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density-function-theory
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A density functional theory study of cyclization of citronellal
, Article Reaction Kinetics and Mechanism ; Vol. 37, Number 2 , May , 2012 , pp. 173-182 ; Gholami, M. R ; Irani, M ; Siadati, A ; Sharif University Of Technology
Abstract
A theoretical study of the kinetics and mechanism of the cyclization of citronellal in the gas phase was performed using density functional theory methods at the B3LYP level of theory with 6-311G, 6-311G*, 6-31G**, 6-311G**, 6-311 þ G and 6-311 þ þ G basis sets at 298.15 K, 433.15 K, and 473.15 K. Equilibrium molecular geometries and harmonic vibrational frequencies of the reactant, transition state and products were calculated. Rate constants and activation thermodynamic parameters were calculated and showed a fairly good agreement with experimental results. The effect of solvent polarity on the reaction was studied. These calculations indicated that the reaction proceeds through an...
The role of strain on the quantum spin hall effect and band inversion in stanene
, Article Computational Condensed Matter ; Volume 10 , 2017 , Pages 1-9 ; 23522143 (ISSN) ; Shodja, H. M ; Ojaghnezhad, F ; Sharif University of Technology
Elsevier B.V
2017
Abstract
Examination of the role of strain on the quantum spin hall (QSH) effect and band inversion for the monolayer of tin, stanene, is of interest. To this end, several uniaxial and biaxial strain loadings along the armchair (AC)- and zigzag (ZZ)-directions are applied using first principles calculations based on density functional theory (DFT). We observe QSH insulator as well as semi-metallic property associated with the strained stanene. © 2017 Elsevier B.V
Adsorption onto zeolites: molecular perspective
, Article Chemical Papers ; Volume 75, Issue 12 , 2021 , Pages 6217-6239 ; 03666352 (ISSN) ; Mousavi Khadem, S. S ; Seidi, F ; Hamed Mashhadzadeh, A ; Zarrintaj, P ; Habibzadeh, S ; Mohaddespour, A ; Rabiee, N ; Lima, E. C ; Shokouhimehr, M ; Varma, R. S ; Saeb, M. R ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH
2021
Abstract
2D minerals are among key elements of advanced systems, but the need for understanding their interactions/reactions with materials and systems in which they are involved necessitates tracking their molecular and atomic monitoring. Zeolitic structures are microporous materials formed in the nature through volcanic activities or synthesis. Because of their outstanding physicochemical properties like cation exchange capacity and excellent adsorption properties, zeolites have found application in diverse chemical processes, e.g., gas adsorption, water purification, and wastewater treatment. Prediction of zeolite performance for a targeted application saves time and expense as such projection...
Structural and electronic properties of YBa2Cu3O 7 and YSr2Cu3O7 under mechanical and strontium chemical pressures
, Article Physical Review B - Condensed Matter and Materials Physics ; Volume 70, Issue 13 , 2004 , Pages 134509-1-134509-9 ; 01631829 (ISSN) ; Mossalla, B ; Akhavan, M ; Sharif University of Technology
2004
Abstract
Calculations of structural and electronic properties of two YBa 2Cu3O7 (YBCO) and YSr2Cu 3O7 (YSCO) high-Tc cuprate isofamilies for ambient and high mechanical pressures (-15 GPa≤pm≤15 GPa) have been carried out by pseudopotential density functional theory in the local density approximation employing VASP code. We have analyzed the changes of bond lengths and equilibrium ionic positions due to mechanical pressure on YBCO and YSCO. Negative pressure causes separation of the YBCO unit cell into Cu(1)-O(1)-O(4) and CuO2-Y-CuO2 blocks, similar to the effect of oxygen reduction in YBCO. We have also found that the nonlinear dependence for ionic positions by mechanical pressure, especially for...
Cluster approach to corrosion inhibition problems: Interaction studies
, Article Materials Chemistry and Physics ; Volume 86, Issue 2-3 , 2004 , Pages 311-314 ; 02540584 (ISSN) ; Lashgari, M ; Parsafar, Gh. A ; Sharif University of Technology
2004
Abstract
The interaction energies of 3,5 di-methyl pyridine (A) and 2,4 di-methyl pyridine (B) on the (100) surface of body-centered cubic (bcc) iron were determined via a cluster model and ab initio quantum chemical calculations at density functional theory level. The obtained energies were used to compare the inhibition behavior of these molecules for iron corrosion in hydrochloric acid solution. The iron surface and its adsorption sites (on-top, bridge, hollow) were considered as some clusters taken from two-layered 〈100〉 planes, i.e. Fe1(1), Fe4(2,2), and Fe5(4,1). So, the process for which quantum chemical calculations was carried out consists of adsorption of molecule A (B) on these clusters....
