Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules

1994 ◽  
Vol 116 (6) ◽  
pp. 2515-2525 ◽  
Author(s):  
M. J. Hwang ◽  
T. P. Stockfisch ◽  
A. T. Hagler
Keyword(s):  
Force Field ◽  
Functional Group ◽  
Force Fields ◽  
Class Ii

Derivation of Class II Force Fields. III. Characterization of a Quantum Force Field for Alkanes

1994 ◽  
Vol 34 (2) ◽  
pp. 195-231 ◽  
Author(s):  
J.R. Maple ◽  
M.-J. Hwang ◽  
T.P. Stockfisch ◽  
A.T. Hagler
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Class Ii ◽  
Quantum Force

Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules

1994 ◽  
Vol 15 (2) ◽  
pp. 162-182 ◽  
Author(s):  
J. R. Maple ◽  
M.-J. Hwang ◽  
T. P. Stockfisch ◽  
U. Dinur ◽  
M. Waldman ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Group ◽  
Force Fields ◽  
Class Ii ◽  
Quantum Force

Derivation of Class II Force Fields. 7. Nonbonded Force Field Parameters for Organic Compounds

1999 ◽  
Vol 103 (33) ◽  
pp. 6998-7014 ◽  
Author(s):  
Carl S. Ewig ◽  
Thomas S. Thacher ◽  
Arnold T. Hagler
Keyword(s):  
Force Field ◽  
Organic Compounds ◽  
Force Fields ◽  
Class Ii ◽  
Force Field Parameters

Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds

1998 ◽  
Vol 19 (4) ◽  
pp. 430-458 ◽  
Author(s):  
J. R. Maple ◽  
M.-J. Hwang ◽  
K. J. Jalkanen ◽  
T. P. Stockfisch ◽  
A. T. Hagler
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Class Ii ◽  
Quantum Force ◽  
Related Compounds

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

2001 ◽  
Vol 22 (15) ◽  
pp. 1782-1800 ◽  
Author(s):  
Carl S. Ewig ◽  
Rajiv Berry ◽  
Uri Dinur ◽  
Jörg-Rüdiger Hill ◽  
Ming-Jing Hwang ◽  
...  
Keyword(s):  
Force Field ◽  
Organic Compounds ◽  
Force Fields ◽  
Class Ii ◽  
Mechanical Force ◽  
Quantum Mechanical ◽  
General Quantum

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Leela Dodda ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Organic Molecules ◽  
Force Fields ◽  
Liquid Density ◽  
Small Organic Molecules ◽  
Automated Generation ◽  
Energy Of Hydration ◽  
Novel Method ◽  
Force Field Parameters

<div><div><div><p>Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites. As a proof of concept, we have re-derived a complete set of parameters for 109 small organic molecules, and assessed the accuracy by comparing computed liquid properties with experiment. QUBEKit gives highly competitive results when compared to standard transferable force fields, with mean unsigned errors of 0.024 g/cm3, 0.79 kcal/mol and 1.17 kcal/mol for the liquid density, heat of vaporization and free energy of hydration respectively. This indicates that the derived parameters are suitable for molecular modelling applications, including computer-aided drug design.</p></div></div></div>

A Transferable, Polarisable Force Field for Ionic Liquids

2019 ◽  
Author(s):  
Kateryna Goloviznina ◽  
José N. Canongia Lopes ◽  
Margarida Costa Gomes ◽  
Agilio Padua
Keyword(s):  
Ionic Liquids ◽  
Force Field ◽  
Force Fields ◽  
Dipole Moments ◽  
Van Der Waals Interactions ◽  
First Principles Calculations ◽  
Ion Diffusion ◽  
Fixed Integer ◽  
Molecular Compounds ◽  
Induced Dipoles

A general, transferable polarisable force field for molecular simulation of ionic liquids and their mixtures with molecular compounds is developed. This polarisable model is derived from the widely used CL\&P fixed-charge force field that describes most families of ionic liquids, in a form compatible with OPLS-AA, one of the major force fields for organic compounds. Models for ionic liquids with fixed, integer ionic charges lead to pathologically slow dynamics, a problem that is corrected when polarisation effects are included explicitly. In the model proposed here, Drude induced dipoles are used with parameters determined from atomic polarisabilities. The CL\&P force field is modified upon inclusion of the Drude dipoles, to avoid double-counting of polarisation effects. This modification is based on first-principles calculations of the dispersion and induction contributions to the van der Waals interactions, using symmetry-adapted perturbation theory (SAPT) for a set of dimers composed of positive, negative and neutral fragments representative of a wide variety of ionic liquids. The fragment approach provides transferability, allowing the representation of a multitude of cation and anion families, including different functional groups, without need to re-parametrise. Because SAPT calculations are expensive an alternative predictive scheme was devised, requiring only molecular properties with a clear physical meaning, namely dipole moments and atomic polarisabilities. The new polarisable force field, CL\&Pol, describes a broad set set of ionic liquids and their mixtures with molecular compounds, and is validated by comparisons with experimental data on density, ion diffusion coefficients and viscosity. The approaches proposed here can also be applied to the conversion of other fixed-charged force fields into polarisable versions.<br>

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