Arabian, S.,
Gordanshekan, A.,
Farhadian, M.,
Solaimany nazar a.r., A.R.,
Tangestaninejad, S.,
Sabzyan, H. Chemical Engineering Journal (13858947)488
This study investigated the photocatalytic adsorption, degradation, and mineralization of Cefixime (CFX) through hydrothermally synthesized Bi2WO6(36 %)/g-C3N4(54 %)/ZIF-67(10 %) dual S-scheme heterojunction (BCZ). Full characterization analysis for the fresh and reused photocatalyst was explored to study the formation of heterojunction, stability, and reusability of the BCZ. VB-XPS, Mott-Schottky plots, and UV–Vis DRS defined the band structure and electron transfer mechanism of BCZ. The effects of ten operating condition factors, including reaction time, initial concentration of CFX, the dosage of photocatalyst, reaction temperature, initial pH of the reaction, visible and UV intensity, and concentration of Na2SO4, NaOH, and NaCl in the reaction solution were experimentally investigated. These factors were then modeled through artificial neural networks (ANN). The number of neurons, training algorithm, and the type of activation functions in the ANN were optimized by mean squared error metric followed by the visualizations of the ANN predictions. Two cost functions (the ratio of instantaneous CFX concentration to initial CFX concentration (C/C0) and the ratio of photocatalyst dosage to the amount of CFX removed) were employed to optimize the value of these operating condition factors separately and simultaneously through single and multi-objective genetic algorithms. Coupling LC-MS results and DFT calculations, a degradation pathway for Cefixime was proposed and then analyzed by QSAR. The toxicity of the treated solution was investigated using the wheat seed culture, along with MIC and MBC testing conducted by E. coli and S. aureus, and its eco-friendliness was confirmed by TOC and COD. Furthermore, ICP-OES confirmed that BCZ is a green photocatalyst. © 2024 Elsevier B.V.
Asghari, S.,
Mohammadpoor baltork, I.,
Sabzyan, H.,
Tangestaninejad, S.,
Moghadam, M.,
Mirkhani, V. Journal of Environmental Chemical Engineering (22133437)12(6)
Iodine capture from gas phase has gained enormous environmental importance due to the harmful effects of iodine pollution on human and other living organisms. In the current paper, an amine-linked covalent organic framework (AL-COF) is prepared by the partial in-situ reduction of the imine-linked COF (IL-COF) under the Eschweiler–Clarke conditions. The flexibility of the AL-COF and its synergic effect with the stronger hydrogen-bond donor ability of amine –HC–NH– compared to the imine –C[dbnd]N– linkages, led to a significant increase in the iodine adsorption capacity of the COF from 2.7 g.g−1 for the IL-COF to 5.0 g.g−1 for the AL-COF at 85 °C and atmospheric pressure. The specific surface area, and pore volume of the IL-COF were altered respectively from 70 m2.g−1 and 0.0642 cm3.g−1 to 58 m2.g−1 and 0.0811 cm3.g−1 for AL-COF. The iodine adsorption type was investigated using the FT-IR, XPS, Raman and DRS analyses. The adsorption of iodine on these two relative COFs is studied deeply with density-functional theory (DFT) computations employing B3LYP/LANL2DZ method. The UV-Vis absorption spectra obtained by TD-DFT method include charge transfer transitions between the iodine species (I−, I2, and I3−) and the designed IL-COF and AL-COF models. Also, various possible COF-iodine structures of the adsorption complexes were optimized and investigated based on the charge distribution and reduced density gradient (RDG). The computational and experimental results show compatible trends for the observed adsorption of iodine over these COFs surfaces. © 2024 Elsevier Ltd
Khalili, A.,
Mohammadpoor baltork, I.,
Mirkhani, V.,
Moghadam, M.,
Tangestaninejad, S.,
Notash, B.,
Sabzyan, H. Journal of Molecular Liquids (18733166)397
In this research, a calixarene-based acidic ionic liquid immobilized on Fe3O4 magnetic nanoparticles coated with epoxy-functionalized silica (Calix-AIL-MN) was successfully synthesized and characterized by various spectroscopic and analytical techniques such as FT-IR, VSM, TEM, SEM, EDX, elemental-mapping, TGA, ICP and elemental analysis. This catalytic system showed excellent activity in the selective synthesis of 4-amino-1,3,4-thiadiazolo-2-yl-2H-chromen-2-ones and 6H,7H-chromeno[4,3-d][1,3,4]thiadiazolo[3,2-a]pyrimidines through the one-pot three-component reaction of 4-aminocoumarin, aldehydes, and 2-amino-1,3,4-thiadiazoles under thermal conditions and microwave irradiation, respectively. Short reaction times, high to excellent yields, simple workup, easy recovery and reuse of the catalyst, and solvent-free conditions are the most prominent features of this method, which make it a green and sustainable process for the synthesis of these very important fused heterocycles. © 2024 Elsevier B.V.
Sedighi, M.,
Talaie m.r., M.R.,
Sabzyan, H.,
Aghamiri, S. Sustainable Materials and Technologies (22149929)38
To develop an appropriate metal-organic framework to capture CO2 from dry flue gas, understanding the roles of structural modifications, location of primary adsorption sites and underlying adsorption mechanisms is crucial. Herein, effects of type, position and concentration of nitrogen-containing functional groups and C/N-substituted ligands are investigated on overall CO2/N2 adsorption process performance and mechanism of pristine and metal-substituted MIL-101 MOFs. In this investigation, density functional theory computations, grand-canonical Monte-Carlo, and molecular dynamics simulations are applied. Taguchi-based overall evaluation criteria objective function is also used to assess the overall adsorption performances of these MIL-101 MOFs in terms of CO2 uptake capacity, CO2/N2 selectivity, isosteric heat of adsorption and mass transfer resistance. The PBE/DZVP computations resulted in the CO2-framework binding energies ranging from −3.85 to −21.01 kJ/mol implying an acid-base type of physisorption. A correlation is introduced to estimate the CO2 uptake capacity from binding affinity and pore diameter of these MIL-101 MOFs. Mechanistic investigations show that to enhance CO2 uptake capacity and CO2/N2 selectivity, functionalization of the linker ligands is more successful than functionalization of the open metal sites having strong interactions with CO2 molecules. Results also showed that the best possible scenario to improve the overall adsorption process performance of MIL-101 is to substitute the C atom(s) of the BDC ligands with the N atom(s), regardless of the central metal atom type. The comprehensive molecular design approach introduced in this work can be used as a methodology by scientists for the development of new MOFs for practical CO2 capture applications. © 2023 Elsevier B.V.
Journal of Molecular Structure (00222860)1275
Cyclic voltammetry, UV-vis spectroscopy and (TD)DFT/6-311++G(d,p) computations are applied to investigate electronic and steric effects of substitutions in a series of 3,5-disubstituted 4,5-dihydro-1,2,4-oxadiazoles (DHOZs). Compared to the σ-electron-donating/accepting substitutions on the C5-position, the π-electron-donating/accepting substitutions on the C3-position have larger effects on the frontier molecular orbitals energies, and consequently, on their oxidation peak potentials and UV-vis transitions. Furthermore, the σ-/π-electron-donating/accepting effects of substitution are larger for the LUMO energies. The trend of the results of the computational UV-vis spectra are in agreement with that of the experimental data. The frontier molecular orbitals and molecular electrostatic potential (MEP) surfaces of the optimized structures 1, 4 and 11, as representative, shows that the electrochemical oxidation occurs mainly from the heterocyclic ring, especially the N4 atom having lone pair in the sp3 orbital. © 2022
Asghari, S.,
Mohammadpoor baltork, I.,
Sabzyan, H.,
Tangestaninejad, S.,
Moghadam, M.,
Mirkhani, V.,
Rastegari, F. Applied Materials Today (23529415)35
Compared to the traditionally made imine-linked covalent organic frameworks (COFs), amine-linked COFs provided by in-situ reduction of the linkages represent significant potential for advanced applications, including catalysis and sensing. The current paper deals with preparing a partially reduced COF with secondary amine groups (IR-COF) via in-situ reduction of imine linkages as a dual-functional material adopted for heterogeneous catalysis and acid-sensing. This COF was synthesized using formic acid as a reductant and catalyst in a solvothermal reaction between 2,4,6-tris-(4-formyl-phenoxy)-1,3,5-triazine and p-phenylenediamine. The IR-COF was used as a basic organocatalyst for the efficient synthesis of tetrahydro-4H-chromenes through the Knoevenagel-Michael cyclocondensation. Excellent yields, short reaction times, easy workup, absence of toxic organic solvents, easy recovery, and reusability of the catalyst are outstanding aspects of this catalytic method, making it convenient and useful for fine chemical synthesis. Moreover, the immediate naked-eye color change of IR-COF upon exposure to the hydrochloric acid by protonating the secondary amine groups was investigated. The (time-dependent) density functional theory (TD)DFT PBE/DNP+ method was used to investigate the mechanism of color change during the sensing. The appearance of a new absorption band at higher wavelengths upon protonation is proved to be due to intermolecular or interlayer electron transitions. © 2023 Elsevier Ltd
Physical Chemistry Research (23452625)11(4)pp. 707-723
Molecular docking was applied to investigate interactions between 1638 approved drugs, SARS-CoV-2 virus proteins (spike, nonstructural proteins NSP3, NSP7, NSP8, NSP9, NSP10, NSP12, NSP15, NSP16, and NSP10-NSP16 complex), and the human angiotensinconverting enzyme 2 (ACE2) protein and its Spike@ACE2 complex. Structures of these approved drugs were fully optimized using the universal force field (UFF), and their lowest energy conformations were used for docking on the (co)crystallized structures of the target proteins taken from the protein data bank (PDB). The docking procedure was performed in two stages, and the results were evaluated based on four docking scores (ranking indices), which were used to measure the comparative affinities of the studied drugs towards the SARSCoV-2 virus proteins. Details of the positions, orientations, and interactions of the first three highest-ranked drugs in the binding pocket of the COVID-19 spike, NSP7, and human ACE2 proteins (as representatives) were visualized and analyzed. Based on the results of this molecular docking study, vazegepant, dasabuvir, vitamin E, fosamprenavir, raltegravir, canagliflozin, biliverdin, and imatinib drugs can be considered promising for further molecular mechanics/dynamics simulations and clinical studies to improve the screening process © 2023, Physical Chemistry Research. All Rights Reserved.
Journal of Photochemistry and Photobiology A: Chemistry (18732666)432
A series of 3,5-disubstituted 4,5-dihydro-1,2,4-oxadiazoles (DHOZs) were considered to elucidate electronic effects of the substitutions on their UV-light sensitivities. Based on the proposed electron-transfer induced photo-oxidation in this study, the rate of photoreaction is dependent more on the electronic nature of the substituent on the C5-position of the heterocyclic ring than on the C3-position. Also, the electron-accepting ability of solvent significantly facilitates this photo-induced electron-transfer process. In addition, results of the computational studies carried out on the species along the photochemical reaction path steps approve that the photo-oxidation reaction proceeds via tunneling electron transfer process from the excited state of DHOZs to the solvent molecule, forming a radical cation complex intermediate, followed by proton transfer resulting in the formation of the radical pair complex intermediate. Structural relaxation of this radical pair intermediate resulted in the formation of the final oxidized product in a single step, which shows that the last step of photo-oxidation reaction consists of the transfer of the second electron/proton (hydrogen) to the solvent. These computational results thus explain how the relative rate of the photo-oxidation reaction affected by the nature of the substitutions. In addition, photo-isomerization of oxadiazole (OZ) containing the trans-5-styryl substitution to the cis-5-styryl isomer and the following photo-cyclization reaction are studied experimentally and computationally. © 2022 Elsevier B.V.
Sedighi, M.,
Talaie m.r., M.R.,
Sabzyan, H.,
Aghamiri, S.,
Chen, P. Fuel (00162361)308
The primary objective of the present research is to evaluate the equilibrium and kinetics of CO2 and N2 adsorption into different varieties of MIL-101 including Cr-, Al-, and Fe-based amine-functionalized MIL-101 metal organic frameworks (MOF) using grand canonical Monte-Carlo (GCMC) and molecular dynamics (MD) simulation methods. In the present study, an attempt is also made to clarify the adsorption mechanisms. To achieve this goal, the adsorption isotherms and self-diffusion coefficients of CO2 and N2 in these MIL-101 MOF adsorbents are computed at different temperatures using the universal force field (UFF). Isosteric heat of adsorption and the selectivity values of the CO2/N2 mixture are also calculated. Among the three computed atomic point charge models, including the QM-based Mulliken population analysis, electrostatic potential (ESP) derived, and semi-empirical charge equilibration (QEq) methods, the latter produces more accurate results compared to the others. The results show that molecular simulation using GCMC and MD methods with UFF and QEq can be an appropriate alternative to experiment for predicting equilibrium and kinetic data of the CO2 and N2 adsorption into different varieties of MIL-101. The radial distribution functions (RDF) indicate that the metal centers are dominant active sites compared to the amine groups in the amine-functionalized Cr-based MIL-101. However, it is not the case for the amine-functionalized Al- and Fe- based MIL-101 frameworks, for which the amine groups are more capable than metal sites to capture CO2 molecules. © 2021 Elsevier Ltd
Journal of Physical Chemistry B (15205207)126(49)pp. 10347-10359
Reactive molecular dynamics simulations (RMD) have been carried out to investigate structural alterations of the dodecamer double-strand B-DNA due to the oxidation/nitration modifications introduced to its guanine bases, including 8-oxoguanine, 8-nitroguanine, and 5-guanidino-4-nitroimidazole, considering two distribution patterns. These modifications may arise in the case of cancer treatment using oxidative/nitrosative reactive nitrogen species as anticancer agents. Results show that these mutations affect structural characteristics of the B-DNA dodecamer in the order 8-nitroguanine > 5-guanidino-4-nitroimidazole ≫ 8-oxoguanine. For instance, the base-pair per turn for these modified B-DNA are changed respectively to 9.79, 10.88 and 10.58 from 10.51 in the native defect-free B-DNA, which is compatible with the experimental value of 10.10. In addition, these mutations allow more water molecules to diffuse into the dodecamer structure and consequently increase the possibility of the penetration of reactive and nonreactive species toward constituting nucleic base-pairs. The largest variation of the B-DNA structure is observed for the mutated B-DNA with 8-nitroguanine modifications applied to its separated CG base-pairs along the dodecamer chain. The structural changes introduced by these nitro-/oxo-modified guanine bases can be considered as a critical step in the damage of the DNA structure and alterations of its function. © 2022 The Journal of Physical Chemistry A. All right reserved.
