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Can anion interaction accelerate transformation of cytosine tautomers? Detailed view form QTAIM analysis
, Article Structural Chemistry ; Volume 23, Issue 6 , 2012 , Pages 1843-1855 ; 10400400 (ISSN) ; Tehrani, Z. A ; Fattahi, A ; Jamshidi, Z ; Sharif University of Technology
Abstract
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...
Hydration strongly affects the molecular and electronic structure of membrane phospholipids
, Article Journal of Chemical Physics ; Volume 136, Issue 11 , 2012 ; 00219606 (ISSN) ; Partovi Azar, P ; Jadidi, T ; Nafari, N ; Maass, P ; Tabar, M. R. R ; Bonn, M ; Bakker, H. J ; Sharif University of Technology
Abstract
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
Adsorption and solar light activity of transition-metal doped TiO 2 nanoparticles as semiconductor photocatalyst
, Article Journal of Materials Science: Materials in Electronics ; Volume 23, Issue 3 , 2012 , Pages 659-667 ; 09574522 (ISSN) ; Simchi, A ; Jafari, T ; Sharif University of Technology
Abstract
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...
Charge transport properties in nanocomposite photoanodes of DSSCs: Crucial role of electronic structure
, Article EPJ Applied Physics ; Volume 57, Issue 2 , February , 2012 ; 12860042 (ISSN) ; Taghavinia, N ; Iraji Zad, A ; Marandi, M ; Tajabadi, F ; Sharif University of Technology
Abstract
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...
Tunneling properties of nonplanar molecules in a gas medium
, Article Physical Review A - Atomic, Molecular, and Optical Physics ; Volume 84, Issue 6 , 2011 ; 10502947 (ISSN) ; Bassi, A ; Sharif University of Technology
Abstract
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
Directed motion of C60 on a graphene sheet subjected to a temperature gradient
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 83, Issue 4 , 2011 ; 15393755 (ISSN) ; Neek Amal, M ; Ejtehadi, M. R ; Sharif University of Technology
Abstract
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
Hydrogen storage in decorated multiwalled carbon nanotubes by Ca, Co, Fe, Ni, and Pd nanoparticles under ambient conditions
, Article Journal of Physical Chemistry C ; Volume 115, Issue 14 , 2011 , Pages 6994-7001 ; 19327447 (ISSN) ; Mortazavi, S. Z ; Mirershadi, S ; Moshfegh, A. Z ; Parvin, P ; Golikand, A. N ; Sharif University of Technology
Abstract
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...
Effect of water-methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels; A molecular dynamics study
, Article Molecular Physics ; Volume 109, Issue 5 , Mar , 2011 , Pages 709-724 ; 00268976 (ISSN) ; Akbarzadeh, H ; Taherkhani, F ; Parsafar, G ; Sharif University of Technology
Abstract
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...
Electrically rotating suspended films of polar liquids
, Article Experiments in Fluids ; Volume 50, Issue 2 , August , 2011 , Pages 419-428 ; 07234864 (ISSN) ; Amjadi, A ; Tonddast Navaei, A ; Ejtehadi, M. R ; Sharif University of Technology
Abstract
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...
Recent progress in inorganic and composite coatings with bactericidal capability for orthopaedic applications
, Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 7, Issue 1 , Feb , 2011 , Pages 22-39 ; 15499634 (ISSN) ; Tamjid, E ; Pishbin, F ; Boccaccini, A. R ; Sharif University of Technology
Abstract
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...
Influence of intermolecular forces on dynamic pull-in instability of micro/nano bridges
, Article ASME 2010 10th Biennial Conference on Engineering Systems Design and Analysis, ESDA2010, 12 July 2010 through 14 July 2010 ; Volume 5 , 2010 , Pages 655-662 ; 9780791849194 (ISBN) ; Ahmadian, M. T ; Sharif University of Technology
Abstract
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
Molecular dynamics simulation and MM-PBSA calculations of sickle cell hemoglobin in dimer form with Val, Trp, or Phe at the lateral contact
, Article Journal of Physical Organic Chemistry ; Volume 23, Issue 9 , March , 2010 , Pages 866-877 ; 08943230 (ISSN) ; Akbarzadeh, H ; Parsafar, G. A ; Sharif University of Technology
Abstract
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...
Poly(citric acid)-block-poly(ethylene glycol) copolymers-new biocompatible hybrid materials for nanomedicine
, Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 6, Issue 4 , Aug , 2010 , Pages 556-562 ; 15499634 (ISSN) ; Adeli, M ; Vossoughi, M ; Sharif University of Technology
Abstract
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...
Theoretical study of CO adsorption on the illuminated TiO2 (0 0 1) surface
, Article Applied Surface Science ; Volume 256, Issue 12 , 2010 , Pages 3795-3798 ; 01694332 (ISSN) ; Sadighi Bonabi, R ; Sharif University of Technology
Abstract
A quantum modeling of the CO adsorption on illuminated anatase TiO2 (0 0 1) is presented. The calculated adsorption energy and geometries of illuminated case are compared with the ground state case. The calculations were achieved by using DFT formalism and the BH and HLYP. Upon photoexcitation, an electron-hole pair is generated. Comparing of natural population in the ground state and the exited state, shows that an electron is trapped in a Ti4+ ion and a hole is localized in an oxygen ion. The photoelectron helps generation of a CO2 molecule on the TiO2 surface. As shown by optimization of these systems, the CO molecule adsorbed vertically on the TiO2 (0 0 1) surface in the ground state...
