Sharif Digital Repository

A general regularity was found based on an effective pair potential of Lennard-Jones LJ (12, 6), for both dense, nonmetallic and nonionic fluids and solids according to which (Z-1) v2 linearly varies with respect to ρ2 for each isotherm, and this equation of state (EoS I) is known as LIR. However, despite the fact that Ne is a simple spherical species, unexpectedly, its solid and liquid phases both show a significant deviation from EoS I. In this work, we have investigated the accuracy of the EoS I for other systems, including quantum light molecules, such as D 2, H 2 and He, in both fluid and solid states at different temperatures. Like Ne, we have noticed that these systems do not well... 

The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and Cu + cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 20-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn 2+ than do with Mg 2+, Ca 2+, and Cu? and therefore stronger interactions lead to higher MIA.... 

Influence of the addition of water molecules (n = 1-6) on the interaction energy between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d, p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the... 

Understanding the nature of the interaction between metal nanoparticles and biomolecules has been important in the development and design of sensors. In this paper, structural, electronic, and bonding properties of the neutral and anionic forms of glutathione tripeptide (GSH) complexes with a Au 3 cluster were studied using the DFT-B3LYP with 6-31+G**-LANL2DZ mixed basis set. Binding of glutathione with the gold cluster is governed by two different kinds of interactions: Auâ€"X (X = N, O, and S) anchoring bond and Au··•·•H-X nonconventional hydrogen bonding. The influence of the intramolecular hydrogen bonding of glutathione on the interaction of this peptide with the gold cluster has been... 

We investigate the structure and electronic properties of phosphatidylcholine (PC) under different degrees of hydration at the single-molecule and monolayer type level by linear scaling ab initio calculations. Upon hydration, the phospholipid undergoes drastic long-range conformational rearrangements which lead to a sickle-like ground-state shape. The structural unit of the tilted gel-phase PC appears to be a water-bridged PC dimer. We find that hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids and consequently guides the interactions of the lipids with other molecules and the communication between cells  

There is an eminent interest to improve the photoactivity of TiO 2 nanostructures via doping with midband gap donors or acceptors to achieve a high solar absorption. In the present work, Cr- and V-doped TiO 2 nanoparticles were prepared via a facile chemical vapor synthesis method. The effect of the transition metals (TM) on the solar light activity of the semiconductor nanoparticles as photocatalyst was examined by degradation of methylene blue and acid red 27. Induced coupled plasma and X-ray photoelectron spectroscopy analyses indicated high efficiency of the doping process in the hot wall reactor without surface covering of the TiO 2 nanoparticles by the dopants. Diffuse reflectance... 

The geometries of the complexes of Be 2+, Mg 2+, and Ca 2+ metal cations with borazine ring were studied. The complexes were optimized at the B3LYP level and the 6-311++G(d,p) basis set. Then, the interaction energies corrected by basis set super position error were calculated in the same level. The results show that interaction energy is strongly dependent on the charge-to-size ratio of the cation. Therefore, Be 2+ cation has the most interaction energy value with respect to Mg 2+ and Ca 2+ metal cations. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to... 

Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate... 

Hydrogen bonding interactions between thymine nucleobase and 2'-deoxythymidine nucleoside (dT) with some biological anions such as F - (fluoride), Cl - (chloride), OH - (hydroxide), and NO 3 - (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory... 

TiO 2 nanorods, TiO 2 nanorod/TiO 2 nanoparticle and TiO 2 nanorod/ZnO nanoparticle composite structures were integrated as photoanodes in backside illuminated dye-sensitized solar cells (DSSCs). Incorporation of TiO 2 nanoparticles into the bare nanorods increased the dye loading and improved the short-circuit current density (J sc) from 2.22 mA/cm 2 to 3.57 mA/cm 2. ZnO nanoparticles electrochemically grown into the TiO 2 nanorod layer could increase the surface area. Nevertheless, this considerably reduced the J sc to 0.57 mA/cm 2 and consequently cell efficiency. Electrochemical impedance spectroscopy (EIS) results showed that ZnO incorporated samples have better effective diffusion... 

We propose a simple, general, and accurate formula for analyzing the tunneling between classical configurations of a nonplanar molecule in a gas medium, as a function of the thermodynamic parameters of the gas. We apply it to two interesting cases: (i) the shift to zero frequency of the inversion line of ammonia, upon an increase in the pressure of the gas; and (ii) the destruction of the coherent tunneling of D 2S 2 molecules in a He gas. In both cases, we compare our analysis with previous theoretical and experimental results  

The nonequilibrium molecular dynamics (NEMD) simulations are performed to calculation the cross drag over a nanotube located in a uniform liquid argon flow. As is known, the behavior of fluid flows in nano-scale sizes is very different from that in microscopic and macroscopic sizes. In this work, our concern is on the flow of argon molecules over a nanotube which occurs in nanoscale sizes. We calculate the cross drag enforced the nanotube at Re<10. In this regard, we use the molecular dynamics and simulate the flow of argon molecules over (6,0), (8,0) and (10,0) nanotubes. The simulations are performed at different velocities and the cross drag coefficient is computed at different Reynolds... 

