An ab initio based investigation of the structural
characteristics of the chain transfer agent in RAFT
polymerization
Eline Dhont
Supervisors: Prof. dr. Marie-Françoise Reyniers, Prof. dr. ir. Dagmar D'hooge
Counsellor: Ir. Gilles Desmet
Master's dissertation submitted in order to obtain the academic degree of
Master of Science in Chemical Engineering
Department of Chemical Engineering and Technical Chemistry
Chairman: Prof. dr. ir. Guy Marin
Faculty of Engineering and Architecture
Academic year 2014-2015
An ab initio based investigation of the structural
characteristics of the chain transfer agent in RAFT
polymerization
Eline Dhont
Supervisors: Prof. dr. Marie-Françoise Reyniers, Prof. dr. ir. Dagmar D'hooge
Counsellor: Ir. Gilles Desmet
Master's dissertation submitted in order to obtain the academic degree of
Master of Science in Chemical Engineering
Department of Chemical Engineering and Technical Chemistry
Chairman: Prof. dr. ir. Guy Marin
Faculty of Engineering and Architecture
Academic year 2014-2015
FACULTY OF ENGINEERING AND ARCHITECTURE
Department of Chemical Engineering and Technical Chemistry
Laboratory for Chemical Technology
Director: Prof. Dr. Ir. Guy B. Marin
Laboratory for Chemical Technology
Declaration concerning the accessibility of the master thesis
Undersigned,
Eline Dhont
Graduated from Ghent University, academic year 2014-2015 and is author of
the master thesis with title:
An ab initio based investigation of the structural characteristics of the chain
transfer agent in RAFT polymerization
The author gives permission to make this master dissertation available for
consultation and to copy parts of this master dissertation for personal use.
In the case of any other use, the copyright terms have to be respected, in
particular with regard to the obligation to state expressly the source when
quoting results from this master dissertation.
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Preface
Before introducing the aim and the results of this master thesis, I would like to express my
gratitude to some people who helped me finishing this research project. First of all, a word of
thanks goes to professor Guy Marin for making this research possible, for providing the
necessary accommodation. In addition, I would like to thank my supervisors professor MarieFrançoise Reyniers and professor Dagmar D’hooge for giving me the opportunity to perform
research about the interesting subject of reversible addition-fragmentation chain transfer
polymerization, and professor Marie-Françoise Reyniers also for providing me guidance and
feedback through the completion of this master thesis.
A special word of thanks goes to my coach Gilles Desmet for supporting me at any time
during this year, for the useful discussions giving me extra insights, for getting me back on
the rails if I was lost, for offering suggestions, for reading and giving comments on my text so
I could make improvements, and for so much more. I am also grateful to Nils De Rybel for
explaining me the kinetic model and for providing me information about the switchable
RAFT CTAs, and to Maarten Sabbe and Pieter Derboven for the interesting scientific
discussions and their critical mind.
On a more personal level, I would like to thank my parents and my brother, for their support
and patience during this five years of studying. I also want to thank my boyfriend, Jeroen, for
his encouragement, curiosity and his patience. An extra word of thanks goes to all the second
master students, especially to Lies, Florence and Brigitte to be at my beck and call.
“It always seems impossible until it’s done”
- Nelson Mandela -
Eline Dhont
June 2015
An ab initio based investigation of the
structural characteristics of the chain transfer
agent in RAFT polymerization
Dhont Eline
Supervisors: Prof. dr. Marie-Françoise Reyniers, Prof. dr. ir. Dagmar R. D’hooge
Counsellor: Ir. Gilles Desmet
Master’s dissertation submitted in order
Master of Science in Chemical Engineering
to
obtain
the
academic
degree
of
Department of Chemical Engineering and Technical Chemistry
Chairman: Prof. dr. ir. Guy B. Marin
Faculty of Engineering and Architecture
Academic year 2014-2015
Abstract
Reversible addition-fragmentation chain transfer (RAFT) polymerization has evolved into a
powerful synthetic tool for polymer chemists. In this work, ab initio calculations of the
forward and reverse rate coefficients have been performed for reactions of different radicals to
several important RAFT chain transfer agents (CTAs). Styrene, methyl methacrylate, methyl
acrylate and n-butyl acrylate have been considered as monomers. The RAFT CTAs that have
been investigated are methyl ethane dithioate (MEDT), methyl benzodithioate (MBDT), 2cyano-2-propyl methyl trithiocarbonate (CPDTmethyl), 2-cyano-2-propyl ethyl trithiocarbonate
(CPDTethyl) and the switchable RAFT CTA 2-cyano-2-propyl N-(4-pyridinyl)-N-methyl
dithiocarbamate (switch). Moreover, a first principles based kinetic model for RAFT
polymerization of styrene, making use of 2-cyano-2-propyl dodecyl trithiocarbonate (CPDT)
as RAFT CTA and azobisisobutyronitrile (AIBN) as initiator, is developed. The RAFT
specific kinetic parameters are determined via ab initio modeling. These parameters are
consequently adjusted and implemented in the kinetic model, whereupon the simulations are
validated with experimental data. In particular, the kinetic model is used to study the
influence of temperature on the RAFT polymerization process.
Keywords
Reversible addition-fragmentation chain transfer (RAFT) polymerization, chain transfer agent
(CTA), ab initio, kinetic modeling
An ab initio based investigation of the
structural characteristics of the chain
transfer agent in RAFT polymerization
Eline Dhont
Supervisors: Prof. dr. Marie-Françoise Reyniers, Prof. dr. ir. Dagmar R. D’hooge
Coach: ir. G. Desmet
Abstract Reversible addition-fragmentation chain transfer
(RAFT) polymerization has evolved into a powerful synthetic
tool for polymer chemists. In this work, ab initio calculations
of the forward and reverse rate coefficients have been
performed for reactions of different radicals to several
important RAFT chain transfer agents (CTAs). Styrene,
methyl methacrylate, methyl acrylate and n-butyl acrylate
have been considered as monomers. The RAFT CTAs that
have been investigated are methyl ethane dithioate (MEDT),
methyl benzodithioate (MBDT), 2-cyano-2-propyl methyl
trithiocarbonate
(CPDTmethyl),
2-cyano-2-propyl
ethyl
trithiocarbonate (CPDTethyl) and the switchable RAFT CTA 2cyano-2-propyl N-(4-pyridinyl)-N-methyl dithiocarbamate
(switch). Moreover, a first principles based kinetic model for
RAFT polymerization of styrene, making use of 2-cyano-2propyl dodecyl trithiocarbonate (CPDT) as RAFT CTA and
azobisisobutyronitrile (AIBN) as initiator, is developed. The
RAFT specific kinetic parameters are determined via ab initio
modeling. These parameters are consequently adjusted and
implemented in the kinetic model, whereupon the simulations
are validated with experimental data. In particular, the kinetic
model is used to study the influence of temperature on the
RAFT polymerization process.
Keywords Reversible addition-fragmentation chain transfer
(RAFT) polymerization, chain transfer agent (CTA), ab initio,
kinetic modeling
Reversible addition-fragmentation chain transfer (RAFT)
polymerization has been put forward as a very interesting
technique for controlling the polymerization as well as for
answering the growing need for designing sustainable
synthetic polymeric materials, due to its versatility. In
RAFT polymerization, typically thiocarbonyl compounds
reversibly react with the growing polymeric radical via a
chain transfer reaction, to protect the growing polymer
chains from bimolecular termination. The principle of
RAFT polymerization is presented in Figure 1.
Figure 1. Mechanism of RAFT polymerization
I. INTRODUCTION
In the last decades, polymers have become ubiquitous in
today’s society, as they are used in numerous applications,
from consumer commodities to highly specialized industrial
products. A major part of these polymers is produced via
free radical polymerization (FRP). In recent years, the field
of FRP has been revolutionized by the development of
methods for controlling the microstructure of polymers.
These controlled radical polymerization (CRP) methods
allow to combine the advantages of conventional radical
polymerization with the ability to control the molar mass
and the molar mass distribution of the polymers, as well as
the composition, the end-group functionality and the
architecture. CRP methods are expected to deliver
significant improvements in the current and future
application fields of polymer chemistry and polymer
science, in high-tech applications such as coatings,
biomedical materials, drug and gene delivery systems, etc.
Eline Dhont is with the Chemical Engineering Department,
Ghent University (UGent), Gent, Belgium.
E-mail: [email protected]
II. METHODOLOGY
A. Ab initio calculations
All the electronic structure calculations in this work have
been performed using the Gaussian-09 package [1]. The ab
initio calculations are performed using BMK with 6311+G** as basis set. For the determination of minimum
energy conformations (reactants and intermediate in Figure
2), an in-house script is used, which scans all possible
conformations, based on rotations of the dihedral angles of
the molecules. The transition states (Figure 2) are optimized
by applying the Berny algorithm [2]. In almost all
calculations
performed,
the
harmonic
oscillator
approximation is applied. However, to correct for the wellknown breakdown of the harmonic oscillator model for
low-frequency vibrational modes, the quasiharmonic
approximation is used. The vibrational frequencies lower
than 30 cm-1 are artificially raised to 30 cm-1. Furthermore,
all vibrational frequencies are scaled with a factor of 0.99
[3]. For the calculation of Gibbs free energies of solvation,
the COSMO-RS theory is used, as implemented in the
COSMOtherm program [4].
The rate and equilibrium coefficients are calculated using
the standard statistical thermodynamic formulas, eq. (1) and
eq. (2):
⁄(
( )
( )
(
)
)
(1)
(2)
Where the activation Gibbs free energy ΔG‡ and the
reaction Gibbs free energy ΔGr respectively, are illustrated
in Figure 2 for the reaction of the styryl radical with methyl
ethane dithioate.
Figure 2. Gibbs free energy diagram of the reaction of the styryl
radical with methyl ethane dithioate as RAFT CTA
B. Kinetic modeling
In the kinetic model, a distinction is made between FRPrelated reactions and RAFT polymerization specific
reaction steps. Only ab initio calculated parameters of the
latter are implemented. Thermal initiation of styrene and
cross termination is not taken into account. The initiator
efficiency is determined via the free volume theory [5]. The
apparent termination rate coefficients are based on the
composite model proposed by Johnston-Hall and Monteiro.
This model is based on the RAFT chain length dependent
termination method presented by Vana et al. [6] and
recently improved by Derboven et al. [7]. The continuity
equations are simultaneously integrated using the numeric
LSODA solver [8].
III. RESULTS AND DISCUSSION
A. Ab initio study
In this work, the so-called pre-equilibrium in the RAFT
mechanism is investigated, since this step strongly
influences the mediating behavior. For the ab initio
calculations, BMK/6-311+G** is initially used in this work,
as it is the recommended DFT method in literature.
However, in a later stage it is suggested that further ab
initio investigations of RAFT polymerization are performed
with M06-2X, due to its better agreement with the reference
values (Table 1).
Table 1. Rate coefficients [L mol-1 s-1] of the addition reactions of
the styryl radical to different RAFT CTAs, calculated at M062X/6-311+G**, at 298.15 K, and reference values
RAFT CTA
M06-2X
MEDT
MBDT
CPDTmethyl
CPDTethyl
1.8E+05
8.3E+06
3.7E+03
1.6E+03
Reference
values
2.8E+06 [9, 10]
4.0E+06 [11]
8.3E+02 [12]
8.3E+02
An investigation of the structural characteristics of the
RAFT chain transfer agent (CTA) on the reactivity is
performed by considering several RAFT CTAs. From Table
2, it is clear that methyl benzodithioate (MBDT) is a more
reactive RAFT CTA than methyl ethane dithioate (MEDT),
due to the stabilization of the RAFT intermediate by the
phenyl substituent. This can be attributed to its ability to
delocalize the unpaired electron in the aromatic ring. When
comparing 2-cyano-2-propyl
ethyl
trithiocarbonate
(CPDTethyl) with MEDT, it can be seen that the latter is
more reactive. A methyl substituent better stabilizes the
intermediate, compared to the cyano isopropyl group. This
can be explained by the positive inductive effect of the
methyl group, while the cyano group in the cyano isopropyl
substituent is strongly electron withdrawing.
Table 2. Rate coefficients [L mol-1 s-1] of the addition reactions of
different radicals to several RAFT CTAs, calculated at BMK/6311+G**, at 298.15 K
RAFT
CTA
MEDT
MBDT
CPDTmethyl
CPDTethyl
switch
switch prot
methyl
styryl
MMA
MA
nBA
6.4E+06
2.6E+07
6.9E+05
5.5E+05
1.4E+03
-
5.9E+02
1.9E+03
8.7E-02
5.5E-02
2.3E-01
-
4.5E+00
4.8E+00
1.2E-02
1.4E-02
3.0E-03
1.1E+05
1.8E+04
7.3E+04
7.3E+01
1.3E+02
1.4E+02
1.4E+09
5.3E+03
3.5E+04
9.7E+00
6.4E+01
1.2E+01
-
Another RAFT CTA that is examined is 2-cyano-2propyl N-(4-pyridinyl)-N-methyl dithiocarbamate, better
known as a switchable RAFT agent. This is a very
promising topic since a switchable RAFT CTA offers good
control over the polymerization of both less-activated and
more-activated monomers, by switching between the
original and the protonated form [13]. After calculations of
the switchable RAFT agent (switch) and its protonated
form (switch prot), represented in Table 2, it becomes clear
that the protonated form is more reactive towards styrene,
methyl methacrylate (MMA), methyl acrylate (MA) and nbutyl acrylate (nBA), compared to its neutral form. This is
in accordance with the principle of switchable RAFT
CTAs, since these monomers belong to the category of
more-activated monomers.
Additionally, the influence of the structure of the radical
on the reactivity with the RAFT CTAs has been
investigated. It can be concluded, looking at the results in
Table 2, that the reactions with MMA have the lowest rate
and equilibrium coefficients, and those with the methyl
radical have the highest coefficients. The radicals in order
of increasing reactivity, and so increasing rate and
equilibrium coefficients, are MMA < styryl < nBA < MA <
methyl. This can be expected because MMA is a tertiary
radical, which is not very reactive. Styrene, nBA and MA
are secondary radicals and have an intermediate reactivity.
The methyl radical is very reactive due to its instability.
This confirms previously obtained results from Goto et al.
[14]. However, in other sources, this order of reactivity is
not recognized [15].
B. Kinetic modeling of RAFT polymerization of styrene
A first principles based kinetic model for RAFT
polymerization of styrene, with 2-cyano-2-propyl dodecyl
trithiocarbonate
(CPDT)
as
RAFT
agent
and
azobisisobutyronitrile (AIBN) as initiator, is developed.
The most important reactions in the RAFT mechanism are
identified, and the activation energy and the preexponential factor of each reaction are determined using ab
initio modeling. A correction of the ab initio calculated
values is necessary to provide an accurate description of the
experimental observations. Two approaches are examined.
In the first approach, the pre-exponential factors of the
addition reactions of the macroradical and the styryl radical
are multiplied with a factor 105. This factor for certain
reactions is obtained by comparing the calculated results
with available kinetic parameters that are able to describe
the experiments well. With this correction factor, a very
good agreement between the model predictions and the
experimental data is obtained. This is presented in Figure 3
for one set of conditions (T = 353.15 K, targeted chain
length = 400, [RAFT CTA]0 / [AIBN]0 = 2 / 1).
radical are additionally raised with a factor 104. A
comparison between the simulated results and the
experimental data is shown in Figure 4 for the same set of
conditions as mentioned before. A good agreement between
modeled and experimental values is observed.
Figure 4. Comparison between the simulation (full line), with ab
initio calculated values, adjusted according to the second
approach, and the experimental data (+)
The influence of temperature is investigated by
comparing different simulations. A higher temperature
results in a faster polymerization, which can be attributed to
the exponential temperature dependence of the propagation
and initiator decomposition rate coefficients. A lower
number of monomer units per chain is observed for a higher
polymerization temperature, due to a higher initiator
decomposition rate coefficient, leading to more and hence
shorter chains. The larger extent of control at a lower
polymerization temperature is reflected in a lower
dispersity and a higher end-group functionality (EGF).
90
Number of monomer units per
chain [-]
140
80
Conversion [%]
70
60
50
40
30
20
10
120
100
80
60
40
20
0
0
0
200
0
400
Time [min]
50
Conversion [%]
100
1.2
1.4
0.8
EGF [-]
Figure 3. Comparison between the simulation (full line), with ab
initio calculated values, adjusted according to the first approach,
and the experimental data (+)
Dispersity [-]
1
1.3
1.2
0.4
1.1
0.2
1
The second approach is based on a scaling with the
propagation reaction. Scaling factors for the kinetic
parameters are determined by comparing the ab initio
calculated parameters for the propagation reaction with the
values originally used in the model. However, using only
these scaling factors for the addition reactions is not
sufficient to have an accurate description of the
experimental observations of RAFT polymerization.
Therefore, similarly as before, the pre-exponential factors
of the addition reactions of the macroradical and the styryl
0.6
0
50
Conversion [%]
100
0
0
50
Conversion [%]
100
Figure 5. Influence of temperature on monomer conversion (top
left), number of monomer units per chain (top right), dispersity
(bottom left) and EGF (bottom right), for RAFT polymerization at
343.15 K (full line) and at 363.15 K (dashed line)
IV. CONCLUSIONS
After a level of theory study, M06-2X seems to be a
promising method to accurately describe the RAFT preequilibrium. Furthermore, an ab initio investigation of
different RAFT CTAs as well as different propagating
radicals is performed. For both, an order of reactivity can
be deduced and interpreted in a logical way. Especially, 2cyano-2-propyl N-(4-pyridinyl)-N-methyl dithiocarbamate
is interesting as this is a switchable RAFT agent, able to
control polymerizations of both less-activated in its neutral
form, and more-activated monomers in its protonated form.
Preliminary ab initio results confirm this.
Kinetic modeling of RAFT polymerization of styrene
using CPDT as RAFT CTA, by the implementation of the
ab initio calculated kinetic parameters, is executed. A
correction of these parameters is necessary to accurately
describe the experimental data. A more extended analysis
of the most important reactions in the RAFT mechanism is
advised, to investigate a more rigourous scaling procedure.
After an investigation of the influence of the temperature, it
can be concluded that a sufficiently low polymerization
temperature is desired for good control of RAFT
polymerization.
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Table of contents
Table of contents………………………………………………………………………………..i
List of figures………………………………………………………………………………….iii
List of tables…………………………………………………………………………………...vi
List of symbols………………………………………………………………………………...ix
Chapter 1
Introduction……………………………………………………………………...1
1.1
Radical polymerization………………………………………………………………………. 1
1.2
Aim of this work……………………………………………………………………………... 3
1.3
Outline……………………………………………………………………………………….. 3
Chapter 2
Literature study…………………………………………………………………. 5
2.1
Mechanism of RAFT polymerization………………………………………………………... 5
2.2
Modeling RAFT polymerization…………………………………………………………… 10
2.2.1
Computational modeling……………………………………………………………….10
2.2.2
Design of RAFT CTAs………………………………………………………………... 11
2.2.3
Structure-reactivity studies……………………………………………………………. 11
2.2.4
Influence of computational methods on results……………………………………….. 19
2.3
Switchable RAFT CTAs……………………………………………………………………. 21
Chapter 3
3.1
Computational methods……………………………………………………….. 23
Ab initio methods…………………………………………………………………………… 23
3.1.1
Introduction…………………………………………………………………………… 23
3.1.2
Hartree-Fock theory…………………………………………………………………… 24
3.1.3
Electron correlation…………………………………………………………………….26
3.1.4
Density functional theory………………………………………………………………29
3.1.5
Parameterized methods………………………………………………………………... 32
3.1.6
Basis sets……………………………………………………………………………….33
3.2
Performance ab initio methods……………………………………………………………... 35
3.3
Computational methods and procedures used in this work………………………………… 37
3.3.1
Ab initio calculations using Gaussian 09……………………………………………… 37
3.3.2
Calculation of thermodynamic quantities……………………………………………... 39
3.3.3
High Performance Computing infrastructure…………………………………………. 40
3.3.4
COSMO-RS…………………………………………………………………………… 40
3.3.5
Calculation of rate and equilibrium coefficients……………………………………….42
i
3.3.6
Kinetic model…………………………………………………………………………..45
Chapter 4
Results and discussion………………………………………………………… 47
4.1
Pre-equilibrium in RAFT mechanism……………………………………………………….47
4.1.1
Level of theory study………………………………………………………………….. 49
4.1.2
Rate coefficients of addition and fragmentation……………………………………….56
4.1.3
Influence of modeling large substituents by smaller groups………………………….. 58
4.1.4
Influence of presence of initiator fragment on styryl radical…………………………..59
4.1.5
Influence of the solvent………………………………………………………………...61
4.2
Structural influences on reactivity………………………………………………………….. 66
4.2.1
Influence of the radical structure……………………………………………………… 66
4.2.2
Influence of RAFT CTA……………………………………………………………….68
4.3
Kinetic modeling of polymerization of styrene with CPDT as RAFT CTA……………… 71
4.3.1
Initiation and propagation reactions…………………………………………………... 71
4.3.2
Reactions in the RAFT mechanism…………………………………………………… 72
4.3.3
Kinetic parameters…………………………………………………………………….. 76
4.3.4
Implementation in the kinetic model and comparison with experimental data……….. 80
4.3.5
Influence of temperature………………………………………………………………. 85
Chapter 5
Conclusions and future recommendations…………………………………….. 88
Chapter 6
References……………………………………………………………………... 91
Appendix A
Conformational analysis…………………………………………………... 105
Appendix B
Optimized geometries for the model reactions…………………………… 107
Appendix C
Optimized geometries for the reactions in the kinetic model…………….. 164
ii
List of figures
Figure 1. The various levels of control from the macromolecule to the material [14] ............... 1
Figure 2. Total number of publications, papers, and patents on RAFT polymerization over the
period 1998 - 2012 [31] .............................................................................................................. 2
Figure 3. Principle of RAFT polymerization [34] ...................................................................... 5
Figure 4. Mechanism of RAFT polymerization [31] .................................................................. 7
Figure 5. Formation of block copolymers via chain extension of macro-RAFT CTAs [14] ..... 8
Figure 6. Reaction of the leaving group R with the initial RAFT CTA [31] ............................. 9
Figure 7. The four lowest doublet configurations of the three-electron-three-center system
[37] ........................................................................................................................................... 12
Figure 8. State correlation diagram for radical addition to double bonds [37] ........................ 13
Figure 9. Delocalization of electron density in case of lone-pair donor Z-groups [14] ........... 14
Figure 10. Chemical structure of the RAFT CTA with R-group = methyl group and Z-group =
methoxy group (top left), methyl group (top center), benzyl group (top right), phenyl group
(bottom left) and hydrogen (bottom right) ............................................................................... 16
Figure 11. Reduced delocalization of the sulfur lone pair onto the double bond [37] ............. 18
Figure 12. Neutral (left) and protonated (right) form of the switchable RAFT CTA [58] ....... 21
Figure 13. Scheme of the switchable RAFT CTA, N-(4-pyridinyl)-N-methyl dithiocarbamate,
controlling both the polymerization of LAMs and MAMs [56]............................................... 22
Figure 14. Canonical structures of dithiocarbamates [58]........................................................ 22
Figure 15. Flow chart of the HF SCF procedure [61] .............................................................. 26
Figure 16. Pre-equilibrium in the RAFT polymerization mechanism [31] .............................. 47
Figure 17. Chemical structure of the RAFT CTA 2-cyano-2-propyl dodecyl trithiocarbonate
.................................................................................................................................................. 49
Figure 18. Gibbs free energy diagram of the reaction of the styryl radical with MEDT ......... 50
Figure 19. Chemical structure of the intermediate (left) and the transition state (right) of the
reaction of a methyl radical with CPDTethyl, with interatomic distances (in Ångstrom) and
angles (in degrees) indicated, optimized via BMK/6-311+G** ............................................... 52
Figure 20. Chemical structure and shape of the LUMO of the CPDT RAFT CTA, with a
methyl group (left) and an ethyl group (right) .......................................................................... 58
Figure 21. Chemical structure and shape of the LUMO of the switchable RAFT CTA ‘switch’
(left) and the simplified version ‘switchmethyl’ (right) ............................................................... 59
iii
Figure 22. Reversible chain transfer of the reaction of a styryl radical with CPDT ethyl, once
with an initiator group attached to the styryl radical (top) and once without an initiator group
attached to the styryl radical (bottom) ...................................................................................... 60
Figure 23. Gibbs free energy diagram of the reaction of the styryl radical with MEDT, in the
gas phase (black) and in styrene (green), the Gibbs free energy differences are expressed in
kJ/mol ....................................................................................................................................... 64
Figure 24. Gibbs free energy diagram of the reaction of the styryl radical with CPDT ethyl, in
the gas phase (black) and in styrene (green), the Gibbs free energy differences are expressed
in kJ/mol ................................................................................................................................... 65
Figure 25. Radical stability as function of the number of alkyl groups on the carbon bearing
the unpaired electron [158] ....................................................................................................... 67
Figure 26. Chemical structure of the switchable RAFT CTA, 2-cyano-2-propyl N-(4pyridinyl)-N-methyl dithiocarbamate (left) and a simplified molecule, methyl N-(4-pyridinyl)N-methyl dithiocarbamate (right) ............................................................................................. 70
Figure 27. Initiation and several propagation reactions for the polymerization of styrene with
AIBN as initiator ...................................................................................................................... 72
Figure 28. Chemical structure of a general RAFT intermediate with groups X, Y and S-Z .... 73
Figure 29. R-radical (top left), styryl radical with initiator group attached (top right),
macroradical of styrene with an initiator group attached (bottom left), dimer radical of styrene
(bottom right)............................................................................................................................ 73
Figure 30. Azobisisobutyronitrile (AIBN) ............................................................................... 74
Figure 31. Reactions concerning the cyano isopropyl radical R0•, included in the kinetic
model ........................................................................................................................................ 75
Figure 32. Reactions concerning the macroradical Ri•, included in the kinetic model............ 75
Figure 33. Reactions concerning the styryl radical St•, included in the kinetic model ............ 76
Figure 34. Arrhenius plot for the reaction of R0• with TR0 in the gas phase, including the
trend line ................................................................................................................................... 77
Figure 35. Arrhenius plot for the reaction of R0• with TR0 in styrene, including the trend line
.................................................................................................................................................. 78
Figure 36. Comparison between the simulation, based on adjusted kinetic parameters obtained
via ab initio modeling (full line) and the experimental data (+), using the first approach,
monomer conversion as function of time (left), number of monomer units per chain as
function of monomer conversion (middle), dispersity as function of monomer conversion
(right), for four sets of conditions............................................................................................. 82
iv
Figure 37. Comparison between the simulation, based on adjusted kinetic parameters obtained
via ab initio modeling (full line) and the experimental data (+), using the second approach,
monomer conversion as function of time (left), number of monomer units per chain as
function of monomer conversion (middle), dispersity as function of monomer conversion
(right), for four sets of conditions............................................................................................. 85
Figure 38. Influence of temperature on monomer conversion (top left), number of monomer
units per chain (top right), dispersity (bottom left) and EGF (bottom right), for RAFT
polymerization of styrene at 343.15 K (full line) and at 363.15 K (dashed line) ..................... 87
Figure 39. Intermediate of the reaction of the styryl radical with CPDTethyl, without (left) and
with (right) conformational analysis....................................................................................... 106
v
List of tables
Table 1. Influence of the Z-group on the reaction enthalpy ΔHr [kJ mol-1], the activation
enthalpy ΔH‡ [kJ mol-1] and the rate coefficient kadd,1 [L mol-1 s-1] for the addition of the
methyl radical, calculated at G3(MP2)-RAD at 0 K and twice 333 K respectively, and on the
equilibrium coefficient K [L mol-1], calculated at W1, R-group = methyl group [37, 52-54] . 16
Table 2. Influence of the methyl radical and different monomer radicals on the reaction
enthalpy ΔHr [kJ mol-1], calculated at G3(MP2)-RAD at 0 K, on the activation enthalpy ΔH‡
[kJ mol-1] and the rate coefficient of addition kadd,1 [L mol-1 s-1], calculated at G3(MP2)-RAD
at 333 K, and on the equilibrium coefficient K [L mol-1], calculated at W1, RAFT CTA =
methyl ethane dithioate [37, 52-54].......................................................................................... 19
Table 3. Influence of the methyl radical and different monomer radicals on the reaction
enthalpy ΔHr
[kJ mol-1] of the addition reaction calculated at three levels of theory:
B3LYP/6-311+G(3df,2p), BMK/6-311+G(3df,3p) and G3(MP2)-RAD at 0 K, RAFT CTA =
methyl ethane dithioate [52] ..................................................................................................... 20
Table 4. Influence of the Z-group on the reaction enthalpy ΔHr [kJ mol-1] of the addition
reaction of a methyl radical, calculated at three levels of theory: B3LYP/6-311+G(3df,2p),
BMK/6-311+G(3df,3p) and G3(MP2)-RAD, at 0 K, R-group = methyl [52] ........................ 20
Table 5. Different RAFT CTAs, with their Z- and R-group .................................................... 48
Table 6. Estimated Arrhenius parameters and thermodynamic parameters for the addition
reaction in RAFT polymerization of styrene with CPDT, valid at a temperature 343 K [147]51
Table 7. Benchmarking of the forward rate coefficients kadd,1 [L mol-1 s-1] of the addition
reactions of the methyl and the styryl radical with different RAFT CTAs (MEDT, MBDT,
CPDTmethyl and CPDTethyl), calculated at different levels of theory, at 298.15 K, with the
literature and experimental data ............................................................................................... 54
Table 8. Benchmarking of the forward equilibrium coefficients K [L mol-1] of the addition
reactions of the methyl and the styryl radical with different RAFT CTAs (MEDT, MBDT,
CPDTmethyl and CPDTethyl), calculated at different levels of theory, at 298.15 K, with the
literature and experimental data ............................................................................................... 55
Table 9. Rate coefficients of the addition and fragmentation reactions in the pre-equilibrium,
calculated at BMK/6-311+G**, at 298.15 K ............................................................................ 57
Table 10. Rate coefficients of addition and fragmentation reactions, shown in Figure 22, with
and without the cyano isopropyl group, calculated at BMK/6-311+G**, at 298.15 K ............ 61
vi
Table 11. Rate and equilibrium coefficients of the model addition reactions in gas phase,
styrene and THF, calculated at BMK/6-311+G**, at 298.15 K. Contributions for solvation are
calculated using COSMO-RS. .................................................................................................. 63
Table 12. Rate and equilibrium coefficients of the model fragmentation reactions in gas phase,
styrene and THF, calculated at BMK/6-311+G**, at 298.15 K. Contributions for solvation are
calculated using COSMO-RS. .................................................................................................. 63
Table 13. Forward rate coefficients kadd,1 [L mol-1 s-1] of addition reactions of the methyl
radical and different monomer radicals (styryl, MMA, MA and nBA) with different RAFT
CTAs (MEDT, MBDT, CPDTmethyl, CPDTethyl, switchmethyl, protonated switchmethyl, switch and
protonated switch), calculated at BMK/6-311+G**, at 298.15 K ............................................ 66
Table 14. Forward equilibrium coefficients K [L mol-1] of addition reactions of the methyl
radical and different monomer radicals (styryl, MMA, MA and nBA) with different RAFT
CTAs (MEDT, MBDT, CPDTmethyl, CPDTethyl, switchmethyl, protonated switchmethyl, switch and
protonated switch), calculated at BMK/6-311+G**, at 298.15 K ............................................ 68
Table 15. Activation Gibbs free energy of the reaction in the gas phase, ΔG‡ [kJ mol-1], rate
coefficient of the addition reaction in the gas phase, kadd,1 [L mol-1 s-1], activation Gibbs free
energy of the reaction in styrene, ΔG‡sol, [kJ mol-1], rate coefficient of the addition reaction in
styrene, kadd,1,sol, [ L mol-1 s-1], for different temperatures T [K], for the reaction of R0 with
TR0. Contributions for solvation are calculated using COSMO-RS........................................ 77
Table 16. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the
addition reactions in RAFT polymerization of styrene using CPDTethyl, in the gas phase and in
styrene. Contributions for solvation are calculated using COSMO-RS. .................................. 78
Table 17. Activation energy Ea [kJ mol-1] and pre-exponential factor A [s-1] for the
fragmentation reactions in RAFT polymerization of styrene using CPDTethyl, in the gas phase
and in styrene. Contributions for solvation are calculated using COSMO-RS. ....................... 79
Table 18. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the
addition of the initiation and propagation reactions, in the gas phase and in styrene.
Contributions for solvation are calculated using COSMO-RS................................................. 80
Table 19. Activation energy Ea [kJ mol-1] and pre-exponential factor A [s-1] for the
fragmentation of the initiation and propagation reactions, in the gas phase and in styrene.
Contributions for solvation are calculated using COSMO-RS................................................. 80
Table 20. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the
addition reactions in RAFT polymerization of styrene using CPDTethyl, in styrene, used in the
first approach ............................................................................................................................ 81
vii
Table 21. Different conditions for RAFT polymerization of styrene using CPDT ethyl,
considered in the kinetic model ................................................................................................ 81
Table 22. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the
propagation reaction, calculated via ab initio and originally used in the model, with the
corresponding scaling factors necessary................................................................................... 83
Table 23. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the
addition reactions in RAFT polymerization of styrene using CPDTethyl, in styrene, used in the
second approach ....................................................................................................................... 83
Table 24. Activation energy Ea [kJ mol-1] and pre-exponential factor A [s-1] for the
fragmentation reactions in RAFT polymerization of styrene using CPDTethyl, in styrene, used
in the second approach ............................................................................................................. 84
Table 25. Forward rate and equilibrium coefficients of the addition reactions of the styryl
radical with CPDTmethyl and CPDTethyl as RAFT CTAs, kadd,1 [L mol-1 s-1] and K [L mol-1]
respectively, calculated at BMK/6-311+G**, at 298.15 K, with and without a conformational
analysis performed .................................................................................................................. 105
Table 26. Forward rate and equilibrium coefficients of the fragmentation reaction of the
intermediate of the styryl radical with CPDTmethyl and CPDTethyl as RAFT CTAs, kfrag,2 [s-1]
and Kβ [L mol-1] respectively, calculated at BMK/6-311+G**, at 298.15 K, with and without a
conformational analysis performed ........................................................................................ 105
viii
List of symbols
Acronyms
Acronym
AIBN
Description
Azobisisobutyronitrile
AO
Atomic Orbital
ATRP
Atom Transfer Radical Polymerization
B
Becke
nBA
n-Butyl Acrylate
BMK
Boese-Martin for Kinetics
CASSCF
Complete Active Space Self-Consistent Field
CBS
Complete-basis-set
CC
Coupled Cluster
CCD
Coupled Cluster with only the Double-excitation operator included
CI
Configuration Interaction
COSMO
COnductor-like Screening MOdel
COSMO-RS
COnductor-like Screening MOdel – Real Solvents
CPDT
2-Cyano-2-Propyl Dodecyl Trithiocarbonate
CPDTethyl
2-Cyano-2-Propyl Ethyl Trithiocarbonate
CPDTmethyl
2-Cyano-2-Propyl Methyl Trithiocarbonate
CRP
Controlled Radical Polymerization
CTA
Chain Transfer Agent
DFT
Density Functional Theory
EGF
End-group functionality
FRP
Free Radical Polymerization
GGA
Generalized Gradient expansion Approximation
GTO
Gaussian-Type Orbital
HB
Hydrogen Bonding
HF
Hartree-Fock
HPC
High Performance Computing
KS
Kohn-Sham
LAM
Less-Activated Monomer
ix
LCAO
Linear Combination of Atomic Orbitals
LCT
Laboratory for Chemical Technology
LDA
Local Density Approximation
LSDA
Local Spin Density Approximation
LSODA
Livermore Solver for Ordinary Differential Equations
LUMO
Lowest Unoccupied Molecular Orbital
LYP
Lee-Yang-Parr
MA
Methyl Acrylate
MAM
More-Activated Monomer
MBDT
Methyl BenzoDiThioate
MCSCF
Multi-Configurational Self-Consistent Field
MEDT
Methyl Ethane DiThioate
MGGA
Meta-Generalized Gradient expansion Approximation
MMA
Methyl MethAcrylate
MO
Molecular Orbital
MPn
Møller-Plesset perturbation theory
NMP
Nitroxide-Mediated Polymerization
ONIOM
Our own N-layered Integrated molecular Orbital and molecular
Mechanics
P
Perdew
PW
Perdew-Wang
RAFT
Reversible Addition-Fragmentation chain Transfer
RAFT-CLD-T
RAFT Chain Length Dependent Termination
SAC
Scaling All Correlation
SCF
Self-Consistent Field
Switch
2-cyano-2-propyl N-(4-pyridinyl)-N-methyl dithiocarbamate
Switchmethyl
Methyl N-(4-pyridinyl)-N-methyl dithiocarbamate
STO
Slater-Type Orbital
STO-NG
Slater-Type Orbital approximated by N Gaussian functions
STY
Styrene
TCL
Targeted Chain Length
THF
TetraHydroFuran
VB
Valence Bonding
x
W1
Weizmann-1
W2
Weizmann-2
xi
Roman symbols
Symbol
A
Unit
Aadd,1
L mol-1 s-1
aeff
m²
aij
-
0
c
Description
Pre-exponential factor in Arrhenius law
1
Pre-exponential factor of the addition reaction of a
growing chain to the RAFT CTA
Effective contact area between two surface segments
MO coefficients
-1
mol L
Standard unit of concentration
-
CI coefficients
-
CI coefficients
-
Adjustable
parameter
in
the
hydrogen
bonding
interaction
Intermediate of the reaction of the RAFT CTA CPDTethyl
CPDTethyl-CH3•
-
CPDTethyl-STY•
-
CPDTmethyl-CH3•
-
CPDTmethyl-STY•
-
Ctr
-
Forward transfer coefficient
C-tr
-
Reverse transfer coefficient
Ea
kJ mol-1
Ea,add,1
kJ mol-1
Eelec
kJ mol-1
Electronic energy of the system
Eexact
kJ mol-1
Energy of the system for the exact wave function
EHB
kJ mol-1
Hydrogen bonding energy
EHF
kJ mol-1
Hartree-Fock energy
Emisfit
kJ mol-1
Specific interaction energy resulting from the “misfit” of
and the methyl radical
Intermediate of the reaction of the RAFT CTA CPDTethyl
and the styryl radical
Intermediate of the reaction of the RAFT CTA
CPDTmethyl and the methyl radical
Intermediate of the reaction of the RAFT CTA
CPDTmethyl and the styryl radical
Activation energy
Activation energy of the addition reaction of a growing
chain to the RAFT CTA
1
The unit of the pre-exponential factor A is the same as the one of the rate coefficient. This is dependent on the
reaction order.
xii
screening charge densities
Exc
kJ mol-1
Exchange and correlation energy
E0
kJ mol-1
Ground state electrical energy of the molecule
Eλ
kJ mol-1
Energy in the Møller-Plesset perturbation theory
E[ρ]
kJ mol-1
Energy per particle
ΔE
kJ mol-1
ΔE‡
kJ mol-1
G
kJ mol-1
kJ mol-1
kJ mol-1
Energy change for a reaction corrected for the zero-point
energy
Energy barrier for a reaction corrected for the zero-point
energy
Gibbs free energy of the system
Gibbs free energy of a molecule in the gas phase,
referred to a state of 1 bar
Gibbs free energy of a molecule in the gas phase,
referred to a state of 1 mol L-1
kJ mol-1
Gibbs free energy of molecule i in the gas phase
kJ mol-1
Gibbs free energy of molecule i in solution
kJ mol-1
Gibbs free energy of solvation of molecule i
ΔGcorr
kJ mol-1
Thermal contributions to the Gibbs free energy
ΔGr
kJ mol-1
Reaction Gibbs free energy
ΔG‡
kJ mol-1
Activation Gibbs free energy of the reaction in gas phase
kJ mol-1
Activation Gibbs free energy of the reaction in solution
kJ mol-1
Activation solvation Gibbs free energy of the reaction
H
Js
H
kJ mol-1
Hi
kJ mol-1
̂
-
Planck’s constant
Enthalpy of the system
One-electron terms arising from the kinetic energy of the
electrons and the nuclear attraction energy
Hamiltonian operator
ΔH‡
kJ mol-1
Activation enthalpy
ΔHr
kJ mol-1
Reaction enthalpy
I•
-
Ixx
kg m2
Moment of inertia about x axis
Iyy
kg m2
Moment of inertia about y axis
Izz
kg m2
Moment of inertia about z axis
Initiator radical
xiii
Jij
kJ mol-1
J[ρ]
kJ mol-1
K
2
K
L mol-1
kadd,1
L mol-1 s-1
kadd,1,sol in styrene
L mol-1 s-1
kadd,1,sol in THF
L mol-1 s-1
kadd,2
L mol-1 s-1
kaddP
L mol-1 s-1
kaddR
L mol-1 s-1
kB
J mol-1 K-1
Two-electron terms associated with Coulomb repulsion
between the electrons
Electrostatic repulsion energy between the electrons
Rate coefficient of a reaction step
Equilibrium coefficient related to the pre-equilibrium, in
the gas phase
Rate coefficient of the addition of a growing chain to the
RAFT CTA, in the gas phase
Rate coefficient of the addition of a growing chain to the
RAFT CTA, in styrene
Rate coefficient of the addition of a growing chain to the
RAFT CTA, in the solvent THF
Rate coefficient of the addition of R• to the macro-RAFT
CTA, in the gas phase
Rate coefficient of the addition of a growing chain to the
macro-RAFT CTA, in the gas phase
Rate coefficient of the addition of R• to the RAFT CTA,
in the gas phase
Boltzmann’s constant
Rate coefficient of the fragmentation of the RAFT
kfrag,1
s-1
adduct radical with formation of a growing chain and the
RAFT CTA, in the gas phase
Rate coefficient of the fragmentation of the RAFT
kfrag,2
s-1
adduct radical with formation of R• and the macroRAFT CTA, in the gas phase
Rate coefficient of the fragmentation of the RAFT
kfrag,2,sol in styrene
s-1
adduct radical with formation of R• and the macroRAFT CTA, in styrene
Rate coefficient of the fragmentation of the RAFT
kfrag,2,sol in THF
s-1
adduct radical with formation of R• and the macroRAFT CTA, in the solvent THF
kfragP
2
s-1
Rate coefficient of the fragmentation of the RAFT
The unit of the rate coefficient is dependent on the reaction order of the reaction step considered.
xiv
adduct radical with formation of a growing chain and the
macro-RAFT CTA, in the gas phase
Rate coefficient of the fragmentation of the RAFT
kfragR
s-1
adduct radical with formation of R• and the RAFT CTA,
in the gas phase
-1 -1
kini
L mol s
Kij
kJ mol-1
kprop
L mol-1 s-1
-1
KP
L mol
KR
L mol-1
ksol
3
Ksol in styrene
L mol-1
Ksol in THF
L mol-1
kt
L mol-1 s-1
or s-1
ktr
L mol-1 s-1
k-tr
L mol-1 s-1
Kβ
L mol-1
Kβ, sol in styrene
L mol-1
Kβ, sol in THF
L mol-1
Rate coefficient of reinitiation
Two-electron terms associated with the exchange of
electronic coordinates
Rate coefficient of the addition of a growing chain to a
monomer
Equilibrium coefficient associated with main equilibrium
Equilibrium coefficient associated with the reaction of
R• with the RAFT CTA
Rate coefficient of a reaction in solvent
Equilibrium coefficient related to the pre-equilibrium, in
styrene
Equilibrium coefficient related to the pre-equilibrium, in
the solvent THF
Rate coefficient of termination by recombination or
disproportionation
Rate coefficient of chain transfer
Rate coefficient associated with the reaction of R• with a
monomer or the macro-RAFT CTA
Equilibrium coefficient related to the pre-equilibrium, in
the gas phase
Equilibrium coefficient related to the pre-equilibrium, in
styrene
Equilibrium coefficient related to the pre-equilibrium, in
the solvent THF
M
-
Molecularity of a reaction
M
-
Monomer
M1
-
Monomer 1 (relating to copolymerization)
3
The unit of the rate coefficient is dependent on the reaction order of the reaction step considered.
xv
M2
-
MBDT-CH3•
-
MBDT-STY•
-
MEDT-CH3•
-
MEDT-STY•
g mol-1
Monomer 2 (relating to copolymerization)
Intermediate of the reaction of the RAFT CTA MBDT
and the methyl radical
Intermediate of the reaction of the RAFT CTA MBDT
and the styryl radical
Intermediate of the reaction of the RAFT CTA MEDT
and the methyl radical
Intermediate of the reaction of the RAFT CTA MEDT
and the styryl radical
Molecular weight of the solvent
N
-
Number of identical non-interacting particles in a system
Δn
-
Change in number of particles upon reaction
Δn‡
-
P(M1)
-
Macro-RAFT CTA based on monomer 1
P(M2)
Change in number of particles between the reactant(s)
and the transition state
-
Macro-RAFT CTA based on monomer 2
i
p (σ)
-
σ-profile
Pm•
-
Growing polymer chain
Pn•
-
Growing polymer chain
qelec
-
Electronic partition function
qmol
-
Molecular partition function
qrot
-
Rotational partition function
qtrans
-
Translational partition function
qvib
-
Vibrational partition function
Qi
-
Molecular partition function of the reactant i
Qj
-
Molecular partition function of the product j
Q‡
-
R
J mol-1 K-1
R•
-
Ri•
-
(RiTR0)•
-
Molecular partition function of the transition state
structure
Universal gas constant
Radical derived from the R-group of the RAFT CTA
Macroradical of styrene with two monomer units and
with an initiator group attached
Intermediate of the reaction of Ri• and the RAFT CTA
xvi
TR0
(RiTRi)•
-
(RiTSt)•
-
R0•
-
(R0TR0)•
-
(R0TRi)•
-
(R0TSt)•
-
S
J mol-1 K-1
Intermediate of the reaction of Ri• and the RAFT CTA
TRi
Intermediate of the reaction of Ri• and the RAFT CTA
TSt
Radical derived from the R-group of the RAFT CTA
Intermediate of the reaction of R0• and the RAFT CTA
TR0
Intermediate of the reaction of R0• and the RAFT CTA
TRi
Intermediate of the reaction of R0• and the RAFT CTA
TSt
Entropy of the system
St•
-
(StTR0)•
-
(StTRi)•
-
(StTSt)•
-
STY•
-
Styryl radical
S=C(Z)SR
-
RAFT CTA
S=C(Z)SPm
-
Macro-RAFT CTA
S=C(Z)SPn
-
Macro-RAFT CTA
ΔS‡
J mol-1 K-1
Activation entropy
ΔSr
J mol-1 K-1
Reaction entropy
Styryl radical with an initiator group attached
Intermediate of the reaction of St• and the RAFT CTA
TR0
Intermediate of the reaction of St• and the RAFT CTA
TRi
Intermediate of the reaction of St• and the RAFT CTA
TSt
T
K
Temperature
Ti
-
TRi
-
RAFT CTA with Ri• attached
TR0
-
RAFT CTA with R0• attached
TSt
-
RAFT CTA with St• attached
Ts[ρ]
kJ mol-1
Operators generating all possible determinants having i
excitations from the reference
Kinetic energy per particle
xvii
̂
-
Operator representing the kinetic energy of the electrons
̂
-
Operator representing the kinetic energy of the nuclei
̂
-
Electron-repulsion term
Vm
m³ mol-1
Molar volume of the ideal gas
m³ mol-1
Molar volume
̂
-
Nuclear-electron attraction term
̂
-
Nuclear-nuclear repulsion term
m³
m³
xi
-
Volume of 1 mol ideal gas at 298.15 K and 1 bar
Volume of 1 mol ideal gas in a concentration of
1 mol L-1
Mole fraction of component i in the mixture
xviii
Greek symbols
Symbol
α
α’
Unit
-
Description
Exponent controlling the width of the GTO
-
Adjustable parameter in the COSMO-RS theory
-
Operator
κ
-
Tunneling correction factor
λ
-
Parameter in Møller-Plesset perturbation theory
kJ mol-1
kJ mol-1
Chemical potential of compound i in the ideal gas
phase
Infinite dilution chemical potential of the compound
i in solution
kJ mol-1
σ-potential of system S
kJ mol-1
Combinatorial term of the chemical potential
kJ mol-1
Chemical potential of compound i in the system S
νi
s-1
Characteristic frequency of harmonic oscillator i
ρ
electrons (cubic Bohr)-1
(σ)
kg m-³
Electron density4
Density of the solvent
Net screening charge density of the surface segment
σ
C m-2
σ'
C m-2
σacceptor
C m-2
Polarization charge of the acceptor
σdonor
C m-2
Polarization charge of the donor
C m-2
of a molecule
Net screening charge density of the surface segment
of a molecule
Adjustable parameter in the hydrogen bonding
interaction
σrot
-
Rotational symmetry number
ϕ
-
Guess wave function
φ
-
Atomic wave function
Partition coefficient describing the partitioning of
Φ
-
the RAFT adduct radical between formation of R•
and Pn•
4
The Bohr radius is a physical constant which is approximately equal to the most probable distance between the
proton and the electron in a hydrogen atom in its ground state.
xix
Partition coefficient describing the partitioning of
ΦB
-
R• between adding to a monomer and reacting with
the macro-RAFT CTA
-
Wave function
-
Coupled cluster wave function
-
Coupled cluster wave function with only the
double-excitation operator included
-
Configuration interaction wave function
-
Hartree-product wave function
-
Exact ground state wave function
-
Møller-Plesset perturbation wave function
-
Complex conjugate of the wave function
xx
Chapter 1
Introduction
1.1 Radical polymerization
In the last decades, polymers have become ubiquitous in today’s society, as they are used in
numerous applications, from consumer commodities to highly specialized industrial products.
A major part of these polymers is produced via free radical polymerization (FRP). In recent
years, the field of FRP has been revolutionized by the development of methods for controlling
the microstructure of polymers [1-6]. These controlled radical polymerization (CRP) methods
allow to combine the advantages of conventional radical polymerization, such as costeffectiveness and easy processing, with the ability to control the molar mass of the polymers.
Moreover, CRP techniques possess the possibility to synthesize a wide range of polymers
with narrow molar mass distributions, efficient control of both the composition and the chainend functionality, as well as the possibility to use a wide range of monomers [7]. In addition,
novel architectures, such as block copolymers, star polymers and grafted polymers, can be
prepared with CRP [8-13]. Control at the macromolecular level is paramount to control and
improve the macroscopic properties of the final materials as can be seen in Figure 1 [14].
Figure 1. The various levels of control from the macromolecule to the material [14]
Currently, the CRP techniques that are receiving most attention are nitroxide-mediated
polymerization (NMP) [15-17], atom transfer radical polymerization (ATRP) [18-20] and
reversible addition-fragmentation chain transfer (RAFT) polymerization [11, 21-23]. The
basic principle of CRP is to protect the growing polymer chains from bimolecular termination
through their reversible trapping into some dormant form.
Chapter 1: Introduction
1
These methods are expected to deliver significant improvements in the current and future
application fields of polymer chemistry and polymer science [5, 24]. CRP techniques have
already shown much potential to produce well-defined polymers with a broad range of
applications, including high performance coatings [11], biomedical materials [25], drug and
gene delivery systems [20, 22], bioactive surfaces and biomaterials [26], light-emitting
nanoporous films [27], self-healing material design [28] and optoelectronic materials [29].
Among these CRP techniques, RAFT polymerization has been put forward as a very
interesting, universal CRP technique. RAFT polymerization is a promising candidate for
answering the growing need for designing sustainable synthetic polymeric materials, from
production to disposal. The global requirements for developing sustainable chemicals and
processes can be achieved by employing environmentally friendly solvents, low temperatures
and alternative sources of energy, due to the versatility of RAFT polymerization [30]. The
increasing importance of RAFT polymerization is illustrated in Figure 2, in which the total
number of publications (= papers and patents) on RAFT polymerization is shown. The term
‘papers’ includes journal articles, communications, letters and reviews, but does not include
conference abstracts [31].
Figure 2. Total number of publications, papers, and patents on RAFT polymerization
over the period 1998 - 2012 [31]
Chapter 1: Introduction
2
1.2 Aim of this work
The aim of this master thesis is to study the effects of the structural characteristics of the chain
transfer agent (CTA) on the reactivity using ab initio methods. Ultimately, this should allow
to make a priori predictions of the polymerization process in order to design new RAFT
CTAs to tackle specific control problems, or, to improve already existing processes.
