Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2′-deoxythymidine with different anions

Abstract

Hydrogen bonding interactions between thymine nucleobase and 2 0 -deoxythymidine nucleoside (dT) with some biological anions such as F -(fluoride), Cl -(chloride), OH -(hydroxide), and NO 3 -(nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311??G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory atoms in molecules (QTAIM) approaches. Donors, acceptors, and orbital interaction energies were also calculated for the hydrogen bonds. Excellent correlations between structural parameter (dR) and electron density topological parameter (q b ) as well as between E(2) and q b have been found. It is interesting that hydrogen bonds with anions can affect the geometry of thymine and 2 0 -deoxythymidine molecules. For example, these interactions can change the bond lengths in thymine nucleobase, the orientation of base unit with respect to sugar ring, the furanose ring puckering, and the C1 0 -N1 glycosidic linkage in dT nucleoside. Thus, it is necessary to obtain a fundamental understanding of chemical behavior of nucleobases and nucleosides in presence of anions.

Tautomerisation of thymine acts against the Hückel 4N + 2 rule. The effect of metal ions and H-bond complexations on the electronic structure of thymine

“…Along with the studies of conventional H-bonds formed between nucleobase pairs, interest in interactions of DNA with anions has recently arisen. [44][45][46] Based on an extensive survey of the Nucleic Acid Database (NDB), Auffinger et al 44 concluded that anions (mostly Cl − and SO 4 − ) do intrude on the first hydration shell of nucleic acids and bind to electropositive amino, imino, and hydroxyl groups. Two types of such complexes formed by H-bonding of the most stable thymine tautomer with anions have recently been studied.…”

“…Along with the studies of conventional H-bonds formed between nucleobase pairs, interest in interactions of DNA with anions has recently arisen. [44][45][46] Based on an extensive survey of the Nucleic Acid Database (NDB), Auffinger et al 44 concluded that anions (mostly Cl − and SO 4…”

Nucleoside–AuCl4− interactions as studied by electrospray ionization mass spectrometry

“…The reason is that nucleic acids contain phosphate groups and they exist as anions (thus it is clear that they are not prone to interaction with other anions). On the other hand, there are a few interesting papers devoted to the interaction of inorganic anions with nucleobases or nucleosides . Furthermore, it has been found that organic anions may stabilize the octamer made of the G‐quadruplex .…”

Structural and electronic properties of alumaphosphinine complexes with metal ions: A theoretical study

“…The sign of H(r) determines whether the accumulation of charge at a given point (r) is stabilizing (H(r) < 0) or destabilizing (H(r) > 0). The energies for interaction of phosphorous atom and metal cation (E P M ) are calculated by the following equation [26][27][28][29]:…”