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Influence of the addition of water molecules ( n = 1-6) on the interaction energy between Li, Na, K cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the electron density (ρ( r)) in the cage critical points generated upon complexation and the distance between metal cation and centroid of phenyl ring in indole molecule. [ABSTRACT FROM AUTHOR]

The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li, Na, K, Mg, Ca, Zn, and Cu cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 2′-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn than do with Mg, Ca, and Cu and therefore stronger interactions lead to higher MIA. In both free molecules and their complexes, the Syn orientation of the base is stabilized by an intramolecular O5′-H···N3 hydrogen bond and the anti orientation of the base is stabilized by an intramolecular C-H···O hydrogen bond formed between the (C8-H8) and the O5′ atom of the sugar moiety. It is also interesting to mention that linear correlation between calculated MIA values and the atomic numbers ( Z) of the metal ions of Li, Na, and K were found. Furthermore, the influences of metal cationization on the strength of the N-glycosidic bond, torsion angles, angle of pseudorotation ( P), and intramolecular C-H···O and O-H···O hydrogen bonds have been studied. Natural bond orbital (NBO) analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of interactions. [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]