In the first part of this master thesis, the RAFT pre-equilibrium is explored by using model
compounds (cf. sections 4.1 and 4.2). First of all, a comparison of different ab initio methods
is desired. Furthermore, it is aimed to investigate the structural influences of several important
RAFT CTAs as well as of different propagating radicals on the reactivity, based on the rate
coefficients for the addition and fragmentation reactions. Also the thermodynamic and kinetic
parameters of reactions in the gas phase and reactions performed in a solvent will be
compared as well.
The acquired insights are then applied in the second part of this work (cf. section 4.3), to
model RAFT polymerization of styrene, using 2-cyano-2-propyl dodecyl trithiocarbonate
(CPDT) as RAFT CTA and azobisisobutyronitrile (AIBN) as initiator. The RAFT specific
kinetic parameters have to be determined via ab initio modeling. These parameters will
consequently be implemented in the kinetic model, whereupon the simulations will be
validated with experimental data. Also a closer look is taken at the initiation and propagation
reactions. In particular, the kinetic model will be used to study the influence of temperature on
conversion, number of monomer units per chain, dispersity and end-group functionality.
1.3 Outline
Chapter 2 consists of a literature study in which the mechanism of RAFT polymerization is
explained in detail. Moreover, a summary of the most important results of the ab initio
modeling of RAFT polymerization reported in literature, is presented. The last part in the
literature study introduces the switchable RAFT CTA.
In Chapter 3, a concise introduction elucidating the theoretical concepts of ab initio modeling
is presented. Furthermore, the performance of different computational methods is
investigated. Next, specifically the computational methods and procedures used in this work
are clarified, including the calculation of the basic thermodynamic properties using statistical
thermodynamics, as well as the use of the COSMO-RS theory to take into account solvent
effects. At the end, some information about the kinetic model is provided.
Chapter 1: Introduction
3
The results obtained in this work, as well as the discussion of these results, are presented in
Chapter 4. First, the results of the level of theory study are discussed, followed by a
discussion of the solvent effects, the influence of the RAFT CTA and the influence of the
propagating radical. In the second part, a kinetic study of RAFT polymerization of styrene, by
making use of CPDT as RAFT CTA and AIBN as initiator, is performed by the
implementation of the ab initio calculated kinetic parameters in the in-house kinetic model.
After adapting the ab initio calculated values with the necessary correction factors, the output
of the simulations is compared with available experimental data. Also the initiation and
propagation reactions are investigated, and a closer look is taken at the influence of
temperature on conversion, number of monomer units per chain, dispersity and end-group
functionality.
Finally, the most important conclusions are summarized in Chapter 5, including some
recommendations for future research on RAFT polymerization by ab initio and kinetic
modeling.
Chapter 1: Introduction
4
Literature study
Chapter 2
The RAFT process appears as one of the most interesting CRP techniques. Due to its
versatility, it can be used for a wider range of monomers in both homogeneous and
heterogeneous environments and it is less sensitive to impurities [32, 33]. Moreover, RAFT
polymerization is additionally interesting due to its strong resemblance to free radical
polymerization and the absence of a toxic catalyst [23]. Therefore, it is a very promising
technique to prepare high-performance polymers for a wide range of applications, such as
drug and gene delivery, diagnostic applications, tissue engineering and regenerative medicine,
membrane science, bioconjugation as well as in the synthesis of polymers with optoelectronic
properties [14, 31].
In RAFT polymerization, typically thiocarbonyl compounds, known as RAFT CTAs,
reversibly react with the growing polymeric radical via a chain transfer reaction [34]. The
principle of RAFT polymerization is schematically presented in Figure 3. In the next
paragraph, the mechanism of RAFT polymerization is thoroughly described.
Figure 3. Principle of RAFT polymerization [34]
2.1 Mechanism of RAFT polymerization
The RAFT process employs a fundamentally different conceptual approach compared to other
controlled radical polymerization techniques, such as NMP and ATRP, in that it relies on a
degenerative chain transfer process and does not make use of a persistent radical effect5 [35,
36] to establish control. An important consequence of such an approach is that the RAFT
process features quasi-identical rates of polymerization as the conventional free radical
polymerization process. This is due to the ideal behavior of the RAFT CTA at steady state
5
The persistent radical effect explains the highly specific formation of the cross-coupling product between two
radicals of which one is persistent (long-lived) and the other transient, in case both radicals are formed at equal
rates. The initial buildup in concentration of the persistent species, caused by the self-termination of the transient
radical, leads to a high cross reaction rate.
Chapter 2: Literature study
5
such that its presence in a polymerization medium does not affect the polymerization rate
[14].
One of the sensitive aspects of radical polymerization processes is the termination that can
occur between two radicals leading to a lower molecular weight of the polymer. Protecting the
propagating species from bimolecular termination is possible by trapping it reversibly as a
dormant species. Equilibria between active and dormant propagating species play a crucial
role by providing equal probability for all chains to grow and allow for the production of
polymers with a low dispersity. A delicate balance of the rates of the various reactions is
required to ensure that equilibrium between dormant and active polymeric species is
established rapidly, the exchange between the two forms is rapid and the equilibrium
concentration of the dormant form is orders of magnitude greater than that of the active
species [37].
In the RAFT process, control of the molecular weight is achieved using RAFT CTAs which
are dithio- or trithioester compounds. A further investigation of these RAFT CTAs is given in
paragraph 2.2.3. The propagating radical adds to the thiocarbonyl sulfur center of the
dithioester to produce an intermediate carbon-centered radical as can be seen in Figure 4. This
carbon-centered radical can then undergo β-scission in two directions, either to form the
propagating radical again or to liberate a new carbon-centered radical, known as the leaving
group. The R-group of the RAFT CTA is chosen such that it undergoes β-scission from the
RAFT adduct radical in preference to the propagating chain, but is still capable of reinitiating
polymerization. As a result, the initial RAFT CTA, S=C(Z)SR, is rapidly converted into a
macro-RAFT CTA, (3) in Figure 4 [37].
Chapter 2: Literature study
6
(1)
(2)
(3)
(4)
(3)
(3)
Figure 4. Mechanism of RAFT polymerization [31]
Ideally, the final product of the RAFT process, which is called the macro-RAFT CTA, is a
polymer chain carrying a thiocarbonylthio end-group ((3) in Figure 4). This structure
resembles the initial RAFT CTA with a polymeric leaving group instead of the R-group. The
macro-RAFT CTA can be employed in the polymerization of a new monomer resulting in
chain extension and hence the formation of block copolymers. This mechanism can be seen in
Figure 5. A crucial feature for the successful formation of block copolymers via this method
is the stability of the propagating macroradical associated with each block. The RAFT adduct
radical in the block copolymer formation must be able to form either a macroradical based on
the monomer of the original macro-RAFT CTA P(M1) or the macroradical based on the new
monomer P(M2), as can be seen in the third reaction of the mechanism in Figure 5. A
preferred fragmentation toward the P(M1) macroradical is crucial, because generating P(M2)
macroradicals will only result in homopolymers [14].
Chapter 2: Literature study
7
Figure 5. Formation of block copolymers via chain extension of macro-RAFT CTAs [14]
The efficiency of the RAFT process is determined by the values of two transfer coefficients,
Ctr and C-tr [31]. The forward transfer coefficient Ctr is equal to the ratio of the rate coefficient
of chain transfer ktr to the rate coefficient of propagation kprop, as shown in equation (2.1). The
reverse transfer coefficient C-tr, given in (2.2), equals the ratio of the rate coefficient k-tr
associated with the reaction of the transfer agent-derived radical (R•) with a monomer or the
macro-RAFT CTA to the rate coefficient kadd,2 as indicated in Figure 4.
(2.1)
(2.2)
The transfer rate coefficients are given by the formulas (2.3) and (2.4) in which Φ is a
partition coefficient which describes the partitioning of the intermediate radical ((2) in Figure
4) between starting materials and products, and Φβ is a partition coefficient describing the
partitioning of the transfer agent-derived radical (R•) between addition to a monomer and
reaction with the macro-RAFT CTA [31].
(2.3)
(2.4)
For highly active RAFT CTAs, the forward transfer coefficient Ctr must be higher than one,
which means that the rate coefficient of chain transfer is higher than the propagation rate
Chapter 2: Literature study
8
coefficient. This indicates that transfer occurs faster than propagation by reaction with
monomer, which is desired for the control of the polymerization.
Next to the transfer coefficients, several equilibrium coefficients can be defined for a RAFT
polymerization process:
(2.5)
(2.6)
(2.7)
(2.8)
KP is associated with the main equilibrium between species (3) and (4) from Figure 4. K and
Kβ are related to the pre-equilibrium, between (1) and (2) and between (2) and (3),
respectively. The equilibrium coefficient KR is related with the reaction of the expelled radical
with the initial RAFT CTA, which is shown in Figure 6. This coefficient would be equal to KP
if R• would be a propagating radical.
kadd,R
kfrag,R
Figure 6. Reaction of the leaving group R with the initial RAFT CTA [31]
The properties of RAFT CTAs are often discussed in terms of the value of the equilibrium
coefficient K. A low value of K is not desired because the addition of the propagating radical
to the RAFT CTA has to be sufficiently fast to be able to control the polymerization. A high
K is not desired as well because it generally implies a low fragmentation rate for the radical
adduct and an increased likelihood for retardation and/or side reactions involving this species.
Rate retardation means that the rate of polymerization is reduced compared to free radical
polymerization. Another phenomenon that can have a profound effect on the reaction kinetics
is an inhibition period or a period of slow polymerization, where at the beginning of the
polymerization no, or extremely little, polymerization activity is observed over a defined
period of time. Worth to notice is that RAFT CTAs most prone to rate retardation and
inhibition effects, are those carrying Z-groups that most effectively stabilize the adduct
radicals. In addition to the Z-group, the R-group plays an important role in determining the
Chapter 2: Literature study
9
kinetics of the pre-equilibrium, as the R-group co-determines the stability of the preequilibrium adduct radicals and must efficiently initiate macromolecular growth. A RAFT
CTA that carries a very poor leaving group or one that inefficiently reacts with the monomer
will either not control the polymerization process or induce strong inhibition [31].
2.2 Modeling RAFT polymerization
2.2.1 Computational modeling
The kinetics and thermodynamics of the individual reactions in a RAFT polymerization
process are hard to obtain via experimental approaches without taking into account modelbased assumptions. This is because not the rates and equilibrium coefficients of the individual
reactions are experimentally observed, but rather the overall polymerization rate, the
concentrations of some of the major species and the average molecular weight distribution of
the resulting polymer [37]. From these measured quantities, the individual rate and
equilibrium coefficients can be determined by assuming a kinetic scheme and often making
simplifying assumptions such as the steady-state assumption [38]. In case of a very extended
reaction scheme, such as in RAFT polymerization, it becomes necessary to restrict the number
of adjustable parameters via further simplifications such as neglecting chain length effects and
side reactions [37].
Computational quantum chemistry offers an attractive solution to this problem, as it allows
the individual reactions to be studied without making assumptions. It is possible to predict the
kinetics and thermodynamics of chemical reactions from first principles, meaning that only
the laws of quantum mechanics and a few fundamental physical constants, such as the masses
and charges of the electron, proton and neutron, are used [39]. Moreover, such calculations
yield a range of additional properties such as the geometries and vibrational frequencies of the
reactants, products and transition structures.
These first principles, or ab initio, calculations come in a variety of methods, as discussed in
paragraph 2.2.4 and more fundamentally in Chapter 3. Provided that calculations for the
individual reactions in a RAFT polymerization are performed at an appropriately high level of
theory, and the rate and equilibrium coefficients are determined, the resulting values can then
be used to study structure-reactivity trends. Another advantage is that the number of
adjustable parameters in a kinetic analysis of experimental data can be reduced or, ultimately,
the kinetic behavior of a RAFT polymerization system can be predicted only starting from
Chapter 2: Literature study
10
these first principles. Such predictions could be compared directly with experimental data so
as to provide a test of the validity of the kinetic model. Moreover, having identified a suitable
kinetic model, the combination of ab initio and kinetic modeling can be used to test new
RAFT CTAs and optimize reaction conditions, prior to experiment.
2.2.2 Design of RAFT CTAs
The ultimate goal of computational modeling of RAFT polymerization is to design new
RAFT CTAs to tackle any specific control problem, or, to improve a certain process. First, a
selection of promising RAFT CTAs is made by taking into account the reactivity of the
polymeric propagating radical and the RAFT CTAs themselves. Also information about the
mechanism, kinetics and thermodynamics of the individual steps, as present in the mechanism
of RAFT polymerization (Figure 4), has to be considered. In a second step, the candidate
RAFT CTAs are tested with direct calculations using model propagating radicals. Having
established computationally that a certain RAFT CTA is likely to be successful, one could
then pursue experimental testing. After comparing the results of both approaches, general
conclusions about the performance of the RAFT CTAs can be drawn.
The kinetic requirements of a successful RAFT CTA are now fairly well understood: i) it
should have a reactive C=S bond (kadd,1 high), but not too reactive, such that the intermediate
radical undergoes fragmentation at a reasonable rate (typically K < 106 L mol-1), ii) the Rgroup should fragment preferentially from the intermediate radical in the pre-equilibrium, and
also be capable of reinitiating polymerization, and iii) there should be no side reactions [14,
37].
2.2.3 Structure-reactivity studies
2.2.3.1 Introduction
Next to the calculation of the rate or equilibrium coefficients of individual reactions,
additional mechanistic information such as the geometries, charges, spin densities and
relevant energetic quantities such as radical stabilization energies of the adduct radical can be
calculated via computational modeling. This information can greatly assist in the
interpretation of structure-reactivity trends.
A reactive double bond in the RAFT CTA plays a crucial role to get a sufficiently fast
reaction. A C=S double bond is much more effective than other types of double bonds, like a
C=C double bond, that would serve the same purpose. This can be explained via the curvecrossing model [40] that was developed by Pross and Shaik [41-43]. This model is a
Chapter 2: Literature study
11
theoretical framework for explaining barrier formation in chemical reactions. In radical
addition to double bonds, the four lowest doublet configurations of the three-electron-threecenter system, formed by the unpaired electron at the radical carbon (R) and the electron pair
of the π bond in X=Y (A), may contribute to the ground state wave function. These
configurations are shown below in Figure 7. The first one (RA) corresponds to the
arrangement of electrons in the reactants, the second configuration (RA3) represents that of
the products and the third (R+A-) and fourth configuration (R-A+) are possible charge-transfer
configurations [37].
Figure 7. The four lowest doublet configurations of the three-electron-three-center system [37]
In Figure 8, a state correlation diagram is given, showing how the energies of the different
configurations can vary as a function of the reaction coordinate. In the beginning of the
reaction, the reactant configuration is the lowest-energy configuration and dominates the
reaction profile. The reason therefore is the stabilizing influence of the bonding interaction in
the π bond of the reactant configuration, which is an antibonding interaction in the product
configuration. As the reaction proceeds, the unpaired electron on the radical becomes able to
interact with the double bond leading to destabilization of the reactant configuration and
stabilization of the product configuration. Therefore, beyond the transition structure, the
product configuration is lower in energy than the reactant configuration and dominates the
wave function. The charge-transfer configurations are high in energy, however, in the vicinity
of the transition structure they are both stabilized by Coulomb interactions. Because of these
interactions, their energy is sometimes sufficiently low to interact with the ground state wave
function [37, 44].
Chapter 2: Literature study
12
Figure 8. State correlation diagram for radical addition to double bonds [37]
The principle of curve-crossing leads to an explanation for the high reactivity of
thiocarbonyls. As the relative energies of the reactant and product configurations converge
towards each other, the increasing interaction between the alternate configurations stabilizes
the ground state wave function and a stronger interaction is observed with decreasing energy
difference between the alternative configurations. The π bond of a thiocarbonyl is much
weaker than that of an alkene, because of the poorer overlap between the π orbitals of the
sulfur and carbon atom. This reduced π bond strength results in a greatly reduced singlettriplet gap for the thiocarbonyl species, hence a strong interaction, low barriers and early
transition structures for radical addition [37]. The low barrier results in a fast addition
reaction, which is necessary to control the RAFT polymerization process. Because of the early
transition structures, the influence of the exothermicity on the addition reaction is greatly
reduced, meaning that the proportionality constant α in the Evans-Polanyi relationship6 (2.9)
is much smaller than in the case of late transition structures [37, 45, 46]. Therefore, dithioester
compounds are used as RAFT CTAs while alkenes are not suitable. Studies of prototypical
systems have shown that C=C, C=O and C≡C bonds all have significantly larger singlet-
6
The Evans-Polanyi rule states a linear relationship between the activation energy and the reaction enthalpy of
reactions within one family.
Chapter 2: Literature study
13
triplet gaps than C=S bonds. As a result, the above mentioned bonds are less reactive to
radical addition than C=S bonds, and so less desired as RAFT CTAs [14].
(2.9)
Not only a reactive double bond in the RAFT CTA is required, the chemical nature of the
other substituents, R and Z, is critical to a controlled polymerization. The degree of control
that can be achieved depends strongly on the tendency for addition of the propagating radical
Pn• to the C=S bond and the subsequent release of that radical from the intermediate carboncentered radical. These two tendencies for addition and release depend on the steric and
electronic properties of R and Z. Moreover, these properties determine the magnitude of the
individual rate coefficients that govern the pre-equilibrium. Most of the variation in the preequilibrium seems to stem from variations in the fragmentation rates. The addition rate
coefficient appears to be largely insensitive to variations in the RAFT CTA structure, as is
evident from published experimental values for polymeric systems with different RAFT CTA
structures, which show close agreement with one another [47-49].
Some structure-reactivity data are available from experimental studies, but computational
chemistry is an additional powerful tool to confirm and explain the observed trends.
Moreover, predictions about the ‘best’ combinations of R- and Z-groups can be made, which
is very useful for designing RAFT CTAs (cf. paragraph 2.2.2).
2.2.3.2 Effect of the Z-group
The Z-group in RAFT CTAs has an influence on the stability of both the RAFT CTA and the
RAFT adduct in two main ways. First, if the Z-group has a free electron-pair such as OR, NR2
or SR, a better stabilization of the RAFT CTA is obtained, due to delocalization of the
electron density into the C=S bond as shown in Figure 9.
Figure 9. Delocalization of electron density in case of lone-pair donor Z-groups [14]
The second effect is the destabilization of RAFT CTAs if Z is electron deficient due to σwithdrawal. This property can be clearly observed with the RAFT CTAs that have CN or CF3
as Z-group [37].
Chapter 2: Literature study
14
Considering RAFT adduct radicals, the effects of Z are somewhat more complicated. If Z is a
π-acceptor group such as Ph or CN, a major increase in stability is gained [50]. Stabilization
by π-acceptor groups is common for carbon-centered radicals, and in RAFT adduct radicals
the effect can be enhanced because the lone-pair donor SR-groups can engage in captodative
effects7 [51]. One would think that the presence of a lone-pair donor Z-group should be an
additional stabilizing feature (as in other carbon-centered radicals), but in RAFT adduct
radicals this is not always true. The reason is that the delocalization of electron density from a
SR-group onto a carbon radical center places the unpaired electron into a higher-energy
orbital, which makes further delocalization onto a second SR-group much less favorable. A
RAFT adduct radical already has two lone-pair donor SR-groups even before considering Z,
so a third interaction involving a lone-pair donor Z-group is not favorable anymore. However
enhanced stabilization will be observed when Z is a stronger lone-pair donor than SR. Making
the situation more complicated, also the second effect of the Z-groups plays a role. RAFT
adduct radicals are strongly destabilized by σ-withdrawal which means that only those Zgroups for which lone-pair donation is stronger than σ-withdrawal (and stronger than the lonepair donation by an SR-group) will lead to enhanced stabilization [37].
In Table 1, the reaction enthalpies ΔHr for the addition of a methyl radical to several
important RAFT CTAs are given, as well as the activation enthalpies ΔH‡. Furthermore, the
equilibrium coefficients K and the rate coefficients kadd,1 for these addition reactions are
presented. The Z-group is varied to study the influence of these substituents, while a methyl
group as R-group is considered. These enthalpies, expressed in kJ mol-1, and the rate
coefficients, expressed in L mol-1 s-1, are calculated at G3(MP2)-RAD, which is a high-level
composite procedure (cf. Chapter 3). The values of the equilibrium coefficients, expressed in
L mol-1, are calculated at the W1-ONIOM method after optimization of the geometry at
B3LYP/6-31G(d). The reaction enthalpies are calculated at 0 K while the activation enthalpies
and the rate coefficients are calculated at 333 K [34, 37, 52-54].
7
Captodative effects involve the stabilization of radicals by the synergistic effect of an electron withdrawing and
an electron donating group in radical reactions.
Chapter 2: Literature study
15
Table 1. Influence of the Z-group on the reaction enthalpy ΔHr [kJ mol-1], the activation enthalpy ΔH‡
[kJ mol-1] and the rate coefficient kadd,1 [L mol-1 s-1] for the addition of the methyl radical, calculated at
G3(MP2)-RAD at 0 K and twice 333 K respectively, and on the equilibrium coefficient K [L mol-1],
calculated at W1, R-group = methyl group [37, 52-54]
ΔH‡
[kJ mol-1]
9.2
4.4
0.6
ΔHr
[kJ mol-1]
-29.2
-64.2
-72.3
-74.2
-95.2
Z
OCH3
CH3
CH2Ph
H
Ph
K
[L mol-1]
8.2
3.8 E+07
1.9 E+08
1.7 E+11
kadd,1
[L mol-1 s-1]
1.2 E+06
8.7 E+06
5.4 E+07
The different RAFT CTAs with a methyl group as R-group, and with the Z-group equal to a
methoxy group, methyl group, benzyl group, phenyl group and hydrogen are shown in Figure
10.
S
S
S
S
S
CH3
S
CH3
CH3
O
CH3
H3C
S
S
CH3
S
S
CH3
H
Figure 10. Chemical structure of the RAFT CTA with R-group = methyl group and Z-group = methoxy
group (top left), methyl group (top center), benzyl group (top right), phenyl group (bottom left) and
hydrogen (bottom right)
Looking at Table 1, the strong effect of the Z-substituent is clearly visible, which is expected
because the Z-group is directly attached to the carbon bearing the unpaired electron in the
RAFT adduct radical. The ranking of the different Z-groups, from least to most exothermic
reaction, is as follows: OCH3 < CH3 < CH2Ph < H < Ph. Using a phenyl group as Z-group
corresponds with the most exothermic reaction between the methyl radical and the RAFT
CTA. This is because the phenyl substituent is expected to stabilize the RAFT intermediate to
a great degree due to its ability to delocalize the unpaired electron in the aromatic ring. The
greater exothermicity of the addition reaction for the benzyl-substituted agent, compared to
the methyl group as Z-group, may reflect a greater release of steric strain upon reaction [34].
Chapter 2: Literature study
16
Looking at the difference between the methoxy-substituted and the methyl-substituted RAFT
CTAs, a much more exothermic reaction is observed in the latter case. This can be explained
by the σ-withdrawal effect of alkoxy groups, resulting in a destabilization of the RAFT adduct
radical. The addition reaction is not favored due to this destabilizing effect, resulting in a
lower enthalpy difference when using the methoxy-substituted RAFT CTA [9].
When comparing the ranking of the Z-groups based on the reaction enthalpy and on the
activation enthalpy, it can be observed that the most exothermic reaction corresponds to the
lowest activation enthalpy. This means that thermodynamically favored reactions are also
kinetically favorable because of the low enthalpy barrier, which is recognized as the Evans
Polanyi relationship (paragraph 2.2.3.1). A low activation enthalpy leads furthermore to a low
activation energy, which will be explained in Chapter 3 (equation (3.50)). As a consequence,
a higher rate coefficient of addition is expected in accordance with the Arrhenius law (3.48),
which is confirmed looking at the values in Table 1.
Because of the higher rate coefficient of addition using a RAFT CTA with a phenyl Z-group
compared to a benzyl Z-group, it is confirmed that the phenyl substituent stabilizes the
intermediate radical in RAFT polymerization better than the benzyl substituent because
phenyl is a good π-acceptor group, leading to a stable RAFT adduct radical. It can also be
concluded that radical addition is very fast and values for kadd,1 are in line with experimental
values (kadd,1 = 106 – 108 L mol-1 s-1) [54, 55].
Generally spoken, it is worth mentioning that the qualitative effects of the substituents on the
forward addition reactions are much smaller than those on the reverse fragmentation
reactions, as mentioned before. This is due to the high reactivity of the C=S bond and the
early transition structures for the addition reactions [53]. This can be seen in Table 1 by the
larger differences between the equilibrium coefficients, compared to the rate coefficients.
The equilibrium coefficients of the reactions with different Z-groups, are almost proportional
to, and show the same trends as, the reaction enthalpies, because no, or only small, entropic
differences are expected. Specifically, the reactions with the methyl R-groups have very high
equilibrium coefficients and, within this class of reactions, the phenyl- and benzyl-substituted
RAFT CTAs have a considerably higher equilibrium coefficient than the RAFT CTA with
methyl as Z-group. A previous kinetic study showed that rate retardation becomes significant
when the equilibrium coefficient exceeds 106-107 L mol-1 [34]. On this basis, the RAFT CTAs
with phenyl and benzyl substituents in the Z-position should show strong rate retardation.
Chapter 2: Literature study
17
However, it is clear that RAFT CTAs with more realistic R-groups have equilibrium
coefficients that are considerably lower than those with methyl R-groups. Hence, it is possible
that the use of non-methyl R-groups on phenyl- or benzyl-substituted RAFT CTAs would
relieve this rate retardation [34].
2.2.3.3 Effect of the R-group
The steric and electronic properties of the R-group influence the chain transfer in two
reinforcing ways: one effect on the R• radical and the opposite effect on the RAFT CTA. The
presence of π-acceptor groups as α-substituents within R• radicals, as well as the capacity for
hyperconjugative interactions provided by α-CH3 substituents, confer enhanced stability. On
the other hand, destabilization of the RAFT CTAs, due to the presence of α-CH3 groups or πacceptor α-substituents in the R-group, has to be taken into account. This is because of the
unfavorable steric interactions, primarily induced by methylation. The π-acceptor groups
destabilize the RAFT CTAs by reducing the capacity for delocalization of the sulfur lone pair
onto the double bond, as can be seen in Figure 11 [37].
Figure 11. Reduced delocalization of the sulfur lone pair onto the double bond [37]
Important to notice is that synergistic effects between the Z- and R-group can occur, which
can cause a breakdown of the previously described structure-reactivity trends [37].
2.2.3.4 Effect of the methyl radical and different monomer radicals
Table 2 compares reaction enthalpies for the addition of different radicals to methyl ethane
dithioate (MEDT) as RAFT CTA (both R- and Z-groups are methyl groups). Also the
activation enthalpies, rate coefficients and equilibrium coefficients of these reactions are
given in Table 2 [52].
Chapter 2: Literature study
18
Table 2. Influence of the methyl radical and different monomer radicals on the reaction enthalpy ΔHr
[kJ mol-1], calculated at G3(MP2)-RAD at 0 K, on the activation enthalpy ΔH‡ [kJ mol-1] and the rate
coefficient of addition kadd,1 [L mol-1 s-1], calculated at G3(MP2)-RAD at 333 K, and on the equilibrium
coefficient K [L mol-1], calculated at W1, RAFT CTA = methyl ethane dithioate [37, 52-54]
ΔHr
[kJ mol-1]
ΔH‡
[kJ mol-1]
K
[L mol-1]
kadd,1
[L mol-1 s-1]
Benzyl radical
-34.2
4.9
2.7
2.8 E+06
Styryl radical
-35.9
-
1.1
-
Methyl acrylate radical
-55.9
-
-
-
Methyl radical
-64.2
9.2
3.8 E+07
1.2 E+06
Radical
Considering the different radicals in Table 2, some significant differences can be observed. It
can be seen that the reaction between a methyl radical and the RAFT CTA MEDT is the most
exothermic one. The one with methyl acrylate radical is quite exothermic as well. The benzyl
radical and styryl radical have similar values for the reaction enthalpy of the addition reaction
which could be expected due to the similar chemical structure [52]. Again, as mentioned in
section 2.2.3.2, more or less the same trend between the reaction enthalpy and equilibrium
coefficient is observed [37]. A more exothermic reaction corresponds to a higher equilibrium
coefficient.
Comparing the trend in the reaction enthalpy and the activation enthalpy for the different
radicals considered, leads to the opposite conclusion as in the study of the effect of the Zgroup (cf. paragraph 2.2.3.2). The reaction of the methyl radical is more exothermic and a
higher activation enthalpy is observed, compared to the reaction of the benzyl radical. This
unexpected observation is also commented upon in literature. Coote et al. have noted that the
addition of the benzyl radical to S=C(CH3)SCH3 is slightly faster (factor 2) than the addition
of the methyl radical, which arises from a lower reaction barrier for the first reaction. This is
somewhat unusual because the benzyl radical is larger and more stable than the methyl radical
[53]. The significance might be disputable looking at the small difference.
2.2.4 Influence of computational methods on results
In Table 3, the reaction enthalpies of the addition reaction of different radicals to MEDT are
calculated at different levels of theory with different basis sets: B3LYP/6-311+G(3df,2p),
BMK/6-311+G(3df,3p) and G3(MP2)-RAD (cf. Chapter 3). Coote et al. [52] have
investigated that none of the DFT methods, including B3LYP and BMK, provide an adequate
Chapter 2: Literature study
19
substitute for G3(MP2)-RAD, and that errors in all the DFT methods are highly
nonsystematic for various radicals. However, BMK tends to perform slightly better than other
DFT methods. New functionals would be desirable to model the absolute and relative values
of the enthalpies for addition reactions [52].
Table 3. Influence of the methyl radical and different monomer radicals on the reaction enthalpy ΔHr
[kJ mol-1] of the addition reaction calculated at three levels of theory: B3LYP/6-311+G(3df,2p), BMK/6311+G(3df,3p) and G3(MP2)-RAD at 0 K, RAFT CTA = methyl ethane dithioate [52]
B3LYP
BMK
G3
ΔHr [kJ mol-1]
ΔHr [kJ mol-1]
ΔHr [kJ mol-1]
Methyl radical
-56.8
-76.3
-64.2
Benzyl radical
0.3
-29.2
-34.2
Styryl radical
11
-20.5
-35.9
Methyl acrylate radical
-7.8
-40.4
-55.9
Radical
Table 4 shows the influence of the Z-group on the reaction enthalpy of the addition reaction
of the methyl radical to a RAFT CTA with a methyl group as R-group, calculated at the three
different levels of theory mentioned above. Again, some differences between the results
obtained at different levels of theory can be observed. However, the trends, when varying the
Z-group of the RAFT CTA, are systematic for the three methods. The values calculated at
B3LYP are always higher than the values at BMK and G3, and the values at G3 are
systematically higher than at BMK. This is the case for all the reactions considered in Table 4.
Table 4. Influence of the Z-group on the reaction enthalpy ΔHr [kJ mol-1] of the addition reaction of a
methyl radical, calculated at three levels of theory: B3LYP/6-311+G(3df,2p), BMK/6-311+G(3df,3p) and
G3(MP2)-RAD, at 0 K, R-group = methyl [52]
B3LYP
BMK
G3
ΔHr [kJ mol-1]
ΔHr [kJ mol-1]
ΔHr [kJ mol-1]
OCH3
-23.7
-37.1
-29.2
CH3
-56.8
-76.3
-64.2
CH2Ph
-59.5
-81.1
-72.3
H
-68.9
-88.2
-74.2
Ph
-83.2
-104.3
-95.2
Z
Chapter 2: Literature study
20
2.3 Switchable RAFT CTAs
A new class of stimuli-responsive RAFT CTAs has recently been reported [56-58]. These, socalled switchable RAFT CTAs, can offer good control over the polymerization of both “lessactivated” monomers (LAMs) and “more-activated” monomers (MAMs), by switching
between the original and the protonated form of the RAFT CTA, shown in Figure 12. The R’substituent, as well as the pyridinyl substituent, influence the electron density on the
dithiocarbamate nitrogen, which in turn influences the electron density on the C=S double
bond. The modification of the electronic properties of the dithiocarbamate nitrogen has to be
simple, able to be performed in situ, rapid and reversible. Protonation of a conjugated
nitrogen, or interaction of a conjugated nitrogen with a Lewis acid, meets these criteria,
required for the suitability of the RAFT CTA for both monomer categories [56]. To form the
protonated RAFT CTA, a strong acid has to be used, for example 4-toluenesulfonic acid or
trifluoromethanesulfonic acid, and it should be added in a stoichiometric amount. Using less
than the stoichiometric amount of acid, or using a weaker acid, was found to provide poorer
control [56]. These switchable RAFT CTAs allow the synthesis of poly(MAM)-blockpoly(LAM) with narrow molecular weight distributions [56, 57].
Figure 12. Neutral (left) and protonated (right) form of the switchable RAFT CTA [58]
Benaglia et al. [56, 57] have investigated that N-(4-pyridinyl)-N-methyl dithiocarbamates (R’
= methyl in Figure 12) provide excellent control over polymerization of LAMs, and, after
addition of one equivalent of a protic or Lewis acid, become effective in controlling
polymerization of MAMs. This scheme of switching of the RAFT CTAs and controlling
polymerization of both types of monomers is schematically shown in Figure 13 [56, 57].
Chapter 2: Literature study
21
Figure 13. Scheme of the switchable RAFT CTA, N-(4-pyridinyl)-N-methyl dithiocarbamate,
controlling both the polymerization of LAMs and MAMs [56]
Keddie et al. [58] have shown that another kind of acid/base switchable RAFT CTAs, N-(4pyridinyl)-N-R’ dithiocarbamates, where R’ is an aryl or a pyridinyl substituent, possess
enhanced activity in both the acidified and neutral forms, when compared to that of the parent
class, with R’ equal to a methyl group. The incorporation of aryl substituents enhances
activity of the RAFT CTAs due to their electron withdrawing character. In case of the
protonated form, the contribution of the zwitterionic8 [40] canonical form is reduced. The
canonical structures of dithiocarbamates are generally represented in Figure 14, in which the
zwitterionic form can be seen at the right. Also the control over the molar mass and the
dispersity seems to be better in case of aryl substituents [58].
Figure 14. Canonical structures of dithiocarbamates [58]
8
A zwitterionic compound is a neutral compound, having formal unit electrical charges of opposite sign.
Chapter 2: Literature study
22
Chapter 3
Computational methods
Computational chemistry can be described as chemistry performed using computers rather
than chemicals. This covers a broad range of topics such as molecular mechanics, semiempirical methods and ab initio quantum chemistry. The last one will be studied in detail
because ab initio modeling is performed during this thesis. Ab initio means ‘from the
beginning’ or ‘from first principles’. The difference with other computational methods is that
it is based solely on established laws of quantum mechanics and basic physical constants, as
will be explained in paragraph 3.1.1. As mentioned earlier in paragraph 2.2.1, for ab initio
modeling a variety of levels of theory exists, as well as different basis sets. The level of theory
mainly determines the manner in which electron exchange and electron correlation are taken
into account while the basis set provides a description of the atomic orbitals and the electron
distribution. The most accurate methods require enormous computational resources, their
computational cost scaling exponentially with the size of the system. Cheaper methods can be
used to study much larger systems but are not that reliable. To apply ab initio methods to
reactions present in the RAFT mechanism, the most computationally efficient methods that
still deliver acceptable accuracy, must be selected based on the benchmarking of small model
systems that show a similar kinetic behavior to the polymeric reactions [37].
3.1 Ab initio methods
3.1.1 Introduction
The computational theory is based on the fundamental postulate of quantum mechanics. This
postulate states that a wave function
operators which act upon
exists for every chemical system and that appropriate
, return the observable properties of the system. Mathematically,
this postulate is given in (3.1) [44, 59, 60].
(3.1)
In this formula,
is an operator and
this equation holds,
is a scalar value for some property of the system. When
is called an eigenfunction and
an eigenvalue. The wave function does
not have a physical meaning but the product of the wave function with its complex conjugate
|
| represents the probability density. The Schrödinger equation is obtained when the
Chapter 3: Computational methods
23
Hamiltonian operator ̂ , represented in (3.2), is considered and the energy E is the observable
property of the system.
̂
̂
̂
̂
̂
̂
(3.2)
In formula (3.2), ̂ represents the kinetic energy of the nuclei, ̂ the kinetic energy of the
electrons, ̂
the nuclear-nuclear repulsion, ̂
the nuclear-electron attraction and ̂
the
electron-electron repulsion [61]. The power of the quantum mechanical postulate as expressed
in equation (3.1), is that if a molecular wave function is available, it is possible to calculate
several physical observable properties by application of the corresponding operator [44].
Solving the Schrödinger equation requires two levels of approximation. The first one is the
Born-Oppenheimer approximation, in which it is assumed that the nuclei are infinitely heavy
so they are clamped at certain positions in space. Furthermore, the nuclear kinetic energy is
neglected and the nuclear-nuclear repulsion term is constant because of the fixed positions of
the nuclei. Basically, the Born-Oppenheimer approximation means that the motion of the
electrons no longer depends on the motion of the nuclei. However, the motion of the electrons
clearly depends on the positions of the nuclei. Similarly, the motion of the nuclei no longer
depends on the detailed motion of the electrons but only on an average property, the energy of
the electrons for a given nuclear configuration [61-64]. The second approximation is the
variational principle for the ground state wave function. The variational theorem states that
the energy determined from any appropriate wave function will always be greater than the
energy for the exact wave function Eexact. This theorem is given in equation (3.3), where
is
the exact ground state wave function [61, 62, 65, 66].
〈 〉
⟨ |̂| ⟩
⟨
|̂ |
⟩
(3.3)
3.1.2 Hartree-Fock theory
Pretending that the electrons do not interact with each other, which means that ̂
= 0, the
Hamiltonian operator would be separable. This means that its many-electron wave function
can be constructed as a product of one-electron wave functions, resulting in a Hartree-product
wave function
. This is given in (3.4), in which N is the number of electrons and ϕi are
called the molecular orbitals (MO). Each molecular orbital consists of a spatial part and a spin
part. The Hartree form of the wave function is sometimes called the independent electron
approximation because this form does not allow for instantaneous interaction of the electrons.
The electrons instead feel the averaged field of all electrons in the system [61, 65, 67].
Chapter 3: Computational methods
24
(
)
( )
( )
( )
(3.4)
This functional form has at least one major shortcoming: it fails to satisfy the antisymmetry
principle. One of the postulates of the quantum mechanics states that the total wave function
must be antisymmetric with respect to the interchange of electron coordinates. This
shortcoming was overcome by Fock by adding signed permutations. The antisymmetrized
wave function can be written as a Slater determinant (3.5) and is called the Hartree-Fock (HF)
wave function, because of the combination of the Hartree-product wave function and the
inclusion of the antisymmetry by Fock. This functional form ensures the electrons are all
indistinguishable and each electron is associated with every orbital [61, 67].
√
[
( )
( )
( )
]
( )
(3.5)
The Hartree-Fock method follows a self-consistent field (SCF) procedure to determine the
molecular orbitals and the energy. First, each molecular orbital is written as a linear
combination of atomic orbitals (AOs), also called basis functions, shown in (3.6).
( )
Where
are the basis functions and
∑
( )
(3.6)
are MO coefficients. The construction of this basis
functions is explained in more detail in paragraph 3.1.6.1. If the wave function is normalized,
the expectation value of the energy is given by equation (3.7). For the HF wave function, this
can be written as formula (3.8), where Hi involves one-electron terms arising from the kinetic
energy of the electrons and the nuclear attraction energy, Jij involves two-electron terms
associated with the Coulomb repulsion between the electrons and Kij involves two-electron
terms associated with the exchange of electronic coordinates [61, 65].
⟨ |̂ | ⟩
∑
∑(
(3.7)
)
(3.8)
The Hartree-Fock energy can be written in terms of the MO coefficients [67]. The oneelectron parts of the energy for example are given in (3.9).
Chapter 3: Computational methods
25
⟨ |̂| ⟩
∑
⟨ |̂| ⟩
(3.9)
The MO coefficients aij can be determined using the variational theorem, explained in the
previous paragraph 3.1.1. The energy of the exact wave function serves as a lower bound of
the calculated energy, so the MO coefficients can be simply adjusted until the total energy of
the system is minimized. Thus computing the HF energy implies the determination of the MO
coefficients. However, to compute the MO coefficients, the HF energy must be minimized
according to the variational principle. This leads to an iterative procedure, which is developed
by Hartree and called the SCF method. A flow chart of the Hartree-Fock SCF procedure is
given in Figure 15 [61].
Guess a set of MO coefficients aij
Use MO coefficients to compute Hi, Jij and Kij
Solve the HF equations for the energy and new
MO coefficients
Are the new MO coefficients different?
YES
NO
Self-consistent field converged
Figure 15. Flow chart of the HF SCF procedure [61]
In the Hartree-Fock method, all electron correlation is ignored because it is based on the
assumption that each electron sees all of the others as an average field. The Hartree-Fock
theory provides a very well defined energy which can be converged in the limit of an infinite
basis set, and the difference between that converged energy and reality is called the electron
correlation energy [44, 68].
3.1.3 Electron correlation
As no electron correlation is included in the Hartree-Fock method, methods have been
developed to compute the electron correlation energy. Two components have to be taken into
Chapter 3: Computational methods
26
account in the correlation energy: dynamic and static correlation. The dynamic correlation is
the energy associated with the movement of electrons as they try to avoid each other, which is
important in bond breaking processes. The static part arises from deficiencies in the single
determinant wave function and is important in stretched bonds and low-lying excited states.
More advanced theories such as configuration interaction (CI) [69-71], Møller-Plesset
perturbation theory (MPn) [72-74] and coupled cluster theory (CC) [75, 76] can describe the
dynamic correlation [77]. To describe the static correlation, one has to use multiconfigurational SCF (MCSCF) methods [78-80], such as complete active space SCF
(CASSCF) [81, 82].
3.1.3.1 Configuration interaction method
In the configuration interaction method, different configurations are created by ‘exciting’ one
or more electrons from occupied to virtual orbitals, which are orbitals that are not occupied.
These configurations can be mixed together to obtain a better approximation of the wave
function
, which is shown in (3.10).
∑∑
∑∑
(3.10)
Herein i and j are the indices of the occupied MOs in the HF reference wave function
while a and b are the indices of the virtual MOs in
. The CI coefficients
,
,
… can be
determined via the variational method. If all possible excited configurations are included, a
full-CI wave function is obtained. This is the most complete treatment possible for a given set
of basis functions. Unless this full-CI wave function is used, no size consistency9 is
guaranteed. The consequences of methods that are not size consistent are poor dissociation
energies and poor treatment of larger systems, because the correlation energy per component
tends to zero as the number increases [44, 61, 83].
3.1.3.2 Møller-Plesset perturbation theory
The core of the Møller-Plesset perturbation theory is to create a more tractable operator by
removing some particularly unpleasant portion of the original one. It is possible to estimate
the eigenfunctions and eigenvalues of the more complete operator, by using exact
9
A method is size consistent if it yields M times the energy of a single molecule when applied to M noninteracting molecules.
Chapter 3: Computational methods
27
eigenfunctions and eigenvalues of the simplified operator [44]. In the Møller-Plesset
perturbation theory, the Hamiltonian is divided into two parts, given in (3.11).
̂
The perturbation,
̂
̂
(3.11)
̂ , is assumed to be small. The wave function and energy are then
expanded as a power series in , respectively shown in formula (3.12) and (3.13).
(3.12)
(3.13)
Where
and
the expansion at
are the HF wave function and energy respectively. MPn is obtained by truncating
. The disadvantage of this method is that convergence problems may occur
for large orders, but the biggest advantage is the size consistency [44, 61, 84, 85].
3.1.3.3 Coupled cluster theory
The coupled cluster theory is based on the following form of the full-CI wave function.
(3.14)
With T the cluster operator, given in (3.15).
(3.15)
Where n is the total number of electrons and the various Ti operators generate all possible
determinants having i excitations from the reference. The most prominent example is the
double excitation operator T2, shown in (3.16).
∑∑
(3.16)
Where the amplitudes t are determined by the constraint that equation (3.14) has to be
satisfied. Using the exponential of T ensures size consistency which is not the case for
truncated CI approaches. This can be illustrated by considering a Taylor expansion of T2,
(3.17).
(
)
(3.17)
Where CCD implies coupled cluster with only the double-excitation operator included. As
each application of T2 induces double excitations, the square of this operator generates
quadruple excitations and the cube sextuple excitations and so on. It is exactly the failure to
include these excitations in CI that makes that method not size consistent [44, 61, 62, 86].
Chapter 3: Computational methods
28
3.1.3.4 Multi-configurational SCF methods
Only occupied orbitals contribute to the electronic energy, in contrast to the virtual orbitals.
Hence, there is no driving force to optimize the geometry of the virtual orbitals, it is only
required that they are orthogonal to the occupied MOs. Thus, the quality of the shape of an
orbital depends on whether it is an occupied orbital or not. A multi-configurational selfconsistent field wave function can be used, which takes into account combinations of
configurations, weighted with a factor proportional to their relevance. Permitting all possible
arrangements of active electrons among active orbitals in the MCSCF expansion is typically
referred to as having chosen a ‘complete active space’ (CAS), known as CASSCF [44, 62].
3.1.4 Density functional theory
For the development of the density functional theory (DFT), one was looking for a useful
physical observable, that permitted a priori construction of the Hamiltonian operator. The
Hamiltonian depends only on the position and atomic number of the nuclei and the total
number of electrons. The dependence on the total number of electrons immediately suggests
that the electron density can be a useful physical observable, since, integrated over all space,
it gives the total number of electrons. Moreover, because the nuclei are point charges, it
should be obvious that their positions correspond to local maxima in the electron density.
Furthermore, it can be shown that the nuclear atomic numbers are also available from the
density. The arguments above indicate that, given a known density, one could form the
Hamiltonian operator, solve the Schrödinger equation and determine the wave functions and
energy eigenvalues [65].
Energy is separable into kinetic and potential components and this property is used for the
development of early density functional10 models. These density functionals are based on a
simple model system, i.e. the uniform electron gas, a system with a constant electron density.
It consists of an infinite number of bound electrons that move against a positively charged
background. The total energy of this system is infinite and the energy is therefore expressed in
terms of energy per particle, given in equation (3.18) [65].
[ ]
[ ]
∫
̅ ( ̅) ( ̅)
[ ]
[ ]
(3.18)
The first term in the right hand side of equation (3.18) stands for the kinetic energy, the
second term represents the electrostatic attraction energy between the positive background
10
A functional is a function whose argument is also a function.
Chapter 3: Computational methods
29
and the electrons, the third term is the electrostatic repulsion energy between the electrons and
the fourth term is a combination of exchange and correlation energy.
The last term has to be estimated and can be split in the exchange energy, Ex, and the
correlation energy, Ec, as is represented in equation (3.19).
[ ]
[ ]
[ ]
(3.19)
The exchange energy and the correlation energy are separately estimated by making use of
some approximations. An extrapolation towards nonhomogeneous systems can be made by
assuming that the energy per electron at a certain position r depends only on the density at that
position, the ‘local’ value of the density. This is known as the local density approximation
(LDA), leading to local density functionals. Systems including spin polarization must use the
spin-polarized formalism, and its greater generality is sometimes referred to as ‘local spin
density approximation’ (LSDA) [65, 87, 88].
Another possibility is the application of the generalized gradient expansion approximation
(GGA), for which semi-local functionals are introduced. In that case, the correlation or
exchange energy functional will depend not only on the local value of the density, but on the
extent to which the density is locally changing, i.e. the gradient of the density. The slope of
the density gives information about the position in the molecular system. A large slope
indicates a position near the nucleus while a small slope represents a position far from the
nucleus. Moreover, the functional has to fulfill as much exact properties as possible such as a
correct asymptotic behavior [44, 65, 87-89].
The meta-GGA (MGGA) is essentially an extension of the GGA in which also the second
derivative of the density, i.e. the Laplacian is taken into account. An alternative MGGA
formalism that is more numerically stable, is to include in the exchange correlation potential a
dependence on the kinetic energy density [44, 65, 87, 88].
When specifically looking at the estimation of the exchange energy, GGA functionals are
proposed in the following form (3.20).
[ ]
With a dimensionless gradient ( ⃗)
∫ ⃗[
|⃗⃗⃗⃗⃗⃗|( ⃗)
( ⃗)
( ( ⃗))] ( ⃗)
. The correction term
(3.20)
( ( ⃗)) becomes more
important if there is more variation in the density, meaning that a larger gradient is present.
Using this form, the right behavior for a homogeneous electron gas is obtained and for
Chapter 3: Computational methods
30
nonhomogeneous systems a correction is introduced [65, 87-89]. Many people introduced
exchange functionals, from which the first, widely popular, GGA exchange functional was
developed by Becke [65]. The functional is shown below, where the parameter β is fitted to
reproduce the Hartree-Fock exchange energies of the noble gases.
( ( ⃗))
( ⃗)
( ⃗)
( (⃗))
(3.21)
Becke’s exchange energy functional gives the correct asymptotic behavior. For small
gradients of the density, the LDA exchange energy density is found, while for larger
gradients, the correction term becomes much more important.
Analogously for the estimation of the correlation energy, different advanced functionals are
proposed by Perdew (P86), Perdew-Wang (PW91), Lee-Yang-Parr (LYP) and many more
[44, 87].
When making use of GGA, an exchange and a correlation energy functional have to be
selected, leading to, for example, the BLYP method, which uses Becke’s exchange functional
and the correlation functional proposed by Lee-Yang-Parr [65]. Hybrid functionals are also
very often used. They include a mixture of Hartree-Fock exchange with DFT exchangecorrelation. It is concluded that inclusion of HF exchange in a hybrid functional makes up for
an underestimation by pure functionals of the importance of ionic terms in describing polar
bonds [90]. The B3LYP functional, for example, incorporates three terms for exchange: one
deduced from LDA, one representing the HF exchange with Kohn- Sham (KS) orbitals [9193], and one introduced by Becke with the correct asymptotic behavior [65]. B3LYP with
large basis sets seems to be particularly robust [94, 95].
Another important hybrid functional, which is used for the calculations performed in this
work, is BMK [96], standing for Boese-Martin for Kinetics. This powerful functional
combines excellent performance for barrier heights with performance rivaling the best
available hybrid functionals (such as B97-1) for thermochemistry, and at least B3LYP-quality
performance for other properties. To achieve this, two “penalty functions” were constructed.
One consists of a large number of molecular dissociation energies, gradients at equilibrium
geometries, and other equilibrium properties, while the other function is constructed from a
moderately large number of accurately known reaction barrier heights. After investigation of
these two penalty functions, a new functional is optimized for a combined penalty function in
which barrier heights were assigned larger weights. In the BMK functional, the kinetic energy
Chapter 3: Computational methods
31
density is included, which appears to correct the excess exact exchange mixing for ground
state properties [96].
3.1.5 Parameterized methods
Many advanced theories, like full CI or MP4, can only be applied to a small fraction of the
chemically interesting systems because of their computational expense. And, with scaling
behaviors on the order of N10, it cannot be expected that this will improve soon. As a result,
parameterized methods are developed [97], in which an improved predictive accuracy with a
still acceptable computational cost is pursued. It is possible to scale the correlation energies,
because the fraction of the full correlation energy that is calculated is often quite consistent
over a fairly large range of structures. This method emphasizes the ‘scaling all correlation’
(SAC) energy assumption. Another option is an extrapolation method, based on estimates of
the HF limit, as explained before in paragraph 3.1.2. The selection of the functional form for
the asymptotic behavior may be considered as parametric [44, 98].
Multilevel methods carry the approach that an additive behavior for the correlation energy is
assumed. The first effort was the so-called G1 theory of Pople and co-workers [99], which
was followed very rapidly by an improved modification, the G2 theory [100]. Furthermore,
another extension was made, leading to G3 [101], which is faster (typically about twice as
fast), more efficient and more accurate than G2. Improved basis sets for the third-row nontransition elements are present in G3 [102], which is an amelioration compared to G2. The G3
method was already used in the literature study of the effects of structural characteristics of
RAFT CTAs (cf. Chapter 2).