The binding of Mg 2+, Ca 2+, Zn 2+ and Cu + metal cations to 2′-deoxyguanosine has been analyzed, using the hybrid B3LYP, Density Functional Theory (DFT) method and 6311++G(d,p) orbital basis sets. Coordination geometries, absolute metal ion affinities, and free energies for the most stable complexes formed by Mg 2+, Ca 2+, Zn 2+ and Cu + with the nucleoside, 2′-deoxyguanosine, have been determined. Furthermore, the influences of metal cationization on the strength of the N-glycosidic bond, torsion angles and angle of Pseudorotation (P) have been studied. With respect to the results, it has been found that metal binding significantly changes the values of the phase angle of Pseudorotation... 

Water molecules are one of the important molecules in nanofluidics. Its structure and its behavior can change with Temperature and cut-off distance parameters. In this study temperature and cut-off distance effects on the nano-scale water molecules behavior are investigated by molecular dynamics simulations. Many water molecular models have been developed in order to help discover the structure of water molecules. In this study, the flexible three centered (TIP3P-C) water potential is used to model the inter- and intramolecular interactions of the water molecules. In this simulation, we have been studied 512 water molecules with periodic boundary conditions and in a simulation box with 25... 

The solubility of sulfur dioxide (SO2) and carbon dioxide (CO2) at P = 1 bar in a series of imidazolium-based room-temperature ionic liquids (RTILs) is calculated by Monte Carlo simulation in NPT ensemble using the OPLS-UA force field and Widom particle insertion method. The studied ILs were 1-butyl-3-methylimidazolium ([bmim]+) tetrafluoroborate ([BF4]-), [bmim]+ hexafluorophosphate ([PF 6]-), [bmim]+ bromide ([Br]-), [bmim]+ nitrate ([NO3]-), [bmim]+ bis-(trifluoromethyl) sulfonylimide ([Tf2N]-), and 1-ethyl-3-methylimidazolium tetrafluoroborate ([emim][BF4]). To validate the simulations, the liquid density of studied ILs and the solubility of CO2 in [bmim][PF6] was compared with... 

Hexagonal array of Cu@CuO core-shell nanoparticles (NPs) on the a-C:H thin film was prepared by codeposition of RF-sputtering and RF-PECVD. The trace of hexagonal NPs supperlattice was recognized by AFM image and XRD result. On the basis of localized surface plasmon resonance (LSPR) of core-shell NPs, the prepared array detected a low flow rate of CO gas at room temperature. XPS results indicate that the surface of Cu@CuO core-shell NPs have no chemical reaction with CO molecule. The physical absorption of CO molecule on the surface of Cu@CuO core-shell NPs increases the LSPR absorbance and causes a red shift in LSPR wavelength. These experimental results are in agreement with Mie theory... 

Equations of state based on the statistical associating fluid theory for potentials of variable range (SAFT-VR) and the perturbed chain statistical associating fluid theory (PC-SAFT) have been used to model the PVT behavior of ionic liquids and the solubility of H2S in six imidazolium-based ionic liquids. The studied systems included [bmim][PF6], [hmim][PF6], [bmim][BF4], [hmim][BF4], [bmim][NTF2] and [hmim][NTF2] at various temperatures and pressures.For pure components, parameters of the models have been obtained by fitting the models to experimental data on liquid densities; the average relative deviation between the calculated and experimental densities for ionic liquids is less than... 

Nonequilibrium molecular dynamics simulations are used to study the motion of a C60 molecule on a graphene sheet subjected to a temperature gradient. The C60 molecule is actuated and moves along the system while it just randomly dances along the perpendicular direction. Increasing the temperature gradient increases the directed velocity of C60. It is found that the free energy decreases as the C60 molecule moves toward the cold end. The driving mechanism based on the temperature gradient suggests the construction of nanoscale graphene-based motors  

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... 

A nonlocal harmonic elastic rod model is proposed to describe the elastic behavior of short DNA molecules. We show that the nonlocal interactions contribute to effective bending energy of the molecule and affect its apparent persistence length. It is also shown that the anomalous behavior which has been observed in all-atom molecular dynamic simulations [A. K. Mazur, Biophys. J. 134, 4507 (2006)] can be a consequence of both nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA