Literature DB >> 17388420

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator.

Pedro E M Lopes1, Guillaume Lamoureux, Benoît Roux, Alexander D Mackerell.   

Abstract

The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the aromatic compounds benzene and toluene. Parameters were optimized for benzene and then transferred directly to toluene, with parameters for the methyl moiety of toluene taken from the previously published work on the alkanes. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the electrostatic parameters, for the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters. The absolute values of the Lennard-Jones parameters were determined by comparing computed and experimental heats of vaporization, molecular volumes, free energies of hydration, and dielectric constants. The newly developed parameter set was extensively tested against additional experimental data such as diffusion constants, heat capacities at constant pressure, and isothermal compressibilities including data as a function of temperature. Moreover, the structures of liquid benzene, liquid toluene, and solutions of each in water were studied. In the case of benzene, the computed and experimental total distribution function were compared, with the developed model shown to be in excellent agreement with experiment.

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Year:  2007        PMID: 17388420      PMCID: PMC2519011          DOI: 10.1021/jp0663614

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


  23 in total

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3.  Electron density distribution in stacked benzene dimers: a new approach towards the estimation of stacking interaction energies.

Authors:  Oleg A Zhikol; Oleg V Shishkin; Konstantin A Lyssenko; Jerzy Leszczynski
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4.  Potential energy surface for the benzene dimer and perturbational analysis of pi-pi interactions.

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5.  High-accuracy quantum mechanical studies of pi-pi interactions in benzene dimers.

Authors:  Mutasem Omar Sinnokrot; C David Sherrill
Journal:  J Phys Chem A       Date:  2006-09-21       Impact factor: 2.781

6.  Multicoefficient extrapolated density functional theory studies of pi...pi interactions: the benzene dimer.

Authors:  Yan Zhao; Donald G Truhlar
Journal:  J Phys Chem A       Date:  2005-05-19       Impact factor: 2.781

7.  A density-functional study on pi-aromatic interaction: benzene dimer and naphthalene dimer.

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Journal:  J Chem Phys       Date:  2005-09-08       Impact factor: 3.488

8.  Polarizable empirical force field for alkanes based on the classical Drude oscillator model.

Authors:  Igor V Vorobyov; Victor M Anisimov; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2005-10-13       Impact factor: 2.991

9.  CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

Authors:  Sandeep Patel; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-01-15       Impact factor: 3.376

10.  Benzene forms hydrogen bonds with water.

Authors:  S Suzuki; P G Green; R E Bumgarner; S Dasgupta; W A Goddard; G A Blake
Journal:  Science       Date:  1992-08-14       Impact factor: 47.728

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  68 in total

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Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

5.  Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Authors:  Bin Lin; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-08-28       Impact factor: 3.488

Review 6.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
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7.  Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

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Journal:  J Comput Aided Mol Des       Date:  2017-02-11       Impact factor: 3.686

Review 8.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

9.  Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Authors:  Fang-Yu Lin; Pedro E M Lopes; Edward Harder; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2018-04-17       Impact factor: 4.956

10.  Recent Developments and Applications of the CHARMM force fields.

Authors:  Xiao Zhu; Pedro E M Lopes; Alexander D Mackerell
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2011-06-28
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