Alternative multilevel methods that have some similarities to G2, G3 and their variants, are
the CBS (Complete-Basis-Set) methods of Petersson and co-workers [103, 104]. A key
difference between the Gn models and the CBS models is that in the latter, results for
different levels of theory are extrapolated to the complete-basis-set limit in defining a
composite energy, instead of assuming basis set incompleteness effects to be completely
accounted for by additive corrections, which is the case in the Gn models. In this work, CBSQB3 is used in the benchmarking study (section 4.1.1). This method involves five steps: the
first one is a geometrical optimization at the B3LYP level with 6-311G(2d,d,p) as basis set,
the second step is the implementation of thermal corrections, the third one is a frequency
calculation, the fourth step is single-point calculations employing CSSD(T), MP4SDQ and
MP2 methods, and the last step is a CBS extrapolation [105].
Chapter 3: Computational methods
32
The Weizmann-1 (W1) and Weizmann-2 (W2) models of Martin and de Oliveira [106, 107]
are similar to the CBS models in that extrapolation schemes are used to estimate the infinite
basis set limits for SCF and correlation energies. A key difference between the two, however,
is that the W1 and W2 models set as a benchmark goal an accuracy of 1 kJ mol-1 on
thermochemical quantities. Because they include empirically derived parameters, multilevel
models nearly always outperform single-level calculations at an equivalently expensive level
of theory [44, 98, 108].
3.1.6 Basis sets
A basis set is a set of mathematical functions from which the wave function is constructed, as
mentioned before in paragraph 3.1.2. The basis functions must be chosen such that their form
is useful in a chemical sense. That is, the functions should have large amplitudes in regions
where the electron probability density is large, and small amplitudes where the probability
density is small.
3.1.6.1 Basis functions
A guess ϕ for the wave function is often constructed as a linear combination of atomic orbitals
(LCAO) (3.22) [60, 109, 110].
∑
Where
are atomic wave functions and a coefficient
set of N functions
(3.22)
is associated with each function. The
is called the basis set, and the more atomic orbitals are included into the
basis, the better the basis will represent the true molecular orbital space. Mathematically, an
atomic orbital can be described by a Slater determinant, which is an antisymmetric sum of all
possible ways to distribute the electrons in a system [65]. Each atomic orbital is written as a
linear combination of one or more Slater-type orbitals (STOs), equal to the product of the
corresponding radial wave function and the spherical harmonic [65]. A STO can be
approximated as a linear combination of Gaussian-type orbitals (GTO), called a contracted
basis function. It is often referred to as STO-NG, which means ‘Slater-Type Orbital
approximated by N Gaussian functions’. The individual Gaussians from which the STO is
formed are referred to as primitive Gaussians [111, 112]. The general functional form of a
normalized GTO in atom-centered Cartesian coordinates is given in (3.23) [44, 113].
Chapter 3: Computational methods
33
(
)
(
)
[
( )
( ) ( ) (
)
]
(
)
(3.23)
Herein, α is an exponent controlling the width of the GTO, and i, j and k are non-negative
integers that represent the nature of the orbital. A linear combination of Gaussian functions is
desirable, because of the combination of the computational efficiency of the GTOs with the
proper radial shape of the STOs. If GTOs were to be used individually to represent atomic
orbitals, they would fail to exhibit radial nodal behavior at the nucleus (r=0) and at infinite
distance of the nucleus (r=∞) [44].
3.1.6.2 Split valence functions
One way to increase the flexibility of a basis set is to ‘decontract’ it. One could for example
construct two basis functions for each atomic orbital, called a double-ζ basis. This basis would
yield a better description of the charge distribution compared to a minimal basis. This can also
be extended to a triple-ζ basis. Valence orbitals can vary widely as a function of chemical
bonding, so having flexibility is more important there than in the core, leading to the
development of ‘split-valence’ or ‘valence-multiple-ζ’ basis sets. In such basis sets, core
orbitals are still represented by a single contracted basis function, while valence orbitals are
split into arbitrarily many functions. For example the basis set 4-31G means that the core
orbitals are represented by one Slater-type function, which is approximated by four
Gaussians. The valence orbitals in contrast, are represented by the linear combination of two
Slater-type functions, one build from three Gaussian functions, the other from only one [65].
3.1.6.3 Polarization functions
Using s and p functions centered on the atoms do not provide sufficient mathematical
flexibility to adequately describe the wave function for e.g. the pyramidal geometry. Because
of the utility of AO-like GTOs, this flexibility is almost always added in the form of basis
functions corresponding to one quantum number of higher angular momentum than the
valence orbitals. A star * implies a set of d functions added to polarize the p functions, a
second star implies p functions on the hydrogen and helium atom [44, 65].
3.1.6.4 Diffuse functions
When a basis set does not have the flexibility necessary to allow a weakly bound electron to
be localized far from the remaining electron density, significant errors in energies and other
molecular properties can occur. To address this limitation, diffuse basis functions are often
Chapter 3: Computational methods
34
added to the standard basis sets. Diffuse functions are Gaussians with very small exponents
and decay slowly with distance from the nucleus. A rough rule of thumb is that diffuse
functions should have an exponent about a factor of four smaller than the smallest valence
exponent [44]. In the Pople family of basis sets, the presence of diffuse functions is indicated
by a ‘+’ in the basis set name. One plus indicates that heavy atoms have been augmented with
an additional one s and one set of p functions having small exponents, while the presence of
diffuse s functions on the hydrogen atom is indicated with a second plus. Particularly for the
calculation of acidities and electron affinities, and for the correct description of anions and
weak bonds, diffuse functions are absolutely required [44, 65, 114].
3.2 Performance ab initio methods
The big advantage of DFT is that the simple three-dimensional electron density can be used
instead of the complex many-dimensional wave function to describe interacting electrons.
DFT optimizes an electron density while MO theory optimizes a wave function. So, to
determine a particular molecular property using DFT, we need to know how that property
depends on the density [115], while to determine the same property using a wave function, we
need to know the correct quantum mechanical operator. As there are more well-characterized
operators than there are generic property functionals of the density, wave functions clearly
have broader utility. This could be a disadvantage of DFT but this approach is still the most
cost-effective method to achieve a given level of accuracy [44, 114, 116].
There is a key difference between the HF theory and DFT. HF is a deliberately approximate
theory, whose development was motivated by the ability to solve the relevant equations
exactly, while DFT is an exact theory, but the relevant equations must be solved
approximately because a key operator has an unknown form. Because of the approximate
form of the exchange-correlation functional [115], errors of DFT, for example
underestimation of barriers of chemical reactions, underestimation of energies of dissociating
molecular ions, overestimation of the binding energies of charge transfer complexes, are not
ascribed to failure of the theory itself. They originate from the delocalization error of
approximate functionals, which is the tendency of most functionals to spread out electron
density artificially due to the dominating Coulomb term that pushes electrons apart [44, 65].
A major shortcoming of the DFT methods is that they typically fail to model long-range
dispersion interactions, which arise from electron correlation. DFT typically neglects longrange dispersion because the exchange-correlation term is typically assumed to be a
Chapter 3: Computational methods
35
functional of the local electron density, or of the gradient of the electron density. A
consequence of this assumption is that only local contributions to the electron correlation are
included. There have recently been some functionals developed that are capable of modeling
dispersion interactions, such as M05 and M06. These functionals do not contain an explicit
dispersion term but they have been parameterized to systems governed by dispersion
interactions and have shown some success for modeling dispersion bound complexes.
Furthermore, also a DFT-D approach is available, which is introduced by Grimme [117]. This
means that the standard DFT total energy is corrected with an empirical dispersion term, for
example the Lennard-Jones potential. This approach is very popular because it is
computationally not expensive due to the a posteriori energy correction and gives good results
[44, 65, 118]. In the benchmarking study (section 4.1.1), M06-2X is one of the methods that is
considered. This is a high-nonlocality functional with double the amount of nonlocal
exchange (2X), and it is parameterized only for nonmetals. This functional may be classified
as hybrid meta-generalized gradient-approximation [119].
In literature [120, 121] it is noted that the scaling behavior of DFT is no worse than N3, where
N is the number of basis functions used to represent the KS orbitals. This is better than HF by
a factor of N, and also substantially better than other methods that also include electron
correlation. However, scaling does not tell anything about the absolute time required for
calculations. As a rule of thumb, for programs that use approximately the same routines and
algorithms to carry out HF and DFT calculations, the cost of a DFT calculation on moderately
sized molecules, say 15 heavy atoms, is double that of the HF calculation with the same basis
set [120, 121].
Regarding efficiency, it is important to note that SCF convergence in DFT is sometimes more
problematic than in HF. Because of similarities between the KS and HF orbitals, this problem
can often be very effectively alleviated by using the HF orbitals as an initial guess for the KS
orbitals [115]. Because the HF orbitals can usually be generated quite quickly, the extra step
can ultimately be time-saving if it sufficiently improves the KS SCF convergence [44, 122].
In general, geometries and frequencies can be calculated at relatively low levels of theory,
such as B3LYP/6-31G(d) [37]. However, very high level composite procedures such as W1
are essential for accurate absolute values of the energies. Low-cost approximations to this
high level of theory can be obtained via an ONIOM-based11 [123-125] procedure in which the
system is divided in different regions which are calculated at different levels of theory. For
11
ONIOM stands for Our own N-layered Integrated molecular Orbital and molecular Mechanics.
Chapter 3: Computational methods
36
example, the inner core is studied at W1 while the core is calculated at G3(MP2)-RAD and
the full system at ROMP2/6-311G(3df,2p) [37]. It should be stressed that popular DFT
methods such as B3LYP fail to model the energetics of polymerization-relevant reactions,
with possible errors of 50 kJ mol-1 [37].
3.3 Computational methods and procedures used in this work
3.3.1 Ab initio calculations using Gaussian 09
The ab initio calculations have been performed by making use of the Gaussian-09 package,
revision D.01 [126, 127]. The typical structure of an input file is cursively given below.
%mem=1500MB
%nproc=4
#p $leveloftheory/$basisset opt freq int=ultrafine
$name calculation
$charge $multiplicity12
$Geometry of the molecule (Z-matrix or Cartesian coordinates)
$one blank line at the end
In the input file, the %mem command controls the amount of dynamic memory to be used by
Gaussian, and %nproc is the number of processors required. To generate additional output, #p
should be added. This additional information includes messages at the beginning and end of
each link, giving assorted machine-dependent information as well as convergence information
in the SCF. The keyword opt requests that an optimization is performed, adding the keyword
ts means the optimization of a transition state rather than a minimum. To compute force
constants and the resulting vibrational frequencies, the keyword freq is required.
Optimizations of large molecules which have many low frequency vibrational modes will
often proceed more reliably when the integration grid for the calculation is set finer, using
int=ultrafine [127].
Input geometries are created using ChemCraft [128], version 1.6, or Molden [129]. Minimum
energy conformations are determined using an in-house script, which scans all possible
12
Multiplicity is the number of possible orientations, calculated as 2S+1, of the spin angular momentum
corresponding to a given total spin quantum number (S), for the same spatial electronic wave function.
Chapter 3: Computational methods
37
conformations, based on rotations of the dihedral angles of the molecules. Important to
mention is that for large molecules, a conformational analysis is performed for the fragments
in the molecule separately, which are basically the reactants or the products of the reaction
(cf. section 4.3). When combining the fragments in the intermediates, only a rotation about
the formed C-S bond (between the fragment and the sulfur atom) is considered, and not again
all the possible rotations within the fragments itself due to computational limitations. To
indicate the influence of a conformational analysis, a few calculations are made with and
without a conformational analysis, and the results are presented and compared in Appendix A.
Transition state geometries vary much more than equilibrium geometries [130], so specific
algorithms are necessary to determine transition structures. In the Gaussian-09 package, the
Berny algorithm is used to optimize the saddle points [127]. The Berny geometry
optimization is based on an earlier program, written by H.B. Schlegel [131], in which the
optimization stops when the default convergence criteria of Gaussian-09 are reached. In
appendix B and C, all the geometries of the molecules considered can be found, for the model
reactions as well as for the reactions implemented in the kinetic model.
In most of the calculations performed, the harmonic oscillator approximation is applied, as
represented by (3.28) in paragraph 3.3.2.1. However, in case of vibrational frequencies lower
than 30 cm-1, this approximation deviates significantly from the original potential well [132].
To correct for this well-known breakdown of the harmonic oscillator model for low-frequency
vibrational modes, the quasiharmonic approximation is used. This is the same as the harmonic
oscillator approximation, except that vibrational frequencies lower than 30 cm-1 are artificially
raised to 30 cm-1 [133].
All the results, such as the optimized geometry and the thermodynamic properties (paragraph
3.3.2.2), are represented in an output file. Furthermore, information about spin densities,
frequencies and partition functions (paragraph 3.3.2.1) is available. Using this information, it
is possible to calculate the rate and equilibrium coefficient as explained in section 3.3.5. It has
to be remarked that the vibrational, translational and rotational partition function, responsible
for the thermal contributions to enthalpy and entropy, are subject to scaling factors. These are
empirically determined via a least-squares approach and available in literature [134]. In this
work, all vibrational frequencies are scaled with a factor of 0.99.
Chapter 3: Computational methods
38
3.3.2 Calculation of thermodynamic quantities
3.3.2.1 Partition functions
The function which relates microscopic quantities with macroscopic thermodynamic
properties is the molecular partition function qmol [135, 136]. This function can be factorized
as shown in (3.24).
(3.24)
In this formula, qelec is the electronic partition function, qtrans the translational, qrot the
rotational and qvib the vibrational partition function, given respectively in (3.25), (3.26), (3.27)
and (3.28) [135].
(3.25)
(
)
(
) √
∏
(3.26)
(3.27)
(3.28)
Where,
E0 is the ground state electrical energy of the molecule,
kB is Boltzmann’s constant (1.380658∙10-23 J mol-1 K-1),
T is the temperature, expressed in Kelvin,
m the molecular mass,
h is Planck’s constant (6.6260755∙10-34 J s),
the rotational symmetry number,
Ixx, Iyy and Izz the moments of inertia,
i the index of the harmonic oscillator,
3N-6 the number of harmonic oscillators and
the characteristic frequency of each harmonic oscillator.
3.3.2.2 Derivation of thermodynamic properties from the partition function
The entropy S, enthalpy H and Gibbs free energy G of the system can be derived from the
molecular partition function, according to formulas (3.29), (3.30) and (3.31) respectively
[135]. Herein, N is the number of identical non-interacting particles.
Chapter 3: Computational methods
39
(
(
)
(
)
)
(
(3.29)
)
(3.30)
(
)
(
)
(3.31)
3.3.3 High Performance Computing infrastructure
The calculations are performed on the High Performance Computing (HPC) infrastructure of
the University of Ghent [137]. This infrastructure consists of seven clusters, which are being
hosted in three datacenters in Ghent. Especially the so-called ‘raichu’ cluster is used for this
master thesis, which has 64 computing nodes, 32 GB RAM/node and is only suited for singlenode jobs. Octa-core Intel processors of 2.6 GHz with the Sandy Bridge technology are used.
Each cluster has a queue, so a calculation or job is sent to a queue and the system will decide
on which of the nodes it will be calculated [137].
3.3.4 COSMO-RS
COSMO-RS, which stands for COnductor-like Screening MOdel for Real Solvents, is used to
calculate Gibbs free energies of solvation in this work. This theory is based on the interaction
of molecular surfaces, as computed by quantum chemical methods, to predict thermodynamic
equilibria of fluids and liquid mixtures. First, a COSMO (COnductor-like Screening MOdel)
calculation is performed, in which the solute molecule is calculated in a virtual, ideal
conductor environment. In such an environment, the solute molecule induces a polarization
charge density on the interface between the molecule and the conductor, i.e. on the molecular
surface. On this surface, each segment is characterized by its area and the screening charge
density σ. These charges act back on the solute and generate a more polarized electron density
than in vacuum. During the quantum chemical self-consistency algorithm, the solute molecule
is thus converged to its energetically optimal state in a conductor with respect to the electron
density. In the COSMO-RS theory, a liquid is considered as an ensemble of closely packed
ideally screened molecules. An electrostatic interaction arises from the contact of two
different screening charge densities. The specific interaction energy per unit area resulting
from this “misfit” of screening charge densities is given by (3.32) [138, 139].
Chapter 3: Computational methods
40
(
)
(
)
(3.32)
Where,
aeff is the effective contact area between two surface segments,
α’ is an adjustable parameter and
σ and σ’ are the net screening charge densities of the surface segments of two molecules.
Also hydrogen bonding (HB) can be written as a function of the polarization charges of two
interacting surface segments, σacceptor and σdonor (3.33). In this formula,
and
are
adjustable parameters. A HB interaction can be expected if two sufficiently polar surfaces of
opposite polarity are in contact [138, 139].
(
The σ-potential
)
(
)
(
(
))
(3.33)
( ) is a measure for the affinity of the system S to the surface of polarity σ.
This quantity can be calculated with formula (3.34) [138].
( )
Herein,
[∫
( )
(
( ( )
( ) is determined by (3.35), where
(
)
(
)))
]
(3.34)
( ) is the so-called σ’-profile, a distribution
function which gives the relative amount of surface with polarity σ’ on the surface of the
molecule i, and xi the mole fraction of this component in the mixture [138].
( )
∑
( )
(3.35)
The chemical potential of compound i in the system S can now be calculated by integration of
( ) over the surface of the compound, shown in (3.36). Herein,
is a combinatorial term
to take into account size and shape differences of the molecules in the system [138].
∫
( )
( )
(3.36)
Once this chemical potential is known, it is possible to calculate the Gibbs free energy of
solvation of the molecule i, Gisolv. This can be calculated in two possible reference
frameworks: the “molar” framework and the “COSMO-RS reference” framework. In the first
case, the reference state of the calculation is 1 L of ideal gas and 1 L of liquid solvent, and the
free energy of solvation is computed as given in formula (3.37). Herein,
dilution chemical potential of the compound in solution,
Chapter 3: Computational methods
is the infinite
the chemical potential of the
41
compound in the ideal gas phase,
ideal gas and
the density of the solvent,
the molar volume of the
the molecular weight of the solvent [139].
(
)
(
)
(3.37)
In the second reference framework, 1 bar of ideal gas and 1 mol of liquid solvent is taken as
the reference state of the calculation. Formula (3.38) is used to calculate the Gibbs free energy
of solvation [139].
(
)
(3.38)
The way in which the surface charges match, is a measure for the solvation energy. A good
match, for example between a very positive and a very negative surface, results in attraction
of the two molecules towards each other [138, 139].
The COSMO-RS theory is used in this work, as implemented in the COSMOtherm program,
to calculate Gibbs free energies of solvation, in the reference framework of 1 bar of ideal gas
and 1 mol of solvent [139]. Once this is known, the Gibbs free energy of molecule i in
solution,
, can be calculated using (3.39), as the sum of the Gibbs free energy of
molecule i in the gas phase,
, and the Gibbs free energy of solvation of molecule i,
.
(3.39)
3.3.5 Calculation of rate and equilibrium coefficients
Having obtained the geometries, frequencies, energies and partition functions of reactants,
products, intermediates and transition structures, it is possible to calculate the rate coefficient
k(T) and equilibrium coefficient K(T) of the chemical reaction, using the standard statistical
thermodynamic formulas (3.40) and (3.41) respectively [53, 140, 141].
( )
( )
( )
( )
( )
(
⁄(
∏
∏
∏
)
⁄(
)
)
(3.40)
(3.41)
In these formulas, κ(T) is the tunneling correction factor, c0 is the standard unit of
concentration (mol L-1), R the universal gas constant (8.3142 J mol-1 K-1), m is the
Chapter 3: Computational methods
42
molecularity13 of the reaction and Δn the change in number of particles upon reaction, Q‡, Qi
and Qj are the molecular partition functions of the transition state structure, reactant i and
product j respectively, ΔE‡ the energy barrier for the reaction, corrected for the zero-point
vibrations and ΔE is the zero-point corrected energy change for the reaction [37]. This
approach is known as the classical transition state theory.
Formulas (3.40) and (3.41) can be rephrased in terms of the Gibbs free energy, which are used
in this work. The rate coefficient is based on the activation Gibbs free energy ΔG‡, while the
equilibrium coefficient is based on the Gibbs free energy of reaction ΔGr, (3.42) and (3.43)
respectively. In these formulas, the tunneling correction factor κ is assumed to be one. The
unit of the rate coefficient depends on the molecularity of the reaction. For a monomolecular
reaction, k is expressed in s-1, while for a bimolecular reaction, the unit of k is L mol-1 s-1. The
unit of the equilibrium coefficient depends on the number of reactants and products, as this
coefficient equals the ratio of the product concentrations to the reactant concentrations. For
addition reactions, K is expressed in L mol-1, while the unit of K for fragmentation reactions is
mol L-1.
⁄(
( )
( )
(
)
(3.42)
)
(3.43)
It is important to mention that the Gibbs free energies have to be referred to a standard state of
1 mol L-1. The values for the molecules in the gas phase,
, obtained from Gaussian, are
referred to a pressure of 1 bar. A correction factor is needed to compensate for this different
reference state. This is shown in formula (3.44), in which
gas at 298.15 K and 1 bar, and
is the volume of 1 mol ideal
is the volume of 1 mol ideal gas in a concentration
of 1 mol L-1. This correction factor is equal to 7.926 kJ mol-1. It has to be noted that the
translational term in the Gibbs free energy is the only term which is dependent on the
concentration of the solute. Therefore, the translational concentration correction factor has to
be added, as shown in (3.44) [142].
(
)
(3.44)
13
The molecularity m of a reaction is defined as the number of molecules, radicals or ions that participate in that
reaction.
Chapter 3: Computational methods
43
When the reaction is performed in a solvent, the rate coefficient of the reaction, ksol, is
calculated via formula (3.45). In this formula,
is the activation Gibbs free energy of
the reaction in solution. This quantity is calculated as the sum of the activation Gibbs free
energy of the reaction in the gas phase and the activation solvation Gibbs free energy,
, via equation (3.46). The Gibbs free energies in case of reactions in a solvent, are
referred to a standard state of 1 mol L-1, so no correction factor has to be added.
(
( )
)
(3.45)
(3.46)
If the molecules are quite extensive (cf. section 4.3), it is no longer possible to perform the
frequency calculation at the BMK/6-311+G** level within the restricted duration of 72 hours
for a calculation, which is imposed by the HPC. For these molecules, the following procedure
is used. For the RAFT intermediates, an optimized geometry is determined at B3LYP/631G(d), including a frequency calculation. The obtained structure is re-optimized at BMK/6311+G**, without the performance of a frequency calculation. Using this methodology, it is
possible to estimate the Gibbs free energy of an intermediate at the BMK level, knowing that
the Gibbs free energy G is calculated by making use of formula (3.47). In this formula, the
electronic energy Eelec is calculated at BMK/6-311+G**, while the thermal contributions to
the Gibbs free energy ΔGcorr are determined at B3LYP/6-31G(d) at the desired temperature,
taking into account a scaling factor of 0.99.
(3.47)
For the transition states, again a geometry optimization and frequency calculation are
performed with B3LYP/6-31G(d). Furthermore, a single-point calculation at BMK/6311+G** is carried out on the optimized structure. The Gibbs free energy of a transition state
is calculated in a similar way as for the intermediates.
The rate coefficient can also be calculated based on activation enthalpies and entropies,
according to the well-known Arrhenius law (3.48). The pre-exponential factor A is given in
formula (3.49) while the activation energy Ea is calculated using (3.50).
( )
Chapter 3: Computational methods
(
)
(3.48)
44
( )
(
( )
(
( )
)
(3.49)
)
(3.50)
In these formulas, Δn‡ is the change in the number of particles between the reactant(s) and the
transition state, ΔH‡ and ΔS‡ are the calculated changes in enthalpy and entropy between the
reactant(s) and the transition state [135].
Another method to calculate A and Ea is by fitting the values of the rate coefficients at
specified temperatures to the Arrhenius relationship. A plot of the logarithm of the rate
coefficient, ln(k), versus the inverse of the temperature, T-1, is constructed. The equation of
the trend line should look like (3.51), in which the slope of the trend line is equal to –Ea/R and
the intercept equals ln(A). Once the slope and the intercept of the trend line are known, it is
possible to calculate the values for Ea and A, by using formulas (3.52) and (3.53) respectively.
( )
( )
(3.51)
(3.52)
(
)
(3.53)
The latter method is used in this work for the determination of A and Ea, which are necessary
parameters as input in the kinetic model for RAFT polymerization (cf. section 4.3).
3.3.6 Kinetic model
For modeling of RAFT polymerization of styrene, by making use of CPDT as CTA and AIBN
as initiator, an existing kinetic model is used. A distinction is made between FRP-related
reactions and RAFT polymerization specific reaction steps. Only the kinetic parameters of the
addition and fragmentation reactions in the RAFT mechanism are adapted by making use of
ab initio modeling. In this work, thermal initiation of styrene and cross termination are not
taken into account.
The initiator efficiency used in the kinetic model is determined via the free volume theory,
based on Buback et al. [143]. This parameter accounts for the fraction of initiator radicals
originating from the initiator molecule, that actually initiate chain growth in a conventional
FRP process. The apparent termination rate coefficients are based on the composite model
proposed by Johnston-Hall and Monteiro [144]. This model is based on the RAFT chain
Chapter 3: Computational methods
45
length dependent termination (RAFT-CLD-T) method presented by Vana et al. [145] and
recently improved by Derboven et al. [28].
The continuity equations are simultaneously integrated using the numeric LSODA (Livermore
Solver for Ordinary Differential Equations) solver [146], which is an algorithm designed for
large dimension non-stiff and stiff problems. This solver combines the backward differential
formulas for stiff equations and the Adams method for non-stiff equations, and automatically
switches between both, depending on the nature of the set of ordinary differential equations.
Chapter 3: Computational methods
46
Chapter 4
Results and discussion
4.1 Pre-equilibrium in RAFT mechanism
The pre-equilibrium in the RAFT mechanism (Figure 4 in paragraph 2.1) is the most
interesting step because this step strongly influences the mediating behavior, and hence
assures a controlled polymerization. Moreover, it is very hard to examine the pre-equilibrium
experimentally, hence there is not much known about this step. Therefore, a closer look is
taken at the pre-equilibrium (Figure 16) in this work.
Figure 16. Pre-equilibrium in the RAFT polymerization mechanism [31]
In Table 5, the R- and Z-groups of the different examined RAFT CTAs are represented with
chemical formulas. To explore the addition and fragmentation reaction of the pre-equilibrium
in RAFT polymerization, simple model compounds are considered. The reactions with methyl
ethane dithioate (MEDT), the smallest and most simple RAFT CTA, and with methyl
benzodithioate (MBDT), a slightly larger RAFT CTA, are considered (cf. Table 5). Both these
RAFT CTAs are basic model compounds, often used in computational studies of RAFT
polymerization [9, 37, 52, 53]. As radicals, first a methyl radical is considered, which is
extended later on to a styryl radical. This allows a comparison of the calculated results with
the results available in literature.
Chapter 4: Results and discussion
47
Table 5. Different RAFT CTAs, with their Z- and R-group
RAFT CTA
Z-group
R-group
MEDT
-CH3
-CH3
CH3
MBDT
-CH3
CH3
CPDTmethyl
H3C
-S-CH3
N
CH3
CH3
CPDTethyl
H3C
-S-CH2CH3
CH3
CH3
H3C
N
switch
H3C
CH3
N
CH3
N
CH3
+
N
H
N
CH3
H3C
protonated switch
N
H3C
N
CH3
H3C
N
switchmethyl
-CH3
CH3
N
H3C
N
protonated switchmethyl
+
H
Chapter 4: Results and discussion
N
CH3
-CH3
48
In the next step, 2-cyano-2-propyl dodecyl trithiocarbonate (CPDT) is considered because an
extensive dataset of experimental data is already available [147]. However, this molecule,
represented in Figure 17, is quite extensive leading to the implementation of a simplification.
Therefore, instead of a dodecyl group, a methyl or an ethyl group is used, indicated as
CPDTmethyl and CPDTethyl respectively. This RAFT CTA will also be used in a kinetic model
study.
Figure 17. Chemical structure of the RAFT CTA 2-cyano-2-propyl dodecyl trithiocarbonate
Finally, 2-cyano-2-propyl N-(4-pyridinyl)-N-methyl dithiocarbamate, which is a switchable
RAFT CTA and indicated as switch, is investigated. Also in the case of the switchable RAFT
CTA, a simplified form
is
modeled as
well,
methyl
N-(4-pyridinyl)-N-methyl
dithiocarbamate. In this CTA, the R-group is a methyl group instead of a cyano isopropyl
group and it is indicated as switchmethyl. For both RAFT CTAs, the neutral and the protonated
form are examined because the principle of switchable RAFT CTAs is based on the
modification of the electronic properties, as explained in section 2.3. This RAFT CTA is
considered because it is nowadays a promising topic, due to the possibility of coupling
otherwise incompatible monomers [56, 57]. Numerous investigations are ongoing at the
moment about this RAFT CTA, also in the laboratory for chemical technology [148].
4.1.1 Level of theory study
The reaction parameters of the addition and fragmentation steps with the RAFT compounds
shown in Table 5 have been calculated using different levels of theory: CBS-QB3, BMK and
M06-2X. The results of these calculations are compared with the results found in literature
[37, 53, 54, 149] and with the experimental data available [147], to test the validity and the
accuracy of the used methods. Specifically, the rate coefficient and the equilibrium coefficient
of the addition reactions are considered. These are calculated via the earlier mentioned
formulas, (3.42) and (3.43) respectively. To illustrate these, a Gibbs free energy diagram of
the reaction of the styryl radical with MEDT as RAFT CTA can be seen in Figure 18. The
Chapter 4: Results and discussion
49
reaction Gibbs free energy ΔGr, as well as the activation Gibbs free energy ΔG‡, are clearly
indicated. These quantities are used for the calculation of the rate and equilibrium coefficient
of the addition reaction. The results of the forward rate coefficient kadd,1 calculated for
different reactions, at 298.15 K, and the corresponding reference values from literature or
experimental data are represented in Table 7. Similarly, the results of the forward equilibrium
coefficient K are given in Table 8.
Figure 18. Gibbs free energy diagram of the reaction of the styryl radical with MEDT
At first instance, the calculations have only been performed with CBS-QB3 and BMK, as
these are recommended in literature [52, 96, 105]. Later on, an investigation of the M06-2X
method is added [119, 150, 151]. The results obtained with CBS-QB3 and BMK are first
discussed, while at the end, the results calculated with M06-2X are investigated.
First of all, the reaction of a methyl radical with MEDT is investigated. The calculated results,
for two levels of theory, BMK/6-311+G** and CBS-QB3, are given in Table 7 and Table 8,
together with the reference values. For the equilibrium coefficient, both methods give a
similar value, which is however three orders of magnitude higher than the reference value.
Looking at the values of the rate coefficient of addition, a very good agreement between the
reference value, calculated at G3(MP2)-RAD and the calculated value at BMK/6-311+G** is
obtained. The value of CBS-QB3 is two orders of magnitude higher than those.
Furthermore, also the reaction between MEDT and the styryl radical is considered. The
equilibrium coefficient from the literature lies between the calculated value at BMK/6311+G** and the one at CBS-QB3. No reference value of the addition rate coefficient is
Chapter 4: Results and discussion
50
found. However, the value for the reaction between MEDT and the benzyl radical instead of
the styryl radical is added in Table 7. In this case, the value calculated at CBS-QB3 is very
similar to the reference value, the value calculated at BMK deviates almost four orders of
magnitude.
Also the reactions with the RAFT CTA MBDT are considered. The reaction of a methyl
radical with MBDT shows the same trend as that with MEDT. The reaction of the styryl
radical with MBDT is only calculated at BMK/6-311+G**, because the molecules appearing
in this reaction are too large to allow a calculation at the CBS-QB3 level. The same trends as
in the case of MEDT as RAFT CTA are recognized.
Nathalie Ghyselinck obtained experimental values for RAFT polymerization of styrene with
CPDT as RAFT CTA, at a temperature of 343 K [147]. The estimated Arrhenius parameters
as well as the thermodynamic parameters are given in Table 6. From these parameters, the
equilibrium coefficient K and the addition rate coefficient kadd,1, both at 298.15 K, are
determined and used as reference values, shown in Table 7 and Table 8.
Table 6. Estimated Arrhenius parameters and thermodynamic parameters for the addition reaction in
RAFT polymerization of styrene with CPDT, valid at a temperature 343 K [147]
Aadd,1 [L mol-1 s-1]
-1
6.8E+15
Ea,add,1 [kJ mol ]
7.4E+01
ΔHr [kJ mol-1]
-3.5E+01
ΔSr [J mol-1 K-1]
-7.0E+01
Note that for the ab initio calculations two simplifications are implemented. Instead of a
dodecyl group, a methyl or an ethyl group is used. In the next paragraph, the influence of this
simplification is investigated. Moreover, the calculations at CBS-QB3 are performed with a
methyl radical instead of a styryl radical, because these calculations would be too
computationally expensive at the CBS-QB3 level of theory. In contrast, results with the styryl
radical are obtained for the method BMK. It seems that the equilibrium coefficient calculated
with BMK/6-311+G** differs four orders of magnitude from the experimental value. Looking
at the values of the rate coefficient of addition, the reference value lies between the value
calculated at BMK and the one calculated at CBS-QB3.
A very good agreement between the reaction of a methyl or a styryl radical and the CPDT
RAFT CTA with a methyl and ethyl group is clear from Table 7 and Table 8, for calculations
performed with CBS-QB3 as well as for those at BMK. At maximum, a difference of a factor
two between both methyl and ethyl group instead of the dodecyl group is observed, which is
Chapter 4: Results and discussion
51
acceptable. It can be concluded that a methyl group can be used instead of the dodecyl group
in CPDT, with limited consequences for the results. In practice however, an ethyl group will
be used because of the possible convergence problems when methyl groups are used.
It can be concluded that BMK will be used for the calculations in this work with as basis set
6-311+G**. The calculated values are more or less in accordance with the reference values
and it is still possible to calculate larger complexes, in contrast to CBS-QB3. Furthermore, it
is decided to use an ethyl group in the RAFT CTA CPDT instead of the dodecyl group
present, because this substitution only has a small influence on the reactivity.
To get an idea of the interatomic distances as well as the angles in the molecules, the chemical
structures of the intermediate as well as the transition state of the reaction of a methyl radical
with CPDTethyl are shown in Figure 19. Some interatomic distances are shown, expressed in
Ångstrom, as well as some angles, expressed in degrees. Both chemical structures are
optimized via BMK/6-311+G**. It is clear that the geometry of the molecule is different in
both cases. Not only the distances between the RAFT CTA and the methyl radical differ
significantly (1.842 Ångstrom in the intermediate, 2.670 Ångstrom in the transition state),
also a difference in the angles and the positions of different fragments is observed.
Figure 19. Chemical structure of the intermediate (left) and the transition state (right) of the reaction of a
methyl radical with CPDTethyl, with interatomic distances (in Ångstrom) and angles (in degrees) indicated,
optimized via BMK/6-311+G**
After investigating the results obtained at the M06-2X level with 6-311+G** as basis set, it is
clear that the results generally correspond very well with the values found in literature as well
as with the experimental data, with at most a difference of one order of magnitude. Certainly
for the reactions of the different RAFT CTAs with the styryl radical, M06-2X has a much
better performance than BMK. Only for the equilibrium coefficient of the reaction of a methyl
Chapter 4: Results and discussion
52
radical with MEDT and MBDT, there is a large difference between the calculated values and
the values reported in literature. In that case, the results obtained with M06-2X are very
similar to those obtained with BMK or CBS-QB3, but differ three to even five orders of
magnitude from the reported values in literature, calculated at W1. Even though, it can be
concluded that it is advised to use M06-2X in further ab initio investigations of RAFT
polymerization.
Chapter 4: Results and discussion
53
Chapter 4: Results and discussion
Table 7. Benchmarking of the forward rate coefficients kadd,1 [L mol-1 s-1] of the addition reactions of the methyl and the styryl radical with different RAFT CTAs
(MEDT, MBDT, CPDTmethyl and CPDTethyl), calculated at different levels of theory, at 298.15 K, with the literature and experimental data
Model reactions
a
CBS-QB3
BMK/6-311+G**
M06-2X/6-311+G**
Reference values
MEDT + CH3• → MEDT-CH3•
3.9E+08
6.4E+06
2.2E+07
1.2E+06a
MBDT + CH3• → MBDT-CH3•
MEDT + STY• → MEDT-STY•
MBDT + STY• → MBDT-STY•
5.1E+08
4.3E+06
-
2.6E+07
5.9E+02
1.9E+03
3.6E+08
1.8E+05
8.3E+06
5.4E+07a
2.8E+06a,b
4.0E+06c
CPDTmethyl + CH3•→CPDTmethyl-CH3•
CPDTethyl + CH3• → CPDTethyl-CH3•
CPDTmethyl + STY• → CPDTmethyl-STY•
CPDTethyl + STY• → CPDTethyl-STY•
1.1E+08
7.4E+07
-
6.9E+05
5.5E+05
8.7E-02
5.5E-02
7.8E+05
9.7E+05
3.7E+03
1.6E+03
8.3E+02d
8.3E+02d
Calculated at G3(MP2)-RAD [53, 54]
Calculated for benzyl radical
c
Calculated for dithiobenzoate (R-group not specified) [149]
d
Experimental values [147]
b
54
Chapter 4: Results and discussion
Table 8. Benchmarking of the forward equilibrium coefficients K [L mol-1] of the addition reactions of the methyl and the styryl radical with different RAFT CTAs
(MEDT, MBDT, CPDTmethyl and CPDTethyl), calculated at different levels of theory, at 298.15 K, with the literature and experimental data
Model reactions
d
e
CBS-QB3
BMK/6-311+G**
M06-2X/6-311+G**
Reference values
MEDT + CH3• → MEDT-CH3•
4.1E+10
1.1E+10
2.2E+10
3.8E+07e
MBDT + CH3• → MBDT-CH3•
MEDT + STY• → MEDT-STY•
MBDT + STY• → MBDT-STY•
3.7E+15
2.0E+02
-
1.3E+15
6.4E-02
1.8E+04
1.1E+16
4.8E+00
6.7E+06
1.7E+11e
1.1E+00e
1.5E+05e
CPDTmethyl + CH3• → CPDTmethyl-CH3•
1.2E+12
7.0E+10
8.1E+10
-
CPDTethyl + CH3• → CPDTethyl-CH3•
1.2E+12
1.3E+11
8.2E+10
-
CPDTmethyl + STY• → CPDTmethyl-STY•
-
1.2E-01
4.4E+02
7.4E+03d
CPDTethyl + STY• → CPDTethyl-STY•
-
1.7E-01
5.0E+02
7.4E+03d
Experimental values [147]
Calculated at W1 [37]
55
4.1.2 Rate coefficients of addition and fragmentation
The pre-equilibrium step of RAFT polymerization consists of two parts. For the model
reactions considered, the rate coefficients of the formation as well as the fragmentation of the
intermediate, considering the pre-equilibrium (Figure 16), are given in Table 9. These rate
coefficients are all calculated at BMK/6-311+G**, at a temperature of 298.15 K.
For the reactions of the methyl radical with the RAFT CTAs MEDT and MBDT, the
intermediate fragments to the left or to the right with the same rate coefficient. This can be
explained because in both cases, a methyl radical is formed. These rate coefficients are very
low because of the instability of a methyl radical. Also the rate coefficients of addition are the
same in both directions, because of the identical reactions, due to the symmetry. These values
are much higher, which is again due to the unstable methyl radical, which prefers to react
quickly.
Looking at the reactions of the styryl radical with MEDT and MBDT, kfrag,1 is much higher
(factor 108-1010) than kfrag,2, because of the formation of a methyl radical in the second part of
the reaction. Based on the same reasoning, it can be understood why kadd,2 is a factor 105-106
higher than kadd,1.
The intermediate proceeds to the right, with the formation of a macro-RAFT CTA and the Rradical, cyano isopropyl radical, for the reactions of the styryl radical and the methyl radical
with CPDTmethyl and CPDTethyl. The cyano isopropyl radical is more stable than either the
methyl or styryl radical, as the cyano group is strongly electron withdrawing [152]. This
results in higher values of kfrag,2, compared to kfrag,1, and in addition, for the reactions of the
methyl radical, the values of kadd,1 are higher than kadd,2. The latter observation is due to the
instability of the methyl radical. Considering the reactions of the styryl radical, the latter is not
observed. This can be due to the stability of the macro-RAFT CTA, compared to the stability
of CPDT(m)ethyl, or to the relatively small difference in stability between the styryl and cyano
isopropyl radical.
In the remainder of this work, only the first part of the reaction is considered, because this is
the most important step to control the polymerization. Once the polymerization is started, the
chain equilibration step (cf. Figure 4) dominates.
Chapter 4: Results and discussion
56
Chapter 4: Results and discussion
Table 9. Rate coefficients of the addition and fragmentation reactions in the pre-equilibrium, calculated at BMK/6-311+G**, at 298.15 K
Model reactions
kadd,1 [L mol-1 s-1] kfrag,1 [s-1] kfrag,2 [s-1] kadd,2 [L mol-1 s-1]
MEDT + CH3• 
 MEDT-CH3• 
 MEDT + CH3•
6.4E+06
5.8E-04
5.8E-04
6.4E+06
MBDT + CH3• 
 MBDT-CH3• 
 MBDT + CH3•
2.6E+07
1.9E-08
1.9E-08
2.6E+07
MEDT + STY• 
 MEDT-STY• 
 S=C(CH3)S-STY + CH3•
5.9E+02
9.2E+03
1.7E-05
2.7E+08
MBDT + STY• 
 MBDT-STY• 
 S=C(C6H5)S-STY + CH3•
1.9E+03
1.0E-01
8.0E-10
3.2E+09
CPDTmethyl + CH3• 
 CPDTmethyl-CH3• 
 S=C(SCH3)S-CH3 + C(CH3)2CN•
6.9E+05
9.9E-06
3.4E+07
3.6E-01
CPDTethyl + CH3• 
 CPDTethyl-CH3• 
 S=C(SCH3)S-CH2CH3 + C(CH3)2CN•
5.5E+05
4.1E-06
1.7E+07
5.5E+00
CPDTmethyl + STY• 
 CPDTmethyl-STY• 
 S=C(SCH3)S-STY + C(CH3)2CN•
8.7E-02
7.5E-01
1.1E+05
4.6E+00
CPDTethyl + STY• 
 CPDTethyl-STY• 
 S=C(SCH2CH3)S-STY + C(CH3)2CN•
5.5E-02
3.3E-01
9.8E+05
5.1E+02
57
4.1.3 Influence of modeling large substituents by smaller groups
Ab initio calculations require a lot of time and resources. Hence a typical methodology of
simplifying the molecules is often implemented [13]. In this work, the dodecyl group of
CPDT is replaced, once by a methyl group, once by an ethyl group. By comparing the results
with methyl and ethyl group (paragraph 4.1.1), the influence of the extra methyl group is
investigated. It could be observed that this influence is negligible so the dodecyl group can be
replaced by a smaller substituent, without a significance influence on the results. By changing
the methyl group to an ethyl group, the shape of the lowest unoccupied molecular orbital
(LUMO) does not significantly change, as is clear from Figure 20, confirming the negligible
difference in results between both simplified RAFT CTAs.
Figure 20. Chemical structure and shape of the LUMO of the CPDT RAFT CTA,
with a methyl group (left) and an ethyl group (right)
Subsequently, it was also attempted to replace the cyano isopropyl group in the switchable
RAFT CTA by a methyl group. The influence of this substitution is investigated (paragraph
4.2.2) and in this case, it was clear that it was not allowed to replace the cyano isopropyl
group. The differences between the results of the reactions with switch and with switchmethyl
are significant. In Figure 21, the LUMO orbitals of both structures are represented. It can be
seen that the shape of the lobes is different, depending on the R-group of the RAFT CTA.
Especially, the shape around the sulfur atom, attached to the R-group, is certainly different.
This is most likely due to the fact that the cyano isopropyl group has very different electronic
properties than the methyl group, because the cyano isopropyl group is both more bulky and
electron withdrawing. It can be concluded that the shape of the LUMO orbital changes
fundamentally, depending on the R-group of the switchable RAFT CTA. This leads to
significant differences between the results of the reactions with switch and with switchmethyl.
Chapter 4: Results and discussion
58
Figure 21. Chemical structure and shape of the LUMO of the switchable RAFT CTA ‘switch’ (left) and
the simplified version ‘switchmethyl’ (right)
It can be concluded that one always has to check if the simplification of the molecules is
allowed. Depending on the type of molecules and substituents considered, the consequences
on the results can be limited [13]. However, replacing large substituents by smaller ones, can
sometimes lead to incorrect results and conclusions.
4.1.4 Influence of presence of initiator fragment on styryl radical
Within this section, a limited study about the influence of the presence of the initiator group,
in the propagating radical and in the RAFT CTA, is performed. In this investigation, the
cyano isopropyl radical is used as initiator radical. In Figure 22, the two reactions that are
considered, are shown. The first reaction is the one of a styryl radical with an initiator group
attached, with the RAFT CTA CPDTethyl. In the second reaction, a styryl radical without a
cyano isopropyl group, reacts with CPDTethyl. In both cases, also the fragmentation of the
formed RAFT intermediate into a cyano isopropyl radical and a macro-RAFT CTA with the
styryl radical attached, is investigated.
Chapter 4: Results and discussion
59
Figure 22. Reversible chain transfer of the reaction of a styryl radical with CPDTethyl, once with an
initiator group attached to the styryl radical (top) and once without an initiator group attached to the
styryl radical (bottom)
The rate coefficients for the different addition and fragmentation reactions in Figure 22,
calculated at BMK/6-311+G**, at 298.15 K, are represented in Table 10, according to the
notations in Figure 16. It is clear that the cyano isopropyl group has a significant influence
when attached to the styryl radical. When this substituent is absent, a much higher rate
coefficient kadd,1 (about a factor 103) is observed. This can be due to steric hindrance in the
presence of the initiator group, making the addition of the styryl radical to CPDTethyl more
difficult. Also the fragmentation of the RAFT intermediate into the styryl radical and the
original RAFT CTA occurs at a much higher rate in the absence of the cyano isopropyl group.
Considering the second part of the pre-equilibrium, the addition and fragmentation of the
cyano isopropyl radical to the macro-RAFT CTA, the presence of the initiator group on the
styryl fragment has a more limited effect. In the presence of the initiator group, the RAFT
intermediate definitely prefers fragmentation towards the macro-RAFT CTA, while without
the initiator group, the RAFT intermediate fragments in both directions with a similar rate
coefficient. The similar values for kadd,2 in both cases mean that the reactivity of the cyano
isopropyl group is hardly affected by the presence of the additional group attached to the
macro-RAFT CTA.
Chapter 4: Results and discussion
60
Table 10. Rate coefficients of addition and fragmentation reactions, shown in Figure 22, with and without
the cyano isopropyl group, calculated at BMK/6-311+G**, at 298.15 K
With initiator
Without initiator
kadd,1 [L mol-1 s-1]
kfrag,1 [s-1]
kfrag,2 [s-1]
kadd,2 [L mol-1 s-1]
1.5E-05
8.9E-01
1.9E+01
2.4E+04
3.2E+06
3.7E+04
6.3E+00
1.0E+00
The conclusion of this computational investigation is that the presence of an initiator group
has an important influence on the reactivity. Hence, a different reactivity for a styryl radical
induced by thermal initiation is expected.
4.1.5 Influence of the solvent
To study the influence of a solvent, the rate and equilibrium coefficients for some model
reactions are calculated in styrene and in tetrahydrofuran (THF), and then compared with the
gas phase values. The results of the calculated coefficients in both phases are represented in
Table 11 for the addition reactions and in Table 12 for the fragmentation reactions. The
notations of the rate and equilibrium coefficients are according to Figure 4.
For the addition reactions of the methyl radical, represented in Table 11, it can be seen that
the solvation does not have a significant influence on the reactions with MEDT and MBDT.
This means that the reactants, transition state and products are more or less equally stabilized
by the solvents. The reaction of CPDTmethyl and CPDTethyl in contrast, proceeds considerably
faster when performed in styrene or THF. This is due to the stronger stabilizing effect of the
transition state, leading to a lower Gibbs free energy barrier and a higher rate coefficient as a
result. Also the equilibrium coefficient is higher for these reactions performed in solvent.
Analogous to the addition of the methyl radical, also the addition of the styryl radical with
MEDT and MBDT is not significantly influenced by the presence of a solvent. In Table 11,
also the rate and equilibrium coefficients of the reaction of the styryl radical with CPDT(m)ethyl
are represented. Again, similar to the reactions of the methyl radical, higher rate coefficients
are observed in case of solvation. For these reactions however, in contrast to those with a
methyl radical, a lower equilibrium coefficient is observed in solution, which indicates that
the reactants are more stabilized than the product.
Similar conclusions can be drawn about the fragmentation reactions. The results for the
fragmentation reactions are shown in Table 12. It has to be remarked that the equilibrium
Chapter 4: Results and discussion
61
coefficient Kβ is determined as the ratio of the addition to the fragmentation rate coefficient,
as defined in (2.7).
The relatively small influence of the solvent is due to the apolarity of the methyl radical and
the very low polarity of the styryl radical. Stronger solvation effects, meaning for example a
difference in the equilibrium constant of six orders of magnitude, can be expected for
reactions with acrylates, because of their greater polarity and their greater potential for
hydrogen bonding [13].
The argumentations before are illustrated with the Gibbs free energy diagrams of two
examples, shown in Figure 23 and Figure 24. The first example is the reaction of the styryl
radical with MEDT, performed in styrene as solvent, the second one illustrates the reaction of
the styryl radical with CPDTethyl, also in styrene.
Chapter 4: Results and discussion
62
Chapter 4: Results and discussion
Table 11. Rate and equilibrium coefficients of the model addition reactions in gas phase, styrene and THF, calculated at BMK/6-311+G**, at 298.15 K.
Contributions for solvation are calculated using COSMO-RS.
kadd,1
[L mol-1 s-1]
6.4E+06
2.6E+07
kadd,1,sol in styrene
[L mol-1 s-1]
4.6E+06
5.0E+07
kadd,1,sol in THF
[L mol-1 s-1]
3.9E+06
5.0E+07
K
[L mol-1]
1.1E+10
1.3E+15
Ksol in styrene
[L mol-1]
2.0E+10
2.6E+15
Ksol in THF
[L mol-1]
1.7E+10
2.7E+15
CPDTmethyl +CH3• → CPDTmethyl-CH3•
CPDTethyl +CH3• → CPDTethyl-CH3•
6.9E+05
5.5E+05
6.2E+07
6.5E+07
7.5E+07
8.3E+07
7.0E+10
1.4E+11
6.3E+12
1.6E+13
7.7E+12
2.0E+13
MEDT + STY• → MEDT-STY•
MBDT + STY• → MBDT-STY•
CPDTmethyl + STY• → CPDTmethyl -STY•
CPDTethyl + STY•→ CPDTethyl -STY•
5.9E+02
1.9E+03
8.7E-02
5.5E-02
4.3E+02
9.5E+02
4.6E-01
2.5E-01
4.1E+02
1.0E+03
5.0E-01
3.0E-01
6.4E-02
1.8E+04
1.2E-01
1.7E-01
4.6E-02
9.3E+03
8.2E-02
1.2E-01
4.4E-02
9.9E+03
9.9E-02
1.7E-01
Model reactions
MEDT + CH3• → MEDT-CH3•
MBDT + CH3• → MBDT-CH3•
Table 12. Rate and equilibrium coefficients of the model fragmentation reactions in gas phase, styrene and THF, calculated at BMK/6-311+G**, at 298.15 K.
Contributions for solvation are calculated using COSMO-RS.
