Directory UMM :wiley:Public:journals:jcc:suppmat:21:
Figure 1
Initial geometries of model compounds
Interaction Parameter Optimization
Partial Atomic Charges
I
VDW Parameters
III
Internal Parameter Optimization
Bonds
II
Angles
Torsions
Impropers, Urey-Bradley
IV
Crystal and solution condensed phase MD simulations
Parameter Optimization Complete
Figure 2A
5'
O
O
P
N
O
O
P
3'
P and τ
H2 N
NH
N
O
O
N
NH2
O
N
O
P
O
N
O
O
O
O
3'
O
O
P
5'
O
Figure 2B
H
O
P
O
O
O
O
(-)
CH2
O
P
O
H
O
O
P
O
O
O
Base
CH3
H
CH3
O
O
CH2
(-2)
O
P
O
Base
O
O
O
O
H
O
Figure 3
A
O
B
H
O
CH2
H
1
CH2 CH
2
O
CH2
CH2
CH2
H
O
H
1
O
H
CH2 CH2
O
H
C
H
O
H
3,4
H
O3
H3 C
1
H
O
H
2
O4
P
O1
H
O
CH3
O2
H
Figure 3, continued
H
H
D
5
O
H
4
O
H
H61
H
H
H2
C2
O
H
H
C4
E
H
H1
H
2
H21 N
2
3
H
H22
O
C6
N1
C2
N3
4
H
H
H
O
O
O6
H
H
O
6
H
5
1
H
H
O
H
H
8
O
O
O
7
H9
H
O
H
N9
H
H
6
C8 H8
O
3
H
N7
C5
N3
H
H62
C6
N1
1
2
N6
O
H
O
H
C5
C4
H
7
N7
H
C8 H8
8
N9
9
H9
O
H
H
O
H
Figure 3, continued
F
H
H
H
H
O
6
H
5
O4
H5
C4
H6
C5
C6
N1
O
H
G
O
H
O
H
H
H
O
H3
N3
H
CH3
C2
7
O2
H
O
H
H
C6
H6
N1
O
H
1
O
H
O
7
H5
5
H42
H41
N4
C4
C5
8 H C6
6
N1
O
H
O
6
1
H
H
H
C2
O2
H1
H
O
O
H
H
3
2
H
H3
O
H
H
4
C2
O2
O
4
N3
N3
O
H
O
O
H
H
H
H
H
H1
H
H
H
C4
C5
H
H
H
O
O4
3
2
5
6
O
4
H1
1
H
H
H
3
2
H
O
H
Figure 4
14
12
G
A
G
G
10
8
6
H
G
G
4
2
G
G
H
F
0
H
F
G
H
F
G
H
F
G
H
F
0
H
F
F
H
F
H
F
G
G
H
F
G
G
G
F
H
G
G
H
F
H
F
H
F
H
F
H
F
120
180
G
H
F
H
G
H
F
H
F
G
60
G
G
H
F
G
H
F
240
F
H
G
G
H
F
H
F
300
F
360
0.5
B
0.4
G
0.3
G
0.2
F
H
F
H
G
F
H
F
0.1
0
F
G
H
0
F
H
G
H
F
H
G
F
H
G
30
G
60
Gamma (degrees)
H
F
G
H
F
G
90
F
G
H
H
F
G
120
Figure 5
14
12
A
10
8
6
4
2
0
14
12
B
10
8
6
4
2
0
0.1
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
Gamma (degrees)
240
300
360
Figure 6
4
A
1
3
2
1
1
1
1
1 1
1
1
1
0
1
11
0.08
B
0.06
0.04
0.02
0
0.08
C
0.06
0.04
0.02
0
0
60
120
180
Alpha (degrees)
240
300
360
Figure 7
4
A
1
3
2
1
1
1
1
1 1
1
1
1
0
1
11
0.1
B
0.08
0.06
0.04
0.02
0
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
Zeta (degrees)
240
300
360
Figure 8
8
A
6
4
2
0
8
B
6
4
2
0
0.08
C
0.06
0.04
0.02
0
0.08
D
0.06
0.04
0.02
0
0
60
120
180
Beta (degrees)
240
300
360
Figure 9
8
6
4
2
A
0
8
6
4
2
B
0
0.08
0.06
0.04
0.02
C
0
0.08
0.06
0.04
0.02
D
0
0
60
120
180
Epsilon (degrees)
240
300
360
Figure 10
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0.1
0.08
0.06
0.04
0.02
C
0
0.1
0.08
0.06
0.04
D
0.02
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 11
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 12
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 13
