Supplemental Material
Diffusional Motion of Redox Centers in Carbonate Electrolytes
Kee Sung Han1, Nav Nidhi Rajput2, Xiaoliang Wei3, Wei Wang3, Jian Zhi Hu4, Kristin A.
Persson2 and Karl T. Mueller*1,5
1
2
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory,
Richland, WA 99352, USA
Environmental Energy Technologies Division, Lawrence Berkeley National Laboratory,
Berkeley, CA 94720, USA
3
Energy & Environmental Directorate, Pacific Northwest National Laboratory, Richland,
WA 99352, USA
4
5
Fundamental and Computational Sciences Directorate, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
Department of Chemistry, Pennsylvania State University, University Park, PA 16802,
USA
*Corresponding author:
Dr. Karl T. Mueller
Tel: 509-371-6550
e-mail: [email protected]
EC
O
O
1
O
O
3
2
1
3
H3C
Fc1N112+
EMC
PC
O
O
1
H C
O
3
4
O
2
3
O
CH3
4
1
EC(1,3)
1`
R
EMC(1)
R``
R` EMC(3)
EMC(4)
2``
1``
PC(4)
PC(2)
5.5
5.0
PC(4)
4.5
4.0
PC(1)
3.5
3.0
2.5
2.0
1.5
1.0
0.5
1
H Chemical Shift (ppm from TMS)
Figure 1S 1H NMR spectrum of 0.85 M Fc1N112-TFSI dissolved in EC/PC/EMC (4:1:5). The
numerals on the chemical structures indicate the molecular 1H positions corresponding to the
indicated resonances.
PC
EMC
EC/PC/EMC
PC
EC
EMC
Covection compenstion
PC
EMC
EC/PC/EMC
PC
EC
EMC
D (m2/s)
10-7
10-8
10-9
10-10
3.0
3.2
3.4
3.6
1000/T (K-1)
Figure 2S Diffusion coefficients of electrolytes only (PC, EMC and the mixture of
EC/PC/EMC) as a function of inverse temperature. Without gradients for convection
compensation, bipolar pulsed gradient stimulated echo experiments showed larger
apparent D values over most of the temperature range. At ambient temperature, 283 K
(3.533 × 1000/T K-1), the apparent diffusion coefficients are the same regardless of
applying convection compensation gradients.
Dapp (m2/s)
10-9
20 °C
0 °C
-30 °C
-40 °C
10-10
0
50
100
150
200
250
300
Diffusion time,  (ms)
Figure 3S Apparent diffusion coefficients of EC/PC/EMC as a function of diffusion time,
Δ, show typical restricted diffusion due to the coexistence of liquid and solid phases at
lower temperature. At 20 °C the apparent diffusion coefficient does not vary with
diffusion time because self-diffusion in the liquid state is occurring.
1.0
PC
EMC
EC/PC/EMC
0.9
0.8
DFc1N112/DTFSI
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
0.25 M
0.85 M
Saturated
Fc1N112-TFSI concentrations (molar ratio)
Figure 4S The diffusion coefficient ratio (DFc1N112/DTFSI) as a function of Fc1N112-TFSI
concentration when Fc1N112-TFSI is dissolved in PC, in EMC, and in EC/PC/EMC.
4
N(Fc1N112)-O(PC)
N(Fc1N112)-O(EMC)
3
N(Fc1N112)-O(EC)
g (r)
N(TFSI)-O(PC)
N(TFSI)-O(EMC)
2
N(TFSI)-O(EC)
1
0
0
2
4
6
8
10
12
14
r (Å)
Figure 5S Radial distribution function (RDF) of 0.25 M Fc1N112-TFSI in EC/PC/EMC at 323 K
for the nitrogen (N) atom of Fc1N112+ and the nitrogen (N) atom of TFSI- (See Scheme 1) with
carbonyl oxygens of PC (blue), EMC (red) and EC (green).