MEDT-CH3• → MEDT + CH3•
MBDT-CH3• → MBDT + CH3•
CPDTmethyl-CH3• -> S=C(SCH3)S-CH3 + C(CH3)2CN•
kfrag,2
[s-1]
5.8E-04
1.9E-08
3.4E+07
kfrag,2,sol in
-1
styrene [s ]
2.3E-04
1.9E-08
1.6E+08
kfrag,2,sol in
-1
THF [s ]
2.3E-04
1.9E-08
1.7E+08
Kβ
[L mol-1]
1.1E+10
1.3E+15
1.1E-08
Kβ,sol in styrene
[L mol-1]
2.0E+10
2.6E+15
2.8E-08
Kβ,sol in THF
[L mol-1]
1.7E+10
2.7E+15
3.8E-08
CPDTethyl-CH3• -> S=C(SCH3)S-CH2CH3 + C(CH3)2CN•
1.7E+07
1.3E+08
1.2E+08
3.3E-07
8.2E-07
1.2E-06
MEDT-STY• -> S=C(CH3)S-STY + CH3•
MBDT-STY• -> S=C(C6H5)S-STY + CH3•
CPDTmethyl-STY• -> S=C(SCH3)S-STY + C(CH3)2CN•
CPDTethyl-STY• -> S=C(SCH2CH3)S-STY + C(CH3)2CN•
1.7E-05
8.0E-10
1.1E+05
9.8E+05
1.1E-03
7.1E-08
3.0E+06
2.6E+06
1.5E-03
8.0E-08
2.8E+06
2.3E+06
1.7E+13
4.0E+18
4.3E-05
5.2E-04
1.0E+14
2.0E+19
3.3E-06
6.4E-05
1.2E+14
2.3E+19
5.1E-06
1.0E-04
Model reactions
63
Chapter 4: Results and discussion
Transition state 2
Transition state 1
100.3
89.8
79.9
75.5
58.0
57.2
6.8
Propagating radical + RAFT CTA
+
7.6
Intermediate
Macro-RAFT CTA
+ R-group of the RAFT CTA
+
64
Figure 23. Gibbs free energy diagram of the reaction of the styryl radical with MEDT, in the gas phase (black) and in styrene (green),
the Gibbs free energy differences are expressed in kJ/mol
Chapter 4: Results and discussion
Transition state 1
Transition state 2
80.2
76.5
38.8
4.4
Propagating radical + RAFT CTA
+
5.2
Intermediate
36.4
24.0
18.7
Macro-RAFT CTA +
R-group of the RAFT CTA
+
65
Figure 24. Gibbs free energy diagram of the reaction of the styryl radical with CPDTethyl, in the gas phase (black) and in styrene (green),
the Gibbs free energy differences are expressed in kJ/mol
4.2 Structural influences on reactivity
4.2.1 Influence of the radical structure
In Table 13, the rate coefficients of the addition reaction of the methyl radical and different
monomer radicals to some RAFT CTAs are given, calculated at BMK/6-311+G**, at 298.15
K and expressed in L mol-1 s-1. Styrene, methyl methacrylate (MMA), methyl acrylate (MA)
and n-butyl acrylate (nBA) are considered as monomers. The RAFT CTAs used are MEDT,
MBDT, CPDTmethyl, CPDTethyl, switchmethyl, protonated switchmethyl, switch and protonated
switch.
Table 13. Forward rate coefficients kadd,1 [L mol-1 s-1] of addition reactions of the methyl radical and
different monomer radicals (styryl, MMA, MA and nBA) with different RAFT CTAs (MEDT, MBDT,
CPDTmethyl, CPDTethyl, switchmethyl, protonated switchmethyl, switch and protonated switch), calculated at
BMK/6-311+G**, at 298.15 K
RAFT CTA
methyl
styryl
MMA
MA
nBA
MEDT
MBDT
CPDTmethyl
CPDTethyl
6.4E+06
2.6E+07
6.9E+05
5.9E+02
1.9E+03
8.7E-02
4.5E+00
4.8E+00
1.2E-02
1.8E+04
7.3E+04
7.3E+01
5.3E+03
3.5E+04
9.7E+00
5.5E+05
5.5E-02
1.4E-02
1.3E+02
6.4E+01
switchmethyl
switchmethyl prot
switch
switch prot
1.6E+05
1.4E+03
-
1.1E+02
2.4E+07
2.3E-01
-
5.4E+00
6.4E+03
3.0E-03
1.1E+05
2.7E+04
9.1E+05
1.4E+02
1.4E+09
3.9E+03
9.8E+05
1.2E+01
-
Looking at the influence of the methyl radical and the different monomer radicals, it can be
seen that the reactions with MMA have the lowest rate coefficient, and those with the methyl
radical have the highest rate coefficient. The radicals in order of increasing reactivity, and so
increasing rate coefficients, are MMA < styryl < nBA < MA < methyl. This is in accordance
with earlier results of Goto et al. [153], who concluded that the styryl radical is more reactive
than the MMA radical. However, it has to be remarked that this order does not correspond
with the ‘classical’ dependence of the rate coefficients: styryl < methacrylates < acrylates
[154-156]. Another source even states acrylates < styryl < methacrylates as possible order of
reactivity [157].
Chapter 4: Results and discussion
66
A possible explanation for the obtained order of reactivity is suggested in what follows. The
relatively low reactivity of the MMA radical can be explained by the presence of three alkyl
groups on the carbon bearing the unpaired electron, making it thus a tertiary radical. These
alkyl groups can donate electron density to the electron poor species. A low bonding
dissociation energy of the C-H bond in the MMA radical indicates a stable, less reactive
radical. In contrast, the methyl radical CH3• has no alkyl groups on the carbon bearing the
unpaired electron, explaining why CH3• is not stable and very reactive. The radicals of
styrene, nBA and MA, are secondary radicals with a reactivity between those of the MMA
radical and CH3•. A schematic representation of this order of stability is shown in Figure 25
[158]. The last three radicals mentioned are stabilized by resonance. This is especially true for
the styryl radical due to the large amount of equivalent resonance structures. For the nBA and
MA radicals, the resonance structures have less of a stabilizing influence since formal positive
charges on oxygen are appearing.
Figure 25. Radical stability as function of the number of alkyl groups
on the carbon bearing the unpaired electron [158]
For the protonated form of switchmethyl however, this trend is not observed, which is due to the
concept of the switchable RAFT CTA, which will be explained in the next paragraph 4.2.2 .
The equilibrium coefficients of the model addition reactions are represented in Table 14. The
reactivities explained above, can be recognized in Table 14 as well. The equilibrium
coefficient increases in the following order: MMA < styryl < nBA < MA < methyl. A higher
equilibrium coefficient means that the equilibrium lies more to the right. This can also be
assigned to the reactivity of the radicals: the more reactive a radical, the more the reaction will
occur, and the equilibrium will shift away from the reactive radical. This general trend is
observed for all the reactions considered. Sometimes the order of two radicals is swapped but
in those cases, the values lie in the same order of magnitude.
Chapter 4: Results and discussion
67
Looking at the equilibrium coefficients of the reactions with switchmethyl, the order of radicals
mentioned above is not recognized. However, the equilibrium coefficients of the reactions
with styryl, MA and nBA radicals have a similar order of magnitude so no clear trend can be
stated. In case of the reactions with switch, the values for styryl and nBA are very close to
each other, leading to the acceptance of the order of monomers given before. As mentioned
previously, the reactivity trend of the monomers is not recognized in the equilibrium
coefficients of the reactions with the protonated form of switchmethyl.
The results for the reactions with MEDT as RAFT CTA correspond to those found in
literature. In Table 2 in section 2.2.3.4, it can be seen that the reaction enthalpy becomes more
negative in the following order: styryl < MA < methyl. A more exothermic reaction
corresponds to a higher equilibrium coefficient, due to the small entropic effects. This trend is
also present in the calculated equilibrium coefficients.
Table 14. Forward equilibrium coefficients K [L mol-1] of addition reactions of the methyl radical and
different monomer radicals (styryl, MMA, MA and nBA) with different RAFT CTAs (MEDT, MBDT,
CPDTmethyl, CPDTethyl, switchmethyl, protonated switchmethyl, switch and protonated switch), calculated at
BMK/6-311+G**, at 298.15 K
RAFT CTA
methyl
styryl
MMA
MA
nBA
MEDT
MBDT
CPDTmethyl
CPDTethyl
1.1E+10
1.3E+15
7.0E+10
1.4E+11
6.4E-02
1.8E+04
1.2E-01
1.7E-01
1.3E-05
7.3E-01
1.2E-04
1.0E-04
9.1E+00
7.6E+05
1.8E+03
3.4E+02
1.9E+00
2.8E+05
1.4E+01
1.6E+01
switchmethyl
switchmethyl prot
switch
1.1E+13
9.6E+10
7.8E+00
6.8E+06
1.3E-01
2.6E-04
5.0E+02
2.5E-07
3.0E+00
2.0E+03
5.8E+01
2.3E-01
2.3E+02
5.6E-01
-
-
7.0E+05
1.6E+11
-
switch prot
4.2.2 Influence of RAFT CTA
Considering Table 13 and Table 14, also the influence of the RAFT CTA can be discussed.
The rate coefficient of addition as well as the equilibrium coefficient for MBDT are higher
than for MEDT. This is because the phenyl substituent is expected to stabilize the RAFT
intermediate to a much greater degree due to its ability to delocalize the unpaired electron in
the aromatic ring. This was already mentioned in the literature study (paragraph 2.2.3.2) [34].
Furthermore, in the literature study, it was shown in Table 1 that the rate coefficient of
Chapter 4: Results and discussion
68
addition differs more or less one order of magnitude between the reaction of the methyl
radical with MEDT and MBDT. The difference between the calculated results, represented in
Table 13, is much smaller, only a factor 2. The difference in equilibrium coefficients between
reaction with both RAFT CTAs is higher, almost four orders of magnitude, according to
literature. Also in the results shown in Table 14, a higher difference in equilibrium
coefficients can be seen, more or less in accordance with the literature.
The calculated results indicate that the rate coefficient of the addition reaction with
CPDTmethyl is lower than with MEDT, one to four orders of magnitude, depending on the
monomer. This means that a methyl substituent better stabilizes the intermediate, compared to
the cyano isopropyl group. This can be explained by the positive inductive effect of the
methyl group, while the cyano isopropyl substituent has an electron withdrawing character.
As a radical is electron deficient, an electron donating group attached to the radical, is
preferred for stability [159].
As already mentioned before in paragraph 4.1.1, the difference between the reactivity of
CPDTmethyl and CPDTethyl is negligible, leading to the conclusion that a methyl or ethyl group
can be used to replace the dodecyl group, originally present in the RAFT CTA CPDT. It can
be seen, in Table 13 as well as in Table 14, that the difference between the rate coefficients of
addition and the equilibrium coefficients of the reactions with both RAFT CTAs are very
small, at most a factor six, which is acceptable, looking at the accuracy of the computational
methods.
Looking at the switchable RAFT CTAs, it is known that they can offer good control over the
polymerization of both “less-activated” monomers and “more-activated” monomers, as
described in the literature study (paragraph 2.3). This is obtained by switching between the
neutral and the protonated form of the RAFT CTA. In this work, the switchable RAFT CTA
2-cyano-2-propyl N-(4-pyridinyl)-N-methyl dithiocarbamate, further indicated as switch, is
investigated. Also a simplified molecule, named switchmethyl, in which the cyano isopropyl
group is replaced by a methyl group, is used in the calculations. This is performed to see the
influence of the presence of the cyano isopropyl group and to see if the simplified chemical
structure is representative for the original, larger structure. The chemical structures of both
RAFT CTAs are presented in Figure 26.
Chapter 4: Results and discussion
69
N
S
S
S
S
CH3
N
N
H3C
CH3
N
CH3
N
CH3
Figure 26. Chemical structure of the switchable RAFT CTA, 2-cyano-2-propyl N-(4-pyridinyl)-N-methyl
dithiocarbamate (left) and a simplified molecule, methyl N-(4-pyridinyl)-N-methyl dithiocarbamate (right)
To investigate the switchable RAFT CTA, the reactions of a methyl radical and different
monomer radicals with both the neutral and protonated form of the switchable RAFT CTA, as
well as of its simplified structure, are performed. The results of the forward rate coefficients
of the addition reactions with the switchable RAFT CTAs are included in Table 13. The
equilibrium coefficients for the same set of reactions are shown in Table 14.
The influence of the protonation of the switchable RAFT CTAs is very clear from Table 13
and Table 14. For the polymerizations of styrene, MMA, MA and nBA, the protonated forms
of switch as well as switchmethyl lead to higher rate coefficients of addition (up to a factor 108)
and higher equilibrium coefficients (up to a factor 1012). This strong trend is in accordance
with the principle of the switchable RAFT CTAs. The neutral form of the RAFT CTAs offers
good control over the polymerization of LAMs. In contrast, the protonated form is appropriate
as RAFT CTA for the polymerization of MAMs, such as styrene, MMA, MA and nBA [56,
58]. This explains the higher rate and equilibrium coefficients for the reactions of the
protonated forms with monomers as styrene, MMA, MA and nBA.
To see the influence of the cyano isopropyl group in the switch RAFT CTA, the reactions are
calculated by making use of the original switch RAFT CTA, as well as the switchable RAFT
CTA with a methyl group attached instead of the cyano isopropyl group. A significant
difference between the rate coefficient of the addition reaction with switch and switchmethyl is
observed in Table 13, a difference of two or three orders of magnitude. The differences in the
equilibrium coefficient lie in the same range, so it can be concluded that methyl N-(4pyridinyl)-N-methyl dithiocarbamate is not representative for 2-cyano-2-propyl N-(4pyridinyl)-N-methyl dithiocarbamate. Furthermore, it is observed that the differences between
the reactions with the neutral and protonated form are much larger in case of the switch RAFT
CTA, compared to the simplified structure.
Chapter 4: Results and discussion
70
4.3 Kinetic modeling of polymerization of styrene with CPDT as
RAFT CTA
In this section, RAFT polymerization of styrene, with CPDT as RAFT CTA and AIBN as
initiator, is modeled by making use of an existing kinetic model. In contrast to what is
previously done, the kinetic parameters necessary as input are not obtained via parameter
estimation or via literature, but via ab initio modeling of the different reaction steps. Also
solvent effects are taken into account for the calculation of the kinetic parameters. First, a
look is taken at the initiation and propagation reactions, followed by an investigation of the
reactions in the RAFT mechanism.
4.3.1 Initiation and propagation reactions
The initiation reaction and several propagation reactions are considered, and the chemical
structures are given in Figure 27. The reaction of the initiator radical with styrene is
considered, indicated as initiation. Also the reaction of a styryl radical with an initiator group
attached, with the monomer styrene, indicated by ‘propagation 1 with the initiator group
attached’ is calculated. Moreover, the reaction of a macroradical with two monomer units and
an initiator group attached with the monomer styrene, ‘propagation 2 with the initiator group
attached’ is considered, as well as the propagation reaction of styrene, without taking into
account the initiator group.
Chapter 4: Results and discussion
71
Figure 27. Initiation and several propagation reactions for the polymerization of styrene
with AIBN as initiator
4.3.2 Reactions in the RAFT mechanism
To determine the reactions to account for in the kinetic model, a general form of the RAFT
intermediate is considered, shown below in Figure 28.
Chapter 4: Results and discussion
72
X
S
S
C
Y
S
Z
Figure 28. Chemical structure of a general RAFT intermediate with groups X, Y and S-Z
For the considered RAFT CTA in this study, CPDT, the Z-group in Figure 28 is a dodecyl
group. As discussed in paragraph 4.1.3, the length of the alkyl chain does not seem to have a
big influence on the reactivity. Because of computational constraints, an ethyl group has
therefore been chosen to model the reactions. Note that an alkyl group will not be split off due
to β-scission because of the instability of alkyl radicals. For the X- and Y-group, different
possibilities exist: i) the initiator radical, ii) the R-radical, which is the cyano isopropyl radical
for CPDT, iii) the styryl radical with an initiator group attached, iv) a macroradical of styrene
with an initiator group attached or v) the dimer radical of styrene. The initiator radical can
vary, depending on the initiator used. The other radicals are represented in Figure 29.
H3C
CH3
CH
H3C
C
N
N
H3C
N
CH3
HC
n
H3C
CH3
HC
Figure 29. R-radical (top left), styryl radical with initiator group attached (top right), macroradical of
styrene with an initiator group attached (bottom left), dimer radical of styrene (bottom right)
Combining these X and Y groups with each other, and considering the Z-group as fixed, leads
to 25 addition and 25 fragmentation reactions. However, in this work, AIBN (Figure 30) is
used as initiator, meaning that the initiator radical and the R-radical are representing the same
chemical structure.
Chapter 4: Results and discussion
73
Figure 30. Azobisisobutyronitrile (AIBN)
Furthermore, supposing a polymerization temperature below 373 K, thermal initiation of
styrene is neglected [160, 161], and therefore dimer formation is not taken into account. These
two simplifications lead to a reduction of the number of reactions to be considered, 18
reactions are left, compared to the 50 reactions originally. Also a third approximation is
implicitly used here, related to the chain length dependence of the macroradical in RAFT
polymerization. It is shown in earlier studies [8, 13] that chain length effects for the first few
steps are highly significant, while they converge rapidly once the second monomer unit is
added. Therefore, only a macroradical with two monomer units (n = 2) is considered as
propagating radical. Typically, kinetic models are based on this approximation. The reactions
considered are represented in Figure 31, Figure 32 and Figure 33, including the chemical
structures. Figure 31 shows the reactions with the cyano isopropyl radical (R0•), Figure 32
those with the macroradical (Ri•) and Figure 33 gives the reactions in the model with the
styryl radical with an initiator group attached (St•). Following symbols are used:
R0• is the radical of the R-group of the RAFT CTA,
Ri• is the macroradical of styrene with two monomer units and with an initiator group
attached,
St• is the styryl radical with an initiator group attached,
TR0 is the original RAFT CTA CPDTethyl,
TRi is a RAFT CTA with the macroradical attached
and TSt is a RAFT CTA with the styryl radical attached.
Chapter 4: Results and discussion
74
Figure 31. Reactions concerning the cyano isopropyl radical R0•, included in the kinetic model
Figure 32. Reactions concerning the macroradical Ri•, included in the kinetic model
Chapter 4: Results and discussion
75
Figure 33. Reactions concerning the styryl radical St•, included in the kinetic model
4.3.3 Kinetic parameters
In the kinetic model, the input parameters are the activation energy and the pre-exponential
factor of each reaction, to clearly see the temperature dependence. In section 3.3.5, the
procedure for the determination of the pre-exponential factor and the activation energy,
present in the Arrhenius relationship, is described. Also the formulas for the calculation of the
rate coefficients at different temperatures, for reactions in the gas phase as well as for
reactions performed in solvent, are mentioned in that section. For the reactions present in the
model, the rate coefficients are determined at the following temperatures: 333.15 K, 353.15
K, 373.15 K and 393.15 K. These comprise the temperature interval in which the
polymerization of styrene is typically carried out [23, 160, 161].
For the reaction of R0• with TR0, schematically represented in Figure 31, this procedure is
explicitly elaborated. The activation Gibbs free energy of the reaction in the gas phase is
calculated at the four above mentioned temperatures. Using these values, the rate coefficient
of the addition reaction is calculated at each temperature. Similarly, for the reaction
Chapter 4: Results and discussion
76
performed in styrene, the activation Gibbs free energy is calculated at each temperature,
leading to the determination of the rate coefficients of addition. All these quantities are
represented in Table 15.
Table 15. Activation Gibbs free energy of the reaction in the gas phase, ΔG‡ [kJ mol-1], rate coefficient of
the addition reaction in the gas phase, kadd,1 [L mol-1 s-1], activation Gibbs free energy of the reaction in
styrene, ΔG‡sol, [kJ mol-1], rate coefficient of the addition reaction in styrene, kadd,1,sol, [ L mol-1 s-1], for
different temperatures T [K], for the reaction of R0 with TR0. Contributions for solvation are calculated
using COSMO-RS.
T
[K]
3.3E+02
3.5E+02
3.7E+02
3.9E+02
ΔG‡
[kJ mol-1]
6.96E+01
7.30E+01
7.64E+01
7.98E+01
kadd,1
[L mol-1 s-1]
2.35E+03
3.37E+03
4.80E+03
6.54E+03
ΔG‡sol
[kJ mol-1]
6.39E+01
6.57E+01
6.75E+01
6.93E+01
kadd,1,sol
[L mol-1 s-1]
6.6E+02
1.4E+03
2.8E+03
5.1E+03
Once these values are known, an Arrhenius plot is made for the reaction in the gas phase as
well as for the reaction in styrene, respectively Figure 34 and Figure 35.
9.2E+00
ln k add,1 [-]
8.8E+00
8.4E+00
8.0E+00
y = -2241.4x + 14.482
7.6E+00
2.5E-03
2.7E-03
2.9E-03
3.1E-03
T-1 [K-1]
Figure 34. Arrhenius plot for the reaction of R0 • with TR0 in the gas phase, including the trend line
Chapter 4: Results and discussion
77
9.0E+00
ln k add,1,sol [-]
8.0E+00
7.0E+00
y = -4461.9x + 19.884
6.0E+00
5.0E+00
2.5E-03
2.7E-03
2.9E-03
T-1
3.1E-03
[K-1]
Figure 35. Arrhenius plot for the reaction of R0• with TR0 in styrene, including the trend line
Looking at the equations of the trend lines, the activation energy and the pre-exponential
factor can be determined from the slope and the intercept respectively. The results are
included in Table 16. In this table, the activation energy and pre-exponential factor for the
addition reactions are represented. Table 17 shows the kinetic parameters for the
fragmentation reactions. In both tables, it is clear that the solvent has a significant influence.
The activation energy is 10 – 30 kJ mol-1 higher, while the difference in the pre-exponential
factor is about four or five orders of magnitude.
Table 16. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the addition
reactions in RAFT polymerization of styrene using CPDTethyl, in the gas phase and in styrene.
Contributions for solvation are calculated using COSMO-RS.
Gas phase
Ea [kJ mol-1]
A [L mol-1 s-1]
In styrene
Ea [kJ mol-1]
A [L mol-1 s-1]
R0• +TR0 → (R0TR0)•
R0• +TRi → (R0TRi)•
R0• +TSt → (R0TSt)•
1.6E+01
2.1E+01
2.4E+01
7.5E+04
2.5E+05
5.5E+04
3.7E+01
4.1E+01
4.2E+01
1.2E+09
5.3E+09
1.2E+09
Ri• +TR0 → (RiTR0)•
Ri• +TRi → (RiTRi)•
Ri• +TSt → (RiTSt)•14
4.4E+01
2.4E+01
1.3E+01
1.2E+05
1.4E+04
5.7E+04
6.6E+01
5.4E+01
5.3E+01
4.3E+09
1.9E+09
2.8E+09
St• +TR0 → (StTR0)•
St• +TRi → (StTRi)•14
St• +TSt → (StTSt)•14
5.8E+01
3.9E+01
2.4E+01
3.7E+05
6.8E+04
4.4E+05
6.8E+01
6.5E+01
4.6E+01
4.1E+09
3.3E+09
5.7E+09
14
For these reactions, the Berny algorithm to find the transition state did not succeed. Instead, the geometry of
the maximum energy structure along a scan of the reaction coordinate has been used to calculate the energies.
Chapter 4: Results and discussion
78
Table 17. Activation energy Ea [kJ mol-1] and pre-exponential factor A [s-1] for the fragmentation
reactions in RAFT polymerization of styrene using CPDTethyl, in the gas phase and in styrene.
Contributions for solvation are calculated using COSMO-RS.
(R0TR0)• → R0• + TR0
(R0TRi)• → R0• + TRi
(R0TSt)• → R0• + TSt
Gas phase
Ea [kJ mol-1]
A [s-1]
4.7E+01
2.2E+14
4.9E+01
8.8E+14
4.3E+01
5.7E+14
In styrene
Ea [kJ mol-1]
A [s-1]
4.8E+01
2.1E+14
4.6E+01
5.6E+14
4.0E+01
4.1E+14
(RiTR0)• → Ri• + TR0
(RiTRi)• → Ri• + TRi
(RiTSt)• → Ri• + TSt15
7.3E+01
5.7E+01
5.2E+01
2.3E+14
1.3E+14
5.9E+14
7.4E+01
5.7E+01
5.2E+01
2.1E+14
1.3E+14
5.9E+14
(StTR0)• → St• + TR0
(StTRi)• → St• + TRi15
(StTSt)• → St• + TSt15
7.5E+01
7.6E+01
5.7E+01
1.4E+15
4.3E+14
9.2E+14
6.0E+01
5.6E+01
6.6E+01
4.3E+14
4.3E+14
8.0E+14
For the initiation and propagation reactions, the results of Ea and A for the addition reactions
are shown in Table 18, those for the fragmentation reactions are given in Table 19. The
activation energy of the addition propagation reaction, taking into account two monomer units
and no initiator group, equals 53.8 kJ mol-1, if the reaction is performed in styrene. This
corresponds more or less to the value of 50 kJ mol-1 found in literature for the micro-emulsion
polymerization of styrene [162]. Furthermore, it has to be remarked that, for addition, the
difference in the activation energy between propagation 1
and propagation 2
with initiator group
with initiator group
of a monomer radical
of a macroradical is significant, while the difference in the
pre-exponential factor is negligible. This means that the entropy does not change significantly
between the two reactions, in contrast to the enthalpy, according to formulas (3.49) and
(3.50). The position of the attached initiator fragment relative to the unpaired electron is
probably the underlying reason. Therefore, chain length dependence cannot be neglected in
the beginning of the polymerization, which is in accordance with the literature [8, 13]. It can
be concluded that propagation cannot completely accurately be described using only one rate
coefficient of propagation, especially in the beginning of the polymerization. Further
investigation of kinetic models with different propagation rate coefficients is suggested.
Looking at the reactions of the macroradical with two monomer units, once with and once
without the initiator group attached, it can be seen that the presence of an initiator group has
an important influence on the reactivity, due to the significant difference in the activation
15
For these reactions, the Berny algorithm to find the transition state did not succeed. Instead, the geometry of
the maximum energy structure along a scan of the reaction coordinate has been used to calculate the energies.
Chapter 4: Results and discussion
79
energy for the addition performed in solvent. The same observation is recognized in
paragraph 4.1.4.
Table 18. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the addition of the
initiation and propagation reactions, in the gas phase and in styrene. Contributions for solvation are
calculated using COSMO-RS.
Initiation
Propagation 1 with initiator group
Propagation 2 with initiator group
Propagation
Gas phase
Ea [kJ mol-1] A [L mol-1 s-1]
3.9E+01
3.5E+05
4.4E+01
4.1E+05
4.6E+01
3.7E+05
4.1E+01
3.0E+05
In styrene
Ea [kJ mol-1] A [L mol-1 s-1]
4.8E+01
2.5E+09
5.5E+01
3.1E+09
6.2E+01
6.5E+09
5.4E+01
3.6E+09
Table 19. Activation energy Ea [kJ mol-1] and pre-exponential factor A [s-1] for the fragmentation of the
initiation and propagation reactions, in the gas phase and in styrene. Contributions for solvation are
calculated using COSMO-RS.
Initiation
Propagation 1 with initiator group
Propagation 2 with initiator group
Propagation
Gas phase
Ea [kJ mol-1]
A [s-1]
1.3E+02
3.1E+15
1.2E+02
1.3E+15
1.2E+02
1.7E+15
1.2E+02
1.5E+15
In styrene
Ea [kJ mol-1]
A [s-1]
1.2E+02
3.1E+15
1.2E+02
1.3E+15
1.3E+02
3.1E+15
1.2E+02
2.6E+15
4.3.4 Implementation in the kinetic model and comparison with experimental data
The kinetic parameters, obtained via ab initio modeling, are implemented in the in-house
kinetic model. However, they are not able to accurately describe the experimental
observations of RAFT polymerization. Therefore, in order to have a better prediction,
correction factors have to be taken into account. In this work, two approaches are
investigated.
In the first approach, the ab initio calculated values for the pre-exponential factors of the
addition reactions of Ri• and St• are multiplied with 105, in order to get a good agreement
between the simulated and the experimental values. This factor for certain reactions is
obtained by comparing the calculated results with available kinetic parameters that are able to
describe the experiments well. The ab initio calculated parameters for the fragmentation
reactions are used without correction. The parameters for the addition reactions, used in this
first approach, are given in Table 20. The results obtained with the kinetic model are
represented in Figure 36. Herein, the monomer conversion is plotted as function of the
Chapter 4: Results and discussion
80
polymerization time, the number of monomer units per chain is given as function of the
monomer conversion and the dispersity is also represented as function of the monomer
conversion. The plots are given for four different conditions, which differ in temperature,
targeted chain length (TCL) and ratio of initial concentration of RAFT CTA to initiator. These
are listed in Table 21. It is clear that a good agreement between the model, based on corrected
kinetic parameters calculated via ab initio modeling, and the experiments is obtained with this
approach.
Table 20. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the addition
reactions in RAFT polymerization of styrene using CPDTethyl, in styrene, used in the first approach
Ea [kJ mol-1]
A [L mol-1 s-1]
R0• +TR0 → (R0TR0)•
R0• +TRi → (R0TRi)•
R0• +TSt → (R0TSt)•
3.7E+01
4.1E+01
4.2E+01
1.2E+09
5.3E+09
1.2E+09
Ri• +TR0 → (RiTR0)•
Ri• +TRi → (RiTRi)•
Ri• +TSt → (RiTSt)•
6.6E+01
5.4E+01
5.3E+01
4.3E+14
1.9E+14
2.8E+14
St• +TR0 → (StTR0)•
St• +TRi → (StTRi)•
St• +TSt → (StTSt)•
6.8E+01
6.5E+01
4.6E+01
4.1E+14
3.3E+14
5.7E+14
Table 21. Different conditions for RAFT polymerization of styrene using CPDTethyl,
considered in the kinetic model
Condition 1
Condition 2
Condition 3
Condition 4
Temperature [K]
TCL [-]
343.15
343.15
353.15
363.15
200
200
400
200
Chapter 4: Results and discussion
[RAFT CTA]0 /
[AIBN]0 [-]
1/1
5/1
2/1
1/1
81
Figure 36. Comparison between the simulation, based on adjusted kinetic parameters obtained via ab
initio modeling (full line) and the experimental data (+), using the first approach, monomer conversion as
function of time (left), number of monomer units per chain as function of monomer conversion (middle),
dispersity as function of monomer conversion (right), for four sets of conditions
The second approach is based on a scaling with the propagation reaction. The ab initio values
for the activation energy and the pre-exponential factor of the propagation reaction are
compared with the values for the propagation reaction originally used in the model, as is
Chapter 4: Results and discussion
82
shown in Table 22. It can be deduced that the ab initio calculated activation energies are about
2.1 kJ mol-1 too high and the pre-exponential factors are a factor 1.2E+02 too high. These
scaling factors are used to adapt the kinetic parameters of the reactions in RAFT
polymerization. However, using only these scaling factors for the addition reactions is not
sufficient to have an accurate description. Therefore, similarly as before, an additional
correction factor of 104 is needed for the addition reactions of Ri• and St•. The parameters for
the addition reactions, used in the second approach, are given in Table 23, while those for the
fragmentation reactions are shown in Table 24. In Figure 37, the same quantities are plotted as
for the first approach, for the same sets of conditions. Again, a good agreement between
predicted and experimental values is obtained.
Table 22. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the propagation
reaction, calculated via ab initio and originally used in the model, with the corresponding scaling factors
necessary
Ab initio
In model
Scaling factor
Ea [kJ mol-1]
5.4E+01
3.3E+01
A [L mol-1 s-1]
3.6E+09
4.2E+07
-2.1E+01
1.2E-02
Table 23. Activation energy Ea [kJ mol-1] and pre-exponential factor A [L mol-1 s-1] for the addition
reactions in RAFT polymerization of styrene using CPDTethyl, in styrene, used in the second approach
Ea [kJ mol-1]
A [L mol-1 s-1]
R0• +TR0 → (R0TR0)•
R0• +TRi → (R0TRi)•
R0• +TSt → (R0TSt)•
1.6E+01
1.9E+01
2.0E+01
1.4E+07
6.2E+07
1.4E+07
Ri• +TR0 → (RiTR0)•
Ri• +TRi → (RiTRi)•
Ri• +TSt → (RiTSt)•
4.5E+01
3.3E+01
3.2E+01
4.9E+07
2.2E+07
3.3E+07
St• +TR0 → (StTR0)•
St• +TRi → (StTRi)•
St• +TSt → (StTSt)•
4.6E+01
4.3E+01
2.5E+01
4.8E+07
3.9E+07
6.7E+07
Chapter 4: Results and discussion
83
Table 24. Activation energy Ea [kJ mol-1] and pre-exponential factor A [s-1] for the fragmentation
reactions in RAFT polymerization of styrene using CPDTethyl, in styrene, used in the second approach
(R0TR0)• → R0• + TR0
(R0TRi)• → R0• + TRi
(R0TSt)• → R0• + TSt
Ea [kJ mol-1]
2.7E+01
2.5E+01
1.9E+01
A [s-1]
2.5E+12
6.5E+12
4.8E+12
(RiTR0)• → Ri• + TR0
(RiTRi)• → Ri• + TRi
(RiTSt)• → Ri• + TSt
5.3E+01
3.6E+01
3.1E+01
2.4E+12
1.5E+12
6.8E+12
(StTR0)• → St• + TR0
(StTRi)• → St• + TRi
(StTSt)• → St• + TSt
3.9E+01
3.5E+01
4.5E+01
5.0E+12
5.0E+12
9.4E+12
Chapter 4: Results and discussion
84
Figure 37. Comparison between the simulation, based on adjusted kinetic parameters obtained via ab
initio modeling (full line) and the experimental data (+), using the second approach, monomer conversion
as function of time (left), number of monomer units per chain as function of monomer conversion
(middle), dispersity as function of monomer conversion (right), for four sets of conditions
4.3.5 Influence of temperature
Comparing the first and fourth set of conditions in Figure 36 and Figure 37, the influence of
the temperature is investigated. In the first set, the temperature equals 343.15 K, the second
set is performed at 363.15 K, while the other parameters are kept constant. As expected and
Chapter 4: Results and discussion
85
confirmed in Figure 38 (top left), a higher temperature results in a higher conversion after a
specified polymerization time (dashed line). This effect can be attributed to the exponential
temperature dependence of the propagation and initiator decomposition rate coefficients.
Looking at the upper right graph in Figure 38, a lower number of monomer units per chain for
a particular monomer conversion is observed at a higher temperature. This can also be due to
the higher initiator decomposition rate coefficient, leading to more and hence shorter chains.
A higher dispersity is observed, at the lower left plot in Figure 38, for the polymerization at
363.15 K (dashed line), compared to the simulation at 343.15 K (full line). This can be
understood by the smaller extent of control at a higher polymerization temperature, possibly
due to higher rate coefficients of the fragmentation reactions. The better control at lower
temperatures is additionally reflected in a higher end-group functionality (EGF; bottom right
in Figure 38). It can be summarized that better control of RAFT polymerization is obtained at
sufficiently low polymerization temperatures.
90
Number of monomer units per
chain [-]
140
80
Conversion [%]
70
60
50
40
30
20
10
120
100
80
60
40
20
0
0
0
200
Time [min]
Chapter 4: Results and discussion
400
0
50
Conversion [%]
100
86
1.2
1.4
0.8
EGF [-]
Dispersity [-]
1
1.3
1.2
0.6
0.4
1.1
0.2
1
0
50
Conversion [%]
100
0
0
50
Conversion [%]
100
Figure 38. Influence of temperature on monomer conversion (top left), number of monomer units per
chain (top right), dispersity (bottom left) and EGF (bottom right), for RAFT polymerization of styrene at
343.15 K (full line) and at 363.15 K (dashed line)
Chapter 4: Results and discussion
87
Chapter 5 Conclusions and future
recommendations
Kinetic and thermodynamic parameters for a number of model RAFT reactions have been
performed using three levels of theory, CBS-QB3, BMK/6-311+G** and M06-2X/6311+G**. CBS-QB3 is too computationally expensive to be of practical use. The parameters
obtained with BMK/6-311+G** are consistent with the reference values from literature and
with available experimental data. This method was initially used in this master thesis as it is
also the recommended DFT method in literature. However, it is suggested that a closer look to
the use of M06-2X should be taken for further ab initio investigations of RAFT
polymerization as the calculated results look promising. This was not possible anymore in the
limited timeframe of this thesis.
Furthermore, it was investigated if large substituents in molecules can be modeled by smaller
groups. It is concluded that long alkyl groups can be substituted by a methyl or an ethyl
group. As a consequence, the RAFT CTA 2-cyano-2-propyl dodecyl trithiocarbonate can be
accurately described by 2-cyano-2-propyl (m)ethyl trithiocarbonate. However, a cyano
isopropyl group cannot be replaced by a methyl group, as was examined for the switchable
RAFT CTA. In this framework, also the influence of an initiator group in RAFT
polymerization, attached to the propagating radical or attached to the RAFT CTA, is
considered. It is clear that the presence of an initiator group has an important influence on the
reactivity.
An investigation of some model reactions of the methyl and the styryl radical, in the gas
phase as well as performed in a solvent (styrene and tetrahydrofuran), shows a relatively small
influence of the solvent. This is due to the apolarity of the methyl radical and the very low
polarity of the styryl radical. Stronger solvation effects can be expected for reactions with
acrylates, because of their greater polarity and their greater potential for hydrogen bonding.
To investigate the structural characteristics of the chain transfer agent in RAFT
polymerization on the reactivity, several important RAFT CTAs were examined in this work.
Methyl benzodithioate is a more reactive RAFT CTA than methyl ethane dithioate, due to the
stabilization of the RAFT intermediate by the phenyl substituent. This can be attributed to its
ability to delocalize the unpaired electron in the aromatic ring. When comparing 2-cyano-2-
Chapter 5: Conclusions and future recommendations
88
propyl ethyl trithiocarbonate with methyl ethane dithioate, it is clear that the latter is more
reactive. A methyl substituent as R-group better stabilizes the intermediate, compared to the
cyano isopropyl group. This can be explained by the positive inductive effect of the methyl
group, while the cyano isopropyl substituent has an electron withdrawing character.
Another RAFT CTA that is examined is 2-cyano-2-propyl N-(4-pyridinyl)-N-methyl
dithiocarbamate, better known as a switchable RAFT CTA. This is a very promising topic
since a switchable RAFT CTA offers good control over the polymerization of both lessactivated in its neutral form, as well as more-activated monomers, in its protonated form.
After calculations of the switchable RAFT CTA and its protonated form, it becomes clear that
the protonated form is more reactive towards styrene, methyl methacrylate, methyl acrylate
and n-butyl acrylate, compared to the neutral form. This is in accordance with the principle of
switchable RAFT CTAs, since these monomers belong to the category of the more-activated
monomers.
Additionally, the influence of the structure of the radical on the reactivity with the RAFT
CTAs has been investigated. It was observed that the reactions with the MMA radical have
the lowest rate and equilibrium coefficients, and those with the methyl radical have the
highest coefficients. The radicals in order of increasing reactivity, and so increasing rate and
equilibrium coefficients, are MMA < styryl < nBA < MA < methyl. This can be expected
because MMA is a tertiary radical, which is not very reactive. Styryl, nBA and MA are
secondary radicals and have an intermediate reactivity. The methyl radical is very reactive
due to its instability. However, this order of reactivity does not correspond with the classical
order of monomer reactivity, stated in literature.
In the last part of this master thesis, a first principles based kinetic model for RAFT
polymerization of styrene, with 2-cyano-2-propyl dodecyl trithiocarbonate as RAFT CTA and
azobisisobutyronitrile as initiator, is developed. First, the initiation and propagation reactions
are considered. It can be concluded that propagation cannot accurately be described with one
rate coefficient of propagation, due to the chain length dependence. Further studies of kinetic
models with different propagation rate coefficients are recommended.
The most important reactions in the RAFT mechanism are identified and kinetic parameters
are calculated using ab initio modeling. A correction of the ab initio calculated values is
necessary to provide an accurate description of the experimental data. Two approaches are
examined. In the first approach, the pre-exponential factors of the addition reactions of the
Chapter 5: Conclusions and future recommendations
89
macroradical and the styryl radical are multiplied with a factor 105. With these correction
factors, a very good agreement between the model predictions and the experimental data is
obtained. The second approach is based on scaling with the propagation reaction.
Additionally, the addition reactions with the macroradical and the styryl radical are raised
with 104. A good agreement between modeled and experimental values is observed. A more
extended analysis of the most important reactions in the RAFT mechanism is advised, to
investigate a more rigorous scaling procedure.
In particular, the kinetic model is used to investigate the influence of temperature by
comparing different simulations. A higher temperature results in a faster polymerization,
which can be attributed to the exponential temperature dependence of the propagation and
initiator decomposition rate coefficients. A lower number of monomer units per chain is
observed for a higher polymerization temperature, due to a higher initiator decomposition rate
coefficient, leading to more and hence shorter chains. The larger extent of control at a lower
polymerization temperature is reflected in a lower dispersity and a higher end-group
functionality. It can be concluded that a sufficiently low polymerization temperature is desired
for good control of RAFT polymerization.
Chapter 5: Conclusions and future recommendations
90
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Makromolekulare Chemie-Macromolecular Chemistry and Physics, 1992. 193(6): p.
1249-1260.
Chapter 6: References
104
Appendix A Conformational analysis
In this section, the importance of a conformational analysis is demonstrated. Therefore, the
reaction between the styryl radical and CPDTmethyl as well as the reaction of the styryl radical
with CPDTethyl are considered. The results for the structures optimized via the keyword ‘opt’
in Gaussian are shown in Table 25 and Table 26, as well as the results after the performance
of a conformational analysis. It can be clearly seen in Table 25 that the conformational
analysis has a significance influence on the values of both the rate and equilibrium
coefficients of the addition reactions, about a factor 100 for both quantities of both reactions.
Looking at the results for the fragmentation reactions in Table 26, again a significant
difference is observed for the rate coefficients, while the difference between the equilibrium
coefficients is at maximum one order of magnitude.
Table 25. Forward rate and equilibrium coefficients of the addition reactions of the styryl radical with
CPDTmethyl and CPDTethyl as RAFT CTAs, kadd,1 [L mol-1 s-1] and K [L mol-1] respectively, calculated at
BMK/6-311+G**, at 298.15 K, with and without a conformational analysis performed
CPDTmethyl + STY• → CPDTmethyl-STY•
CPDTethyl + STY• → CPDTethyl-STY•
kadd,1 [L mol-1 s-1]
without
with
2.0E-04 8.7E-02
1.1E+00 5.5E-02
K [L mol-1]
without
with
4.9E-03 1.2E-01
2.4E-02 1.7E-01
Table 26. Forward rate and equilibrium coefficients of the fragmentation reaction of the intermediate of
the styryl radical with CPDTmethyl and CPDTethyl as RAFT CTAs, kfrag,2 [s-1] and Kβ [L mol-1] respectively,
calculated at BMK/6-311+G**, at 298.15 K, with and without a conformational analysis performed
CPDTmethyl-STY• → S=C(SCH3)S-STY +
C(CH3)2CN•
CPDTethyl-STY• → S=C(SCH2CH3)S-STY
+ C(CH3)2CN•
kfrag,2 [s-1]
without
with
Kβ [L mol-1]
without
with
1.6E+07 1.05E+05
5.4E-04
4.3E-05
1.4E+08 9.77E+05
8.0E-04
5.2E-04
To illustrate the influence of a conformational analysis on the chemical structure of a
molecule, the intermediate of the reaction of the styryl radical with CPDTethyl is shown in
Figure 39. On the left, the optimized structure is shown without a conformational analysis
executed, while on the right, the chemical structure after the performance of a conformational
analysis can be seen. A clearly difference between both structures is observed, certainly by
Appendix A: Conformational analysis
105
looking at the orientation of the cyano isopropyl group. This results in differences in the rate
and equilibrium coefficient, as explained earlier and shown in Table 25 and Table 26.