Environmental Science and Pollution Research (09441344)29(6)pp. 9173-9192
Magnetic nano-size copper iron binary oxide is synthesized via a sol–gel method using copper and iron nitrates as precursors and citric acid, chicken egg white, and starch as stabilizers followed by annealing at 400 °C and 800 °C in air. The TG-DTG, XRD, FESEM, EDX, VSM, and FT-IR and UV–Vis DRS spectroscopy methods are used for thermal, structural, magnetic, and optoelectronic characterizations. Depending on the stabilizer and annealing temperature, pure CuFe2O4, (CuFe2O4,CuO) or (CuFe2O4,CuO,Fe2O3) phases are formed with nano-size particles of 20–65 nm, having optical band gaps in the range of 2.15–2.60 eV (577–477 nm). Photocatalytic activities of the synthesized nano-size copper iron binary oxide samples are examined for degradation of Nile Blue textile dye displayed first-cycle removal (from water solution) efficiencies of 86.7–93.3%. Considering usage of non-toxic metals and low-cost green stabilizers, good degradation performances, and easy/efficient (magnetic) recyclability, this nano-size catalyst is suggested for further optimization studies for industrial applications. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Materials Today Communications (23524928)26
Performance of the proposed lead-free mixed halide iron perovskite CH3NH3FeI2Br as the light absorber layer of the perovskite solar cells is evaluated based on the analysis of the calculated optical properties. Crystal structure of this mixed halide iron perovskite is optimized at spin-polarized DFT GGA-PBE/FP-LAPW+lo level of theory. Structural analysis shows that the optimized unit cell parameters of this CH3NH3FeI2Br perovskite are all smaller than their corresponding values for the pure iodide iron perovskite CH3NH3FeI3. Thermodynamic analysis based on the total SCF energies calculated for the CH3NH3FeI2Br, CH3NH3FeI3, I2 and Br2 lattices shows also that the mixed halide iron perovskite CH3NH3FeI2Br is more stable than the pure iodide iron perovskite CH3NH3FeI3 by 1477.5 kJmol−1. Band structure, density of states and band gaps are calculated with the GGA-PBE(mBJ)/FP-LAPW+lo method. Analysis of the results show that the mixed halide iron perovskite CH3NH3FeI2Br is a direct band gap semiconductor having band gaps of 3.041 and 0.689 eV for its spin-up and spin-down states, respectively. The absorption spectrum calculated for the mixed halide iron perovskite MAFeI2Br and its corresponding Brewster angles calculated for the TiO2/perovskite and perovskite/spiro interfaces, the proposed mixed halide iron perovskite MAFeI2Br can be regarded as a promised candidate for application as light-harvesting layer of perovskite solar cells due to its good optical performance in the 500–630 nm range of wavelengths of the sunlight spectrum. Stability of the proposed CH3NH3FeI2Br perovskite is also validated based on the analysis of the calculated octahedral and Goldschmidt tolerance factors (0.465 and 1.009, respectively). © 2020 Elsevier Ltd
Physical Chemistry Chemical Physics (14639084)22(23)pp. 13070-13083
In this paper, we have reported a molecular dynamics (MD) study on the properties of three different magnetic imidazolium-based ionic liquids in the absence and presence of an external magnetic field. In this regard, the volumetric properties such as density and isobaric expansion coefficient, dynamical properties, namely, viscosity, mean square displacement of ions, diffusion coefficients, transport numbers of cations and anions, and electrical conductivity, and structural properties such as radial distribution function (RDF) and spatial distribution function (SDF) of [emim][FeCl4], [bmim][FeCl4] and [hmim][FeCl4] have been studied at different temperatures using molecular dynamics simulations. After studying the different volumetric, structural, and dynamical properties of the above-mentioned magnetic ILs in the absence of a magnetic field, we investigated the effect of an external magnetic field on the structural properties of one of these systems, i.e., [bmim][FeCl4]. In this regard, we established different contributions in the interactions between the external magnetic field and the studied magnetic ionic liquid (MIL). The number density profiles of the studied MIL before and after imposing an external magnetic field of 1.5 T showed a significant variation in the molecular distribution. The results indicated that the external magnetic field reduced the intensity of RDFs due to the reduction in the interactions between different ion sites as a result of changes in their orientations. After applying the external magnetic field, it was observed that due to the oppositely directed forces on the cations and anions, they moved in opposite directions. The snapshots showed that the static motion of the anion was smaller because of its small size. In the presence of an external magnetic field, the ions distributed more homogeneously compared to that observed in the absence of this field. The results of this study can be used in the rational and accurate design of viscomagnetic fluids and reaction systems in the presence and absence of magnetic fields. © the Owner Societies.
Physical Chemistry Research (23452625)8(4)pp. 629-644
Reactive molecular dynamics simulations (RMDS) with the ReaxFF force field are used to study nucleation and growth of silica nanoparticles during flame synthesis from tetramethoxysilane (TMOS). Two reactive systems (A and B) are considered and formation and/or consumption of various reactants, intermediates and products are followed. In the RMDSs of system A (TMOS, O2, SiO2 and Ar), the temperature-dependence of the formation of initial SimOn seeds show that formation of transient SiO3C3H9 intermediate is an important stage in the conversion of TMOS to the initial SimOn seeds, which then aggregate to produce silica nanoparticles. Increasing temperature speeds up this conversion. Results of the RMDSs on system B (TMOS, O2, Ar and (SimOn); the SimOn seeds play the role of the initial silica nanoparticles) show that at 2100 K, application of weak EFs (~1 V/A) narrows the size distribution of the silica nanoparticles compared to that in the absence of EF while by application of stronger EFs (4-8 V/A), the initial SimOn nanoparticles split into smaller species. In the absence of EF, increasing temperature from 1500 K to 3000 K increases sizes of the nanoparticles. The radial distribution functions, coordination numbers, and atomic compositions are used to characterize nanoparticles and evolution of the reaction. © 2020 Iranian Chemical Society.
Ekramian, E.,
Aghamiri, S.,
Talaie m.r., M.R.,
Sabzyan, H. Fluid Phase Equilibria (03783812)508
In this work, a grand canonical Monte Carlo (GCMC) simulation was performed to evaluate the performance of three types of modifications on the adsorption isotherms of pristine and modified crystal structures of two metal organic frameworks (MOFs) of Zn-MOF-74 and Zn-IRMOF-13. These modifications were: (i) doping by nickel and magnesium ions, (ii) functionalization with OH, CH3, and NH2 groups, and (iii) ion exchange with magnesium and copper ions. The CO2 working capacity, CO2/N2 selectivity, and selection parameters of each pristine and modified structures was calculated. The results showed that among all of modified structures, the copper ion exchange modification of Zn-MOF-74 has the largest selection parameter of 2858 and 250, and this modification can increase the selection parameters by 590 and 455% than the pristine structure, in the pressure ranges of 10–100 kPa, and 100–1000 kPa, respectively. Therefore, among all of structure modifications studied in this work, the adsorbent structure modification with copper ion exchange and the application of Cu-MOF-74 is the most appropriate for both vacuum and pressure swing adsorption processes. © 2019
Structural Chemistry (15729001)31(2)pp. 809-821
Bistability of the proposed [(phenanthroline)2FeII/III–(terephthalate)–CoIII/II(phenanthroline)2]3+ binuclear complex, arising from intramolecular FeII/III ↔ CoIII/II charge transfer, is investigated based on energetics, geometries, atomic charges, electric polarizabilities, and IR and UV-Vis spectra obtained computationally at (TD)DFT-B3LYP/LANL2DZ level of theory. Two distinct stable states are obtained which have different characteristics, including structures, charge distributions, and spectroscopic properties. Also, the well-defined first-order saddle point obtained between these two states using the QST3 search method, having a 1.182 eV activation (barrier) energy for the FeIICoIII → FeIIICoII reaction, furthermore approves bistability in this complex. This value of activation energy suggests that switching between the two charge distribution states FeII–CoIII and FeIII–CoII in this complex may be induced by electric field and/or infrared radiation, and thus, it can be candidate as an infrared radiation- or electric field-driven molecular two-state switch. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.
Journal of Physics Condensed Matter (09538984)32(46)
Structural and optical properties of methylammonium iron iodide perovskite CH3NH3FeI3 are studied at DFT-PBE(mBJ)/FP-LAPW + lo level of theory to assess feasibility of the replacement of the toxic lead with the non-toxic iron in the perovskite layer of solar cells. Starting from experimental crystal structure of the Pb perovskite, volume and aspect ratio (c/a) and atomic positions are optimized for the CH3NH3FeI3 structure, and its electronic and optical characteristics are calculated. An index, measuring the raw optical performance of the light harvesting layer of a solar cell is introduced and calculated for the two Fe and Pb perovskites. Comparative values of this index shows that the iron perovskite CH3NH3FeI3 has an acceptable optical performance, ∼61% that of the Pb perovskite CH3NH3PbI3. Analysis of the Brewster angles (θ B) calculated for the TiO2/perovskite and perovskite/spiro interfaces shows that the Fe perovskite solar cell can have better optical harvesting performance by a factor of 1.32, which improves its comparative overall performance up to 80%. As a conclusion, application of iron perovskite CH3NH3FeI3 is promising, especially due to its much lower costs and significantly alleviated environmental hazards of the incorporating solar cells. © 2020 IOP Publishing Ltd.
Journal of Molecular Structure (00222860)1207
Some 3,5-disubstituted 4,5-dihydro-1,2,4-oxadiazoles (DHOZs) were synthesized, and steric and electronic effects of the substituents on the heterocyclic ring C3- and C5-positions were investigated using the NMR and UV–Vis spectroscopies, and (TD)DFT/6-311++G(d,p) computations. The NMR and UV–Vis spectroscopic characteristics of the synthesized compounds could be explained in terms of the π- and σ-electronic effects of the C3- and C5-aryl substitutions on the heterocyclic ring, respectively. Computational NMR chemical shifts and spin-spin coupling constants of the C5–H and N4–H protons display a Karplus correlation with corresponding H–C5–N4–H dihedral angle. The experimental and computational 1H NMR chemical shifts of the C5–H proton show very good compatibility. Conformational analysis on the o-nitro and o-methoxyphenyl C5-substituted DHOZs showed intramolecular interactions affecting their structural and spectroscopic features. © 2020 Elsevier B.V.
Journal of Molecular Liquids (18733166)318
The corrosion of iron carbide was investigated in the water at 298 K and 500 K as a weak electrolyte and a solution of hydrochloric acid at 298 K, using the reactive force field molecular dynamics. The thickness of the passive film, the formed species, and two-dimensional radial distribution function were investigated. The species FeO5H10, FeO4H8, and FeO3H6 were recognized as the products of corrosion reaction in the water at 500 K and FeO5H10, FeO4H8, and FeO5H9 in acidic solution at 298 K. The quantum mechanics calculations have shown that the more stable products in water and acidic solution are FeO4H8 and FeO5H9, respectively. © 2020 Elsevier B.V.
Acta Physica Polonica A (05874246)137(6)pp. 1175-1181
Electron dynamics in gold (Aun) nanoparticles in the absence and presence of electric field is studied using molecular dynamics simulations. For this dynamics, motion of electrons is treated classically by considering a force field including Coulomb and van der Waals interaction potentials for the electron–electron (e−–e−), electron-ionic core (e−–Au+) and ionic core-ionic core (Au+–Au+) pairs of species. These electrons and ionic cores are set initially at the alternative sites of a set of identical twin fcc lattices. Electric current and conduction are evaluated for the Aun gold nanoparticles of different sizes (n = 2048, 2816, 3328, and 3840) in electric field of 0.001 V/Å strength. Results of this study show a non-linear dependence of electric conduction on the size of the gold nanoparticles. © 2020 Polish Academy of Sciences. All rights reserved.