(a)
(b)
10-9
1.7 M Fc1N112-TFSI dissolved in EC/PC/EMC
EC expt
EC sim
PC expt
PC sim
EMC expt
EMC sim
Fc1N112+ expt
Fc1N112+ sim
TFSI- expt
TFSI- sim
0.25 M Fc1N112-TFSI dissolved in EC/PC/EMC
EC expt
EC sim
PC expt
PC sim
EMC expt
EMC sim
+
Fc1N112 expt
Fc1N112+ sim
TFSI- expt
TFSI- sim
D (m2/s)
D (m2/s)
10-9
10-10
10-10
3.1
3.2
3.3
3.4
3.5
3.6
3.7
10-11
3.1
3.2
1000/T (K-1)
3.3
3.4
3.5
3.6
3.7
1000/T (K-1)
Figure 6S The diffusion coefficients of Fc1N112+, TFSI-, EC, PC and EMC in (a) 0.25
and (b) 1.7 M Fc1N112-TFSI dissolved in EC/PC/EMC as a function of temperature
comparing MD simulations and PFG-NMR measurements.
* Force field parameters and geometry
Representative Gromacs input files, topology files and coordinate files
are available upon request.
ethylene carbonate geometry
atom_number name
1
2
3
4
5
6
7
8
9
10
C2E
H2E
H2E
OSE
CE
OE
OSE
C1E
H1E
H1E
x
y
2.098
1.558
2.048
1.668
2.758
2.738
3.888
3.518
3.498
4.128
2.149
1.369
2.079
3.429
4.229
5.449
3.489
2.169
2.139
1.399
z (coordinates in nm)
2.514
3.054
1.424
2.994
2.814
2.854
2.594
3.014
4.104
2.534
Lennard-Jones parameters [atomtypes ]
name
OE
CE
OSE
C1E
C2E
H2E
H1E
mass
15.99940
12.01100
15.99940
12.01100
12.01100
1.00800
1.00800
sigma(nm)
2.96000e-01
3.75000e-01
3.00000e-01
3.50000e-01
3.50000e-01
2.42000e-01
2.42000e-01
epsilon(KJ/mol)
8.7864000e-01
4.393200e-01
7.11280e-01
2.7614400e-01
2.7614400e-01
6.276100e-02
6.276100e-02
atoms charges
atom
atom number
OE
CE
OSE
C1E
C2E
H2E
H1E
charge
1
2
3
4
5
6
7
-0.558
0.927
-0.46
0.236
0.236
0.020
0.020
bond parameters
; atom(i)
CE
CE
C1E
C2E
C1E
C1E
C2E
atom(j)
OE
OSE
OSE
OSE
C2E
H1E
H2E
b0
0.1229
0.13270
0.1410
0.1410
0.1526
0.1090
0.1090
kb
238488.0
89537.6
133888
133888
129704
138490.4
138490.4
mass
15.99940
12.01100
15.99940
12.01100
12.01100
1.00800
1.00800
angle parameters
atom(i)
H2E
H2E
H2E
OSE
C2E
OSE
OSE
OE
CE
C2E
C2E
OSE
H1E
atom(j)
atom(k)
C2E
C2E
C2E
C2E
OSE
CE
CE
CE
OSE
C1E
C1E
C1E
C1E
th0
H2E
OSE
C1E
C1E
CE
OE
OSE
OSE
C1E
OSE
H1E
H1E
H1E
cth
109.0
109.5
109.0
109.5
116.9
123.4
111.5
123.4
116.9
109.5
109.0
109.5
109.0
146.440
146.440
146.440
209.200
347.270
347.270
387.438
347.270
347.270
209.200
146.440
146.440
146.440
dihedral parameters
atom(i)
C1E
OSE
OSE
CE
atom(j)
C2E
C2E
CE
OSE
atom(k)
atom(l)
phi0
OSE
C1E
OSE
C1E
CE
OSE
C1E
C2E
000.00
000.00
000.00
000.00
cp
4.8116
0.60249
4.8116
4.8116
n
3
3
3
3
***********************************************************************
******************
ethyl methyl carbonate geometry
atom_number name
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
C1M
O1M
O2M
O3M
C2M
C3M
C4M
H1M
H2M
H3M
H4M
H5M
H6M
H7M
H8M
x
y
z (coordinates in nm)
