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Items: 1 to 20 of 166

1.

A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models.

Whitfield TW, Varma S, Harder E, Lamoureux G, Rempe SB, Roux B.

J Chem Theory Comput. 2007;3(6):2068-2082.

2.

Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models.

Davis JE, Rahaman O, Patel S.

Biophys J. 2009 Jan;96(2):385-402. doi: 10.1016/j.bpj.2008.09.048.

3.

Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.

Li H, Ngo V, Da Silva MC, Salahub DR, Callahan K, Roux B, Noskov SY.

J Phys Chem B. 2015 Jul 23;119(29):9401-16. doi: 10.1021/jp510560k. Epub 2015 Feb 4.

4.

Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations.

Cau√ęt E, Bogatko S, Weare JH, Fulton JL, Schenter GK, Bylaska EJ.

J Chem Phys. 2010 May 21;132(19):194502. doi: 10.1063/1.3421542.

PMID:
20499974
5.

The Solvation Structure of Na(+) and K(+) in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations.

Rowley CN, Roux B.

J Chem Theory Comput. 2012 Oct 9;8(10):3526-35. doi: 10.1021/ct300091w. Epub 2012 Apr 19.

PMID:
26593000
6.

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model.

Zhu X, MacKerell AD Jr.

J Comput Chem. 2010 Sep;31(12):2330-41. doi: 10.1002/jcc.21527.

7.

Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field.

Wu JC, Piquemal JP, Chaudret R, Reinhardt P, Ren P.

J Chem Theory Comput. 2010 Jul 13;6(7):2059-2070.

9.

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field.

Luo Y, Jiang W, Yu H, MacKerell AD Jr, Roux B.

Faraday Discuss. 2013;160:135-49; discussion 207-24.

10.

Thermodynamics of small alkali metal halide cluster ions: comparison of classical molecular simulations with experiment and quantum chemistry.

Vlcek L, Uhlik F, Moucka F, Nezbeda I, Chialvo AA.

J Phys Chem A. 2015 Jan 22;119(3):488-500. doi: 10.1021/jp509401d. Epub 2015 Jan 9.

PMID:
25513841
11.
12.

Dissociation of NaCl in water from ab initio molecular dynamics simulations.

Timko J, Bucher D, Kuyucak S.

J Chem Phys. 2010 Mar 21;132(11):114510. doi: 10.1063/1.3360310.

PMID:
20331308
13.

Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.

Savelyev A, MacKerell AD Jr.

J Phys Chem B. 2014 Jun 19;118(24):6742-57. doi: 10.1021/jp503469s. Epub 2014 Jun 9.

15.
16.

Hydration structure of salt solutions from ab initio molecular dynamics.

Bankura A, Carnevale V, Klein ML.

J Chem Phys. 2013 Jan 7;138(1):014501. doi: 10.1063/1.4772761.

PMID:
23298049
17.

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.

Izvekov S, Parrinello M, Burnham CJ, Voth GA.

J Chem Phys. 2004 Jun 15;120(23):10896-913.

PMID:
15268120
18.

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies.

Atta-Fynn R, Bylaska EJ, Schenter GK, de Jong WA.

J Phys Chem A. 2011 May 12;115(18):4665-77. doi: 10.1021/jp201043f. Epub 2011 Apr 18.

PMID:
21500828
19.

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.

Baker CM, Anisimov VM, MacKerell AD Jr.

J Phys Chem B. 2011 Jan 27;115(3):580-96. doi: 10.1021/jp1092338. Epub 2010 Dec 17.

20.

Solvation of the Guanidinium Ion in Pure Aqueous Environments: A Theoretical Study from an "Ab Initio"-Based Polarizable Force Field.

Houriez C, Meot-Ner Mautner M, Masella M.

J Phys Chem B. 2017 Dec 11. doi: 10.1021/acs.jpcb.7b07874. [Epub ahead of print]

PMID:
29182348

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