Sharif Digital Repository

Three new Cu(I) complexes containing bidentate N^N donor ligands with the general formula [Cu(N^N)2][PF6] (N^N = 2,3-diphenyl-6,7-di-p-tolyl-1,4,5,8-tetraazaphenanthrene (L1), 2,3-diphenyl-6,7-di(2-thienyl)-1,4,5,8-tetraazaphenanthrene (L2), and 2,3-diphenyl-6,7-di-p-fluorophenyl-1,4,5,8-tetraazaphenanthrene (L3), were prepared by the reaction of [Cu(CH3CN)4][PF6] with two equivalents of the N^N ligand. Single-crystal X-ray diffraction analysis confirmed that in each complex the metal displays a distorted tetrahedral geometry surrounded by the four N atoms of the two sterically hindered substituted tetraazaphenanthrene (TAP) ligands. Density functional theory (DFT) and time-dependent density... 

The pKa value for protonated forms of different benzo-substituted quinuclidines in aqueous solution has been calculated using DFT methods (MP2//B3LYP, B3LYP and M06-2X) and 6-311++G(d,p) basis set and are compared with corresponding experimental values. The results were obtained from different theoretical methods so close to the corresponding experimental values but the best agreement were achieved with B3LYP/6-311+G(d,p) level of theory. The average error was found to be less than 1.6pKa unit. Relative pKa values were computed for each protonated benzo-substituted quinuclidine using quinuclidine as a reference. Solvation was included in the calculations in all used different methods using... 

The electron transport characteristics of a 1,10-dimethylene-1,10-dicarba-closo-decaborane (10-vertex carborane) single molecular conductor is investigated via the density functional-based non-equilibrium Green's function (DFT-NEGF) method. We consider three configurations for the molecular wire sandwiched between two Au(1 0 0) electrodes: the hollow site, top site and bridge site positions. Our results show that the energetically favorable hollow site configuration has a higher current intensity than the other configurations. The projection of the density of states (PDOS) and the transmission coefficients T(E) of the two-probe system at zero bias are analyzed, and it suggests that the... 

(Equation present) Density functional theory (DFT) was used to investigate the acidity of the various silica alkyl sulfonic acids. In this regard, cluster models with various alkyl spacer lengths were selected to mimic the surface of silica gel. The effects of distance from the surface and the role of hydrogen bond (H-bond) on the ΔHacidity values of these catalysts were investigated. DFT calculations revealed that a notable gap of ΔH acidity values exists between the structures considering lateral hydrogen bonding with the surface of the silica HB structure and the structures with omitted surface interactions (non-HB structures). Natural bonding orbital (NBO) and quantum theory of atoms in... 

In this study, the drastic influence of the boron atom on the acidity of alcohol has been considered. 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 BH 2CH2OH, BF2CH2OH alcohols, respectively, which are much smaller than that of CH3OH (with ΔHacid = 374.9 kcal/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 unoccupied orbital of boron atom with the electron pairs... 

In this study, electronic structure, stability, and tendency to exchange electron of neutral, anionic, and cationic RhxCu4-x (x = 0-4) small clusters were investigated by density functional theory calculations. For neutral small clusters, it was found that the most stable structures of Rh4, Rh3Cu and Rh2Cu2 have distorted tetrahedral shape while the most stable structures of RhCu3 and Cu4 have quasi-planer shape. Adding charges to the clusters, caused shapes of the most stable structures undergo variations. Stabilities of the neutral, anionic, and cationic clusters decrease linearly with increasing the copper content. In addition, calculated chemical harnesses indicated that the small... 

For the first time, the mechanism of Fischer esterification between acetic acid and ethanol over silica-functionalized propylsulfonic acid (silica-propyl-SO3H) catalyst was explored by means of computational modeling techniques. For this purpose, 6-edge-atom cage-like cluster comprising Si-O-Si sequences has been selected to represent the surface of the catalyst. The results indicate that the reaction goes through concerted transition states. In all optimized structures no proton (H+) transfer occurs from catalyst to the substrates and the role of the catalyst is via the activation of the substrates through the formation of strong hydrogen bonds (H-bonds). Furthermore, the energetic diagram... 

