Sharif Digital Repository

Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of upmost importance in the living cell. Thymol derivatives exhibit various antioxidant activities and potential health benefits. Exploration of structure-radical scavenging activity (SAR) was approached with a wide range of thymol derivatives. To accomplish this task, the DPPH experimental assay along with quantum-chemical calculations were also employed for these compounds. By comparing the structural properties of the derivatives of interest, their antioxidant activity was explained by the formation of an intramolecular hydrogen bond and the presence of unsaturated double bond (–CHdouble bond; length... 

Three dimensional calculations of electronic dynamics of CH4 in a strong laser field are presented with time-dependent density-functional theory. Time evolution of dipole moment and electron localization function is presented. The dependence of dissociation rate on the laser characters is shown and optimal effective parameters are evaluated. The optimum field leads to 76% dissociation probability for Gaussian envelope and 40 fs (FWHM) at 10 16 W cm-2. The dissociation probability is calculated by optimum convolution of dual short pulses. By combining of field assisted dissociation process and Ehrenfest molecular dynamics, time variation of bond length, velocity and orientation effect are... 

CdS nanocrystals were thermochemically (thermally activated) synthesized thorough the reaction between CdSO4 and Na2S 2O3 in an aqueous solution. Thioglycolic Acid (TGA) was used as the capping agent and catalyst of the reaction. The method was based on heat activated dissociation of Na2S2O3 and controllable release of S and free electrons in the solution. CdS NCs were formed by heating the sample solution at 96 C for 1 h. The results of optical spectroscopy and transmission electron microscopy demonstrated round shape NCs with sizes about 3.0 nm. The nanocrystals were also luminescent and represented a broad emission with a peak located at 515 nm and FWHM of 160 nm. Several samples were... 

Using cluster-based density functional theory we investigate adsorption configurations of an acetophenone molecule on a Si(001) surface and their follow-up proton transfer processes. We examine two possible types of dative-adsorption configurations, up-right standing and flat, as well as compute their follow-up kinetically preferable on-dimer, interdimer, and inter-row proton transfers. Energetics of possible conversions between the achieved adsorption configurations are computed as well. Using all the data obtained, we theoretically illustrate reaction pathways leading to detached hydrogen positions captured in STM imaging of a Si(001) surface exposed to acetophenone vapor at room... 

Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the... 

Conversion of CH4 molecule into higher hydrocarbons using two different wavelengths of 248 nm KrF laser and 355 nm of third harmonic of Nd:YAG laser is studied experimentally and theoretically. The stable products are analyzed and the effect of pressure on conversion of methane is measured. The detected reaction products are C2H2, C2H4, and C2H6. The conversion efficiency of 33.5% for 355 nm in comparison to 2.2% conversion for 248 nm for C2H2 is achieved. The potential of laser parameters as an important variable in controlling of final products is investigated  

The effects of laser field and laser pulse width on the dissociation probability of C-H bond of CH4 have been investigated. Calculation of time dependent Schrödinger equation by grid spectral method is carried out and it is produced optimistic results in comparison to the earlier Quasi-classical calculations. The results show that there is an excellent match with experimental data. In this work, a number of results in the emerging field of laser with intensity of I = 8 × 1013 W cm-2 and pulse duration of 100 fs are presented. The present modulated field leads to more than 20% improvement in the dissociation probability  

Bromophenols are known as antioxidant radical scavengers for some biomolecules such as those in marine red alga. Full understanding of the role played by bromophenols requires detailed knowledge of the radical scavenging activities in probable pathways, a focus of ongoing research. To gain detailed insight into two suggested pathways, H-atom transfer and electron transfer, theoretical studies employing first principle quantum mechanical calculations have been carried out on selected bromophenols. Detailed investigation of the aforementioned routes revealed that upon H-atom abstraction or the electron transfer process, bromophenols cause an increase in radical species in which the unpaired... 

The optimum convolution of dual short pulse for producing the maximum wakefield and the highest dissociation probability of CH4 has been investigated. By using three fundamental shapes of pulses though four different arrangements, the generated wake are considered in plasma. It is found that when the first and second pulses were rectangular-triangular and sinusoidal pulse shapes, respectively, the resultant wakefield amplitude is the highest. This effect opens up a new novel way by pulse shaping mechanism in the photo dissociation dynamics of molecules and controlling of chemical reactions in the desired channels by short pulse intense lasers for reducing the computation time of genetic... 

The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our... 

N,N′,N″-triethylenethiophosphoramide (Thiotepa) and its oxo analogue (Tepa) as the major metabolite are trifunctional alkylating agents with a broad spectrum of antitumor activity. In vivo and vitro studies show alkylation of DNA by Thiotepa and Tepa can follow two pathways, but it remains unclear which pathway represents the precise mechanism of action. In pathway 1, these agents are capable of forming cross-links with DNA molecules via two different mechanisms. In the first mechanism, the ring opening reaction is initiated by protonating the aziridine, which then becomes the primary target of nucleophilic attack by the N7-Guanine. The second one is a direct nucleophilic ring opening of... 

