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


Kurt B., Temel H.

CHEMICAL PHYSICS LETTERS, vol.775, 2021 (Journal Indexed in SCI) identifier identifier

  • Publication Type: Article / Article
  • Volume: 775
  • Publication Date: 2021
  • Doi Number: 10.1016/j.cplett.2021.138656
  • Title of Journal : CHEMICAL PHYSICS LETTERS
  • Keywords: Boron, Aromatic, AMBER, Parameterization, FORCE-FIELD PARAMETERS, DERIVING ATOMIC CHARGES, OPTIMIZATION, SOFTWARE, PARAMFIT, VFFDT, DNA

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.