Journal of Photochemistry and Photobiology A: Chemistry (18732666)389
Photooxidation of various 2-pyrazolines is studied experimentally and computationally. Experimental results show that the electron-donating/withdrawing substituents increases/decreases the rate of this photoreaction. The proposed light-induced electron-transfer mechanism explains the steric and electronic effects of the substituents, co-planarity of the aryl rings substitutions, orientations of the C3-aryl ring towards the C3=N2 double bond and the solvent on the irradiation time for completion of reaction. Computational (TD)B3LYP/6-311++G(d,p) results, including frontier orbital energies, UV–vis transitions, electrostatic potential, CHELPG charges, are used to find and describe tunneling electron-transfer process and its associated structural relaxations which form the rate-determining step of the reaction, and to justify the effect of substitutions on the rate of reaction. The intermediate complex formed after the first electron transfer proceeds the proton transfer step only in its triplet state. Triplet excited states of 2-pyrazolines may have little contribution to the electron transfer step. Cyclic voltammetric measurements support the photochemical results. © 2019 Elsevier B.V.
Materials Today Communications (23524928)22
Proton conductivity of Na3 (2, 4, 6-trihydroxy-1, 3, 5-benzenetrisulfonate) framework (β-PCMOF2) is studied in anhydrous and humid conditions using molecular dynamics simulation in the temperature range of 303-423 K. To obtain results compatible with experiments force field parameters for proton is adjusted. The Grotthuss mechanism for proton conduction of β-PCMOF2 is proved by obtaining an activation energy in the range of (− 0.261, − 0.101 eV). The effect of the electric field on proton conductivity is also investigated. Proton conduction is reduced with temperature which is in agreement with the experiments. The RDF plots obtained in the absence of electric field and the effect of electric field on the proton MSD show that the protons transport through the oxygen atoms of sulfonate groups of the framework and their movements in the x and y directions are more than that in the z-direction. Simulations are carried out in the presence of protonated water and 1, 2, 4-triazole molecules rejected possibility of the vehicle. © 2019 Elsevier Ltd
Computational and Theoretical Chemistry (2210271X)1155pp. 9-19
Computational study at DFT-B3LYP/LANL2DZ level of theory is carried out to evaluate structural, bonding and energetic characteristics of cis/trans isomers of the [(CO) 2 (benzoate)M II/III (terephthalate)] 0/1+ complexes with 3d transition metals M = V, Cr, Mn, Fe and Co. Results of this study show that all cis/trans isomers of these complexes in their two oxidation states are stable with distinctly different structures. As a general trend, for all cis/trans isomers of these complexes, the M–O(benzoate) and M–O(terephthalate) bonds are shorter for the M III oxidation state of the metal ion compared to those for the corresponding M II oxidation state. Also, structure of the set of four M–O bonds are almost asymmetric such that the optimized M II/III –O (terephthalate) bond lengths are slightly longer than the M II/III –O(benzoate) bond lengths. The coordination M–O bonds structure of the cis/trans isomers of the [(CO) 2 (benzoate)Co II (terephthalate)] complex have the most asymmetries, and interestingly, its trans isomer is more asymmetric than its cis isomer. The M III complexes have larger electric dipole moments compared to their corresponding M II complexes. Furthermore, cis/trans isomerization has no significant effect on the size of electric dipole moment for the M II complexes. © 2019 Elsevier B.V.
Materials Science and Engineering C (09284931)94pp. 410-416
Accurate and fast measurement of the iron ion in biological, pharmaceutical and medical samples is of great applied importance. In this work, a novel optical sensor (optode) for the Fe(III) ion is fabricated based on the immobilization of morin (2′,3,4′,5,7-pentahydroxyflavone) on a triacetylcellulose membrane. Chemical binding of the Fe(III) ion with the immobilized morin is monitored spectrophotometrically at 334 nm. The prepared optode shows excellent response over a wide range of concentrations from 1.06 × 10−10 to 4.73 × 10−5 M with a detection limit of 4.23 × 10−11 M Fe(III). Effects of the factors determining sensitivity of the optode are studied and optimized. The prepared optical sensor shows good selectivity toward the Fe(III) ion in the presence of a number of other metal ions. The developed sensor is applied successfully and satisfactorily for the determination of iron in three pharmaceutical, one plasma and two serum samples. In addition, concentration of the Fe(III) ion in two tap water samples is measured using standard addition method. Density functional theory (TD) B3LYP/6-311++G** method is used to investigate structure and binding characteristics, and calculate the UV–Vis spectrum of the Fe(III)-morin complex. © 2018
International Journal of Quantum Chemistry (1097461X)119(7)
Bistability of the four cis/trans isomers of the proposed iron-cobalt binuclear complex [(CO) 2 (benzoate-)Fe II/III (-terephthalate-)Co III/II (-benzoate)(CO) 2 ] 1+ , arising from the Fe II/III ↔ Co III/II intramolecular charge transfer (IMCT) is investigated computationally at (TD)DFT-B3LYP/LanL2DZ level of theory. Energies, geometries, atomic charges, and the UV-Vis spectra are considered in this investigation. Results approve IMCT bistability of all cis/trans isomers by locating two stable states with distinctly different structures and charge distributions (Fe II -Co III and Fe III -Co II oxidation states). Also, well-defined first-order saddle points between these two IMCT states are found and characterized using QST2/QST3 method. Based on the analysis of the calculated charge distributions and the 0.35-1.66 eV activation (barrier) energies of the Fe II -Co III ↔ Fe III -Co II IMCT reactions, it can be predicted that electric field or NIR radiation may be used to switch between the two IMCT states of this bistable binuclear complex. It is also found that the cis/trans isomerization has significant effects on the energetics of this IMCT reaction, and that the trans-Fe II/III -trans-Co III/II isomer is the best candidate for prospective switching application due to having the least energy dissipation and the largest charge transfer. © 2018 Wiley Periodicals, Inc.
Soltani m., M.,
Minakar, R.,
Memarian, H.R.,
Sabzyan, H. Journal of Physical Chemistry A (15205215)123(13)pp. 2820-2830
Cyclic voltammetry is used to derive HOMO energies of the 1-phenyl-2-pyrazolines containing electron-donating or electron-withdrawing substituted phenyl rings and or naphthalenyl substitution on the C 3 - or C 5 -positions of the heterocyclic ring to investigate the steric and electronic effects of the aryl substitutions and the type of aryl system on their electrochemical behaviors. The optical HOMO-LUMO gaps needed for the calculation of LUMO (excited state) energies of these compounds are obtained from their UV-vis spectra. Results show that the substitution on the C 3 -aryl ring has significant effect via its π-donor/acceptor ability, compared to the σ-donor/acceptor ability of the C 5 -aryl ring, on the CV oxidation peak and onset potentials. Comparative analysis showed very good agreement between the experimentally obtained HOMO and (apparent) LUMO energies and the (TD)DFT/6-311++G(d,p) calculated ground and excited states energies. These computational results indicate also that for all chloro- and methoxy-substituted 2-pyrazolines, the HOMO → LUMO is the most intense transition. While the strong acceptor NO 2 substitution on all positions of either C 3 - or C 5 -aryl rings, except for one compound, increases the intensity of the HOMO → LUMO+1 (LUMO+2) transition significantly, the first (the first two) transition(s) HOMO → LUMO (and HOMO → LUMO+1) has (have) much smaller or negligible intensity (intensities). © 2019 American Chemical Society.
Journal Of The Iranian Chemical Society (1735207X)16(5)pp. 963-978
Abstract: Electric field effects on the kinetics of SiO 2 formation, and the growth of silica nanoparticles formed in the flame (fumed silica) are studied theoretically and computationally, considering combustion of SiCl 4 in the H 2 /O 2 flame. An existing mechanism for the gas-phase part of this flame synthesis reaction is improved and used to derive instantaneous concentrations of the involved species. Quantum (DFT) computations are used to obtain thermodynamic data required for the calculation of equilibrium concentrations and reaction rate constants, assuming an overall (high temperature) equilibrium state. Kinetics equations based on a modified 43-step 24-species mechanism are established and solved to obtain concentrations at different temperatures and EF strengths. These concentrations are used as inputs for the Monte Carlo simulation of the growth of silica nanoparticles, considering also possibility of atomic displacements and vacancies. Effects of homogeneous electric field of different strengths on the growth of silica nanoparticles are investigated. Results of this study show that electric field changes the preferences of different paths of the mechanism of this flame synthesis reaction and changes composition of the flame via controlling orientation of the dipolar species, which consequently determine characteristics of the grown silica nanoparticles. Furthermore, EF effect is larger at lower temperatures. © 2019, Iranian Chemical Society.
Communications in Theoretical Physics (02536102)71(4)pp. 441-454
Electronic and vibrational intra-molecular thermoelectric-like figures of merit (ZTγ M) are introduced for single molecule nanoelectronic system, using quantum theory of atoms in molecule. These figures of merit are used to describe intra-molecular or local energy dissipation/transition (as in Joule-like, Peltier-like, and Thomson-like effects) in field effect molecular devices. The ZTγ Mfigures of merit are computed for two proposed molecular devices. Analysis of the results shows that ZTγ M depends almost non-linearly on the electric field (EF) strength. Also, the intra-molecular Joule-like heating plays a dominant role in the local energy dissipation, and intra-molecular Thomson-like heating is generally larger than the intra-molecular Peltier-like heating. Introduction of ZTγ Mcan be applied to extend the analysis of thermoelectric heating down to molecular and intra-molecular levels, and thus can be used to predict characteristics and performance of any candidate multi-terminal or multi-pole molecular systems prior to their application in real nanoelectronic circuits. © 2019 Chinese Physical Society and IOP Publishing Ltd
Molecular Physics (00268976)117(1)pp. 110-121
Recently, we reported molecular dynamics simulations of stable cyclotron motions of ions and water molecules in a carbon nanotorus, induced by different rotating electric fields (EFs). This study is devoted to the calculation and characterisation of the magnetic field (MF) induced by these cyclotron motions. Results show that carbon nanotorus containing ions or water molecules acts as an EF-to-MF transducer. Components of the instantaneous induced MF show large-scale oscillations superimposed by strong fluctuations arising respectively from overall circular motion and random collisions of moving species. Analysis of the space-dependencies of the induced MF components shows that the induced MF is maximum at the centre of the nanotorus. The MF induced by cyclotron motion of ions follows the orders B(Ca2+) > B(Na+) ≈ B(K+) at E = 1.0 V/nm and B(E = 1.0 V/nm) > B(E = 0.5 V/nm) > B(E = 0.1 V/nm). The time-averaged induced MF of the cyclotron motion of 81 water molecules is almost 102 times stronger than that of ions. The induced MF strength is decreased with increasing distance from nanotorus and decays effectively at about 17.3–18.1 and 15.9–18.2 nm along the z-axis of the nanotorus for ions and water molecules, respectively. The magnitude of the MF induced by cyclotron motions of water molecules and ions, respectively, decreases and increases in the nanotorus with freed carbon atoms. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.
Journal of Physical Chemistry C (19327447)123(49)pp. 29932-29945
Physicochemical properties of the nanostructured complex systems, formed between the deferrioxamine B (DFO) siderophore ligand and Zr(IV), Hf(IV), or Fe(III) metal ions at the gold-thiol electrode surface, are determined by different surface, electrochemical, and solution techniques, and the systems are characterized. The results obtained from separate experiments show that the DFO can accumulate and complex the M ions [M: Fe(III), Hf(IV), or Zr(IV)] on the gold-mercaptopropionic acid (Au-MPA) surface efficiently but with different affinities as Zr(IV) > Hf(IV) > Fe(III), leading to different surface morphologies and organizations, and structural diversity of the Au-MPA-DFO-M complexes as Fe(III) > Hf(IV) > Zr(IV). Furthermore, the Fe(III) ions of the Au-MPA-DFO-Fe(III) surface are replaced rapidly by both Hf(IV) and Zr(IV) ions but with different kinetics; the replacement of Zr(IV) is ∼three times faster than that of Hf(IV) at highly acidic solution. Thus, the DFO can be used to identify and differentiate the behaviors of these important heavy metal ions. To our knowledge, this is one of the few cases in which Hf(IV) and Zr(IV) ions show different behaviors. The results of this study are important and can improve our physicochemical insights into the behavior of these ions in conjunction with siderophores, regarding the natural and industrial environments, metal refinery and nuclear power plants, human biological systems, soil contamination, agricultural products, and foods. © 2019 American Chemical Society.
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy (13861425)222
Non-linear optical (NLO) behavior of some phenanthrene-based organic molecules is studied using quantum computational MP2 and B3LYP methods with cc-pVDZ basis set. The design of these molecules is based on possible intramolecular charge transfer between electron donor and electron acceptor groups via an aromatic bridge. The –NO2, –CN, –CF3, –C(CF3)[dbnd]C(CF3)2, –SO3H and –C(CN)[dbnd]C(CN)2 acceptors and the –NH2, –N(CH3)2 and pyrrolidinyl donors have been considered. The HOMO and LUMO energies, polarizabilities and first hyperpolarizabilities are calculated for the optimized structures both in the gas phase and in the conductor-like polarizable continuum model (CPCM) of different solvents. Moreover, the energies of the vertical transitions in the UV–Vis range having large oscillator strengths and their corresponding adiabatic transition energies are calculated using TD-DFT-B3LYP/cc-pVDZ method. Also, UV–Vis and infrared spectra are simulated for these designed molecules. Results show that these phenanthrene derivatives have generally very good NLO behavior. Also, NLO properties are enhanced when (–C(CN)[dbnd]C(CN)2 & –NH2) and (–NO2 & pyrrolidinyl) pairs of (acceptor & donor) groups are used. The approach adopted in the present quantum computational study can be used for similar studies for better description and understanding of the NLO responses of the electron donor-bridge-acceptor systems with π-conjugated bridges. © 2019 Elsevier B.V.
