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

• DOI: 10.1021/acs.jpcb.8b01172
• Publication Date: 2018-03-20T17:17:32Z
• Authors: Yoshio Okiyama; Tatsuya Nakano; Chiduru Watanabe; Kaori Fukuzawa; Yuji Mochizuki; Shigenori Tanaka
• Keywords: Fragment molecular orbital; Polarizable continuum model; Implicit solvation; Poisson–Boltzmann equation; Biomolecule

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