Sharif Digital Repository

In this study, drastic influence of the intramolecular cation-π interaction on the basicity of selected amines has been considered. The optimized minimum energy geometries of different studied amines and their protonated structures were determined by using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. Geometry optimizations indicate that the most stable structures of protonated amines are stabilized by intramolecular cation-π interaction. The proton affinity (PA) of selected amines is controlled by the strength of intramolecular cation-π interaction of ammonium with aromatic ring. These cation-π interactions strongly influence the basicity of amines. Natural bond orbital (NBO)... 

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 2+, Ca 2+, Zn 2+, 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 20-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 2+ than do with Mg 2+, Ca 2+, and Cu? and therefore stronger interactions lead to higher MIA.... 

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... 

Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate... 

The binding of Mg 2+, Ca 2+, Zn 2+ and Cu + metal cations to 2′-deoxyguanosine has been analyzed, using the hybrid B3LYP, Density Functional Theory (DFT) method and 6311++G(d,p) orbital basis sets. Coordination geometries, absolute metal ion affinities, and free energies for the most stable complexes formed by Mg 2+, Ca 2+, Zn 2+ and Cu + with the nucleoside, 2′-deoxyguanosine, have been determined. Furthermore, the influences of metal cationization on the strength of the N-glycosidic bond, torsion angles and angle of Pseudorotation (P) have been studied. With respect to the results, it has been found that metal binding significantly changes the values of the phase angle of Pseudorotation... 

The optimized minimum-energy geometries of different macrocyclic amines and their protonated structures were determined by using ab initio and density functional theory (DFT) calculations. All the gas phase optimizations and energy calculations were performed at the DFT/B3LYP/6-311++G(d,p) level of theory. The HF/6-31 + G(d,p) level was used for all single point calculations in the solution phase. Geometry optimizations indicate that the most stable structures are stabilized by intramolecular hydrogen bonds. The proton affinity (PA) of macrocyclic amines is controlled by the strength of intramolecular hydrogen bonds of macrocyclic amines. These hydrogen bonds strongly influence the basicity...