Sharif Digital Repository

Nowadays, there is no doubt about the importance of investigation of physicochemical properties of nucleosides in order to determine the structure of these biopolymers. Nucleotides have a variety of roles in cellular metabolism. They are the constituents of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), the molecular repositories of genetic information. The metal ions play a significant role in several biological processes. Synthesis, replication, and cleavage of DNA and RNA as well as their structure integrity are affected by the presence of these ionized metals in the cell nucleus. To understand the role of cations in the biophysics of DNA, it is necessary first to... 

Acidity values of some compound (e.g., alkanes, alcohols, carboxylic acids and amines) with or without boron substitute have been studied theoretically to evaluate the influence of boron on acidity of organic functional groups. We have derived the unoccupied reactive orbital that show the maximum localization on the boron pπ atomic orbital overlapping with the lone-pair orbital of an electron donor. Localization of unoccupied reactive orbital on the boron pπ atomic and the polarizability of the boron center are two factors which affect acidity values of functional groups. Conformational searching was performed using MM (Molecular Mechanics). The most important conformations were optimized at... 

There is no satisfactory agreement between theory and experiment in the Hartree-Fock (HF) and density functional theory (DFT) calculation for metals, semiconductors and metals. It is clear that this discrepancy is attributed to the neglecting of correlation. For example, experimentally
LiF have the largest band gap about 13.6 eV among the alkali halides and show an exciton peak at 12.6 eV . Brener have obtained a value of 22.9 eV for LiF band gap in the HF approximation. DFT has been very successful tool in calculating the ground-state properties of materials. As
we expect, the band gap in LiF are underestimated in the local density approximation (LDA) calculation (about 8.3 eV) .... 

This work investigates adsorption and possible dissociation of a number of small molecules on small clusters and carbonic surface. Theoretical study of carbon monoxide adsorption on SixGe4_x(x=0–4) nano-clusters has been carried out using MPW1B95 density functional. The geometry, adsorption energy, charge distribution, and vibrational frequency of CO adsorption on all possible structures were investigated. The maximum vibrational frequency changes occur in the bridge structures while the most stable structures occur when CO adsorbs on one silicon atom in a flat surface. Adsorption energies of CO on one Si atom are by far more negative than the corresponding value for on Ge atom. Theoretical... 

In this work we have studied conformation of ranitidine by dynamic nuclear magnetic resonance spectroscopy (DNMR) in four different solvents: chloroform, acetone, dimethylsulfoxide, and deuteriumoxide. Ranitidine has three tatumeric forms of enamine, nitoic acid, and imine, but its stable structure is enamine. Temperature dependent 1HNMR spectra of ranitidine which reportet at 500MHz were consistent with the following free activation of energies ΔG# (kcal mol-1): chloroform = 16.2; acetone = 15.4; dimethylsulfoxide = 15.1. The experimental results were confirmed by DFT theoretical calculations at the B3LYP/6-311++G (d, p) level of theory. It was also proved that ranitidine has the form of... 

In Li batteries, lithium ions are exchanged between two electrodes, along with the accompaning electron transfer to maintain riability good ionic conductivities and electrolytes stability are achived through additives to the electrolyte. Such matrial should possess good anions acceptability. This work investigates the potential of aza-ethers in this regard. The softness criteris is basically employed. DFT calculation for selected molecules of different size, substituents and interacting atoms are used to correlate softness, electrophilicity, Fukui no, etc to the usefulness of the corresponding matrials  

Hydrogen bonding is an important weak interaction encountered in gas, liquid, as well as solid phase. The hydrogen bond plays a very vital role in many life processes and is one of the most frequently used terms in chemistry and biology. Amides have several applications as drugs, antibacterials and antifungals. Different substituents can affect the acidity of amides. Investigation have shown that hydroxyl function group can increase the acidity of many organic molecules through interamolecular hydrogen bonding. The goal of this project is to investigate the acidity of cyclic amides and barbiturates by adding hydroxyl group in the gas and solution phase. All the gas phase optimizations and... 

