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Merge pull request #32 from molssi-seamm/dev
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Added parameters for TFSI - bis[(trifluoromethyl)sulfonyl]imide to CL&P ff
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@seamm
seamm authored Sep 13, 2023
2 parents fd3bb18 + 1152568 commit fcb9ebb
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3 changes: 3 additions & 0 deletions HISTORY.rst
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History
=======

2023.9.13 -- Added parameters for TFSI to CL&P/OPLSAA
* Parameters for TFSI - bis[(trifluoromethyl)sulfonyl]imide

2023.9.8 -- Added more typing for OPLS-AA
* cyclopropane -CH2-, -CHR-, and -CR2-
* hexafluorobenzene
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241 changes: 203 additions & 38 deletions forcefield_step/data/oplsaa.frc
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! Version Ref Function Label
!--------- --- ------------------------------ ------
2023.01.29 1 atom_types oplsaa CL&P-oplsaa
2023.01.29 1 equivalence oplsaa CL&P-oplsaa
2023.01.29 1 charges oplsaa CL&P-oplsaa
2023.01.29 1 nonbond(12-6) oplsaa CL&P-oplsaa
2023.01.29 1 quadratic_bond oplsaa CL&P-oplsaa
2023.01.29 1 quadratic_angle oplsaa CL&P-oplsaa
2023.08.21 1 quadratic_angle oplsaa
2023.08.26 1 tabulated_angle CL&P-oplsaa
2023.01.29 1 torsion_opls oplsaa
2023.01.29 1 atom_types oplsaa CL&P
2023.01.29 1 equivalence oplsaa CL&P
2023.01.29 1 charges oplsaa CL&P
2023.01.29 1 nonbond(12-6) oplsaa CL&P
2023.01.29 1 quadratic_bond oplsaa CL&P
2023.01.29 1 quadratic_angle oplsaa CL&P
2023.08.21 1 quadratic_angle oplsaa CL&P
2023.08.26 1 tabulated_angle CL&P
2023.01.29 1 torsion_opls oplsaa CL&P
2023.01.29 1 improper_opls oplsaa
2023.01.29 1 templates oplsaa
#end
Expand All @@ -32,21 +32,20 @@
2023.01.29 1 templates oplsaa


#define CL&P-oplsaa
#define CL&P

! Version Ref Function Label
!--------- --- ------------------------------ ------
2023.01.29 1 atom_types oplsaa CL&P-oplsaa
2023.01.29 1 equivalence oplsaa CL&P-oplsaa
2023.01.29 1 charges oplsaa CL&P-oplsaa
2023.01.29 1 nonbond(12-6) oplsaa CL&P-oplsaa
2023.01.29 1 quadratic_bond oplsaa CL&P-oplsaa
2023.01.29 1 quadratic_angle oplsaa CL&P-oplsaa
2023.08.21 1 quadratic_angle oplsaa
2023.08.21 1 simple_fourier_angle CL&P-oplsaa
2023.01.29 1 torsion_opls oplsaa
2023.01.29 1 improper_opls oplsaa
2023.01.29 1 templates oplsaa
2023.01.29 1 atom_types CL&P
2023.01.29 1 equivalence CL&P
2023.01.29 1 charges CL&P
2023.01.29 1 nonbond(12-6) CL&P
2023.01.29 1 quadratic_bond CL&P
2023.01.29 1 quadratic_angle CL&P
2023.08.21 1 quadratic_angle CL&P
2023.08.21 1 simple_fourier_angle CL&P
2023.01.29 1 torsion_opls CL&P
2023.01.29 1 templates CL&P
#end