Figure 39. Intermediate of the reaction of the styryl radical with CPDTethyl,
without (left) and with (right) conformational analysis
Appendix A: Conformational analysis
106
Appendix B Optimized geometries for
the model reactions
RAFT CTAs
MEDT
C 0.000000
S 1.231951
S 0.400861
C -1.220728
H -0.966867
H -1.795572
H -1.795572
C -1.460676
H -1.542345
H -1.968101
H -1.968101
0.545648 0.000000
1.625949 0.000000
-1.181712 0.000000
-2.057500 0.000000
-3.119768 0.000000
-1.827027 0.898150
-1.827027 -0.898150
0.939390 0.000000
2.026461 0.000000
0.537167 -0.884222
0.537167 0.884222
MBDT
C -1.037269
S -1.689559
S -2.141676
C -1.142622
H -1.874135
H -0.451677
H -0.602244
C 0.432924
C 1.237510
C 1.034092
C 2.618520
C 2.418212
C 3.212392
H 0.770240
H 0.417528
H 3.231596
H 2.877030
H 4.288861
-0.471860
-1.964741
0.914849
2.306692
2.968933
1.931610
2.845023
-0.232516
-0.997971
0.708283
-0.805594
0.874808
0.127008
-1.737965
1.278043
-1.392045
1.585603
0.265974
-0.101872
-0.303693
0.029534
0.721614
1.190189
1.477117
-0.056158
-0.057404
0.800227
-0.909214
0.822869
-0.905161
-0.031361
1.441527
-1.597535
1.499853
-1.585196
-0.021440
CPDTmethyl
C -2.156546
C -1.983322
C -3.082592
S -0.396670
C 0.971532
S 0.907151
C -2.058122
N -2.208182
S 2.450087
C 3.762260
H -1.374532
0.284944
-0.219870
-1.253263
-1.190195
-0.041452
1.551637
0.878278
1.707362
-0.971920
0.283114
0.992995
1.608485
0.164209
-0.188688
-0.072282
0.071193
0.438468
-0.812506
-1.593563
-0.286977
-0.040141
1.879380
Appendix B: Optimized geometries for the model reactions
107
H
H
H
H
H
H
H
H
-3.129549
-2.128386
-4.060872
-2.978102
-3.023397
3.618875
3.749389
4.695504
0.779921
-0.570274
-0.776823
-1.609060
-2.102625
1.112120
0.642156
-0.242787
1.697376
2.288809
-0.077385
-1.216162
0.497813
-0.733583
0.989507
-0.253466
CPDTethyl
C -2.576423
C -2.372076
C -3.431363
S -0.750421
C 0.577062
S 0.444840
C -2.475914
N -2.649642
S 2.093358
C 3.381099
C 4.757636
H -1.822006
H -3.567139
H -2.523958
H -4.426653
H -3.303317
H -3.350566
H 3.178921
H 3.268031
H 4.944181
H 4.855420
H 5.530014
0.238048
-0.264448
-1.336044
-1.179410
0.013974
1.608058
0.828206
1.648273
-0.870001
0.431017
-0.205019
0.974272
0.698422
-0.613796
-0.893192
-1.691346
-2.180754
1.236267
0.818736
-1.017818
-0.597886
0.556433
1.586084
0.144957
-0.216022
-0.073040
0.101210
0.450378
-0.835618
-1.621284
-0.201898
0.048896
-0.176279
1.861131
1.664897
2.269225
-0.117423
-1.241041
0.473987
-0.659704
1.063187
0.531288
-1.192205
-0.030755
switchmethyl
S 0.955898
C 1.232078
S 2.907013
N 0.302237
C 0.638065
H 1.717467
H 0.200877
H 0.262183
C -1.070878
C -2.075198
C -1.475475
C -3.410686
C -2.833340
H -1.852307
H -0.749106
H -4.200680
H -3.160634
N -3.799023
C 2.721871
H 3.470949
H 1.725716
H 2.897838
2.060339
0.493419
0.080077
-0.529617
-1.790406
-1.900659
-2.633368
-1.786204
-0.276931
-0.960375
0.603587
-0.719077
0.761463
-1.661048
1.154058
-1.239662
1.439171
0.119585
-1.400509
-1.284122
-1.399701
-2.331921
-0.732675
-0.301938
0.209704
-0.319823
-0.986359
-1.033149
-0.444404
-2.015902
-0.083683
-0.777614
0.932158
-0.437120
1.180049
-1.571329
1.516674
-0.973928
1.964698
0.515165
1.301529
2.087076
1.746704
0.761585
Appendix B: Optimized geometries for the model reactions
108
switchmethyl prot
S -1.611652 2.042001
C -1.407849 0.481559
S -2.523045 -0.359934
N -0.319707 -0.305360
C -0.629397 -1.061631
H -1.713098 -1.151564
H -0.196224 -2.064134
H -0.257823 -0.531719
C 0.934704 -0.134618
C 2.047899 -0.723445
C 1.223677 0.628217
C 3.315294 -0.534948
C 2.515424 0.769013
H 1.920049 -1.302990
H 0.434068 1.104093
H 4.188731 -0.951524
H 2.781136 1.337649
N 3.535251 0.196927
C -1.813667 -2.052215
H -2.455285 -2.543099
H -0.793678 -2.007531
H -1.862645 -2.599473
H 4.484599 0.324670
switch
S -0.070643
C 0.304013
S 2.022703
N -0.561848
C -0.293622
H 0.652518
H -0.255698
H -1.106682
C -1.891900
C -2.920155
C -2.165966
C -4.198819
C -3.484545
H -2.729073
H -1.375225
H -5.030798
H -3.743428
N -4.482014
C 2.873893
C 4.179712
H 3.974927
H 4.782316
H 4.749334
C 3.162061
H 3.661334
H 3.819962
H 2.242650
C 1.998339
N 1.293411
1.914561
0.862360
0.828146
0.009783
-0.961827
-0.734835
-1.970738
-0.906613
-0.100812
0.710474
-1.080821
0.502179
-1.197066
1.487880
-1.721593
1.117161
-1.947360
-0.428830
-0.276295
-0.741801
-1.316650
0.133933
-1.362495
0.472320
-0.205820
1.318706
0.847155
-1.431129
-2.319171
0.588581
0.177165
-0.894305
0.708373
1.927171
2.009643
1.875794
2.811189
0.271730
0.950080
-0.905345
0.470705
-1.324544
1.853669
-1.472076
0.959099
-2.208138
-0.642416
-1.072518
-1.807820
-1.455561
-0.130471
-0.972102
0.919889
-0.306190
-0.991031
-0.881749
-1.947348
-2.431324
-1.523157
-2.676341
-0.342703
-0.812146
0.606578
-0.290976
1.053399
-1.544057
0.985473
-0.625396
1.796485
0.618795
0.283449
-0.396350
-1.301895
-0.654877
0.302045
1.597286
2.298039
1.383891
2.049153
0.532193
0.722537
Appendix B: Optimized geometries for the model reactions
109
switch prot
S -0.200190
C -0.569475
S -2.227766
N 0.332115
C 0.106118
H -0.908162
H 0.196301
H 0.814969
C 1.470063
C 2.421672
C 1.780783
C 3.562260
C 2.943181
H 2.265639
H 1.118791
H 4.308169
H 3.221391
N 3.811399
C -2.197333
C -3.692448
H -4.136324
H -4.238129
H -3.779931
C -1.564272
H -1.652627
H -2.090777
H -0.505612
C -1.469503
N -0.883546
H 4.667546
2.965373
1.423531
0.827183
0.555332
0.484705
0.825361
-0.543914
1.145539
0.101648
-0.626929
0.289094
-1.103858
-0.212791
-0.819725
0.839246
-1.662060
-0.086676
-0.894311
-1.039592
-1.435296
-1.232587
-0.879990
-2.504630
-1.346337
-2.417746
-0.787638
-1.077560
-1.758056
-2.358486
-1.252978
-0.211240
0.141666
-0.126249
0.843750
2.299686
2.505186
2.649649
2.810266
0.292686
1.071662
-1.091635
0.486798
-1.605027
2.123092
-1.746056
1.040688
-2.644881
-0.823850
-0.431357
-0.396252
0.580815
-1.164482
-0.609382
-1.803164
-2.010969
-2.580919
-1.821152
0.620959
1.406016
-1.229576
Radicals
methyl
C 0.000000 0.000000 -0.000045
H 0.000000 1.082746 0.000091
H -0.937686 -0.541373 0.000091
H 0.937686 -0.541373 0.000091
styryl
C 0.460053
C 0.024472
C -0.546818
C -1.328353
C -1.894089
C -2.298646
H 0.761354
H -0.240091
H -1.635712
H -2.640162
H -3.353687
C 1.834650
-0.303697
1.053607
-1.314079
1.369918
-0.986288
0.358182
1.850440
-2.356626
2.411529
-1.775299
0.611907
-0.657925
-0.000047
0.000038
-0.000011
0.000059
-0.000011
0.000005
0.000189
-0.000025
0.000140
-0.000019
0.000005
-0.000112
Appendix B: Optimized geometries for the model reactions
110
C
H
H
H
H
2.958722 0.338612 -0.000085
3.928909 -0.163044 -0.005436
2.915827 0.997304 -0.878927
2.922132 0.990098 0.884513
2.081484 -1.716292 0.000554
MMA
C 2.188391
H 2.800399
H 1.788825
H 2.864238
C 1.089251
C -0.294532
O -0.621004
O -1.197264
C -2.561313
H -2.787603
H -2.792201
H -3.139589
C 1.439013
H 1.854264
H 0.572335
H 2.220617
-0.896775
-0.813028
-1.909559
-0.717775
0.119015
-0.355858
-1.523717
0.644134
0.248440
-0.347142
-0.345270
1.172478
1.576113
1.860638
2.206169
1.784550
-0.004818
0.904601
-0.069954
-0.852496
0.010828
0.003441
0.000384
0.000549
-0.002638
-0.891320
0.886143
-0.005145
0.001963
-0.976837
0.201142
0.743749
MA
C
H
H
H
C
C
O
O
C
H
H
H
H
2.534213
3.123807
2.406714
3.123892
1.211418
-0.032027
-0.107282
-1.111787
-2.373298
-2.481250
-2.481273
-3.120297
1.139110
0.011244
-0.281288
1.095591
-0.281442
-0.672337
0.090513
1.298800
-0.711172
-0.057407
0.570089
0.570245
-0.850969
-1.755330
0.000018
-0.879702
0.000098
0.879625
0.000012
-0.000019
-0.000017
-0.000033
0.000040
0.889126
-0.888950
-0.000090
-0.000018
nBA
C 4.201458
H 4.728119
H 4.271605
H 4.728982
C 2.776524
C 1.691552
O 1.841171
O 0.485029
C -0.649868
H -0.608640
H -0.607823
H 2.509278
C -1.902719
H -1.885447
H -1.886407
C -3.185270
-0.360924
-0.755871
0.728681
-0.754236
-0.793401
0.183063
1.384843
-0.408465
0.457465
1.103168
1.104299
-1.845432
-0.411959
-1.062794
-1.063960
0.437440
-0.000985
-0.880618
-0.002005
0.878873
0.000135
0.000206
-0.000636
0.001372
0.001257
0.885900
-0.882505
0.000988
0.000140
-0.882344
0.881780
-0.000014
Appendix B: Optimized geometries for the model reactions
111
H
H
C
H
H
H
-3.187747 1.094095 -0.879050
-3.188664 1.092993 0.879834
-4.456054 -0.427979 -0.001145
-5.358456 0.190878 -0.001073
-4.488687 -1.071894 -0.886662
-4.489452 -1.073175 0.883424
Intermediates
MEDT-methyl
C 0.023002
S -1.488184
S 1.331091
C 2.839455
H 3.682732
H 2.825124
H 2.931978
C 0.044062
H -0.697519
H -0.183621
H 1.022894
C -2.643215
H -3.614530
H -2.302703
H -2.730688
0.251927
-0.612637
-0.779915
0.178994
-0.481937
0.421764
1.083188
1.749939
2.201126
2.065002
2.165462
0.149440
-0.321260
-0.059102
1.224789
-0.246060
-0.559379
0.351204
-0.096639
0.114613
-1.161012
0.507051
-0.099575
-0.766264
0.930549
-0.359179
0.670660
0.502889
1.686401
0.505435
MEDT-styryl
C 2.160656
S 0.529805
S 3.252387
C 4.919277
H 5.633259
H 5.042003
H 5.084506
C 2.447601
H 1.800703
H 2.268572
H 3.486896
C -0.501855
C -0.030944
H -0.629969
H -0.135077
H 1.021512
C -1.950822
C -2.442612
C -2.823802
C -3.778635
C -4.162525
C -4.644114
H -1.775410
H -2.452800
H -4.143850
H -4.826078
H -5.683672
H -0.359022
0.411413
-0.069987
-0.942887
-0.164996
-0.987906
0.335986
0.530848
1.809125
2.519912
1.914489
2.097550
0.417920
-0.324174
-0.008048
-1.405767
-0.108814
0.161413
-1.144879
1.235689
-1.368226
1.014395
-0.289239
-1.989653
2.252551
-2.385053
1.859108
-0.464282
1.494420
-0.402606
-0.881131
-0.076880
-0.177729
-0.102995
-1.140089
0.646235
0.077836
-0.445088
1.160060
-0.109409
0.624247
1.881174
2.742914
1.762521
2.087191
0.258925
0.117368
0.044834
-0.216639
-0.286949
-0.417391
0.259670
0.140668
-0.323208
-0.444431
-0.676048
0.751754
Appendix B: Optimized geometries for the model reactions
112
MEDT-MMA
C 1.733781
S 0.063384
S 2.629147
C 4.380984
H 4.965600
H 4.689794
H 4.531054
C 2.281665
H 1.645303
H 2.318472
H 3.298144
C -0.965515
C -0.266675
H -0.915831
H -0.056492
H 0.671726
C -1.263336
H -1.933525
H -0.333828
H -1.731680
C -2.252196
O -2.906937
C -4.097776
H -3.875856
H -4.828456
H -4.476046
O -2.637370
0.271184
-0.074134
-1.129374
-0.563067
-1.418936
-0.297313
0.274167
1.672747
2.343110
2.047371
1.736091
0.531655
0.202825
0.490410
-0.864787
0.756985
2.035444
2.358229
2.605047
2.258379
-0.291040
-0.014592
-0.759215
-1.828663
-0.572711
-0.413523
-1.088026
-0.533882
-0.974362
0.061379
0.048909
0.392695
-0.963988
0.732248
-0.462187
-1.045208
0.573078
-0.866329
0.522439
1.842351
2.675987
1.926548
1.920888
0.386983
1.193689
0.471081
-0.572844
0.400191
-0.728613
-0.967076
-1.003146
-0.175884
-1.928530
1.209998
MEDT-MA
C -1.612881
S -0.075714
S -2.893611
C -4.421430
H -5.251879
H -4.484630
H -4.459563
C -1.694821
H -0.904186
H -1.580747
H -2.656206
C 0.974930
C 0.556624
H 1.140080
H 0.729152
H -0.504110
C 2.412287
O 2.976651
C 4.306238
H 4.334470
H 4.976767
H 4.593457
O 2.971467
H 0.865976
-0.551144
-0.159567
0.628799
-0.298055
0.358122
-1.220417
-0.508768
-1.557690
-2.304620
-1.083634
-2.081803
0.326987
1.683797
1.917854
2.467095
1.670720
0.328984
-0.871806
-0.999271
-0.776654
-0.314138
-2.033971
1.282129
-0.481720
-0.125629
-0.899780
-0.434685
0.011813
-0.256836
-0.568990
1.081596
0.990799
0.874947
1.978415
0.991076
0.589755
1.153382
2.051321
0.412251
1.418821
0.087084
0.216686
-0.280479
-1.350086
0.244481
-0.096712
-0.379737
1.315195
Appendix B: Optimized geometries for the model reactions
113
MEDT-nBA
C -2.638699
S -1.244675
S -4.188261
C -5.405315
H -6.376267
H -5.176490
H -5.428140
C -2.477668
H -1.510482
H -2.526363
H -3.260472
C -0.437354
C -1.265581
H -0.806575
H -1.318825
H -2.279125
C 0.946997
O 1.841417
C 3.171904
H 3.135340
H 3.561318
O 1.202395
H -0.316763
C 4.015686
H 3.992777
H 3.567299
C 5.469942
H 5.905887
H 5.482984
C 6.332978
H 7.363439
H 6.357119
H 5.932483
-0.763569
-0.008451
-0.029998
-1.320162
-0.955157
-2.264464
-1.447521
-1.652727
-2.162007
-1.080892
-2.417001
0.867731
2.063923
2.521747
2.813952
1.744338
1.278982
0.312554
0.558549
0.754004
1.457363
2.334877
0.111629
-0.669664
-0.847025
-1.547058
-0.498109
0.389136
-0.311436
-1.729651
-1.591741
-1.919856
-2.624088
-0.090879
-0.866959
-0.526011
-0.028786
-0.369955
-0.526831
1.054532
1.113065
1.071128
2.053273
1.156354
0.595222
1.060416
1.944221
0.268484
1.318099
0.107907
0.307339
-0.163316
-1.240476
0.327109
-0.401842
1.373762
0.157981
1.239990
-0.322886
-0.313706
0.162392
-1.394788
0.005941
-0.335094
1.084411
-0.483250
MBDT-methyl
C 0.896440
S 1.865496
S 1.865532
C 1.075614
H 1.672577
H 1.118617
H 0.044375
C -0.554895
C -1.288034
C -1.288022
C -2.679035
C -2.679024
C -3.386479
H -0.747169
H -0.747151
H -3.216923
H -3.216902
H -4.471566
C 1.075513
H 1.118514
-0.000006
-1.447309
1.447273
2.711447
3.618228
2.373702
2.903524
0.000012
-0.922921
0.922953
-0.917129
0.917184
0.000033
-1.617607
1.617626
-1.625921
1.625983
0.000038
-2.711480
-2.373764
0.000008
-0.318277
0.318293
-0.774384
-0.653923
-1.810767
-0.476873
0.000000
-0.787569
0.787571
-0.785842
0.785837
-0.000004
-1.422375
1.422384
-1.408333
1.408327
-0.000002
0.774358
1.810752
Appendix B: Optimized geometries for the model reactions
114
H
H
0.044272 -2.903508
1.672445 -3.618277
0.476827
0.653879
MBDT-styryl
C 1.349617
S -0.365767
S 2.124387
C 3.692666
H 4.188761
H 3.455031
H 4.333930
C -1.176304
C -0.856291
H -1.343939
H -1.211640
H 0.222560
C -2.657448
C -3.455556
C -3.253022
C -4.818295
C -4.618326
C -5.404959
H -3.007161
H -2.644258
H -5.422470
H -5.064568
H -6.465742
H -0.763861
C 2.045560
C 1.630206
C 3.155249
C 2.297009
C 3.811154
C 3.390926
H 0.797789
H 3.469270
H 1.968003
H 4.650333
H 3.906928
-0.860392
-0.976039
-2.424150
-2.298486
-3.264565
-2.128218
-1.503185
0.210928
-0.186831
0.514268
-1.196544
-0.153289
0.214953
-0.916508
1.361964
-0.894818
1.387201
0.258253
-1.820576
2.242677
-1.778844
2.286695
0.274577
1.200295
0.408291
1.546278
0.555154
2.760712
1.775973
2.887257
1.447983
-0.293762
3.613539
1.865434
3.836955
-0.245781
-0.660205
0.057909
-0.912202
-0.795253
-1.963212
-0.531775
0.558942
2.005594
2.692048
2.227455
2.180696
0.229889
0.455858
-0.309849
0.158180
-0.604839
-0.370951
0.856895
-0.495575
0.337320
-1.017641
-0.600486
0.349753
-0.118563
-0.855015
0.751239
-0.730154
0.873625
0.134034
-1.544812
1.350440
-1.316377
1.556998
0.230213
MBDT-MMA
C -0.825029
S 0.825273
S -1.129534
C -2.807453
H -2.939507
H -2.827685
H -3.591966
C 1.588198
C 0.997843
H 1.545917
H 1.089514
H -0.054047
C 1.447967
H 2.015817
H 0.398161
0.838828
0.536348
2.523902
2.859565
3.941284
2.555880
2.350833
-0.600765
-0.311482
-0.892615
0.745186
-0.603053
-2.083643
-2.703099
-2.381763
-0.292414
-0.848758
0.150940
-0.547027
-0.472815
-1.594762
0.012292
0.484309
1.865646
2.614215
2.124155
1.895176
0.096542
0.802089
0.147693
Appendix B: Optimized geometries for the model reactions
115
H
C
O
C
H
H
H
O
C
C
C
C
C
C
H
H
H
H
H
1.825915
3.062596
3.622288
4.980497
5.076687
5.616432
5.254432
3.652780
-1.834945
-2.859111
-1.822612
-3.820693
-2.794046
-3.799470
-2.864713
-1.049949
-4.585679
-2.771101
-4.553076
-2.264852
-0.175435
-0.432397
-0.031043
1.047153
-0.550373
-0.302427
0.322288
-0.204715
-0.132034
-1.327798
-1.132738
-2.318371
-2.230155
0.701112
-1.395479
-1.062625
-3.162770
-3.006803
-0.911159
0.454268
-0.728931
-0.885521
-0.735438
-0.164147
-1.904454
1.371859
-0.182098
0.793549
-1.044581
0.896954
-0.940465
0.029421
1.489297
-1.803282
1.664390
-1.622755
0.109689
MBDT-MA
C -0.569297
S 0.827952
S -0.612840
C -2.359193
H -2.411798
H -2.577974
H -3.062706
C 1.577358
C 2.463973
H 2.960509
H 1.854303
H 3.235426
C 2.297054
O 3.553379
C 4.276129
H 3.774683
H 4.351601
H 5.263948
O 1.784055
C -1.573716
C -2.306345
C -1.844149
C -3.264360
C -2.807200
C -3.525812
H -2.078462
H -1.304652
H -3.801481
H -3.004559
H -4.274411
H 0.747659
0.760996
0.283593
2.482632
2.948301
4.029363
2.704911
2.448711
-1.121934
-1.949961
-2.745496
-2.405727
-1.329951
-0.491335
-0.153079
0.522789
1.457390
-0.105175
0.721171
-0.294683
-0.190481
0.024289
-1.368123
-0.891069
-2.275832
-2.045037
0.895217
-1.543521
-0.712270
-3.165424
-2.756170
-1.706163
-0.516583
-1.493624
-0.117709
-0.504484
-0.357190
-1.545125
0.161356
-0.501138
-1.435920
-0.871420
-2.220357
-1.898393
0.680239
0.388500
1.413164
1.676637
2.304509
0.998414
1.747646
-0.073214
1.119670
-0.812898
1.542379
-0.383533
0.794695
1.725546
-1.738397
2.468947
-0.974090
1.128499
-0.101045
MBDT-nBA
C -0.955557 -1.437739 0.132423
S -2.352724 -0.882856 -0.808971
Appendix B: Optimized geometries for the model reactions
116
S
C
H
H
H
C
C
H
H
H
C
O
C
H
H
O
H
C
H
H
C
H
H
C
H
H
H
C
C
C
C
C
C
H
H
H
H
H
-1.271026
0.049049
-0.154296
1.041323
-0.035194
-2.780048
-4.187554
-4.445985
-4.242724
-4.913489
-1.719280
-0.596694
0.548704
0.688426
0.358584
-1.847962
-2.701408
1.755467
1.568733
1.878778
3.037253
2.896776
3.216282
4.263157
5.166987
4.119707
4.435311
0.335759
1.310478
0.680160
2.561284
1.935384
2.887797
1.054850
-0.051740
3.284108
2.174664
3.865225
-1.814652
-0.853181
-0.975507
-1.238473
0.195175
0.732130
1.153342
2.103764
1.296944
0.395441
1.732927
1.583316
2.324305
2.146741
3.393620
2.528245
0.529482
1.848172
2.009538
0.768265
2.586753
3.667441
2.418159
2.127073
2.656815
2.314214
1.054030
-1.627171
-2.487471
-0.943596
-2.639799
-1.100869
-1.945148
-3.055477
-0.287065
-3.313905
-0.562457
-2.067465
1.839850
2.710885
3.777198
2.475276
2.423137
0.048706
-0.369942
0.106896
-1.451845
-0.066225
-0.384461
0.322176
-0.118104
-1.190002
0.025909
-1.274632
1.118996
0.682172
1.751377
0.527611
0.260800
0.389770
-0.808262
1.066392
0.750555
2.136172
0.932569
-0.493405
0.076712
-1.689775
-0.510579
-2.265919
-1.681647
0.964941
-2.148136
-0.060938
-3.177990
-2.136965
CPDTmethyl-methyl
S 1.697337 -1.667915
S -0.652240 -0.102266
C -1.899383 -0.062519
C -3.149020 -0.503019
N -4.134070 -0.833247
C -2.073796 1.369192
H -2.373175 2.054108
H -2.845477 1.376422
H -1.129997 1.706107
C -1.491578 -1.052602
H -0.544905 -0.732750
H -2.260134 -1.062643
H -1.375309 -2.062839
C 3.482094 -1.274383
H 3.664364 -0.817474
H 3.821580 -0.617491
-0.122404
-1.082881
0.368949
-0.267502
-0.759588
0.912837
0.116221
1.690525
1.349235
1.473085
1.915723
2.252995
1.074553
0.109392
1.081728
-0.692623
Appendix B: Optimized geometries for the model reactions
117
C
S
H
C
H
H
H
0.932679 -0.085675 -0.311931
1.613182 1.325581 0.529311
3.994680 -2.236988 0.048024
1.205764 2.687449 -0.642766
1.575126 3.601489 -0.173014
1.711970 2.520408 -1.594284
0.126759 2.747310 -0.788766
CPDTmethyl-styryl
C 5.560202 -0.752619
C 4.584739 -1.686301
C 3.276009 -1.272764
C 2.922984 0.080650
C 3.906384 1.007234
C 5.217273 0.596299
C 1.505981 0.552346
C 0.888624 0.019398
S 0.494398 0.031037
C -1.095224 0.744681
S -2.525689 -0.059888
C -2.923618 -1.434592
C -4.344487 -1.906968
C -2.923107 -0.844513
N -2.910394 -0.382069
C -1.909511 -2.590610
S -1.142728 2.483062
C -2.686123 2.666807
H -0.902506 -2.246124
H -2.198573 -3.378340
H -1.907712 -2.998293
H -4.342512 -2.273620
H -4.643788 -2.725620
H -5.068906 -1.094257
H -2.601844 2.115555
H -3.539064 2.314132
H -0.123154 0.410197
H 0.835254 -1.072580
H 1.504180 0.334603
H 2.525827 -2.008244
H 3.642433 2.057320
H 4.842911 -2.737473
H 5.967943 1.328666
H 6.578451 -1.074737
H 1.488423 1.643512
H -2.781084 3.738136
-0.246847
0.112386
0.364900
0.263719
-0.106502
-0.356484
0.534618
1.832622
-0.966948
-0.645397
-1.322878
-0.080460
-0.453854
1.263243
2.316009
-0.153877
-0.295937
0.693266
0.085680
0.550751
-1.168364
-1.484781
0.207682
-0.365113
1.629965
0.112168
1.969023
1.832887
2.682420
0.638670
-0.197407
0.195835
-0.636832
-0.440733
0.536913
0.883400
CPDTmethyl-MMA
C -0.575074 0.325670
S 0.841286 -0.345598
S -1.067671 1.962174
C -2.064925 2.531750
H -2.201231 3.604290
H -3.033989 2.034448
H -1.508847 2.353065
C 2.319218 0.734220
C 2.562523 1.864498
0.115522
-0.694135
-0.337791
1.103170
0.948228
1.121171
2.024453
-0.144801
-1.154264
Appendix B: Optimized geometries for the model reactions
118
H
H
H
C
H
H
H
C
O
C
H
H
H
O
S
C
C
H
H
H
C
H
H
H
C
N
3.464228
2.706402
1.713078
2.130971
3.062308
1.339679
1.886069
3.446768
3.768884
4.761680
4.425333
5.698294
4.892028
3.966307
-1.612338
-3.005454
-2.456990
-3.276353
-1.996900
-1.710526
-3.670489
-2.949395
-4.013033
-4.533355
-3.976495
-4.750878
2.420818
1.461786
2.550803
1.255004
1.727011
2.006770
0.450607
-0.305498
-0.854538
-1.876930
-2.705934
-1.482401
-2.203426
-0.605790
-0.778387
-1.253514
-1.557871
-1.888292
-0.673410
-2.353924
-2.488908
-3.309765
-2.270734
-2.793322
-0.151806
0.697645
-0.870400
-2.157862
-1.153501
1.283783
1.615000
1.303185
1.978236
-0.261338
0.906468
0.866202
0.238655
0.464553
1.897346
-1.301383
1.025171
-0.177947
-1.580779
-2.228234
-2.026688
-1.512207
0.465041
0.498117
1.480152
-0.135444
-0.234772
-0.270896
CPDTmethyl-MA
C 0.231006 -0.034337
S -0.932395 -1.359602
S 0.473388 0.971671
C 0.957137 2.601090
H 0.963606 3.291189
H 1.953152 2.546502
H 0.210143 2.908874
C -2.521699 -0.515242
C -3.377502 -1.526462
H -4.324003 -1.061582
H -3.611654 -2.389506
H -2.853316 -1.861843
C -3.214200 -0.019350
O -2.714666 1.149242
C -3.250374 1.675128
H -3.069879 0.983032
H -4.326137 1.839812
H -2.732179 2.618097
O -4.092045 -0.603855
S 1.291864 -0.002390
C 2.957135 -0.672610
C 2.767007 -1.909918
H 3.746555 -2.300472
H 2.202783 -1.663727
H 2.229834 -2.679316
C 3.749322 -0.998594
H 3.239393 -1.796609
H 3.835343 -0.120293
0.237506
0.353980
1.670409
0.958196
1.804690
0.519996
0.226301
0.884453
1.647917
1.940061
1.019601
2.545588
-0.377245
-0.779942
-1.992308
-2.818469
-1.892761
-2.162260
-0.949702
-1.170232
-0.550101
0.340809
0.636864
1.242865
-0.220602
-1.834030
-2.379982
-2.479489
Appendix B: Optimized geometries for the model reactions
119
H 4.756391 -1.333527 -1.566907
C 3.648365 0.394068 0.188661
N 4.207411 1.229590 0.746940
H -2.221118 0.331640 1.503419
CPDTmethyl-nBA
C 0.478963 -0.757551
S -0.518880 -2.075819
S 0.661752 -0.537536
C 0.551958 1.295629
H 0.799304 1.507098
H 1.282742 1.775084
H -0.465429 1.614940
C -2.116483 -1.911310
C -2.810036 -3.274600
H -3.759727 -3.197617
H -3.030689 -3.609765
H -2.178324 -4.014019
C -2.973158 -0.843358
O -2.575102 0.383151
C -3.311012 1.476485
H -3.340575 1.353239
H -4.338719 1.433183
O -3.894646 -1.074032
S 1.491297 0.064637
C 3.271895 -0.379815
C 3.416341 -1.876628
H 4.464716 -2.102767
H 2.807483 -2.157893
H 3.100879 -2.458876
C 4.111951 0.034779
H 3.822432 -0.575681
H 3.963371 1.090394
H 5.173015 -0.126660
C 3.674060 0.440613
N 4.016049 1.102140
H -1.831141 -1.578948
C -2.610677 2.769018
H -2.501387 2.784265
H -3.268403 3.607552
C -1.241193 2.952560
H -0.635034 2.054482
H -1.387223 3.043252
C -0.489781 4.183372
H 0.475003 4.305377
H -1.070906 5.099049
H -0.299431 4.090708
0.102932
-0.514523
1.849085
2.023622
3.065875
1.371329
1.792936
0.445690
0.459248
0.996651
-0.557252
0.956765
-0.224822
0.108968
-0.461971
-1.549556
-0.087523
-0.958501
-1.089661
-0.622305
-0.307255
-0.085132
0.554038
-1.177243
-1.850112
-2.709429
-2.092854
-1.636465
0.531128
1.407104
1.445597
-0.057700
1.034789
-0.319339
-0.733149
-0.574153
-1.816798
-0.203654
-0.704837
-0.361057
0.871861
CPDTethyl-methyl
S 1.694965 -1.131347
S -0.940043 -0.137056
C -2.172878 -0.364692
C -3.298650 -1.057701
N -4.188999 -1.587809
C -2.648528 0.995687
H -3.084458 1.603863
-0.073497
-1.081891
0.365127
-0.277528
-0.775381
0.911952
0.116032
Appendix B: Optimized geometries for the model reactions
120
H
H
C
H
H
H
C
H
H
C
S
C
H
H
H
C
H
H
H
-3.406329
-1.799050
-1.568846
-0.714322
-2.321339
-1.237910
3.374764
3.437652
3.472622
0.598191
0.948612
0.196273
0.412195
0.656780
-0.881249
4.426143
4.296484
4.370574
5.425994
0.836746
1.523643
-1.249565
-0.737375
-1.427013
-2.209949
-0.352525
0.187087
0.358485
0.234099
1.770357
2.998206
3.976533
2.913538
2.845639
-1.465235
-2.191520
-1.995890
-1.030022
1.687076
1.353062
1.468820
1.918139
2.244334
1.067454
0.065759
1.011776
-0.757422
-0.305679
0.520856
-0.627243
-0.192498
-1.612296
-0.694520
-0.012868
0.795140
-0.967390
0.081241
CPDTethyl-styryl
C 5.759285 -0.447724
C 4.854757 -1.407209
C 3.510893 -1.076657
C 3.050748 0.218420
C 3.963909 1.170064
C 5.309972 0.842560
C 1.593746 0.599370
C 1.000387 0.200081
S 0.659902 -0.210043
C -0.998597 0.371706
S -2.323008 -0.651631
C -2.578022 -1.941529
C -3.944861 -2.585500
C -2.635961 -1.237193
N -2.670240 -0.686841
C -1.454396 -2.994125
S -1.244125 2.120701
C -2.764689 2.249197
C -3.167506 3.724351
H -0.486346 -2.532130
H -1.664018 -3.740656
H -1.413130 -3.488478
H -3.907376 -3.040758
H -4.159065 -3.367751
H -4.747279 -1.844795
H -2.530617 1.824849
H -3.544743 1.649628
H -0.043646 0.515031
H 1.039772 -0.881608
H 1.571269 0.683029
H 2.816861 -1.832218
H 3.617453 2.174261
H 5.195808 -2.413872
H 6.004817 1.594180
H 6.804918 -0.704881
-0.121389
0.341022
0.520088
0.241330
-0.230996
-0.407817
0.432539
1.788673
-0.988068
-0.764749
-1.361417
0.002792
-0.312258
1.289126
2.298229
0.022922
-0.614187
0.443725
0.539580
0.221393
0.797112
-0.951434
-1.306549
0.422339
-0.288677
1.421268
-0.029662
1.862641
1.941692
2.589463
0.875248
-0.459454
0.562166
-0.769447
-0.258147
Appendix B: Optimized geometries for the model reactions
121
H 1.484934
H -2.373997
H -3.395017
H -4.061227
1.674745 0.282357
4.325355 0.993570
4.138489 -0.447020
3.816152 1.164745
CPDTethyl-MMA
C 0.417478 0.034478
S -1.074959 -0.563523
S 1.088763 1.559951
C 2.051865 2.217190
H 2.584617 1.379886
H 1.329418 2.617852
C -2.411324 0.740821
C -2.533312 1.748903
H -3.363420 2.436558
H -2.731729 1.236570
H -1.611297 2.327749
C -2.151998 1.420467
H -3.020766 2.034768
H -1.279926 2.072241
H -1.993387 0.691822
C -3.653187 -0.167103
O -4.022362 -0.519394
C -5.127592 -1.415404
H -4.898057 -2.351732
H -6.017198 -0.968962
H -5.281490 -1.589204
O -4.216911 -0.536576
S 1.370323 -1.140456
C 2.778766 -1.661563
C 2.263806 -1.929363
H 3.090912 -2.278192
H 1.845354 -1.024656
H 1.490970 -2.701978
C 3.370020 -2.931058
H 2.614462 -3.720984
H 3.688616 -2.737995
H 4.238102 -3.265764
C 3.800399 -0.603238
N 4.613114 0.210399
C 3.023936 3.288519
H 2.499720 4.099219
H 3.759664 2.847424
H 3.558646 3.718897
-0.086399
0.637407
0.509893
-0.936434
-1.387286
-1.651831
0.242960
1.394391
1.191636
2.336889
1.479127
-1.105769
-1.366028
-1.029623
-1.901461
0.227267
-1.000995
-1.091046
-0.576470
-0.639909
-2.155453
1.221004
-1.007011
0.154586
1.577524
2.205163
2.023359
1.541249
-0.495122
-0.495938
-1.523038
0.081228
0.165346
0.164001
-0.434284
0.081209
0.243304
-1.286956
CPDTethyl-MA
C -0.125421
S 1.130250
S -0.518591
C -1.032298
H -1.667735
H -0.121632
C 2.617638
C 3.502309
H 4.393248
H 3.835448
-0.177190
-0.807193
-1.094744
0.217482
0.925671
0.717882
-1.011353
-2.124611
-2.238120
-1.881921
-0.201013
-1.274107
1.258027
2.469722
1.936597
2.804827
-0.151428
-0.713939
-0.088881
-1.726127
Appendix B: Optimized geometries for the model reactions
122
H
C
O
C
H
H
H
O
S
C
C
H
H
H
C
H
H
H
C
N
H
C
H
H
H
2.954582
3.341767
2.783922
3.343710
3.259218
4.397633
2.767200
4.288492
-1.151281
-2.811798
-2.611237
-3.587074
-2.065863
-2.049542
-3.566146
-3.023803
-3.659965
-4.570029
-3.548395
-4.142081
2.219763
-1.790424
-1.181731
-2.713743
-2.055006
-0.728360
-0.110546
0.772286
0.844378
-0.122328
1.128828
1.602598
-0.790271
-0.854176
-1.231650
-1.934830
-2.176897
-1.296773
-2.859857
-2.122103
-3.062536
-1.627254
-2.335895
0.029611
1.006898
0.835856
3.621310
4.116915
3.256695
4.365205
-3.069528
0.327151
1.155374
2.464689
2.967177
2.412584
2.993199
0.613243
1.103574
0.266014
-1.085449
-1.519978
-1.783999
-0.929233
1.276504
1.404319
2.246933
0.896738
0.089612
-0.032213
-1.251539
-0.448275
-1.210959
-0.906238
0.309917
CPDTethyl-nBA
C 0.384982 -0.840616
S -0.682991 -2.199671
S 0.647488 -0.345702
C 0.637854 1.510516
H 1.230401 1.786924
H -0.401869 1.811148
C -2.233085 -1.832046
C -2.972537 -3.150906
H -3.895985 -2.960358
H -3.246475 -3.617077
H -2.347052 -3.837440
C -3.079145 -0.837589
O -2.626488 0.406745
C -3.342627 1.437952
H -3.433110 1.156120
H -4.350714 1.503409
O -4.036251 -1.133815
S 1.397425 -0.290803
C 3.170467 -0.727241
C 3.264946 -2.155681
H 4.309585 -2.387267
H 2.670771 -2.263599
H 2.902113 -2.860042
C 3.994453 -0.559766
H 3.658127 -1.291220
H 3.882209 0.446228
H 5.053345 -0.730418
C 3.635526 0.254902
N 4.027223 1.034029
0.042061
-0.322342
1.718542
1.602930
0.728809
1.452668
0.658350
0.891415
1.446030
-0.058291
1.466546
-0.128795
0.012217
-0.684755
-1.738886
-0.262969
-0.789809
-1.300285
-0.798594
-0.240190
-0.006177
0.669136
-0.993578
-2.094068
-2.833501
-2.507177
-1.876834
0.194029
0.943482
Appendix B: Optimized geometries for the model reactions
123
H
C
H
H
C
H
H
C
H
H
H
C
H
H
H
-1.899607 -1.372840 1.590624
-2.564989 2.737856 -0.510680
-2.397457 2.906799 0.561199
-3.195749 3.562798 -0.865195
-1.224989 2.744085 -1.265571
-0.661950 1.840487 -1.009035
-1.422157 2.694781 -2.343783
-0.380791 3.986930 -0.945916
0.561937 3.980316 -1.501206
-0.918061 4.907029 -1.202234
-0.140376 4.027761 0.122850
1.240938 2.086472 2.886342
0.689246 1.757590 3.772533
2.288061 1.787045 2.982869
1.199345 3.179790 2.847985
switchmethyl-methyl
S 1.350430 1.518891
C 1.128406 -0.026956
S 2.589155 -0.852511
N -0.011276 -0.783813
C 0.090412 -1.940091
H 1.136474 -2.240638
H -0.499105 -2.775654
H -0.262320 -1.696981
C -1.268365 -0.319788
C -2.449715 -0.851229
C -1.424230 0.691298
C -3.679349 -0.359015
C -2.705408 1.098444
H -2.430391 -1.622253
H -0.558691 1.137140
H -4.595372 -0.765860
H -2.832211 1.876051
N -3.829680 0.595832
C 1.867819 -1.803604
H 2.681749 -2.401234
H 1.481976 -1.118525
H 1.074771 -2.460557
C 2.096134 2.571762
H 2.391064 3.503688
H 1.357963 2.776716
H 2.973197 2.076950
-1.095880
-0.232124
0.366215
-0.524019
-1.412081
-1.467822
-1.021589
-2.422930
-0.155889
-0.707115
0.814077
-0.268417
1.164691
-1.466124
1.288329
-0.691827
1.914820
0.646245
1.772934
2.188368
2.529013
1.412531
0.221159
-0.265472
0.998785
0.639562
switchmethyl-styryl
S 0.472548 -1.297624
C -0.433504 -1.480304
S 0.127326 -2.686204
N -1.784026 -1.111271
C -2.800317 -2.140722
H -2.374444 -3.104247
H -3.674616 -1.944380
H -3.117603 -2.184351
C -2.146287 0.229868
C -3.430477 0.633365
C -1.251344 1.250999
-1.605998
-0.085176
1.102203
-0.083253
-0.291873
-0.011011
0.336087
-1.342559
-0.150507
-0.562621
0.226201
Appendix B: Optimized geometries for the model reactions
124
C
C
H
H
H
H
N
C
H
H
H
C
H
C
H
H
H
C
C
C
C
C
C
H
H
H
H
H
-3.738008
-1.677174
-4.179428
-0.248991
-4.728753
-0.988912
-2.895296
-0.406538
-0.192081
0.154989
-1.477275
2.219744
2.474902
3.117774
3.067215
2.823639
4.153553
2.281379
2.140329
2.453143
2.171145
2.479583
2.337138
1.978136
2.561184
2.056598
2.613465
2.356185
1.994259
2.572359
-0.079042
1.018171
2.312386
3.362805
2.962764
-1.843176
-2.532936
-0.915514
-1.638425
-0.944775
-1.774578
-0.981796
-1.962729
-0.225227
-0.786759
0.352124
1.596236
0.317730
2.776698
1.500017
2.732994
1.642703
-0.642828
3.731531
1.456558
3.652403
-0.572270
0.167216
-0.883062
0.564714
-0.890576
0.458667
-0.220502
2.655318
3.474204
2.781176
2.612723
-1.013984
-0.351970
-2.260632
-2.741155
-2.993473
-1.966124
-0.234613
-0.866341
1.155319
-0.125036
1.901765
1.263293
-1.938832
1.652234
-0.628803
2.978411
1.839994
switchmethyl-MMA
S -0.657599 0.553020
C -0.044318 -0.843428
S -0.862999 -2.380862
N 0.860918 -0.756399
C 0.484340 -1.266422
H -0.404797 -1.885484
H 1.299673 -1.862829
H 0.242255 -0.449079
C 2.077746 -0.095500
C 2.824636 0.314799
C 2.636460 0.176196
C 4.048433 0.954278
C 3.865435 0.821660
H 2.474904 0.153154
H 2.125497 -0.118050
H 4.629005 1.274100
H 4.304180 1.029658
N 4.577216 1.214808
C -1.562491 1.680111
C -2.116798 2.808047
H -2.677152 3.512019
H -1.292433 3.344277
H -2.793170 2.418756
C -0.614684 2.224100
H -1.160216 2.918135
H -0.200397 1.428634
-1.509724
-0.616367
-0.957332
0.442532
1.758662
1.648200
2.181213
2.449595
0.304257
1.425252
-0.960658
1.223790
-1.029396
2.436570
-1.868120
2.086679
-2.002710
0.030944
-0.274705
-1.156085
-0.532164
-1.634555
-1.919150
0.802101
1.453171
1.419691
Appendix B: Optimized geometries for the model reactions
125
H
C
O
O
C
H
H
H
C
H
H
H
0.207287
-2.709478
-3.845278
-2.295256
-3.268156
-4.134894
-3.590844
-2.773335
0.516274
0.825084
0.124278
1.357599
2.765371
0.845468
0.886386
0.030272
-0.875091
-0.330306
-1.564669
-1.418967
-3.582282
-3.624959
-4.554483
-3.303554
0.325904
0.292666
-0.091655
1.267998
1.782306
2.164100
0.997644
2.587384
-0.717721
0.327725
-1.023901
-1.354069
switchmethyl-MA
S 0.642084 -0.378866
C 0.199183 0.832804
S 1.158304 2.324697
N -0.663660 0.583448
C -0.181751 0.737989
H 0.750864 1.300037
H -0.921903 1.275387
H 0.022177 -0.234873
C -1.942464 0.073812
C -2.673205 -0.523226
C -2.580211 0.147940
C -3.959491 -0.997468
C -3.865780 -0.362944
H -2.264371 -0.628622
H -2.086485 0.603096
H -4.528371 -1.459929
H -4.365281 -0.304299
N -4.562901 -0.931640
C 1.439362 -1.804143
C 0.477931 -2.567969
H 0.978300 -3.453623
H 0.145211 -1.949381
H -0.397716 -2.891149
C 2.699271 -1.285325
O 3.801691 -1.358024
O 2.430218 -0.707925
C 3.529126 -0.085128
H 4.323140 -0.811276
H 3.923178 0.729063
H 3.132275 0.301827
C -0.081852 3.559034
H -0.349481 3.384381
H 0.397379 4.535503
H -0.968002 3.514787
H 1.772801 -2.431545
-1.750768
-0.537044
-0.574462
0.530994
1.901728
1.880135
2.503481
2.366115
0.325807
1.370956
-0.928683
1.110302
-1.061668
2.367456
-1.777274
1.914298
-2.026105
-0.073593
-0.815348
0.099650
0.507678
0.933365
-0.468612
-0.143282
-0.609994
1.031434
1.691693
1.881851
1.077770
2.630494
0.010010
1.053152
-0.086952
-0.624953
-1.646277
switchmethyl-nBA
S 0.510030 -2.105016 0.657857
C 0.494297 -0.386778 1.081817
S -0.479315 0.044128 2.500103
N 1.034427 0.617085 0.276439
C 0.180909 1.707069 -0.187783
Appendix B: Optimized geometries for the model reactions
126
H
H
H
C
C
C
C
C
H
H
H
H
N
C
C
H
H
H
C
O
O
C
H
H
C
H
H
H
H
C
H
H
C
H
H
C
H
H
H
-0.761126
0.668273
-0.042327
2.348388
2.787601
3.310612
4.121698
4.610563
2.119967
3.049121
4.466418
5.359240
5.031729
-0.460579
0.092455
-0.419969
-0.065180
1.162599
-1.934341
-2.743342
-2.222107
-3.570053
-4.246511
-3.810686
0.490262
0.459304
0.015006
1.520870
-0.353499
-3.657653
-2.948395
-4.661080
-3.394487
-2.427825
-4.153996
-3.407673
-2.630717
-3.230941
-4.371488
switchmethyl
S 1.496854
C 1.138186
S 2.439730
N -0.047182
C 0.077471
H 1.130820
H -0.481214
H -0.284402
C -1.258164
C -2.462722
C -1.408948
C -3.677670
C -2.654937
H -2.444538
H -0.539339
1.668903
2.673079
1.611940
0.560769
1.360637
-0.275906
1.279341
-0.267237
2.033426
-0.911735
1.894843
-0.907087
0.487741
-2.282514
-1.470357
-1.763528
-0.402606
-1.658805
-2.049971
-2.928047
-0.753065
-0.430430
-0.789209
-0.961036
1.457786
2.316618
1.717937
1.144899
-3.354788
1.080767
1.381453
1.316090
1.865269
1.559004
1.594556
3.385222
3.679391
3.930486
3.713506
0.357442
-0.017326
-1.257913
-0.179231
-1.251482
0.420985
-1.651837
-0.071076
-1.773676
1.256728
-2.480207
0.390604
-1.090036
-0.942553
-2.117208
-3.040472
-1.965581
-2.234720
-0.649120
-0.524401
-0.527963
-0.154562
-0.938283
0.771357
3.182496
2.510426
4.130700
3.356753
-1.126390
0.022641
0.804826
0.399759
-1.273538
-1.688299
-2.017871
-1.046202
-0.331112
-1.978293
-0.641811
prot-methyl
1.570528 -0.857523
-0.007828 -0.135367
-1.055745 0.445411
-0.608180 -0.656398
-1.577516 -1.757554
-1.830411 -1.864999
-2.490720 -1.533112
-1.139747 -2.694045
-0.208860 -0.233437
-0.683968 -0.844352
0.712041 0.854285
-0.257607 -0.382844
1.088520 1.262386
-1.370202 -1.678971
1.114228 1.354914
Appendix B: Optimized geometries for the model reactions
127
H
H
N
C
H
H
H
C
H
H
H
H
-4.613035
-2.815534
-3.764588
1.527424
2.246271
1.194008
0.687484
2.871487
2.996388
2.595656
3.788642
-4.676912
-0.587287 -0.820028
1.778320 2.082613
0.609875 0.649059
-2.067883 1.689688
-2.805209 2.052776
-1.438023 2.515087
-2.582840 1.220545
2.198390 0.195799
3.243497 -0.094496
2.130645 1.248626
1.644911 -0.002596
0.912703 0.967240
switchmethyl
S 0.584941
C -0.389347
S 0.064009
N -1.755955
C -2.761760
H -2.295285
H -3.611742
H -3.107548
C -2.104401
C -3.434509
C -1.160893
C -3.748207
C -1.548647
H -4.207225
H -0.139777
H -4.739216
H -0.864324
N -2.819671
C -0.647173
H -0.434591
H -0.162596
H -1.727030
C 2.310142
H 2.517437
C 3.264554
H 3.241528
H 3.010559
H 4.283014
C 2.320913
C 2.291091
C 2.332831
C 2.270454
C 2.305399
C 2.271274
H 2.281147
H 2.373012
H 2.272414
H 2.330683
H 2.273374
H -3.077978
prot-styryl
-1.346379 -1.560291
-1.504078 -0.097593
-2.665381 1.155338
-1.123480 -0.214958
-2.171455 -0.448882
-3.135545 -0.252630
-2.048724 0.228428
-2.145834 -1.488129
0.175545 -0.231856
0.593839 -0.555079
1.205121 0.083051
1.925529 -0.560585
2.512700 0.060218
-0.115978 -0.814520
0.962544 0.347264
2.287816 -0.808067
3.319322 0.296701
2.859429 -0.260250
-1.843169 2.647197
-2.508535 3.486414
-0.877483 2.802032
-1.728258 2.540387
-0.985716 -0.885386
-1.791824 -0.179489
-1.084793 -2.084362
-2.090240 -2.512325
-0.369810 -2.871567
-0.872112 -1.746184
0.342093 -0.158018
1.561217 -0.852249
0.362458 1.243861
2.772101 -0.158432
1.574624 1.941008
2.783052 1.241290
1.567380 -1.937869
-0.576561 1.789353
3.707674 -0.709959
1.574790 3.026370
3.725348 1.780602
3.838127 -0.276209
Appendix B: Optimized geometries for the model reactions
128
switchmethyl
S 0.710478
C 0.000709
S 0.674277
N -0.932928
C -0.586528
H 0.309643
H -1.411651
H -0.353730
C -2.092025
C -2.918420
C -2.568689
C -4.091211
C -3.755299
H -2.633826
H -2.007906
H -4.739928
H -4.159991
N -4.494924
C 1.581418
C 2.325386
H 2.899430
H 1.606296
H 3.016836
C 0.579039
H 1.111973
H 0.072567
H -0.157174
C 2.503130
O 2.117245
O 3.734568
C 4.651609
H 4.298218
H 4.749390
H 5.599413
H -5.367059
C -0.756433
H -1.022953
H -0.416601
H -1.604690
prot-MMA
-0.357147
0.933651
2.534299
0.709866
1.146924
1.759891
1.722907
0.283154
0.061451
-0.371585
-0.225638
-1.029088
-0.876664
-0.203566
0.080970
-1.381158
-1.098658
-1.275099
-1.560862
-2.515786
-3.234200
-3.071575
-1.982515
-2.314137
-3.067455
-1.644269
-2.824715
-0.686788
-0.107605
-0.617957
0.216596
1.249966
-0.131766
0.131143
-1.764423
3.637040
3.597081
4.644606
3.370594
-1.474147
-0.507846
-0.765514
0.530685
1.895515
1.840063
2.324087
2.524896
0.313205
1.400011
-1.008367
1.150988
-1.179631
2.428927
-1.879303
1.944523
-2.160101
-0.115695
-0.286255
-1.232651
-0.638848
-1.841656
-1.886447
0.596199
1.187828
1.291404
-0.030176
0.572095
1.555624
0.105556
0.821937
0.818332
1.852336
0.293186
-0.272936
-0.393698
0.663277
-0.642215
-1.025976
switchmethyl
S 0.695986
C 0.224071
S 1.058823
N -0.635623
C -0.128449
H 0.805212
H -0.853169
H 0.080680
C -1.875095
C -2.646761
C -2.489891
C -3.902472
C -3.751571
H -2.259328
prot-MA
-0.327961
0.855279
2.397832
0.547671
0.711719
1.267729
1.261309
-0.263060
0.058132
-0.480224
0.053614
-0.970950
-0.442936
-0.524808
-1.761001
-0.541973
-0.605037
0.539392
1.911519
1.862168
2.518777
2.363378
0.340284
1.418859
-0.954276
1.185673
-1.108998
2.426818
Appendix B: Optimized geometries for the model reactions
129
H
H
H
N
C
C
H
H
H
C
O
O
C
H
H
H
C
H
H
H
H
H
-1.973207
-4.516012
-4.260145
-4.436400
1.508350
0.563104
1.090557
0.214502
-0.295867
2.762051
3.861910
2.478649
3.595001
4.334816
4.058407
3.191791
-0.208966
-0.425757
0.235844
-1.113817
1.859392
-5.367377
0.454622
-1.395404
-0.450598
-0.950652
-1.753819
-2.569335
-3.449335
-1.989395
-2.911491
-1.236081
-1.305372
-0.684722
-0.143722
-0.924081
0.660112
0.235420
3.565991
3.369734
4.558661
3.509912
-2.350425
-1.321226