Dichlorosilane adsorption on the Al, Ga, and Zn-doped fullerenes
, Article Monatshefte fur Chemie ; Volume 153, Issue 5-6 , 2022 , Pages 427-434 ; 00269247 (ISSN) ; Yousefi Siavoshani, A ; Bazargani, M ; Turki Jalil, A ; Ramezani, M ; Poor Heravi, M. R ; Sharif University of Technology
Springer
2022
Abstract
Density functional theory calculations are utilized for probing the effect of doping Al, Ga, and Zn atoms on the sensing performance of a C60 fullerene in detecting the dichlorosilane (DS) gas. We predicted that the interaction of pure C60 with DS is physisorption, and the sensing response (SR) of C60 is 8.6. The adsorption energy of DS changes from − 21.4 to − 84.4, − 86.7, and − 90.7 kJ/mol, by doping the Al, Ga, and Zn metals, respectively. Also, the corresponding SR meaningfully rises to 33.7, 52.3, and 92.9, indicating that the Zn transition metal much more increases the sensitivity of fullerene compared to the Al and Ga metals. Our theoretical results further support the fact that the...
Bare and functionalized nanodiamonds in aqueous media: a theoretical study
, Article Diamond and Related Materials ; Volume 89 , 2018 , Pages 301-311 ; 09259635 (ISSN) ; Shojaei, A ; Sharif University of Technology
Abstract
Nanodiamond particles, basically those produced by detonation method, are acquiring progressive attraction in different fields such as material, biomedical, and environmental engineering. Aqueous environments are usually dealt with at different stages of preparation, preservation, and application of these particles. The aim of this article is to perform a systematic first-principles density functional theory analysis on the interaction of C35 ultrasmall octahedral nanodiamond and its full homogeneous carboxylated and aminated forms, with water derived specie, namely, neutral, protonated, and deprotonated water and (H2O)20 water cluster. The effect of solvent media on the interactions has...
Acidity enhancement of α-carbon of beta diketones via hydroxyl substituents: A density functional theory study
, Article Journal of Physical Organic Chemistry ; Volume 34, Issue 3 , 2021 ; 08943230 (ISSN) ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2021
Abstract
Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd
Electro-optical properties of APS and APhS linkers on silicon thin film: A DFT study
, Article Applied Surface Science ; Volume 605 , 2022 ; 01694332 (ISSN) ; Darvish, G ; Faez, R ; Sharif University of Technology
Elsevier B.V
2022
Abstract
APS (3-Aminopropyl) trimethoxysilane) and APhS (p-Aminophenyl) trimethoxysilane) are the most commonly used linkers on a silicon surface. We investigate the surface properties of the structures, including APS or APhS on a silicon substrate. The studied structures consist of APS or APhS linkers with one, two, or three bonds with a substrate, which is a thin layer of Si with crystal orientation 〈1 0 0〉 or 〈1 1 1〉. Using a first-principles study based on density functional theory (DFT), we investigated the electronic and optical properties of the silicon-linker interface, such as interface states, orbital location, dielectric function, and photon absorption. The effects of linker type, number...
Metal-Organic cubane cage with trimethylplatinum(IV) vertices
, Article Inorganic Chemistry ; Volume 61, Issue 1 , 2022 , Pages 15-19 ; 00201669 (ISSN) ; Jamali, S ; Mahmoudi, S ; Samouei, H ; Nayeri, S ; Chabok, S. M. J ; Jamshidi, Z ; Sharif University of Technology
American Chemical Society
2022
Abstract
Herein we describe the synthesis and characterization of the first platinum(IV) metal-organic cage [(Me3PtIV)8(byp)12](OTf)8 (2), in which the organometallic moieties trimethylplatinum(IV) (PtMe3) occupied the corners of a cubane structure and 4,4′-bipyridine ligands used as linkers. The first-principles density functional theory calculations showed that the highest occupied molecular orbitals were localized on the PtMe3 moieties, while the lowest unoccupied molecular orbitals were distributed on the organic linkers. © 2021 American Chemical Society
Comparing the nature of quantum plasmonic excitations for closely spaced silver and gold dimers
, Article Journal of Chemical Physics ; Volume 156, Issue 7 , 2022 ; 00219606 (ISSN) ; Asadi-Aghbolaghi, N ; Morad, R ; Mahmoudi, E ; Sen, S ; Maaza, M ; Visscher, L ; Sharif University of Technology
American Institute of Physics Inc
2022
Abstract
In the new field of quantum plasmonics, plasmonic excitations of silver and gold nanoparticles are utilized to manipulate and control light-matter interactions at the nanoscale. While quantum plasmons can be described with atomistic detail using Time-Dependent Density Functional Theory (DFT), such studies are computationally challenging due to the size of the nanoparticles. An efficient alternative is to employ DFT without approximations only for the relatively fast ground state calculations and use tight-binding approximations in the demanding linear response calculations. In this work, we use this approach to investigate the nature of plasmonic excitations under the variation of the...
