Literature DB >> 26606351

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters.

Bruno A C Horta1, Patrick F J Fuchs2,3,4, Wilfred F van Gunsteren1, Philippe H Hünenberger1.   

Abstract

A new parameter set (53A6OXY) is developed for the GROMOS force field, that combines reoptimized parameters for the oxygen-containing chemical functions (alcohols, ethers, aldehydes, ketones, carboxylic acids, and esters) with the current biomolecular force field version (53A6) for all other functions. In the context of oxygen-containing functions, the 53A6OXY parameter set is obtained by optimization of simulated pure-liquid properties, namely the density ρliq and enthalpy of vaporization ΔHvap, as well as solvation properties, namely the free energies of solvation in water ΔGwat and in cyclohexane ΔGche, against experimental data for 10 selected organic compounds, and further tested for 25 other compounds. The simultaneous refinement of atomic charges and Lennard-Jones interaction parameters against the four mentioned types of properties provides a single parameter set for the simulation of both liquid and biomolecular systems. Small changes in the covalent parameters controlling the geometry of the oxygen-containing chemical functions are also undertaken. The new 53A6OXY force-field parameters reproduce the mentioned experimental data within root-mean-square deviations of 22.4 kg m(-3) (ρliq), 3.1 kJ mol(-1) (ΔHvap), 3.0 kJ mol(-1) (ΔGwat), and 1.7 kJ mol(-1) (ΔGche) for the 35 compounds considered.

Entities:  

Year:  2011        PMID: 26606351     DOI: 10.1021/ct1006407

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  17 in total

1.  Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations.

Authors:  Monika Laner; Bruno A C Horta; Philippe H Hünenberger
Journal:  Eur Biophys J       Date:  2014-08-24       Impact factor: 1.733

Review 2.  Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

Authors:  Pnina Dauber-Osguthorpe; A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

3.  On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters.

Authors:  Zhixiong Lin; Chris Oostenbrink; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2014-02-07       Impact factor: 1.733

4.  A fast and high-quality charge model for the next generation general AMBER force field.

Authors:  Xibing He; Viet H Man; Wei Yang; Tai-Sung Lee; Junmei Wang
Journal:  J Chem Phys       Date:  2020-09-21       Impact factor: 3.488

5.  Using MD Simulations To Calculate How Solvents Modulate Solubility.

Authors:  Shuai Liu; Shannon Cao; Kevin Hoang; Kayla L Young; Andrew S Paluch; David L Mobley
Journal:  J Chem Theory Comput       Date:  2016-03-02       Impact factor: 6.006

6.  Force Fields for Small Molecules.

Authors:  Fang-Yu Lin; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2019

7.  Structure of a protein-detergent complex: the balance between detergent cohesion and binding.

Authors:  Jonathan Khao; Jaime Arce-Lopera; James N Sturgis; Jean-Pierre Duneau
Journal:  Eur Biophys J       Date:  2011-09-08       Impact factor: 1.733

8.  Investigation of the effect of erythrosine B on amyloid beta peptide using molecular modeling.

Authors:  Juho Lee; Inchan Kwon; Seung Soon Jang; Art E Cho
Journal:  J Mol Model       Date:  2016-03-28       Impact factor: 1.810

Review 9.  An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Authors:  Justin A Lemkul; Jing Huang; Benoît Roux; Alexander D MacKerell
Journal:  Chem Rev       Date:  2016-01-27       Impact factor: 60.622

10.  Braun's Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall.

Authors:  Firdaus Samsudin; Alister Boags; Thomas J Piggot; Syma Khalid
Journal:  Biophys J       Date:  2017-10-03       Impact factor: 4.033

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