Supporting Information
The role of solvent and dendritic architecture on the redox
core encapsulation
Rakhee C. Pani, Yaroslava G. Yingling*
911 Partners Way, Department of Materials Science and Engineering, North Carolina State
University, Raleigh, NC 27695, USA
S1
Figure S1. Dendrimer shape tensor. The aspect ratio of dendrimers in explicit water
(left) and chloroform (right). Dendrimers with hydrophilic carboxyl peripheral groups
(top); alternating –COOH and alkyl [(CH2)9CH3] peripheral groups (middle); long chain
alkyl peripheral [(CH2)9CH3] groups (bottom) respectively.
The shape of the dendrimers and their folding can be accessed from their aspect ratio
obtained from time evolution of their principal moments of inertia (Iz>Iy>Ix). The
presence of symmetry and globular shape is evident from an aspect ratio ~1. A high
aspect ratio indicates a deviation from the globular shape of the dendrimers towards a
more elliptical configuration.
S2
Figure S2. Position of the redox iron-sulfur core
The translocation of the redox core was calculated as the distance between the center
of mass of redox core and dendrimer (as seen from the 3D schematic representation) in
(a) water and (b) chloroform.
S3
Figure S3. Radial density of the peripheral branch point and radial density of the
solvent molecules. The density profile of the peripheral branch point (left); of the solvent
molecules (right);
(a)-(b) -COOH peripheral groups: The density shows a minimum at a distance of 1nm
with an initial rise at 0.75 nm and again at 1.5 nm away from the core. The initial rise in
chloroform indicates the presence of monomer groups near the core. The other peak
indicates the accumulation of branch point at a distance close to the core whereas the
branch points lie at a distance of 1.75nm from the core in chloroform.
(c)- (d) carboxyl and alkyl -[(CH2)9CH3] peripheral groups: The radial density peaks at
distance of 1.75 nm from the core ;
(e ),(f) ;-[(CH2)9CH3] : Radial density of the peripheral group peaks at a distance 1.2 nm
from the core in explicit water and at 1.75 nm from core in explicit chloroform.
In each plot we have represented the distribution of solvent molecules for each branch
points. We do not find a discriminating change in the density of solvents at branch
points for different peripheral groups.
S4
Figure S4. Convergence with time of the van der Waals energy for dendrimer
configurations in water and chloroform.
S5
Figure S5. The radial density of the surface monomers densities of the peripheral
groups with respect to the redox core changes in presence of water and chloroform.
The carboxyl groups mostly lie at the periphery in D1 and D2. Formation of dense core
is mainly due to the back folding of alkyl groups, as suggested by the rise in radial
density. However, with chloroform the density of the monomer groups decreased. In
D1 the hydrophilic –COOH groups were concentrated close to the core in chloroform. In
chloroform D2 and D3 are observed as hollow dendrimers with atomic densities lying at
periphery.
S6
Figure S6. Number of solvent contacts with the redox core Fe4S4 as a function of time
and solvent accessible surface area of the dendrimers as a function of hydrodynamic
radius (Rg) (a),(c) Water (b),(d) Chloroform.
S7
Figure S7. Number of solvent contacts at all branch points, Dendrimer with –COOH
terminal groups, with –COOH and -[(CH2)9CH3] terminal and all alkyl -[(CH2)9CH3]
terminal groups respectively in (a) water and (b)chloroform. In the legend the order of
branch points were counted away from the core.
These results were in supplement to the time correlation of the solvent contacts with the
core and dendrimer surface. The distribution of the solvent molecules at the branch
points in explicit water indicates the decrease in the solvent contacts at every branch as
the dendrimer folds. The number of water molecules at the first branch point declines
with incorporation of the hydrophobic alkyl groups as we move towards dendrimer with [(CH2)9CH3] surface groups. In explicit chloroform the solvent contacts at the branch
points indicate a slight decline with some degree of fluctuation. This was also evidenced
by the relaxation time of the solvent contacts and indicates confinement of solvent
molecules.