-1.814195
1.971791
-2.065958
-0.055370
-0.845354
0.040772
0.424684
0.896354
-0.542265
-0.148275
-0.610323
1.035318
1.752404
1.942696
1.175905
2.691261
0.051019
1.102011
-0.045471
-0.555841
-1.692174
-0.201359
switchmethyl
S 0.657578
C 0.700081
S 0.161361
N 0.993724
C -0.021613
H -0.753321
H 0.441907
H -0.546027
C 2.135410
C 2.310951
C 3.233851
C 3.481566
C 4.376203
H 1.529461
H 3.179776
H 3.651729
H 5.236761
N 4.488863
C -0.556906
C -0.134860
H -0.820300
H -0.170194
H 0.874794
C -1.958880
O -2.733561
O -2.210538
C -3.533699
H -4.262932
H -3.635759
C 1.196671
H 0.960907
H 0.941412
prot-nBA
-2.058598
-1.231098
-2.165749
0.146511
1.017833
0.382613
1.682280
1.599750
0.679616
2.096583
-0.136097
2.609681
0.447282
2.785788
-1.213579
3.675122
-0.130630
1.795486
-1.123939
0.301193
0.699658
0.965495
0.299413
-1.250530
-2.104431
-0.301481
-0.314195
-0.366298
-1.219338
-1.482208
-0.434246
-2.075078
-1.006395
0.547965
1.933085
0.681967
1.294198
1.788653
2.028266
0.528290
0.205568
0.103823
-0.221229
-0.383712
-0.686713
0.391282
-0.164803
-0.485751
-1.002859
-0.769887
-2.090593
-2.457646
-3.213387
-1.593287
-2.877025
-1.497974
-1.815818
-0.595462
-0.016320
-0.830400
0.589498
3.298669
3.489723
4.179501
Appendix B: Optimized geometries for the model reactions
130
H
H
C
H
H
C
H
H
C
H
H
H
H
2.254037 -1.612084 3.063520
-0.549685 -1.768925 -2.974122
-3.710688 0.953161 0.811368
-2.982215 0.965204 1.631934
-4.700388 0.897232 1.281443
-3.604606 2.248321 -0.011777
-2.626359 2.286538 -0.507071
-4.353766 2.225349 -0.812749
-3.806954 3.504733 0.850227
-3.058117 3.561596 1.648565
-3.729697 4.415587 0.249566
-4.794394 3.499093 1.323135
5.344876 2.200310 -1.128427
switch-methyl
S 0.169025 2.609874
C -0.425124 1.061684
S -2.191694 0.956366
N 0.390985 0.178878
C 0.150904 -0.032060
H -0.819286 0.391950
H 0.128864 -1.100375
H 0.927526 0.461990
C 1.518951 -0.390164
C 2.449569 -1.119922
C 1.794019 -0.277862
C 3.556495 -1.682097
C 2.937953 -0.882183
H 2.325831 -1.263912
H 1.139033 0.278249
H 4.272319 -2.250835
H 3.152496 -0.797402
N 3.818965 -1.577732
C -2.577798 -0.766204
C -4.117710 -0.817641
H -4.584678 -0.607304
H -4.457051 -0.079217
H -4.428128 -1.813966
C -1.905010 -1.017860
H -2.202792 -2.001586
H -2.224319 -0.248395
H -0.817281 -0.994831
C -2.120735 -1.760129
N -1.780229 -2.548088
C 1.615719 2.938496
H 1.293575 2.978730
H 2.384495 2.177781
H 2.000652 3.913533
-0.541262
0.111830
0.211045
0.818760
2.248219
2.502836
2.478487
2.846314
0.238104
1.004989
-1.141758
0.370692
-1.653168
2.069508
-1.798948
0.960372
-2.716333
-0.930760
-0.454813
-0.555581
0.410115
-1.287141
-0.884256
-1.814190
-2.192465
-2.522133
-1.723966
0.529701
1.294517
0.552002
1.593797
0.407494
0.246015
switch-styryl
S 0.189738 -0.761347 2.017983
C -0.701061 -0.563214 0.489165
S -1.934748 -1.806387 0.232027
N -0.309191 0.296933 -0.531538
C -0.089042 -0.240064 -1.878958
H -0.485065 -1.252459 -1.918094
Appendix B: Optimized geometries for the model reactions
131
H
H
C
C
C
C
C
H
H
H
H
N
C
C
H
H
H
C
H
H
H
C
N
C
H
C
C
C
C
C
C
H
H
H
H
H
C
H
H
H
-0.620584
0.981879
-0.041772
0.614868
-0.413999
0.848747
-0.119409
0.940927
-0.913012
1.351669
-0.408466
0.501242
-3.525378
-4.643441
-4.443267
-4.714128
-5.598726
-3.764302
-4.714893
-3.803308
-2.964721
-3.424196
-3.359373
1.934700
1.903337
2.504433
3.259242
2.345765
3.851379
2.930945
3.686828
3.375250
1.750415
4.434706
2.795292
4.140616
2.768288
3.790157
2.349893
2.807856
0.368755
-0.269358
1.641955
2.429446
2.300431
3.777235
3.652264
2.016977
1.771493
4.385811
4.161394
4.399827
-0.828052
-1.891117
-2.646597
-2.378015
-1.408554
0.219081
0.732028
-0.280320
0.962521
-0.172622
0.337603
-0.217893
0.869984
-0.818217
-0.002032
-2.172305
-0.528523
-2.697781
-1.878507
1.053189
-2.809791
0.117005
-3.747634
-2.289043
-0.589912
-0.221316
-0.138581
-1.675317
-2.615173
-2.108671
-0.303826
-1.272230
0.888587
-1.005542
1.034883
-2.216946
1.689177
-1.754187
1.951885
0.119755
-0.070925
-0.110800
-0.875117
0.865737
-0.338490
1.028250
0.847050
1.999974
1.038234
-1.384108
-2.412411
1.625107
1.523568
0.352726
-0.499615
0.029777
-1.651046
-1.123262
-1.967158
-0.265797
0.677271
-2.300573
-1.364503
-2.863658
2.867641
2.735434
3.772445
2.997622
switch-MMA
S -0.996732
C 0.249988
S 0.971205
N 0.403797
C 0.071584
H -0.061730
H 0.880515
H -0.860601
C 0.708340
C 0.669909
C 1.082640
C 1.002391
C 1.387787
H 0.399504
-0.303766
-0.488418
-2.107316
0.395794
-0.053271
-1.134870
0.182970
0.419251
1.738813
2.665441
2.243566
3.996172
3.594797
2.373036
-1.826383
-0.577595
-0.515633
0.492227
1.847818
1.827550
2.543156
2.184366
0.289161
1.349302
-0.973603
1.097019
-1.096180
2.354713
Appendix B: Optimized geometries for the model reactions
132
H
H
H
N
C
C
H
H
H
C
H
H
H
C
N
C
C
H
H
H
C
H
H
H
C
O
O
C
H
H
H
1.124737
0.979040
1.677121
1.355304
2.806677
3.476364
3.048188
3.335319
4.547771
3.372178
4.453644
3.176374
2.917795
3.010706
3.196598
-2.608577
-3.704893
-4.691723
-3.609331
-3.626173
-2.752548
-3.744177
-2.005911
-2.630373
-2.700759
-2.366050
-3.252325
-3.436614
-4.074622
-2.472180
-3.908674
1.599316
4.712568
3.987827
4.475748
-1.787588
-3.167456
-3.911086
-3.499211
-3.083240
-0.744266
-0.654307
-1.070214
0.235438
-1.340439
-1.004485
-0.007362
-0.394833
-0.208259
0.221757
-1.448360
1.463313
1.634311
1.753704
2.100953
-0.998986
-2.149332
-0.440641
-1.298732
-2.144701
-1.678061
-0.685621
-1.841312
1.915455
-2.068423
-0.093489
-0.225411
-0.413708
0.263460
-1.445918
-0.208510
-1.204622
-1.056471
-2.229648
-1.045461
1.161384
2.245119
-0.893444
-1.913301
-1.475580
-2.812539
-2.190737
-0.475507
-0.046302
0.265705
-1.354852
0.277188
0.233264
1.356537
2.480936
2.214234
2.829452
3.247886
switch-MA
S -1.103583
C 0.238619
S 1.178209
N 0.350807
C 0.311474
H 0.445150
H 1.122167
H -0.658836
C 0.318725
C 0.122243
C 0.496824
C 0.115072
C 0.466847
H -0.015973
H 0.653928
H -0.033501
H 0.607039
N 0.278685
C 2.976830
C 3.797726
H 3.583469
H 3.554697
H 4.865119
-0.434337
-0.478833
-1.980059
0.426054
-0.064225
-1.143722
0.382321
0.162064
1.803213
2.701416
2.377010
4.071557
3.762135
2.357576
1.764697
4.765955
4.207545
4.614951
-1.404534
-2.679340
-3.464639
-3.043618
-2.443257
-1.593055
-0.426355
-0.455574
0.625305
2.006812
1.994920
2.587891
2.463240
0.412288
1.480605
-0.864491
1.221672
-0.991701
2.496472
-1.741297
2.045823
-1.974244
0.017407
-0.451451
-0.744394
-0.014701
-1.746173
-0.699071
Appendix B: Optimized geometries for the model reactions
133
C
H
H
H
C
N
C
C
H
H
H
C
O
O
C
H
H
H
H
3.229467
4.295754
2.932349
2.665519
3.313428
3.594852
-2.565273
-3.587136
-4.459893
-3.144432
-3.929809
-3.131325
-4.087513
-2.416598
-2.821091
-3.850736
-2.750852
-2.136203
-2.171079
-0.307778
-0.058298
-0.674830
0.597346
-0.907790
-0.525288
0.088985
0.777628
1.074949
1.666863
0.098329
-1.160159
-1.768786
-1.509244
-2.707180
-2.616306
-3.558231
-2.830026
0.767206
-1.499074
-1.514324
-2.485041
-1.265539
0.892066
1.939051
-0.545633
-1.451289
-0.862378
-1.905405
-2.235629
0.114305
-0.276716
1.186954
1.848167
2.202582
1.166552
2.686460
0.214494
switch-nBA
S -0.362214
C -0.512351
S 0.458952
N -1.049263
C -0.204224
H 0.688713
H -0.738411
H 0.105761
C -2.306823
C -2.710776
C -3.247209
C -3.985893
C -4.488496
H -2.061138
H -3.020255
H -4.300624
H -5.217217
N -4.873305
C -0.699174
C 0.025378
H 1.021580
H 0.117364
H -0.556760
C -2.082273
H -2.693321
H -1.961721
H -2.597956
C -0.835456
N -0.944620
C 0.177049
C -0.246598
H 0.080875
H -1.333507
H 0.216304
C 1.687142
-1.072215
0.273599
1.698695
0.105921
0.328214
0.865890
0.929442
-0.629796
-0.466950
-0.941650
-0.584321
-1.488321
-1.150791
-0.887798
-0.245665
-1.853675
-1.240373
-1.603964
3.156904
4.372603
4.501373
4.227681
5.279114
2.932897
3.831710
2.737792
2.090427
3.360447
3.539740
-2.497659
-3.807918
-4.653553
-3.841292
-3.911194
-2.397591
-1.849135
-0.696702
-1.104188
0.577229
1.754584
1.444588
2.494163
2.189260
0.765274
2.028753
-0.279547
2.171181
-0.009554
2.891706
-1.280917
3.146338
-0.812202
1.185650
-0.795570
-1.414005
-0.982635
-2.493712
-1.223024
-1.429797
-1.294865
-2.498673
-0.964804
0.655343
1.785648
-0.757464
-1.421365
-0.809456
-1.523887
-2.405848
-0.585377
Appendix B: Optimized geometries for the model reactions
134
O 2.485751 -3.080183 -1.164403
O 2.013739 -1.437209 0.280338
C 3.414029 -1.182569 0.462581
H 3.880896 -2.071616 0.901967
H 3.866344 -1.014005 -0.518391
H -0.320121 -2.348770 0.204134
C 3.546118 0.030505 1.377991
H 2.979690 -0.163807 2.296074
H 3.085270 0.896953 0.886522
C 5.012023 0.346351 1.734220
H 5.018026 1.165242 2.461744
H 5.457950 -0.519859 2.239458
C 5.876073 0.740294 0.522341
H 5.424363 1.577645 -0.021176
H 6.876264 1.047756 0.842175
H 5.996982 -0.090288 -0.179875
switch prot-methyl
S -0.289629 2.582881
C -0.589461 1.113127
S -2.281410 0.677904
N 0.428958 0.482156
C 0.260336 0.404412
H -0.642109 0.947247
H 0.155301 -0.638618
H 1.116642 0.867663
C 1.471526 -0.139851
C 2.463434 -0.810760
C 1.637641 -0.182586
C 3.489166 -1.471630
C 2.691079 -0.860305
H 2.410046 -0.840512
H 0.936012 0.312019
H 4.249273 -2.009343
H 2.848243 -0.928128
N 3.594543 -1.491132
C -2.440383 -1.062124
C -3.838484 -1.553139
H -3.931674 -1.592312
H -4.599728 -0.878728
H -4.009841 -2.554442
C -2.285239 -1.019572
H -2.380397 -2.030451
H -3.069139 -0.387425
H -1.311165 -0.615678
C -1.393216 -1.903275
N -0.545056 -2.533499
C 1.222882 3.268259
H 1.037907 3.435375
H 2.082028 2.613480
H 1.400334 4.224293
H 4.360098 -1.995015
-0.761032
0.161562
0.405870
0.917740
2.378855
2.650421
2.693358
2.878552
0.335820
1.117797
-1.085719
0.502469
-1.629779
2.196135
-1.742799
1.056880
-2.699913
-0.845160
-0.329574
0.098841
1.186437
-0.303948
-0.307134
-1.859655
-2.269734
-2.284069
-2.146093
0.267020
0.720035
0.038359
1.100503
-0.116085
-0.458604
-1.275596
switch prot-styryl
S 0.231173 -1.152527
C -0.585692 -0.821186
1.835511
0.312906
Appendix B: Optimized geometries for the model reactions
135
S
N
C
H
H
H
C
C
C
C
C
H
H
H
H
N
C
C
H
H
H
C
H
H
H
C
N
C
H
C
C
C
C
C
C
H
H
H
H
H
C
H
H
H
H
-1.737152
-0.197749
0.170809
0.062779
-0.498864
1.214657
-0.233358
0.230417
-0.758276
0.127056
-0.831714
0.647732
-1.120164
0.450201
-1.244301
-0.397061
-3.404999
-4.371294
-4.037579
-4.435604
-5.367417
-3.873085
-4.831644
-3.998796
-3.145392
-3.228896
-3.057282
1.919391
1.756789
2.628492
3.280860
2.708400
4.002144
3.421705
4.069661
3.240018
2.210007
4.515797
3.478489
4.630019
2.706960
3.680789
2.180890
2.875223
-0.474794
-2.050329
0.217685
-0.136939
-1.211641
0.370110
0.132464
1.513238
2.536811
1.948981
3.851532
3.281380
2.298991
1.236770
4.656551
3.654089
4.210756
-1.146488
-2.101982
-2.304778
-3.044218
-1.651051
-0.830588
-0.301993
-1.765188
-0.206454
0.095488
1.077950
-0.343678
0.731469
-0.603952
0.459210
-1.885654
0.248070
-2.095955
-1.030433
1.454822
-2.719984
1.077782
-3.093895
-1.198677
-0.873197
-0.375771
-0.668838
-1.950155
5.192602
-0.218763
-0.559760
-1.942473
-2.061210
-2.643751
-2.128321
-0.202131
-1.089329
1.058369
-0.733371
1.344256
-2.056540
1.786290
-1.382755
2.274409
0.461036
-0.249171
-0.978085
-1.998141
-0.426064
-1.014407
1.182000
1.150816
1.734209
1.706473
-1.014729
-1.586625
1.701645
1.818518
0.385830
-0.252207
-0.174866
-1.431388
-1.356052
-1.988568
0.183282
0.311119
-1.907260
-1.779402
-2.902588
2.916786
2.948730
3.854151
2.831158
0.694205
switch prot-MMA
S -1.191405 -0.017129 -1.437001
C -0.043374 -0.555717 -0.218006
S 0.174510 -2.301470 -0.072141
N 0.555074 0.305986 0.731817
C 0.351400 0.013558 2.163785
H -0.260681 -0.878816 2.248166
H 1.318564 -0.150726 2.646744
H -0.195188 0.836102 2.633869
C 1.360594 1.324272 0.377627
Appendix B: Optimized geometries for the model reactions
136
C
C
C
C
H
H
H
H
N
C
C
H
H
H
C
H
H
H
C
N
C
C
H
H
H
C
H
H
H
C
O
O
C
H
H
H
H
1.921876
1.722683
2.772681
2.580636
1.708797
1.332832
3.228458
2.892052
3.092085
2.025086
2.239227
1.983462
1.618143
3.288490
2.402804
3.468307
1.818785
2.203216
2.797939
3.398392
-2.507829
-3.462166
-4.314914
-2.947753
-3.843928
-1.926008
-2.751161
-1.324296
-1.325298
-3.125463
-2.603910
-4.256423
-4.885875
-4.223865
-5.122203
-5.794222
3.731270
2.193671
1.587744
3.197003
2.608129
2.067473
0.987630
3.866647
2.830527
3.394665
-2.610552
-4.089588
-4.270185
-4.725111
-4.355338
-2.336955
-2.539729
-2.991432
-1.297326
-1.734097
-1.021069
1.070023
1.404576
1.967066
2.027425
0.506422
2.342213
2.990896
2.115417
2.884743
0.173468
-0.001978
-0.388882
-1.269429
-2.107194
-0.729703
-1.617259
4.139966
1.365914
-0.982835
0.996027
-1.277445
2.416955
-1.791237
1.715793
-2.291289
-0.302375
-0.343749
0.040924
1.087332
-0.596980
-0.117891
-1.810972
-1.961797
-2.462696
-2.081723
0.546645
1.219298
-0.602667
-1.760225
-1.368100
-2.497722
-2.248445
0.026240
0.342114
0.905852
-0.708835
0.481068
1.551964
0.102787
1.041356
1.270470
1.960807
0.552424
-0.548858
switch prot-MA
S -1.159000 -0.571603
C 0.038665 -0.718578
S 0.704012 -2.334004
N 0.324354 0.319943
C 0.192475 0.033044
H -0.156250 -0.989006
H 1.166270 0.145645
H -0.558368 0.694124
C 0.795359 1.519883
C 1.026242 2.562377
C 1.122630 1.817881
C 1.551349 3.757603
C 1.646654 3.035531
H 0.813093 2.426259
H 0.979819 1.086560
H 1.752267 4.566028
H 1.927042 3.293062
-1.421557
-0.135557
0.111136
0.776412
2.218251
2.333762
2.704053
2.654976
0.388920
1.342528
-0.973845
0.940302
-1.301104
2.392236
-1.755676
1.633315
-2.315702
Appendix B: Optimized geometries for the model reactions
137
N
C
C
H
H
H
C
H
H
H
C
N
C
C
H
H
H
C
O
O
C
H
H
H
H
H
1.853380
2.557244
3.194835
3.040332
2.755108
4.269634
2.787985
3.859998
2.401871
2.280622
3.068697
3.444711
-2.426537
-3.319209
-4.096835
-2.729197
-3.809672
-3.146456
-2.738241
-4.228511
-4.955139
-4.321155
-5.288787
-5.805666
-1.883953
2.251787
3.983591
-2.151833
-3.466635
-3.606704
-4.309789
-3.445298
-1.926160
-1.824050
-2.783472
-1.022123
-1.009043
-0.089558
0.645765
1.038909
1.726263
1.539836
0.164280
-0.017335
0.044591
-0.669982
-1.362321
-2.124683
-0.657481
-1.818759
1.505491
4.874297
-0.358472
-0.253885
0.239727
1.311846
-0.301044
0.036641
-1.758545
-1.957408
-2.315473
-2.104347
0.514850
1.093375
-0.776583
-1.958993
-1.613417
-2.730539
-2.391214
0.396511
1.526771
0.022237
1.045093
1.502945
1.809516
0.541860
-0.378856
-0.628030
switch prot-nBA
S -0.008837 -1.076067
C -0.417276 0.166730
S 0.178347 1.794700
N -0.921885 -0.168306
C -0.118442 0.185553
H 0.816556 0.621499
H -0.661086 0.906925
H 0.114431 -0.717855
C -2.144498 -0.708205
C -2.641560 -1.013900
C -3.019789 -0.984271
C -3.900174 -1.524585
C -4.264726 -1.496608
H -2.055156 -0.824503
H -2.712261 -0.794206
H -4.319824 -1.753940
H -4.962137 -1.710448
N -4.689710 -1.759667
C -1.348568 2.912874
C -0.791965 4.351708
H -0.135144 4.541691
H -0.234117 4.508274
H -1.624164 5.061117
C -2.293899 2.637849
H -3.162373 3.302131
H -1.764133 2.826231
H -2.643873 1.602835
C -2.040299 2.654969
-1.834095
-0.658406
-0.979209
0.623248
1.806762
1.466627
2.425085
2.378961
0.790830
2.096776
-0.308369
2.249775
-0.078691
2.983653
-1.326156
3.222179
-0.880123
1.178429
-0.878638
-0.906137
-0.054365
-1.833960
-0.875892
-2.061956
-2.002253
-2.998998
-2.053717
0.391782
Appendix B: Optimized geometries for the model reactions
138
N -2.590946 2.418948 1.372915
C 0.752710 -2.446997 -0.804511
C 0.564609 -3.771371 -1.545025
H 1.035553 -4.575792 -0.973098
H -0.497374 -3.995317 -1.668296
H 1.046523 -3.740165 -2.525126
C 2.231181 -2.102671 -0.608904
O 3.123236 -2.644974 -1.191879
O 2.389096 -1.121613 0.277314
C 3.743878 -0.675431 0.501741
H 4.319490 -1.509037 0.917729
H 4.180064 -0.408996 -0.464074
H 0.240043 -2.436665 0.160107
C 3.693318 0.507261 1.462212
H 3.164430 0.197917 2.371615
H 3.116283 1.319425 0.999930
C 5.099391 1.018732 1.837060
H 4.985866 1.802085 2.593804
H 5.663690 0.207865 2.313977
C 5.896704 1.576371 0.644403
H 5.331843 2.361425 0.129223
H 6.841237 2.011710 0.982434
H 6.139066 0.798780 -0.086397
H -5.620031 -2.133300 1.320134
Transition states
MEDT-methyl-TS
C 0.082416 0.526019
S -1.443260 0.420484
S 1.147991 -0.881215
C 2.736883 -0.408239
H 3.374792 -1.289930
H 3.207404 0.429517
H 2.593910 -0.179331
C 0.597179 1.720217
H -0.161148 2.504097
H 0.821906 1.443979
H 1.518570 2.111085
C -2.993145 -0.944670
H -3.161342 -0.135341
H -3.757543 -1.172746
H -2.252242 -1.699597
-0.166268
-0.778914
-0.371830
0.433165
0.340324
-0.083927
1.490171
0.605087
0.603869
1.642771
0.159269
0.981122
1.680045
0.248810
1.211937
MEDT-styryl-TS
C 2.239415 0.687228
S 0.628633 0.794344
S 3.071246 -0.840794
C 4.812618 -0.588269
H 5.311144 -1.542355
H 5.300802 0.190441
H 4.864722 -0.356776
C 3.006181 1.776417
-0.248821
-0.637836
-0.635461
-0.088473
-0.273099
-0.676819
0.976352
0.466568
Appendix B: Optimized geometries for the model reactions
139
H
H
H
C
C
H
H
H
C
C
C
C
C
C
H
H
H
H
H
H
2.370291
3.315171
3.912983
-0.790658
-0.057621
-0.574358
0.018838
0.957917
-2.081612
-2.630717
-2.826517
-3.871176
-4.063020
-4.595251
-2.083102
-2.413780
-4.276823
-4.616614
-5.561095
-0.574018
2.657532
1.450146
2.052459
-0.129170
-1.403847
-1.958299
-2.058928
-1.189998
-0.103886
-1.235709
1.100592
-1.164679
1.166315
0.032576
-2.171948
1.983437
-2.046395
2.100297
0.082852
0.725324
0.565479
1.468228
-0.083494
1.200723
1.517241
2.315140
0.644821
1.860286
0.547442
-0.100144
0.519446
-0.728423
-0.111597
-0.738907
-0.106096
1.000152
-1.215273
-0.117743
-1.231328
1.835813
MEDT-MMA-TS
S 0.188197
C -1.189788
S -2.171040
C 2.097961
C 3.112684
H 4.087997
H 3.245266
H 2.818818
C 2.271797
H 3.103058
H 1.376001
H 2.516314
C 1.419904
O 1.550420
O 0.612001
C -0.085188
H 0.616269
H -0.759702
H -0.646460
C -3.584599
H -3.234676
H -4.217879
H -4.157138
C -1.588609
H -2.630758
H -0.938286
H -1.477683
-1.735327
-1.079188
-0.054458
-0.239786
-0.711176
-0.245160
-1.795718
-0.437117
-0.659018
-0.097330
-0.463821
-1.723391
1.035540
1.655625
1.450979
2.665378
3.477829
2.551933
2.874613
0.494187
1.025322
-0.349260
1.179165
-1.238748
-1.560300
-1.975423
-0.280751
-0.564841
0.085105
-0.977607
0.129332
-0.875021
-0.667642
-0.806523
-1.889492
1.565778
2.020047
2.156727
1.622784
-0.181523
-1.209836
0.814917
0.573160
0.365471
-0.280549
1.484670
0.069036
0.955463
0.348950
-0.560165
1.532504
1.634539
2.006890
2.057129
MEDT-MA-TS
C 1.660564 0.444720 -0.579015
S 0.219184 0.879747 -1.273881
S 1.880141 -1.261309 -0.168868
C 3.572571 -1.363061 0.551929
H 3.695785 -2.409581 0.838806
Appendix B: Optimized geometries for the model reactions
140
H
H
C
H
H
H
C
C
H
H
H
C
O
C
H
H
O
H
H
4.331943
3.662391
2.753584
2.462988
2.927430
3.699933
-1.395581
-0.464805
0.237174
-1.031031
0.082949
-2.161208
-3.085221
-3.831022
-3.165480
-4.388064
-1.990452
-1.789577
-4.514885
-1.100769
-0.735493
1.431501
2.426122
1.460886
1.152213
1.195212
1.290566
2.119264
1.464218
0.352107
-0.042620
0.085045
-1.084404
-1.885953
-1.427070
-1.064530
2.094434
-0.801007
-0.186522
1.439726
-0.238028
-0.578771
0.844970
-0.715274
0.690586
1.857423
1.731487
2.784380
1.985623
0.498485
-0.466791
-0.773039
-1.104986
0.103405
1.121102
0.229639
-1.573037
MEDT-nBA-TS
C -2.712318
S -1.217491
S -2.777555
C -4.566926
H -4.605065
H -5.130133
H -4.984991
C -3.992624
H -3.772169
H -4.462768
H -4.715955
C -0.276498
C -1.497893
H -2.255601
H -1.244951
H -1.909363
C 0.696022
O 1.818368
C 2.804342
H 2.360333
H 3.113364
O 0.518287
H 0.084611
C 3.977056
H 4.368734
H 3.615605
C 5.096027
H 5.443023
H 4.692813
C 6.284580
H 7.071062
H 6.721727
H 5.966611
-0.401636
-0.126309
-1.373358
-1.469540
-2.044182
-1.995965
-0.477482
0.173977
0.724262
0.853503
-0.618466
1.883993
2.437495
2.709017
3.341370
1.711743
1.145169
0.873317
0.097022
-0.858201
0.622923
0.812118
2.313379
-0.107496
0.871776
-0.603297
-0.943595
-0.446482
-1.916818
-1.156687
-1.753163
-0.197696
-1.677271
0.805484
1.468300
-0.670826
-1.099221
-2.027155
-0.326987
-1.275620
1.366050
2.281702
0.644176
1.590373
0.183624
-0.478832
0.261125
-1.052447
-1.186828
-0.632665
0.049915
-0.628974
-0.931201
-1.539536
-1.781283
1.111840
0.324357
0.625279
1.233090
-0.319766
-1.234410
-0.626642
0.632021
0.159580
0.930721
1.541824
Appendix B: Optimized geometries for the model reactions
141
MBDT-methyl-TS
C 0.813298 0.151927
S 1.887948 -0.999043
S 1.447042 1.773890
C -0.011030 2.906393
H 0.414972 3.902551
H -0.637463 2.654401
H -0.594750 2.877879
C 2.920825 -2.296957
H 3.252486 -1.382836
H 1.980123 -2.744406
H 3.622364 -2.872137
C -0.632316 -0.133620
C -1.360740 -0.822564
C -1.270341 0.222218
C -2.705335 -1.128431
C -2.607790 -0.109624
C -3.331788 -0.776355
H -0.861520 -1.111880
H -0.703085 0.725997
H -3.262067 -1.649344
H -3.083702 0.149034
H -4.375887 -1.024737
-0.362680
-0.848234
0.014977
-0.052546
-0.191858
-0.909050
0.866628
1.439730
1.914641
1.732221
0.848936
-0.150576
-1.133838
1.049711
-0.928457
1.262251
0.270163
-2.052747
1.826206
-1.701058
2.202995
0.432654
MBDT-styryl-TS
C -4.386152 -2.146675
C -3.636035 -2.346566
C -2.620697 -1.456181
C -2.352284 -0.334460
C -3.116442 -0.139261
C -4.116521 -1.045207
C -1.240942 0.584695
S -1.448372 2.347021
C -3.253246 2.647898
S 0.249449 0.047667
C 1.627707 -0.490493
C 2.957711 -0.406145
C 3.752088 0.763571
C 5.031494 0.804705
C 5.557781 -0.308583
C 4.785794 -1.472344
C 3.508647 -1.521986
C 1.027214 0.545067
H -3.335866 3.719366
H -3.597425 2.091064
H -3.844200 2.383488
H 1.491973 0.503465
H 1.159190 1.559603
H -0.044982 0.370747
H 3.360711 1.637606
H 2.910693 -2.424314
H 5.624706 1.709468
H 5.186124 -2.339197
H 6.555907 -0.269894
H 1.176854 -1.478263
H -2.024726 -1.615086
0.480118
-0.682806
-1.025561
-0.220512
0.944554
1.296465
-0.579059
-0.346316
-0.602870
-1.064415
1.101433
0.561219
0.663035
0.118690
-0.547759
-0.664671
-0.121053
2.008450
-0.798530
-1.475607
0.273101
3.005150
1.620172
2.132937
1.172388
-0.216597
0.210702
-1.181537
-0.972062
1.115332
-1.918200
Appendix B: Optimized geometries for the model reactions
142
H
H
H
H
-2.898236 0.707586 1.587865
-3.839965 -3.200496 -1.321283
-4.683041 -0.892809 2.209956
-5.171647 -2.845557 0.749884
MBDT-MMA-TS
S 0.706223
C -0.509475
S -0.334243
C 2.704208
C 3.813452
H 4.783598
H 3.705991
H 3.830094
C 2.440064
H 3.285488
H 1.534657
H 2.355234
C 2.383323
O 2.915176
O 1.402015
C 1.008972
H 1.819055
H 0.750599
H 0.143946
C -1.547480
H -1.561898
H -2.548423
C -1.717115
C -3.003225
C -1.584249
C -4.131434
C -2.717438
C -3.992691
H -3.109899
H -0.588994
H -5.118753
H -2.604109
H -4.872561
H -1.174692
-0.301581
0.476683
2.226649
-0.883442
-0.489983
-0.787179
-1.002604
0.588924
-2.352311
-2.806499
-2.531459
-2.862330
0.081229
1.155994
-0.353069
0.544613
0.681551
1.518879
0.087346
2.674465
1.904282
2.823118
-0.222904
0.219183
-1.364759
-0.475684
-2.043076
-1.604385
1.086021
-1.695510
-0.139714
-2.918666
-2.140137
3.611721
-1.751486
-0.926295
-0.684914
-0.271367
-1.205659
-0.778691
-2.166884
-1.364451
-0.070107
0.470692
0.509418
-1.034415
0.800021
0.941943
1.614745
2.642572
3.364950
2.218436
3.124479
0.632861
1.405323
0.228620
-0.417688
-0.773681
0.388681
-0.340878
0.837778
0.472308
-1.418943
0.664872
-0.642189
1.469499
0.814288
1.052610
MBDT-MA-TS
C -0.449880
S 0.548330
S 0.046283
C -1.357967
H -1.193800
H -2.303081
H -1.355432
C 2.025567
C 3.113070
H 3.835139
H 2.699769
H 3.660321
C 2.192536
O 3.325000
0.176961
-0.973149
1.865947
2.871523
3.875883
2.474800
2.893968
-1.711236
-2.420406
-2.860349
-3.235495
-1.731727
-0.375501
0.227634
-0.954419
-1.617601
-1.121272
-0.475183
-0.871854
-0.847638
0.614107
0.368678
-0.378432
0.325725
-0.979249
-1.025843
0.942429
0.552374
Appendix B: Optimized geometries for the model reactions
143
C
H
H
H
O
C
C
C
C
C
C
H
H
H
H
H
H
3.514553
2.700131
3.547175
4.466084
1.384758
-1.688943
-1.827397
-2.710078
-2.978409
-3.867840
-4.004891
-1.005967
-2.588552
-3.069344
-4.658107
-4.902076
1.213932
1.559077
2.199099
1.589174
1.885656
0.155002
-0.171620
0.167982
-0.888371
-0.202937
-1.235547
-0.893978
0.664208
-1.165960
0.040884
-1.779494
-1.173483
-2.278703
1.010579
0.659481
2.103199
0.591065
1.675897
-0.208523
1.147553
-0.851724
1.842694
-0.155239
1.192661
1.654848
-1.893924
2.896649
-0.663141
1.736113
0.809818
MBDT-nBA-TS
C -1.174214
S -0.707182
S -0.052447
C -0.959710
H -0.404612
H -1.976744
H -0.969415
C 0.250399
C -1.001297
H -1.605350
H -0.751319
H -1.591812
C 0.971935
O 2.211766
C 2.970905
H 2.421335
H 3.079707
O 0.502411
H 0.820786
C 4.324543
H 4.822786
H 4.163711
C 5.218404
H 5.365669
H 4.706982
C 6.584872
H 7.208642
H 7.126398
H 6.463410
C -2.443497
C -2.429352
C -3.666768
C -3.625941
C -4.861183
C -4.844050
H -1.476718
H -3.670530
0.439290
-0.808640
1.799338
3.101434
4.022999
3.198527
2.884791
-2.520008
-3.133650
-3.566740
-3.936631
-2.388237
-1.528063
-1.307693
-0.297566
0.649233
-0.565282
-0.946561
-3.027894
-0.199275
-1.175279
0.032055
0.874957
0.640601
1.844998
0.987156
1.754643
0.036226
1.249224
0.415909
0.489805
0.266638
0.418311
0.220282
0.295276
0.540346
0.189936
-0.984329
-1.976727
-0.822950
0.116736
-0.072528
-0.264759
1.184289
-0.289901
0.254422
-0.546168
0.964870
0.793335
0.513866
0.058492
0.722473
0.669156
1.779790
1.468975
-1.060937
0.026883
0.071970
-1.032647
0.669463
1.731363
0.631166
-0.026409
0.442027
0.022180
-1.082992
-0.209094
1.194226
-0.881569
1.907306
-0.162546
1.232602
1.712139
-1.964148
Appendix B: Optimized geometries for the model reactions
144
H -3.605589
H -5.803490
H -5.773478
0.450406 2.992232
0.117444 -0.691539
0.248512 1.791511
CPDTmethyl-methyl-TS
S 1.992153 -1.690170
S -0.679881 -0.793327
C -2.037992 0.163014
C -3.244270 -0.521167
N -4.200834 -1.030053
C -2.094928 1.644886
H -2.172198 1.730794
H -2.974892 2.112048
H -1.195889 2.157405
C -1.962875 -0.022038
H -1.069197 0.467357
H -2.845149 0.440464
H -1.944264 -1.081930
C 3.619146 -0.976634
H 3.634045 -0.718484
H 3.825653 -0.095318
C 0.878629 -0.330749
S 1.283139 1.099263
H 4.343287 -1.766138
C 1.916318 2.900599
H 2.991790 2.854114
H 1.459920 2.382140
H 1.381984 3.728208
-0.230606
-0.688906
0.215248
-0.288341
-0.670543
-0.211207
-1.297233
0.243824
0.132021
1.743961
2.132748
2.198189
2.006410
0.221040
1.280190
-0.387256
0.069311
0.786135
0.007997
-1.080313
-0.962674
-1.914716
-0.629860
CPDTmethyl-styryl-TS
S -2.703943 1.889317
S -2.155230 -0.895178
C -0.807654 -1.859815
C -1.422807 -3.189039
N -1.883254 -4.234640
C -0.563463 -1.252700
H -1.482896 -1.241474
H 0.192194 -1.844900
H -0.188538 -0.233690
C 0.483523 -1.978187
H 0.900374 -0.985504
H 1.218222 -2.574977
H 0.278958 -2.455358
C -4.035700 0.825554
H -3.616926 0.020964
H -4.621791 1.500586
H -4.661224 0.418507
C -1.662674 0.832476
S -0.352432 1.534267
C 1.593646 2.204893
C 0.891849 2.776648
H 0.223726 3.587889
H 0.291756 2.026138
H 1.623841 3.175222
C 2.469648 1.058006
C 2.598548 0.281603
0.291215
-0.911924
0.015638
0.166179
0.291873
1.408962
1.999078
1.934764
1.296258
-0.814759
-0.992305
-0.263064
-1.775459
0.984457
1.588404
1.613285
0.190444
-0.694264
-1.435989
0.054746
1.256493
0.960937
1.781602
1.974964
0.132884
1.309430
Appendix B: Optimized geometries for the model reactions
145
C
C
C
C
H
H
H
H
H
H
3.227807
3.432046
4.051862
4.156357
2.051019
3.144213
3.523486
4.617732
4.802352
1.794046
0.671792
-0.833702
-0.445220
-1.209515
0.564632
1.256723
-1.411046
-0.725991
-2.081146
2.894648
-1.001229
1.340899
-0.966280
0.204689
2.202393
-1.913193
2.256097
-1.849170
0.232103
-0.760150
CPDTmethyl-MMA-TS
C -0.703224 0.656426
S 0.558637 0.185044
S -1.187274 2.358298
C -2.655145 2.538272
H -3.476358 1.923509
H -2.405334 2.292789
C 2.720379 0.911509
C 3.041490 2.178787
H 3.895302 2.679899
H 3.316459 1.974417
H 2.192900 2.868704
C 2.095312 0.991935
H 2.855848 1.277943
H 1.317496 1.762396
H 1.673461 0.033441
C 3.440929 -0.308005
O 3.309766 -1.319009
C 3.936064 -2.540430
H 3.528272 -2.910328
H 5.014829 -2.401812
H 3.722833 -3.239554
O 4.082397 -0.402918
S -1.496583 -0.444237
C -2.636070 -1.510819
C -1.882393 -2.369504
H -2.602461 -2.999034
H -1.347400 -1.753900
H -1.162568 -3.004883
C -3.390091 -2.390118
H -2.672948 -3.025334
H -3.934105 -1.780047
H -4.102393 -3.028458
C -3.585534 -0.612335
N -4.331362 0.092808
H -2.918386 3.596028
-0.179619
-1.132074
-0.227548
0.867804
0.499212
1.899305
0.276322
-0.458629
0.025267
-1.494478
-0.428714
1.637452
2.380619
1.653026
1.945146
-0.145113
0.727841
0.360684
-0.583918
0.248836
1.169269
-1.165659
1.033311
-0.029204
-1.057401
-1.591750
-1.780944
-0.535320
0.992921
1.520402
1.717707
0.461673
-0.702658
-1.220616
0.787145
CPDTmethyl-MA-TS
C 0.279201 0.777331
S -0.047963 -0.659116
S -0.870520 2.118849
C -0.630073 3.169644
H -1.402120 3.939005
H 0.353651 3.640736
H -0.792276 2.553620
0.734434
1.489177
0.938829
-0.557130
-0.484682
-0.563752
-1.444352
Appendix B: Optimized geometries for the model reactions
146
C
C
H
H
H
C
O
C
H
H
H
O
H
S
C
C
H
H
H
C
H
H
H
C
N
-1.449743
-2.102324
-2.716138
-1.348014
-2.759119
-2.172085
-3.400476
-4.137117
-3.615314
-4.269427
-5.101909
-1.710229
-0.561560
1.670187
2.883152
3.457433
2.678594
4.206814
3.936613
3.997225
4.456009
4.761740
3.599334
2.268127
1.866963
-1.923589
-2.953742
-3.630272
-3.563731
-2.492225
-0.759744
-0.627065
0.515065
1.427693
0.520039
0.444470
0.025081
-2.186789
1.157856
-0.265429
-0.430651
-0.686325
-1.229340
0.505240
0.135223
1.074915
-0.647049
0.250799
-1.511650
-2.500155
-0.214152
0.656501
0.043200
1.161264
1.397133
-0.737999
-0.214263
-0.623915
-0.321572
-1.709359
-0.121515
-1.538356
-0.779095
-0.315827
-0.197324
1.221638
1.939462
1.213450
1.520544
-1.197143
-0.877375
-1.205954
-2.208021
-0.681095
-1.108026
CPDTmethyl-nBA-TS
C -1.525685 0.691787
S -0.168340 -0.264526
S -1.276793 2.405634
C -2.941931 3.195596
H -2.745043 4.237889
H -3.596065 2.745415
H -3.392377 3.147592
C 0.847776 0.079105
C -0.166611 0.927015
H -1.160782 0.471710
H 0.104080 1.047252
H -0.201724 1.924740
C 2.097130 0.704177
O 2.969526 -0.207788
C 4.197188 0.294147
H 3.975351 0.982347
H 4.717529 0.863744
O 2.319532 1.891361
H 0.881141 -0.990359
C 5.026005 -0.895819
H 5.195363 -1.572399
H 4.454129 -1.454720
C 6.373956 -0.451134
H 6.934477 0.116725
H 6.194982 0.233610
C 7.219445 -1.642016
H 8.173744 -1.308904
H 7.435098 -2.326394
H 6.690561 -2.208752
-0.622079
-0.580362
-1.017667
-1.001949
-1.263119
-1.749874
-0.009582
1.718426
2.417733
2.377600
3.477100
1.972425
1.256106
0.800735
0.271080
-0.552221
1.049336
1.268019
1.900672
-0.200598
0.645816
-0.950942
-0.793565
-0.040388
-1.631990
-1.273914
-1.693092
-0.446251
-2.047839
Appendix B: Optimized geometries for the model reactions
147
S
C
C
H
H
H
C
H
H
H
C
N
-3.213788
-3.313175
-2.580268
-2.787899
-1.506450
-2.928228
-2.895823
-3.459897
-1.828438
-3.103941
-4.765768
-5.892683
0.265122
-1.615154
-2.134316
-3.203545
-1.989562
-1.612208
-2.342219
-1.963531
-2.204756
-3.410946
-1.788347
-1.947163
-0.228177
-0.060842
1.193586
1.307006
1.074050
2.087811
-1.355475
-2.210473
-1.529372
-1.239721
0.134590
0.291963
CPDTethyl-methyl-TS
S 1.877082 -1.270392
S -0.898679 -0.801159
C -2.395162 -0.050931
C -3.478629 -0.916614
N -4.343101 -1.570136
C -2.671502 1.399897
H -2.752996 1.459518
H -3.614778 1.735407
H -1.861487 2.045183
C -2.309371 -0.203676
H -1.507879 0.423798
H -3.258249 0.120587
H -2.128725 -1.244479
C 3.396408 -0.314089
H 3.320344 -0.031062
H 3.406228 0.592973
C 0.566641 -0.097924
S 0.739268 1.384157
C 1.122609 3.239566
H 0.721007 2.666091
H 0.497650 3.997285
H 2.197246 3.325572
C 4.618858 -1.199569
H 4.591012 -2.112053
H 4.683545 -1.481608
H 5.526939 -0.647923
-0.197821
-0.674914
0.205369
-0.298132
-0.679853
-0.241417
-1.328906
0.202808
0.099529
1.737182
2.128361
2.176733
2.014084
0.239105
1.290437
-0.368659
0.085830
0.792285
-1.089447
-1.915960
-0.632582
-0.987923
-0.030286
0.572130
-1.084892
0.231789
CPDTethyl-styryl-TS
S 2.403948 -1.994221
S 2.041302 0.910426
C 0.955742 2.372597
C 1.747466 3.495844
N 2.343588 4.385939
C -0.420412 2.357681
H -0.299730 2.274586
H -0.942179 3.294004
H -1.012861 1.520881
C 0.855498 2.524080
H 0.292425 1.689371
H 0.328854 3.456879
H 1.849471 2.560313
C 4.032036 -1.437354
-0.401749
0.262876
-0.244102
0.294057
0.709628
0.453959
1.536907
0.229305
0.081658
-1.775753
-2.193941
-2.002589
-2.226668
0.296180
Appendix B: Optimized geometries for the model reactions
148
H
H
C
S
C
C
H
H
H
C
C
C
C
C
C
H
H
H
H
H
H
C
H
H
H
3.870717
4.430042
1.347247
-0.176521
-1.640406
-0.823950
0.150202
-0.651651
-1.336609
-2.898226
-3.356056
-3.707861
-4.565136
-4.910950
-5.348258
-2.767424
-3.372580
-4.902682
-5.514308
-6.289322
-1.517381
4.961942
4.555417
5.118235
5.934537
-1.039466
-0.648227
-0.557500
-0.779928
-1.709769
-1.406422
-1.899072
-0.332793
-1.770613
-1.054801
0.070901
-1.531970
0.682440
-0.913666
0.198769
0.455409
-2.394987
1.538966
-1.297288
0.679554
-2.700875
-2.656951
-3.450500
-3.060010
-2.361418
1.300265
-0.344763
-0.489985
-1.115386
0.679355
1.905905
1.850188
2.030379
2.808348
0.390588
1.116727
-0.669733
0.796044
-0.988674
-0.257987
1.943103
-1.238931
1.371821
-1.805692
-0.504851
0.252246
0.326707
0.960266
-0.677941
0.731918
CPDTethyl-MMA-TS
C -0.601683 0.355105
S 0.736750 0.034255
S -1.350339 1.950133
C -2.851072 1.976759
H -3.502956 1.158741
H -2.533260 1.826708
C 2.727908 1.149363
C 2.876641 2.409338
H 3.632297 3.058569
H 3.207873 2.193092
H 1.933955 2.963927
C 2.061488 1.209757
H 2.746396 1.658183
H 1.170982 1.845251
H 1.787843 0.216744
C 3.634664 0.032252
O 3.633363 -0.939084
C 4.446236 -2.068938
H 4.123797 -2.547520
H 5.494242 -1.774021
H 4.320113 -2.747389
O 4.311200 -0.018656
S -1.234938 -0.792255
C -2.178206 -2.078190
C -1.289003 -2.854947
H -1.893245 -3.623780
H -0.862197 -2.200707
H -0.474902 -3.331998
C -2.789602 -3.016673
-0.257933
-1.169041
-0.405168
0.685487
0.376619
1.717964
0.232088
-0.567946
-0.097022
-1.584742
-0.594424
1.574565
2.310998
1.527319
1.935340
-0.104916
0.821502
0.536346
-0.392313
0.435517
1.380083
-1.105842
1.006427
-0.003598
-0.987878
-1.482028
-1.748284
-0.436511
1.060483
Appendix B: Optimized geometries for the model reactions
149
H
H
H
C
N
C
H
H
H
-1.983848
-3.428441
-3.387952
-3.254647
-4.100560
-3.531333
-2.869203
-3.842360
-4.423630
-3.503593 1.616968
-2.467257 1.755842
-3.784776 0.561417
-1.379357 -0.721657
-0.831241 -1.274710
3.338374 0.494602
4.161581 0.778923
3.482703 -0.543709
3.384952 1.126365
CPDTethyl-MA-TS
C 0.275810 0.585042
S 0.252167 -0.927573
S -1.112761 1.662185
C -1.143520 2.786230
H -0.268832 3.439032
H -1.114082 2.137357
C -0.894216 -2.356195
C -1.287034 -3.552370
H -1.766905 -4.303918
H -0.404940 -4.019474
H -1.999903 -3.286028
C -1.861525 -1.342770
O -3.071927 -1.503621
C -4.043351 -0.518607
H -3.711177 0.462366
H -4.212190 -0.473878
H -4.954199 -0.819967
O -1.602795 -0.432443
H 0.011709 -2.389807
S 1.558097 1.293957
C 3.022288 0.124664
C 3.640504 -0.018545
H 2.936418 -0.464521
H 4.528481 -0.656518
H 3.936776 0.970617
C 4.023589 0.794069
H 4.299517 1.781840
H 4.923206 0.174970
H 3.595071 0.895868
C 2.648733 -1.182912
N 2.437710 -2.200938
C -2.438077 3.605315
H -2.481523 4.276236
H -3.317177 2.955545
H -2.485689 4.214740
0.791688
1.465472
1.060683
-0.418583
-0.396200
-1.297865
-0.299740
0.512638
-0.131952
0.959290
1.296142
-0.731792
-0.174504
-0.489834
-0.136816
-1.569307
0.027654
-1.489704
-0.895963
-0.227917
-0.208366
1.194665
1.896670
1.130748
1.553374
-1.183289
-0.803876
-1.246069
-2.183061
-0.770502
-1.259911
-0.359562
-1.223123
-0.390233
0.547880
CPDTethyl-nBA-TS
C 1.174541 0.588140
S 1.075760 -0.929277
S -0.186208 1.709879
C -0.141543 2.831278
H 0.741381 3.470870
H -0.089941 2.179963
C -0.067071 -2.302053
C -0.520774 -3.491905
0.788252
1.442843
1.018496
-0.462778
-0.408164
-1.339053
-0.370381
0.419197
Appendix B: Optimized geometries for the model reactions
150
H
H
H
C
O
C
H
H
O
H
S
C
C
H
H
H
C
H
H
H
C
N
C
H
H
H
C
H
H
C
H
H
C
H
H
H
-1.002088
0.332437
-1.249681
-0.988976
-2.217654
-3.160958
-2.771980
-3.270372
-0.676398
0.854970
2.516308
3.935576
4.500814
3.758925
5.368334
4.818288
4.992962
5.291624
5.871121
4.602457
3.533874
3.302945
-1.424481
-1.421620
-2.310629
-1.500287
-4.481221
-4.815237
-4.315567
-5.565107
-5.220238
-5.713432
-6.902865
-7.282119
-6.784738
-7.662201
-4.224012
-3.988836
-3.210057
-1.254308
-1.376848
-0.360632
0.604723
-0.309604
-0.351172
-2.359491
1.264385
0.041803
-0.142696
-0.574427
-0.809828
0.830407
0.686485
1.658408
0.035618
0.817129
-1.243802
-2.247139
3.670354
4.343331
3.033442
4.279126
-0.705521
-1.691339
-0.781358
0.345933
1.329574
0.426217
0.007082
-0.959839
-0.051316
0.764684
-0.246382
0.889271
1.182130
-0.822655
-0.299156
-0.629576
-0.283899
-1.718888
-1.569349
-0.939372
-0.175502
-0.124272
1.296263
1.967628
1.251828
1.679905
-1.055636
-0.653181
-1.097360
-2.067547
-0.716956
-1.227280
-0.455047
-1.318139
-0.524012
0.450978
0.051600
-0.293907
1.132777
-0.240586
0.102335
-1.324900
0.437342
0.089493
1.524730
0.220729
switchmethyl-methyl-TS
S 1.121619 1.503283
C 1.246919 0.053165
S 2.814897 -0.352563
N 0.238009 -0.908899
C 0.503714 -2.219310
H 1.579175 -2.386621
H 0.022662 -3.006275
H 0.133809 -2.258408
C -1.094257 -0.547486
C -2.168372 -1.283428
C -1.409072 0.525407
C -3.470047 -0.906335
C -2.743595 0.804198
H -2.019397 -2.124408
H -0.626691 1.122012
H -4.310247 -1.467278
H -2.998693 1.628155
N -3.772439 0.111932
-1.215411
-0.436187
0.340013
-0.338336
-0.931129
-0.955352
-0.343310
-1.963604
-0.100687
-0.622000
0.753068
-0.279542
1.018141
-1.286527
1.205147
-0.683246
1.680567
0.518303
Appendix B: Optimized geometries for the model reactions
151
C 2.369724
H 3.161355
H 1.414128
H 2.327479
C 0.415306
H 0.880463
H 0.944370
H -0.653590
-1.629640 1.595916
-1.590070 2.347085
-1.372693 2.054787
-2.629589 1.162025
3.577618 0.373625
3.243625 1.293241
4.300289 -0.234791
3.463375 0.243357
switchmethyl-styryl-TS
S 0.372955 -0.794062
C -1.185916 -1.222887
S -1.511216 -2.874789
N -2.315964 -0.400748
C -3.189629 -0.756916
H -3.146103 -1.836884
H -4.220301 -0.464648
H -2.863463 -0.271719
C -2.349759 0.893283
C -3.077981 1.923649
C -1.705771 1.212064
C -3.112922 3.180828
C -1.813578 2.501723
H -3.597538 1.772140
H -1.152414 0.456323
H -3.669995 3.985207
H -1.325137 2.753882
N -2.499809 3.486927
C -3.178789 -2.710220
H -3.314889 -3.613256
H -3.206405 -1.830999
H -3.963184 -2.651968
C 1.711900 0.087692
H 1.093340 0.981054
C 1.428688 -0.967982
H 0.359732 -1.022279
H 1.742508 -1.959906
H 1.957334 -0.743606
C 2.995917 0.231488
C 4.016145 -0.743943
C 3.252258 1.375579
C 5.236191 -0.571103
C 4.471239 1.540693
C 5.472515 0.568653
H 3.851657 -1.634622
H 2.474751 2.127678
H 6.008205 -1.328126
H 4.646426 2.426335
H 6.425030 0.698130
-0.905711
-0.539241
0.080944
-0.722622
-1.836987
-1.984135
-1.616154
-2.767055
-0.217773
-0.836707
0.994141
-0.229791
1.498181
-1.774102
1.538775
-0.705663
2.436935
0.910358
0.849573
1.448862
1.494246
0.093899
1.059598
1.078282
2.091952
2.316678
1.755039
3.030709
0.414453
0.520845
-0.381985
-0.126814
-1.027914
-0.903357
1.117513
-0.484651
-0.028043
-1.630881
-1.407194
switchmethyl-MMA-TS
S 1.169447 -1.393091 -0.967819
C -0.114325 -0.385620 -0.583466
S -0.274960 1.090424 -1.583988
N -0.976068 -0.586002 0.478141
C -0.522018 -1.455008 1.568698
Appendix B: Optimized geometries for the model reactions
152
H
H
H
C
C
C
C
C
H
H
H
H
N
C
C
H
H
H
C
H
H
H
C
O
O
C
H
H
H
C
H
H
H
0.471270
-1.213867
-0.480010
-2.376128
-3.193785
-2.997575
-4.566825
-4.380958
-2.775006
-2.419119
-5.215418
-4.880791
-5.163226
3.262614
4.184884
5.230639
4.069779
3.990773
3.354733
4.356252
2.622752
3.217968
2.962907
3.350658
2.168632
1.825554
2.719090
1.337193
1.151333
