Search for: molecules
Total 258 records
Ionization and Dissociation of the Chlorine Molecule by the Femtosecond Ti: Sapphire Laser Radiation, M.Sc. Thesis Sharif University of Technology ; Sadighi-Bonabi, Rasoul
Ionization probability of Cl2 molecule is studied by irradiation of 800 nm Ti: Sapphire laser pulses at intensities of 1014 Wcm-2 to 1016 Wcm-2 with the Gaussian package. Molecular orbital symmetry and orientation of the molecule dipole moment with laser field polarization axis are very effective in ionization probability. The results show that the most ionization probability for the intensity of 1014 wcm-2 is at 900 and also 50 at intensity of 1016 wcm-2. Due to the lack of intrinsic dipole moment, variation of dipole moment with the intensity, bond length and time evolution of dipole moment are investigated. It is found that there is a linear dependance of these parameters with ionization...
The intramolecular cation-π interaction of some aryl amines and its drastic influence on the basicity of them: AIM and NBO analysis, Article Computational and Theoretical Chemistry ; Vol. 1036 , May , 2014 , pp. 51-60 ; ISSN: 2210271X ; Fattahi, A ; Hashemi, M. M ; Sharif University of Technology
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)...
Theoretical investigation on the structure and properties of alumazine⋯m complexes (M = Li+, Na+, K+, Be2+, Mg2+, and Ca2+), Article Journal of Theoretical and Computational Chemistry ; Volume 12, Issue 5 , August , 2013 ; 02196336 (ISSN) ; Sharif University of Technology
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...
Thermochemical properties of some vinyl chloride-induced DNA lesions: Detailed view from NBO & AIM analysis, Article Structural Chemistry ; Volume 23, Issue 6 , 2012 , Pages 1987-2001 ; 10400400 (ISSN) ; Torabifard, H ; Fattahi, A ; Sharif University of Technology
Etheno-damaged DNA adducts such as 3,N4- ethenocytosine, N 2,3-ethenoguanine, and 1,N2-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gasphase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare...
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
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...
Dithiocarbamic acids and thiols as nucleophiles in the Bargellini reaction, Article Scientia Iranica ; Volume 19, Issue 3 , June , 2012 , Pages 551-554 ; 10263098 (ISSN) ; Saidi, M. R ; Sharif University of Technology
Dithiocarbamic acids and thiols are employed in the Bargellini reaction to generate useful intermediates for the synthesis of organic molecules. This is the first time that dithiocarbamic acids are used as nucleophile in this reaction
Theoretical study of borazine: cation-π (Be 2+, Mg 2+, and Ca 2+) interaction, Article Structural Chemistry ; 2012 , Pages 1-7 ; 10400400 (ISSN) ; Sharif University of Technology
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...
Inhibition effect of 3,5 bis (2-pyridil) 4-amino 1,2,4 triazole and 1-10 phenantrolin on corrosion of mild steel in acid solutions, Article British Corrosion Journal ; Volume 37, Issue 1 , 2002 , Pages 76-80 ; 00070599 (ISSN) ; Hosseini, M. G ; Ghorbani, M ; Sharif University of Technology
IOM Communications Ltd 2002
The inhibition effects of 3.5 bis (2-pyridil) 4-amino 1,2,4 triazole (NBTA) and 1-10 phenantrolin (PHEN), on corrosion of mild steel in acid solutions, (sulphuric acid and hydrochloric acid) were studied. The Tafel polarisation and ac impedance techniques were employed. Results obtained reveal that both compounds are relatively good inhibitors. The inhibition efficiencies of NBTA are higher in hydrochloric acid than in sulphuric acid. This has been attributed to the synergistic effect of chloride ions present in hydrochloric acid. The mechanism of inhibition of PHEN is believed to be owing to the formation of insoluble chelates between the organic molecules and atom/ion on the metal surface....
Design and synthesis of new family of ionic liquids based on 2-iminium-1,3-dithiolanes: A combined theoretical and experimental effort, Article Journal of Molecular Structure ; Vol. 1056-1057, issue. 1 , January , 2014 , p. 56-62 ; Shakourian-Fard, M ; Farvardin, M. V ; Raeesi, M ; Hashemi, M. M ; Behzadi, H ; Sharif University of Technology
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...