Expand Down Expand Up @@ -10719,11 +10718,61 @@
"description": "Fluorine in PF6-",
"overrides": []
}
},
"Nbt": {
"2023.09.213": {
"smarts": [
"[N:1](~[S](~[O])~[O])~[S](~[O])~[O]",
"[N-1:1](~[S](~[O])~[O])~[S](~[O])~[O]"
],
"description": "N- in bis(sulfonyl)imide",
"overrides": []
}
},
"Sbt": {
"2023.09.213": {
"smarts": [
"[N](~[S:1](~[O])~[O])~[S:2](~[O])~[O]",
"[N](~[S:1](~[O])~[O])~[S:2](~[O])~[O]"
],
"description": "S in bis(sulfonyl)imide",
"overrides": []
}
},
"Obt": {
"2023.09.213": {
"smarts": [
"[N](~[S](~[O:1])~[O:2])~[S](~[O:3])~[O:4]",
"[N-1](~[S](~[O:1])~[O:2])~[S](~[O:3])~[O:4]"
],
"description": "O in bis(sulfonyl)imide",
"overrides": []
}
},
"Cbt": {
"2023.09.213": {
"smarts": [
"[N](~[S](~[O])(~[O])[C:1](F)(F)F)~[S](~[O])(~[O])[C:2](F)(F)(F)",
"[N-1](~[S](~[O])(~[O])[C:1](F)(F)F)~[S](~[O])(~[O])[C:2](F)(F)(F)"
],
"description": "O in bis(trifluormethanesulfonyl)imide",
"overrides": []
}
},
"Fbt": {
"2023.09.213": {
"smarts": [
"[N](~[S](~[O])(~[O])C([F:1])([F:2])[F:3])~[S](~[O])(~[O])C([F:4])([F:5])([F:6])",
"[N-1](~[S](~[O])(~[O])C([F:1])([F:2])[F:3])~[S](~[O])(~[O])C([F:4])([F:5])([F:6])"
],
"description": "F in bis(trifluormethanesulfonyl)imide",
"overrides": []
}
}
}


#atom_types CL&P-oplsaa
#atom_types CL&P

> Atom type definitions for any variant of oplsaa

Expand All @@ -10732,10 +10781,17 @@
2023.01.29 1 P 30.974 P 6 Phosphorous
2023.01.29 1 F 18.998 F 1 Fluorine
2023.01.29 1 FP 18.998 F 1 Fluorine in PF6-
2023.09.13 3 N 14.007 N 2 generic N in CL&P
2023.09.13 3 S 32.060 S 4 generic S in CL&P
2023.09.13 3 O 15.999 O 1 generic O in CL&P
2023.09.13 5 Nbt 14.007 N 2 N- in bis(trifluoromethanesulfonyl)imide anion
2023.09.13 5 Sbt 32.060 S 4 S in bis(trifluoromethanesulfonyl)imide anion
2023.09.13 5 Fbt 18.998 F 1 F in bis(trifluoromethanesulfonyl)imide anion
2023.09.13 5 Obt 15.999 O 1 O in bis(trifluoromethanesulfonyl)imide anion
2023.09.13 5 Cbt 15.999 C 4 C in bis(trifluoromethanesulfonyl)imide anion



#equivalence CL&P-oplsaa
#equivalence CL&P

! Equivalences
! -------------------------------------------
Expand All @@ -10744,21 +10800,29 @@
2023.01.29 1 P P P P P P
2023.01.29 1 F F F F F F
2023.01.29 1 FP FP F FP F F
2023.09.13 5 Nbt Nbt N N N N
2023.09.13 5 Sbt Sbt S S S S
2023.09.13 5 Fbt Fbt Fbt Fbt Fbt Fbt
2023.09.13 5 Obt Obt O O O O
2023.09.13 5 Cbt Cbt C C C C



#charges CL&P-oplsaa
#charges CL&P


! Version Ref I Charge
!--------- ---- -------- ------
2023.01.29 2 F -0.12
2023.01.29 2 FP -0.39
2023.01.29 2 P 1.34
2023.09.13 3 Nbt -0.660
2023.09.13 3 Sbt 1.020
2023.09.13 3 Fbt -0.160
2023.09.13 3 Obt -0.530
2023.09.13 3 Cbt 0.350