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 14
6
A
J
J
4
J
JJ
JJ
J
JJ
J
J
J
J
J
J
2
J
1
J
JJ
J
JJ
J
J
JJ
JJ
JJ
JJ
J
JJ
J
J
J
J
0
J JJ
JJ
J
JJ
J J
JJ
J J JJ J
1
6
J
J
J
JJ 1J
JJ JJ
J
J
J J
4
J
J
J
JJ
J
J
2
J
J
J
J
J
J
J
J
J
J
J
JJ
J
J
J
J
J
J
JJ
J
J
J
J
JJ
J
JJ
0
J
J
JJ J J
J J JJ
JJ
JJ
B
J J
JJ
0.1
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
Pseudorotation angle (degrees)
240
300
360
Figure 15
0.12
A
0.08
0.04
0
0.12
B
0.08
0.04
0
0
60
120
180
Delta (degrees)
240
300
360
Figure 16
16
J
J
J
J
J
J
J
J
12
J
J
J
J
J
8
J
J
J
4
J
J
J
J
J
J
0
JJ
0
60
120
180
H-O2'-C2'-C3' dihedral (degrees)
240
300
J
360
Figure 17
10
J
J J
8
A
J
J
J
J
6
4
J J
2
0
JJ
J J
J
JJ J JJ J
JJ
J
J
J J JJ J J J J J
J J JJ
J J J
J J
JJ
J
JJ
JJ J
JJ
J J
J
JJ
J
10
B
8
J
6
J
J
J
4
J J
J
2
0
J
J JJ
J
JJJJJJJ
J
J
JJ
J
J J J
JJ JJ JJ JJ J
J
J
J
J J J
J
J
JJJ
J
J
JJ
J
J
J
J
JJJ
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
Pseudorotation angle (degrees)
240
300
360
Figure 18
0.08
A
0.04
0
0.08
B
0.04
0
0.08
C
0.04
0
0.16
D
0.08
0
0.04
E
0.02
0
0.08
F
0.04
0
0.08
G
0.04
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
Figure 19
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0.04
H
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
Initial geometries of model compounds
Interaction Parameter Optimization
Partial Atomic Charges
I
VDW Parameters
III
Internal Parameter Optimization
Bonds
II
Angles
Torsions
Impropers, Urey-Bradley
IV
Crystal and solution condensed phase MD simulations
Parameter Optimization Complete
Figure 2A
5'
O
O
P
N
O
O
P
3'
P and τ
H2 N
NH
N
O
O
N
NH2
O
N
O
P
O
N
O
O
O
O
3'
O
O
P
5'
O
Figure 2B
H
O
P
O
O
O
O
(-)
CH2
O
P
O
H
O
O
P
O
O
O
Base
CH3
H
CH3
O
O
CH2
(-2)
O
P
O
Base
O
O
O
O
H
O
Figure 3
A
O
B
H
O
CH2
H
1
CH2 CH
2
O
CH2
CH2
CH2
H
O
H
1
O
H
CH2 CH2
O
H
C
H
O
H
3,4
H
O3
H3 C
1
H
O
H
2
O4
P
O1
H
O
CH3
O2
H
Figure 3, continued
H
H
D
5
O
H
4
O
H
H61
H
H
H2
C2
O
H
H
C4
E
H
H1
H
2
H21 N
2
3
H
H22
O
C6
N1
C2
N3
4
H
H
H
O
O
O6
H
H
O
6
H
5
1
H
H
O
H
H
8
O
O
O
7
H9
H
O
H
N9
H
H
6
C8 H8
O
3
H
N7
C5
N3
H
H62
C6
N1
1
2
N6
O
H
O
H
C5
C4
H
7
N7
H
C8 H8
8
N9
9
H9
O
H
H
O
H
Figure 3, continued
F
H
H
H
H
O
6
H
5
O4
H5
C4
H6
C5
C6
N1
O
H
G
O
H
O
H
H
H
O
H3
N3
H
CH3
C2
7
O2
H
O
H
H
C6
H6
N1
O
H
1
O
H
O
7
H5
5
H42
H41
N4
C4
C5
8 H C6
6
N1
O
H
O
6
1
H
H
H
C2
O2
H1
H
O
O
H
H
3
2
H
H3
O
H
H
4
C2
O2
O
4
N3
N3
O
H
O
O
H
H
H
H
H
H1
H
H
H
C4
C5
H
H
H
O
O4
3
2
5
6
O
4
H1
1
H
H
H
3
2
H
O
H
Figure 4
14
12
G
A
G
G
10
8
6
H
G
G
4
2
G
G
H
F
0
H
F
G
H
F
G
H
F
G