In this study, orthosilicate materials with chemical formula of Li2MSiO4 (M one or two transition metal/metals) were investigated experimentally and theoretically as cathode material of Li-ion batteries. The most important material in this category i.e. Li2FeSiO4 was synthesized by three methods including nitrate-based sol-gel, oxalate-based solid state reaction and oxide-based solid state reaction. Based on XRD and SEM evaluations, grain size of synthesized powders was estimated to be between 15 to 100 nanometers. Of these three methods, oxide-based solid state reaction was employed in this study for the first time. This syntheses method is very important due to the significant lower... 

In this study, using the B3LYP/6-3111++g(d,p) computational level, we have explored the possibility of formation of some organic and bioorganic cation-cation clusters (CCC) in the absence of any anionic stabilizing species. Furthermore, we have shown the existence of a barrier energy for exothermic dissociation of these clusters. Herein, we have selected some biomolecules such as the chloroquine (CQ) antimalarial drug . The selected molecules possess the basic sites and can function as both hydrogen bond donors and acceptors. Also, a facile and direct synthetic route toward the rhodanine derivatives and thiazolidine-2,4-diones via a three-component coupling of carbon disulfide, primary... 

The synthesis, characterization, structural and computational studies of mononuclear Re(I) tricarbonyl complexes of 2,2'-bipyridine (2,2′-bpy) and 2,9-dimethylphenanthtroline (2,9-Me2Phen), [Re(CO)3(NN)(X)], where NN=2,2′-bpy,X=Br (1) and X=–ONO (3); NN=2,9-Me2 Phen, X=Br (2) and X= –ONO (4), were reported. The complexes characterized by crystallographic and spectroscopic methods and elemental analyses. In each complex, the Re(I) center showed the distorted octahedral geometry. Single crystal X-ray diffraction data revealed the endo-nitrito (κ1–ONO) coordination in complexes 3 and 4. It has been shown that the replacement of the bromo ligand in complexes 1 and 2, either by AgOTf/NaNO2 in a... 

In this study, electrochemical oxygen reduction reaction (ORR) was studied on Cu, Pd, Rh, Pd-Cu and Rh-Cu alloys in alkaline solution. Pd-Cu and Rh-Cu alloys were prepared by electrochemical methods. On copper electrode it is found that direct oxygen reduction is accompanied by the electrochemical reductions of copper oxides. Also, mechanism and kinetics of reaction change as the amount of copper oxides increase on the surface. For electrodeposited alloys, it is indicated that the reactivity of Pd-Cu and Rh-Cu alloys toward oxygen reduction is higher than pure Pd and pure Rh. The maximum reactivity among Pd-Cu alloys is related to the sample with 24.5% copper content while the maximum... 

Hydrogen bond is a type of molecular bonds which occurs between hydrogen and a highly electronegative atom( usually F, N and O) and results to special properties. Polyols and multihydroxyl compounds are among substances which have special properties such as acidity due to the existence of hydrogen bond in their molecular structure. Acidity in these compounds is a result of having stable anions due to intramolecular hydrogen bands. The existence of an electronegative group in addition to hydroxyl groups leads to increase the acidity in these substances. In this project acidities of some polyols and multihydroxyl compounds were calculated in both gas phase and solution phase( DMSO,... 

The unique properties of graphene due to the presence of massless Dirac fermions, high surface to volume ratio, high crystal quality in 2D, and high mechanical strength, recommend it as a promising material for technologies such as nanoelectromechanical systems (NEMS) and nanosensors. Use of graphene in nanodevices is accompanied by induced strains and stresses. Therefore it is important to study the mechanical properties of graphene. In present thesis, we synthesized graphene using both mechanical cleavage of graphite and chemical method. In the chemical method graphene oxide is prepared by oxidation and exfoliation of graphite. The graphene oxide sheets were reduced to prepare graphene... 

The silicon vacancy in silicon carbide is a strong emergent candidate for applications in quantum information processing. 4H, 6H and 3C polytypes of SiC all host coherent and optically addressable defect spin states. Electron paramagnetic resonance (EPR) and optically detected magnetic resonance (ODMR) investigations suggest that silicon vacancy point defects in SiC possess properties similar to those of the NV center in diamond. We provide a new theoretical frame to explain a wider range of experimental results. Employing a proposed generalized Hubbard model, with the help of electronic structure programs, DFT, second quantization, and various computational approaches, we obtain new...