Understanding atomic bonding and electronic distributions of a DNA molecule using DFT calculation and BOLS-BC model

Anlin Deng; Hanze Li; Maolin Bo; ZhongKai Huang; Lei Li; Chuang Yao; Fengqin Li

doi:10.1016/j.bbrep.2020.100804

Understanding atomic bonding and electronic distributions of a DNA molecule using DFT calculation and BOLS-BC model

Biochem Biophys Rep. 2020 Aug 30:24:100804. doi: 10.1016/j.bbrep.2020.100804. eCollection 2020 Dec.

Authors

Anlin Deng¹, Hanze Li¹, Maolin Bo¹, ZhongKai Huang¹, Lei Li¹, Chuang Yao¹, Fengqin Li²

Affiliations

¹ Chongqing Key Laboratory of Extraordinary Bond Engineering and Advanced Materials Technology (EBEAM), Yangtze Normal University, Chongqing, 408100, China.
² Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.

Abstract

Deoxyribonucleic acid (DNA) is an important molecule that has been extensively researched, mainly due to its structure and function. Herein, we investigated the electronic behavior of the DNA molecule containing 1008 atoms using density functional theory. The bond-charge (BC) model shows the relationship between charge density and atomic strain. Besides, the model mentioned above is combined with the bond-order-length-strength (BOLS) notion to calculate the atomic cohesive energy, the bond energy, and the local bond strain of the DNA chain. Using the BOLS-BC model, we were able to obtain information on the bonding features of the DNA chain and better comprehend the associated properties of electrons in biological systems. Consequently, this report functions as a theoretical reference for the precise regulation of the electrons and the bonding states of biological systems.

Keywords: BOLS-BC Model; Charge density; DFT calculation; DNA.