CHARMM force field parameters for 2′-hydroxybiphenyl-2-sulfinate, 2-hydroxybiphenyl, and related analogs

Yue Yu, Ishan A. Fursule, Landon C. Mills, Derek L. Englert, Brad J. Berron, Christina M. Payne

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

2′-Hydroxybiphenyl-2-sulfinate (HBPS) desulfinase (DszB) catalyzes the cleavage of the carbon-sulfur bond from HBPS in the final step of microbial 4S pathway desulfurization reactions. DszB is notable for its substrate specificity and exhibits product inhibition, both of which hinder the overall 4S pathway turnover rate. To understand the molecular-level contributions to substrate and inhibitor binding to DszB, we plan to perform molecular dynamic simulations bound to an array of naphthenic molecules and biphenyl analogues of HBPS. However, many of the small molecules we are interested in are not included in standard force field packages, and thus, we must first produce accurate molecular mechanics force fields. Here, we develop and validate CHARMM-compatible force field parameters for the HBPS substrate, the 2-hydroxybiphenyl product, and potential inhibitors including: 2,2′-biphenol, 2-biphenyl carboxylic acid, 1,8-naphthosultam, and 1,8-naphthosultone. The selected molecules represent biphenyl compounds having both a single and double functional group and the planar naphthenic molecule class, all likely present in the oil-rich environment surrounding DszB-producing microorganisms. The Force Field Toolkit (ffTK) in VMD was used to optimize charge, bond distance, angle, and dihedral parameters. Optimized geometries were determined from quantum mechanical calculations. Molecular simulations of the molecules in explicit and implicit water solutions were conducted to assess the abilities of optimized parameters to recapitulate optimized geometries. Calculated infrared (IR) spectra were obtained and compared with experimental IR spectra for validation of the optimized MM parameters.

Original languageEnglish
Pages (from-to)32-42
Number of pages11
JournalJournal of Molecular Graphics and Modelling
Volume72
DOIs
StatePublished - Mar 1 2017

Bibliographical note

Publisher Copyright:
© 2016 Elsevier Inc.

Keywords

  • Biodesulfurization
  • Dibenzothiophene
  • Organosulfur compound
  • Parameterization
  • Petroleum refining

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

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