Australian Journal of Chemistry (14450038)71(5)pp. 348-359
Electric dipole moments, polarizabilities, and IR, Raman, optical rotatory dispersion, and electronic and vibrational circular dichroism spectra of the four cis-trans isomers of the proposed [(CO)2(benzoate)FeII/III(terephthalate) CoIII/II(benzoate)(CO)2]+ binuclear complex, having bistablity due to intramolecular charge transfer (IMCT), is investigated using the time-dependent density functional theory ((TD)DFT) B3LYP/6-31G(d,p)[LanL2DZ] method. Results show that the two FeII-CoIII and FeIII-CoII IMCT states of this binuclear complex have distinctly different spectroscopic, optical, and electric response properties, and are sensitive to the cis-trans arrangement of the ligands around the two metallic centres. Furthermore, intrinsic reaction coordinates inter-connecting the two IMCT states are identified using the Duschinsky matrix method. Only one or two of the normal coordinates remain almost (above 80 %) intact during the IMCT reaction which denotes global changes in the bonding strengths and potential energy hypersurface of this bistable binuclear complex. Analysis of the calculated spin densities characterizes the IMCT transition state structures of the trans-trans, cis-cis, and trans-cis isomers as early, early, and late transition states, respectively. © 2018 CSIRO.
Journal of Physics B: Atomic, Molecular and Optical Physics (09534075)51(7)
Contributions of the pre-ionized H2 (PI-H2) and ionized subsystems of the two-electron H2 system to its high-order harmonic generation in eight-cycle sin2-like ultrafast intense laser pulses are calculated and analyzed based on the solution of the time-dependent Schrödinger equation for the one-dimensional two-electronic H2 system with fixed nuclei. The laser pulses have λ = 390 and 532 nm wavelengths and I = 1 ×1014, 5 ×1014, 1 ×1015 and 5 ×1015 W cm-2 intensities. It is found that at the two lower intensities, the PI-H2 subsystem dominantly produces the HHG spectra. However, at the two higher intensities, both PI-H2 and ionized subsystems contribute comparably to the HHG spectra. In the subsystem, the symmetry of the populations of (I) and (II) regions (left and right regions of subsystem) is broken by increasing the laser intensity. Complex patterns and even harmonics also appear at these two higher intensities. For instance, at 1 ×1015 W cm-2 intensity and λ = 532 nm wavelength, the even harmonics are appeared near cutoff region. Interestingly, at 5 ×1015 W cm-2 intensity and λ = 390 nm wavelength, the even harmonics replaced by the odd harmonics with red shift. At λ = 390 and 532 nm wavelengths and I = 1 ×1015 intensity, the two-electron cutoffs corresponding to nonsequential double-recombination with maximum return kinetic energy of 4.70Up are detected. The HHG spectra of the whole H2 system obtained with and without nuclear dynamics treated classically are approximately similar. However, at 1 ×1015 W cm-2 intensity and λ = 532 nm wavelength, if we take into account nuclear dynamics, the even harmonics which are appeared near cutoff region, replaced by the odd harmonics with blue shift. © 2018 IOP Publishing Ltd.
Computational and Theoretical Chemistry (2210271X)1128pp. 42-47
Contribution of inter-ring torsional motion of 2,2′-difluorobiphenyl (DFBPh) to the NMR chemical shifts (CSs) and lineshapes is investigated using B3LYP/aug-cc-PVDZ computations. The anharmonic potential energy curve for this vibrational motion is calculated by a relaxed scan over the whole span of its coordinate, inter-ring dihedral angle D. The NMR CS curves for the most affected 1H, 13C and 19F nuclei are calculated as functions of D for these relaxed structures using IGAIM method. Lineshapes arising from the unaveraged NMR CSs are simulated for each vibrational state, and their corresponding state averages and the thermally averaged values at two temperatures are calculated. Lineshape broadening in slow regime is significant especially for the 19F nuclei. The averaged CSs differ slightly, but detectably, from their corresponding equilibrium values. It is thus concluded that for accurate evaluation of the NMR CSs and experimentally compatible NMR spectra, such vibrational analysis is necessary. © 2018 Elsevier B.V.
Molecular Simulation (08927022)44(4)pp. 263-273
Molecular dynamics (MD) simulations of the transport of ions in nano-confined spaces such as nanotori, which can be regarded as a good analogue of ion accelerators and cyclotrons, can help smart design of nanoelectronic devices for various prospective applications including local control of electron transfer, switching molecular and nano circuits and also photodynamic therapy. In this regard, a cyclotron motion is established for the Na+, Ca2+ and K+ ions inside a rigid carbon nanotorus by applying gigahertz homogeneous rotating electric fields (EF) of 0.01–1.00 V/nm strengths and 16–128 GHz frequencies. The ion-wall collisions result in a fluctuation in the instantaneous position of the ions lagging behind the direction of the EF. Analysis of the variations of the position vector of the ion with respect to the instantaneous direction of the EF, measured in terms of the lagging angle (Formula presented.), shows that for all three ions, narrow distributions towards the desired value of (Formula presented.) are achieved by increasing strength and decreasing frequency of the EF. Under similar conditions, average values of the acquired velocities of ions follow the order: (Formula presented.) which reflects their relative charge/mass ratios and interactions with the nanotorus carbon atoms. The results show that, more stable motion could be obtained with stronger EF and lower frequency. Lighter ions with higher electric charge are more appropriate for the induction of nanocyclotron motion. Continuous cyclotron motion could also be established with the relaxed nanotorus and in a nanotorus of larger radius. © 2017 Informa UK Limited, trading as Taylor & Francis Group.
Australian Journal of Chemistry (14450038)71(5)pp. 380-388
Various 5-carboethoxy-2-oxo-1,2,3,4-tetrahydropyridines and their corresponding oxidation products containing methoxy or nitro groups on different positions of the C 4 -aryl ring were synthesized and the effect of steric and electrostatic interactions of these aryl substituents on the characteristic peaks in 1 H NMR spectra were investigated. In addition, the intermolecular interaction of the parent compound and its oxidized form with solvent was experimentally investigated. For this, 1 H NMR spectra of these compounds at different concentrations and temperatures in [D6]DMSO and CDCl 3 were investigated. For comparison of the dimerization ability of these heterocyclic compounds with different conformations, the binding electronic energies, the total enthalpies and free energies of dimerization in the gas and solution phases, and the QTAIM (quantum theory of atoms-in-molecules) analysis were determined. These interactions were also studied using density functional theory at the B3LYP/6-311++G(d,p) level. The theoretical results are in good agreement with the experimental results and indicate that the electronic effect of the methoxy and nitro groups on the C 4 -aryl ring influences the electron density of the heterocyclic ring via the σ bond and, consequently, the chemical shift of the heterocyclic ring protons. © CSIRO.
Journal of Molecular Structure (00222860)1173pp. 903-917
A series of aryl substituted 1-phenyl-2-pyrazolines containing electron-donating and electron-withdrawing substituents on different positions of the C3– or C5-aryl groups were synthesized and their steric and electronic effects on characteristic spectral data were investigated by experimental spectroscopic methods (UV–Vis, IR and NMR) and DFT computations. Whereas the C5-aryl group of the heterocyclic ring behaves as σ-donor/acceptor substituent, the π-donor/acceptor ability of the C3-aryl group depends on the co-planarity of the substituent with the aryl ring and also the extent of the orientation of this C3-aryl ring towards the C[dbnd]N double bond of the heterocyclic ring. A significant through conjugation of the lone pair on the N1-atom towards the C3-aryl ring is observed when the electron-withdrawing nitro group is located on the para-position of this aryl ring. The experimental spectroscopic results for the substitution effects are also supported by (TD)DFT/6-311++G(d,p) computed UV–Vis spectra. Experimental and theoretical NMR chemical shifts and spin-spin coupling constants obtained for these 2-pyrazolines validated by Karplus diagram approves the structures predicted for these compounds. © 2018 Elsevier B.V.
Computational and Theoretical Chemistry (2210271X)1099pp. 75-86
Quantum chemical calculations based on density functional theory (DFT) and X-ray crystal structure analysis of some ethyl 4-aryl-6-methyl-2-oxo-1,2,3,4-tetrahydropyridine-5-carboxylates (THPYs) were applied in order to elucidate the effect of variations of the additional substituent on the C4-aryl ring on the molecular geometry, conformation and packing of molecules in the crystalline lattice. Due to the presence of the C4 stereocenter, these compounds exist as a racemic mixture in the crystal structure. Intermolecular interactions between the potential hydrogen donor (N[sbnd]H) and hydrogen acceptor (2-CO) of the heterocycle in the enantiomeric pair forming a sheet like dimeric structure, which provides especial stability to the crystal packing. The existence of the short intramolecular interactions (C[sbnd]H⋯π) and (C[sbnd]H⋯O) are a key feature which imparts also additional stability to the molecular conformation in the solid state. Most computational data including conformation of the heterocycle, the values of the bond lengths and angles are well in agreement with the experimental data. Ring flip calculations for 4-phenyl substituent explain the extreme torsional strain caused by the eclipsing of the carbon-hydrogen bonds in 3-CH2 moiety with the neighboring C4[sbnd]Caryl and C4[sbnd]H bonds and also the changes of some characteristic bond lengths and angles. These calculations indicate the more favored pseudo-axial orientation of the phenyl group over the pseudo-equatorial orientation. © 2016 Elsevier B.V.
Chemical Physics Letters (00092614)686pp. 26-33
The mean square displacement and the self-diffusion coefficients of hydrogen molecules along both crystallographic and Cartesian coordinates inside the MOF-508a were calculated in the temperature range of 77–900 K. The self-diffusion is increased with temperature and also with hydrogen molecules loading up to a certain point after which it is decreased. Activation energy and binding energy of hydrogen molecules to the MOF sites were calculated for each loading. Analysis of the radial distribution functions shows that hydrogen molecules prefer to bind to the nitrogen and carbon atoms of the MOF. Furthermore, correlation between the hydrogen molecules increases with temperature. © 2017 Elsevier B.V.
Physical Chemistry Chemical Physics (14639084)19(46)pp. 31138-31155
The effects of the orientation, wavelength and carrier-envelope phase of laser pulses on the spin fluctuation in HeH2+ and LiH3+ molecular ions in their bound electronic states, during their interactions with linearly polarized intense laser pulses, were investigated by solving numerically the time-dependent Dirac equation with the Foldy-Wouthuysen transformation. The results of this study showed that an increase in the wavelength of the laser pulse at a fixed intensity reduces the lifetime of the coherent spin states and increases the sensitivity of the spin vector to the applied laser field in both HeH2+ and LiH3+ species. This sensitivity also depends on the carrier-envelope phase of the laser pulse due to the asymmetry of these systems. Furthermore, the influence of spin-orbit coupling on the dynamics of the spin in the interaction of the highly charged atomic species, N6+, with ultra-intense laser pulses was investigated by considering different initial orbitals and spin polarizations. The results show that significantly different spin-forces are induced when an interaction starts with two parallel and perpendicular polarized spin states with respect to the direction of the laser pulse propagation. Furthermore, spin-orbit coupling affects the quantization of the spin space and results in asymmetric spin fluctuation depending on the initial spin polarization state and the electron orbital momentum, which is induced by the electric field of the laser pulse. © 2017 the Owner Societies.
Zeitschrift fur Naturforschung - Section A Journal of Physical Sciences (09320784)72(1)pp. 1-7
First principle density functional theory methods, local density and Perdew-Burke-Ernzerhof generalized gradient approximations with Goedecker pseudopotential (LDA-G & PBE-G), are used to study the electric field effects on the binding energy and atomic charges of bilayer graphene (BLG) at the Γ point of the Brillouin zone based on two types of unit cells (α and β) containing nC=8-32 carbon atoms. Results show that application of electric fields of 4-24 V/nm strengths reduces the binding energies and induces charge transfer between the two layers. The transferred charge increases almost linearly with the strength of the electric field for all sizes of the two types of unit cells. Furthermore, the charge transfer calculated with the α-type unit cells is more sensitive to the electric field strength. The calculated field-dependent contour plots of the differential charge densities of the two layers show details of charge density redistribution under the influence of the electric field. © 2017 Walter de Gruyter GmbH, Berlin/Boston.
Physical Chemistry Chemical Physics (14639084)19(19)pp. 12384-12393
A nano-flow is induced by applying gigahertz rotating electric fields (EFs) of different strengths and frequencies on a carbon nanotorus filled with water molecules, using molecular dynamics simulations. This nano-flow, which may also be regarded as a molecular cyclotron motion, needs a rising time to establish and to follow the rotating EF depending on the applied EF strength and frequency. For establishment of a steady cyclotron motion in the carbon nanotorus, EFs of higher strengths and lower frequencies are required. Furthermore, the response of the orientations of the water molecules to the direction of the rotating EF is faster than that of their positions. In this study, it is also shown that the free motion of the nanotorus carbon atoms speeds up establishment of cyclotron motion. © 2017 the Owner Societies.
