Development of AMBER parameters for molecular dynamics simulations of boron compounds containing aromatic structure

Kurt B., Temel H.

CHEMICAL PHYSICS LETTERS, vol.775, 2021 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 775
  • Publication Date: 2021
  • Doi Number: 10.1016/j.cplett.2021.138656
  • Journal Name: CHEMICAL PHYSICS LETTERS
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Chemical Abstracts Core, INSPEC
  • Keywords: Boron, Aromatic, AMBER, Parameterization, FORCE-FIELD PARAMETERS, DERIVING ATOMIC CHARGES, OPTIMIZATION, SOFTWARE, PARAMFIT, VFFDT, DNA
  • Yozgat Bozok University Affiliated: Yes

Abstract

In this study, the Amber force field parameters for benzodioxaboroles which are boron compounds containing aromatic structure, were produced. The Root-Mean-Square Deviation (RMSD) value between the minimized geometries and x-ray structures was found to be very close to the values obtained by the quantum mechanical calculation. Then, an anti-cancer boron compound was used as ligand, molecular dynamics simulation of the DNA-Ligand complex was successfully performed and the previously reported experimentally anti-cancer feature was approved by the molecular dynamics simulation. As a result, the library of parameters needed to perform molecular dynamics simulation of benzodioxaborole compounds was produced successfully.