First-principle electronic structure study of Ni-doped BaFe2-xNixAs2 (x = 0, 1, 2) superconductor
, Article Physica C: Superconductivity and its Applications ; Vol. 506, issue , 2014 , p. 151-153 ; Khosroabadi, H ; Abolhassani, M. R ; Akhavan, M ; Sharif University of Technology
Abstract
The electronic structure of BaFe2-xNixAs2 (x = 0, 1, 2) as a function of Ni doping has been investigated. Electronic density of states and the band structures are calculated within the first-principle density functional theory for non-magnetic phase. Pseudopotential quantum espresso code in the generalized gradient approximation has been used. Lattice and ionic position parameters of the system have been taken from the experimental data and have been optimized to find the equilibrium structure parameters. The electronic structure is characterized by a sharp Fe/Ni3d peak close to the Fermi level and is dominated by Fe/Ni3d and As4p hybridized states similar to the other Fe-based...
Theoretical investigation of Li2MnSiO4 as a cathode material for Li-ion batteries: A DFT study
, Article Journal of Materials Chemistry A ; Volume 1, Issue 8 , 2013 , Pages 2847-2855 ; 20507488 (ISSN) ; Asgari, S ; Mustarelli, P ; Sharif University of Technology
2013
Abstract
Transition metal lithium orthosilicates are of interest as cathode materials for lithium batteries. Density functional theory (DFT) calculations were performed to evaluate the structural and electrochemical properties of the different polymorphs of Li2MnSiO4. Our computational studies predict superior properties for the Pmn21 polymorph even after extraction of two Li per formula unit. We state that the shortcomings observed for Li2MnSiO4 as a cathode are caused by two mechanisms. Switching of the magnetic state occurs during the first cycles. The subsequent transition, under delithiated conditions, from the Pmn21 or Pmnb polymorphs to the electrochemically weakest P21/n polymorph is the...
A computational investigation on the influence of different π spacer groups in the bithiazole-based organic dye sensitizers on the short-circuit photocurrent densities of dye-sensitized solar cells
, Article Journal of Photochemistry and Photobiology A: Chemistry ; Volume 333 , 2017 , Pages 70-78 ; 10106030 (ISSN) ; Hadipour, N. L ; Parsafar, G ; Sharif University of Technology
Elsevier B.V
2017
Abstract
A series of experimentally synthesized metal free organic dyes based on the 2-Cyano-3-(5-(5'-(4-(diphenylamino)phenyl)-4,4'-dihexyl-2,2'-bithiazol-5-yl)thiophen-2-yl)acrylic acid (dye 1) were investigated, based on computational methods to shed light on how a tiny difference in π-linker of sensitizer, C[tbnd]C and thiophene moiety as the additional π spacer group in dyes 2 and 3 respectively, has a significant impact on the short-circuit photocurrent densities (JSC) in Dye-sensitized solar cells (DSSCs). Although dyes 2 and 3 have similar redshifts in comparison to dye 1 in the UV–vis absorption spectra, there is a significant difference between JSC values of these dyes resulting in...
Theoretical Study of Metallochlorophylls of Forth Period Elements in Periodic Table
, M.Sc. Thesis Sharif University of Technology ; Parsafar, Gholamabbas (Supervisor)
Abstract
In this study, some properties of metallochlorophylls - compounds produced by replacing Mg2+ in tetrapyrrolic ring of chlorophyll b with divalent ions – of the forth period transit elements of the periodic table have been investigated. Using DFT/B3LYP method and DGDZVP basis set, structures of these compounds were optimized and the energy of electronic levels, Gibbs free energy of formation of complex, contribution of atomic orbitals to formation of molecular orbitals and partial charges in these molecules were computed. The results show that some properties of these complexes cannot be justified by the common theories of complexes. Among these properties is the negligible effect of...