Journal Of The Iranian Chemical Society (1735207X)14(8)pp. 1815-1826
Quantum dynamics of electron transfer (capture) phenomenon during the H–He2+ collision is investigated by solving two-dimensional time-dependent Schrödinger equation numerically using a third-order split operator technique. Results of this study, represented as the snapshots of the electron wavepacket time evolution, show significantly different dynamics for the electron of different initial orbitals (1s, 2s, 2px and 2py) of the incoming hydrogen atom. This electron transfer dynamics is also detailed by calculating expansion coefficients of the projection of the evolving wavepacket onto the stationary eigenfunctions of the H and He+ species to investigate evolution of the electron density around each nucleus during the collision. The instantaneous and overall electron densities captured by the He2+ nucleus from the H atom are calculated and analyzed. It is also shown evidently and concluded that due to its quantum nature, electron crawls from one nucleus to the other in an electron transfer process during an atom–ion collision. © 2017, Iranian Chemical Society.
Journal of Materials Science: Materials in Electronics (09574522)28(12)pp. 8546-8553
Nickel cobaltite nano-composites have been prepared by a modified sol–gel process using nickel–cobalt acetates as precursors and citric acid-monoethylene glycol as stabilizers followed by calcination at 400 and 650 °C in air. X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM) and thermogravimetry (TG-DTG), and energy dispersive X-ray (EDX), Fourier transform infrared (FTIR) and UV–Vis diffuse reflectance (UV–Vis DRS) spectroscopies were used for structural, thermal, and opto-electronic characterization of the prepared nano-powders. XRD results showed that using acetate as precursor and calcination at 400 °C results in a pure nickel cobaltite phase (NiCo2O4), while at 650 °C, nickel cobaltite with NiO impurity is produced. The nano-structured nickel cobaltite photocatalyst was composed of nano-size crystalline phases with an average size of 25 nm. The optical band gap energy of the nano-structured nickel cobaltite photocatalyst was 2.00 (640) and 3.20 eV (387.5 nm) from the UV–Vis DRS absorption spectra. The photo-catalytic activity of the synthesized nickel cobaltite nano-composite photo-catalysts for degradation of Reactive Red RB azo textile dye was examined. The nano-structured nickel cobaltite photocatalyst exhibited high photocatalytic activity for the photo-degradation of Reactive Red RB which is related to the optical absorption in the visible (640 nm) and UV (387.5 nm) irradiation, electron–hole separation and high surface area of the nano size particles (average size of 25 nm). © 2017, Springer Science+Business Media New York.
Memarian, Hamid Reza,
Memarian, H.R.,
Sabzyan, H.,
Sanchooli, E. COMPUTATIONAL AND THEORETICAL CHEMISTRY (2210271X)1093pp. 9-19
Density functional theory at the B3LY13/6-31++G(d,p) level was applied to study structural, electronic and bonding characteristics of various 5-unsubstituted 4,6-diaryl-2-oxo-1,2,3,4-tetrahydropyrimidines (THPMs). To elucidate the steric and electronic effects of the substituents on the characteristic parameters obtained from the optimized structures, additional electron-donating and electron-withdrawing substituents were considered to be at different aryl positions, which are already located on the C-4 and C-6 positions of the heterocyclic ring. Results of this study show that the six-membered heterocyclic ring in half of these compounds adopts a pseudo-boat conformation with a pseudo-axial orientation of the C-4-aryl substituent; in other cases a twisted chair conformation is observed. The extent of deviation of the N-1 and C-4 atoms from the boat plane depends on the type and position of the additional substituent on both aryl rings. Dihedral angle scanning elucidates the intramolecular interaction regarding the steric and electronic effects of the additional substituent, and its location on the aryl groups at the C-4 and C-6 positions on the total energy content of the molecule. (C) 2016 Elsevier B.V. All rights reserved.
Journal of Chemical Physics (10897690)144(13)
Electron transfer (ET) process and its dependence on the system parameters are investigated by solving two-dimensional time-dependent Schrödinger equation numerically using split operator technique. Evolution of the electron wavepacket occurs from the one-electron species hydrogen atom to another bare nucleus of charge Z > 1. This evolution is quantified by partitioning the simulation box and defining regional densities belonging to the two nuclei of the system. It is found that the functional form of the time-variations of these regional densities and the extent of ET process depend strongly on the inter-nuclear distance and relative values of the nuclear charges, which define the potential energy surface governing the electron wavepacket evolution. Also, the initial electronic state of the single-electron atom has critical effect on this evolution and its consequent (partial) electron transfer depending on its spreading extent and orientation with respect to the inter-nuclear axis. © 2016 AIP Publishing LLC.
Zeitschrift fur Naturforschung - Section A Journal of Physical Sciences (09320784)71(4)pp. 315-320
Effects of the size of the unit cell on energy, atomic charges, and phonon frequencies of graphene at the Γ point of the Brillouin zone are studied in the absence and presence of an electric field using density functional theory (DFT) methods (LDA and DFT-PBE functionals with Goedecker-Teter-Hutter (GTH) and Troullier-Martins (TM) norm-conserving pseudopotentials). Two types of unit cells containing nC = 4-28 carbon atoms are considered. Results show that stability of graphene increases with increasing size of the unit cell. Energy, atomic charges, and phonon frequencies all converge above nC = 24 for all functional-pseudopotentials used. Except for the LDA-GTH calculations, application of an electric field of 0.4 and 0.9 V/nm strengths does not change the trends with the size of the unit cell but instead slightly decreases the binding energy of graphene. Results of this study show that the choice of unit cell size and type is critical for calculation of reliable characteristics of graphene.
Journal Of The Iranian Chemical Society (1735207X)13(8)pp. 1395-1404
X-ray crystal structure analysis and quantum chemical calculations based on the density functional theory (DFT) were used for structural and electronic characterizations of three 2,3-dihydroquinazolin-4(1H)-ones (DHQZs). The occurrence of the C2-stereocenter in the heterocyclic ring causes the formations of both R- and S-enantiomers. X-ray diffraction technique indicates that these compounds exist as a racemic mixture in the crystal structure, and the enantiomers are orientated to each other via hydrogen bonding between the potential hydrogen donor (N3–H) and acceptor species (C4 = O group) in each layer under the formation of an enantio-syndio packing. Additional intermolecular and intramolecular interactions affect the orientations of the molecules adopted in the crystal packing, especially the orientation of the ring substitution. Most computational data, including the bond lengths and angles, are well in agreement with the experimental data. Dihedral angle scanning elucidates the effect of the nature and the location of the additional substituent on the aryl group at C2-position on the total energy content of the molecule. © 2016, Iranian Chemical Society.
Polymer Science - Series A (0965545X)58(3)pp. 487-498
Barrier properties of pristine polyethylene (PE) and polyethylene/montmorillonite-clay (PE/MMT) nanocomposite films with different MMT layers configurations were studied using molecular dynamics simulation within NVT ensemble. The force field parameters were optimized for bond lengths, bond angles and torsion angles of the MMT structure. A special simulation box was designed to simulate the diffusion of oxygen, nitrogen and methane, through pristine PE and PE/MMT nanocomposite films. The diffusion coefficients of these gases and the tortuosity values were calculated and analyzed. Results showed that the configuration of clay nanoparticles has strong effect on the barrier properties of the nanocomposite films. The parallel configuration for layered silicates was predicted to have a low diffusion coefficient and a high tortuosity parameter for gas diffusive molecules. The simulation could also indicate that the diffusion coefficient of oxygen is higher than those of nitrogen and methane gases in the examined systems which can be attributed to the smaller kinetic diameter of oxygen. © 2016, Pleiades Publishing, Ltd.
Mahmoudzadeh, M.,
Fassihi, A.,
Dorkoosh, F.,
Heshmatnejad, R.,
Mahnam, K.,
Sabzyan, H.,
Sadeghi, A. Pharmaceutical Research (07248741)32(12)pp. 3899-3915
Purpose: Chitosan-based polymeric micelles (CBPMs) are considered as promising carriers for delivery of anticancer drugs, imaging agents and genes. To optimize the physicochemical, pharmaceutical and biological properties of CBPMs, the molecular mechanisms behind the self-assembly behavior of chitosan (CHI) amphiphilic derivatives are elucidated. Methods: This study has two stages. In the experimental stage, dexamethasone (DEX) as a hydrophobic group is grafted to CHI in three degrees of substitution in order to obtain CHI derivatives with different degrees of hydrophobicity. These new CHI amphiphilic derivatives (CHI-DEXs) form micelles in water where their critical aggregation concentration (CAC), size and zeta potential are measured. Through comparing the results of these measurements, the change of self-assembly behavior of CHI-DEXs in response to increasing their hydrophobicity is evaluated. Correlating this evaluation with the results of the 13 MD simulations conducted on CHI-DEXs in atomistic molecular dynamics (MD) simulation stage, reveals the molecular mechanisms behind the self-assembly behavior of CHI-DEXs. Results: Our evaluation of the experimental results reveals that increasing hydrophobicity of a CHI amphiphilic derivative would not necessarily cause it to form micelles with lower CAC value, smaller size and lower zeta potential. The MD simulations reveal that there exists a balance between intra- and inter-chain interactions which is responsible for the self-assembly behavior of CHI amphiphilic derivatives. Conclusion: An increase in DS of the hydrophobic group triggers a cascade of molecular events that shifts the balance between intra- and inter-chain interactions leading to changes in the CAC, size and zeta potential of the CBPMs. © 2015 Springer Science+Business Media New York.
Journal Of The Iranian Chemical Society (1735207X)12(4)pp. 581-586
Potential energy curves (PECs) of the lowest singlet and triplet states of the HCl2+ dication have been calculated using density functional theory with the B3LYP and HSE06 functionals and coupled cluster CCSD(T) method, all with 6-311G(3df,3pd) basis set. Analysis of the results of all three methods shows that the triplet state is a pure 3∑- state, while the singlet state is a mixture of the 1Δ and 1∑+ states. Spectroscopic constants and Franck-Condon factors corresponding to the transitions from the ground state neutral HCl to these dicationic states have been calculated and compared to the available experimental and computational data. While the calculated spectroscopic constants and equilibrium bond lengths of the PECs obtained by the HSE06 functional are in good agreement with the available data, the predicted vertical offset of the PECs differ significantly with those observed experimentally. Inclusion of a set of floating basis functions corresponding to the Li ghost atom does not improve the results within the available experimental resolution. Addition of centrifugal term to the potential energy decreases the well depth and well width at barrier and increases the barrier height. © 2014 Iranian Chemical Society.
Electrochimica Acta (00134686)180pp. 722-736
Oxinate-aluminum nanostructures constructed on gold-mercaptopropionic acid using 5-Amino-8-hydroxyquinoline complex of aluminum(III), Au-MPA-5A8HQ-Al(III), are prepared for the first time via in-situ and ex-situ approaches, and their physiochemical characteristics are studied by cyclic and differential pulse voltammetry, electrochemical impedance spectroscopy, attenuated total reflectance Fourier-transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The electrochemical signal background observed for the in-situ prepared nanostructures is large and superimposed by some faradaic effects, while, it is small, smooth, and featureless for the ex-situ prepared nanostructures. To find the source of these features, effects of several parameters (like solvent, preparation method, and linking spacer between the complex and Au surface) are studied. These features are attributed to the intercalation and physical adsorption of the free 5A8HQ molecules onto the Au-MPA-5A8HQ structure when prepared via in-situ method. Nanostructures with minimum backgrounds in their electrochemical responses could be obtained via in-situ assembling of 5A8HQ from DMF solvent onto the Au-MPA surface, and then, accumulation of Al(III) onto the 5A8HQ layer, and also via ex-situ formation of 5A8HQ:Al(III) complex in the ethanol phase first, and then, transferring the complex onto the Au-MPA surface. The equilibrium constants for the intercalation and adsorption processes are calculated for the first time based on the collected experimental surface quantities. © 2015 Elsevier Ltd. All rights reserved.
Journal of Molecular Liquids (18733166)211pp. 1060-1073
Adsorption of the nickel and copper ions from single and bi-component solutions by nanostructure γ-alumina is studied experimentally and described by thermodynamic and kinetic modeling. Effects of the contact time, temperature and pH on these adsorptions are investigated. Kinetics of adsorption is studied by fitting the time-dependent data into different mechanisms, among which the pseudo-second order mechanism has been found successful. To model adsorption equilibrium, Freundlich isotherm resulted in the best fitting. With a 200 ppm initial concentration, maximum adsorption capacity at 40 °C for the Ni2 + and Cu2 + ions is measured to be 49.7 mg g- 1 and 31.3 mg g- 1. The Langmuir-Freundlich model could describe the two-component adsorption successfully. © 2015 Published by Elsevier B.V.
