Sharif Digital Repository

In this study, drastic influence of the intramolecular cation-π interaction on the basicity of selected amines has been considered. The optimized minimum energy geometries of different studied amines and their protonated structures were determined by using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. Geometry optimizations indicate that the most stable structures of protonated amines are stabilized by intramolecular cation-π interaction. The proton affinity (PA) of selected amines is controlled by the strength of intramolecular cation-π interaction of ammonium with aromatic ring. These cation-π interactions strongly influence the basicity of amines. Natural bond orbital (NBO)... 

The preparation and catalytic activity of molybdenum(VI) dioxido complex [MoO2L(C2H5OH)] (L = N′-[1-(2- hydroxynaphthyl)ethylidene]-2-hydroxy benzohydrazide) are reported. The reaction of the respective benzohydrazide ligand and the Mo(VI) dioxido precursor, [MoO2(acac)] (acac = acetylacetonate), in ethanol afforded the [MoO2L(C2H5OH)] complex. Structure of the complex was unequivocally established by single-crystal X-ray crystallography. The X-ray structure of complex reveals a six coordinate molybdenum center with a distorted octahedral geometry. By using the AIM analysis, topological properties of the electron density were analyzed to define the bond path between atoms. The AIM... 

Thiotepa (N,N′,N″-triethylenethiophosphoramide) and its major metabolite (Tepa) as trifunctional alkylating agents has recently been used in cancer therapy. In vivo and vitro studies show the possible pathways of alkylation of DNA by Thiotepa and Tepa. Two pathways are suggested, but the main pathway of mechanism remains unclear. In pathway 1, forming cross-links with DNA molecules can be carried out via two different mechanisms. In first mechanism, these agents undergo the ring opening reaction which is initiated by protonating aziridine, which then becomes the main target of nucleophilic attack by the N7-Guanine of DNA. The second probable mechanism is ring opening of aziridyl group by... 

With the specific target of calculating the pK a values of boronic acids (RB(OH) 2) in aqueous solution we inquired the solute-solvent interactions of these acids and their corresponding conjugate base. Relative pK a values were computed for each boronic acid using methylboronic acid (CH 3B(OH) 2) as a reference. All gas phase computations were performed at (MP2/6-311++G(d,p)//B3LYP/6-31+G(d)) level of theory. Solvation was included in the calculations using the polarized continuum model (PCM) at the HF/6-31G(d,p) level. The geometry optimization of studied structures was performed with DFT computation and the optimized structures were used to carry out Natural Bond Orbital (NBO) analysis.... 

An extensive GIAO (gauge-including atomic orbital) calculation has been made within Hartree-Fock (HF), density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2), in conjunction with selected basis sets for the prediction of 19F chemical shift values of 26 different F nuclei in small fluorine-containing molecules. The effect of four factors, namely, electron correlation treatment, triple-ξ valence shell, diffuse function and polarization function were assessed using a systematic comparison of the results. Based on types of series, the optimized wave functions were proposed for different molecules. An additional comparison of the principal components of the... 

In this paper, we explore theoretically energetic and structural properties of the possible cations formed via hydride ion abstraction at various sites of sugar part of cytosine nucleosides by employing B3LYP exchange-correlation functional with 6-311++G (d,p) orbital basis sets. In general, the hydride ion abstracted sugar cations of cytosine nucleosides have the following stability sequence: caH2′ > caH1′ > caH3′ > caH4′ > caH5′ for cytidine and caH1′ > caH4′ > caH3′ > caH5′ > caH2′ for deoxycytidine. Furthermore, the effect of solvent environment on the stability order of cations integral equation formalism of the polarized model (IEF-PCM) was employed to model aqueous solution. The... 

Abstraction of hydrogen atom from DNA and RNA subunits leads to formation of a neutral radical. The formation of these radicals can lead to harmful structural alternations and formation of multiple lesions in helixes of DNA and RNA. In the present work, we explore theoretically energetic and structural properties of the possible radicals formed via hydrogen atom abstraction at various sites of sugar part of cytosine nucleosides by employing B3LYP exchange-correlation functional with 6-311++G (d,p) orbital basis sets. Two types of free radicals may be found by hydrogen abstraction of sugar part of cytosine nucleosides: carbon centered radicals and the oxygen centered radicals. The computation... 

Gas phase amino proton chemical shifts in the 54 of amines have been predicted using Gauge-independent atomic orbital (GIAO) method and optimally selected wave function. The effects of electron correlation, triple-ξ valance shell, diffuse function, and polarization function on calculated amino proton chemical shifts have been investigated using factorial design as a multivariate technique. Different optimized wave functions for different groups of amines were recommended. A wave function as the best level of the theory is proposed for homologue amines covered. In this context, B3LYP/6-311+G and HF/6-311+G wave functions have been recommended as the best and the most efficient level of theory... 

Exploring deprotonation properties of silica-functionalized propylsulfonic acid catalyst (silica-propyl-SO3H) is the subject of various experimental and theoretical researches. In the current study, the structure of the silica-propyl-SO3H has been simulated using density functional theory (DFT) methods by mimicking the surface of the silica in the form of cubic cage-like nanoclusters of silicon and oxygen. The values of ΔHacidity for gas-phase deprotonation are calculated considering various possible interactions of the propylsulfonic acid on the surface of the silica. Our investigations indicate that interactions of sulfonic acid (-SO3H) head... 

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... 

