Literature DB >> 28627890

Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization.

Xin Cindy Yan1, Michael J Robertson1, Julian Tirado-Rives1, William L Jorgensen1.   

Abstract

The atomic point-charge model used in most molecular mechanics force fields does not represent well the electronic anisotropy that is featured in many directional noncovalent interactions. Sulfur participates in several types of such interactions with its lone pairs and σ-holes. The current study develops a new model, via the addition of off-atom charged sites, for a variety of sulfur compounds in the OPLS-AA and OPLS/CM5 force fields to address the lack of charge anisotropy. Parameter optimization is carried out to reproduce liquid-state properties, torsional and noncovalent energetics from reliable quantum mechanical calculations, and electrostatic potentials. Significant improvements are obtained for computed free energies of hydration, reducing the mean unsigned errors from ca. 1.4 to 0.4-0.7 kcal/mol. Enhanced accuracy in directionality and energetics is also obtained for molecular complexes with sulfur-containing hydrogen and halogen bonds. Moreover, the new model reproduces the unusual conformational preferences of sulfur-containing compounds with 1,4-intramolecular chalcogen bonds. Transferability of the new force field parameters to cysteine and methionine is verified via molecular dynamic simulations of blocked dipeptides. The study demonstrates the effectiveness of using off-atom charge sites to address electronic anisotropy, and provides a parametrization methodology that can be applied to other systems.

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Year:  2017        PMID: 28627890      PMCID: PMC5816952          DOI: 10.1021/acs.jpcb.7b04233

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  42 in total

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Review 2.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Authors:  William L Jorgensen; Julian Tirado-Rives
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development.

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4.  Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.

Authors:  Dmitry Lupyan; Yuriy A Abramov; Woody Sherman
Journal:  J Comput Aided Mol Des       Date:  2012-10-06       Impact factor: 3.686

5.  Influences of solvent water on protein folding: free energies of solvation of cis and trans peptides are nearly identical.

Authors:  A Radzicka; L Pedersen; R Wolfenden
Journal:  Biochemistry       Date:  1988-06-14       Impact factor: 3.162

6.  Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations.

Authors:  Alexandre V Morozov; Tanja Kortemme; Kiril Tsemekhman; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-26       Impact factor: 11.205

7.  Halogen bonding--a novel interaction for rational drug design?

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Authors:  Mahbub Alam; Rebekah E Beevers; Tom Ceska; Richard J Davenport; Karen M Dickson; Mara Fortunato; Lewis Gowers; Alan F Haughan; Lynwen A James; Mark W Jones; Natasha Kinsella; Christopher Lowe; Johannes W G Meissner; Anne-Lise Nicolas; Benjamin G Perry; David J Phillips; William R Pitt; Adam Platt; Andrew J Ratcliffe; Andrew Sharpe; Laura J Tait
Journal:  Bioorg Med Chem Lett       Date:  2007-03-30       Impact factor: 2.823

9.  Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins.

Authors:  Peng Zhou; Feifei Tian; Fenglin Lv; Zhicai Shang
Journal:  Proteins       Date:  2009-07

10.  Halogen bonding in supramolecular chemistry.

Authors:  Pierangelo Metrangolo; Franck Meyer; Tullio Pilati; Giuseppe Resnati; Giancarlo Terraneo
Journal:  Angew Chem Int Ed Engl       Date:  2008       Impact factor: 15.336

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  2 in total

1.  Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s.

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Journal:  J Cheminform       Date:  2019-08-07       Impact factor: 5.514

2.  Efficient Crystal Structure Prediction for Structurally Related Molecules with Accurate and Transferable Tailor-Made Force Fields.

Authors:  Alessandra Mattei; Richard S Hong; Hanno Dietrich; Dzmitry Firaha; Julian Helfferich; Yifei Michelle Liu; Kiran Sasikumar; Nathan S Abraham; Rajni Miglani Bhardwaj; Marcus A Neumann; Ahmad Y Sheikh
Journal:  J Chem Theory Comput       Date:  2022-08-05       Impact factor: 6.578

  2 in total

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