Journal of Molecular Graphics and Modelling (10933263)57pp. 9-19
The deacylation step of acylated Candida Antarctica lipase B, which was acylated with methylcaprylate (MEC) and acetylcholine (ACh), has been studied by using density functional theory method. Free energies of the entire reaction were calculated for enzyme deacylation by water and hydrogen peroxide that represented hydrolysis and perhydrolysis reactions, respectively. The calculations displayed that a stepwise mechanism there was with the enzyme-product complex being a deep minimum on the free energy surfaces of both of two reactions. The tetrahedral intermediate formation was the rate-determining step of all reactions, which needed 8.1 to 10.5 kcal mol-1 for activation in different reactions. In the second stage of the reaction, fewer free energy barriers, between 4.7 and 5.9 kcal mol-1, were identified to enable the proton transfer from His224 to Ser105 and the breakdown of the tetrahedral intermediate. These calculated activation free energies approved theoretical possibility of both of two reactions for two substrates. Finally, an applied tool examined the interactions role in the stability and energy levels of different chemical species. © 2015 The Authors. Published by Elsevier Inc.
Yaghoobi nia, N.,
Farahani, P.,
Sabzyan, H.,
Zendehdel, M.,
Oftadeh, M. Physical Chemistry Chemical Physics (14639084)16(23)pp. 11481-11491
A combined experimental and computational investigation conducted to understand the nature of the interactions between cobalt II/III redox mediators ([Co(bpy)3]2+/3+) and their impact on the performance of the corresponding dye-sensitized solar cells (DSCs) is reported. The fully optimized equilibrium structures of cobalt(ii/iii)-tris-bipyridine complexes in the gas phase and acetonitrile solvent are obtained by the density functional B3LYP method using LanL2DZ and 6-31G(d,p) basis sets. The harmonic vibrational frequencies, infrared intensities and Raman scattering activities of the complexes are also calculated. The scaled computational vibrational wavenumbers show very good agreement with the experimental values. Calculations of the electronic properties of the complexes are also performed at the TD-B3LYP/6-31G(p,d)[LanL2DZ] level of theory. Detailed interpretations of the infrared and Raman spectra of the complexes in different phases are reported. Detailed atomic orbital coefficients of the frontier molecular orbitals and their major contributions to electronic excitations of the complexes are also reported. These results are in good agreement with the experimental electrochemical values. Marcus diagram is derived for the electron transfer reaction Co(ii) + D35+ → Co(iii) + D35 using the Co-N bond length as a reaction coordinate. © 2014 the Partner Organisations.
Match (03406253)72(2)pp. 359-373
An asymmetry index (AI) is introduced to measure deviation of the electron density distribution in a molecule from any given symmetry. This AI is calculated by summing all point-wise differences between electron density distributions before and after symmetry operation. A minimum asymmetry index (MAI) rule is also introduced to evaluate uniquely the extent of asymmetry of a molecule with respect to any reference symmetry operation. This MAI rule prescribes where to locate the reference element of symmetry. The overall MAI for a given molecule with respect to a certain symmetry point group is calculated by averaging over AIs of all symmetry elements appearing in its character table. The proposed AI and the MAI rule are used to measure electron density asymmetry of the NX3, NX2Y/NXY2 and NXYZ (X, Y, Z = H, F, Cl, Br) series of molecules referenced to the C3V symmetry.
Nickmand, Z.,
Aghamiri, S.,
Reza talaie khozanie, M.,
Sabzyan, H. Separation Science and Technology (15205754)49(4)pp. 499-505
Grand canonical Monte Carlo (GCMC) simulation is used to model adsorption of CO 2 and SO 2 molecules by the pure and functionalized single walled carbon nanotubes (SWCNT and FSWCNT). Simulations are conducted for two cases: i) without and ii) with a 5.75 Å clearance between the CNT wall and the walls of the simulation box. Results show that the adsorption capacity for the SO 2 molecules is generally higher than that of the CO 2 molecules, especially at low pressures. Although for both molecules, the inside adsorption is higher at low pressures, the outside adsorption becomes larger above 10 and 2 bar for CO 2 and SO 2, respectively. At 5 bar, the total amounts of adsorption for case (ii) is higher by ∼ 42% and ∼ 271% for CO 2 and SO 2, respectively, compared with those for case (i). Functionalization does not show significant effect on the adsorption of the CO 2 and SO 2 gases. Adsorption of CO 2 and SO 2 gases in the FSWCNT are rather more sensitive to the parameters of the force field, especially those used for the functionalized carbon atoms, than the number of carbon atoms affected by functional groups. The effects of non-spherical interactions on the adsorption isotherms have also been examined. © 2014 Copyright Taylor and Francis Group, LLC.
Analytica Chimica Acta (00032670)825pp. 34-41
Gold electrode surface is modified via covalent attachment of a synthesized thiol functionalized with 8-hydroxyquinoline, p-((8-hydroxyquinoline)azo) benzenethiol (SHQ), for the first time. The behavior of the nanostructured electrode surface (Au-SHQ) is characterized by electrochemical techniques including cyclic and differential pulse voltammetry (CV and DPV), and electrochemical impedance spectroscopy (EIS). The modified surface is stable in a wide range of potentials and pHs. A surface pKa of 6.0±0.1 is obtained for Au-SHQ electrode using surface acid/base titration curves constructed by CV and EIS measurements as a function of pH. These results helped to determine the charge state of the surface as a function of pH. The gold modified electrode surface showed good affinity for sensing the Al(III) ion at pH 5.5. The sensing process is based on (i) accumulation and complex formation between Al(III) from the solution phase and 8HQ function on the Au electrode surface (recognition step) and (ii) monitoring the impedance of the Au-SHQ-Al(III) complex against redox reaction rate of parabenzoquinone (PBQ) (signal transduction step). The PBQ is found to be a more suitable probe for this purpose, after testing several others. Thus, the sensor was tested for quantitative determination of Al(III) from the solution phase. At the optimized conditions, a linear response, from 1.0×10-11 to 1.2×10-5M Al(III) in semi-logarithmic scale, with a detection limit of 8.32×10-12M and mean relative standard deviation of 3.2% for n=3 at 1.0×10-7M Al(III) is obtained. Possible interferences from coexisting cations and anions are also studied. The results show that many ions do not interfere significantly with the sensor response for Al(III). Validity of the method and applicability of the sensor are successfully tested by determination of Al(III) in human blood serum samples. © 2014 Elsevier B.V.
Structural Chemistry (15729001)25(4)pp. 1207-1216
Effects of the inclusion of a set of 6-311++Gfloating basis functions (FBFs) corresponding to the H, He, Li, Be, B, and C atoms, located at the center of molecular cage on the structural and bonding characteristics of the T d symmetric adamantane (A), tetrafluoroadamantane (TFA) and tetracyanoadamantane (TCA), and their anions are studied using B3LYP/(6-311++G+ FBF) method. Results show that neutral A, TFA, and TCA are stabilized most, by 3.22, 10.43, and 3.36 kJ/mol, when, respectively, Be, B, and B FBFs are used. Application of FBF results in much higher stabilizations for the negative ions of adamantanes. The highest stabilization energies for the negative ions A -, TFA -, and TCA - (36.49, 42.35, and 12.73 kJ/mol) are all obtained with the Li FBF. To detail effects of the FBF on the electronic structures of adamantanes, nuclei-independent chemical shift at the cage center is also calculated and analyzed. These results show explicitly that for accurate description of the molecular properties of cage compounds, such as adamantanes and diamondoids, the use of FBF is necessary. Application of the FBF affects also the vertical and adiabatic ionization potentials and electron affinities calculated for these cage species. © 2014 Springer Science+Business Media New York.
Keshavarz, E.,
Farrokhpour h., H.,
Sabzyan, H.,
Noorisafa, Z.,
Kivimäki a., ,
Richter r., Physical Review A - Atomic, Molecular, and Optical Physics (10502947)89(5)
Single-photon multiple ionization of the argon dimer van der Waals complex, Ar2, is studied by the photoelectron-photoion-photoion coincidence technique using synchrotron radiation in the photon-energy range of 255-340 eV, which covers the Ar 2p and Ar 2s ionization continua. Dissociation processes into Ar++Ar+, Ar++Ar2+, Ar++Ar3+, and Ar2++Ar2+ ion pair channels are observed. The Ar++Ar+ and Ar++Ar2+ channels show the most intense ion-ion coincidences, compared to other observed dissociative channels. For the four observed channels the intensities are integrated and compared as functions of photon energy. © 2014 American Physical Society.
Journal Of The Iranian Chemical Society (1735207X)11(6)pp. 1513-1532
The electronic and vibrational atomic responses to external electric field (EF) are computed to detail intramolecular energy transfer in a proposed molecular nanoelectronic field-effect system. The parallel and perpendicular electronic and vibrational contributions to intramolecular energy transfer are computed using, respectively, quantum theory of atoms-in-molecule and an energy partitioning scheme based on normal modes vibrational analysis. The symmetrical and asymmetrical intramolecular energy transfers are interpreted, respectively, as Peltier-like and Joule-like effects and quantified in terms of appropriate coefficients. Dependencies of these coefficients on EF are investigated. In addition, a semiclassical temperature model is introduced to describe symmetrical and asymmetrical temperature distributions which are attributed, respectively, to the Joule-like and Peltier-like heatings. This procedure can be used to map out intramolecular energy distribution in molecular nanoelectronic systems. © 2014 Iranian Chemical Society.
Structural Chemistry (15729001)25(1)pp. 85-94
Steric and the electronic effects caused by the substituents in the 1-, 4-, and 5-positions of substituted 2-oxo-1,2,3,4-tetrahydropyrimidines were investigated using density functional theory at the B3LYP/6-31++G(d,p) level. Results of this study show that the heterocyclic ring adopts a pseudo-boat conformation, in which the C4 and N1 atoms are deviated from ring planarity. The C4-substituent occupies a pseudo-axial position and the space orientation of the substituent depends on the type and position of the additional substituent in this aryl group. The heights of the C4 and N1 atoms from the boat plane and the orientation of 5-CO moiety toward the heterocyclic ring depend on the electronic and steric effects of the substituents in the various positions. Ring flip calculations for 4-phenyl substituent explain the extreme steric effect caused by the substituent in the 1-position. These calculations indicate the more favored pseudo-axial orientation of the phenyl group over the equatorial orientation. © 2013 Springer Science+Business Media New York.
Journal Of The Iranian Chemical Society (1735207X)11(3)pp. 871-945
Diatomic dications and dianions are attractive species for quantum chemists and spectroscopists. In comparison with neutral diatomics, these species show a wealth of potential behaviors arising mainly from the presence of residual Coulomb repulsion at the separated ions limit. Due to the stability of dications, numerous reports have been published on their potential curves, vibrational states, stability, and spectroscopic properties. In contrast, there are only a few reports on the stability and potential curves of dianions, since the strong correlation effects in dianions introduce some difficulties in the calculations of their potentials and properties, and perhaps, because they have not been observed in the laboratory due to their short lifetimes. In this review article, interesting subjects related to dications and dianions, the methods used to study their characteristics, and the achievements of these studies are described. Furthermore, the present research topics open on dications and dianions are reviewed. This report would thus serve researchers interested in the examination of quantum dynamical treatment on reactive scattering of ions and the laser-matter interactions and their subsequent phenomena such as vibrational wavepacket evolution, tunneling dissociation, vibronic coupling, and tunneling ionization for which dianions and dications can be regarded as prototypical species. © 2013 Iranian Chemical Society.
Ahmadi h., H.,
Maghari a., ,
Sabzyan, H.,
Niknam a.r., ,
Vafaee, M. Physical Review A - Atomic, Molecular, and Optical Physics (10502947)90(4)
High-order-harmonic generation is investigated for H2+ and D2+ with and without a Born-Oppenheimer approximation by a numerical solution of a full dimensional electronic time-dependent Schrödinger equation under four-cycle intense laser pulses of 800 nm wavelength and I=4, 5, 7, and 10×1014 W/cm2 intensities. For most harmonic orders, the intensity obtained for D2+ is higher than that for H2+, and the yield difference increases as the harmonic order increases. Only at some low harmonic orders, H2+ generates more intense harmonics compared to D2+. The results show that nuclear motion, ionization probability, and system dimensionality must be simultaneously taken into account to properly explain the isotopic effects on high-order-harmonic generation and to justify experimental observations. © 2014 American Physical Society.
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy (13861425)117pp. 95-101
The QCISD(T)/aug-cc-pVQZ and CIS/aug-cc-pVQZ calculations have been carried out to obtain potential energy curves (PECs) of the Cl22- diatomic dianion in order to address possibility of its formation in the merged beam fragmentation of Cl2- questioned based on the observation of the Cl-+Cl+e - channel. Results show that two of the excited states, namely A 1Σg and a3Σg are metastable with PECs having wells deep enough to suite several bound states, with minima located at Re = 2.8280 Å and Re = 2.5972 Å, and Coulomb barriers of 1648.288 and 1403.835 cm-1 heights located at 4.0320 and 3.6130 Å, respectively. Transition probabilities and tunneling predissociation lifetimes corresponding to these metastable states are also calculated and analyzed. Ground state X1Σg and excited states B1Σu, C1 Πg and D1Πu calculated for this dianion are all repulsive. Calculated Franck-Condon factors suggest that Cl22- can be produced in its excited states via an electron impact process initiating from the ground states of Cl2 and Cl2-. © 2013 Elsevier B.V. All rights reserved.
