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Literature DB >> 23621692

Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields.

Markus K Dahlgren¹, Patric Schyman, Julian Tirado-Rives, William L Jorgensen.

Abstract

The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10 arylpyridinones for parametrization in the OPLS all-atom force fields. Bond stretching, angle-bending, and torsional parameters were developed to reproduce the MP2 geometries and torsional energy profiles. The transferability of the new parameters was tested through their application to three additional biaryls. The torsional energetics for the 33 biaryl molecules are analyzed and factors leading to preferences for planar and nonplanar geometries are identified. For liquid biphenyl, the computed density and heat of vaporization at the boiling point (255 °C) are also reported.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Hydrocarbons, Aromatic

Year: 2013 PMID： 23621692 PMCID： PMC3707137 DOI： 10.1021/ci4001597

Source DB: PubMed Journal: J Chem Inf Model ISSN： 1549-9596 Impact factor: 4.956

25 in total

Review 1. Force fields for protein simulations.

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

Review 2. The many roles of computation in drug discovery.

Authors: William L Jorgensen
Journal: Science Date: 2004-03-19 Impact factor: 47.728

3. The evolution of synthetic oral drug properties.

Authors: John R Proudfoot
Journal: Bioorg Med Chem Lett Date: 2005-02-15 Impact factor: 2.823

Review 4. 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

5. 4-(4-fluoro-3-phenoxyphenyl)-6-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carbonitrile and the 6-(4-methylphenyl)- analogue.

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6. Nonpeptidic inhibitors of human leukocyte elastase. 2. Design, synthesis, and in vitro activity of a series of 3-amino-6-arylopyridin-2-one trifluoromethyl ketones.

Authors: J R Damewood; P D Edwards; S Feeney; B C Gomes; G B Steelman; P A Tuthill; J C Williams; P Warner; S A Woolson; D J Wolanin
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7. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction.

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Authors: P Kamatchi; G Jagadeesan; M Pramesh; P T Perumal; S Aravindhan
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9. 2-Phenyl-1H-imidazole.

Authors: Maryam Mehdizadeh Barforoush; Soheila Naderi; Ali Reza Ghanbarpour; Alireza Azhdari Tehrani; Hamid Reza Khavasi
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2011-11-09

10. N-(2-Fluoro-phen-yl)-5-[(4-meth-oxy-phen-yl)amino-meth-yl]-6-methyl-2-phenyl-pyrimidin-4-amine.

Authors: Jerzy Cieplik; Janusz Pluta; Iwona Bryndal; Tadeusz Lis
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1. Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking.

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Journal: J Chem Theory Comput Date: 2021-02-12 Impact factor: 6.006

10. Surface Reconstructions in Organic Crystals: Simulations of the Effect of Temperature and Defectivity on Bulk and (001) Surfaces of 2,2':6',2″-Ternaphthalene.

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Journal: Cryst Growth Des Date: 2015-12-02 Impact factor: 4.076

Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields.

Review 1. Force fields for protein simulations.

Review 2. The many roles of computation in drug discovery.

3. The evolution of synthetic oral drug properties.

Review 4. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

5. 4-(4-fluoro-3-phenoxyphenyl)-6-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carbonitrile and the 6-(4-methylphenyl)- analogue.

6. Nonpeptidic inhibitors of human leukocyte elastase. 2. Design, synthesis, and in vitro activity of a series of 3-amino-6-arylopyridin-2-one trifluoromethyl ketones.

7. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction.

8. Ethyl 2-benzyl-3-[3-(4-chloro-phen-yl)-1-phenyl-1H-pyrazol-4-yl]-4,6-dioxo-5-phenyl-octa-hydro-pyrrolo-[3,4-c]pyrrole-1-carboxyl-ate.

9. 2-Phenyl-1H-imidazole.

10. N-(2-Fluoro-phen-yl)-5-[(4-meth-oxy-phen-yl)amino-meth-yl]-6-methyl-2-phenyl-pyrimidin-4-amine.

1. Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking.

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

3. Systematic Study of Effects of Structural Modifications on the Aqueous Solubility of Drug-like Molecules.

4. Picomolar inhibitors of HIV reverse transcriptase featuring bicyclic replacement of a cyanovinylphenyl group.

5. Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design.

6. General van der Waals potential for common organic molecules.

7. Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors.

8. Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.

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

10. Surface Reconstructions in Organic Crystals: Simulations of the Effect of Temperature and Defectivity on Bulk and (001) Surfaces of 2,2':6',2″-Ternaphthalene.