H
F
0
H
F
F
H
F
H
F
G
G
H
F
G
G
G
F
H
G
G
H
F
H
F
H
F
H
F
H
F
120
180
G
H
F
H
G
H
F
H
F
G
60
G
G
H
F
G
H
F
240
F
H
G
G
H
F
H
F
300
F
360
0.5
B
0.4
G
0.3
G
0.2
F
H
F
H
G
F
H
F
0.1
0
F
G
H
0
F
H
G
H
F
H
G
F
H
G
30
G
60
Gamma (degrees)
H
F
G
H
F
G
90
F
G
H
H
F
G
120
Figure 5
14
12
A
10
8
6
4
2
0
14
12
B
10
8
6
4
2
0
0.1
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
Gamma (degrees)
240
300
360
Figure 6
4
A
1
3
2
1
1
1
1
1 1
1
1
1
0
1
11
0.08
B
0.06
0.04
0.02
0
0.08
C
0.06
0.04
0.02
0
0
60
120
180
Alpha (degrees)
240
300
360
Figure 7
4
A
1
3
2
1
1
1
1
1 1
1
1
1
0
1
11
0.1
B
0.08
0.06
0.04
0.02
0
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
Zeta (degrees)
240
300
360
Figure 8
8
A
6
4
2
0
8
B
6
4
2
0
0.08
C
0.06
0.04
0.02
0
0.08
D
0.06
0.04
0.02
0
0
60
120
180
Beta (degrees)
240
300
360
Figure 9
8
6
4
2
A
0
8
6
4
2
B
0
0.08
0.06
0.04
0.02
C
0
0.08
0.06
0.04
0.02
D
0
0
60
120
180
Epsilon (degrees)
240
300
360
Figure 10
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0.1
0.08
0.06
0.04
0.02
C
0
0.1
0.08
0.06
0.04
D
0.02
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 11
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 12
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 13
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
Chi (degrees)
240
300
360
Figure 14
6
A
J
J
4
J
JJ
JJ
J
JJ
J
J
J
J
J
J
2
J
1
J
JJ
J
JJ
J
J
JJ
JJ
JJ
JJ
J
JJ
J
J
J
J
0
J JJ
JJ
J
JJ
J J
JJ
J J JJ J
1
6
J
J
J
JJ 1J
JJ JJ
J
J
J J
4
J
J
J
JJ
J
J
2
J
J
J
J
J
J
J
J
J
J
J
JJ
J
J
J
J
J
J
JJ
J
J
J
J
JJ
J
JJ
0
J
J
JJ J J
J J JJ
JJ
JJ
B
J J
JJ
0.1
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
Pseudorotation angle (degrees)
240
300
360
Figure 15
0.12
A
0.08
0.04
0
0.12
B
0.08
0.04
0
0
60
120
180
Delta (degrees)
240
300
360
Figure 16
16
J
J
J
J
J
J
J
J
12
J
J
J
J
J
8
J
J
J
4
J
J
J
J
J
J
0
JJ
0
60
120
180
H-O2'-C2'-C3' dihedral (degrees)
240
300
J
360
Figure 17
10
J
J J
8
A
J
J
J
J
6
4
J J
2
0
JJ
J J
J
JJ J JJ J
JJ
J
J
J J JJ J J J J J
J J JJ
J J J
J J
JJ
J
JJ
JJ J
JJ
J J
J
JJ
J
10
B
8
J
6
J
J
J
4
J J
J
2
0
J
J JJ
J
JJJJJJJ
J
J
JJ
J
J J J
JJ JJ JJ JJ J
J
J
J
J J J
J
J
JJJ
J
J
JJ
J
J
J
J
JJJ
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
Pseudorotation angle (degrees)
240
300
360
Figure 18
0.08
A
0.04
0
0.08
B
0.04
0
0.08
C
0.04
0
0.16
D
0.08
0
0.04
E
0.02
0
0.08
F
0.04
0
0.08
G
0.04
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360
Figure 19
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0.04
H
0.02
0
0
60
120
180
Dihedral Angle (degrees)
240
300
360