Thermal wall model effect on the lid-driven nanocavity flow simulation using the molecular dynamics method, Article Numerical Heat Transfer, Part B: Fundamentals ; Volume 63, Issue 3 , Jan , 2013 , Pages 248-261 ; 10407790 (ISSN) ; Sabouri, M ; Jafari, S ; Sharif University of Technology
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...
Investigation of salts behavior at liquid–liquid interfaces, Article Springer Proceedings in Mathematics and Statistics, 26 August 2013 through 30 August 2013 ; Volume 117 , July , 2015 , Pages 265-270 ; 21941009 (ISSN) ; 9783319123066 (ISBN); 9783319123066 (ISBN) ; Bahramian, A ; Soltani, M ; Pourafshary, P ; Sarikhani, K ; Chen, P ; Ejtehadi, M. R ; Makarov R. N ; Melnik R. V. N ; Kotsireas I. S ; Shodiev H ; Cojocaru M. G ; Cojocaru M. G ; Makarov R. N ; Melnik R. V. N ; Kotsireas I. S ; Shodiev H ; Sharif University of Technology
Springer New York LLC 2015
We have used molecular dynamics simulation to investigate hydrophilic– hydrophobic interfaces between calcium chloride (CaCl2) aqueous solutions and normal hexane. The results demonstrate the increasing impact of salt concentration on the liquid–liquid interfacial tension, hence, negative adsorption of CaCl2 according to Gibbs adsorption isotherm. Moreover, we calculated the density profiles of hexane, water, and the counter ions. The results reveal an electrical double layer near the interface and the less affinity of calcium cations toward the interface than that of chloride anions. Orientation of water molecules at the studied concentrations may result in developing a positively charged...
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
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
Comprehensive reactive receiver modeling for diffusive molecular communication systems: reversible binding, molecule degradation, and finite number of receptors, Article IEEE Transactions on Nanobioscience ; Volume PP, Issue 99 , 2016 ; 15361241 (ISSN) ; Arjmandi, H ; Burkovski, A ; Schober, R ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc 2016
This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nanomachine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nanomachine can participate in a reversible bimolecular reaction with receiver receptor proteins. Thereby, we distinguish between two scenarios. In the first scenario, we assume that the entire surface of the receiver is covered by receptor molecules. We derive a closed-form...
Soluble butyl substituted copper phthalocyanine as alternative hole-transporting material for solution processed perovskite solar cells, Article Electrochimica Acta ; Volume 212 , 2016 , Pages 929-933 ; 00134686 (ISSN) ; Chen, Q ; Lin, Y. W ; Wang, Y. L ; Nouri, E ; Xu, Z. X ; Lianos, P ; Sharif University of Technology
Copper phthalocyanine can effectively act as alternative small molecule hole transporting material in perovskite solar cells. In order to produce solution processed devices, a soluble copper phtalocyanine has been synthesized by n-butyl substitution and it was compared to commercially available tert-butyl substituted copper phthalocyanine. It was found that the configuration of the butyl chain plays a very important role in film conductivity and in the subsequent efficiency of solar cells, n-bytyl derivative being the most effective hole transporter. Such a result is due to the fact that n-butyl derivative allows better packing of the molecules in the film and stronger π-π interaction
Ion pump based bio-synthetic modulator model for diffusive molecular communications, Article 17th IEEE International Workshop on Signal Processing Advances in Wireless Communications, SPAWC 2016, 3 July 2016 through 6 July 2016 ; Volume 2016-August , 2016 ; 9781509017492 (ISBN) ; Jamali, V ; Ahmadzadeh, A ; Burkovski, A ; Schober, R ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
In diffusive molecular communication (DMC), the transmitter has to be able to control the release of signaling molecules for modulation of the information bits. In natural cells, pumping ions is an important control mechanism for releasing molecules which is carried out by ion pumps embedded in the membrane. The activity of the ion pumps is controlled by a driving parameter. In particular, light driven pumps are controlled by light intensity and enable a high degree of spatial and temporal control for modulation functionality. In this paper, a modulator based on ion pumps is proposed for DMC which controls the release rate of the molecules from the transmitter by modulating a light intensity...
