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Cyclobutane - puckering

Cyclobutane - puckering

Owned by Pavan Behara
Last updated: Jun 24, 2021
3 min read

Parameters applied to this are:

C4H8 ['a2', 'a7', 'a9', 'b1', 'b83', 'n16', 'n2', 't2', 't3', 't4']



System

Bonds

Angles

Dihedrals

Impropers

FF



RMSD

RMSD

RMSD

RMSD

1.0.0

1_19370395_C4H8

0.019

2.663

23.27

0

1.2.0

1_19370395_C4H8

0.019

2.674

23.247

0

1.3.0

1_19370395_C4H8

0.019

2.701

23.249

0

2.0.0 rc1

1_19370395_C4H8

0.018

2.604

23.243

0

2.0.0 refit w/ dd

1_19370395_C4H8

0.017

2.254

16.588

0

 

QM in green, dark orange is with Sage refit with inclusion of dihedral rmsd in optgeo target objective function.

 

Rest all below are from

1.0.0 - yellow, 1.2.0 - magenta

1.3.0 - cyan, 2.0.0 rc1 - wheat tint

 

 

Change in parameters with the inclusion of dihedral rmsd

diff between 2.0.0 rc and reift w/ dd

Δ(pararmeter)

Δ(pararmeter)



smarts

parameter

angle in degrees

k in kcal/(mol*rad**2)



 

a2

0.34

0.71



"[#1:1]-[#6X4:2]-[#1:3]"

a7

2.3

12.35



"[#6r4:1]-;@[#6r4:2]-;@[#6r4:3]"

a9

0.82

17.51



"[!#1:1]-[#6r4:2]-;!@[#1:3]"



length in ang.

k in kcal/(ang**2*mol)



 

b1

0.00

2.18



"[#6X4:1]-[#6X4:2]"

b83

0.00

0.15



"[#6X4:1]-[#1:2]"



k1 in kcal/mol

k2 in kcal/mol

k3 in kcal/mol

 

t2

-0.05

0.03

0.02

"[#6X4:1]-[#6X4:2]-[#6X4:3]-[#6X4:4]"

t3

-0.01





"[#1:1]-[#6X4:2]-[#6X4:3]-[#1:4]"

t4

-0.03





"[#1:1]-[#6X4:2]-[#6X4:3]-[#6X4:4]"

% change in parameter values

Parameter

Sage rc1

Sage refit w/ dd

% change

a2, angle

115.60

115.27

-0.29%

a2, k

97.55

98.26

0.73%

a7, angle

122.17

119.88

-1.88%

a7, k

77.00

64.65

-16.04%

a9, angle

119.14

119.96

0.69%

a9, k

90.36

107.87

19.38%









b1, length

1.52

1.52

0.12%

b1, k

529.24

527.06

-0.41%

b83, length

1.09

1.09

-0.17%

b83, k

740.09

740.25

0.02%









t2, k1

0.09

0.14

50.83%

t2, k2

0.32

0.28

-10.64%

t2, k3

0.32

0.31

-4.85%

t3, k1

0.19

0.20

7.09%

t4, k1

0.10

0.13

25.66%

*angle in degrees, angle k in kcal/(ang**2*mol), bond length in angstroms, bond k in kcal/(ang**2*mol), torsion k in kcal/mol

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