Literature DB >> 20161692

Developing Force Fields from the Microscopic Structure of Solutions.

Elizabeth A Ploetz1, Nikolaos Bentenitis, Paul E Smith.   

Abstract

We have been developing force fields designed for the eventual simulation of peptides and proteins using the Kirkwood-Buff (KB) theory of solutions as a guide. KB theory provides exact information on the relative distributions for each species present in solution. This information can also be obtained from computer simulations. Hence, one can use KB theory to help test and modify the parameters commonly used in biomolecular studies. A series of small molecule force fields representative of the fragments found in peptides and proteins have been developed. Since this approach is guided by the KB theory, our results provide a reasonable balance in the interactions between self-association of solutes and solute solvation. Here, we present our progress to date. In addition, our investigations have provided a wealth of data concerning the properties of solution mixtures, which is also summarized. Specific examples of the properties of aromatic (benzene, phenol, p-cresol) and sulfur compounds (methanethiol, dimethylsulfide, dimethyldisulfide) and their mixtures with methanol or toluene are provided as an illustration of this kind of approach.

Entities:  

Year:  2010        PMID: 20161692      PMCID: PMC2821164          DOI: 10.1016/j.fluid.2009.11.023

Source DB:  PubMed          Journal:  Fluid Phase Equilib        ISSN: 0378-3812            Impact factor:   2.775


  11 in total

1.  Infrared spectroscopy of size-selected water and methanol clusters.

Authors:  U Buck; F Huisken
Journal:  Chem Rev       Date:  2000-11-08       Impact factor: 60.622

2.  A Kirkwood-Buff derived force field for the simulation of aqueous guanidinium chloride solutions.

Authors:  Samantha Weerasinghe; Paul E Smith
Journal:  J Chem Phys       Date:  2004-08-01       Impact factor: 3.488

3.  A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Authors:  Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

4.  Modeling nonionic aqueous solutions: the acetone-water mixture.

Authors:  Aurlien Perera; Franjo Sokolić
Journal:  J Chem Phys       Date:  2004-12-08       Impact factor: 3.488

5.  The Amber biomolecular simulation programs.

Authors:  David A Case; Thomas E Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J Woods
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

6.  Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues.

Authors:  Zhitao Xu; Harry H Luo; D Peter Tieleman
Journal:  J Comput Chem       Date:  2007-02       Impact factor: 3.376

7.  Molecular basis of the apparent near ideality of urea solutions.

Authors:  Hironori Kokubo; Jörg Rösgen; D Wayne Bolen; B Montgomery Pettitt
Journal:  Biophys J       Date:  2007-08-10       Impact factor: 4.033

8.  A Kirkwood-Buff derived force field for amides.

Authors:  Myungshim Kang; Paul E Smith
Journal:  J Comput Chem       Date:  2006-10       Impact factor: 3.376

9.  A Kirkwood-Buff derived force field for thiols, sulfides, and disulfides.

Authors:  Nikolaos Bentenitis; Nicholas R Cox; Paul E Smith
Journal:  J Phys Chem B       Date:  2009-09-10       Impact factor: 2.991

10.  Microstructure of neat alcohols: a molecular dynamics study.

Authors:  Larisa Zoranić; Franjo Sokolić; Aurélien Perera
Journal:  J Chem Phys       Date:  2007-07-14       Impact factor: 3.488

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  20 in total

1.  A Kirkwood-Buff force field for the aromatic amino acids.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  Phys Chem Chem Phys       Date:  2011-09-19       Impact factor: 3.676

2.  Kirkwood-Buff integrals for ideal solutions.

Authors:  Elizabeth A Ploetz; Nikolaos Bentenitis; Paul E Smith
Journal:  J Chem Phys       Date:  2010-04-28       Impact factor: 3.488

3.  Local Fluctuations in Solution: Theory and Applications.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  Adv Chem Phys       Date:  2013       Impact factor: 1.000

4.  Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization.

Authors:  Mark S Miller; Wesley K Lay; Adrian H Elcock
Journal:  J Phys Chem B       Date:  2016-04-21       Impact factor: 2.991

5.  Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other.

Authors:  Casey T Andrews; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2013-10-08       Impact factor: 6.006

6.  Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for liquid mixtures.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  J Chem Phys       Date:  2015-03-07       Impact factor: 3.488

7.  Local fluctuations in solution mixtures.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  J Chem Phys       Date:  2011-07-28       Impact factor: 3.488

Review 8.  Toward an understanding of biochemical equilibria within living cells.

Authors:  Germán Rivas; Allen P Minton
Journal:  Biophys Rev       Date:  2017-12-12

9.  Theory and Simulation of Multicomponent Osmotic Systems.

Authors:  Sadish Karunaweera; Moon Bae Gee; Samantha Weerasinghe; Paul E Smith
Journal:  J Chem Theory Comput       Date:  2012-10-09       Impact factor: 6.006

10.  Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.

Authors:  Wesley K Lay; Mark S Miller; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2017-04-28       Impact factor: 6.006

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