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

Kurt B., Temel H.

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

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 775
  • Basım Tarihi: 2021
  • Doi Numarası: 10.1016/j.cplett.2021.138656
  • Dergi Adı: CHEMICAL PHYSICS LETTERS
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Chemical Abstracts Core, INSPEC
  • Anahtar Kelimeler: Boron, Aromatic, AMBER, Parameterization, FORCE-FIELD PARAMETERS, DERIVING ATOMIC CHARGES, OPTIMIZATION, SOFTWARE, PARAMFIT, VFFDT, DNA
  • Yozgat Bozok Üniversitesi Adresli: Evet

Özet

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.