Density functional theory is used in a spin-polarized plane wave pseudopotential implementation to investigate molecular oxygen adsorption and dissociation on graphite and nickel-doped graphite surfaces. Molecular oxygen physisorbs on graphite surface retaining its magnetic property. The calculated adsorption energy is consistent with the experimental value of 0.1eV. It is found that substituting a carbon atom of the graphite surface by a single doping nickel atom (2.8% content) makes the surface active for oxygen chemisorption. It is found that the molecular oxygen never adsorbs on doping nickel atom while it adsorbs and dissociates spontaneously into atomic oxygens on the carbon atoms... 

Bridgehead C-H bond dissociation enthalpies of 105.7 ± 2.0, 102.9 ± 1.7, and 102.4 ± 1.9 kcal mol -1 for bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, and adamantane, respectively, were determined in the gas phase by making use of a thermodynamic cycle (i.e., BDE(R-H) = ΔH° acid(H-X) - IE(H •) + EA(X •)). These results are in good accord with high-level G3 theory calculations, and the experimental values along with G3 predictions for bicyclo[1.1.1]pentane, bicyclo[2.1.1]hexane, bicyclo[3.1.1]heptane, and bicyclo[4.2.1]nonane were found to correlate with the flexibility of the ring system. Rare examples of alkyl anions in the gas phase are also provided  

The adsorption and dissociation of H2O2 on small PdxM3-x (M=Pt, Cu; x = 1-3) clusters is investigated using the B3PW91 hybrid density functional method. Natural bond orbitals are analysed to obtain partial charges on atoms, dipole moments, bond orders, and hybrid orbitals of the PdxM3-x-H2O2 systems. The calculated adsorption energies are in the range of -0.32 to -2.12 eV. Generally, H2O2 adsorbs on top positions through one of its oxygen atoms and only in a few cases reacts with the cluster through both oxygen and hydrogen sides. In the latter case the cluster sites which are negatively charged interact with the hydrogen atoms. Interestingly, on the triplet Pd2Pt cluster, H2O2 dissociates... 

We report a study on hydrogen storage in Ca, Co, Fe, Ni, and Pd decorated multiwalled carbon nanotubes (MWCNTs) by using two techniques: volumetric and electrochemical. The results showed that hydrogen molecules are adsorbed on the defect sites and transported to the spaces between adjacent carbon via diffusion through both defect sites and opened tips into the layers. Hydrogen storage capacity can be improved in the decorated MWCNT by Co, Fe, Ni, and Ca metals in two approaches: (i) H2 adsorption via Kubas interaction and (ii) dissociation of H2 molecules on the metal particles. The results reveal that Pd are more effective catalyst for hydrogen storage process. It was found that... 

The fragmentation dynamics of CH4 and H2CO molecules have been studied with ultra-short pulses at laser intensityof up to 1015Wcm-2. Three dimensional molecular dynamics calculations for finding the optimized laser pulses are presented based on time-dependent density functional theory and quantum optimal control theory. A comparison of the results for orientation dependence in the ionization process shows that the electron distribution for CH4 is more isotropic than H2CO molecule. Total conversion yields of up to 70% at an orientation angle of 30o for CH4 and 65% at 900 for H2CO are achieved which lead to enhancement of dissociation probability  

(GraphPresented) The quantum optimal control theory in conjunction with time dependent density functional theory is used to optimize the laser pulse shape for dissociation of nitrogen molecule. For several initial peak intensities and frequency ranges, the optimum shapes are produced and compared to determine the most efficient pulse. Ehrenfest molecular dynamics model is also used to test the dissociation process. The corresponding snapshots of density and time dependent electron localization function are presented. It is noticed that when the frequency ranges of laser pulses are doubled, it leads to 60% faster dissociation of N2 molecule  

The effect of strong femto-second laser pulses on the dissociation probability of methane has been investigated analytically in various arrangements. The ellipticity dependence of the dissociation probability at intensities from 1014 W cm-2 to 1016 W cm-2 for Ti:Sapphire laser is presented. A reliable calculation of the dissociation probability based on 3D time-dependent Schrodinger equation with an improved model of time-dependent density-functional theory is presented. These calculations are carried out for three different cases of elliptically polarized laser pulse, optimum convolution of dual short pulses, and two-color mixed nonresonant laser pulses. It is found that the rescattering... 

Based on the quantum mechanics principles and classically calculated dressed potential surfaces by using field assisted dissociation model the dissociation probability for CH4 + molecule exposed with a 100 femtosecond 8 Jcm-2 Ti:sapphire laser pulses is calculated. Using the gradient optimization method two tailored rectangular laser pulses for controlling the dissociation of C-H bond of CH4 + molecule along laser pulse direction is found. In the proposed optimization method, the complicacy of solving Schrodinger wave equation is reduced by using classical method and in contrast to the usual controlling and pulse shaping methods of chemical reactions, the experimental data is not needed and... 

The present article deals with super-swelling behavior of crosslinked homopolymer of 2-acrylamido-2-methylpropane sulfonic acid, poly(AMPS), in binary mixtures of dimethyl sulfoxide (DMSO) and various polar solvents including water, mono-, and polyhydric alcohols, and amide solvents such as N-methyl pyrrolidone. Extraordinary phase transition sequences including a new unusual swelling phenomenon, referred to as "overentrant" swelling, was observed for this polymeric organogel in the solvent/DMSO mixtures. The swelling behaviors were preliminarily explained based on the major interactions involved in the solvation process and dielectric constant of the swelling media. It was established that...