Application of the Approximate 3D-Reference Interaction Site Model (RISM) Molecular Solvation Theory to Acetonitrile as Solvent

2020 ◽  
Vol 124 (22) ◽  
pp. 4590-4597 ◽  
Author(s):  
Dipankar Roy ◽  
Andriy Kovalenko
Keyword(s):  
Interaction Site ◽  
Site Model ◽  
Reference Interaction Site ◽  
Solvation Theory

scholarly journals Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory

2021 ◽  
Vol 22 (10) ◽  
pp. 5061
Author(s):  
Dipankar Roy ◽  
Andriy Kovalenko
Keyword(s):  
Ligand Binding ◽  
Molecular Simulation ◽  
Solvation Energy ◽  
Modeling Framework ◽  
Time Step ◽  
Interaction Site ◽  
Energy Calculations ◽  
Site Model ◽  
Reference Interaction Site ◽  
Solvation Theory

The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé–Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work.

Role of Mg2+Ions in DNA Hydrolysis byEcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics

2018 ◽  
Vol 122 (39) ◽  
pp. 9061-9075 ◽  
Author(s):  
Itaru Onishi ◽  
Shunya Sunaba ◽  
Norio Yoshida ◽  
Fumio Hirata ◽  
Masayuki Irisa
Keyword(s):  
Molecular Dynamics ◽  
Dna Hydrolysis ◽  
Interaction Site ◽  
Site Model ◽  
Reference Interaction Site

Multigrid solver for the reference interaction site model of molecular liquids theory

2011 ◽  
Vol 32 (9) ◽  
pp. 1982-1992 ◽  
Author(s):  
Volodymyr P. Sergiievskyi ◽  
Wolfgang Hackbusch ◽  
Maxim V. Fedorov
Keyword(s):  
Molecular Liquids ◽  
Multigrid Solver ◽  
Interaction Site ◽  
Site Model ◽  
Reference Interaction Site

The Excluded Volume Problem in the Polymer Reference Interaction Site Model

1999 ◽  
Vol 32 (6) ◽  
pp. 2016-2027 ◽  
Author(s):  
Erik Nies ◽  
Suxin Wang ◽  
Rob H. C. Janssen ◽  
Peter Cifra
Keyword(s):  
Excluded Volume ◽  
Interaction Site ◽  
Site Model ◽  
Volume Problem ◽  
Reference Interaction Site
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