6.593
5.803
6.003
7.773
4.523
4.853
4.413
4.453
3.723
4.993
4.803
3.933
5.203
3.433
4.503
5.286
5.156
5.686
5.076
4.476
6.556
3.496
3.956
5.226
7.246
7.116
5.976
2.736
2.996
4.016
4.540
5.630
3.390
4.590
5.530
3.410
6.680
4.560
5.580
2.570
4.350
3.260
6.620
6.650
7.640
Lennard-Jones parameters [atomtypes ]
name
C1M
O1M
O2M
O3M
mass
12.01
16.00
16.00
16.00
sigma(nm)
3.75000e-01
3.00000e-01
3.00000e-01
2.96000e-01
epsilon(KJ/mol)
4.393200e-01
7.11280e-01
7.11280e-01
8.7864000e-01
C2M
C3M
C4M
H1M
H2M
H3M
H4M
H5M
H6M
H7M
H8M
12.01
12.01
12.01
1.008
1.008
1.008
1.008
1.008
1.008
1.008
1.008
3.50000e-01
3.50000e-01
3.50000e-01
2.42000e-01
2.42000e-01
2.42000e-01
2.42000e-01
2.42000e-01
2.42000e-01
2.42000e-01
2.42000e-01
2.7614400e-01
2.7614400e-01
2.7614400e-01
6.276100e-02
6.276100e-02
6.276100e-02
6.276100e-02
6.276100e-02
6.276100e-02
6.276100e-02
6.276100e-02
atoms charges
atom
C1M
O1M
O2M
O3M
C2M
C3M
C4M
H1M
H2M
H3M
H4M
H5M
H6M
H7M
H8M
atom number
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
charge
0.878000
-0.449000
-0.420000
-0.556000
0.408000
0.186000
-0.373000
-0.029000
-0.029000
0.023000
0.023000
0.023000
0.105000
0.105000
0.105000
mass
12.01
16.00
16.00
16.00
12.01
12.01
12.01
1.008
1.008
1.008
1.008
1.008
1.008
1.008
1.008
bond parameters
; atom(i)
C1M
C1M
C1M
C3M
C2M
C2M
C2M
C2M
C3M
C3M
C3M
C4M
C4M
C4M
atom(j)
O1M
O2M
O3M
O2M
O1M
C4M
H1M
H2M
H3M
H4M
H5M
H6M
H7M
H8M
b0
0.1343
0.1343
0.1214
0.1439
0.1439
0.1535
0.1093
0.1093
0.1093
0.1093
0.1093
0.1092
0.1092
0.1092
kb
171972.6649
171972.6649
270941.6565
126063.4896
126063.4896
126732.3562
140446.1987
140446.1987
140446.1987
140446.1987
140446.1987
141031.9762
141031.9762
141031.9762
angle parameters
atom(i)
C1M
C1M
O2M
O3M
O3M
C4M
atom(j)
O2M
O1M
C1M
C1M
C1M
C2M
atom(k)
C3M
C2M
O1M
O1M
O2M
O1M
th0
115.14
115.14
111.38
123.33
123.33
108.42
cth
266.0510368
266.0510368
319.6517626
317.4748303
317.4748303
283.4000239
H1M
H2M
H3M
H4M
H5M
C2M
C2M
C2M
C4M
C4M
H1M
H3M
H3M
H4M
H6M
H6M
H7M
C2M
C2M
C3M
C3M
C3M
C4M
C4M
C4M
C2M
C2M
C2M
C3M
C3M
C3M
C4M
C4M
C4M
O1M
O1M
O2M
O2M
O2M
H6M
H7M
H8M
H1M
H2M
H2M
H4M
H5M
H5M
H7M
H8M
H8M
108.82
108.82
108.82
108.82
108.82
110.05
110.05
110.05
110.07
110.07
109.55
109.55
109.55
109.55
108.35
108.35
108.35
212.5749446
212.5749446
212.5749446
212.5749446
212.5749446
193.8799155
193.8799155
193.8799155
193.838371
193.838371
163.8183086
163.8183086
163.8183086
163.8183086
164.8652303
164.8652303
164.8652303
dihedral parameters
atom(i)
O2M
O1M
O3M
O3M
C4M
H1M
H2M
H3M
H4M
H5M
H6M
H7M
H8M
H1M
H2M
H1M
H2M
H1M
H2M
atom(j)
atom(k)
atom(l)
C1M
C1M
C1M
C1M
C2M
C2M
C2M
C3M
C3M
C3M
C4M
C4M
C4M
C2M
C2M
C2M
C2M
C2M
C2M
O1M
