Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions

Bin Lin, Ka Yiu Wong, Char Hu, Hironori Kokubo, Bernard Pettitt

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.

Original languageEnglish (US)
Pages (from-to)1626-1632
Number of pages7
JournalJournal of Physical Chemistry Letters
Volume2
Issue number13
DOIs
StatePublished - Jul 7 2011
Externally publishedYes

Fingerprint

Solvation
radial distribution
Free energy
Distribution functions
solvation
Electrostatics
distribution functions
free energy
electrostatics
continuums
simulation
alanine
retaining
complex systems
Alanine
Peptides
peptides
Large scale systems
Scanning
scanning

ASJC Scopus subject areas

  • Materials Science(all)

Cite this

Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions. / Lin, Bin; Wong, Ka Yiu; Hu, Char; Kokubo, Hironori; Pettitt, Bernard.

In: Journal of Physical Chemistry Letters, Vol. 2, No. 13, 07.07.2011, p. 1626-1632.

Research output: Contribution to journalArticle

@article{73265f7edcdb4277ad4ab1519a6f13e4,
title = "Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions",
abstract = "Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.",
author = "Bin Lin and Wong, {Ka Yiu} and Char Hu and Hironori Kokubo and Bernard Pettitt",
year = "2011",
month = "7",
day = "7",
doi = "10.1021/jz200609v",
language = "English (US)",
volume = "2",
pages = "1626--1632",
journal = "Journal of Physical Chemistry Letters",
issn = "1948-7185",
publisher = "American Chemical Society",
number = "13",

}

TY - JOUR

T1 - Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions

AU - Lin, Bin

AU - Wong, Ka Yiu

AU - Hu, Char

AU - Kokubo, Hironori

AU - Pettitt, Bernard

PY - 2011/7/7

Y1 - 2011/7/7

N2 - Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.

AB - Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.

UR - http://www.scopus.com/inward/record.url?scp=79960164079&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79960164079&partnerID=8YFLogxK

U2 - 10.1021/jz200609v

DO - 10.1021/jz200609v

M3 - Article

VL - 2

SP - 1626

EP - 1632

JO - Journal of Physical Chemistry Letters

JF - Journal of Physical Chemistry Letters

SN - 1948-7185

IS - 13

ER -