Calculation of H/D carbon-12/carbon-13, and carbon-12/carbon-14 fractionation factors from valence force fields derived for a series of simple organic molecules

1972 ◽  
Vol 94 (26) ◽  
pp. 9002-9012 ◽  
Author(s):  
S. R. Hartshorn ◽  
V. J. Shiner
Keyword(s):  
Organic Molecules ◽  
Force Fields ◽  
Valence Force ◽  
Carbon 14 ◽  
Fractionation Factors

Protium -Deuterium Fractionation Factors for Organic Molecules Calculated From Vibrational Force Fields

1989 ◽  
Vol 44 (5) ◽  
pp. 337-354
Author(s):  
Vernon J. ◽  
Shiner Jr. ◽  
Thomas E. Neumann
Keyword(s):  
Organic Molecules ◽  
Force Fields ◽  
Small Organic Molecules ◽  
Valence Force ◽  
Bond Lengths ◽  
Mechanistic Analysis ◽  
Fractionation Factors

New valence force fields have been calculated for forty-seven small organic molecules and used to calculate protium-deuterium fractionation factors. Factors for molecules of the type CH3X and HCOX have been found to correlate with the electronegativities of X and the CX bond lengths. The effects of cumulative substitution on a given C atom on the alpha CH fractionation factors have been examined. Some uses of the factors in mechanistic analysis are discussed.

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>

scholarly journals Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

2021 ◽  
Author(s):  
David Peter Kovacs ◽  
Cas van der Oord ◽  
Jiri Kucera ◽  
Alice Allen ◽  
Daniel Cole ◽  
...  
Keyword(s):  
Cluster Expansion ◽  
Organic Molecules ◽  
Force Fields ◽  
Atomic Cluster ◽  
Expansion Force

scholarly journals Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

2021 ◽  
Author(s):  
David Peter Kovacs ◽  
Cas van der Oord ◽  
Jiri Kucera ◽  
Alice Allen ◽  
Daniel Cole ◽  
...  
Keyword(s):  
Cluster Expansion ◽  
Organic Molecules ◽  
Force Fields ◽  
Atomic Cluster ◽  
Expansion Force

scholarly journals Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

2021 ◽  
Author(s):  
David Peter Kovacs ◽  
Cas van der Oord ◽  
Jiri Kucera ◽  
Alice Allen ◽  
Daniel Cole ◽  
...  
Keyword(s):  
Cluster Expansion ◽  
Organic Molecules ◽  
Force Fields ◽  
Atomic Cluster ◽  
Expansion Force

Comparisons of different force fields in conformational analysis and searching of organic molecules: A review

Tetrahedron ◽  
2021 ◽  
Vol 79 ◽  
pp. 131865
Author(s):  
Toby Lewis-Atwell ◽  
Piers A. Townsend ◽  
Matthew N. Grayson
Keyword(s):  
Conformational Analysis ◽  
Organic Molecules ◽  
Force Fields

scholarly journals A unified picture of the covalent bond within quantum-accurate force fields: From organic molecules to metallic complexes’ reactivity

2019 ◽  
Vol 5 (5) ◽  
pp. eaaw2210 ◽  
Author(s):  
Alessandro Lunghi ◽  
Stefano Sanvito
Keyword(s):  
Organic Molecules ◽  
Energy Surface ◽  
Force Fields ◽  
Covalent Bond ◽  
Organometallic Compounds ◽  
Molecular Systems ◽  
Physical Chemical ◽  
Atomistic Models ◽  
General Potential ◽  
Unified Description

Computational studies of chemical processes taking place over extended size and time scales are inaccessible by electronic structure theories and can be tackled only by atomistic models such as force fields. These have evolved over the years to describe the most diverse systems. However, as we improve the performance of a force field for a particular physical/chemical situation, we are also moving away from a unified description. Here, we demonstrate that a unified picture of the covalent bond is achievable within the framework of machine learning–based force fields. Ridge regression, together with a representation of the atomic environment in terms of bispectrum components, can be used to map a general potential energy surface for molecular systems at chemical accuracy. This protocol sets the ground for the generation of an accurate and universal class of potentials for both organic and organometallic compounds with no specific assumptions on the chemistry involved.

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