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... 

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,... 

In this study, some properties of metallochlorophylls - compounds produced by replacing Mg2+ in tetrapyrrolic ring of chlorophyll b with divalent ions – of the forth period transit elements of the periodic table have been investigated. Using DFT/B3LYP method and DGDZVP basis set, structures of these compounds were optimized and the energy of electronic levels, Gibbs free energy of formation of complex, contribution of atomic orbitals to formation of molecular orbitals and partial charges in these molecules were computed. The results show that some properties of these complexes cannot be justified by the common theories of complexes. Among these properties is the negligible effect of... 

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... 

Many of the significant reactions in chemistry and biology are related to bimolecular nucleophilic substitution (SN2) reactions which have been studied first by Hughes and Ingold in the 1930s. Afterward, many organic chemists have continued this work. Up to now, numerous experimental kinetic and theoretical researches have studied the mechanism of these reactions. Since most SN2 reactions occur in solution, a large number of these studies have been devoted to the solvent effects. One of these effects that has been examined extremely is H-bonding via protic solvents that lowers the energy of an anionic nucleophile relative to the transition state, in which the charge is more diffuse, and... 

The advent and advancement of technology through the conversion of Gas-Synthesis (a mixture of CO and H) into liquid hydrocarbons, by Fischer- Tropsch synthesis (FTS) gives more promising future in this field. Metals such as cobalt, nickel, zinc and iron are used as catalysts for FTS. Studies have shown that the surface structure of metal catalyst has a great influence on the process, and leads to different products and transition states. Iron has been known the most used and the most cost-effective metal catalyst in FTS. Different surfaces of Iron have different catalytic roles. In our work, Fe(100) -that is the most stable after Fe(110) and is known as the most active iron’s surface in... 

Schiff bases are used as prevalent ligands in coordination chemistry and are prepared easily. Their application as mild inhibitory agents for prevention of various steel’s corrosion in acidic solution has been proved. When their structure is altered, multi-purpose application for them is found. This property has led to a motive for research and study. In this study, electronic properties of a group of Schiff bases are investigated. The goal of this study is using quantum mechanics (QM) as a tool for specifying electronic properties of some of these bases. With respect to QM calculation which is done by density functional theory (DFT), their properties as inhibitory agents are studied. First,... 

Optimized structure of the chlorophyll a and b molecules was obtained for LDA and GGA approximation by SIESTA package. Calculation illustrate that tails are curved in the optimized structure for both chlorophyll a and chlorophyll b molecules; in addition, Antennas, which are attached to the head of molecules, are located in optimized-spatial state. This optimized structure of chlorophyll a is similar to the calculated structure in ref [42]. Electrical dipole are calculated from ground state electron density of chlorophylls. Total electrical dipole of chlorophyll a for GGA and LDA approximation are 4.662 and 4.813 Debay, and these value for chlorophyll b are 1.435 and 1.302 Debay,... 

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  

Recently, The interest of using the coherent and incoherent photons in chemical synthesis have been raised considerably. In this project, theoretical calculations due to investigation of irradiation’s effects on Fischer- Tropsch synthesis have done. Fischer – Tropsch synthesis is the process that converts synthesis gas, i.e. a mixture of carbon monoxide and hydrogen, in to a wide range of long chain hydrocarbons and oxygenates. We invest the first chapter of this project to introduce of Fischer- Tropsch synthesis and its importance. Following in the next chapter we have analyzed the photocatalyst in microscopic scale. In third chapter, we have claimed the necessary theories which are useful... 

Quantum calculation based on the density functional theory (DFT) level and 6-311++G (d,p) basis set was employed to study the relation between the structure and radical scavenging activity of a series of hydroxybenzohydroxamic acid derivatives, namely: [HU]; hyroxyurea, [TX]; 3,4,5-trihydroxybenzamidoxime, [DX]; 3,4-dihydroxybenzohydroxamic acid, [4-HBA]; 4-hydroxybenzohydroxamic acid, [2,3-DHBA]; 2,3-Dihydroxybenzohydroxamic acid, [3,5-DHBA]; 3,5-Dihydroxybenzohydroxamic acid and [2-HBA]; 2-hydroxybenzohydroxamic acid in the gas phase, water and benzene environments. The hydrogen bond property of the studied structures and their radicals as well as radical cations was investigated using... 

It is believed that intramolecular hydrogen bonding and also conjugation can affect the acidity power of organic molecules. But simultaneous effects of intramolecular hydrogen bonding and conjugation have not investigated systematically yet. In this project, we choose Ascorbic acid as a basic structure. Then we have changed its structure conveniently, and have explored the roles of hydrogen bonding and conjugation on the acidity of this molecule by using B3LYP functional with the 6-311++G(d,p) basis set. After that we similarly investigate these effects on the acidity of three different systems, including enols, enamines and alcohols. In this project we probe the effect of different hydrogen... 

A study of the electro-oxidation and surface reactions of C1 compounds on Ni and Cu electrodes, Ni(111) and Cu (111) has been performed by methods of cyclic voltammetry, BOC-MP and DFT. The diffusion coefficients and activation energies of the electro-oxidation of methanol and formaldehyde in alkaline solution on Ni electrode have been derived. Values around 2.27×10-6 cm2s-1, 1.98×10-5cm2s-1, 12.15 Kcal mol-1 and 11.65 Kcal mol-1 have been obtained respectively. In theoretical study , the elimination of hydrogen from CH3 and CH2 groups has been proposed as a mechanism in surface reactions of methanol and formaldehyde on Ni(111) ... 

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... 

Entropy is one of the important quantities in thermodynamics. In this project has tried to make this quantity as a bridge between quantum and thermodynamics. Entropy has many definitions that the Shannon entropy is chosen in this work. By this definition of entropy, we are able to define the entropy for a electronic system in molecules. By this definition, we are seeking an answer for this question,”whether entropy has a similar application in quantum like thermodynamics or not?”. To elucidate this hypothesis, simple diatomic molecules are computed. In fact, displacement of the Shannon entropy has investigated in bond making process. The question is that whether we can use this quantity to... 

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...