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In this study, the drastic influence of the boron atom on the acidity of alcohol has been con-sidered. The calculated ΔHacid (320.9--338.1 kcal/mol) and pKa range of boron containing alcohol (--0.1--9.4) indicate that the boronation of alcohol leads to considerable enhancement of its acidity. For instance, we have obtained the ΔHacid values 338.1, 335.2 kcal/mol and the pKa values 4.12, 2.81 for BH2CH2OH, BF2CH2OH alcohols, respectively, which are much smaller than that of CH3OH (with ΔHacid = 374.9kcal/mol and pKa = 15). The increase in the acidity of boronated alcohol can be related to the stabilization of alkoxy ion due to overlap of unoc-cupied orbital of boron atom with the electron pairs of negative oxygen. All gas phase computations were performed at MP2/6-311++G(d,p)//(B3LYP/6-31+G(d)) level. The primary results indicate that the presence of boron atom in an alcohol might make it as acidic as nitric acid. The geometry optimization of studied structures was performed with DFT computation and optimized structures were used to carry out natural bond orbital (NBO) analysis. NBO analysis revealed that the increase in the acidity of boron-containing alcohols is due to the charge transfer from the negative oxygen (in deprotonated structure) to the empty orbital of --BH2 and --BF2. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of bonds formed in the deprotonated structure. [ABSTRACT FROM AUTHOR]

The radical cations of DNA constituents generated by the ionizing radiation initiate an alteration of the bases, which is one of the main types of cytotoxic DNA lesions. These cation radical spices are known for their role in producing nucleic acid strand break. In this study, the gas-phase intrinsic chemical properties of the gaseous radical cations of cytosine and its base pair with guanine were examined by employing density functional theory (B3LYP) with the 6-311++G(d,p) basis set. Structures, geometries, adiabatic ionization energies, adiabatic electron affinities, charge distributions, molecular orbital analysis and proton-transfer process of these molecules were investigated. The influence of cation radical formation on acidities of multiple sites in cytosine molecule was investigated. Results of calculations revealed that cytosine radicals formed by deprotonation of cytosine cation radicals can exothermically abstract hydrogen atoms from thiol groups, phenol, and α-positions of amino acid. Furthermore, comparison of acidity value of N-H sites of cytosine cation radical with the known proton affinities (PA) of organic and biological molecules implied that cytosine cation radical can exothermically transfer onto basic sites of amino acids and peptides. [ABSTRACT FROM AUTHOR]

In view of better understanding interactions of amino acids and peptides with metallic cations in the isolated state, the model system histidine–M2+ (M2+ = Mg2+, Ca2+, Zn2+) has been studied theoretically. The computations have been performed with the help of the density functional theory (DFT) and the B3LYP functional. The extended basis set was the standard 6-311++G**. All the molecular complexes obtained by the interaction between several energetically low-lying tautomers/conformers/zwitterions of histidine and the cations on different binding sites were considered. Our study shows that complexes of histidine with Mg2+, Ca2+, Zn2+ are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with oxygen and two nitrogen atoms: one from the terminal NH2 and one from the imidazole ring. All computations indicate that the metal ion affinity (MIA) decreases on going from Zn2+ to Mg2+ and Ca2+, for the considered amino acid. This indicates that histidine prefers to bind to the transition metal cation rather than alkali earth metals. The influence of theses cations on the acidity of histidine were also considered. As expected, upon metal complexation, proton dissociation of histidine becomes much more favorable, that is, its acidity becomes much less endothermic. [ABSTRACT FROM AUTHOR]

The gas-phase metal affinities of histidine Li+, Na+ and K+ ions have been determined theoretically employing the hybrid B3LYP exchange–correlation functional and using 6-311++G** basis sets. All computations indicate that the metal ion affinity decreases on going from Li+ to Na+ and K+ for the considered amino acid. Different types of M+ coordinations on several histidine conformers/tautomers were considered in detail. The optimized structures indicate that Li+ and Na+ prefer a tri-dentate coordination, bonding with a nitrogen atom of imidazole ring (Nτ), –NH2, and an oxygen atom of a carbonyl, while in the K+-histidine lowest-energy conformer, the cation appears to be bi-coordinated to both oxygen atoms of the zwitterionic form by the energy values not too far from that of tri-coordination. We also performed the DFT calculations for proton dissociation energy of histidine both in the presence and absence of alkali metal ions. Our results also reveal that the acidity of histidine dramatically increases upon metal ion complexation. [ABSTRACT FROM AUTHOR]