Journal of Physics B: Atomic, Molecular and Optical Physics (09534075)47(10)
Dynamics of the two-dimensional H+2 under 30- and 40-cycle xuv (45 and 90 nm) laser pulses is investigated by numerical solution of the time-dependent Schrödinger equation beyond the dipole and Born-Oppenheimer approximations for two orientations (θ = 0° and θ = 90° referenced to the molecular axis) of the laser polarization. Dynamics of the electron and nuclei are treated in quantum and classical approaches, respectively. The ground, first and second excited states of H +2 are considered as initial states for different laser field intensities in the range of (4×1016 - 4×10 19 W cm-2). For parallel orientation (θ = 0°), a negligibly small difference is seen for high-order harmonic generation (HOHG) spectra obtained with the dipole and non-dipole Hamiltonians for all three electronic states. While, for the perpendicular orientation (θ = 90°), non-dipole forces attenuate the HOHG spectra for the initial ground and the second excited states. For the initial first excited state and orientation θ = 90°, the motion of nuclei considerably increases the HOHG yield within the dipole approximation, but decreases it partially beyond dipole approximation. It is shown that contribution of the motion of nuclei to the HOHG yield depends on the extent of the increase in the separation between nuclei. © 2014 IOP Publishing Ltd Printed in the UK.
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy (13861425)132pp. 672-677
Electronic stabilities, structures, properties, and spectroscopic constants of the halogen oxide dianions OBr2- and OCl2- and their singly charged anions which are of astrophysical and laboratory interests have been studied. The X2Σ states of OBr2- and OCl 2- are metastable with PECs having smooth wells with minima located at R = 1.859 Å and 1.776 Å, and Coulomb barriers of 40402.54987 cm-1 and 43746.63462 cm-1 heights located at R RCB = 2.100 Å and 1.922 Å, respectively, both without any vibrational states. While, the B2Σ state of OBr2- and the A2Σ state of OCl2- are metastable with PECs having wells deep enough to suite several bound states, with minima located at Re = 1.773 Å and 1.6430 Å, and Coulomb barriers of 191437.45813 cm-1 and 180550.70294 cm-1 heights located at RRCB = 2.658 Å and 2.4480 Å, with De = 1.26470 eV and 1.60837 eV, respectively. The OBr- and OCl- singly charged anions are stable in their ground states. Based on the calculated Frank-Condon factors, it is concluded that metastable excited state OBr2- and OCl2- dianions and ground state OBr- and OCl- singly charged anions can be formed via electron capture processes. © 2014 Elsevier B.V. All rights reserved.
Sadeghi googheri, M.S.,
Housaindokht, M.R.,
Sabzyan, H. Journal of Molecular Graphics and Modelling (10933263)54pp. 131-140
Candida Antarctica lipase B (CALB), a specific enzyme to catalyze the hydrolysis of esters, can be a good candidate for acetylcholine (ACh) hydrolysis instead of acetylcholinesterase. The catalytic mechanism of the CALB acylation, as the first stage in the hydrolysis reaction, with ACh and methylcaprylate (MEC) has been examined by using density functional theory technique. The significant emphasis of this article is on the free energy barriers for the acylation step of hydrolysis reactions. Computed free energy barriers of the first step are 9.2 and 15.9 kcal mol-1, but for the second step are 7.9 and 11.6 kcal mol-1 for MEC and ACh respectively. Activation free energies are in the comparable and acceptable range and imply both of two reactions are theoretically possible. The stability role of the adjacent amino acids was examined by using two applied tools. It is exposed that the oxyanion hole residues decrease energy barriers by stabilizing the transition state structures. © 2014 Elsevier Inc. All rights reserved.
Journal Of The Iranian Chemical Society (1735207X)11(5)pp. 1265-1274
Some selected 5-acetyl-2-methoxydihydropyrimidines (DHPMs) are synthesized and the electronic effect of the substituent on the 4-position of the heterocyclic ring on the ratio of the possible tautomeric forms is investigated using dynamic NMR experiments. The results of this study indicate that these compounds coexist in two tautomeric 1,4- and 3,4-forms in the solution and their tautomeric ratios depend on the electronic nature of the additional substituent on the 4-phenyl substituent, the nature of solvent used for NMR study and also on the temperature. B3LYP/6-31 ++G**computational studies in the gas and solution phases elucidate the effect of the additional substituent on the phenyl ring on the structural, electronic and bonding characteristics of the tautomeric forms in these compounds. Furthermore, solvation of these DHPMs determines the relative stabilities of the two tautomers in the solution phase, which cannot be probed by model solvents adopted in SCRF calculations. © 2014 Iranian Chemical Society.
Zanjanchi, F.,
Hadipour, N.L.,
Sabzyan, H.,
Beheshtian, J. Journal Of The Iranian Chemical Society (1735207X)11(1)pp. 111-121
Electronic absorption spectra and the frontier orbitals of 1-arylazo-2-naphtol dyes are computed and analyzed in four models, namely in the gas phase (model I), in a solvent (model I + CPCM), adsorbed on the cellulose surface (model II), and model II in the presence of solvent (model II + CPCM) via time-dependent density functional theory (TD-DFT) and conductor-like polarizable continuum model (CPCM) at the B3LYP/6-31G**level of theory. A bathochromic shift is observed for the λmax peak due to both short-range and long-range interactions of the non-ionic dyes with cellulose, while the ionic dyes exhibit hypsochromic shift in their λmax peak. The results predict that the studied dyes should be nearly yellow after being adsorbed on cellulose with excellent color strength. Furthermore, the ionic dyes are suitable for the dyeing of cellulose fibers. The nuclear magnetic resonance (NMR) chemical shieldings calculated for the azo dyes in the gas phase and adsorbed states and for their tautomeric equilibrium mixtures show that the NMR technique can be used successfully to follow the dyeing process. © 2013 Iranian Chemical Society.
Physical Chemistry Research (23452625)2(1)pp. 41-52
In the first part of this work, correlation between optical activity and elements of magnetic susceptibility tensor (MST) for five classes of model small molecules containing a single chiral center has been studied using quantum computational techniques at DFT-B3LYP level of theory with 6-311G basis set. Several molecular properties are used to reduce the MST elements prior to the examination of the correlation. This study showed a close correlation between optical activity and the off-diagonal MST elements reduced by the electronic spatial extent . In the second part of this work, effects of the type of substitutions and their distances from the chiral center on the optical activity of these molecules have been investigated. Results of this work show that optical activity is reduced effectively upon distancing the substitution groups from the chiral center. Furthermore, the set of substitutions with higher electron densities and larger differences in their electronic structures result in higher optical activity.
Journal of Molecular Liquids (18733166)182pp. 48-56
The (CO) elimination reaction of cyclopropylmethoxy (fluoro/chloro) carbenes (C-X, X=H, F, Cl) and its consequent rearrangement products are studied computationally using B3LYP/6-311++G** method. Results of this study show that the reaction proceeds via a first TS corresponding to the cyclopropylmethoxy (chloro/fluoro) carbenes (C-X, X=H, F, Cl). The negative mode of this TS species corresponds to the elimination of the CO molecule, consistent with the experimentally proposed mechanism. Effects of the X substitution on the electronic and energetic properties of this conversion which is an intermediate step of the conversion of 3-cyclopropylmethoxy-3-(fluoro/ chloro) diazirines (D-X, X=H, F, Cl) to different products are also investigated. Calculations are also carried out for reactants and products of this reaction at the same level of theory. Nuclear quadrupole coupling constants and asymmetry parameter of the 35Cl and 14N nuclei have also been calculated and analyzed for reactants, TSs and products, as probes of the reaction coordinate. © 2013 Elsevier B.V.
Nickmand, Z.,
Do d.d., ,
Nicholson d., ,
Aghamiri, S.,
Khozanie, M.R.T.,
Sabzyan, H. Adsorption (15728757)19(6)pp. 1245-1252
We have used Grand Canonical Monte Carlo simulation to study argon adsorption at 87 K in wedge shaped mesopores. The structural parameters, including mean pore size, wall length and wedge angle, were varied to investigate their effects on the size, shape and the position of the hysteresis loop. Although the effects of pore size have been studied previously, the wall length and wedge angle have received little attention. We find that the wedge angle can have a significant effect on the existence, position, size and shape of the hysteresis loop, while the wall length affects the adsorptive capacity associated with the loop and the behaviour of the isotherm beyond the loop. The results of this work have far-reaching consequences for the characterization of pore size distribution where it is commonly assumed, when constructing a kernel of local isotherms, that pore size is uniform, since even a small deviation from a constant pore width can shift the condensation and evaporation pressures significantly and thus lead to an incorrect estimation of pore size. © 2013 Springer Science+Business Media New York.
Journal of Physics B: Atomic, Molecular and Optical Physics (13616455)46(24)
Effects of the laser pulse wavelength and intensity on the high harmonic generation (HHG) production from the ionic and homolytic pre-ionization transient states of the two-electron H2 system exposed to ultrashort intense laser pulses are studied by solving the time-dependent Schrödinger equation. It is found that for the populated homolytic species in each half cycle of the laser pulse having enough strength, a pair of strong and weak HHG radiations are produced simultaneously. For the populated ionic species divided into two regions, in each half cycle, one of the ionic regions has a strong radiation and the other ionic region has a weak HHG radiation. The HHG spectra of the homolytic and ionic species are almost the same, except that in some limited parts of the HHG spectrum, one of them dominates the other. © 2013 IOP Publishing Ltd.
Memarian, H.R.,
Ranjbar, M.,
Sabzyan, H.,
Habibi, M.H.,
Suzuki, T. Journal of Molecular Structure (00222860)1048pp. 196-201
X-ray crystal structure analysis and quantum chemical calculations based on density functional theory (DFT) were used for structural and electronic characterizations of two 1,2,3,4-tetrahydropyrimidine derivatives (THPMs), namely, ethyl 6-methyl-4-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5- carboxylate (1) and methyl 4-(4-bromophenyl)-1,6-dimethyl-2-oxo-1,2,3,4- tetrahydropyrimidine-5-carboxylate (2). The results of these studies revealed that the heterocyclic ring adopts a quasi-boat conformation, in which the 4-aryl group occupies the pseudo-axial position. The occurrence of the C 4-stereocenter in the heterocyclic ring causes the formation of both R- and S-enantiomers. X-ray diffraction technique indicates that both compounds exist as a racemic mixture in the crystal structure and the enantiomers are orientated to each other via hydrogen bonding between N3-H as donor and the C2=S or C2=O groups as acceptor species, in each layer under formation of an enantio-syndio packing. Most computational bond lengths and angles are well in agreement with experimental data, and support the pseudo-axial orientation of the C4-aryl substitution. © 2013 Elsevier B.V. All rights reserved.
Saghaei, L.,
Sakhi, H.,
Sabzyan, H.,
Shahlaei, M.,
Shamshirian, D. Medicinal Chemistry Research (10542523)22(4)pp. 1679-1688
The quantitative relationship between molecular properties and pharmaceutical activities of 19 antimalarial 3-hydroxypyridinones is studied using B3LYP/6-311++G**structural, electronic, and thermochemical characteristics. In this QSAR study, stepwise-multilinear regression (MLR) and principle component regression (PCR) are utilized based on volume, HOMO, nCrH2, and nHDon descriptors selected from a number of descriptor sets calculated and examined. The MLR coefficients are evaluated by cross-validation and external test sets methods. Regression coefficients of R 2 = 0.882 and R 2 = 0.874 are obtained, respectively, for the MLR and PCR predicted pIC50 values as referenced to their experimental values. Results of PCR predict the same trend for the predicted IC50 approving validity of the MLR results. Based on the present MLR and PCR analyses, pIC50 value is calculated for six candidate antimalarial drugs designed in this work, two of which are found to have promising antimalarial activity as high as that of the two best already synthesized and examined drugs. © 2012 Springer Science+Business Media, LLC.
Surface Science (00396028)616pp. 100-103
In this paper layer-by-layer (LBL) assembly of calf thymus DNA (ct-DNA) onto gold-mercaptopropionic acid self-assembled monolayer via Zr(IV) ion glue, Au-MPA-Zr(IV)-ct-DNA SAM, is monitored by scanning tunneling microscopy (STM) technique. The STM images of Au-MPA-Zr(IV) template show well-organized arrays of rod-like peaks. ct-DNA has been immobilized on the Au-MPA-Zr(IV) surface in hilly forms, implying globular structure for the immobilized ct-DNA. This immobilization strategy offers a simple and fast method to prepare the Au-MPA-Zr(IV)-ct-DNA template with promising applications for immobilization and study of the other compounds. © 2013 Elsevier B.V.