The gas-phase metal affinities of histidine Li+, Na+ and K+ ions have been determined theoretically employing the hybrid B3LYP exchangecorrelation 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 (N τ), 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... 

Density functional theory (DFT) using the B3LYP functional and the split-valance 6-311++G** basis sets have been used to investigate the structures of 24 derivatives of glucose and galactose which present sequences of atoms in anomeric configurations of the C-C bond in C-glycosides, C-O bond in glycosides, C-S bond in thioglycosides, C-N bond in glycosylamines, and C-F/Cl bond in glycosyl halides. Values of the vicinal coupling constants, 3JCXCH (X = C, O, S), for mentioned compounds were calculated in water and methanol solvents by using PCM method and new Karplus equations were derived. © 2007 Elsevier B.V. All rights reserved  

Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including gulose, allose, altrose, and talose, are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C2-4 atoms. The basis sets effect in evaluation of the possibility intramolecular hydrogen bonding (H-bonds) in the selected rare sugars was studied from 6-31G* to 6–311 ++ G(d,p) basis sets using DFT, AIM, and NBO methods. The results show that the selected rare sugars are more stable at 6–311 ++ G(d,p) basis sets compared to 6-31G* because their electronic energies were reduced... 

The synthesis, characterization, structural and computational studies of mononuclear Re(I) tricarbonyl complexes of 2,2′-bipyridine (2,2′-bpy) and 2,9-dimethylphenantroline (2,9-Me2Phen), [Re(CO)3(NN)(X)], where NN = 2,2′-bpy, X = Br (1) and X = [sbnd]ONO (3); NN = 2,9-Me2Phen, X = Br (2) and X = [sbnd]ONO (4), are reported. The complexes characterized by crystallographic and spectroscopic methods and elemental analyses. In each complex the Re(I) centre shows 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... 

A combined experimental and computational study was carried out on the gas phase pyrolysis reaction of diallylsulfoxide. Allylalcohol and Thioacrolein were detected as the major products during a unimolecular reaction. Experimental kinetic studies were carried out via a static system over the pressure of 21-55 torr and temperature of 435.2-475.1 K. Based on the experiments, the reaction is homogeneous and proceeds through a zwitterionic intermediate. Computational studies at the DFT (B3LYP) and QCISD(T) levels with 6-311++G(d,p) basis set indicated a two-step concerted pathway as the possible route. Comparison between the experimental and theoretical activation parameters for the most... 

Ab initio, DFT, Monte Carlo statistical mechanics and atom in molecule methods have been applied to investigate the hydrogen bonding effect of protic solvents, apart from the bulk properties, on the reaction of cyclopentadiene and vinyl acetate. The results show that methanol accelerates the rate of the reaction more than water. DFT calculations demonstrate that the interaction of the carbonyl group oxygen atom with solvent molecules in transition state is stronger and more effective than the ether-type oxygen atom. Also, when the solvent molecule is near the oxygen of the carbonyl group the rate of reaction is larger than when it is near the ether-type oxygen. In addition, methanol... 

In the present work, adsorption of hydrogen molecules over a metal organic framework (MOF-5) has been investigated by using first principles density functional theory (DFT). Different strategies have been applied for improving hydrogen storage, i.e. metal doping, boron substitution and functionalization. The metal atoms used for enhancing hydrogen adsorption include Li, Ca and Sc. It is found that the binding energy between these metal atoms and MOF is not enough to prevent clustering. Therefore a number of carbon atoms are substituted by boron atoms and it is indicated that boron substitution enhances the binding energies, significantly. Also the results reveal that boron substituted MOF... 

