Literature DB >> 26498002

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

Alexei Nikitin1, Yury Milchevskiy1, Alexander Lyubartsev2.   

Abstract

A molecular mechanics force field of the AMBER/OPLS family for perfluoroalkanes, noble gases, and their mixtures with alkanes has been proposed. We had to abandon the traditional Lorentz-Berthelot combining rules for the Lennard-Jones potential to be able to uniformly describe these substance classes and their mixtures. Instead, the Waldman-Hagler rules developed for noble gases were used for all of these elements except hydrogen. Hydrogen is considered to be a particular substance to which the usual Lorentz-Berthelot rules are applied. The proposed rules have little effect on the organic chemistry of H, C, N, and O elements but make it compliant with the chemistry of heavy elements. Because of assigning a relatively high partial charge of -0.37e to fluorine atoms, the new force field reproduces the mutual insolubility of higher liquid alkanes and perfluoroalkanes.

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Year:  2015        PMID: 26498002     DOI: 10.1021/acs.jpcb.5b07233

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


  5 in total

Review 1.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

2.  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

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

Authors:  Alexei Nikitin
Journal:  J Comput Aided Mol Des       Date:  2019-11-25       Impact factor: 3.686

4.  The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations.

Authors:  Vijaya Kumar Hinge; Nikolay Blinov; Dipankar Roy; David S Wishart; Andriy Kovalenko
Journal:  J Comput Aided Mol Des       Date:  2019-11-04       Impact factor: 3.686

5.  Ligand and Structure-Based Virtual Screening in Combination, to Evaluate Small Organic Molecules as Inhibitors for the XIAP Anti-Apoptotic Protein: The Xanthohumol Hypothesis.

Authors:  Angeliki Mavra; Christos C Petrou; Manos C Vlasiou
Journal:  Molecules       Date:  2022-07-28       Impact factor: 4.927

  5 in total

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