Supramolecular complexation of C60 with L1-L5 were studied in toluene, chloroform and 1,2-dichlorobenzene solvents using UV–vis, fluorescence, 1H, 13C NMR spectroscopy as well as density functional theory (DFT) calculations. The Job’s plot of continuous variation method established 1:1 stoichiometry for L1-L5/C60. Binding constants (K) calculated for L1-L5/C60 were also determined employing UV–vis and fluorescence spectroscopy. Both steady-state and time-resolved fluorescence spectroscopic surveys showed remarkable fluorescence quenching phenomenon for L1-L5 in the presence of C60 which was primarily attributed to involvement of a static process. The observed fluorescence quenching in L1–L5... 

The coordination geometries, electronic features, absolute metal ion affinities, geometrical multiplicity and binding strength for the complexes formed by Mg2+, Ca2+, Zn2+ and Cu+ with cytidine and deoxycytidine have been determined theoretically employing the hybrid B3LYP exchange-correlation functional and using 6-311++G(d,p) orbital basis sets. Our study shows that the most stable coordination modes of cytosine nucleosides with these cations are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with three oxygen atoms: one from the carbonyl oxygen of cytosine moiety and two from the sugar unit (i.e., O5′ and O4′).... 

A joint theoretical and experimental study of the kinetic and mechanism of the rearrangement of allyl p-tolyl ether was performed in order to study the kinetic and mechanism of the reaction. Experimental studies were performed in gas phase over a temperature range of 493.15-533.15 K. The experimental Arrhenius parameters of this reaction were measured to be Ea = 36.08 kcal mol-1, ΔS# = -7.88 cal mol-1 K-1, and Log A = 11.74, experimentally. Using GC for the mixture of the reaction with and without cyclohexene demonstrated that the reaction is clean without any radical intermediates. The experimental results show that the studied reaction is unimolecular and proceeds through a concerted... 

Coupling of side chain dynamics over long distances is an important component of allostery. Methionine side chains show the largest intrinsic flexibility among methyl-containing residues but the actual degree of conformational averaging depends on the proximity and mobility of neighboring residues. The 13C NMR chemical shifts of the methyl groups of methionine residues located at long distances in the same protein show a similar scaling with respect to the values predicted from the static X-ray structure by quantum methods. This results in a good linear correlation between calculated and observed chemical shifts. The slope is protein dependent and ranges from zero for the highly flexible... 

According to the importance of polyanion cathode materials in intercalation batteries, they may play a significant role in energy-storage systems. Here, evaluations of LiMBO3 and NaMBO3 (M = Mn, Fe, Co, Ni) as cathode materials of Li-ion and Na-ion batteries, respectively, are performed in the density functional theory (DFT) framework. The structural properties, structural stability after deintercalation, cell voltage, electrical conductivity, and rate capability of the cathodes are assessed. As a result, Li compounds have more structural stability and energy density than Na compounds in the C2/c frame structure. Cell voltage is increased by increasing the atomic number of the transition... 

The corrosion inhibition of glycine-based dithiocarbamates with benzyl (BDTC) and propyl (PDTC) groups were investigated for cold rolled carbon steel (CRS) in 0.5 M HCl, indicating that the compounds as mixed type inhibitors significantly reduced the corrosion rate of the CRS due to the formation of a stable protective film on the metal surface. As confirmed by ATR-FTIR, SEM, AFM, XPS and theoretical studies, chemically adsorbed BDTC molecule is a better corrosion inhibitor with higher corrosion efficiency of about 98% at room temperature and a better thermal stability attributed to the Fe-S and Fe-N bindings, and in addition, to the presence of the benzene ring in the molecular structure. ©... 

27Al, 17O and 13C chemical shieldings of aluminum acetylacetonate complex, Al(acac)3, were calculated at some Density Functional Theory (DFT) levels of theory. In these calculations the X-ray structures of its different polymorphs were used. Using these calculated data observed discrepancies between the X-ray crystallography and solid state NMR experiment were explained in terms of the quality of the NMR data. In this survey we resorted to the simulated spectra using our calculated chemical shifts. Inorder toconfirm our conclusions, electric field gradient (EFG) tensors of the 27Al and 17O nuclei were calculated at the same levels of theory as used in the chemical shielding calculations. On... 

A combined theoretical and experimental kinetic and mechanism of diallyl disulfide pyrolysis reaction in the gas phase was studied in a static system over the temperature range of 586.7-621.2 K and a total pressure of 72 Torr in the presence of cyclohexene as radicals inhibitor. The experimental results show that the reaction is homogeneous, unimolecular and proceeds through a radical mechanism. Theoretical calculations at the B3LYP level using the 6-31G*, 6-31++G* and 6-311++G* basis sets confirm the radical mechanism for the diallyl disulfide pyrolysis. The calculated kinetic and activation parameters especially at the B3LYP/6-31G* level are in good agreement with the experimental data. ©... 

The molecular behavior of some pyridine derivatives as corrosion inhibitors of iron and aluminum in acid media, were studied quantum electrochemically. The calculations were made for three conditions; isolated inhibitor molecule, metal cluster, and finally polarized continuum media. It is concluded that for aluminum the vertical adsorption through nitrogen atom is prevailing, while for iron both vertical and planar adsorptions (through π electrons of aromatic ring) are possible, but the vertical is predominant. The inhibitor chemical potential (μ) and the extent of charge transfer (ΔN) to the metal were determined. A linear correlation between each of these and the inhibition efficiencies... 

The mechanism and kinetic aspects of the retro-ene reaction of allyl n-butyl sulfide and its deuterated derivative were studied using four different types of density functional theory (DFT) methods with eight different levels of the basis sets. Vibrational frequency analysis confirmed that the stationary points include the transition state (TS) structure with only one imaginary frequency. Mechanistic studies on the retro-ene process rejected the step-wise mechanism and confirmed that the reaction proceeds through a six-centered cyclic transition state. Theoretical calculations show that propene elimination from the reactant can occur through an asynchronous concerted mechanism. A primary...