-1.307620
-1.046425
-1.043611
-2.372604
-1.134813
-1.365854
-2.500980
-0.448238
-0.061523
-0.707620
0.052410
-0.550839
0.169592
-1.025506
0.357181
-0.747354
-0.179138
-0.723943
-1.029711
-0.889655
-2.072012
-0.369038
-1.638083
-1.553235
-1.388930
-2.680867
0.709770
1.607306
0.927617
2.285392
2.874808
2.714584
2.280232
2.249543
2.158389
3.245980
2.067561
1.883036
2.405277
1.244769
0.311812
1.382858
-0.916373
1.171120
-1.011103
2.355830
-1.775970
1.989205
-1.956805
0.001517
0.050634
-1.101637
-0.790888
-1.417231
-1.947430
1.249733
1.699041
2.017586
0.946938
0.257183
-0.450083
1.326751
1.564253
1.788877
0.684913
2.421342
-0.588802
0.466596
-0.950371
-0.736203
switchmethyl-MA-TS
S -1.298459 -1.757464
C -0.059453 -0.633724
S 0.025997 0.486176
N 0.814128 -0.484575
C 0.396062 -1.002061
H -0.604920 -0.629750
H 1.090710 -0.644634
H 0.390083 -2.097519
C 2.206061 -0.328912
C 2.999130 0.402201
C 2.841208 -0.917303
C 4.365254 0.513491
C 4.214985 -0.728866
H 2.566464 0.894528
H 2.280673 -1.509243
H 4.996400 1.081716
H 4.726575 -1.176875
N 4.974414 -0.030801
C -3.309228 -0.813725
C -4.391703 -1.590068
H -5.359999 -1.412094
0.457564
0.413316
1.805622
-0.640902
-1.949311
-2.170490
-2.708356
-1.952133
-0.423932
-1.318398
0.676522
-1.063662
0.833262
-2.182036
1.390891
-1.743013
1.681932
-0.010196
-0.638260
0.049029
-0.440465
Appendix B: Optimized geometries for the model reactions
153
H
H
C
O
O
C
H
H
C
H
H
H
H
H
-4.191075 -2.664798 0.005920
-4.482005 -1.277048 1.091649
-3.141171 0.602880 -0.307208
-3.734788 1.199183 0.558649
-2.204760 1.192603 -1.085631
-1.969831 2.567371 -0.818359
-2.876218 3.154589 -0.991329
-1.656354 2.705837 0.220482
1.024659 1.925064 1.229085
0.769111 2.156664 0.194126
0.723554 2.752186 1.876276
2.094728 1.742069 1.330788
-2.984753 -1.117983 -1.627530
-1.182837 2.878223 -1.506660
switchmethyl-nBA-TS
S -1.560886 -2.260119
C -0.230340 -1.389042
S -0.119007 -1.157680
N 0.693831 -0.803949
C 0.305055 -0.573542
H -0.659679 -0.065272
H 1.056496 0.056976
H 0.233499 -1.521289
C 2.082303 -0.868557
C 2.942894 0.164652
C 2.646487 -1.973216
C 4.302805 0.047301
C 4.021679 -1.975851
H 2.565559 1.051707
H 2.030024 -2.808592
H 4.986079 0.841722
H 4.479402 -2.824114
N 4.845041 -0.993771
C -3.467783 -0.757525
C -4.619480 -1.633081
H -5.572487 -1.159217
H -4.569590 -2.599771
H -4.624732 -1.791909
C -3.103256 0.360092
O -3.579596 0.590020
O -2.121101 1.114006
C -1.636467 2.190867
H -2.437059 2.925344
H -1.357506 1.807261
C 1.027314 0.261375
H 0.876170 1.018918
H 0.737344 0.665206
H 2.069145 -0.059457
C -0.442750 2.804146
H 0.302407 2.016781
H -0.766216 3.167654
C 0.190856 3.952731
H -0.563137 4.728650
H 0.498613 3.582944
C 1.401713 4.567804
-0.464238
0.062750
1.833726
-0.773045
-2.170016
-2.188651
-2.644019
-2.714942
-0.496526
-0.890102
0.152827
-0.605906
0.390422
-1.387320
0.464679
-0.896965
0.894079
0.025581
-0.836372
-0.442236
-0.718027
-0.952226
0.638423
0.039646
1.124999
-0.502225
0.294032
0.440221
1.282298
2.109102
1.339091
3.082022
2.132394
-0.431970
-0.612396
-1.414948
0.370259
0.551502
1.356990
-0.349351
Appendix B: Optimized geometries for the model reactions
154
H 2.182766 3.816100 -0.508897
H 1.113486 4.966158 -1.328114
H 1.838100 5.385414 0.232071
H -3.233097 -0.633520 -1.888346
switchmethyl
S -0.159890
C -1.172696
S -1.211009
N -2.150637
C -3.527963
H -3.592207
H -4.232027
H -3.785053
C -1.820212
C -2.790426
C -0.493763
C -2.427265
C -0.207069
H -3.812457
H 0.294885
H -3.126698
H 0.785782
N -1.159964
C -2.140497
H -2.051124
H -1.681554
H -3.194449
C 2.401827
H 2.242182
C 2.860691
H 2.428113
H 2.599722
H 3.954589
C 2.597657
C 3.095465
C 2.302630
C 3.295130
C 2.492874
C 2.991370
H 3.352208
H 1.934242
H 3.715199
H 2.277547
H 3.168843
H -0.915668
prot-styryl-TS
-1.729725 -1.516645
-1.434705 -0.253446
-2.519512 1.152479
-0.382311 -0.275033
-0.820173 -0.540894
-1.888540 -0.336620
-0.291816 0.107627
-0.651072 -1.592605
0.917335 -0.319819
1.921958 -0.635400
1.368749 -0.034372
3.240532 -0.657884
2.702645 -0.071320
1.669957 -0.879392
0.673426 0.221392
4.031546 -0.902197
3.079006 0.145764
3.614962 -0.381089
-1.556674 2.420606
-2.140368 3.339413
-0.577950 2.566126
-1.463921 2.155830
-1.608693 -0.928559
-2.556823 -0.424309
-1.672694 -2.356615
-2.538967 -2.863696
-0.774261 -2.923249
-1.783891 -2.393860
-0.470150 -0.072823
0.770781 -0.549602
-0.579966 1.312640
1.837102 0.322234
0.494864 2.174052
1.711112 1.685666
0.882524 -1.597623
-1.527718 1.696351
2.765531 -0.054701
0.383838 3.232313
2.539533 2.364405
4.597053 -0.408236
switchmethyl prot-MMA-TS
S 0.615044 -1.202981 -1.060229
C -0.196073 0.126418 -0.554624
S 0.091402 1.715378 -1.279455
N -1.131555 0.070896 0.539239
C -0.564226 0.139157 1.891122
H 0.490755 0.406195 1.804008
H -1.083733 0.898638 2.484245
H -0.640162 -0.835440 2.385904
Appendix B: Optimized geometries for the model reactions
155
C
C
C
C
C
H
H
H
H
N
C
C
H
H
H
C
H
H
H
C
O
O
C
H
H
H
C
H
H
H
H
-2.420380
-3.342213
-2.948685
-4.653823
-4.271468
-3.024350
-2.308708
-5.384265
-4.713197
-5.101974
3.057117
3.696706
4.732647
3.173414
3.733772
2.721408
3.649588
2.073272
2.254193
3.242495
3.800944
2.717231
2.944856
4.016271
2.476361
2.504787
-0.967506
-0.663244
-0.788681
-2.023839
-6.077974
switchmethyl
S 0.731540
C -0.035164
S 0.331012
N -1.005804
C -0.476357
H 0.598335
H -0.948528
H -0.651204
C -2.309800
C -3.278415
C -2.806679
C -4.603786
C -4.145847
H -2.987417
H -2.133281
H -5.369801
H -4.565056
N -5.021346
C 3.175359
C 3.901628
H 4.897162
H 3.376770
H 4.051160
-0.199630
-0.390223
-0.310784
-0.669034
-0.590479
-0.332043
-0.186153
-0.827871
-0.688202
-0.764934
-1.375619
-2.129127
-2.383161
-3.072137
-1.529876
-2.108777
-2.318528
-1.528836
-3.072268
0.092410
0.707455
0.693620
2.099462
2.313018
2.614983
2.414430
2.856999
2.860910
3.844664
2.605221
-0.976873
0.319478
1.399548
-1.009095
1.134083
-1.193341
2.431255
-1.873227
1.918994
-2.178236
-0.137368
0.078097
-1.047930
-0.774119
-1.235054
-1.958806
1.344185
1.899275
2.001798
1.120450
0.077619
-0.794585
1.167247
1.257283
1.249959
0.414123
2.204027
-0.293213
0.754374
-0.724320
-0.398875
-0.304487
prot-MA-TS
-1.665980 -0.514344
-0.223522 -0.435307
1.079295 -1.572280
0.056593 0.591157
0.334095 1.932707
0.503245 1.846049
1.231489 2.344138
-0.518380 2.597929
-0.128208 0.364391
0.007367 1.410941
-0.475639 -0.934962
-0.193991 1.143085
-0.659926 -1.124032
0.253256 2.422572
-0.606942 -1.772205
-0.108553 1.905172
-0.928678 -2.086721
-0.518299 -0.100624
-1.401816 0.652255
-2.481155 -0.074677
-2.621985 0.374558
-3.437643 0.000788
-2.212512 -1.122913
Appendix B: Optimized geometries for the model reactions
156
C
O
O
C
H
H
C
H
H
H
H
H
H
3.381945 -0.001114 0.264026
4.042266 0.366354 -0.673210
2.737070 0.856396 1.088063
2.957873 2.240380 0.824239
4.022842 2.476252 0.888960
2.599871 2.498755 -0.176781
-0.573473 2.531885 -0.888555
-0.230853 2.752236 0.123788
-0.310008 3.361515 -1.548642
-1.653132 2.377397 -0.917461
2.736432 -1.590870 1.626871
2.406432 2.784497 1.592034
-6.008893 -0.666336 -0.269376
switchmethyl
S -0.369513
C -0.664959
S -0.117680
N -1.350430
C -0.598366
H 0.452010
H -0.686028
H -0.968288
C -2.661540
C -3.388450
C -3.411126
C -4.730668
C -4.750561
H -2.904597
H -2.933641
H -5.320152
H -5.357172
N -5.390607
C 2.203214
C 2.479876
H 3.451814
H 1.725424
H 2.539265
C 2.730846
O 3.315034
O 2.489309
C 3.063289
H 4.133579
H 2.609197
C -0.395218
H 0.181614
H -0.020054
H -1.456136
H -6.386080
C 2.818993
H 1.738821
H 3.256031
C 3.418230
H 4.494935
H 2.986878
C 3.181367
prot-nBA-TS
2.455305 -0.138257
0.919530 0.338376
0.323077 1.910133
-0.013129 -0.518401
-0.514403 -1.676750
-0.253904 -1.539548
-1.603647 -1.736687
-0.057606 -2.600957
-0.232385 -0.375923
-1.052202 -1.298868
0.348114 0.700041
-1.247297 -1.127482
0.106874 0.804151
-1.517521 -2.145963
0.989763 1.429167
-1.854899 -1.804370
0.530853 1.595965
-0.678433 -0.094403
2.570600 -1.044892
4.010346 -0.777354
4.286596 -1.215259
4.655231 -1.236728
4.201808 0.296491
1.548685 -0.131261
1.781089 0.896240
0.294815 -0.574210
-0.763834 0.203071
-0.571350 0.328341
-0.757480 1.201366
-1.495940 1.817856
-1.926179 0.996891
-1.883871 2.767648
-1.733542 1.725628
-0.835642 0.005101
-2.080476 -0.526390
-2.234703 -0.659712
-2.021400 -1.530286
-3.274460 0.237229
-3.114052 0.367975
-3.319395 1.245462
-4.608896 -0.487847
Appendix B: Optimized geometries for the model reactions
157
H
H
H
H
2.110551 -4.809096 -0.606230
3.633418 -4.597047 -1.485059
3.618392 -5.442893 0.068259
1.878250 2.244035 -2.027853
switch-methyl-TS
N 4.153429 -1.476053
C 3.837961 -1.416552
C 2.625505 -0.926508
C 1.664724 -0.455166
C 1.993119 -0.523080
C 3.230904 -1.033606
N 0.394075 -0.020429
C 0.044884 -0.282915
C -0.303106 0.963489
S -2.118337 0.877420
C -2.568940 -0.897799
C -2.375277 -1.801902
N -2.246499 -2.532840
S 0.344229 2.277123
C -4.079703 -0.827391
C -1.760337 -1.398905
C 0.527281 4.570742
H -0.985381 0.014060
H 0.148363 -1.345831
H 0.693936 0.306765
H 2.461397 -0.922078
H 1.305481 -0.182108
H 4.589289 -1.778921
H 3.491071 -1.091446
H -4.651235 -0.445350
H -4.234126 -0.172440
H -4.442563 -1.830836
H -2.133695 -2.383448
H -1.885133 -0.698636
H -0.699740 -1.492587
H 0.621400 5.205262
H -0.441140 4.464397
H 1.418687 4.263324
-0.660473
0.627777
1.122776
0.217296
-1.148561
-1.519600
0.652606
2.055984
-0.030097
0.024354
-0.419752
0.723616
1.601314
-0.788369
-0.745044
-1.631224
0.826397
2.230546
2.279106
2.714548
2.191383
-1.911052
1.325963
-2.573808
0.104684
-1.606361
-0.987416
-1.932354
-2.461275
-1.390666
-0.045953
1.298095
1.357260
switch-styryl-TS
S 0.123494 -1.350420
C -0.230033 -0.063358
S 0.802575 1.412321
N -1.161386 -0.061979
C -0.726840 0.328807
H 0.171491 0.935566
H -1.506978 0.907602
H -0.489963 -0.566573
C -2.388340 -0.739737
C -3.074437 -1.183239
C -3.031856 -0.938282
C -4.323656 -1.790296
C -4.277957 -1.552319
H -2.664607 -1.068599
H -2.573298 -0.629109
-1.489628
-0.494018
-0.683306
0.539025
1.885535
1.807857
2.383024
2.473779
0.432321
1.574774
-0.804392
1.423529
-0.826377
2.568683
-1.733726
Appendix B: Optimized geometries for the model reactions
158
H
H
N
C
C
H
H
H
C
H
H
H
C
N
C
H
C
C
C
C
C
C
H
H
H
H
H
C
H
H
H
-4.855148
-4.780229
-4.930635
-0.402784
0.449774
1.313415
0.797801
-0.162778
-1.594180
-2.210126
-1.217886
-2.217924
-0.886309
-1.271786
2.172212
1.530146
2.824642
2.414371
3.838952
2.989627
4.412098
3.990513
1.638501
4.173402
2.662980
5.189620
4.439145
2.683073
3.595794
1.940936
2.922024
-2.138307
-1.704267
-1.982089
2.861759
4.029703
4.223747
3.781381
4.935408
2.554996
3.454003
2.254433
1.757354
3.220311
3.533306
-2.589872
-3.278386
-1.578098
-1.374045
-0.736544
-0.381485
0.254294
0.441953
-2.014011
-0.861400
-0.245907
0.888708
1.218308
-3.051614
-3.652547
-3.677663
-2.212432
2.306658
-1.778925
0.257455
-0.765113
-1.312994
-0.671709
-2.318947
-1.358128
-1.690861
-1.800612
-2.672188
-1.283092
0.576559
1.613456
-0.603004
-0.060982
0.190575
1.530772
-0.326390
2.315856
0.464448
1.785954
1.943229
-1.350590
3.342523
0.050057
2.397330
-1.939588
-1.811763
-2.441946
-2.598644
switch-MMA-TS
S 1.547134 -0.248884
C 0.089818 -0.081513
S -0.621466 1.573746
N -0.542875 -1.108455
C 0.206458 -2.346318
H 1.193944 -2.101056
H -0.338565 -2.951161
H 0.325828 -2.912231
C -1.963365 -1.229558
C -2.603471 -1.713703
C -2.748133 -0.931227
C -3.988774 -1.875475
C -4.126659 -1.128035
H -2.045727 -1.952748
H -2.299806 -0.563040
H -4.510110 -2.244576
H -4.759244 -0.904487
N -4.743282 -1.597196
C 3.413701 0.550424
C 3.103809 2.018530
H 3.931224 2.525641
H 2.983081 2.479569
H 2.194557 2.176364
-1.771217
-0.952593
-0.981072
-0.309661
-0.071456
0.319659
0.652154
-1.002643
-0.272001
0.872944
-1.389066
0.841960
-1.300385
1.772083
-2.304191
1.721739
-2.155854
-0.218216
-0.454139
-0.313857
0.205508
-1.297534
0.268099
Appendix B: Optimized geometries for the model reactions
159
C
H
H
H
C
O
O
C
H
H
H
C
C
H
H
H
C
H
H
H
C
N
4.508459
5.485720
4.542970
4.361325
3.182547
2.439797
3.856242
3.710094
4.053212
2.665113
4.324878
-1.328086
-1.132217
-0.063334
-1.587345
-1.603610
-0.608574
-0.963405
-0.813045
0.472526
-2.773981
-3.910834
0.161512
0.474435
-0.916808
0.668730
-0.267889
0.038815
-1.431227
-2.253291
-1.726682
-2.541513
-3.134352
1.995479
3.528828
3.754128
4.040507
3.895524
1.281823
1.708026
0.211649
1.419582
1.718295
1.558324
-1.416609
-1.021101
-1.579780
-2.375374
0.750050
1.659446
0.740619
1.889768
2.784558
2.034431
1.706090
0.722888
0.814757
0.841674
-0.037597
1.731853
1.879920
2.824367
1.883115
1.800628
0.751228
0.805559
switch-MA-TS
S 1.613614
C 0.171703
S -0.497718
N -0.458425
C 0.301123
H 1.237008
H -0.294259
H 0.517142
C -1.877854
C -2.484845
C -2.694977
C -3.871455
C -4.072002
H -1.900266
H -2.273323
H -4.367395
H -4.729518
N -4.657174
C 3.265898
C 4.402370
H 5.210205
H 4.826320
H 4.064010
C 3.331158
O 2.492481
O 4.402060
C 4.514657
H 4.544127
H 3.668881
H 5.445479
C -1.188754
C -0.976896
-0.300481
-0.119530
1.554510
-1.125415
-2.350083
-2.081427
-2.982035
-2.891164
-1.224477
-1.685441
-0.933899
-1.834527
-1.117351
-1.919451
-0.587143
-2.186675
-0.901434
-1.565079
0.881235
1.085361
1.658955
0.130844
1.643503
-0.077404
-0.179688
-0.886131
-1.870522
-1.403447
-2.563101
-2.401239
1.995199
3.528097
-1.819732
-0.983245
-1.011089
-0.319250
-0.034587
0.458671
0.622305
-0.961923
-0.231262
0.941043
-1.326864
0.956712
-1.190885
1.824235
-2.262805
1.857841
-2.029319
-0.082873
-0.416875
-1.377027
-0.900781
-1.698348
-2.253888
0.681726
1.557250
0.613672
1.630467
2.618522
1.593701
1.430596
0.693033
0.766787
Appendix B: Optimized geometries for the model reactions
160
H
H
H
C
H
H
H
C
N
H
0.093977
-1.434773
-1.437772
-0.459412
-0.794343
-0.672276
0.621691
-2.637463
-3.776539
2.569887
3.744042 0.783783
4.035730 -0.086503
3.907280 1.684011
1.287418 1.847479
1.728777 2.792192
0.219389 1.867702
1.410436 1.747352
1.737757 0.742180
1.603812 0.815313
1.696022 -0.246015
switch-nBA-TS
S -0.464062 -0.897534
C 0.829548 -0.395511
S 1.973192 -1.713854
N 1.023819 0.885762
C -0.100662 1.824753
H -0.979562 1.380212
H 0.167573 2.745392
H -0.318780 2.046220
C 2.319185 1.463173
C 2.583865 2.356082
C 3.334092 1.211269
C 3.843902 2.951150
C 4.556799 1.863130
H 1.835423 2.582554
H 3.176014 0.535784
H 4.076174 3.644962
H 5.362024 1.686988
N 4.814370 2.722518
C -1.871493 -2.191710
C -2.747210 -2.968498
H -3.411546 -3.641878
H -3.380957 -2.303959
H -2.137443 -3.578574
C -2.371069 -1.074671
O -1.732130 -0.516126
O -3.605003 -0.682274
C -4.153884 0.432093
H -4.156201 0.216843
H -3.514980 1.308726
C 2.518137 -1.500456
C 2.776440 -2.957909
H 1.831078 -3.505543
H 3.481446 -3.465841
H 3.198669 -2.944165
C 1.453000 -0.832305
H 1.764534 -0.924157
H 1.334053 0.224503
H 0.483370 -1.316626
C 3.797151 -0.774578
N 4.819860 -0.260517
H -0.998091 -2.675852
C -5.564895 0.671289
H -5.518468 0.848119
H -6.161107 -0.236318
-1.989752
-1.048456
-0.595363
-0.635487
-0.739660
-0.269873
-0.224062
-1.789960
-0.489950
0.553077
-1.416771
0.613870
-1.250266
1.304812
-2.249209
1.418045
-1.959173
-0.267348
-0.426364
-1.366928
-0.806827
-1.959089
-2.038489
0.370811
1.243081
0.016009
0.717173
1.791505
0.557554
1.202365
1.660235
1.670758
0.996610
2.669687
2.088127
3.134086
1.853678
1.949538
1.268526
1.371657
-0.001608
0.190118
-0.891100
0.342790
Appendix B: Optimized geometries for the model reactions
161
C
H
H
C
H
H
H
-6.239104
-5.631683
-6.269608
-7.664377
-8.129204
-7.656287
-8.298363
1.864634 0.888494
2.766152 0.738492
1.684553 1.970446
2.113530 0.368452
2.964795 0.874916
2.323702 -0.706500
1.235676 0.533217
switch prot-MMA-TS
S 1.060736 -1.331168
C 0.019717 -0.253627
S -0.050278 1.391277
N -0.851399 -0.597287
C -0.226184 -0.725643
H 0.764860 -0.270889
H -0.826608 -0.209095
H -0.118108 -1.782005
C -2.081169 -1.086615
C -2.922671 -1.542298
C -2.607147 -1.158821
C -4.199567 -1.948674
C -3.889414 -1.581435
H -2.592264 -1.549335
H -2.015574 -0.856365
H -4.885453 -2.275165
H -4.339861 -1.632707
N -4.666056 -1.955947
C 3.525272 -1.471232
C 4.181711 -2.062616
H 5.236073 -2.282879
H 3.709373 -3.010653
H 4.166076 -1.370119
C 3.254429 -2.352618
H 4.209357 -2.603864
H 2.624157 -1.866722
H 2.798867 -3.295844
C 3.609320 -0.002149
O 4.145071 0.728946
O 3.020623 0.454628
C 3.173003 1.852672
H 4.229320 2.104107
H 2.773714 2.425381
H 2.624479 2.065374
C -1.064807 2.553495
C -1.156880 3.842287
H -0.151253 4.225114
H -1.662571 3.656727
H -1.718399 4.597367
C -0.378174 2.834695
H -0.980978 3.547904
H -0.258634 1.927285
H 0.605345 3.271700
C -2.417471 2.021422
N -3.480311 1.623005
H -5.620236 -2.247106
-1.194555
-0.537417
-1.232293
0.547255
1.870779
1.825562
2.625436
2.141308
0.300617
1.358254
-1.025048
1.082829
-1.224355
2.386974
-1.878767
1.855632
-2.208398
-0.182695
-0.074523
-1.283657
-1.054557
-1.560655
-2.126576
1.108681
1.597284
1.853512
0.792171
0.071685
-0.721671
1.197988
1.432955
1.558030
0.591556
2.351058
-0.142554
-0.996868
-1.191957
-1.946993
-0.439087
1.206545
1.778479
1.800023
1.021961
0.069208
0.249863
-0.356725
Appendix B: Optimized geometries for the model reactions
162
switch prot-MA-TS
C 0.083871 -0.564604
S 1.004640 -1.798471
S 0.284168 1.052716
C -0.400391 2.379297
C 3.289490 -1.888795
C 4.195980 -2.642228
H 4.391173 -2.087001
H 5.165833 -2.804670
H 3.785715 -3.627667
C 3.331825 -0.429988
O 4.223066 0.153392
C 4.310452 1.573635
H 3.365919 2.018436
H 4.536331 1.900083
H 5.115254 1.850928
O 2.608175 0.181861
H 2.749914 -2.410581
N -0.906806 -0.755737
C -0.414588 -1.071561
H -0.939190 -0.459109
H -0.563196 -2.133578
H 0.648201 -0.828134
C -2.202071 -0.923566
C -2.653600 -0.841835
C -3.188613 -1.189352
C -3.987207 -0.932354
C -4.507797 -1.263154
H -1.960395 -0.684190
H -2.930060 -1.302409
H -4.378790 -0.855200
H -5.295072 -1.428567
N -4.890022 -1.124489
H -5.875031 -1.166639
C 0.342265 2.411483
H 1.415004 2.514932
H -0.021125 3.263746
H 0.187288 1.499061
C -0.179391 3.688847
H 0.890525 3.837693
H -0.698619 3.669543
H -0.560685 4.527777
C -1.842261 2.177932
N -2.969975 2.030664
-0.441748
-1.003343
-1.163955
-0.004224
0.437590
-0.475497
-1.395316
0.020861
-0.712152
0.597877
-0.196380
-0.136263
-0.463873
0.881786
-0.815643
1.359796
1.221227
0.573063
1.923703
2.662536
2.146240
1.964936
0.242997
-1.109789
1.238744
-1.387530
0.886131
-1.924580
2.281381
-2.394811
1.612070
-0.400105
-0.631173
1.343429
1.169545
1.927141
1.918198
-0.799722
-0.968536
-1.760791
-0.210481
0.197625
0.364318
Appendix B: Optimized geometries for the model reactions
163
Appendix C Optimized geometries for
the reactions in the kinetic model
Reactions in the kinetic model
RAFT CTAs
TR0
C 3.431305
C 2.372068
C 2.576076
S 0.750363
C -0.577063
S -0.444748
C 2.476395
N 2.650229
S -2.093444
C -3.381184
C -4.757793
H 3.303540
H 4.426631
H 3.350108
H 3.566820
H 1.821663
H 2.523360
H -3.267649
H -3.179512
H -4.856066
H -4.943855
H -5.530196
-1.336203
-0.264580
0.237526
-1.179336
0.014033
1.608113
0.828279
1.648607
-0.869843
0.431148
-0.205181
-1.691149
-0.893535
-2.181102
0.697780
0.973751
-0.614492
0.819294
1.236098
-0.598617
-1.017618
0.556249
-0.215826
0.145131
1.586449
-0.073551
0.100855
0.450052
-0.835166
-1.620541
-0.202221
0.048721
-0.175415
-1.241004
-0.116749
0.473899
1.665633
1.861510
2.269352
1.062795
-0.660350
-1.191075
0.532689
-0.029900
TRi
S 2.398613
C 2.318151
S 3.408642
C 4.374573
H 4.920730
H 3.660914
C 5.312721
H 6.011168
H 5.896670
H 4.753372
S 1.157644
C 0.319549
H -0.215297
C 1.307872
C 1.578869
C 2.464541
C 3.091840
C 2.828619
C 1.943772
-1.199036
-0.918891
-1.635025
-2.860973
-2.309724
-3.524875
-3.617169
-2.937725
-4.342497
-4.160894
0.095639
1.245438
1.856785
2.159959
2.056354
2.944915
3.944580
4.054376
3.169631
-1.286487
0.331203
1.548462
0.561186
-0.206423
0.068404
1.508931
2.005929
0.933820
2.275516
1.226767
-0.002896
0.735522
-0.709944
-2.079328
-2.696101
-1.952809
-0.583895
0.029341
Appendix C: Optimized geometries for the reactions in the kinetic model
164
H
H
H
H
C
H
H
H
N
C
C
C
H
H
H
H
H
H
H
H
H
C
C
C
C
C
H
C
H
C
H
C
H
H
C
1.109771
3.779677
3.309306
1.744958
-0.711992
-1.049040
-0.236517
-1.562242
-1.499273
-2.389551
-3.503449
-4.424538
-4.829449
-5.258338
-3.880729
-3.717907
-2.340265
-3.447910
-4.748893
-5.088681
-3.655787
-4.295083
-3.364140
-2.651189
-1.945503
-2.546296
-1.983705
-3.147177
-3.055444
-3.860719
-4.328579
-3.964113
-4.509913
2.665887
-2.884629
1.275129
4.633108
4.830162
3.255483
0.522298
1.224571
-0.316084
-0.414370
1.365431
1.268990
1.171886
2.400099
2.422967
2.338884
3.332169
1.260422
2.158559
0.186227
-0.109907
-0.220711
-1.012974
-0.130648
-0.831950
-1.091337
0.024891
-2.419134
-2.640626
-3.459351
-4.480700
-3.186915
-3.992755
-1.868237
-1.646322
2.848859
1.211785
-2.665808
-2.433554
0.003945
1.094535
-0.892895
-1.666645
-1.404436
0.837445
3.386838
2.665476
1.696134
1.893982
2.909590
1.187463
1.715262
-0.440030
0.175874
-2.408198
2.949302
1.205715
1.882344
1.954245
-2.037358
-0.857398
-0.091238
-0.423648
0.479862
-1.137022
-0.780252
-2.305370
-2.861954
-2.755382
-3.667467
-3.758543
0.268956
TSt
C -1.049013
C -1.032608
C -1.119615
C -1.226164
C -1.245279
C -1.156487
C -1.349073
C -2.004358
C -2.397516
C -2.924169
N -3.337762
S 0.232931
C 1.532738
S 1.389029
S 3.072397
C 4.317981
C 5.698173
C -3.529590
C -1.213450
4.476148
3.602166
2.221219
1.698454
2.587387
3.963177
0.206492
-0.606581
-2.091436
-2.217537
-2.300477
-0.472087
-0.351087
-0.194477
-0.477649
-0.637996
-0.848450
-2.484324
-3.074495
0.230133
1.316527
1.115026
-0.179528
-1.265949
-1.066196
-0.459324
0.674694
0.393428
-0.981925
-2.051474
-1.211670
-0.001369
1.631003
-0.885801
0.468999
-0.164375
1.378061
0.575597
Appendix C: Optimized geometries for the reactions in the kinetic model
165
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-2.924729
-1.377395
4.274991
4.017815
5.728151
5.978037
6.446979
-1.098467
-1.327811
-0.950008
-1.176749
-0.982190
-1.976499
-3.169226
-4.413824
-3.815467
-0.413365
-0.814897
-1.560153
-0.060105
-0.604144
0.273958
-1.480066
-1.762628
-0.005268
-0.936032
1.557446
2.193945
3.990822
4.634244
5.547731
0.094220
-2.354967
-1.857489
-3.530370
-2.882899
-2.962495
-4.103973
0.915403
1.567362
1.067105
1.096365
-0.763852
-0.802447
0.628895
1.970673
-2.275734
2.326753
-1.919136
0.389552
-1.351942
2.403787
1.234280
1.238441
-0.139435
1.588591
0.446330
Radicals
R0
C
C
N
C
H
H
H
C
H
H
H
-0.309097
1.088056
2.250785
-1.064762
-0.394829
-1.713567
-1.718255
-1.064640
-1.712991
-1.718580
-0.394624
-0.000010
-0.000033
-0.000048
-1.300679
-2.162078
-1.362721
-1.359916
1.300738
1.363082
1.359796
2.162068
0.000047
-0.000002
-0.000009
-0.000049
-0.003056
0.884124
-0.880889
0.000026
-0.884447
0.880560
0.003642
Ri
C
C
C
C
C
C
C
C
C
C
C
C
N
C
C
C
C
C
-4.148586
-3.113999
-3.505566
-4.840979
-5.837413
-5.477481
-1.762971
-0.580821
0.761209
0.762813
1.699206
1.319843
1.015316
1.930264
2.223874
3.269203
4.040280
3.752796
0.616200
-0.263794
-1.399779
-1.627800
-0.744928
0.378328
0.011155
-0.835561
-0.051759
1.055419
2.276252
2.908200
3.389506
-1.028442
-1.708669
-2.632665
-2.896727
-2.233179
-0.734453
-0.295513
0.472373
0.779936
0.341280
-0.419901
-0.633187
-0.249662
-0.300486
0.783492
0.545364
-0.737763
-1.736580
-0.207283
0.983496
1.043045
-0.091736
-1.285782
Appendix C: Optimized geometries for the reactions in the kinetic model
166
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
2.705274
3.196570
1.472715
-2.752924
-3.876327
-5.114111
-6.243742
-6.878323
-0.500385
-0.710176
-1.569820
0.810746
1.631883
2.489437
3.480417
4.342956
4.854190
-0.258080
1.028965
3.413424
3.813086
3.469339
2.085862
0.423224
1.755751
-1.310168
1.890641
3.309790
-2.102031
1.486601
-2.501483
1.065377
-0.929857
-1.698364
-1.257895
0.879212
0.433040
-1.522446
-0.796237
-3.147685
-2.431508
-3.613253
1.443468
0.628349
1.233124
2.789884
1.366669
4.200991
3.612842
2.859580
-1.340215
0.485012
1.676772
0.814850
-1.325136
1.364209
-0.765970
0.585587
-0.929486
0.756034
-1.261994
-1.283938
1.875447
-2.273612
1.975375
-2.175320
-0.045319
0.877247
1.757447
-0.358308
0.394899
1.406630
1.516492
1.728515
2.633684
St
C
C
C
C
C
C
C
C
C
C
N
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-3.937168
-3.016222
-1.709144
-1.267439
-2.226305
-3.528207
0.054557
1.183416
2.267862
2.821774
3.256786
3.416786
1.651396
-1.017981
-1.915666
-3.326247
-4.234642
-4.956681
1.691682
0.824814
0.286688
4.194853
3.019520
3.869170
2.410432
0.838737
1.249989
-0.301797
-1.329194
-1.036910
0.312920
1.339379
1.035106
0.674965
-0.266438
-0.360067
0.991440
2.041898
-1.285608
-0.881930
-1.851944
2.376211
-2.365511
1.837069
-0.538418
0.060008
-1.285042
1.736994
-1.350709
-2.289846
-0.916381
-0.935295
-0.234452
-1.887163
0.355571
0.107288
-0.259210
-0.393114
-0.133551
0.231303
-0.761406
-1.062900
0.065925
0.296610
0.465730
-0.398036
1.383570
-0.444212
-0.226926
0.202303
0.422593
0.641660
-1.979481
-1.238790
-0.805343
0.367701
-0.577678
-1.322818
2.169150
1.721905
1.217531
Appendix C: Optimized geometries for the reactions in the kinetic model
167
Intermediates
R0-TR0
C 3.376089
C 2.907476
C 3.943397
S 1.325069
C 0.078426
S -0.948532
C -2.422556
C -3.248807
N -3.896696
C 2.640804
N 2.445487
S -0.146642
C -1.165903
C -0.387804
C -3.205001
C -1.967696
H 2.628987
H 4.309260
H 3.550054
H 4.898121
H 3.613026
H 4.090352
H -1.460406
H -2.065062
H -0.070312
H 0.496102
H -1.030792
H -2.578073
H -3.497251
H -4.108782
H -2.843938
H -1.307784
H -1.433908
0.999470
-0.429952
-1.482501
-0.883976
0.153464
-0.455892
-1.250769
-0.178551
0.661604
-0.559046
-0.635202
1.704380
2.712676
3.145206
-1.976061
-2.217522
1.736842
1.207348
1.087428
-1.287356
-2.493045
-1.409760
3.568990
2.144554
2.278169
3.729899
3.765938
-2.764463
-1.283641
-2.426504
-2.706369
-2.974846
-1.688677
-0.439024
-0.117700
-0.563683
-1.053391
-0.315885
0.990591
0.094785
-0.476481
-0.920485
1.321404
2.451753
-1.109882
0.060927
1.306273
1.209210
-1.010109
-0.140664
0.096211
-1.514699
-0.065932
-0.312762
-1.645405
-0.552992
0.301341
1.891434
1.036251
1.939840
1.634356
2.002949
0.787530
-1.449556
-0.579345
-1.802819
R0-TRi
C 3.848987
H 4.890375
C 4.859513
C 5.825896
C 5.768976
C 4.757668
C 3.787455
C 2.640906
C 3.100032
C 3.505470
C 4.651925
C 3.923739
C 2.319723
N 1.393554
C -1.889258
S -1.846824
C -1.918983
-0.742398
-1.231775
-1.358732
-2.135320
-2.294213
-1.674721
-0.883599
-0.245386
0.581751
2.059586
2.187005
2.723347
2.779342
3.337799
0.673159
1.798383
3.453441
-2.195942
-4.015623
-2.937785
-2.295606
-0.908951
-0.171182
-0.803115
-0.021682
1.207566
0.936217
-0.094438
2.271761
0.420627
0.030741
-0.594237
0.774484
-0.078264
Appendix C: Optimized geometries for the reactions in the kinetic model
168
C
S
C
C
C
C
N
S
H
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-1.858373
-3.115925
-4.516141
-3.987909
-5.254144
-5.413933
-6.126779
-0.579935
-1.233199
-0.648621
-0.798649
-1.612327
-2.295926
-2.155769
-1.335843
0.222557
1.635816
-1.052101
-2.846429
-2.683588
-1.927480
-0.909655
-3.319522
-3.442044
-4.831883
-6.085187
-5.646856
-4.559580
-0.288491
-1.718419
-2.932105
-2.682659
0.291081
1.579837
2.008216
3.096969
6.613083
6.510862
4.725974
2.104418
2.296615
3.957287
4.358932
5.513000
4.949811
4.812281
4.164451
3.124784
4.549203
0.779929
-0.318385
-1.698073
0.396962
-0.463556
-0.575668
-0.461825
-0.181532
-1.723317
-3.076487
-3.914069
-3.411457
-2.067374
-1.228564
-0.795760
-1.347053
3.500366
3.483475
4.462324
5.528771
4.505732
-1.581812
-2.183435
-2.330166
-0.227042
1.361249
0.559056
-3.473008
-4.958559
-4.064069
-1.667247
0.176795
-2.118325
-1.843660
-0.143233
-2.614442
-2.902648
-1.818945
0.421468
0.600681
0.095778
1.806985
1.607320
3.234234
2.215406
3.779431
2.650134
0.987866
-1.872254
-1.181861
-0.750408
-0.034317
-2.337519
-3.232450
-0.946123
2.923364
1.537853
1.196451
1.957457
3.070180
3.415197
2.653102
0.712507
0.418492
-0.738235
-0.653167
1.701640
0.503826
1.529883
0.107543
-1.562197
-0.455294
0.312575
-0.363890
0.793517
0.323396
1.680900
3.659711
4.276000
1.206021
-0.357376
1.323598
-2.703498
-2.868985
-0.400584
0.905351
-0.708127
1.952406
1.686665
-1.074730
0.252953
-0.199947
2.659896
2.121707
3.015120
R0-TSt
C -0.073884
C -0.450440
C -0.978674
C -1.135659
C -0.761765
C -0.236085
4.488825
3.795702
2.510767
1.886665
2.589199
3.882496
-0.864234
-2.019528
-1.922281
-0.675136
0.476636
0.380839
Appendix C: Optimized geometries for the reactions in the kinetic model
169
C
C
C
C
N
S
C
S
C
C
N
S
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-1.723087
-2.228954
-3.120146
-4.032658
-4.742681
-0.617312
0.853001
1.988759
2.576487
1.424922
0.536294
1.336866
2.919216
2.708656
-3.983136
-2.301235
3.097191
3.680756
-2.826738
-1.391640
3.628354
3.276838
2.000944
2.322069
3.662130
-1.262757
-0.867159
-0.337778
0.038479
0.331870
-2.560422
-3.318035
-4.633810
-4.603991
-1.746437
-1.593593
-2.970983
2.305004
3.474783
3.918343
4.034909
3.307135
4.517157
0.481342
0.062357
-1.215027
-1.311915
-1.374778
-0.801040
-0.950655
0.413225
0.564955
0.384488
0.245076
-2.605899
-2.837438
-2.800756
-1.060813
-2.526239
2.016017
-0.448910
0.907387
-0.057806
-2.074506
-3.814107
-3.571630
-1.826358
-2.969289
1.975246
2.137766
4.259762
4.415685
5.493049
0.444963
-0.942770
-0.184508
-1.947377
-2.740043
-2.428188
-3.365850
2.733068
2.196704
2.155212
-0.257404
-1.472645
-0.325379
-0.626959
0.765336
0.895558
-0.262813
-1.165052
-1.458116
-0.492514
-0.456568
1.335521
2.226600
2.942567
-0.071375
-1.022767
-2.536908
2.175866
1.007005
1.441151
1.693937
1.127341
1.459671
-0.695160
-0.682958
-2.853548
-2.850017
-3.050102
-2.824270
1.456577
-2.994514
1.286424
-0.936799
-1.334529
3.037379
2.110418
2.330697
0.094058
1.836949
1.215495
1.213416
2.452236
0.731222
2.712894
1.639153
1.000443
Ri-TR0
C 3.848987
H 4.890375
C 4.859513
C 5.825896
C 5.768976
C 4.757668
C 3.787455
C 2.640906
C 3.100032
C 3.505470
C 4.651925
-0.742398
-1.231775
-1.358732
-2.135320
-2.294213
-1.674721
-0.883599
-0.245386
0.581751
2.059586
2.187005
-2.195942
-4.015623
-2.937785
-2.295606
-0.908951
-0.171182
-0.803115
-0.021682
1.207566
0.936217
-0.094438
Appendix C: Optimized geometries for the reactions in the kinetic model
170
C
C
N
C
S
C
C
S
C
C
C
C
N
S
H
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
3.923739
2.319723
1.393554
-1.889258
-1.846824
-1.918983
-1.858373
-3.115925
-4.516141
-3.987909
-5.254144
-5.413933
-6.126779
-0.579935
-1.233199
-0.648621
-0.798649
-1.612327
-2.295926
-2.155769
-1.335843
0.222557
1.635816
-1.052101
-2.846429
-2.683588
-1.927480
-0.909655
-3.319522
-3.442044
-4.831883
-6.085187
-5.646856
-4.559580
-0.288491
-1.718419
-2.932105
-2.682659
0.291081
1.579837
2.008216
3.096969
6.613083
6.510862
4.725974
2.104418
2.296615
3.957287
4.358932
5.513000
4.949811
4.812281
4.164451
3.124784
2.723347
2.779342
3.337799
0.673159
1.798383
3.453441
4.549203
0.779929
-0.318385
-1.698073
0.396962
-0.463556
-0.575668
-0.461825
-0.181532
-1.723317
-3.076487
-3.914069
-3.411457
-2.067374
-1.228564
-0.795760
-1.347053
3.500366
3.483475
4.462324
5.528771
4.505732
-1.581812
-2.183435
-2.330166
-0.227042
1.361249
0.559056
-3.473008
-4.958559
-4.064069
-1.667247
0.176795
-2.118325
-1.843660
-0.143233
-2.614442
-2.902648
-1.818945
0.421468
0.600681
0.095778
1.806985
1.607320
3.234234
2.215406
3.779431
2.650134
2.271761
0.420627
0.030741
-0.594237
0.774484
-0.078264
0.987866
-1.872254
-1.181861
-0.750408
-0.034317
-2.337519
-3.232450
-0.946123
2.923364
1.537853
1.196451
1.957457
3.070180
3.415197
2.653102
0.712507
0.418492
-0.738235
-0.653167
1.701640
0.503826
1.529883
0.107543
-1.562197
-0.455294
0.312575
-0.363890
0.793517
0.323396
1.680900
3.659711
4.276000
1.206021
-0.357376
1.323598
-2.703498
-2.868985
-0.400584
0.905351
-0.708127
1.952406
1.686665
-1.074730
0.252953
-0.199947
2.659896
2.121707
3.015120
Ri-TRi
Appendix C: Optimized geometries for the reactions in the kinetic model
171
C
C
S
C
S
C
C
S
C
C
C
C
C
C
H
H
H
C
H
H
H
H
H
H
H
C
C
C
N
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
-1.325599
-1.373059
-0.042852
-0.117142
0.021443
-1.221033
-1.018126
-0.079475
1.280301
-0.245052
-0.005374
-0.537314
-1.299667
-5.834321
-5.839624
-2.550155
-2.112311
-2.639601
-1.707159
-0.353599
0.605834
0.184933
-0.883250
-3.929916
-2.900451
-3.867067
-4.148783
-2.953468
-2.018045
-4.366699
-5.370911
-6.253312
-5.559447
-3.502531
-4.535305
-5.247517
-4.749793
-5.227629
-5.790780
-7.692028
-7.737348
-3.148096
-2.332265
-1.201633
-2.114390
-0.363705
-1.481997
-1.533857
4.589328
5.561022
6.613759
6.681948
7.492064
7.370965
5.493417
3.768732
6.328852
4.808903
4.042048
2.334214
1.857959
0.449391
-0.095072
1.172482
-0.032707
-1.249941
-1.755110
-1.108769
0.050807
1.057580
1.111794
1.660443
1.469576
0.902567
0.565986
-1.499237
-2.645748
-1.761311
-0.305308
0.054696
-0.725200
-1.316405
-2.752791
-3.219634
-3.577192
-3.697736
-2.820239
-2.444380
-3.854455
-3.686211
-4.725596
-3.366160
-1.007750
-2.214799
0.870426
1.924945
2.050705
1.381002
4.398958
4.521036
6.794213
6.735318
6.616507
0.557691
1.604444
2.532988
2.839822
2.214844
2.451584
3.560695
3.015871
1.375171
-0.221991
-0.046452
-1.085134
-0.644443
1.049047
1.187615
2.589088
-1.965755
-1.460810
2.770923
4.049511
5.167340
4.998034
-2.546200
-3.630852
0.004737
3.602211
0.789310
5.862974
6.163831
4.157958
1.913762
0.470362
-2.466913
-0.569511
1.268482
0.737052
0.001626
-0.568312
1.944319
-0.208127
0.319924
-0.512331
2.614689
1.609775
2.503937
1.840618
-1.105250
1.321330
0.163988
-2.320564
1.634294
-0.374062
0.993010
0.378299
0.105325
-1.266450
3.718849
1.440785
1.820878
0.956763
-0.290700
-0.974362
1.249553
2.791305
2.116285
Appendix C: Optimized geometries for the reactions in the kinetic model
172
H
C
H
C
C
C
H
H
H
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
C
C
C
C
C
C
C
H
H
H
H
N
H
H
H
C
5.775414
4.079073
3.302242
4.530451
3.393232
4.894560
4.050772
5.188286
6.046795
5.731757
-5.795094
-4.724695
-6.872839
-6.898407
-4.757878
-3.512840
1.759724
1.228545
2.234134
-3.047810
0.956061
-0.011572
0.974040
2.089199
3.144279
1.671833
1.042932
0.495585
5.709010
2.622611
3.552977
4.652315
5.736369
6.568260
4.932982
2.415808
2.508762
2.936007
5.492779
0.142864
0.586282
0.816758
-1.374207
-1.856382
-2.407190
-2.672782
-3.735143
-4.114985
-4.497921
-2.702732
-1.920504
0.910297
0.366948
1.512103
1.585256
0.457756
-0.245948
-0.923927
-1.119320
0.019712
-1.398652
-0.459536
-4.264043
-3.920821
-1.763059
0.839293
-1.929165
-3.140539
-3.336749
1.286288
0.694059
-0.013676
0.960958
-3.559483
-1.689321
-1.219427
1.692259
-2.882865
-0.202618
-1.020606
-2.498646
-2.331876
-1.643697
-0.734736
-1.334369
0.340380
1.247903
-0.368734
-0.951836
0.358431
1.882166
1.184535
0.235197
-0.490120
-0.417622
-1.812339
-1.888667
0.206657
-3.802490
-2.518591
-4.055546
1.987762
-0.506587
-2.947415
-5.217295
-5.755442
-2.196333
-4.766644
-4.465209
-3.195541
-0.665682
-1.243508
-0.215632
0.197078
-1.046546
0.517068
-1.404966
-0.845746
1.955994
0.673875
1.754417
-1.252663
-2.230994
Ri-TSt
C -6.186487
C -7.206583
C -6.901429
C -5.586557
C -4.559178
C -4.869397
C -3.123717
C -2.913822
C -3.079876
C -4.541753
S -2.549664
C -0.781925
S 0.139507
-0.254486
0.215905
0.645334
0.591344
0.109665
-0.301494
0.036372
-0.697755
-2.247857
-2.708278
1.812397
1.722780
0.216401
1.617647
0.787974
-0.506608
-0.970909
-0.147194
1.154527
-0.637007
-1.976243
-1.943091
-1.716038
-0.780069
-0.729070
-0.720850
Appendix C: Optimized geometries for the reactions in the kinetic model
173
C
C
C
C
C
C
S
C
C
C
C
C
C
C
C
C
N
C
C
C
C
C
C
C
C
N
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
0.841096
1.918921
3.234112
4.023493
5.153654
6.374194
0.007632
1.007584
1.776128
-0.265096
-0.789151
-1.785487
-2.285155
-1.793905
-0.788634
4.599432
4.166601
5.615204
4.032726
4.584954
5.296332
5.466187
4.912906
4.200093
-2.241978
-1.599671
-2.563841
0.301134
1.693500
1.097737
2.369329
2.471495
1.294607
-0.431603
-3.056226
-2.186039
-0.402045
2.136386
1.523877
2.951552
6.401469
6.014253
4.782163
4.478500
3.316415
4.458556
7.162808
6.760529
6.110914
3.774071
5.035038
6.020964
5.716638
-2.173745
-5.360264
-4.074605
0.214863
-0.887078
-0.496077
0.530207
1.331367
0.457680
3.296500
3.441737
4.764478
0.075722
-1.177568
-1.276368
-0.125081
1.127424
1.225669
1.935388
2.404101
2.480306
-1.748564
-2.560518
-3.715970
-4.081240
-3.285755
-2.130434
-2.807331
-3.258340
-2.818147
3.390480
2.593747
5.621040
4.851077
4.792391
1.204389
-2.078130
-0.204695
2.027652
2.200960
-1.111281
-1.809516
-0.013351
3.073227
2.049103
3.141609
0.028257
1.265446
-2.293674
1.084061
-0.026666
-0.318037
-1.512579
-3.562343
-4.978506
-4.332522
-2.253838
0.932167
-0.661952
1.033661
1.083964
0.351601
1.200214
0.487110
0.105234
-0.493215
-2.061153
-2.040138
2.054755
2.408918
3.380910
3.999707
3.627916
2.661699
-0.743891
-1.699440
1.420184
0.007284
1.008750
0.681067
-0.657489
-1.662331
-1.329694
-0.858966
-0.020131
-3.289730
-2.892273
-2.095500
-1.979123
-2.955505
-1.197155
1.128692
1.919397
4.759828
4.090561
2.376974
2.136052
0.644709
-0.591120
0.944952
2.343986
1.673306
2.062895
1.599188
2.054702
-0.321912
1.007674
-0.615121
-2.115838
-2.705081
-0.912532
1.469820
3.649682
-1.977359
1.801784
Appendix C: Optimized geometries for the reactions in the kinetic model
174
H
H
H
H
H
H
H
H
H
H
H
H
-7.686932
-6.414782
-8.230207
-1.896543
-3.598850
-2.488306
-2.652537
-3.165955
-1.517109
-4.603487
-4.919177
-5.179896
1.022659
-0.584652
0.252125
-0.487944
-0.304154
-0.410330
-3.907800
-2.405921
-2.548826
-3.797642
-2.404809
-2.263758
-1.154002
2.626210
1.147161
-2.316341
-2.735001
0.133757
-3.306395
-4.105899
-3.454145
-1.794366
-0.738516
-2.486428
St-TR0
C -0.073884
C -0.450440
C -0.978674
C -1.135659
C -0.761765
C -0.236085
C -1.723087
C -2.228954
C -3.120146
C -4.032658
N -4.742681
S -0.617312
C 0.853001
S 1.988759
C 2.576487
C 1.424922
N 0.536294
S 1.336866
C 2.919216
C 2.708656
C -3.983136
C -2.301235
C 3.097191
C 3.680756
H -2.826738
H -1.391640
H 3.628354
H 3.276838
H 2.000944
H 2.322069
H 3.662130
H -1.262757
H -0.867159
H -0.337778
H 0.038479
H 0.331870
H -2.560422
H -3.318035
H -4.633810
H -4.603991
H -1.746437
H -1.593593
4.488825
3.795702
2.510767
1.886665
2.589199
3.882496
0.481342
0.062357
-1.215027
-1.311915
-1.374778
-0.801040
-0.950655
0.413225
0.564955
0.384488
0.245076
-2.605899
-2.837438
-2.800756
-1.060813
-2.526239
2.016017
-0.448910
0.907387
-0.057806
-2.074506
-3.814107
-3.571630
-1.826358
-2.969289
1.975246
2.137766
4.259762
4.415685
5.493049
0.444963
-0.942770
-0.184508
-1.947377
-2.740043
-2.428188
-0.864234
-2.019528
-1.922281
-0.675136
0.476636
0.380839
-0.626959
0.765336
0.895558
-0.262813
-1.165052
-1.458116
-0.492514
-0.456568
1.335521
2.226600
2.942567
-0.071375
-1.022767
-2.536908
2.175866
1.007005
1.441151
1.693937
1.127341
1.459671
-0.695160
-0.682958
-2.853548
-2.850017
-3.050102
-2.824270
1.456577
-2.994514
1.286424
-0.936799
-1.334529
3.037379
2.110418
2.330697
0.094058
1.836949
Appendix C: Optimized geometries for the reactions in the kinetic model
175
H -2.970983 -3.365850
H 2.305004 2.733068
H 3.474783 2.196704
H 3.918343 2.155212
H 4.034909 -0.257404
H 3.307135 -1.472645
H 4.517157 -0.325379
St-TRi
C -6.186487
C -7.206583
C -6.901429
C -5.586557
C -4.559178
C -4.869397
C -3.123717
C -2.913822
C -3.079876
C -4.541753
S -2.549664
C -0.781925
S 0.139507
C 0.841096
C 1.918921
C 3.234112
C 4.023493
C 5.153654
C 6.374194