O2M
O2M
O1M
O1M
O1M
O1M
O2M
O2M
O2M
C2M
C2M
C2M
C4M
C4M
C4M
C4M
C4M
C4M
C2M
C3M
C3M
C2M
C1M
C1M
C1M
C1M
C1M
C1M
O1M
O1M
O1M
H6M
H6M
H7M
H7M
H8M
H8M
phi0
180
180
180
180
180
0
0
0
0
0
0
0
0
0
0
0
0
0
0
cp
11.28922184
11.28922184
11.28922184
11.28922184
3.344997702
1.601374651
1.601374651
1.601374651
1.601374651
1.601374651
0.0
0.0
0.0
0.652248794
0.652248794
0.652248794
0.652248794
0.652248794
0.652248794
n
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
***********************************************************************
******************
propylene carbonate geometry
atom_number name
1
2
3
4
5
6
7
8
9
10
11
12
13
C2P
H2P
H2P
OAP
CP
OP
OBP
C1P
H1P
C3P
H3P
H3P
H3P
x
y
2.589
3.109
1.719
2.199
3.319
3.479
4.249
3.509
2.919
4.389
4.979
3.759
5.029
3.461
3.301
2.821
4.831
5.451
6.661
4.551
3.331
3.301
2.091
2.121
1.201
2.131
z (coordinates in nm)
2.752
1.812
2.922
2.922
3.392
3.392
3.842
3.942
4.862
3.862
2.942
3.862
4.742
Lennard-Jones parameters [atomtypes ]
name
OP
CP
OAP
C2P
C1P
OBP
C3P
H1P
H2P
H3P
mass
16.0000
12.01100
16.0000
12.01100
12.01100
16.0000
12.01100
1.00800
1.00800
1.00800
sigma(nm)
epsilon(KJ/mol)
2.96000e-01
3.75000e-01
3.00000e-01
3.50000e-01
3.50000e-01
3.00000e-01
3.50000e-01
2.4200e-01
2.42000e-01
2.42000e-01
8.7864000e-01
4.393200e-01
7.11280e-01
2.7614400e-01
2.7614400e-01
7.11280e-01
2.7614400e-01
6.2760000e-02
6.2760000e-02
6.2760000e-02
atoms charges
atom
atom number
OP
CP
OAP
C2P
C1P
OBP
C3P
H1P
H2P
H3P
1
2
3
4
5
6
7
8
9
10
charge
mass
-0.476
0.878
-0.460
0.194
0.349
-0.507
-0.365
0.032
0.008
0.113
16.0000
12.01100
16.0000
12.01100
12.01100
16.0000
12.01100
1.00800
1.00800
1.00800
bond parameters
; atom(i)
CP
CP
CP
C1P
C2P
C1P
C1P
C1P
C2P
C3P
atom(j)
OP
OAP
OBP
OBP
OAP
C2P
C3P
H1P
H2P
H3P
b0
kb
0.1229
0.13270
0.13270
0.1410
0.1410
0.1526
0.1526
0.1090
0.1090
0.1090
238488.0
89537.6
89537.6
133888
133888
129704
129704
138490.4
138490.4
138490.4
angle parameters
atom(i)
H2P
H2P
H2P
OAP
C2P
OAP
OAP
OP
atom(j)
C2P
C2P
C2P
C2P
OAP
CP
CP
CP
atom(k)
H2P
OAP
C1P
C1P
CP
OP
OBP
OBP
th0
cth
109.0
109.5
109.0
109.5
116.9
123.4
111.5
123.4
146.440
146.440
146.440
209.200
347.270
347.270
387.438
347.270
CP
C2P
C2P
C2P
OBP
OBP
H1P
C1P
H3P
OBP
C1P
C1P
C1P
C1P
C1P
C1P
C3P
C3P
C1P
OBP
H1P
C3P
H1P
C3P
C3P
H3P
H3P
116.9
109.5
109.0
109.5
109.5
111.4
109.0
109.0
109.0
347.270
209.200
146.440
146.440
146.440
338.904
146.440
146.440
146.440
atom(k)
atom(l)
dihedral parameters
atom(i)
atom(j)
C1P
OAP
OAP
CP
C2P
C2P
CP
OBP
OAP
C1P
OBP
C1P
CP
OBP
C1P
C2P
phi0
000.00
000.00
000.00
000.00
cp
4.8116
0.60249
4.8116
4.8116
n
3
3
3
3
***********************************************************************
******************
Fc1N112 geometry
