ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

How the stability, reactivity and optical response of the protonated base pairs differ with other biologically important adenine–thymine pairs: a DFT and TD-DFT approach

Ranjan Sutradhar, Sumana Gop, Sumana Chakraborty, and Tripurari Prasad Sinha

Department of Physics, Bose Institute, Kolkata, India

E-mail: rsutradhar.physics@gmail.com

Received: 29 August 2020  Accepted: 16 December 2020

Abstract:

Abstract

The chemical behaviour of six biologically important Adenine (A)–Thymine (T) base pairs formed as a result of the interaction between Watson–Crick(WC) type Adenine, Thymine, rare Adenine (A*) and rare Thymine (T*) bases have been studied using density functional theory (DFT) and time-dependent DFT (TD-DFT). The geometrical optimization and other relevant properties have been calculated by employing the hybrid functional CAM-B3LYP and M06-2X with 6-311++G(d,p) basis set for the reliable treatment of dispersion interaction in the gas phase. The energetic parameters show that the A*T* base pair has the highest binding energy. The characteristic Raman modes due to stretching vibrations show significant change for conformational and structural alteration. The absorption spectra of all AT conformers belong to the UV region and the excitations are due to π → π* and π → ryd* transitions. A distinct absorption peak has been observed for the protonated base pairs at a relatively higher wavelength. Natural transition orbital and molecular orbital analysis define charge transfer states associated with the electronic transitions. The lowest ionization potential, positive electron affinity and least value of hardness of the A*T* compared to the other AT base pairs suggest more reactivity of A*T* base pair than the others in chemical and biological reactions. Naturally, these structural rearrangements affect various biological and chemical processes, therefore, this study may be helpful to find out the best fit between the structurally flexible ligand and receptor and how the interaction will affect the chemistry of these important molecules.

Graphic abstract

Keywords: DNA base pairs; Vibrational spectra; UV–Vis spectra; Reactivity; DFT; TD-DFT

Full paper is available at www.springerlink.com.

DOI: 10.1007/s11696-020-01474-x

Chemical Papers 75 (5) 2159–2172 (2021)