#nonbond(12-6) CL&P-oplsaa
#nonbond(12-6) CL&P

> E = 4 * eps(ij) * [(sigma(ij)*/r(ij))**12 - (sigma(ij)*/r(ij))**6]
>
Expand All @@ -10776,10 +10840,14 @@
2023.01.29 2 F 2.95 0.22175
2023.01.29 2 FP 3.12 0.25520
2023.01.29 2 P 3.74 0.83680
2023.09.13 3 Nbt 3.250 0.71128
2023.09.13 3 Sbt 3.550 1.04600
2023.09.13 5 Fbt 3.118 0.25540
2023.09.13 5 Obt 3.150 0.83736
2023.09.13 3 Cbt 3.500 0.27614



#quadratic_bond CL&P-oplsaa
#quadratic_bond CL&P

> E = K2 * (R - R0)^2

Expand All @@ -10789,10 +10857,12 @@
! Version Ref I J R0 K2
!--------- ---- -------- -------- -------- --------
2023.01.29 3 P F 1.606 3100.0
2023.09.13 3 S N 1.570 3137.0
2023.09.13 3 S O 1.437 5331.0
2023.09.13 3 Sbt Cbt 1.818 1970.0
2023.09.13 3 Cbt Fbt 1.323 3697.0



#quadratic_angle CL&P-oplsaa
#quadratic_angle CL&P

> E = K2 * (Theta - Theta0)^2

Expand All @@ -10802,10 +10872,17 @@
! Version Ref I J K Theta0 K2
!--------- ---- -------- -------- -------- -------- --------
2023.01.29 3 FP P FP 90.0 1165.0
2023.09.13 3 Sbt Nbt Sbt 125.6 671.0
2023.09.13 3 O N S 113.6 789.0
2023.09.13 5 C S N 103.5 764.0
2023.09.13 3 C S O 102.6 870.0
2023.09.13 3 O S O 118.5 969.0
2023.09.13 3 N S O 113.6 789.0
2023.09.13 3 Fbt C S 111.8 694.0
2023.09.13 5 Fbt C Fbt 109.1 644.0



#simple_fourier_angle CL&P-oplsaa
#simple_fourier_angle CL&P

> E = K * [1 - cos(n*Theta)]
>
Expand All @@ -10817,8 +10894,24 @@
!--------- ---- -------- -------- -------- -------- ---
2023.01.29 5 FP P FP 145.6 4

#torsion_opls CL&P

> E = 1/2*V1*[1 + cos(phi1)]
> + 1/2*V2*[1 - cos(2*phi2)]
> + 1/2*V3*[1 + cos(3*phi3)]
> + 1/2*V4*[1 - cos(4*phi4)]

! Version Ref I J K L V1 V2 V3 V4
!--------- ---- -------- -------- -------- -------- ------ ------- ------ ------
2023.09.13 3 C S N S 32.773 -10.420 -3.915 0.0
2023.09.13 3 Fbt C S N 0.0 0.0 1.322 0.0
2023.09.13 3 S N S O 0.0 0.0 -0.015 0.0
2023.09.13 3 Fbt C S O 0.0 0.0 1.451 0.0




#tabulated_angle CL&P-oplsaa
#tabulated_angle CL&P

> Fourier angle with reasonable repulsive 1/R^12 term to keep atoms apart from 0º
> E = K * [1 - cos(n*Theta)] + 1.0/Rij^12
Expand All @@ -10832,9 +10925,9 @@

! Version Ref I J K Eqn K n Rb A zero-shift
!--------- ---- -------- -------- -------- --- -------- --- ------ ------ ----------
2023.10.25 5 FP P FP E 1165.0 4 1.606 2000.0 0.001
2023.08.25 5 FP P FP E 1165.0 4 1.606 2000.0 0.001