Lipid membranes with transmembrane proteins in shear flow
, Article Journal of Chemical Physics ; Volume 132, Issue 2 , 2010 ; 00219606 (ISSN) ; Noguchi, H ; Gompper, G ; Sharif University of Technology
Abstract
The effects of embedded proteins on the dynamical properties of lipid bilayer membranes are studied in shear flow. Coarse-grained molecular simulations are employed, in which lipids are modeled as short polymers consisting of hydrophilic head groups and hydrophobic tail monomers; similarly, transmembrane proteins are modeled as connected hydrophobic double- or triple-chain molecules with hydrophilic groups at both ends. In thermal equilibrium, rigid proteinlike molecules aggregate in a membrane of flexible lipids, while flexible proteins do not aggregate. In shear flow parallel to the membrane, the monolayers of lipid bilayer slide over each other. The presence of transmembrane proteins...
DFT study of NH3(H2O) n=0,1,2,3 complex adsorption on the (8, 0) single-walled carbon nanotube
, Article Computational Materials Science ; Volume 48, Issue 3 , 2010 , Pages 655-657 ; 09270256 (ISSN) ; Beheshtian, J ; Parsafar, G ; Hadipour, N. L ; Sharif University of Technology
Abstract
Theoretical study of NH3(H2O) n=0,1,2,3 adsorption on (8, 0) carbon nanotube was performed at the X3LYP/6-31G* level of density functional theory (DFT). The tube-NH3 interaction was discussed in the terms of binding energy (EB), coupling energy (EC), charge density, molecular orbitals, and dipole moments. The results reveal that addition of water molecules to tube-NH3 system increases the interaction between tube and ammonia molecule
Nonlocal interactions in DNA molecules at nano-scale
, Article Scientia Iranica ; Volume 17, Issue 1 F , 2010 , Pages 23-26 ; 10263098 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
Abstract
In this paper, we try to explain the origin of the anomalous elastic behavior of nanometersized DNA molecules, which has been observed in all-atom molecular dynamic simulations [A.K. Mazur, Biophys. J. 2006]. It is shown that this anomalous behavior is a consequence of nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA. A nonlocal harmonic elastic rod model is proposed, which can successfully describe the elastic behavior of short DNA molecules
Adsorption of proteins at the solution/air interface influenced by added nonionic surfactants at very low concentrations for both components. 3. dilational surface rheology
, Article Journal of Physical Chemistry B ; Volume 119, Issue 9 , January , 2015 , Pages 3768-3775 ; 15206106 (ISSN) ; Aksenenko, E. V ; Lylyk, S. V ; Lotfi, M ; Miller, R ; Sharif University of Technology
Abstract
The influence of the addition of the nonionic surfactants C12 DMPO, C14 DMPO, C10 OH, and C10 EO5 at concentrations between 10-5 and 10-1 mmol/L to solutions of β-casein (BCS) and β-lactoglobulin (BLG) at a fixed concentration of 10-5 mmol/L on the dilational surface rheology is studied. A maximum in the viscoelasticity modulus |E| occurs at very low surfactant concentrations (10-4 to 10-3 mmol/L) for mixtures of BCS with C12 DMPO and C14 DMPO and for mixtures of BLG with C10 EO5 , while for mixture of BCS with C10 EO5 the value of |E| only slightly increased. The |E| values...
Study of self-diffusion in two binary solutions, glycerol-water and methanol-water using diffusion-ordered spectroscopy
, Article Scientia Iranica ; Volume 23, Issue 3 , 2016 , Pages 1175-1183 ; 10263098 (ISSN) ; Tafazzoli, M ; Sharif University of Technology
Sharif University of Technology
Abstract
The concentration and temperature behaviors of the self-diffusion coefficient were analyzed in glycerol-water and methanol-water solutions using Diffusion-Ordered Spectroscopy (DOSY) experiment. Our results indicate that the self-diffusion coefficient dips with increasing concentration and decreasing temperature. The concentration behavior shows that there is hydrogen bond interaction between water and alcohol, which declines the self-diffusion coefficients of both in the aqueous binary mixtures. The self-diffusion activation energies were estimated 13.6, 29.4, and 32.8 (kJ/mol) for methanol and 24.8, 25.5, and 27.6 (kJ/mol) for water in the methanol-water solutions with 0.03, 0.10, and 0.20...
Probing solvent-solvent and solute-solvent interactions in surfactant binary mixtures: Solvatochromic parameters, preferential solvation, and quantum theory of atoms in molecules analysis
, Article RSC Advances ; Volume 6, Issue 22 , 2016 , Pages 18515-18524 ; 20462069 (ISSN) ; Fakhraee, M ; Salari, H ; Gholami, M. R ; Sharif University of Technology
Royal Society of Chemistry
Abstract
The behaviour of solvatochromic absorbance probes (4-nitroaniline, 4-nitroanisole, and Reichardt's dye) within binary mixtures of polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether (Triton X-100 or TX-100)/organic solvents (2-propanol, hexanol, butyl acetate, THF, toluene, and p-xylene) was extensively explored by using solvatochromism and the quantum theory of atoms in molecules (QTAIM). To be more precise, the polarity parameters, ET N, and Kamlet-Taft parameters, such as the hydrogen bond donor ability (HBD) (α), hydrogen bond acceptor ability (HBA) (β), and dipolarity/polarizability (π∗), have been investigated in selected mixtures at 298 K. All binary mixtures exhibit complex...