Ion Channel Based Bio-Synthetic Modulator for Diffusive Molecular Communication, Article IEEE Transactions on Nanobioscience ; Volume 15, Issue 5 , 2016 , Pages 418-432 ; 15361241 (ISSN) ; Ahmadzadeh, A ; Schober, R ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc 2016
In diffusion-based molecular communication (DMC), a transmitter nanomachine is responsible for signal modulation. Thereby, the transmitter has to be able to control the release of the signaling molecules employed for representing the transmitted information. In nature, an important class of control mechanisms for releasing molecules from cells utilizes ion channels which are pore-forming proteins across the cell membrane. The opening and closing of the ion channels is controlled by a gating parameter. In this paper, an ion channel based modulator for DMC is proposed which controls the rate of molecule release from the transmitter by modulating a gating parameter signal. Exploiting the...
Ultrahigh permeable C2N-inspired graphene nanomesh membranes versus highly strained c2n for reverse osmosis desalination, Article Journal of Physical Chemistry B ; Volume 123, Issue 41 , 2019 , Pages 8740-8752 ; 15206106 (ISSN) ; Akhavan, O ; Sharif University of Technology
American Chemical Society 2019
The reverse osmosis (RO) desalination capability of hydrogenated and hydroxylated graphene nanomesh membranes (GNMs) inspired by the morphology of carbon nitride (C2N) has been studied by using molecular dynamics simulation. As an advantage, water permeance of the GNMs is found to be several orders of magnitude higher than that of the available RO filters and comparable with highly strained C2N (S-C2N) as follows: 6,6-H,OH > 12-H > S-C2N > 5,5-H,OH > 10-H. The reverse order is found for salt rejection, regardless of S-C2N. The hydrophilic character of the incorporated -OH functional group is believed to be responsible for linking the water molecules in feed and permeate sides via the...
Efficient high harmonic generation of bromine molecule by controlling the carrier-envelope phase and polarization of driving laser pulse, Article Chemical Physics Letters ; Volume 719 , 2019 , Pages 27-33 ; 00092614 (ISSN) ; Monfared, M ; Sharif University of Technology
Elsevier B.V 2019
The generation of ultrashort attosecond pulse requires both an enhanced high harmonic generation and the spectral-phase control. In the present work, an efficient method is theoretically investigated for extending HHG cutoff energy in Br2 molecule using TDDFT. The effects of molecular orientation and carrier-envelope phase of the laser on the high harmonic spectrum are analyzed. As a result, by the fine modulations of the laser field, the harmonic plateau is enlarged and the position of structure-induced interference minimum shifts. We also provide a physical picture on the intensity dependence of the spectral minima in the harmonic spectra
The impact of salinity on the interfacial structuring of an aromatic acid at the calcite/brine interface: an atomistic view on low salinity effect, Article Journal of Physical Chemistry B ; Volume 124, Issue 1 , December , 2020 , Pages 224-233 ; Badizad, M. H ; Hartkamp, R ; Ayatollahi, S ; Ghazanfari, M. H ; Sharif University of Technology
American Chemical Society 2020
This study aims to elucidate the impact of salinity on the interactions governing the adsorption of polar aromatic oil compounds onto calcite. To this end, molecular dynamics simulations were employed to assess adsorption of a model polar organic molecule (deprotonated benzoic acid, benzoate) on the calcite surface in NaCl brines of different concentration levels, namely, deionized water (DW), low-salinity water (LS, 5000 ppm), and sea water (SW; 45,000 ppm). Calcite was found to be completely covered by several well-ordered water layers. The top hydration layer is very compact and prevents direct adsorption of benzoates onto the substrate. Instead, Na+ ions form a distinct positively...
Graphic: Graph-based hierarchical clustering for single-molecule localization microscopy, Article 18th IEEE International Symposium on Biomedical Imaging, ISBI 2021, 13 April 2021 through 16 April 2021 ; Volume 2021-April , 2021 , Pages 1892-1896 ; 19457928 (ISSN); 9781665412469 (ISBN) ; Aziznejad, S ; Unser, M ; Sage, D ; Sharif University of Technology
IEEE Computer Society 2021
We propose a novel method for the clustering of point-cloud data that originate from single-molecule localization microscopy (SMLM). Our scheme has the ability to infer a hierarchical structure from the data. It takes a particular relevance when quantitatively analyzing the biological particles of interest at different scales. It assumes a prior neither on the shape of particles nor on the background noise. Our multiscale clustering pipeline is built upon graph theory. At each scale, we first construct a weighted graph that represents the SMLM data. Next, we find clusters using spectral clustering. We then use the output of this clustering algorithm to build the graph in the next scale; in...