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Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study
journal contribution
posted on 2018-03-20, 00:00 authored by Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori TanakaIn
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.
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Keywords
surface areastabilityInteraction analysiselectrolyte distributionsolvated biomoleculesab initio methodologyFMO electron densitychemical processesinteractionDickerson dodecamerImplicit SolventFMO-PBSA approachab initio fragmentnonpolar contributionsdispersion effectsDNA StudyDNA duplexespolarizable soluteFragment Molecular Orbital Calculationsmodel showPoisson
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