scholarly journals Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: Application to oxygen and nitrogen compounds.

2021 ◽  
Author(s):  
Marina Pereira Oliveira ◽  
Philippe Hunenberger
Keyword(s):  
Force Field ◽  
Condensed Phase ◽  
Organic Molecules ◽  
Nitrogen Compounds ◽  
Pure Liquid ◽  
Fragment Library ◽  
Systematic Optimization ◽  
Phase Data ◽  
Force Field Parameters ◽  
Large Compound

The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial...

scholarly journals Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

2020 ◽  
Vol 16 (12) ◽  
pp. 7525-7555
Author(s):  
Marina P. Oliveira ◽  
Maurice Andrey ◽  
Salomé R. Rieder ◽  
Leyla Kern ◽  
David F. Hahn ◽  
...  
Keyword(s):  
Force Field ◽  
Pure Liquid ◽  
Systematic Optimization ◽  
Large Compound

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>

Matrix Effects in Matrix Isolation Infrared Spectroscopy

1989 ◽  
Vol 43 (5) ◽  
pp. 781-786 ◽  
Author(s):  
S. Jagannathan ◽  
J. R. Cooper ◽  
C. L. Wilkins
Keyword(s):  
Infrared Spectra ◽  
Condensed Phase ◽  
Organic Molecules ◽  
Matrix Effects ◽  
Matrix Isolation ◽  
Effect Of Temperature ◽  
Infrared Spectrometry ◽  
Data Bases ◽  
Phase Data ◽  
Phase Spectra

A major factor limiting extensive use of matrix isolation gas chromatography-Fourier transform infrared spectrometry is the incompatibility of matrix-isolated spectra with available vapor- or condensed-phase spectral data bases. Here, matrix and surface effects on matrix isolation infrared spectra of organic molecules are investigated. Use of xenon at −215°C (58 K) to obtain matrix isolation spectra that are similar to condensed-phase spectra is demonstrated. Finally, the effect of temperature on reflection-absorption infrared spectra of matrix-isolated molecules is discussed, and guidelines for obtaining and interpreting matrix isolation infrared spectra of gas chromatographic eluants using the existing condensed phase data bases are provided.

scholarly journals Condensed phase properties of n-pentadecane emerging from application of biomolecular force fields

2020 ◽  
Author(s):  
Maciej Bratek ◽  
Anna Wójcik-Augustyn ◽  
Adrian Kania ◽  
Jan Majta ◽  
Krzysztof Murzyn
Keyword(s):  
Force Field ◽  
Condensed Phase ◽  
Chemical Structure ◽  
Computer Modelling ◽  
Hydrocarbon Chains ◽  
Linear Alkanes ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
Force Field Parameters ◽  
Phase Properties

For over 20 years, the OPLS-All Atom (OPLS-AA) force field has been efficiently used in molecular modelling studies of proteins, carbohydrates and nucleic acids. OPLS-AA is successfully applied in computer modelling of many organic compounds, including decane and shorter alkanes, but it fails when employed for longer linear alkanes, whose chemical structure corresponds to hydrocarbon tails in phospholipids constituting cellular membranes. There have been several attempts to address this problem. In this work we compare the ability to reproduce various condensed phase properties by six distinct sets of force field parameters which can be assigned to phospholipid hydrocarbon chains. In this comparison, we include three alternative sets of the OPLS-AA force field, as well as the commonly used CHARMM C36, Slipids, and Berger lipids’ parameters.

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

2016 ◽  
Vol 12 (8) ◽  
pp. 3825-3850 ◽  
Author(s):  
Bruno A. C. Horta ◽  
Pascal T. Merz ◽  
Patrick F. J. Fuchs ◽  
Jozica Dolenc ◽  
Sereina Riniker ◽  
...  
Keyword(s):  
Force Field ◽  
Condensed Phase ◽  
Organic Molecules ◽  
Small Organic Molecules

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

2018 ◽  
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>

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>

Specific force field parameters determination for the hybridab initioQM/MM LSCF method

2002 ◽  
Vol 23 (6) ◽  
pp. 610-624 ◽  
Author(s):  
Nicolas Ferré ◽  
Xavier Assfeld ◽  
Jean-Louis Rivail
Keyword(s):  
Force Field ◽  
Specific Force ◽  
Force Field Parameters

scholarly journals New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (89) ◽  
pp. 48621-48631 ◽  
Author(s):  
Eleanor R. Turpin ◽  
Sam Mulholland ◽  
Andrew M. Teale ◽  
Boyan B. Bonev ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amino Acid Residues ◽  
Charmm Force Field ◽  
Force Field Parameters ◽  
Dynamics Simulations
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