atom_number
name
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
CA
CA
CA
CA
CA
HA
HA
HA
HA
CA
CA
CA
HA
CA
HA
CA
HA
HA
HA
C2
H2
H2
C4
H4
H4
CT
HC
HC
HC
N
C3
H3
H3
H3
C3
x
12.220
11.210
10.430
10.960
12.070
12.550
10.760
10.350
12.270
12.320
12.660
13.240
11.890
13.790
12.600
14.150
13.580
14.570
15.190
9.600
9.950
9.800
7.360
6.290
7.590
7.630
7.600
8.590
6.870
8.130
7.830
8.100
8.390
6.760
7.640
y
z (coordinates in nm)
7.180
6.950
8.110
9.050
8.470
6.370
5.980
9.800
8.670
9.680
8.380
10.10
10.38
8.000
8.120
9.060
11.13
7.410
9.280
8.490
7.930
9.540
8.700
8.680
9.750
7.840
6.770
8.090
8.040
8.300
6.880
6.650
6.200
6.660
9.180
7.850
8.790
8.830
7.950
7.320
7.200
8.860
7.450
6.280
11.110
11.500
10.140
11.810
10.770
12.550
9.930
10.140
11.250
9.760
10.030
10.890
10.250
11.050
10.840
11.290
12.290
12.090
12.740
13.050
9.830
9.480
8.450
10.130
9.610
8.730
36
37
38
39
40
41
H3
H3
H3
X1
X2
Fe
7.830
8.140
6.560
11.470
13.430
12.170
10.220
8.980
9.060
7.860
9.070
8.420
8.990
7.780
8.580
8.120
10.520
9.470
Lennard-Jones parameters [atomtypes ]
name
CA
CA
CA
CA
CA
HA
HA
HA
HA
CA
CA
CA
HA
CA
HA
CA
HA
HA
HA
C2
H2
H2
C4
H4
H4
CT
HC
HC
HC
N
C3
H3
H3
H3
C3
H3
H3
H3
X1
X2
Fe
mass
12.01100
12.01100
12.01100
12.01100
12.01100
1.008000
1.008000
1.008000
1.008000
12.01100
12.01100
12.01100
1.008000
12.01100
1.008000
12.01100
1.008000
1.008000
1.008000
12.01100
1.008000
1.008000
12.01100
1.008000
1.008000
12.01100
1.008000
1.008000
1.008000
14.0067
12.01100
1.008000
1.008000
1.008000
12.01100
1.008000
1.008000
1.008000
0.000001
0.000001
55.847
sigma(nm)
3.55000e-01
3.55000e-01
3.55000e-01
3.55000e-01
3.55000e-01
2.42000e-01
2.42000e-01
2.42000e-01
2.42000e-01
3.55000e-01
3.55000e-01
3.55000e-01
2.42000e-01
3.55000e-01
2.42000e-01
3.55000e-01
2.42000e-01
2.42000e-01
2.42000e-01
3.50000e-01
2.50000e-01
2.50000e-01
3.50000e-01
2.50000e-01
2.50000e-01
3.50000e-01
2.50000e-01
2.50000e-01
2.50000e-01
3.25000e-01
3.50000e-01
2.50000e-01
2.50000e-01
2.50000e-01
3.50000e-01
2.50000e-01
2.50000e-01
2.50000e-01
0.000e-01
0.000e-01
3.110e-01
epsilon(KJ/mol)
2.92880e-01
2.92880e-01
2.92880e-01
2.92880e-01
2.92880e-01
1.25520e-01
1.25520e-01
1.25520e-01
1.25520e-01
2.92880e-01
2.92880e-01
2.92880e-01
1.25520e-01
2.92880e-01
1.25520e-01
2.92880e-01
1.25520e-01
1.25520e-01
1.25520e-01
2.76144e-01
6.27600e-02
6.27600e-02
2.76144e-01
6.27600e-02
6.27600e-02
2.76144e-01
6.27600e-02
6.27600e-02
6.27600e-02
7.11280e-01
2.76144e-01
6.27600e-02
6.27600e-02
6.27600e-02
2.76144e-01
6.27600e-02
6.27600e-02
6.27600e-02
0.00
0.00
2.016
atoms charges
atom
CA
CA
CA
atom number
1
2
3
charge
-0.146844
