Literature DB >> 24007020

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

Bin Lin1, Pedro E M Lopes, Benoît Roux, Alexander D MacKerell.   

Abstract

Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.

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Year:  2013        PMID: 24007020      PMCID: PMC3772949          DOI: 10.1063/1.4818731

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  46 in total

1.  Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator.

Authors:  Edward Harder; Victor M Anisimov; Igor V Vorobyov; Pedro E M Lopes; Sergei Y Noskov; Alexander D MacKerell; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2006-11       Impact factor: 6.006

2.  Preferential solvation in urea solutions at different concentrations: properties from simulation studies.

Authors:  Hironori Kokubo; B Montgomery Pettitt
Journal:  J Phys Chem B       Date:  2007-04-21       Impact factor: 2.991

Review 3.  CHARMM: the biomolecular simulation program.

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

4.  Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

Authors:  Igor Vorobyov; Victor M Anisimov; Shannon Greene; Richard M Venable; Adam Moser; Richard W Pastor; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2007-05       Impact factor: 6.006

5.  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

6.  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

7.  Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

Authors:  Pedro E M Lopes; Guillaume Lamoureux; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2009-09       Impact factor: 3.376

8.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

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.  AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA.

Authors:  Lei Huang; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2013-08-13       Impact factor: 6.006

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  13 in total

1.  Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

Authors:  Meagan C Small; Asaminew H Aytenfisu; Fang-Yu Lin; Xibing He; Alexander D MacKerell
Journal:  J Comput Aided Mol Des       Date:  2017-02-11       Impact factor: 3.686

2.  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

Review 3.  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

4.  Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

Authors:  Pedro E M Lopes; Jing Huang; Jihyun Shim; Yun Luo; Hui Li; Benoît Roux; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2013-12-10       Impact factor: 6.006

5.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

6.  Current status of protein force fields for molecular dynamics simulations.

Authors:  Pedro E M Lopes; Olgun Guvench; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2015

7.  Force Fields for Small Molecules.

Authors:  Fang-Yu Lin; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2019

Review 8.  An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Authors:  Justin A Lemkul; Jing Huang; Benoît Roux; Alexander D MacKerell
Journal:  Chem Rev       Date:  2016-01-27       Impact factor: 60.622

9.  Experimental Atom-by-Atom Dissection of Amide-Amide and Amide-Hydrocarbon Interactions in H2O.

Authors:  Xian Cheng; Irina A Shkel; Kevin O'Connor; John Henrich; Cristen Molzahn; David Lambert; M Thomas Record
Journal:  J Am Chem Soc       Date:  2017-07-17       Impact factor: 15.419

10.  A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields.

Authors:  Bin Lin; Xibing He; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2013-08-29       Impact factor: 2.991

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