Contents lists available at ScienceDirect Chemical Physics journal homepage: www.elsevier.com/locate/chemphys Tuning of structural and magnetic properties by intriguing radical-radical interaction by double electron oxidation in U-A-U′ triplex formation Snehasis Bhunia a,b , Aditya Kumar a , Animesh K. Ojha a, ⁎ a Department of Physics, Motilal Nehru National Institute of Technology, Allahabad 211004, India b Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan ARTICLE INFO Keywords: RNA triplex Coupling constant Broken symmetry approach CASSCF Di-radical ABSTRACT The spin coupling properties of a series of two di-radical centers A % U % and A % U′ % in U-A-U′ triplex were in- vestigated. These two series are considered by intriguing the radical-radical cation (A %+ U %+ and A %+ U′ %+ ), radical-dehydrogenated (A %+ U(-H1) % , A(-H1) % U %+ , A(-H1) % U′ %+ and A %+ U′(-H1)), and dehydrogenated-de- hydrogenated (A(-H1) % U(-H1) % and A(-H1) % U′(-H1) % ) as RNA base couplers. The structural and electronic properties were calculated employing density functional theory (DFT). The di-radical character was identifed by performing DFT and complete active space self-consistent (CASSCF) calculations. The calculated value of cou- pling constant revealed the presence of both types of magnetic interaction i.e. ferromagnetic (FM) and anti- ferromagnetic (AFM). A strong magnetic interaction is found for the radical-dehydrogenated A(-H1) % U %+ series whereas a weak magnetic interaction is observed for radical-radical cation, A %+ U %+ ,A %+ U′ %+ and other di- radical series e.g. A %+ U(-H1) % ,A %+ U′(-H1) % , and A(-H1) % U′(-H1) % . The transformation of FM and AFM coupling with the change in dehydrogenation sites is explained with the help of distribution of spin density. 1. Introduction Knowledge of the nature of binding and sequence specifcity in the triplex formation of a molecule with a diverse class of oligonucleotides is essential due to its great potential in the feld of molecular biology and gene therapy. The existence of specifc binding pattern in the tri- plex molecules has made it important for intensive study. Triplex mo- lecules are mainly formed by duplex and single-strand messenger. Natural and modifed oligonucleotides such as, peptide nucleic acids (PNAs) may have a role for third strand binding to genetic targets [1–3] A RNA duplex may accomplish the third strand by forming a minor- groove and a major-groove triplex, respectively without distracting the stable duplex structure. For shaping RNAs into complex three-dimen- sional architectures, the naturally formed triplexes play an important role [1,4]. The triplex structure of RNA is reported to perform diverse biological functions [5–12]. A triplex containing a regular sequence of U⋅A-U base triples has been found in a stable form in RNA poly(U)⋅poly (A)-poly(U) major-groove in the presence of Mg 2+ ions [13]. The U⋅A-U base triplex was observed frst in RNA pseudoknot of the human telo- merase in absence of Mg 2+ ions [5–7]. In this triplex structure, Wat- son–Crick A-U combines with Hoogsteen U⋅A pairs with two poly(U) strands. The formation of radicals via oxidation and radiation-based ionization of nucleobases has been the subject of immense research interest for the scientifc community due to its biological signifcant [14]. The base radical cation is more acidic rather than its neutral structure, and deprotonates easily to form the base neutral radical. The deprotonated radical can direct to a variety of life degrading phe- nomena, damage to the genetic code and may attribute for developing in electrochemical devices. In this perspective, the understanding of deprotonation mechanism and formation of the radical cation is im- portant to apprehend the relevant way of oxidative damage in DNA and molecular electronics of DNA-based devices [15,16]. During last two decades, experimental and theoretical investigations have been done to shed more light on the radical formation and their consequences. Both, experimental and theoretical exploration had been elucidated on this topic for two decades. The time evolution of base radicals of DNA du- plex and quadruplex was nicely-investigated by employing pulsed electron beams [17–21]. Guanine is recognized as a good hole transfer, thereby extensive studies were done on guanine based radicals [17,20–22]. Theoretical investigations had been done to study the en- ergetic and structural characteristics of both the deprotonated and closed-shell of guanine-cytosine (G-C) [22–25], and adenine-thymine (A-T) base pairs [26,27], as well as the closed-shell and deprotonated base pair of adenine-uracil (A-U) [28,29]. It is reported that the de- protonated nucleobases (or, dehydrogenated nucleobases) can exist in https://doi.org/10.1016/j.chemphys.2019.110527 Received 22 January 2019; Received in revised form 21 July 2019; Accepted 11 September 2019 ⁎ Corresponding author. E-mail addresses: animesh@mnnit.ac.in, animesh198@gmail.com (A.K. Ojha). Chemical Physics 528 (2020) 110527 Available online 12 September 2019 0301-0104/ © 2019 Elsevier B.V. All rights reserved. T