Sharif Digital Repository

Gas-phase acidities of nucleosides, combined with the knowledge of deprotonation sites, could improve our understanding of chemical reactions to biological systems. In this paper, we mainly focus our attention on the influence of cation coordination on acidities of multiple sites in cytosine nucleosides. The acidities of multiple sites in M +-L (where L represents cytosine nucleosides and M + is an alkali metal ion, including Li +, Na + and K +) complexes have been investigated theoretically, employing B3LY P6-311++G(d,p) basis sets. The geometrical characters, gas-phase acidities, sugar puckering and electronic properties of non-deprotonated and/or deprotonated complexes have been... 

Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M3 clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M3 clusters is governed by two major bonding factors: (a) the anchoring N-M and O-M bonds and (b) the nonconventional N-H⋯M and O-H⋯M hydrogen bonds. The nature of these chemical bonds has been investigated based on quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. In the next... 

The pK a of an acyclic aliphatic heptaol ((HOCH 2CH 2CH(OH)CH 2) 3COH) was measured in DMSO, and its gas-phase acidity is reported as well. This tertiary alcohol was found to be 10 21 times more acidic than tert-butyl alcohol in DMSO and an order of magnitude more acidic than acetic acid (i.e., pK a = 11.4 vs 12.3). This can be attributed to a 21.9 kcal mol -1 stabilization of the charged oxygen center in the conjugate base by three hydrogen bonds and another 6.3 kcal mol -1 stabilization resulting from an additional three hydrogen bonds between the uncharged primary and secondary hydroxyl groups. Charge delocalization by both the first and second solvation shells may be used to facilitate... 

Hydrogen bonds are the dominant motif for organizing the three-dimensional structures of biomolecules such as carbohydrates, nucleic acids, and proteins, and serve as templates for proton transfer reactions. Computations, gas-phase acidity measurements, and pKa determinations in dimethyl sulfoxide on a series of polyols indicate that multiple hydrogen bonds to a single charged center lead to greatly enhanced acidities. A new class of Brønsted acids, consequently, is proposed. © 2009 American Chemical Society