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ELECTRONIC SUPPORTING INFORMATION FOR:
DFT characterization of the reaction pathways for terminal- to μ-hydride isomerization in
synthetic models of the [FeFe]-hydrogenase active site.
Giuseppe Zampella, Piercarlo Fantucci and Luca De Gioia
General notes
Even if experimental results suggest that isomerization at the protonated iron atom can be in some
cases be accompanied by isomerisation of the other iron centre, the overall computed energy profile
for the hydride-bond iron atom isomerisation, which is the focus of this work, is only slightly
changed, not affecting the general conclusions (data not shown).
Computational methods
Density functional theory (DFT) calculations have been carried out with the TURBOMOLE 5.7
suite.1 Geometry optimizations and transition state searches have been carried out using the pure
functional B-P86,2,3 in conjunction with a valence triple-ζ basis set with polarization on all atoms,
a level of theory which has been shown to be suited to reliably investigate [FeFe] hydrogenase
models.4-6
Stationary points of the energy hypersurface have been located by means of energy gradient
techniques and a full vibrational analysis has been carried out to further characterize each
stationary point.
The optimization of transition state structures has been carried out according to a procedure based
on a pseudo Newton-Raphson method. Initially, geometry optimization of a guessed transition
state structure is carried out constraining the distance corresponding to the reaction coordinate.
Vibrational analysis at BP86/TZVP level of the constrained minimum energy structures is then
carried out and, if one negative eigenmode corresponding to the reaction coordinate is found, the
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curvature determined at such point is used as starting point in the transition state search. The
location of the transition state structure is carried out using an eigenvector-following search: the
eigenvectors in the hessian are sorted in ascending order, the first one being that associated to the
negative eigenvalue. After the first step, however, the search is performed by choosing the critical
eigenvector with a maximum overlap criterion, which is based on the dot product with the
eigenvector followed at the previous step.
Gibbs free energy (G) values have been obtained from the electronic SCF energy considering three
contributions to the total partition function (Q), namely qtranslational, qrotational, qvibrational, under the
assumption that Q may be written as the product of such terms. In order to evaluate enthalpy and
entropy contributions, the values o temperature and pressure have been set to 273.15 K and 1 bar,
respectively, to reproduce as closely as possible experimental conditions. Rotations have been
treated classically and vibrational modes described according to the harmonic approximation.
All Gibbs free energy differences have been computed by correcting gas phase data with the
inclusion of an implicit treatment of solvent effect (COSMO).7 The ε value has been set to 37.5
(corresponding to acetonitrile).
In light of available experimental data and considering the chemical nature of the ligands, only
low-spin species have been investigated.
1.
Ahlrichs, R.; Bar, M.; Haser, M.; Horn, H.; Kolmel, C., Chemical Physics Letters 1989, 162, 165-169.
2.
Becke, A. D., Phys Rev A 1988, 38, 3098-3100.
3.
Perdew, J. P., Phys Rev B Condens Matter 1986, 33, 8822-8824.
4.
Bertini, L.; Bruschi, M.; de Gioia, L.; Fantucci, P.; Greco, C.; Zampella, G., Atomistic Approaches in Modern Biology: From
Quantum Chemistry to Molecular Simulations 2007, 268, 1-46.
5.
Bruschi, M.; Zampella, G.; Fantucci, P.; De Gioia, L., Coordination Chemistry Reviews 2005, 249, 1620-1640.
6.
Bruschi, M.; Greco, C.; Zampella, G.; Ryde, U.; Pickett, C. J.; De Gioia, L., Comptes Rendus Chimie 2008, 11, 834-841.
7.
Schafer, A.; Klamt, A.; Sattel, D.; Lohrenz, J. C. W.; Eckert, F., Physical Chemistry Chemical Physics 2000, 2, 2187-2193.
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This journal is (c) The Royal Society of Chemistry 2010
Scheme 1S. Other reaction pathways tested by DFT calculations. Structures are schematically
shown only for complex 3 for the sake of clarity. Energies in kcal/mol.
