Literature DB >> 15260773

Coupled reference interaction site model/simulation approach for thermochemistry of solvation: theory and prospects.

Holly Freedman1, Thanh N Truong.   

Abstract

We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from a single molecular dynamics or Monte Carlo simulation. Here we describe in detail the coupled RISM/simulation approach, and offer some error analysis. Finally we give the results of its application to a set of small test molecules in aqueous solution. The success shown in some of our results demonstrates that the coupled RISM/simulation approach is worth considering further as a potentially useful tool in studies of solvated systems, such as aqueous molecular biosystems. (c) 2004 American Institute of Physics.

Year:  2004        PMID: 15260773     DOI: 10.1063/1.1760741

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


  3 in total

1.  Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent.

Authors:  Fumitaka Kamo; Ryosuke Ishizuka; Nobuyuki Matubayasi
Journal:  Protein Sci       Date:  2015-08-06       Impact factor: 6.725

Review 2.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

3.  Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

Authors:  Robert C Harris; Nanjie Deng; Ronald M Levy; Ryosuke Ishizuka; Nobuyuki Matubayasi
Journal:  J Comput Chem       Date:  2016-12-23       Impact factor: 3.376

  3 in total

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