Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: Implementation and DNA Study

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

In this study, an ab initio fragment molecular orbital (FMO) methodology was developed to evaluate the solvent effects on electrostatic interactions, which make a significant contribution to the physical and chemical processes occurring in biological systems. Here, a fully polarizable solute consisting of the FMO electron density was electrostatically coupled with an implicit solvent based on the Poisson-Boltzmann (PB) equation; in addition, the nonpolar contributions empirically obtained from the molecular surface area (SA) were added. Interaction analysis considering solvent-screening and dispersion effects is now available as a powerful tool to determine the local stabilities inside solvated biomolecules. This methodology is applied to a deoxyribonucleic acid (DNA) duplex known as the Dickerson dodecamer. We found that excessively large electrostatic interactions inside the duplex are effectively damped by the screening, and the frontier molecular orbital energies are also successfully lowered. These observations indicate the stability of highly charged DNA duplexes in solution. Moreover, the solvation free energies in the implicit model show fairly good agreement with those in the explicit model while avoiding the costly statistical sampling of the electrolyte distribution. Consequently, our FMO-PBSA approach could yield new insights into biological phenomena and pharmacological problems via this ab initio methodology.

Original languageEnglish
Pages (from-to)4457-4471
Number of pages15
JournalJournal of Physical Chemistry B
Volume122
Issue number16
DOIs
Publication statusPublished - 2018 Apr 26
Externally publishedYes

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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