#templates CL&P-oplsaa
#templates CL&P
{
"P": {
"2023.01.29": {
Expand All @@ -10853,6 +10946,56 @@
"description": "Fluorine in PF6-",
"overrides": []
}
},
"Nbt": {
"2023.09.213": {
"smarts": [
"[N:1](~[S](~[O])~[O])~[S](~[O])~[O]",
"[N-1:1](~[S](~[O])~[O])~[S](~[O])~[O]"
],
"description": "N- in bis(sulfonyl)imide",
"overrides": []
}
},
"Sbt": {
"2023.09.213": {
"smarts": [
"[N](~[S:1](~[O])~[O])~[S:2](~[O])~[O]",
"[N](~[S:1](~[O])~[O])~[S:2](~[O])~[O]"
],
"description": "S in bis(sulfonyl)imide",
"overrides": []
}
},
"Obt": {
"2023.09.213": {
"smarts": [
"[N](~[S](~[O:1])~[O:2])~[S](~[O:3])~[O:4]",
"[N-1](~[S](~[O:1])~[O:2])~[S](~[O:3])~[O:4]"
],
"description": "O in bis(sulfonyl)imide",
"overrides": []
}
},
"Cbt": {
"2023.09.213": {
"smarts": [
"[N](~[S](~[O])(~[O])[C:1](F)(F)F)~[S](~[O])(~[O])[C:2](F)(F)(F)",
"[N-1](~[S](~[O])(~[O])[C:1](F)(F)F)~[S](~[O])(~[O])[C:2](F)(F)(F)"
],
"description": "O in bis(trifluormethanesulfonyl)imide",
"overrides": []
}
},
"Fbt": {
"2023.09.213": {
"smarts": [
"[N](~[S](~[O])(~[O])C([F:1])([F:2])[F:3])~[S](~[O])(~[O])C([F:4])([F:5])([F:6])",
"[N-1](~[S](~[O])(~[O])C([F:1])([F:2])[F:3])~[S](~[O])(~[O])C([F:4])([F:5])([F:6])"
],
"description": "F in bis(trifluormethanesulfonyl)imide",
"overrides": []
}
}
}

Expand Down Expand Up @@ -10923,4 +11066,26 @@ added missing angle parameters
F-CH-O-C(=O) in FEC

from LibParGen on EC and FEC (ethylene carbonate and fluoroethylene carbonate)

#reference 5
@Author Paul Saxe
@Date 2023-09-13
Gouveia, A. S. L. et al. Ionic liquids with anions based on fluorosulfonyl derivatives:
from asymmetrical substitutions to a consistent force field model.
Phys. Chem. Chem. Phys. 19, 29617–29624 (2017).
doi: 10.1039/c7cp06081e

@article{10.1039/c7cp06081e,
year = {2017},
title = {{Ionic liquids with anions based on fluorosulfonyl derivatives: from asymmetrical substitutions to a consistent force field model}},
author = {Gouveia, Andreia S. L. and Bernardes, Carlos E. S. and Tomé, Liliana C. and Lozinskaya, Elena I. and Vygodskii, Yakov S. and Shaplov, Alexander S. and Lopes, José N. Canongia and Marrucho, Isabel M.},
journal = {Physical Chemistry Chemical Physics},
issn = {1463-9076},
doi = {10.1039/c7cp06081e},
pmid = {29083012},
pages = {29617--29624},
number = {43},
volume = {19},
local-url = {file://localhost/Users/psaxe/Downloads/c7cp06081e.pdf}
}
#end
22 changes: 22 additions & 0 deletions tests/test_CLP.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""Tests for atom type assignment for CL&P forcefield forcefield."""


def test_TFSI(oplsaa_assigner, configuration):
"""Test of atom-type assignment bis(trifluoromethanesulfonyl)imide anion"""
correct = (
["Cbt"]
+ 3 * ["Fbt"]
+ ["Sbt", "Obt", "Obt"]
+ ["Nbt"]
+ ["Sbt", "Obt", "Obt"]
+ ["Cbt"]
+ 3 * ["Fbt"]
)
configuration.from_smiles("C(F)(F)(F)S(=O)(=O)[N-]S(=O)(=O)C(F)(F)F")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
raise AssertionError(f"\n result: {result}\ncorrect: {correct}")

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