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... 

A molecularly imprinted xerogel (MIX) for fentanyl was successfully prepared on the inner surface of a copper tube by sol-gel technology. Primarily, the tube was treated by self-assembly monolayers of 3-(mercaptopropyl) trimethoxysilane and then [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane was employed as a precursor for imprinting the template molecule in acidic conditions. During the sol-gel process influential parameters including volume and concentration of fentanyl were carefully investigated to obtain the most efficient and appropriate xerogel. In parallel, a non-imprinted xerogel (NIX) was synthesized in the absence of fentanyl. The extraction efficiencies achieved from MIX and NIX,... 

The nonlinear dynamic and static deflection of a micro/nano gyroscope under DC voltages and base rotation are investigated. The gyroscope undertakes two coupled bending motions along the drive and sense directions and subjected to electrostatic actuations and intermolecular forces. The nonlinear governing equations of motion for the system with the effect of electrostatic force, intermolecular tractions and base rotation are derived using extended Hamilton principle. Under constant voltage, the gyroscope finds the preformed shape. First, the deflection of the micro/nano gyroscope under electrostatic forces is obtained by static and dynamic analyses. Furthermore, the static and dynamic... 

In this paper, we demonstrate the applicability of the perturbation methods to different elastic models of DNA molecule. Two different kinds of perturbation methods are presented to find a first approximation for the force-extension characteristic of DNA in the anisotropic wormlike chain model, and the persistence length of DNA in the asymmetric elastic rod model. In both cases we show that it is meaningful to use the perturbation theory, and a first-order calculation is enough to find the result with an acceptable accuracy  

The incorporation of modified β-cyclodextrin (β-CD) into a poly(N-isopropylacrylamide) (PNIPAAm)/chitosan (PNCS) nanohydrogel was studied. β-CD was functionalized with acrylic groups, with different numbers of vinyl bonds added per β-CD molecule. The surfactant-free dispersion polymerization (SFDP) semi-batch method was used to synthesize the nanohydrogel. Increasing the number of vinyl groups per β-CDAC (β-CD acrylate) molecule induced the formation of smaller nanogels with diameters ranging from 142 to 68 nm. The cyclodextrin-modified dual-responsive nanogels obtained presented an LCST (lower critical solution temperature) in aqueous medium at around 31 C. The incorporation of β-CDAC into... 

In this study, we apply the monitoring master equation describing decoherence of internal states to an optically active molecule prepared in a coherent superposition of nondegenerate internal states interacting with thermal photons at low temperatures. We use vibrational Raman scattering theory up to the first chiral-sensitive contribution, i.e., the mixed electric-magnetic interaction, to obtain scattering amplitudes in terms of molecular polarizability tensors. The resulting density matrix is used to obtain elastic decoherence rates  

The nature of alumazine⋯M (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical... 

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

This work presents a procedure for functionalization of graphene sheets from edges by polyglycerol. Hyperbranched polyglycerol with a bi-dentate aromatic segment in its focal point was synthesized and used to sandwich graphene sheets from the cut-edges. Due to the hydrophobicity of the flat surface of the edge-functionalized graphenes and hydrophilicity of their edges, they changed their conformation from the extended- to the closed-state and formed nanocapsules in aqueous solutions. Spectroscopy and microscopy evaluations showed that the average size for nanocapsules is 300 nm. They were able to encapsulate hydrophobic molecules such as doxorubicin in aqueous solutions with a high loading... 

Interactions of α-D-glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM-B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α-D-glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M.H-O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy... 

Aims. Stars twinkle because their light propagates through the atmosphere. The same phenomenon is expected on a longer time scale when the light of remote stars crosses an interstellar turbulent molecular cloud, but it has never been observed at optical wavelengths. The aim of the study described in this paper is to fully simulate the scintillation process, starting from the molecular cloud description as a fractal object, ending with the simulations of fluctuating stellar light curves. Methods. Fast Fourier transforms are first used to simulate fractal clouds. Then, the illumination pattern resulting from the crossing of background star light through these refractive clouds is calculated... 

Superparamagnetic Iron Oxide Nanoparticles (SPIONs) were synthesized and coated with pseudopolyrotaxanes (PPRs) and proposed as a novel hybrid nanostructure for medical imaging and drug delivery. PPRs were prepared by addition of α-cyclodextrin rings to functionalized polyethylene glycol (PEG) chain with hydrophobic triazine end-groups. Non-covalent interactions between SPIONs and PPRs led to the assembly of SPIONs@PRs hybrid nanomaterials. Measurements of the 1H Nuclear Magnetic Resonance (NMR) relaxation times T1 and T2 allowed us to determine the NMR dispersion profiles. Comparison between our SPIONs@PRs hybrid nano-compound and the commercial SPION compound, Endorem®, showed a higher... 

An accurate molecular dynamics simulation of the nanocavity flow cannot be achieved without considering correct thermal treatments for the molecules both distributed in the flow and located at the cavity walls and without including their interactions correctly. In this study, we specify constant temperature at the nanocavity vertical walls; however, we examine three different thermal wall models, including a rigid wall, a controlled-temperature flexible wall, and a noncontrolled-temperature flexible wall, to model the horizontal wall behaviors. Comparing the results of these three models with each other, it is possible to evaluate the effect of wall model on the resulting temperature and... 

This paper deals with the study of the small scale effect on the pull-in instability of nano-switches subjected to electrostatic and intermolecular forces. Using Eringen's nonlocal elasticity theory, the nonlocal Euler-Bernoulli beam model is derived through virtual displacement principle. The static governing equation which is extremely nonlinear due to the intermolecular and electrostatic attraction forces is solved numerically by differential quadrature method. The accuracy of the present method is verified by comparing the obtained results with the finite difference method and those in the literatures and very good agreement is obtained. Finally a comprehensive study is carried out to...