Literature DB >> 31768728

Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances.

Alexei Nikitin1.   

Abstract

Application of a small radius of the hydrogen atom in molecular-mechanical models of hydrogen bonding improves the estimate of the solvation free energy of organic substances. At the same time, the density and evaporation heat of the bulk water vary slightly and are close to experimental values. Blind testing drug candidates in the SAMPL6 simulation competition showed that using the same Lennard-Jones hydrogen parameters for the hydroxyl, hydroxycarbonyl, amino, and amide groups is enough to predict log P octanol-water with MAE 0.67 and RMSD 0.75.

Entities:  

Keywords:  Expanded ensembles; Free energy; Hybrid Monte Carlo; Molecular dynamics; Molecular mechanics; Water model

Mesh：

Substances：

Year:  2019        PMID： 31768728     DOI： 10.1007/s10822-019-00256-2

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  7 in total

1.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Authors:  Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2004-05-22       Impact factor: 3.488

2.  Canonical sampling through velocity rescaling.

Authors:  Giovanni Bussi; Davide Donadio; Michele Parrinello
Journal:  J Chem Phys       Date:  2007-01-07       Impact factor: 3.488

3.  Molecular-dynamics study of atomic motions in water.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1985-03-01

4.  Computer simulation of the static dielectric constant of systems with permanent electric dipoles.

Authors:  S W De Leeuw; J W Perram; E R Smith
Journal:  Annu Rev Phys Chem       Date:  1986       Impact factor: 12.703

5.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

Authors:  W L Jorgensen; J Tirado-Rives
Journal:  J Am Chem Soc       Date:  1988-03-01       Impact factor: 15.419

6.  AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes.

Authors:  Alexei Nikitin; Yury Milchevskiy; Alexander Lyubartsev
Journal:  J Phys Chem B       Date:  2015-11-05       Impact factor: 2.991

7.  Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

Authors:  Daniel J Cole; Jonah Z Vilseck; Julian Tirado-Rives; Mike C Payne; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2016-04-21       Impact factor: 6.006
  7 in total
  2 in total

1.  Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge.

Authors:  Mehtap Işık; Teresa Danielle Bergazin; Thomas Fox; Andrea Rizzi; John D Chodera; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2020-02-27       Impact factor: 3.686

2.  Identifying misbonded atoms in the 2019 CoRE metal-organic framework database.

Authors:  Taoyi Chen; Thomas A Manz
Journal:  RSC Adv       Date:  2020-07-20       Impact factor: 4.036
  2 in total

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