Sharif Digital Repository

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density Δ2 ρ(r) from Bader's atom in molecules theory. Charge transfer energies based on... 

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... 

Histidine as a natural amino acid is found to be biologically important and is known to function as a nucleophile or enzyme co-factor, or in proton transfer process. The properties of gaseous aromatic amino acid histidine depend on the structural forms it may take in gas-phase. Ab initio method has been used to characterize the gas-phase conformer/tautomers of histidine. Wide range of possible structures for histidine was surveyed at the MM level, and then the geometries of the unique conformers were refined at the B3LYP/6-311++G (d,p) levels. At this theoretical level, 25 conformers were located for both tautomers of histidine i.e., His [NπH] and His [NτH]. The MM level provides a poor... 

In this research, gel production from the extracted pectin gel of shahroud sugar beet pulp has been investigated. The pectin extractions were performed in a cold alkaline solution and a hot acid solution, respectively. The effects of different parameters, such as percent of sugar, pectin concentration, calcium content and quantity of peroxidase enzyme, hardness and content of water absorbed by the gel, were studied. Optimum conditions for production of favorable gel, from extracted pectin in this research are, as follows: Percent of sugar (glucose): 15%, peroxidase enzyme content: (pectin unit) 170 pu/g of pectin, pectin concentration (if only gel water uptake is important): 10%, pectin... 

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... 

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were... 

Liquid-liquid equilibrium (LLE) data, density, viscosity, and interfacial tension for the ternary system of toluene-acetic acid-water were measured at 298.15 K and 101.7 kPa. The Othmer-Tobias and the Hand correlations were used to check the reliability of the experimental tie-lines. Moreover, the distribution coefficient and the separation factor were explored. It was found from the experimental results that a maximum separation factor value happens at an acetic acid mass fraction of 0.02 in the organic phase. Density, viscosity, and interfacial tension were correlated using the appropriate correlations such that the predicted results have excellent agreement with the experimental data. The... 

Interesting properties of ionic liquids lead to their application as sub-component of membrane structures. Supported ionic liquid membranes (SILMs) are porous membranes whose pores are saturated with ionic liquids. Two ionic liquids, pr[mim]2[Tf2N]2 [1,3-di(3-methyl-imidazolium) propane bis(trifluoromethylsulfonyl) imide] and, h[mim]2 [Tf2N]2 [(1,6-di(3-methylimidazolium)hexane bis(trifluoromethylsulfonyl)imide)], were synthesized in our laboratory and stabilized on an alumina porous support. Permeability and permselectivity of carbon dioxide and methane using membranes containing these ionic liquids were then measured. The experiments were performed in the pressure range of 10-50kPa and... 

Salicylic acid-beeswax microspheres were prepared by melt dispersion technique. The effects of formulation parameters on the microscopic characteristic, drug loading and cumulative amount of released drug were investigated by experimental design. Results showed that all of the microparticles were spherical with porous surfaces. The average size of microspheres was 2448 m, the drug content was in the range of 2245 and the encapsulation efficiency was 4693. Drug loading was influenced by emulsification speed as a main factor. All the microspheres had a burst release initially. The emulsifier concentration did not have a significant effect on drug release. The release behaviour of microspheres... 

We introduce a new smooth, non-toxic, biocompatible method for cross-linking of gum tragacanth (GT), a polysaccharide of natural origin, in order to serve as a new supporting matrix for immobilization systems. The modified gum is used as a matrix for the catalysis of the conversion of benzyl penicillin to 6-aminopenicillanic acid (6-APA) by means of Escherichia coli ATCC11105 with penicillin G acylase (PGA) activity. The results show that GT beads can not only serve as a proper matrix for immobilization, but show enhanced hydrolysis rate and stability compared to other immobilization systems used for this reaction. This signifies the potential of GT as a biocompatible matrix for...