S 0.007632
C 1.007584
C 1.776128
C -0.265096
C -0.789151
C -1.785487
C -2.285155
C -1.793905
C -0.788634
C 4.599432
N 4.166601
C 5.615204
C 4.032726
C 4.584954
C 5.296332
C 5.466187
C 4.912906
C 4.200093
C -2.241978
N -1.599671
C -2.563841
H 0.301134
H 1.693500
H 1.097737
H 2.369329
H 2.471495
H 1.294607
H -0.431603
-0.254486
0.215905
0.645334
0.591344
0.109665
-0.301494
0.036372
-0.697755
-2.247857
-2.708278
1.812397
1.722780
0.216401
0.214863
-0.887078
-0.496077
0.530207
1.331367
0.457680
3.296500
3.441737
4.764478
0.075722
-1.177568
-1.276368
-0.125081
1.127424
1.225669
1.935388
2.404101
2.480306
-1.748564
-2.560518
-3.715970
-4.081240
-3.285755
-2.130434
-2.807331
-3.258340
-2.818147
3.390480
2.593747
5.621040
4.851077
4.792391
1.204389
-2.078130
1.215495
1.213416
2.452236
0.731222
2.712894
1.639153
1.000443
1.617647
0.787974
-0.506608
-0.970909
-0.147194
1.154527
-0.637007
-1.976243
-1.943091
-1.716038
-0.780069
-0.729070
-0.720850
1.033661
1.083964
0.351601
1.200214
0.487110
0.105234
-0.493215
-2.061153
-2.040138
2.054755
2.408918
3.380910
3.999707
3.627916
2.661699
-0.743891
-1.699440
1.420184
0.007284
1.008750
0.681067
-0.657489
-1.662331
-1.329694
-0.858966
-0.020131
-3.289730
-2.892273
-2.095500
-1.979123
-2.955505
-1.197155
1.128692
1.919397
Appendix C: Optimized geometries for the reactions in the kinetic model
176
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-3.056226
-2.186039
-0.402045
2.136386
1.523877
2.951552
6.401469
6.014253
4.782163
4.478500
3.316415
4.458556
7.162808
6.760529
6.110914
3.774071
5.035038
6.020964
5.716638
-2.173745
-5.360264
-4.074605
-7.686932
-6.414782
-8.230207
-1.896543
-3.598850
-2.488306
-2.652537
-3.165955
-1.517109
-4.603487
-4.919177
-5.179896
-0.204695
2.027652
2.200960
-1.111281
-1.809516
-0.013351
3.073227
2.049103
3.141609
0.028257
1.265446
-2.293674
1.084061
-0.026666
-0.318037
-1.512579
-3.562343
-4.978506
-4.332522
-2.253838
0.932167
-0.661952
1.022659
-0.584652
0.252125
-0.487944
-0.304154
-0.410330
-3.907800
-2.405921
-2.548826
-3.797642
-2.404809
-2.263758
4.759828
4.090561
2.376974
2.136052
0.644709
-0.591120
0.944952
2.343986
1.673306
2.062895
1.599188
2.054702
-0.321912
1.007674
-0.615121
-2.115838
-2.705081
-0.912532
1.469820
3.649682
-1.977359
1.801784
-1.154002
2.626210
1.147161
-2.316341
-2.735001
0.133757
-3.306395
-4.105899
-3.454145
-1.794366
-0.738516
-2.486428
St-TSt
C 4.264710
C 5.407620
C 6.343543
C 6.124267
C 4.976982
C 4.042077
C 2.818234
C 2.642255
C 3.679414
C 3.861871
N 4.012847
S 1.335693
C -0.040815
S -1.187412
C -2.840927
C -3.841674
C -4.217702
C -5.150257
C -5.717894
C -5.337898
-0.502397
-0.292862
0.674494
1.435922
1.227866
0.251027
0.016102
-1.412362
-1.876738
-0.802438
0.038819
0.488370
0.303801
-0.981723
-0.298189
-1.418229
-1.820867
-2.842627
-3.479787
-3.096395
-2.195023
-2.966347
-2.587711
-1.438505
-0.668442
-1.032790
-0.169544
0.377189
1.450531
2.450572
3.219583
-1.239140
-0.142596
-0.547203
0.034327
-0.181721
-1.471401
-1.650566
-0.543228
0.744031
Appendix C: Optimized geometries for the reactions in the kinetic model
177
C
C
C
C
N
S
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-4.400672
-3.133643
-4.355884
-4.250258
-4.164872
-0.056758
0.490542
0.637609
5.063394
3.106402
-4.288370
-5.726087
-2.244870
-3.270925
1.437191
-0.260929
-0.310959
1.386661
0.955515
-3.777824
-4.102928
-5.433686
-5.767121
-6.446060
-2.721487
3.538439
5.567855
7.234020
6.844475
4.814753
2.669115
1.649353
2.823580
4.932718
5.538944
5.724330
3.809991
2.157596
2.935716
-3.297585
-5.034459
-4.501047
-6.531384
-5.779391
-5.880822
-2.075588
1.029552
1.844387
3.182341
4.220950
0.991723
2.742865
3.450110
-2.228211
-3.121402
2.033150
1.247686
1.659648
0.850326
2.709011
3.221482
3.470094
2.954912
4.484482
-1.336377
-1.783959
-3.142847
-3.591292
-4.272220
-0.121511
-1.250807
-0.882135
0.835298
2.190832
1.813516
-2.137269
-1.472152
0.720668
-3.007622
-1.365276
-2.610695
-3.488652
-2.888434
-3.914339
2.379399
2.762838
1.082697
1.926227
1.099228
0.285337
0.921315
-0.690309
-0.150122
-0.775809
-1.261132
1.495364
1.194342
2.545080
0.848654
2.174606
1.385540
-0.558290
-0.585258
-1.761648
0.651778
0.562371
3.089659
3.169215
2.381022
-2.338297
1.925067
-2.654570
1.609654
-0.684275
1.103632
-2.499476
-3.863928
-3.187168
-1.138820
0.232262
-0.443907
0.833406
0.665769
0.091037
0.380923
1.632002
2.926932
2.665064
1.439236
1.695594
1.711895
1.883077
-0.261485
-1.640558
-0.066400
Transition states
R0-TR0-TS
S 1.084616 -2.214748 -0.840852
S -1.534918 -1.030149 -0.990141
C -2.796408 -0.301584 0.191175
C -2.599940 1.154106 0.298318
Appendix C: Optimized geometries for the reactions in the kinetic model
178
N
C
H
H
H
C
H
H
H
C
H
H
C
S
C
H
H
H
C
H
H
C
H
H
H
H
C
C
N
-2.525609
-2.768159
-1.815740
-3.570688
-2.932788
-4.148591
-4.952970
-4.165494
-4.315918
2.745220
3.428628
2.930981
0.057550
0.505940
2.877447
2.172100
2.698019
3.891328
0.894194
-0.193124
1.368733
0.574710
1.194736
0.884091
-0.500826
0.791365
1.314204
2.704009
3.821600
2.299446
-0.974706
-0.809360
-0.558068
-2.048063
-0.552505
-0.116567
-0.096307
-1.628681
-1.916545
-2.387325
-0.840763
-0.940592
0.210069
-2.523800
-2.058598
-3.602286
-2.346122
3.257992
3.246381
3.089074
2.145188
4.255267
2.981977
2.224546
1.214550
2.215164
1.893913
1.600241
0.360040
1.574537
2.078888
2.192376
1.450051
-0.520608
0.079036
-1.513580
-0.614485
-0.080216
-0.792611
-0.084877
-0.152900
0.957224
1.318467
2.010653
1.299948
1.693334
0.791042
0.904911
1.761404
-1.536854
0.438292
-2.179630
-1.362717
-2.069076
-0.220599
-0.270218
-0.312108
R0-TRi-TS
C -3.541862
H -4.473412
C -4.588089
C -5.775049
C -5.903529
C -4.855695
C -3.660024
C -2.484147
C -2.841489
C -2.941222
C -4.040031
C -3.229862
C -1.639451
N -0.614793
C 1.757618
S 2.074451
C 2.834233
C 2.988111
S 2.495957
C 4.634819
C 4.888744
C 4.373359
C 5.414912
N 6.028771
S 0.663622
-0.948465
-1.636256
-1.028159
-0.330121
0.450225
0.525781
-0.177709
-0.066342
-0.374091
-1.867069
-2.649504
-1.917830
-2.527642
-3.048751
-0.544418
-0.397983
-2.017197
-2.088071
-1.635189
-0.794812
-1.724840
0.660449
-1.045093
-1.261616
0.627628
-2.187150
-4.001550
-3.108052
-2.882485
-1.732018
-0.813424
-1.022025
-0.057113
1.419247
1.855136
1.099657
3.376059
1.620926
1.454358
-0.311498
1.411807
1.850608
3.369220
-1.349603
-2.017941
-3.185440
-2.333790
-0.850063
0.120436
-1.067768
Appendix C: Optimized geometries for the reactions in the kinetic model
179
H
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
0.668298
0.089013
0.002689
0.402616
0.897376
0.989833
0.588037
-0.372150
-1.850599
2.163536
3.800990
3.627806
3.457281
2.018670
4.102472
4.922502
5.851440
5.294397
4.025378
3.618149
-0.370804
0.330444
1.211031
1.377279
-0.226314
-1.938719
-2.425124
-2.617813
-6.591597
-6.821078
-4.973990
-1.722360
-2.090990
-3.798125
-3.842344
-5.005423
-4.115044
-4.195975
-3.273752
-2.458104
2.370574
2.835178
3.855298
5.154953
5.458874
4.452549
3.150986
1.423749
1.349571
-2.795013
-2.087944
-1.285439
-3.041969
-2.036382
-1.610113
-2.771472
-1.487895
1.146665
1.209644
0.746863
3.631015
5.931823
6.472032
4.676522
0.803496
1.707612
2.056402
-1.491012
-0.391081
1.003483
1.146323
-0.785079
0.094397
0.098120
-2.703705
-2.152299
-3.669914
-1.442842
-2.951875
-1.390912
2.607103
0.584509
-0.375036
-0.070124
1.200792
2.161729
1.854465
0.280982
-0.165600
1.478341
1.348137
3.751549
3.633825
3.875445
-3.938145
-2.868578
-3.662260
-2.690031
-1.454463
-3.120660
-1.371157
-0.826714
1.437083
3.152059
1.168656
-1.197583
0.448286
-2.374195
-3.596812
-1.548607
0.071974
-0.384454
2.067666
1.674957
0.027608
1.241575
1.489413
3.579643
3.731738
3.946197
R0-TSt-TS
C -0.740853
C -1.141716
C -1.413462
C -1.293631
C -0.890274
C -0.616676
C -1.616889
C -2.116242
C -3.138947
C -4.280223
N -5.156273
S -0.225034
C 1.296306
S 1.528875
4.442259
4.391293
3.163890
1.966988
2.027259
3.258303
0.653518
-0.482758
-1.477456
-0.703196
-0.093563
0.180178
0.253298
-0.318224
1.473273
0.134729
-0.466143
0.256492
1.596345
2.199875
-0.438584
0.480663
-0.147210
-0.685532
-1.113557
-1.626367
-0.697189
0.849695
Appendix C: Optimized geometries for the reactions in the kinetic model
180
C
C
N
S
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
1.984960
0.709443
-0.333655
2.560802
4.113125
4.349026
-3.664182
-2.547438
3.099663
2.321610
-2.621782
-1.282184
4.045947
4.898629
4.401659
3.543641
5.294966
-1.725356
-0.788883
-1.249526
-0.309031
-0.533464
-2.389785
-2.826432
-4.117307
-4.416357
-2.248300
-1.673678
-3.291099
2.774550
3.432560
3.953855
2.553731
1.488007
3.199245
-2.726599
-3.227059
-3.612760
0.896437
0.714899
1.888246
-2.408153
-2.334922
-2.868644
-2.877463
-0.008519
-1.063984
-0.233665
0.641754
2.833574
1.952420
1.743800
3.129556
1.116256
5.307066
3.287572
5.397542
0.866090
-2.988595
-1.827575
-3.095814
-1.728220
-2.873432
-3.062804
-2.568565
-3.915328
-2.252654
-3.927590
-2.566127
-2.274952
0.648736
1.044555
1.360724
-1.769242
-0.784415
0.171666
0.974666
-1.291845
1.663322
-0.817834
1.328870
0.882527
-0.245913
-1.541804
-0.374828
0.907083
0.705524
-1.506546
2.174864
-0.437992
3.240580
1.945138
-1.187368
1.372181
1.783419
0.578024
-2.148767
-0.913630
-1.629541
2.662765
1.714351
1.369111
-1.045336
-1.453251
-1.068414
Ri-TR0-TS
C -3.483400
H -4.554129
C -4.543662
C -5.583737
C -5.550922
C -4.490031
C -3.442181
C -2.249685
C -2.632695
C -3.048090
C -4.335855
C -3.258701
C -1.949382
N -1.087967
C 1.610761
S 0.373211
C 0.764974
C -0.312841
S 2.979606
-0.766752
-1.779454
-0.927321
0.002362
1.095191
1.251256
0.319543
0.500049
0.707909
-0.537846
-1.221137
-0.094067
-1.526203
-2.305398
-1.185209
-2.405407
-3.886698
-4.940963
-1.694461
-1.702796
-3.271663
-2.596949
-2.626451
-1.758275
-0.865203
-0.817415
0.116529
1.603504
2.443331
1.926763
3.912404
2.422369
2.418266
-0.714940
-1.032510
-0.003984
-0.258508
0.299441
Appendix C: Optimized geometries for the reactions in the kinetic model
181
C
C
C
C
N
S
H
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
4.524405
4.640762
4.613648
5.598427
6.458187
1.322728
2.030627
0.773062
0.515473
1.260267
2.280027
2.552246
1.814490
0.012511
-1.383069
1.757536
0.759114
-1.298140
-0.084489
-0.360485
3.825235
4.613113
5.590774
5.569045
4.557477
3.796776
-0.270132
1.044550
2.857458
3.340830
0.205765
-1.333921
-1.903995
-2.672115
-6.410482
-6.352184
-4.480947
-1.628836
-1.780926
-3.455426
-4.214116
-5.152741
-4.620911
-4.074261
-3.525027
-2.356119
-0.804468
-0.915643
0.651262
-1.593704
-2.199339
0.361673
2.350251
2.973179
4.028001
5.203301
5.362443
4.327984
3.151284
1.735732
1.691078
-4.254601
-3.584545
-4.579968
-5.838241
-5.228929
-0.369387
-1.959119
-0.473881
1.085612
0.695072
1.237352
3.919812
6.000746
6.282180
4.444410
1.068556
1.657366
2.631138
-1.490638
-0.120719
1.829651
2.114178
-0.400950
1.167673
1.430084
-1.615995
-0.492013
-2.044414
0.636087
-0.946367
0.369981
-0.359524
-1.890047
0.135870
0.265875
0.759198
-1.311403
1.871746
0.228308
-0.676305
-0.634646
0.307661
1.210443
1.168739
0.208518
-0.376817
-0.275611
1.045810
0.052236
0.326888
-1.314374
-2.367904
-2.213450
-2.210606
-0.181219
1.226701
-0.287752
-1.418235
-1.340960
0.339278
1.949301
1.045897
-1.471547
-0.133517
-1.691280
-3.320866
-1.776273
-0.203122
0.040261
2.119243
1.678185
0.916647
1.909196
2.590100
3.957766
4.545220
4.322482
Ri-TRi-TS
C -1.980567
C -1.247031
S -0.823826
C 0.029376
S 0.300679
C 1.384522
C 1.135942
S 0.412633
-4.711721
-4.012954
-2.299451
-1.534671
-2.537259
-1.476078
-1.964761
0.093278
-4.037821
-2.891679
-3.430277
-2.076772
-0.634328
0.456142
1.872026
-2.250670
Appendix C: Optimized geometries for the reactions in the kinetic model
182
C
C
C
C
C
C
H
H
H
C
H
H
H
H
H
H
H
C
C
C
N
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
C
H
C
C
C
H
H
-1.227825
0.353161
0.087072
0.597405
1.372728
6.143824
6.182425
2.845610
2.238074
2.850256
1.770275
0.391820
-0.524199
-0.047466
0.980105
4.146226
2.996105
3.845613
3.938232
2.708167
1.736927
4.000254
5.160922
6.076753
5.210945
3.130155
4.038481
4.903509
4.759453
5.129593
5.980330
8.007310
8.130945
3.386956
-0.327341
-1.878401
-2.239544
-2.907673
-1.356778
1.639805
-4.169728
-5.163898
-6.316714
-6.464594
-7.356402
-7.092573
-5.035352
-3.273324
-5.600963
-3.631776
-2.814563
-3.997423
-2.933547
-4.066277
-3.112316
-4.322555
1.412333
-1.195714
-1.632903
-2.854785
-3.633133
0.618729
1.234846
-1.590776
-3.812759
-1.478679
-4.587554
-3.199983
-1.011566
-0.239116
-0.466187
1.240419
0.644981
0.062476
1.543524
2.248515
2.789793
1.564183
2.291448
1.763189
3.310666
1.065905
2.590608
1.041041
-0.440812
2.346204
-1.585583
-1.594704
-0.182151
-2.347013
-4.546167
-3.961599
-5.733637
-4.189899
-4.769015
-3.192458
-1.700058
-2.679927
-2.474890
-1.284589
-1.115957
-3.235045
-3.602825
-1.869018
0.610676
1.956149
2.646493
2.178521
1.610152
3.702502
4.189494
3.906789
-1.167588
2.746051
4.044067
4.486966
3.624776
-2.509576
-3.404160
-1.127394
1.665229
-0.040037
3.960455
5.496852
4.691674
2.421282
0.349000
-2.002288
-0.108357
1.787425
2.266926
1.847556
1.511331
3.813422
1.687495
1.973434
2.084846
4.251889
4.191913
4.146444
2.125322
0.597416
0.668643
-0.728170
-2.773319
0.360740
-2.634755
-1.999619
-3.739574
-4.296752
-4.935973
2.327882
0.910848
0.865685
0.106849
-0.608516
-1.206914
0.071149
1.425441
1.503285
-1.127137
0.678122
0.441572
2.180092
3.034183
2.447543
2.223595
3.491988
Appendix C: Optimized geometries for the reactions in the kinetic model
183
H
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
C
C
C
C
C
C
C
H
H
H
H
N
H
H
H
C
-5.585920
-5.343637
6.016696
4.915098
7.165860
7.235528
4.996054
3.629748
-1.841550
-1.118156
-2.505151
3.024104
-0.689336
0.595236
-0.714406
-2.264568
-3.197728
-1.697623
-0.823706
-0.088532
-5.469715
-2.489972
-3.194274
-4.308817
-4.838973
-6.140651
-4.493403
-2.264090
-2.104897
-2.440277
-5.324715
0.345503
-0.227104
1.774204
1.530148
-0.955651
-0.154342
-0.966226
-0.175866
0.625219
-0.167351
2.963062
2.681333
2.211872
-0.397192
1.405646
5.634544
6.106707
4.377071
0.934044
4.182933
5.154575
4.887732
-0.308032
0.579402
0.541364
-0.496244
4.146976
1.923121
2.290789
-0.460504
1.156112
0.189762
0.444387
3.471125
3.668578
3.623704
2.583983
-0.217241
-0.552144
-1.008963
-2.157580
-1.715062
0.270250
-3.060685
-1.879555
-3.478544
2.342318
-0.221169
-1.659512
-3.725765
-4.619692
-1.916838
-3.712632
-3.213356
-2.055010
-0.559917
-1.159386
0.234128
0.205655
1.810393
1.943418
0.086000
-1.422537
3.710056
0.950440
2.478512
-0.494591
-1.397750
Ri-TSt-TS
C 6.017185
C 7.125391
C 6.945472
C 5.667151
C 4.547481
C 4.737543
C 3.146959
C 2.952477
C 2.949831
C 4.344461
S 2.745707
C 0.972875
S -0.085747
C -1.065849
C -1.881006
C -3.253176
C -4.214923
C -5.412040
C -6.429708
S 0.529921
C -1.302519
0.016802
-0.177013
-0.285150
-0.190114
0.014576
0.105201
0.112701
1.137731
2.649798
3.175670
-1.610885
-1.643816
-0.457960
-0.592684
0.675329
0.475666
-0.294509
-1.062958
-0.133775
-3.199936
-3.120693
1.858365
1.032304
-0.347971
-0.897905
-0.077171
1.308514
-0.654892
-1.790099
-1.394603
-0.977398
-1.250785
-1.441678
-0.947432
1.293940
1.179952
0.477835
1.417322
0.779540
0.077812
-2.173199
-2.295816
Appendix C: Optimized geometries for the reactions in the kinetic model
184
C
C
C
C
C
C
C
C
N
C
C
C
C
C
C
C
C
N
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-1.820000
0.012033
0.629489
1.638997
2.075370
1.493670
0.480904
-4.888572
-4.475736
-6.133071
-3.791853
-4.221715
-4.673765
-4.703389
-4.270669
-3.817322
2.014462
1.292861
2.443881
-1.567790
-1.720961
-1.451333
-2.913285
-1.529388
-1.576305
0.326664
2.860828
1.830401
0.029608
-2.050548
-1.312009
-3.068548
-6.966962
-6.531360
-5.448457
-4.636312
-3.627948
-4.197893
-7.280124
-6.802571
-5.983608
-3.475206
-4.283869
-5.056978
-5.000714
2.088900
5.541160
3.877104
7.801026
6.146126
8.121645
1.991499
3.725566
2.432006
2.423405
3.117833
-4.398208
-0.728329
0.390372
0.216792
-1.066251
-2.182235
-2.016970
-2.026897
-2.789301
-1.865669
1.816690
2.806002
4.044093
4.319850
3.349105
2.112476
2.881592
3.092428
3.460588
-2.233993
-3.002372
-4.505988
-4.354576
-5.290244
-1.519250
1.394404
-1.195510
-3.182640
-2.888811
1.091993
1.449177
-0.145398
-2.443292
-1.171700
-2.557590
0.391761
-1.030339
2.615340
-0.713911
0.604204
0.405572
1.363650
3.552582
5.283402
4.795470
1.089958
-0.283603
0.243325
-0.445347
0.095244
-0.247761
0.926462
1.003054
0.318420
4.531675
3.299280
-2.954236
2.244965
2.857118
3.799600
4.149971
3.537342
2.600914
-0.211067
-0.984380
1.890570
-0.006758
0.890050
0.432277
-0.936005
-1.839901
-1.376792
-0.273572
0.611955
-2.613805
-2.876684
-1.295274
-3.979847
-2.976526
-2.388982
1.042565
2.578300
4.889722
3.796313
2.132921
2.185439
0.646997
-0.407747
1.479506
2.638955
2.391259
2.162647
1.980263
1.960521
-0.295504
0.795948
-0.759465
-2.087781
-2.907611
-1.292974
1.146556
4.265890
-1.973495
1.957646
-0.998734
2.934647
1.460536
-2.265696
-2.555019
0.146222
-2.389447
-3.462572
Appendix C: Optimized geometries for the reactions in the kinetic model
185
H
H
H
H
1.436716
4.301373
4.717424
5.058571
3.149238
4.253543
2.683220
2.995374
-2.906819
-0.789304
-0.077883
-1.788185
St-TR0-TS
C -3.324192
C -3.419362
C -2.930775
C -2.332300
C -2.240616
C -2.733861
C -1.827697
C -1.406537
C -2.551113
C -3.579078
N -4.394663
S 0.541715
C 1.725861
S 2.449696
C 2.575736
C 1.352544
N 0.397631
S 2.342648
C 4.134759
C 4.337787
C -1.936902
C -3.234199
C 2.615092
C 3.819620
H -0.924672
H -0.668572
H 4.549788
H 4.589860
H 3.917738
H 3.855880
H 5.408336
H -3.002425
H -1.788303
H -3.877265
H -2.666913
H -3.710381
H -2.045970
H -1.192229
H -1.447650
H -2.709841
H -3.730936
H -2.477979
H -3.982378
H 1.718095
H 2.692468
H 3.494312
H 3.873454
H 3.776334
H 4.714945
3.394856
2.689811
1.394719
0.758425
1.490215
2.787060
-0.577664
-1.466041
-2.327814
-1.455695
-0.810762
-0.145940
-0.146892
1.432342
1.474965
0.889906
0.445345
-1.666538
-1.596992
-1.768282
-3.195550
-3.226146
2.987245
0.764952
-0.889447
-2.187217
-0.652025
-2.414113
-2.715919
-0.955916
-1.752824
0.849773
1.039518
3.156080
3.327618
4.406745
-1.071940
-3.870434
-2.567369
-3.793583
-2.629118
-3.858794
-3.869593
3.492658
3.122593
3.435772
0.938784
-0.309559
1.181934
-0.703588
-1.911691
-2.000095
-0.879651
0.332483
0.411079
-1.023300
0.114754
0.751339
1.357659
1.847378
-2.065744
-0.923032
-0.436849
1.450755
2.012292
2.472334
-0.176346
-0.672954
-2.178998
1.876712
-0.306439
1.776649
2.017845
0.909596
-0.255923
-0.317065
-0.105093
-2.526368
-2.730352
-2.413089
-2.937512
1.208726
-2.778452
1.349908
-0.632003
-1.966903
1.443008
2.626083
2.367771
-1.075310
-0.782972
0.165096
1.413838
2.859732
1.304312
3.098176
1.840418
1.548510
Appendix C: Optimized geometries for the reactions in the kinetic model
186
St-TRi-TS
C 4.185790 -2.087170 -1.059726
C 5.058864 -2.746220 -1.919491
C 6.001741 -2.027776 -2.664061
C 6.057597 -0.634694 -2.543754
C 5.187901 0.028974 -1.684579
C 4.238340 -0.681409 -0.911557
C 3.336460 0.059418 -0.046129
C 2.641810 -0.544319 1.150587
C 3.174539 -0.003072 2.517467
C 2.956578 1.459758 2.547801
N 2.779612 2.595882 2.552534
S 1.512420 0.567293 -1.600940
C 0.112578 0.643601 -0.702136
S -0.864646 -0.854512 -0.584862
C -2.580259 -0.332020 -0.023535
C -3.266058 -1.622376 0.391918
C -3.616068 -2.598598 -0.551865
C -4.256379 -3.772131 -0.152448
C -4.554944 -3.987201 1.195884
C -4.198101 -3.026404 2.143969
C -3.552158 -1.854779 1.743169
C -3.267856 0.467594 -1.150646
C -4.622228 1.155840 -0.772379
C -4.940850 2.054453 -1.905454
N -5.192866 2.749271 -2.785809
S -0.385790 2.000857 0.336676
C 0.809492 3.339600 -0.112976
C 0.502456 4.567754 0.748829
C 4.682771 -0.293370 2.692854
C 2.362283 -0.638436 3.670347
C -4.488301 2.027035 0.500971
C -5.804441 0.165152 -0.624673
H -2.578706 1.255967 -1.466637
H -3.429976 -0.181805 -2.016654
H 1.812497 2.960351 0.082700
H 0.693336 3.534760 -1.181144
H -0.520796 4.923532 0.596225
H 0.657051 4.344224 1.807636
H 1.188806 5.374166 0.472593
H -3.385933 -2.444154 -1.602043
H -3.272698 -1.111367 2.485097
H -4.522675 -4.518802 -0.894050
H -4.420691 -3.187659 3.194186
H -5.057684 -4.898245 1.504512
H -2.443548 0.290570 0.861113
H 3.444616 -2.661933 -0.514847
H 5.000460 -3.825870 -2.018264
H 6.679326 -2.546804 -3.334239
H 6.781282 -0.067797 -3.121290
H 5.234305 1.111094 -1.596089
H 2.758546 -1.631652 1.169271
H 1.565311 -0.339175 1.119232
H 3.569708 1.117376 0.050772
H 4.841600 -1.375995 2.657861
H 5.271909 0.166299 1.895253
Appendix C: Optimized geometries for the reactions in the kinetic model
187
H
H
H
H
H
H
H
H
H
H
5.040288
2.695207
1.295280
2.509441
-3.618253
-5.384501
-4.379436
-6.739445
-5.893974
-5.658973
St-TSt-TS
C 4.185790
C 5.058864
C 6.001741
C 6.057597
C 5.187901
C 4.238340
C 3.336460
C 2.641810
C 3.174539
C 2.956578
N 2.779612
S 1.512420
C 0.112578
S -0.864646
C -2.580259
C -3.266058
C -3.616068
C -4.256379
C -4.554944
C -4.198101
C -3.552158
C -3.267856
C -4.622228
C -4.940850
N -5.192866
S -0.385790
C 0.809492
C 0.502456
C 4.682771
C 2.362283
C -4.488301
C -5.804441
H -2.578706
H -3.429976
H 1.812497
H 0.693336
H -0.520796
H 0.657051
H 1.188806
H -3.385933
H -3.272698
H -4.522675
H -4.420691
H -5.057684
0.083177 3.655490
-0.253501 4.638424
-0.427485 3.556814
-1.722941 3.656602
2.686928 0.434551
2.638329 0.638269
1.383267 1.378660
0.719398 -0.499927
-0.470301 -1.510297
-0.473448 0.248826
-2.087170
-2.746220
-2.027776
-0.634694
0.028974
-0.681409
0.059418
-0.544319
-0.003072
1.459758
2.595882
0.567293
0.643601
-0.854512
-0.332020
-1.622376
-2.598598
-3.772131
-3.987201
-3.026404
-1.854779
0.467594
1.155840
2.054453
2.749271
2.000857
3.339600
4.567754
-0.293370
-0.638436
2.027035
0.165152
1.255967
-0.181805
2.960351
3.534760
4.923532
4.344224
5.374166
-2.444154
-1.111367
-4.518802
-3.187659
-4.898245
-1.059726
-1.919491
-2.664061
-2.543754
-1.684579
-0.911557
-0.046129
1.150587
2.517467
2.547801
2.552534
-1.600940
-0.702136
-0.584862
-0.023535
0.391918
-0.551865
-0.152448
1.195884
2.143969
1.743169
-1.150646
-0.772379
-1.905454
-2.785809
0.336676
-0.112976
0.748829
2.692854
3.670347
0.500971
-0.624673
-1.466637
-2.016654
0.082700
-1.181144
0.596225
1.807636
0.472593
-1.602043
2.485097
-0.894050
3.194186
1.504512
Appendix C: Optimized geometries for the reactions in the kinetic model
188
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-2.443548
3.444616
5.000460
6.679326
6.781282
5.234305
2.758546
1.565311
3.569708
4.841600
5.271909
5.040288
2.695207
1.295280
2.509441
-3.618253
-5.384501
-4.379436
-6.739445
-5.893974
-5.658973
0.290570
-2.661933
-3.825870
-2.546804
-0.067797
1.111094
-1.631652
-0.339175
1.117376
-1.375995
0.166299
0.083177
-0.253501
-0.427485
-1.722941
2.686928
2.638329
1.383267
0.719398
-0.470301
-0.473448
0.861113
-0.514847
-2.018264
-3.334239
-3.121290
-1.596089
1.169271
1.119232
0.050772
2.657861
1.895253
3.655490
4.638424
3.556814
3.656602
0.434551
0.638269
1.378660
-0.499927
-1.510297
0.248826
Initiation and propagation reactions
Monomer
styrene
C -0.512904
C -0.011532
C 0.406705
C 1.360329
C 1.782621
C 2.264996
H -0.697477
H 0.036093
H 1.728099
H 2.474719
H 3.333639
C -1.960198
C -2.972950
H -4.001012
H -2.821638
H -2.194822
-0.221934
1.092311
-1.283137
1.331014
-1.046095
0.262997
1.933236
-2.304717
2.352559
-1.882463
0.453013
-0.533402
0.338278
-0.008102
1.413216
-1.596935
-0.000480
-0.000661
0.000008
-0.000206
0.000483
0.000395
-0.001309
0.000074
-0.000389
0.000897
0.000730
-0.000809
0.001060
0.000698
0.002968
-0.002408
Radicals
Cyano isopropyl radical
C -0.309097 -0.000010 0.000047
C 1.088056 -0.000033 -0.000002
N 2.250785 -0.000048 -0.000009
C -1.064762 -1.300679 -0.000049
H -0.394829 -2.162078 -0.003056
Appendix C: Optimized geometries for the reactions in the kinetic model
189
H
H
C
H
H
H
-1.713567 -1.362721 0.884124
-1.718255 -1.359916 -0.880889
-1.064640 1.300738 0.000026
-1.712991 1.363082 -0.884447
-1.718580 1.359796 0.880560
-0.394624 2.162068 0.003642
Styryl radical with initiator group attached
C -3.937168 -0.301797 0.355571
C -3.016222 -1.329194 0.107288
C -1.709144 -1.036910 -0.259210
C -1.267439 0.312920 -0.393114
C -2.226305 1.339379 -0.133551
C -3.528207 1.035106 0.231303
C 0.054557 0.674965 -0.761406
C 1.183416 -0.266438 -1.062900
C 2.267862 -0.360067 0.065925
C 2.821774 0.991440 0.296610
N 3.256786 2.041898 0.465730
C 3.416786 -1.285608 -0.398036
C 1.651396 -0.881930 1.383570
H -1.017981 -1.851944 -0.444212
H -1.915666 2.376211 -0.226926
H -3.326247 -2.365511 0.202303
H -4.234642 1.837069 0.422593
H -4.956681 -0.538418 0.641660
H 1.691682 0.060008 -1.979481
H 0.824814 -1.285042 -1.238790
H 0.286688 1.736994 -0.805343
H 4.194853 -1.350709 0.367701
H 3.019520 -2.289846 -0.577678
H 3.869170 -0.916381 -1.322818
H 2.410432 -0.935295 2.169150
H 0.838737 -0.234452 1.721905
H 1.249989 -1.887163 1.217531
Macroradical
C -4.148586
C -3.113999
C -3.505566
C -4.840979
C -5.837413
C -5.477481
C -1.762971
C -0.580821
C 0.761209
C 0.762813
C 1.699206
C 1.319843
N 1.015316
C 1.930264
C 2.223874
C 3.269203
C 4.040280
C 3.752796
C 2.705274
with two monomer units and an initiator group attached
0.616200 -0.734453
-0.263794 -0.295513
-1.399779 0.472373
-1.627800 0.779936
-0.744928 0.341280
0.378328 -0.419901
0.011155 -0.633187
-0.835561 -0.249662
-0.051759 -0.300486
1.055419 0.783492
2.276252 0.545364
2.908200 -0.737763
3.389506 -1.736580
-1.028442 -0.207283
-1.708669 0.983496
-2.632665 1.043045
-2.896727 -0.091736
-2.233179 -1.285782
-1.310168 -1.340215
Appendix C: Optimized geometries for the reactions in the kinetic model
190
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
3.196570
1.472715
-2.752924
-3.876327
-5.114111
-6.243742
-6.878323
-0.500385
-0.710176
-1.569820
0.810746
1.631883
2.489437
3.480417
4.342956
4.854190
-0.258080
1.028965
3.413424
3.813086
3.469339
2.085862
0.423224
1.755751
Macroradical
attached
C -5.053970
C -4.030849
C -2.720787
C -2.404323
C -3.439237
C -4.753548
C -0.973040
C -0.393542
C -0.068200
C 1.284557
C 2.515694
C 2.632713
C 3.863901
C 5.027541
C 4.940332
C 3.717027
H 1.748217
H 3.657851
H 3.923653
H 5.835817
H 5.985655
H -0.586511
H 0.009747
H 1.317846
H -0.992786
H -1.938682
H -3.214452
H -4.254148
H -5.539883
1.890641
3.309790
-2.102031
1.486601
-2.501483
1.065377
-0.929857
-1.698364
-1.257895
0.879212
0.433040
-1.522446
-0.796237
-3.147685
-2.431508
-3.613253
1.443468
0.628349
1.233124
2.789884
1.366669
4.200991
3.612842
2.859580
0.485012
1.676772
0.814850
-1.325136
1.364209
-0.765970
0.585587
-0.929486
0.756034
-1.261994
-1.283938
1.875447
-2.273612
1.975375
-2.175320
-0.045319
0.877247
1.757447
-0.358308
0.394899
1.406630
1.516492
1.728515
2.633684
with two monomer units, without an initiator group
0.536432
1.488937
1.113005
-0.219895
-1.163879
-0.792426
-0.640783
0.124176
-0.480693
-1.110501
-0.442720
0.974689
1.575583
0.803279
-0.593605
-1.204807
1.595649
-2.286651
2.656677
-1.200465
1.280726
-0.959814
0.583524
-2.198318
-1.708284
1.867199
-2.201259
2.525741
-1.541246
-0.397504
-0.397611
-0.097639
0.207489
0.201939
-0.096056
0.519082
1.725738
-0.747114
-0.587266
-0.357292
-0.243317
-0.016602
0.106635
-0.000619
-0.226397
-0.331272
-0.309079
0.066880
0.093715
0.283639
-1.587553
-0.991933
-0.626313
0.770591
-0.099681
0.435993
-0.630630
-0.091617
Appendix C: Optimized geometries for the reactions in the kinetic model
191
H -6.073238 0.828870 -0.629274
H 0.620049 -0.220569 1.951647
H -0.345828 1.199548 1.522433
H -1.018913 -0.022076 2.611668
Intermediates
Initiation C -3.937168
C -3.016222
C -1.709144
C -1.267439
C -2.226305
C -3.528207
C 0.054557
C 1.183416
C 2.267862
C 2.821774
N 3.256786
C 3.416786
C 1.651396
H -1.017981
H -1.915666
H -3.326247
H -4.234642
H -4.956681
H 1.691682
H 0.824814
H 0.286688
H 4.194853
H 3.019520
H 3.869170
H 2.410432
H 0.838737
H 1.249989
intermediate
-0.301797 0.355571
-1.329194 0.107288
-1.036910 -0.259210
0.312920 -0.393114
1.339379 -0.133551
1.035106 0.231303
0.674965 -0.761406
-0.266438 -1.062900
-0.360067 0.065925
0.991440 0.296610
2.041898 0.465730
-1.285608 -0.398036
-0.881930 1.383570
-1.851944 -0.444212
2.376211 -0.226926
-2.365511 0.202303
1.837069 0.422593
-0.538418 0.641660
0.060008 -1.979481
-1.285042 -1.238790
1.736994 -0.805343
-1.350709 0.367701
-2.289846 -0.577678
-0.916381 -1.322818
-0.935295 2.169150
-0.234452 1.721905
-1.887163 1.217531
Propagation 1 with an initiator group attached - intermediate
C -4.148586 0.616200 -0.734453
C -3.113999 -0.263794 -0.295513
C -3.505566 -1.399779 0.472373
C -4.840979 -1.627800 0.779936
C -5.837413 -0.744928 0.341280
C -5.477481 0.378328 -0.419901
C -1.762971 0.011155 -0.633187
C -0.580821 -0.835561 -0.249662
C 0.761209 -0.051759 -0.300486
C 0.762813 1.055419 0.783492
C 1.699206 2.276252 0.545364
C 1.319843 2.908200 -0.737763
N 1.015316 3.389506 -1.736580
C 1.930264 -1.028442 -0.207283
C 2.223874 -1.708669 0.983496
Appendix C: Optimized geometries for the reactions in the kinetic model
192
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
3.269203
4.040280
3.752796
2.705274
3.196570
1.472715
-2.752924
-3.876327
-5.114111
-6.243742
-6.878323
-0.500385
-0.710176
-1.569820
0.810746
1.631883
2.489437
3.480417
4.342956
4.854190
-0.258080
1.028965
3.413424
3.813086
3.469339
2.085862
0.423224
1.755751
-2.632665
-2.896727
-2.233179
-1.310168
1.890641
3.309790
-2.102031
1.486601
-2.501483
1.065377
-0.929857
-1.698364
-1.257895
0.879212
0.433040
-1.522446
-0.796237
-3.147685
-2.431508
-3.613253
1.443468
0.628349
1.233124
2.789884
1.366669
4.200991
3.612842
2.859580
1.043045
-0.091736
-1.285782
-1.340215
0.485012
1.676772
0.814850
-1.325136
1.364209
-0.765970
0.585587
-0.929486
0.756034
-1.261994
-1.283938
1.875447
-2.273612
1.975375
-2.175320
-0.045319
0.877247
1.757447
-0.358308
0.394899
1.406630
1.516492
1.728515
2.633684
Propagation 2 with an initiator group attached - intermediate
C -5.014916 1.273266 -1.045357
C -3.879236 0.411901 -1.137920
C -4.032909 -0.920921 -0.653413
C -5.241819 -1.352180 -0.124117
C -6.343818 -0.488117 -0.051326
C -6.216939 0.830128 -0.516026
C -2.672157 0.907690 -1.695929
C -1.395212 0.147484 -1.910525
C -0.321481 0.395533 -0.796977
C -0.759319 -0.241250 0.517499
C -1.343493 0.545306 1.518348
C -1.808017 -0.026873 2.705549
C -1.687767 -1.401907 2.913245
C -1.099904 -2.197195 1.925701
C -0.641849 -1.622842 0.737837
C 1.058805 -0.091498 -1.293952
C 2.215493 0.118659 -0.281594
C 3.543224 -0.496655 -0.814119
C 3.877383 -1.943786 -0.344548
C 2.763885 -2.864299 -0.658096
N 1.908431 -3.594193 -0.897247
C 2.386135 1.598109 0.052301
C 2.060031 2.087036 1.323200
C 2.204901 3.443726 1.629687
C 2.678810 4.334046 0.665271
C 3.006111 3.858712 -0.608113
Appendix C: Optimized geometries for the reactions in the kinetic model
193
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
2.859225
5.132901
4.135704
-3.191043
-4.923924
-5.330085
-7.064000
-7.284811
-0.957907
-1.574775
-2.661731
-0.259019
-1.444014
-0.188027
-2.266948
-0.997740
-2.048208
1.004175
1.300996
1.939308
3.542071
4.389361
1.681263
3.117496
1.946653
3.375618
2.792860
4.961511
5.971331
5.401707
4.391177
4.974090
3.260979
2.504038
-2.444543
-1.993801
-1.603625
2.294655
-2.370476
1.507466
-0.834336
0.468333
-0.930142
1.957972
1.478313
1.615755
-2.263148
0.600831
-3.267671
-1.850086
-1.151505
0.455043
-0.390888
-0.479464
0.118622
1.401078
2.148678
3.802234
4.543532
5.387398
-2.453435
-1.774974
-3.455652
-3.010405
-1.332259
-1.671077
-0.909842
-1.101633
1.181523
-0.678481
-1.405173
0.242275
-0.461465
0.363717
-2.865195
-1.989315
-1.982972
-0.635962
1.360213
-0.013986
3.463426
2.076618
3.833980
-1.564108
-2.214861
0.646968
-1.910922
-0.489036
2.076183
-1.904385
2.621576
-1.365520
0.901158
-2.181619
-0.884916
-0.783091
1.493530
1.421517
1.750530
Propagation - intermediate
C -4.448059 -1.938642 1.730341
C -3.839703 -0.778210 2.210646
C -3.290329 0.147612 1.318302
C -3.339858 -0.066040 -0.065092
C -3.953925 -1.237695 -0.534545
C -4.502764 -2.165513 0.351900
C -2.732519 0.948001 -1.030328
C -3.787461 1.497238 -2.014304
C -1.531875 0.353291 -1.806176
C -0.378700 -0.157009 -0.912979
C 0.203973 0.921496 -0.006667
C 0.440487 0.657719 1.347675
C 1.024060 1.618808 2.177791
C 1.376544 2.867664 1.664376
C 1.141135 3.146927 0.315223
C 0.562166 2.181514 -0.510044
C 0.744222 -0.797574 -1.796939
C 1.697775 -1.658280 -1.019482
C 2.988994 -1.299988 -0.552839
C 3.565766 -0.009599 -0.745034
C 4.838378 0.280856 -0.271783
Appendix C: Optimized geometries for the reactions in the kinetic model
194
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
5.590615
5.043898
3.773964
2.998419
3.357292
5.251726
5.617878
6.584562
0.250773
1.268907
1.346788
-0.780708
0.169753
0.390606
1.205424
1.409574
1.829941
-1.155017
-1.886335
-2.361373
-3.349588
-4.172308
-4.634602
-2.812693
-4.006960
-3.791447
-4.975148
-4.876161
-0.687564
-1.963747
-2.265481
0.763101
-3.255926
1.272839
-2.719732
-0.451595
-1.422343
-0.000622
-2.657706
-0.948504
-0.313347
2.413577
1.389243
4.116263
3.616055
1.110995
-0.483786
1.786322
2.271925
0.703485
1.932063
1.046137
-1.428489
-0.590975
-3.064737
-2.658964
0.408211
0.614794
0.148730
-1.251306
0.310843
-0.427168
1.142274
0.774160
-2.552910
-2.335208
-0.767676
-0.269796
1.753094
-1.557846
3.223397
-0.094311
2.306709
-2.505280
-2.421677
-0.430085
-2.652816
-2.663707
-1.475343
1.699745
-1.603139
3.279206
-0.032232
2.420395
Transition states
Initiation-TS
C 1.284330 0.332184
C 1.723716 -1.007640
C 2.142720 1.335763
C 2.960202 -1.324826
C 3.380856 1.016584
C 3.795311 -0.315720
H 1.100209 -1.803876
H 1.824156 2.373299
H 3.280590 -2.361392
H 4.022400 1.806906
H 4.759642 -0.567237
C -0.007246 0.721786
C -1.032695 -0.116194
H -1.878036 0.278887
H -0.891046 -1.191859
H -0.180283 1.793231
C -2.394034 -0.400190
C -3.361071 -1.424679
H -4.103072 -1.703995
H -2.823821 -2.333766
H -3.902068 -1.040300
C -1.425655 -0.845714
0.563043
0.491729
0.068285
-0.062056
-0.486455
-0.556942
0.885403
0.119540
-0.103746
-0.863665
-0.986659
1.129956
1.473503
2.026506
1.519134
1.210809
-0.346623
0.208678
-0.552893
0.497084
1.077503
-1.418970
Appendix C: Optimized geometries for the reactions in the kinetic model
195
H
H
H
C
N
-1.959039 -1.045175 -2.359422
-0.665070 -0.085267 -1.611678
-0.925195 -1.770302 -1.114214
-2.883981 0.934857 -0.449947
-3.250584 2.030511 -0.489844
Propagation 1 with an initiator group attached – TS
C 3.915763 -0.470874 1.114128
C 2.687284 -1.020162 0.688589
C 2.593549 -1.463506 -0.649719
C 3.678661 -1.360035 -1.514912
C 4.889487 -0.812021 -1.074200
C 5.001294 -0.368677 0.246445
C 1.579912 -1.111772 1.638466
C 0.314636 -1.568909 1.367878
C -1.005126 0.133845 0.689122
C -0.117221 0.945102 -0.220288
C -0.607637 2.409818 -0.487701
C -0.727699 3.104670 0.812527
N -0.815835 3.639450 1.826376
C -2.150059 -0.631845 0.224054
C -2.274681 -1.106352 -1.103728
C -3.366686 -1.879087 -1.489999
C -4.366362 -2.209597 -0.568144
C -4.258026 -1.757181 0.752074
C -3.168510 -0.985237 1.142595
C -1.978813 2.450993 -1.200933
C 0.455631 3.148012 -1.336597
H 1.666656 -1.896851 -1.011758
H 4.009854 -0.124310 2.139779
H 3.584634 -1.710798 -2.538308
H 5.935345 0.057047 0.600082
H 5.733540 -0.734443 -1.751943
H -0.371790 -1.752051 2.187146
H 0.097372 -2.109832 0.452836
H 1.784532 -0.722602 2.634198
H -1.105135 0.543108 1.692694
H -1.511814 -0.868037 -1.837775
H -3.096083 -0.631865 2.167883
H -3.440518 -2.227451 -2.515860
H -5.028309 -2.005289 1.475970
H -5.216294 -2.810913 -0.873872
H 0.880594 1.014328 0.225711
H 0.007356 0.467213 -1.197953
H -2.757703 1.974441 -0.602183
H -2.272443 3.485954 -1.399219
H -1.902903 1.920439 -2.155654
H 0.158148 4.185675 -1.512388
H 1.428835 3.142405 -0.838364
H 0.554586 2.644575 -2.303585
Propagation 2 with an initiator group attached – TS
C 4.340028 -0.875029 -2.049304
C 3.690112 0.202212 -1.407906
C 4.261307 0.687708 -0.209960
C 5.421174 0.124608 0.311129
Appendix C: Optimized geometries for the reactions in the kinetic model
196
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
N
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
6.050876
5.501927
2.483019
1.726059
0.203348
-0.470249
0.054341
-0.540150
-1.681501
-2.214784
-1.623606
-0.479186
-1.508041
-2.219838
-3.633552
-3.593197
-3.572903
-0.853655
-1.174595
-0.577782
0.356044
0.689131
0.090277
-4.088212
-4.665131
3.789429
3.919408
5.839088
5.981109
6.957290
0.936988
2.115513
2.125492
0.978822
0.936676
-2.058537
-0.117362
-3.099928
-2.147897
-0.996710
0.285860
-2.257590
-1.577201
-2.352812
-1.896785
0.364153
-0.844009
1.418725
0.822191
-3.395943
-4.121229
-5.086610
-5.657912
-4.725165
-4.389714
-0.939785
-1.435765
0.757907
1.797162
1.025524
2.244523
3.019882
4.213943
4.681215
3.934919
2.738539
-0.080683
-0.891783
-1.966394
-1.610375
-0.336319
0.663576
-1.511912
-1.059676
-1.620402
-2.647495
-3.106664
-2.543400
-2.721166
-1.478570
1.512940
-1.266656
0.516943
-2.262488
-1.376202
2.212893
2.471254
0.244426
0.691201
2.659537
2.185460
4.783255
4.288745
5.614558
0.311215
-0.774522
-0.177900
-2.229774
-2.886005
-0.254789
-2.910601
-1.252583
-3.903510
-3.085871
-2.815295
-3.679838
-2.512023
-1.243207
-2.428456
-0.694062
-0.342594
-1.527910
-1.997691
-1.511034
-0.005259
0.388932
1.453534
1.842387
1.180759
0.125143
-0.270132
-0.765112
0.084768
-0.790431
-1.340365
-2.086333
-2.677826
1.312893
2.599028
3.730308
3.593297
2.317054
1.190362
-2.317983
-0.194810
0.315398
-2.973062
1.234893
-2.046305
0.067922
-2.129338
-0.754810
-2.889739
0.680629
1.978452
-1.097031
2.666546
-0.397408
1.484054
-1.647982
-1.134904
0.445867
-1.640334
-0.208948
2.715504
0.203790
4.717979
2.197658
4.471654
-3.160466
-1.788730
-2.714890
-0.591028
0.347663
0.515114
Appendix C: Optimized geometries for the reactions in the kinetic model
197
Propagation - TS
C -2.985769 1.413406
C -2.961728 1.379498
C -4.146102 0.941718
C -4.051982 0.902353
C -5.237274 0.466633
C -5.196893 0.444149
H -2.083450 1.727588
H -4.184367 0.957186
H -4.010325 0.884449
H -6.119854 0.112954
H -6.044563 0.072995
C -1.865774 1.904716
C -0.686953 2.407110
H 0.032983 2.837977
H -0.587335 2.720103
H -1.973905 1.786325
C 0.701605 0.669373
H 0.066461 0.303190
C 1.892074 1.378443
C 2.021781 1.785517
C 2.931435 1.737316
C 3.128297 2.506352
C 4.038196 2.458815
C 4.146330 2.849020
H 1.240654 1.514584
H 2.869776 1.447443
H 3.203919 2.800429
H 4.823078 2.719124
H 5.010872 3.410476
C 0.650595 -0.134023
H 0.981246 0.468648
H -0.391014 -0.411855
C 1.516878 -1.427885
H 2.552942 -1.126236
C 1.470701 -2.149351
H 1.839030 -1.492925
H 0.447039 -2.444770
H 2.088011 -3.052654
C 1.092281 -2.346438
C 1.962352 -2.609605
C -0.178253 -2.941763
C 1.580465 -3.449001
C -0.565006 -3.778765
C 0.315065 -4.037294
H 2.947089 -2.149849
H -0.875745 -2.749187
H 2.271604 -3.640406
H -1.553502 -4.228044
H 0.015426 -4.689316
0.434920
-0.976207
1.084316
-1.698704
0.359939
-1.037137
-1.510198
2.170374
-2.783599
0.884240
-1.604173
1.236902
0.754157
1.442220
-0.279628
2.313457
0.298914
-0.505219
-0.127120
-1.478336
0.765831
-1.913321
0.325088
-1.014334
-2.184056
1.809913
-2.955883
1.029049
-1.353300
1.574359
2.429633
1.773189
1.525227
1.332408
2.888459
3.684238
3.142225
2.871768
0.384077
-0.681137
0.368215
-1.732075
-0.679133
-1.734102
-0.689014
1.178786
-2.547454
-0.673151
-2.548618
Appendix C: Optimized geometries for the reactions in the kinetic model
198