-0.146844
-0.146844
mass
12.01100
12.01100
12.01100
CA
CA
HA
HA
HA
HA
CA
CA
CA
HA
CA
HA
CA
HA
HA
HA
C2
H2
H2
C4
H4
H4
CT
HC
HC
HC
N
C3
H3
H3
H3
C3
H3
H3
H3
X1
X2
Fe
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
-0.146844
-0.146844
0.172827
0.172827
0.172827
0.172827
-0.146844
-0.146844
-0.146844
0.172827
-0.146844
0.172827
-0.146844
0.172827
0.172827
0.172827
-0.465046
0.203392
0.203392
0.010792
0.088320
0.084171
-0.254022
0.088562
0.089744
0.129650
0.265061
-0.354903
0.166661
0.176695
0.171663
-0.454371
0.184265
0.216615
0.180513
0.00
0.0
-0.068765
12.01100
12.01100
1.008000
1.008000
1.008000
1.008000
12.01100
12.01100
12.01100
1.008000
12.01100
1.008000
12.01100
1.008000
1.008000
1.008000
12.01100
1.008000
1.008000
12.01100
1.008000
1.008000
12.01100
1.008000
1.008000
1.008000
14.0067
12.01100
1.008000
1.008000
1.008000
12.01100
1.008000
1.008000
1.008000
0.000001
0.000001
55.847
bond parameters
; atom(i)
CA
CA
CA
CA
CT
C2
C2
N
N
C3
C4
C4
X1
Fe
CA
CA
Fe
atom(j)
CA
HA
N
C2
HC
H2
N
C3
C4
H3
H4
CT
X2
CA
X1
X2
X1
b0
0.1400
0.1080
0.1340
0.1495
0.1090
0.1090
0.1471
0.1471
0.1471
0.1090
0.1090
0.1526
0.3320
0.2060
0.12
0.12
0.2160
kb
392459.2
307105.6
402500.8
284500.0
284512.0
284512.0
307105.6
307105.6
307105.6
284512.0
284512.0
259408.0
999900.0
190.0000
999900.0
999900.0
10.00000
Fe
X2
0.2160
10.00000
angle parameters
atom(i)
atom(j)
CA
CA
CA
CA
CA
H2
H2
C2
C2
C3
C3
H3
H3
N
N
H4
H4
C4
HC
CA
CA
atom(k)
CA
CA
CA
C2
C2
C2
C2
N
N
N
N
C3
C3
C4
C4
C4
C4
CT
CT
X1
X2
th0
CA
HA
C2
H2
N
H2
N
C3
C4
C3
C4
N
H3
H4
CT
H4
CT
HC
HC
X2
X1
cth
120.0
120.0
120.0
109.5
111.2
109.5
109.5
107.2
107.2
107.2
107.2
109.5
109.5
109.5
109.4
107.8
110.7
110.7
107.8
90.00
90.00
527.180
292.880
585.760
418.400
669.440
276.144
292.880
433.462
433.462
433.462
433.462
292.880
292.880
292.880
470.280
276.144
313.800
313.800
276.144
999.999
999.999
dihedral parameters
atom(i) atom(j)
;X
;CA
CA
C2
C2
N
CA
N
N
C4
CA
X1
C2
C3
C4
CT
atom(k)
CA
X2
N
0.4275
H3 0.9875
CT 0.9875
HC -0.979
atom(l) phi0
X
CA
0.8345
0.2745
0.2745
1.216
cp
180.00
30.33
180
0.022
0.128 -1.3900 0.0
0.128 -1.3900 0.0
0.128 -1.3900 0.0
0.709 -0.9460 0.0
2
0.0
0.0
0.0
0.0
2
;(func_type
;(func_type
;(func_type
;(func_type
3)
3)
3)
3)
***********************************************************************
******************
TFSI geometry
atom_number name
1
NJ
2
SJ
3
OJ
4
OJ
5
CJ
6
FJ
7
FJ
8
FJ
9
SJ
10
OJ
11
OJ
12
CJ
13
FJ
14
FJ
x
8.570
8.020
6.840
9.020
7.330
6.600
8.280
6.540
9.440
9.330
9.350
11.180
11.490
11.450
y
13.900
15.350
15.410
16.380
15.680
14.670
15.890
16.750
13.090
11.670
13.420
13.520
13.050
14.810
z (coordinates in nm)
10.430
10.640
11.470
10.790