1 Terminal-H moves through the gap left
by the S-Fe bond cleavage
E Barrier=37.5
2
Terminal-H moves between S and P ligands
toward a FeFe bridging coordination. The μCO ligand tends to coordinate to a single Fe
E Barrier=43.4
3
4
Push-Through and Cross-Over Twist,
i.e.the other two mechanisms which the
Group Theory predicts for intramolecular
rearrangement of octahedral complexes:
E> 50 kcal/mol
P-Fe bond breaks; Berry Pseudo Rotation of the
pentacoordinated coordination geometry: E >
50 kcal/mol
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Figure 1S. Schematic representation of transition states for terminal-hydride isomerization in
complex 1, according to Ray-Dutt (top) and Bailar (bottom) twist reaction pathways.
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Scheme
2S.
Intermediate
species
formed
along
the
isomerization
[(dppv)(CO)Fe(edt)Fe(CO)2(PMe3)H]+, (2).
S
S
P
S
S
P
CO
Fe
P
H
Fe
CO
P
Fe
CO
P
O
H
Fe
2
CO
P
CO
Fe
P
Fe
CO
H
O
Fe
P
P
CO
P
S
S
P
2a
Fe
Fe
O
CO
H
Fe
CO
P
Fe
P
CO
P
Fe
P
2b
CO
CO
O
S
S
P
P
S
S
Fe
P
CO
Fe
S
S
P
P
CO
Fe
P
CO
OC H
H
P
P
CO
CO
S
S
S
S
P
Fe
P
CO
Fe
CO
Fe
H
2e
P
CO
H
P
CO
P
CO
CO
S
S
P
Fe
H
P
Fe
CO
P
S
S
CO
Fe
2f
P
Fe
H
S
S
P
CO
P
CO
P
CO
CO
Fe
Fe
H
2d
P
CO
Fe
OC
CO
H
O
S
S
P
P
Fe
P
S
S
P
H
P
Fe
2c
CO
Fe
OC
OC
P
Fe
OC
H
OC
P
Fe
CO
P
Fe
CO
P
H
P
Fe
P
H
Fe
OC
S
S
P
S
S
P
S
S
CO
O
P
OC CO
H
P
Fe
CO
P
Fe
CO
S
S
P
S
S
Fe
P
P
O
H
S
S
P
CO
CO
Fe
CO
Fe OC
H
P
S
S
P
P
CO
Fe
P
Fe
H
OC
CO
of
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Scheme 3S. Reaction energy profile for isomerization of [(dppv)(CO)Fe(edt)Fe(CO)2(PMe3)H]+,
(2).
6.2
-23.9
G°
23.1
-35.2
-37.4
27.8
-12.6
-17.6
11.2
-17.5
18.9
22.8
23.4
-25.2
13.2
-18.2
2a
16.4
13.3
-35.5
-12.5
2c
2b
2
-19.3
16.0
15.6
-21.1
-23.8
16.0
2d
2f
2e
Reaction Coordinate
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Scheme
4S.
Intermediate
species
formed
along
the
isomerization
of
[(PMe3)2(CO)Fe(edt)Fe(CO)(PMe3)2H], (3).
S
S
P
Fe
OC
P
Fe
S
S
P
OC
P
Fe
P
3
Fe
H
P
P
OC
P
P
O
P
S
S
Fe
H
Fe
P
O
P
Fe
O
Fe
OC
P
O
S
S
P
H
P
P
S
S
H
Fe
P
P
CO
3b
P
P
Fe
OC H
S
S
P
OC
P
Fe
Fe
P
H
O
P
3a
S
S
P
OC
P
Fe
P
H Fe
P
OC
S
S
P
OC
P
Fe
OC
H
P
Fe
S
S
P
P
Fe
OC
OC
P
Fe
OC
S
S
Fe
OC
P
P
Fe
H
3d
P
CO
OC
P
3c
S
S
P
Fe
Fe
H
P
Fe
CO
H
P
P
H
S
S
P
P
P
Fe
P
P
OC
P
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Scheme
5S.
Reaction
energy
profile
for
the
isomerization
[(PMe3)2(CO)Fe(edt)Fe(CO)(PMe3)2H], (3).
G°
28.7
-44.1
-34.5
-2.3
19.8
0.7
3b
-12.1
18.4
-24.8
9.0
3a
10.7
-14.0
-19.2
3c
3
3d
Reaction coordinate
of