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Literature DB >> 23329896

Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents.

Abstract

The representation of chlorine, bromine, and iodine in aryl halides has been modified in the OPLS-AA and OPLS/CM1A force fields in order to incorporate halogen bonding. The enhanced force fields, OPLS-AAx and OPLS/CM1Ax, have been tested in calculations on gas-phase complexes of halobenzenes with Lewis bases, and for free energies of hydration, densities, and heats of vaporization of halobenzenes. Comparisons with results of MP2/aug-cc-pVDZ(-PP) calculations for the complexes are included. Implementation in the MCPRO software also allowed computation of relative free energies of binding for a series of HIV reverse transcriptase inhibitors via Monte Carlo/free-energy perturbation calculations. The results support the notion that the activity of an unusually potent chloro analog likely benefits from halogen bonding with the carbonyl group of a proline residue.

Entities: Chemical Disease Gene Species

Year: 2012 PMID： 23329896 PMCID： PMC3544186 DOI： 10.1021/ct300180w

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

22 in total

Review 1. Force fields for protein simulations.

Authors: Jay W Ponder; David A Case
Journal: Adv Protein Chem Date: 2003

2. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Authors: Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
Journal: J Comput Chem Date: 2004-10 Impact factor: 3.376

Review 3. 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

4. Sigma-hole bonding between like atoms; a fallacy of atomic charges.

Authors: Peter Politzer; Jane S Murray; Monica C Concha
Journal: J Mol Model Date: 2008-03-04 Impact factor: 1.810

5. Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: a new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains.

Authors: Daniel M Himmel; Kalyan Das; Arthur D Clark; Stephen H Hughes; Abdellah Benjahad; Said Oumouch; Jérôme Guillemont; Sophie Coupa; Alain Poncelet; Imre Csoka; Christophe Meyer; Koen Andries; Chi Hung Nguyen; David S Grierson; Eddy Arnold
Journal: J Med Chem Date: 2005-12-01 Impact factor: 7.446

6. Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine.

Authors: Kevin E Riley; Jane S Murray; Jindřich Fanfrlík; Jan Rezáč; Ricardo J Solá; Monica C Concha; Felix M Ramos; Peter Politzer
Journal: J Mol Model Date: 2011-03-04 Impact factor: 1.810

7. Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion.

Authors: William L Jorgensen; Kasper P Jensen; Anastassia N Alexandrova
Journal: J Chem Theory Comput Date: 2007-11-01 Impact factor: 6.006

8. Halogen bonds in biological molecules.

Authors: Pascal Auffinger; Franklin A Hays; Eric Westhof; P Shing Ho
Journal: Proc Natl Acad Sci U S A Date: 2004-11-19 Impact factor: 11.205

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

Authors: Yunxiang Lu; Ting Shi; Yong Wang; Huaiyu Yang; Xiuhua Yan; Xiaoming Luo; Hualiang Jiang; Weiliang Zhu
Journal: J Med Chem Date: 2009-05-14 Impact factor: 7.446

10. Br···O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone.

Authors: Kevin E Riley; Jane S Murray; Peter Politzer; Monica C Concha; Pavel Hobza
Journal: J Chem Theory Comput Date: 2008-12-18 Impact factor: 6.006

40 in total

1. A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions.

Authors: Zhuo Yang; Yingtao Liu; Zhaoqiang Chen; Zhijian Xu; Jiye Shi; Kaixian Chen; Weiliang Zhu
Journal: J Mol Model Date: 2015-05-10 Impact factor: 1.810

2. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Authors: Jonah Z Vilseck; Jakub Kostal; Julian Tirado-Rives; William L Jorgensen
Journal: J Comput Chem Date: 2015-08-27 Impact factor: 3.376

3. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions.

Authors: Ignacio Soteras Gutiérrez; Fang-Yu Lin; Kenno Vanommeslaeghe; Justin A Lemkul; Kira A Armacost; Charles L Brooks; Alexander D MacKerell
Journal: Bioorg Med Chem Date: 2016-06-18 Impact factor: 3.641

4. Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths.

Authors: Antti Siiskonen; Arri Priimagi
Journal: J Mol Model Date: 2017-02-04 Impact factor: 1.810

5. 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

Review 6. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.

Authors: Anders S Christensen; Tomáš Kubař; Qiang Cui; Marcus Elstner
Journal: Chem Rev Date: 2016-04-13 Impact factor: 60.622