Quasi-chemical theory and implicit solvent models for simulations

  title={Quasi-chemical theory and implicit solvent models for simulations},
  author={Lawrence R Pratt and Susan L B Rempe},
  journal={arXiv: Chemical Physics},
A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent model is based upon the quasi-chemical approach, distinct from the common integral equation trunk of the theory of liquid solutions. The idea is geometrically to define molecular-scale regions attached to the solute macromolecule of interest. It is then… 

Figures and Tables from this paper

Dielectric continuum methods for quantum chemistry

  • J. Herbert
  • Physics
    WIREs Computational Molecular Science
  • 2021
This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the

The hydration number of Na+ in liquid water

Hydration theory for molecular biophysics.

Utility of chemical computations in predicting solution free energies of metal ions

Abstract Here, we study quasi-chemical theory (QCT) for the free energies of divalent alkaline earth ions (Ba, Sr, Ca, Mg) in water, emphasizing that: (a) interactions between metal ions and proximal

Quasi-chemical theory of F-(aq): The "no split occupancies rule" revisited.

It is anticipated that other aqueous halide ions might be treated successfully with QCT, provided that the structure of the underlying statistical mechanical theory is absorbed, i.e., that the "no split occupancies" rule is recognized.

Hydrated Anions: From Clusters to Bulk Solution with Quasi-Chemical Theory

Conspectus The interactions of hydrated ions with molecular and macromolecular solution and interface partners are strong on a chemical energy scale. Here, we recount the foremost ab initio theory

Regularizing Binding Energy Distributions and the Hydration Free Energy of Protein Cytochrome C from All-Atom Simulations.

By introducing an external field to temper short-range protein water interactions, the statistical problem of calculating the hydration free energy of the protein cytochrome C is regularized using the potential distribution theorem and potential applications are indicated toward illuminating the role of water, ions, and osmolytes in protein solution thermodynamics, including in protein folding and aggregation.

Hydration of Kr(aq) in Dilute and Concentrated Solutions.

The thermodynamic analysis interconnecting these two approaches shows that they are closely consistent with each other, providing support for both approaches.

Ab initio molecular dynamics calculations of ion hydration free energies.

Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential contributions, absolute AIMD hydration free energies (DeltaG(hyd)) are obtained within a few kcal/mol of Tissandier et al.'s experimental values augmented with the SPC/E water model phi predictions.



Generalized solvent boundary potential for computer simulations

Approaches to obtain statistical properties similar to those of an infinite bulk system from computer simulations of a finite cluster are reviewed. A rigorous theoretical formulation is given for the

Implicit solvent models for protein-ligand binding: Insights based on explicit solvent simulations

This work has studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models, and finds that the solvation free energy calculations are more than 103 faster using the Surface Generalized Born implicit solvent model as compared to FEP simulations with explicit solvent.

Statistical Mechanics:

AbstractPROF. R. H. FOWLER'S monumental work on statistical mechanics has, in this the second edition, in his own modest words, been rearranged and brought more up to date. But the new volume is much

Water A Comprehensive Treatise, edited by F

  • 1973

Stochastic Processes in Physics and Chemistry

Exploring chemistry with electronic structure methods