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In the present density functional theory study, we have compared intrinsic properties of non-natural nucleobases ( acA, acG, acC, and acT nucleobases) such as proton affinities, gas phase acidities, tautomerization, and hydrogen-bonding properties with those in normal Watson-Crick nucleobases (A, G, C, T nucleobases). The hydrogen-bonding interactions in non-natural and Watson-Crick base pairs were studied at B3LYP/6-311++G (d,p) level regarding their geometries, energies, and topological features of the electron density. The quantum theory of atoms-in-molecule (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in base pairs. The electron density ρ( r) as well as its Laplacian $$ \nabla^{2} $$ ρ( r) at the hydrogen bond critical point predicted by QTAIM is strongly correlated with hydrogen bond structural parameter and the second-order perturbation energies in NBO scheme. Our results show that most of hydrogen bonds in normal Watson-Crick and non-natural base pairs must be considered as electrostatic interactions. Results of calculations revealed that energetic values of hydrogen bonds in T- A base pair are more than those in ac T- ac A base pair, while values of hydrogen bonds in C- G base pair and ac C- ac G base pair are almost the same. These results confirmed stability order of stabilization energies of these base pairs. [ABSTRACT FROM AUTHOR]

The relative stabilities and noncovalent interactions of the six low-lying energy tautomers of cytosine nucleobase with some biological anions (such as F, Cl, and CN) have been investigated in gas phase by density functional theory (DFT) method in conjunction with 6-311++G (d,p) atomic basis set. Furthermore, to systematically investigate all possible tautomerisms from cytosine induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase and in a continuum solvent using DFT calculation. We carried out geometrical optimizations with the integral equation formalism of polarizable continuum (IEF-PCM) model to account for the solvent effect, and the results were compared with those in the gas phase. The result of calculation revealed that anions bind mostly in a bidentate manner via hydrogen bond, and stabilization energies of these complexes are larger than those in the case when anions bind in a monodentate manner. The quantum theory of atoms in molecules (QTAIM), natural bonding orbital (NBO) and energy decomposition analysis (EDA) have also been applied to understand the nature of hydrogen bond interactions in these complexes. NBO analysis reveals that the interaction patterns between the anions and the tautomers are σ-type interaction between lone pairs and $$ \sigma_{{_{{{\text{N}}--{\text{H}}}} }}^{*} $$, $$ \sigma_{{_{{{\text{O}}--{\text{H}}}} }}^{*} $$ and $$ \sigma_{{_{{{\text{H}}--{\text{F}}}} }}^{*} $$ antibonding orbitals. Also, according to these theories, the interactions are found to be partially electrostatic and partially covalent. EDA results identify that these bonds have less than 35% covalent character and more than 65% electrostatic, and the covalent character increases in different anions in the order F > CN > Cl. On the other hand, orbital interaction energies of complexes of F anion are more than those of Cl and CN complexes. The lower orbital interaction energies in complexes of Cl and CNanions imply less charge transfer and stronger ionic bond character. Furthermore, relationship between the orbital interaction energy ( E) with hydrogen bonding energy ( E) and the electron density (ρ( r)) with hydrogen bonding energy of F, Cl and CN complexes have also been investigated. [ABSTRACT FROM AUTHOR]

Hydrogen bonding interactions between thymine nucleobase and 2′-deoxythymidine nucleoside (dT) with some biological anions such as F (fluoride), Cl (chloride), OH (hydroxide), and NO (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 (δ R) and electron density topological parameter ( ρ) as well as between E(2) and ρ have been found. It is interesting that hydrogen bonds with anions can affect the geometry of thymine and 2′-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′-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. [ABSTRACT FROM AUTHOR]