The reactions of FeCl3·3H2O and 2-(2′-hydroxyphenyl)-5,6-dihydro-1,3-oxazine (N-O) as a bidentate O, N donor ligand afforded a five-coordinated iron(III) complex, [Fe(N-O) 2Cl], with a distorted trigonal bipyramidal configuration. The complex [Fe(N-O)2Cl] was isolated as an air-stable crystalline solid and was fully characterized, including by single-crystal X-ray structure analysis. The complex [Fe(N-O)2Cl] shows very efficient reactivity in the oxidation of sulfides to their corresponding sulfoxides using urea hydrogen peroxide (UHP) as the oxidant at room temperature under air. To get an insight into the electronic structure of the complex, the experimental studies have been accompanied... 

The molecular characteristics of Crocin (digentiobiosyl-8,8'-diapocarotene-8,8'-oate; C44H64O24), naturally occurring carotenoid pigment compound, such as: the ionization potential (I), electron affinity (A), electronegativity (χ), electrophicility (ω), and hardness have been calculated using Density Functional Theory (DFT) approach with B3LYP/6-31G(d,p) level of theory. The plots of Frontier Molecular Orbital and molecular electrostatic potential (MEP) for Crocin molecule along with the spin density distribution for its cation radical have been demonstrated. For the first time, we indicated the chemically active sites of the Crocin molecule by Fukui functions. Calculated components of... 

The performance of the ab initio and density functional theory (DFT) functional, B3LYP and PBEPBE, in conjunction with selected basis sets for the prediction of 31P shielding constants for small phosphorous- containing molecules is assessed. The effects of applied factors are discussed. By including the electron correlation treatment, B3LYP and PBEPBE are the most accurate methods to compute the chemical shielding for a set of small phosphines that was studied. Also, additional improvements of DFT were obtained by empirical scaling of basis sets in calculation of chemical shifts. For molecules containing only phosphorous and carbon atoms with sp3 hybridization, the PBEPBE/6-311G(d,p) level... 

Adsorption of molecular and atomic oxygen on neutral and negatively charged PdxCu3-x (x=0-3) nano-clusters have been studied by density functional theory. It has been observed that modes and energies of adsorption strongly depend on the charge and composition of the nano-clusters. The most stable adsorption mode for molecular oxygen on neutral Pd/Cu nano-clusters is to bridge Pd-Cu site (adsorption energy=-103.7kJmol-1) while on negatively charged nano-clusters bridging of Pd-Pd or Cu-Cu are more stable adsorption modes (adsorption energies=-140.9 and -172.9kJmol-1). Also, the most stable adsorption mode for atomic oxygen on neutral Pd/Cu nano-clusters is on the hollow site (adsorption... 

Density functional theory (DFT) calculations were performed at the B3LYP/6-311++G(d, p) level to determine coordination geometries, absolute metal ion affinities, and free energies for all possible complexation stable products formed by monovalent metal cations including Li+, Na+, K+ with the nucleoside 2'-Deoxyguanosine. All computations indicate that the metal ion affinity (MIA) decreases on going from Li+ to Na+ and K+ for 2'-Deoxyguanosine. For example, the affinities for the metal ions described above are 75.2, 57.3, 43.4 kcal/mol, respectively. Furthermore, the influence of metal cationization and O 6 protonation on the strength of the N-glycosidic bond, torsion angles and angle of... 

The wave functions for calculating gas phase 19F chemical shifts were optimally selected using the factorial design as a multivariate technique. The effects of electron correlation, triple-ξ valance shell, diffuse function, and polarization function on calculated 19F chemical shifts were discussed. It is shown that of the four factors, electron correlation and the polarization functions affect the results significantly. B3LYP/6-31 + G(df,p) wave functions have been proposed as the best and the most efficient level of theory for calculating 19F chemical shifts. An additional series of fluoro compounds were used as a test set and their predicted 19F chemical shifts values confirmed the...