Directory UMM :wiley:Public:journals:jcc:suppmat:21:

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Figure 1

Interaction Parameter Optimization Partial Atomic Charges

VDW Parameters

Internal Parameter Optimization Bonds

Angles

Torsions

Impropers, Urey-Bradley

Parameter Optimization Complete

Crystal and solution condensed phase MD simulations

I

II

III

IV

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Figure 2A

O

O O P

P O

O

O O

O

P P

O O

O

O N

N N

N

NH O

NH₂ N H₂N

O α

β γ

δ

ε ζ

χ

P and τ 5'

3'

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Figure 2B

O CH₂

O P

O O

O

H O

O

O P

O

H

O Base

O

O P

O

CH₃

O

O P

O CH₃

O Base

CH₂

O

H

(-)

(-2)

O H

α

and

ζ

β

O

(-) (-)

(-)

A

B

C

D

E

F

G

CH₃

O

P

O

CH₃ O O

(OH)

(OH) O

γ

ε

P and

τ

χ

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Figure 3

O CH₂

CH₂ CH₂ CH₂ H

O H

O CH₂

CH₂ CH CH₂

O H

H

O H

H

O H

1

1 2

A

B

H₃C

O1 P

O2 CH₃ O4

O3

H

O H

H O

H

O H

1

2 3,4

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(6)

(7)

Figure 4

Gamma (degrees)

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Figure 5

0 2 4 6 8 10 12 14

A

0 2 4 6 8 10 12 14

B

0 0.02 0.04 0.06 0.08 0.1

C

0 0.02 0.04 0.06 0.08 0.1

0 60 120 180 240 300 360

Gamma (degrees)

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Figure 6

1

1 1 1 1 1 1 1 1 1 1 1

0 1 2 3 4

A

0 0.02 0.04 0.06 0.08

B

0 0.02 0.04 0.06 0.08

0 60 120 180 240 300 360

Alpha (degrees)

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Figure 7

1

1 1 1 1 1 1 1 1 1 1 1

0 1 2 3 4

A

0 0.02 0.04 0.06 0.08 0.1

B

0 0.02 0.04 0.06 0.08 0.1

0 60 120 180 240 300 360

Zeta (degrees)

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Figure 8

0 2 4 6 8

A

0 2 4 6 8

B

0 0.02 0.04 0.06 0.08

0 60 120 180 240 300 360

Beta (degrees) 0

0.02 0.04 0.06 0.08

C

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Figure 9

0 2 4 6 8

A

0 2 4 6 8

B

0 0.02 0.04 0.06 0.08

C

0 0.02 0.04 0.06 0.08

0 60 120 180 240 300 360

Epsilon (degrees)

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Figure 10

0 2 4 6 8 10

A

0 2 4 6 8 10

B

0 0.02 0.04 0.06 0.08 0.1

C

0 0.02 0.04 0.06 0.08 0.1

0 60 120 180 240 300 360

Chi (degrees)

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Figure 11

0 2 4 6 8 10

A

0 2 4 6 8 10

0 60 120 180 240 300 360

Chi (degrees)

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Figure 12

0 2 4 6 8 10

A

0 2 4 6 8 10

0 60 120 180 240 300 360

Chi (degrees)

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Figure 13

0 2 4 6 8 10

A

0 2 4 6 8 10

0 60 120 180 240 300 360

Chi (degrees)

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Figure 14

JJJ J JJJ J JJ J JJJ JJJ J 0.02 0.04 0.06 0.08 0.1

C

0 0.02 0.04 0.06 0.08 0.1

0 60 120 180 240 300 360

Pseudorotation angle (degrees)

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Figure 15

0 0.04 0.08

0.12

_A

0 0.04 0.08 0.12

0 60 120 180 240 300 360

Delta (degrees)

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Figure 16

J J J J J J J J J J J J J J J J J J J J J J J J J

0 4 8 12 16

0 60 120 180 240 300 360

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Figure 17 JJJ J JJJ JJ JJJ JJ 0.02 0.04 0.06 0.08 0.1

0 60 120 180 240 300 360

Pseudorotation angle (degrees)

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Figure 18

0 0.04 0.08

A

0 0.04 0.08

B

0 0.04 0.08

C

0 0.08 0.16

D

0 0.02

0.04

_E

0 0.04 0.08

F

0 0.04 0.08

0 60 120 180 240 300 360

Dihedral Angle (degrees)

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Figure 19

0 0.02 0.04

0 60 120 180 240 300 360

Dihedral Angle (degrees)

H

0 0.02

0.04

_A

0 0.02

0.04

_B

0 0.02

0.04

_C

0 0.02

0.04

_D

0 0.02

0.04

_E

0 0.02

0.04

_F

0 0.02