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 Sun is located inside an enormous local cavity filled with a million degree, ionized hydrogen gas and surrounded by a wall of dense and cold gas, this cavity is known as the Local Bubble (LB). Since the tempreture of Local Bubble is high, the typical singly-ionized atoms or molecules can not survive at this high tempreture. To overcome this problem we should probe the Local Bubble using species which survive under this condition so we have done a whole sky survey in north hemisphere by observing absorptions in the Diffuse Interstellar Bands (DIBs) for sight-lines with distance >300 pc. We have done 30 nights observation and have observed 473 bright stars. We found that the correlations... 

In this paper the free vibration of single walled carbon nanopeapods encapsulating C60 molecules is considered. The nanopeapod is embedded in an elastic medium and clamped at both ends. The Euler-Bernoulli beam model is used for the carbon nanotube and the C60 molecules are considered as lumped masses attached to the beam. Based on the nonlocal elasticity theory the governing equation of motion is derived and the resonance frequencies of the nanopeapod are obtained. The effects of small scale, foundation stiffness and ratio of the fullerenes' mass to the nanotube's mass on the frequencies are studied and some conclusions are drawn  

In this paper, we present an extension of dissipative particle dynamics method in order to study the mixed electroosmotic/pressure-driven micro- or nano-flows. This method is based on the Poisson-Boltzmann equation and has a great potential to resolve the electric double layer (EDL). Hence, apart from studying the bulk flow, it also provides a strong capability in order to resolve the complex phenomena occur inside the EDL. We utilize the proposed method to study the pure electroosmotic and also the mixed electroosmotic/pressure-driven flow through the straight micro-/nano-channels. The obtained results are in good agreement with the available analytical solutions. Furthermore, we study the... 

In the present work, the interaction of hydrogen molecules with defective graphene structures doped by transition metal (TM) atoms is investigated by using first principles density functional theory (DFT). Defective graphene structures include Stone-Wales (SW), 585 and 555-777 and transition metals include early TMs, i.e. scandium (Sc), titanium (Ti) and vanadium (V). It is found that in comparison with the pristine graphene, presence of defects significantly enhances the metal binding. Among three defects, 585 divacancy leads to the strongest binding between graphene and metal. Hydrogen adsorption is then evaluated by sequential addition of hydrogen molecules to the system. The results... 

We explore the interplay between tunneling process and chiral interactions in the discrimination of chiral states for an ensemble of molecules in a biological environment. Each molecule is described by an asymmetric double-well potential and the environment is modeled as a bath of harmonic oscillators. We carefully analyze different time-scales appearing in the resulting master equation at both weak- and strong-coupling limits. The corresponding results are accompanied by a set of coupled differential equations characterizing optical activity of the molecules. We show that, at the weak-coupling limit, chiral interactions prohibit the coherent racemization induced by decoherence effects and... 

An efficient method for synthesis of 2-iminium-1,3-dithiolane as a new family of ionic liquids with reaction of dithiocarbamates with methyl triflouromethanesulfonate was described. Theoretical study on the synthesized ionic liquids was also performed by quantum chemistry calculation. Geometry optimization on the ion pairs was carried out with the B3LYP/6-311++G(d,p) level of theory. The interaction energies were calculated, and corrected by the basis set superposition error (BSSE) calculated by the counterpoise method. The results of natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses indicate that the interactions occur via hydrogen bonding between oxygen... 

The relative stabilities and noncovalent interactions of the six low-lying energy tautomers of cytosine nucleobase with some biological anions (such as F-, Cl-, and CN-) have been investigated in gas phase by density functional theory (DFT) method in conjunction with 6-311++G (d,p) atomic basis set. Furthermore, to systematically investigate all possible tautomerisms from cytosine induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase and in a continuum solvent using DFT calculation. We carried out geometrical optimizations with the integral equation formalism of polarizable continuum (IEF-PCM) model to account for the solvent effect, and the... 

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... 

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  

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... 

Continuing an ongoing study, molecular dynamics (MD) simulations were performed to investigate the effects of methanol concentration on Nafion morphology, such as the size of solvent cluster, solvent location, and polymer structure via the sandwich model. Our survey shows that high methanol concentrations resulted in increment of solvent cluster size in Nafion membrane. The sulfonic acid clusters also befall much in order as subsequent layers of such ionic clusters are formed. The number of neighbouring hydronium ions around a sulfur atom is independent of methanol concentration, but the first shell of hydronium and water around sulfonic acid clusters is broader. Although methanol would... 

Controlled rotation of a suspended soap water film, simply generated by applying an electric field, has been reported recently. The film rotates when the applied electric field exceeds a certain threshold. In this study, we investigate the phenomenon in films made of a number of other liquids with various physical and chemical properties. Our measurements show that the intrinsic electrical dipole moments of the liquid molecules seems to be vital for the corresponding film rotation. All the investigated rotating liquids have a molecular electric dipole moment of above 1 Debye, while weakly polar liquids do not rotate. However, the liquids investigated here cover a wide range of physical... 

This review covers the most recent developments of inorganic and organic-inorganic composite coatings for orthopedic implants, providing the interface with living tissue and with potential for drug delivery to combat infections. Conventional systemic delivery of drugs is an inefficient procedure that may cause toxicity and may require a patient's hospitalization for monitoring. Local delivery of antibiotics and other bioactive molecules maximizes their effect where they are required, reduces potential systemic toxicity and increases timeliness and cost efficiency. In addition, local delivery has broad applications in combating infection-related diseases. Polymeric coatings may present some... 

In this study, influences of intermolecular forces on dynamic pull-in instability of electrostatically actuated beams are investigated. Effects of midplane stretching, electrostatic actuation, fringing fields and intermolecular forces are considered. The boundary conditions of the beams are clamped-free and clamped-clamped. A finite element model is developed to discretize the governing equations and Newmark time discretization is then employed to solve the discretized equations. The results indicate that by increasing the Casimir and van der Waals effects, the effect of inertia on pull-in values considerably increases  

As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and... 

Linear-dendritic ABA triblock copolymers containing poly(ethylene glycol) (PEG) as B block and hyperbranched poly(citric acid) (PCA) as A blocks were synthesized through polycondensation. The molecular self-assembly of synthesized PCA-PEG-PCA copolymers in water led to formation of nanoparticles and fibers in different sizes and shapes depending on the time and size of PCA blocks. Ten days after dissolving PCA-PEG-PCA copolymers in water, the size of fibers had reached several millimeters. Mixing a water solution of fluorescein as a small guest molecule and PCA-PEG-PCA copolymers led to the encapsulation of fluorescein by products of molecular self-assembly. To investigate their potential...