S8
Table S1. Partial Charges 1 of Reduced Iron Sulfur core (with charge of -2)
Partial
Atoms
charges
Fe red
+0.635x2
Feoxd
+0.642x2
Soxd
-0.584x2
Sred
-0.580x2
S
-0.571x2
S
-0.574x2
CH3
+0.016x4
S9
Table S2. Force field parameters for Iron sulfur cluster
MASS
Fe
S
s6
Ss
55.845
32.066
32.066
32.066
BOND
c-s
fe-s6
fe-s
ss-fe
c-s
s-c
227.0
70.0
101.0
101.0
227
227
1.810
2.31
2.27
2.27
1.81
1.81
DIHEDRAL
ca-c-s6-fe
fe-s-c-ca
fe-s6-fe-s6
s-fe-s6-fe
ca-ca-s-fe
ca-s-fe-s6
ss-fe-s6-fe
ca-ca-ss-fe
ca-ss-fe-s6
1
1
1
1
1
1
1
1
1
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
NON
BONDED
s6
s
ss
fe
2.0
2.0
2.0
1.10
0.25
0.25
0.25
0.0125
ANGLE
fe-s-c
s-c-ca
ca-c-s
fe-fe-fe
fe-fe-s6
s6-fe-s
ss-fe-s6
s-fe-s
fe-s-c
ha-c-s
s6-fe-s6
fe-s6-fe
ca-c-fe
ca-ss-fe
18.0
50.0
50.0
18.0
18.0
18.0
18.0
18.0
18.0
50.0
18.0
12.2
18.0
18.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
109.5
109.5
114.7
59.9
52.3
114.1
114.1
104.6
109.5
109.5
104.6
73.0
109.5
109.5
S10
Table S3. Dendrimer Models in different solvent conditions, Radius of gyration at 10 ns
of simulation
Dendrimer
Model 1
Dendrimer
Model 2
Dendrimer
Model 3
Abbreviations
Number of
Water
Molecules
Radius of
gyration,
Rg,nm
Number
of ChCl3
Molecule
s
Radius of
gyration,
Rg
D1-Wat/D1-ChCl3
9089
1.096
1898
1.491
D2-Wat/D2-ChCl3
14808
1.376
3119
1.824
D3-Wat/D3-ChCl3
19066
1.226
7645
2.053
S11
Table S4. Average values of the Principal Moments of inertia (averaged over last 500
snapshots)Iz>Iy>Ix, Aspect ratios of the three Dendrimer Models at different solvent
conditions, Asphericity parameter (δ) as a measure of relative shape anisotropy
Iz
D1-Water
D2-Water
D3-Water
D1-ChCl3
D2-Chcl3
D3-ChCl3
364211423
1353305037
1810187040
9371681173
1336642191
5272140551
Iy
303909569
1265328569
1627868953
696309384
1827320942
4400651127
Ix
247216308
438845806
976978821
512678013
2183558933
2904116276
Iz/Iy
1.19
1.06
1.11
1.34
1.19
1.19
Iz/Ix
1.47
3.08
1.85
1.82
1.63
1.81
Asphericity
parameter
(δ)
0.0129
0.0393
0.0291
0.0308
0.0197
0.0283
S12
Table S5. Free energy change and Entropy change of dendrimers during 10 ns of our
MD simulation in different solvent conditions.
ΔG
ΔS
ΔH
ΔG
ΔS
D1 in
Water
-139.46
540.81±3.75 162103.5
D2 in
Water
-195.94
739.94±30
D3 in
Water
-306.22
875 ± 29.8
ΔH
D1 in
ChCl3
-27.92
576.92±5.12 173048.1
221786.1
D2 in
ChCl3
-25.97
728.43±5.45 218503
262193.8
D3 in
ChCl3
-33.11
890 ± 5.66
266967
With presence of hydrophobic alkyl groups at the periphery the change in free energy of
the dendrimer in water increases which indicates a higher driving force to attain the
stable state. In chloroform the driving force decreases due to the presence of good
solvent conditions and with lipophilic groups the change in free energy or the driving
force is less.
References
Torres, R. A.; Lovell, T.; Noodleman, L.; David, A. Journal of the American Chemical
Society 2003, 125, 1923-1936.
S13