8.940
8.470
8.030
8.900
11.410
11.100
12.810
10.920
9.710
10.890
15
FJ
12.080
12.980
11.740
Lennard-Jones parameters [atomtypes ]
name
NJ
SJ
OJ
CJ
FJ
mass
14.0067
32.0600
15.9994
12.0110
18.9984
sigma(nm)
3.25000e-01
3.55000e-01
2.96000e-01
3.50000e-01
2.95000e-01
epsilon(KJ/mol)
7.1128e-01
1.0460e-00
8.7864e-01
2.7614e-01
2.2175e-01
atoms charges
atom
NJ
SJ
OJ
CJ
FJ
atom number
1
2
3
4
5
charge
-0.66
1.02
-0.53
0.35
-0.16
mass
14.0067
32.0600
15.9994
12.0110
18.9984
bond parameters
; atom(i)
CJ
CJ
SJ
NJ
atom(j)
FJ
SJ
OJ
SJ
b0
kb
0.13230
0.18180
0.14420
0.15700
184850.0
98500.0
266550.0
115650.0
angle parameters
atom(i)
FJ
SJ
CJ
OJ
OJ
CJ
SJ
atom(j)
atom(k)
CJ
CJ
SJ
SJ
SJ
SJ
NJ
th0
FJ
FJ
OJ
OJ
NJ
NJ
SJ
107.100
111.800
102.600
118.500
113.600
100.200
125.600
cth
390.50
347.000
435.000
484.500
394.500
408.000
335.500
dihedral parameters
atom(i)
FJ
SJ
FJ
SJ
atom(j)
CJ
NJ
CJ
NJ
atom(k)
SJ
SJ
SJ
SJ
atom(l)
OJ
OJ
NJ
CJ
phi0
0.000
0.000
0.000
180.00
cp
1.451
-0.015
1.322
-20.840
n
3
3
3
2
***********************************************************************
******************
Parameter file for NPT simulation
define
= -DFLEXIBLE
integrator
= md
dt
= 0.00001
nsteps
= 200000000
Nstxout
= 10000000
nstvout
= 10000000
nstlog
= 10000000
nstenergy
= 10000000
nstxtcout
= 10000000
nstlist
= 10
ns_type
= grid
pbc
= xyz
rlist
= 1.0
vdw-type
= Cut-off
rvdw
= 1.2
coulombtype
= PME
rcoulomb
= 1.0
DispCorr
= EnerPres
fourierspacing
= 0.1
pme_order
=6
ewald_rtol
= 1e-05
ewald_geometry = 3d
epsilon_surface
=0
optimize_fft
= yes
tcoupl
= v-rescale
tc_grps
= system
tau_t
= 0.1
ref_t
= 298
Pcoupl
= Berendsen
Pcoupltype
= isotropic
tau_p
= 2.0
compressibility
= 1.e-05
ref_p
= 1.0
refcoord_scaling
= no
gen_vel
= yes
gen_temp
= 298
gen_seed
= 173529
constraints
= none
constraint_algorithm = lincs
lincs_order
=4
lincs_iter
=4
***********************************************************************
**********************
Parameter for NVT Simulation
define
= -DFLEXIBLE
integrator
= md
dt
= 0.00001
nsteps
= 300000000
Nstxout
= 10000000
nstvout
= 10000000
nstlog
= 10000000
nstenergy
= 10000000
nstxtcout
= 10000000
nstlist
= 10
ns_type
= grid
pbc
= xyz
rlist
= 1.0
vdw-type
= Cut-off
rvdw
= 1.2
coulombtype
= PME
rcoulomb
= 1.0
DispCorr
= EnerPres
fourierspacing
= 0.1
pme_order
=6
ewald_rtol
= 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft
= yes
tcoupl
= v-rescale
tc_grps
= system
tau_t
= 0.1
ref_t
= 323
Pcoupl
= no
Pcoupltype
= isotropic
tau_p
= 2.0
compressibility = 1.e-05
ref_p
= 1.0
refcoord_scaling = no
gen_vel
= yes
gen_temp
= 323
gen_seed
= 173529
constraints
= none
constraint_algorithm = lincs
lincs_order
=4
lincs_iter
=4