A Theoretical Investigation of Adsorption Energy of a Simple Reaction of FTS by Density Functional Theory (DFT)
, M.Sc. Thesis Sharif University of Technology ; Gholami, MohammadReza (Supervisor) ; Alahyfard, MohammadReza (Co-Advisor)
Abstract
The advent and advancement of technology through the conversion of Gas-Synthesis (a mixture of CO and H) into liquid hydrocarbons, by Fischer- Tropsch synthesis (FTS) gives more promising future in this field. Metals such as cobalt, nickel, zinc and iron are used as catalysts for FTS. Studies have shown that the surface structure of metal catalyst has a great influence on the process, and leads to different products and transition states. Iron has been known the most used and the most cost-effective metal catalyst in FTS. Different surfaces of Iron have different catalytic roles. In our work, Fe(100) -that is the most stable after Fe(110) and is known as the most active iron’s surface in...
Theoretical Assessment of the Corrosion Inhibitory Effect of Some Derivatized Benzaldehyde Based Schiff Bases
, M.Sc. Thesis Sharif University of Technology ; Gobal, Freydoon (Supervisor)
Abstract
Schiff bases are used as prevalent ligands in coordination chemistry and are prepared easily. Their application as mild inhibitory agents for prevention of various steel’s corrosion in acidic solution has been proved. When their structure is altered, multi-purpose application for them is found. This property has led to a motive for research and study. In this study, electronic properties of a group of Schiff bases are investigated. The goal of this study is using quantum mechanics (QM) as a tool for specifying electronic properties of some of these bases. With respect to QM calculation which is done by density functional theory (DFT), their properties as inhibitory agents are studied. First,...
A Survey on Electronic Structure of the Chlorophyll Molecules Participating in Photosynthesis Process
, M.Sc. Thesis Sharif University of Technology ; Vesaghi, Mohammad Ali (Supervisor)
Abstract
Optimized structure of the chlorophyll a and b molecules was obtained for LDA and GGA approximation by SIESTA package. Calculation illustrate that tails are curved in the optimized structure for both chlorophyll a and chlorophyll b molecules; in addition, Antennas, which are attached to the head of molecules, are located in optimized-spatial state. This optimized structure of chlorophyll a is similar to the calculated structure in ref [42]. Electrical dipole are calculated from ground state electron density of chlorophylls. Total electrical dipole of chlorophyll a for GGA and LDA approximation are 4.662 and 4.813 Debay, and these value for chlorophyll b are 1.435 and 1.302 Debay,...
DFT study on Thiotepa and Tepa interactions with their DNA receptor
, Article Structural Chemistry ; Volume 24, Issue 1 , February , 2013 , Pages 1-11 ; 10400400 (ISSN) ; Fattahi, A ; Sharif University of Technology
2013
Abstract
Thiotepa (N,N′,N″-triethylenethiophosphoramide) and its major metabolite (Tepa) as trifunctional alkylating agents has recently been used in cancer therapy. In vivo and vitro studies show the possible pathways of alkylation of DNA by Thiotepa and Tepa. Two pathways are suggested, but the main pathway of mechanism remains unclear. In pathway 1, forming cross-links with DNA molecules can be carried out via two different mechanisms. In first mechanism, these agents undergo the ring opening reaction which is initiated by protonating aziridine, which then becomes the main target of nucleophilic attack by the N7-Guanine of DNA. The second probable mechanism is ring opening of aziridyl group by...
Anion interactions of cytosine nucleobase and its nucleosides: detailed view from DFT study
, Article Journal of Molecular Structure: THEOCHEM ; Volume 913, Issue 1-3 , 2009 , Pages 277-283 ; 01661280 (ISSN) ; Fattahi, A ; Sharif University of Technology
2009
Abstract
The noncovalent interactions between cytosine nucleobase with some biological anions such as F-, Cl-, CN-, NO3-, SO42 - and OH- and cytosine nucleosides (i.e., cytidine and deoxycytidine molecules) with F-, Cl-, CN- anions have been demonstrated by DFT study. The molecular geometries, energy properties, H-bonding patterns, dipole moments and charge distribution of these complexes were investigated with the B3LYP method in conjunction with the 6-311++G(d,p) basis set. It has been found that anions can interact with cytosine nucleobase forming hydrogen bonds. In general, these interactions occur via N-H, O-H and C-H substituents of cytosine, cytidine and deoxycytidine. The presence of anions...