Zanjanchi, F.,
Hadipour, N.L.,
Sabzyan, H.,
Beheshtian, J. Journal Of The Iranian Chemical Society (1735207X)10(5)pp. 985-999
Structural, bonding and electronic characteristics of complexes of anthraquinone and 1-arylazo-2-naphtol dyes and cellulose I β are studied using B3LYP density functional method with 6-31G**basis set based on the partially and fully optimized structures. Results reveal that for both partially and fully optimized complexes, there is a stabilizing attraction between dyes and cellulose surface. The hydrazone (Hy) tautomer in anionic state (Hy-SO3 -) shows the strongest interaction with the cellulose surface. Natural bond orbital (NBO) and atoms-in-molecules (AIM) analyses have been carried out to study the nature of azo dyes-cellulose bonds in detail. According to NBO analysis, a remarkable charge transfer occurs between the -SO3 - and -SO3H functional groups of the dye and the cellulose surface which can be regarded as the main source of the large dye-cellulose interaction energy. AIM analysis confirms the existence of hydrogen and van der Waals bonds between the azo dyes and cellulose. Furthermore, a very good agreement is observed between the number of hydrogen bonding sites and dye-cellulose interaction energies. © 2013 Iranian Chemical Society.
Structural Chemistry (15729001)23(6)pp. 1971-1979
Structure and bonding characteristics, and gas phase stepwise basicities of proposed multivalent bases 1,3, 5,7-tetraazatricyclo[3.3.1.1(3,7)]decane, 1,3,5,7,9,10-hexaazatricyclo[ 3.3.1.1(3,7)]decane and tricyclo[3.3.1.1(3,7)] azadecane, named and abbreviated here respectively as tetra-aza-adamantane (TAA), hexa-aza-adamantane (HAA) and deca-aza-adamantane (DAA), have been studied using B3LYP/6-311++G** method. Effects of protonation on the bond lengths and angles, and atomic charges, and on their correlations are studied in detail. Results show that the most affected characteristics by protonation are the N- H bond lengths and the charge of the hydrogen atoms. It is found, interestingly, that in the protonation of DAA, electric charges of the unprotonated nitrogen atoms are increased more than that of the protonated nitrogen atoms. Because of very small effects of protonation on the skeletal C-N and N-N bond lengths, it can be said that the azaadamantane cage volume is not changed significantly upon protonation. The protonation energies approve multivalent nature of these bases with the order of TAA ≈ HAA> DAA. Different isomers for the unprotonated and protonated HAA and DAA are also studied. © Springer Science+Business Media, LLC 2012.
Europhysics Letters (02955075)99(6)
The response of a model molecular electronic device to external electric field is characterized in terms of an index named intramolecular thermoelectric-like coefficient (IMTLC). The electronic IMTLC is introduced and computed based on the density and energy transfers between different pairs of sections of the molecule using quantum theory of atoms-in-molecules. The contribution from nuclear motion to the energy transfer, quantified as vibrational IMTLC, is evaluated using an atomic partitioning scheme based on normal modes vibrational analysis. The dependencies of the electronic and vibrational IMTLCs on the electric-field intensity are studied. Symmetrical and asymmetrical contributions components of the IMTLCs, describing, respectively, the intramolecular Joule-like and Peltier-like effects, are also introduced. A simple semiclassical intramolecular temperature modeling is also introduced to describe intramolecular energy monitoring. © Copyright EPLA, 2012.
Journal Of The Iranian Chemical Society (1735207X)9(5)pp. 805-813
The light sensitivity of various 2-oxo-1,2,3,4- tetrahydropyrimidine-5- carboxamides (THPMs) was investigated by exposing them to UV light in order to elucidate the effects of the nature of the substituents located on the 4- and 5-positions of the heterocyclic ring and also the effect of an oxygen or argon atmosphere on the rate of reaction. The rate of reaction is faster under argon than under oxygen and is influenced by the nature of the substituent on the 4- and 5-positions of the THPM ring. Furthermore, it is found that the dehydrogenation of THPM-amides is faster than that of the corresponding 5-ethoxycarbonyl- and 5-acetyl-THPMs. In contrast to the solution photochemistry, no changes have been observed by irradiation in the solid state. A mechanism concerning an electron transfer from excited THPM to acetonitrile has been proposed for this reaction. © Iranian Chemical Society 2012.
Physical Review A - Atomic, Molecular, and Optical Physics (10502947)85(3)
The mechanism of the formation of doorway quasistates (transient species) prior to the start of ionization of the two-electron molecular H 2 system subjected to an eight-cycle ultrashort intense laser pulse is investigated by solving exactly the one-dimensional (1D) electronic time-dependent Schrödinger equation, including nuclear motion semiclassically. Space of the electron density of the two-electron 1D H 2 system around the nuclei is partitioned into four physicochemically significant partitions, including homolytic (e 1Hα+- Hβ+e 2)∼(e 2Hα+-Hβ+e 1) and ionic (Hα+-Hβ-)∼(Hα - Hβ+) transient species. The underlying mechanisms responsible for the formation and evolution of the homolytic and ionic transient species are explored based on probing variation of the two-electron norms of these states and their corresponding time-dependent high-order harmonic generation spectra. © 2012 American Physical Society.
Comptes Rendus Chimie (18781543)15(11-12)pp. 1001-1011
The electrochemical oxidation of various substituted 2-oxo-1,2,3,4- tetrahydropyrimidines (THPMs) in acetonitrile has been studied using voltammetric methods at a glassy carbon electrode to investigate the steric and electronic effects of the substituents on the 1-, 4- and 5-positions of the heterocyclic ring. Analysis of the results presented in this study shows that the electronic nature and steric hindrance of the substituents, their positions and their orientations towards the heterocyclic ring, determine their effects on the oxidation peak potential. The electron detachment process in this study is also affected by the nature of solvent, which explains the extent of solvation of both neutral THPM and THPM ̇+. Analysis of the computational results obtained at the DFT-B3LYP/6-31++G** level of theory suggests a mechanism in which the first electron removal occurs from the N1 atom. This process is followed by a fast proton removal, resulting in the formation of stable allylic and/or benzylic radicals which then undergo further oxidation to the 2-oxo-1,2-dihydropyrimidines (DHPMs). © 2012 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.
Memarian, H.R.,
Sabzyan, H.,
Soleymani m., M.,
Habibi, M.H.,
Suzuki, T. Journal of Molecular Structure (00222860)998(1-3)pp. 91-98
Density functional theory (DFT) at B3LYP/6-31++G** level has been applied to study structural, electronic and bonding characteristics of some 2-oxo-1,2,3,4-tetrahydropyrimidin-5-carboxamides (THPMs) and their oxidized forms 2-oxo-1,2-dihydropyrimidin-5-carboxamides (DHPMs). Results of this study show that for these THPMs, the six-member ring adopts a boat conformation with a pseudo-axial orientation of the C4- substituent. Experimental and theoretical 1H NMR data obtained for THPMs and their corresponding oxidized forms (DHPMs) are correlated. Thermochemical analysis on THPMs and their corresponding oxidation products show that the oxidation reaction of THPMs to DHPMs is endothermic. © 2011 Elsevier B.V. All rights reserved.
Journal of Electroanalytical Chemistry (15726657)660(1)pp. 37-44
Attachment of natural double strand calf thymus DNA onto gold-mercaptopropionic acid self-assembled monolayer electrode via Zr(IV) ion glue, Au-MPA-Zr(IV)-ds-ct-DNA SAM, is studied. The sequential assembly of the layers on the Au surface is traced by electrochemical methods including cyclic and square wave voltammetries in the presence of methylene blue. The results show that DNA is attached to Zr(IV) via its phosphate groups without any contribution from its bases. Effects of the MB concentration on the behavior of adsorbed MB, ionic strength on the MB adsorption, and pH on the amount of immobilized DNA are studied. The proposed method for the preparation of the new template, the Au-MPA-Zr(IV)-ds-ct-DNA, is relatively simple and fast. Long-term stability of this electrode is tested by keeping the template at pH 3, and carrying out a daily electrochemical study at pH 7.4. Under these circumstances, the Au-MPA-Zr(IV)-ds-ct-DNA electrode showed stable behavior for one week. © 2011 Elsevier B.V. All rights reserved.
Hajipour, M.,
Aghamiri, S.,
Sabzyan, H.,
Seyedeyn-azad, F. Fluid Phase Equilibria (03783812)301(1)pp. 73-79
Configurational-biased Gibbs ensemble Monte Carlo simulations were performed to obtain the phase behavior of the homologous series of primary alcohols from ethanol to 1-heptanol. Molecular interactions in these systems are modeled by a newly developed exp-6 potential in combination with a Coulombic intermolecular potential. Some of exp-6 potential parameters required to describe these alcohols were taken from the previous literature data reported for methanol and n-alkanes. The oxygen's potential parameters were optimized to fit the coexistence curve of these alcohols to the experimental data. Simulated values of saturated liquid and vapor densities, vapor pressures and critical constants of the alcohols are in good agreement with experimental data. The efficiency of the new model in the prediction of binary phase diagram of water/ethanol and n-hexane/1-propanol mixtures is also evaluated. The calculated mole fractions in the vapor and liquid phases of these binary mixtures also show satisfactory agreement with the experimental data. © 2010 Elsevier B.V.
Journal of Physical Chemistry C (19327447)115(16)pp. 8042-8055
Nanostructure assemblies based on ferrioxamation of gold-mercaptopropionic acid, Au-MPA-DFO-Fe(III), are prepared via in-situ and ex-situ approaches for the first time and described by cyclic voltammetry (CV), square wave voltammetry (SWV), electrochemical impedance spectroscopy (EIS) and scanning tunneling microscopy (STM) techniques. The assemblies formed via the two approaches show different structures, topologies, and electrochemical kinetics. The STM images show that the Au-MPA-DFO layer is formed in rodlike arrays with 3-4 nm peak-to-peak distances, while the arrays of the Au-MPA-DFO-Fe(III) layers formed by the in-situ and ex-situ methods, respectively with sharp and round ridges, have similar peak-to-peak distances of 2-3 nm. The CVs reveal that the Fe(III) ion immobilized by the ex-situ method is more stable by 14.48 kJ/mol. The relative amounts of the adsorbed Fe(III) ions via the in-situ and ex-situ methods, ex-situ/in-situ, obtained by CV and EIS are 1.33 ± 0.13 and 1.37 ± 0.19, respectively. Faradaic and impedimetric surface titrations both predict a surface-pKa of ∼9.4 for the Au-MPA-DFO self-assembled monolayer (SAM). © 2011 American Chemical Society.
Zanjanchi, F.,
Hadipour, N.L.,
Sabzyan, H.,
Beheshtian, J. Dyes and Pigments (01437208)89(1)pp. 16-22
Reactivity of gaseous 1-arylazo-2-naphthol dyes and their complexes with cellulose, after adsorption on cellulose, towards singlet molecular oxygen, 1O2, are investigated based on frontier molecular orbital theory. Results reveal that electrophilic reactions may occur predominately for the studied species, with the oxidizing agent 1O2 as electrophile. The -SO3- functionalized 1-arylazo-2-naphtol tautomers (soft nucleophiles) and their complexes with the cellulose are shown to be less reactive towards 1O2 and under thermodynamic control; while the -SO3H functionalized 1-arylazo-2-naphtol tautomers (hard nucleuphiles) and their cellulose complexes are fairly reactive and under kinetic control. According to the frontier molecular orbital theory, the sites more vulnerable for 1O2 attack (the atomic positions and double bounds) are similar for both azo dyes and their complexes with cellulose. Thermodynamic study reveals that the photo-oxidation reactions are exothermic and spontaneous, except for cycloaddition of hydrazone tautomers. TD-DFT calculations confirm the decolorization and color fading phenomenon during the photo-decomposition reaction. © 2010 Elsevier Ltd. All rights reserved.
Journal of Physical Organic Chemistry (10991395)24(5)pp. 414-422
3-Hydroxy-5-(pyrimidin-2-yl)-2H-pyrrol-2-one (HYPO, T1) and 2-hydroxy-5-(pyrimidine-2-yl)-3H-pyrrole-3-one (HYPO, T2) have designed in this research to study potential energy curves for their dynamic motions and possibility of crossing between levels. Study of tautomerism shows that T1 tautomer is more stable than T2 (about 5.83 kJ/mol). Dynamic study of possible motions show rate constants (highest possible) equal to 8.82 M/s for tautomerism, 1.70 × 109 M/s for relative rotation of ring (rr) and 3.67 × 106 M/s for rotation of OH bond (br). Moreover, variations of orbital populations, NBO charges, hybridations, and acceptor-donor interactions in IRC steps have been investigated to study the possibility of non-adiabatic crossing between tautomerism and ring rotation potential energy curves. The data showed that in spite of the fact that these two potentials share three common points, these two potential curves cannot have non-adiabatic crossing because of different symmetries and a large difference between their barrier energies. Copyright © 2010 John Wiley & Sons, Ltd.
Memarian, H.R.,
Soleymani m., M.,
Sabzyan, H.,
Bagherzadeh, M.,
Ahmadi h., H. Journal of Physical Chemistry A (15205215)115(29)pp. 8264-8270
Electrochemical oxidation of a series of 20 substituted 2-oxo-1,2,3,4-tetrahydropyrimidin-5-carboxamides (THPMs) in acetonitrile has been studied using voltammetric methods at a glassy carbon electrode to investigate the influence of the substituents on the 4- and 5-positions of the heterocyclic ring. Analysis of the results shows that the electronic nature and steric hindrance of the substituents, especially their orientations toward the heterocyclic ring, determine their effects on the oxidation potential. Analysis of the computational results obtained at the DFT-B3LYP/6-31++G* level of theory suggests a mechanism in which the first electron removal occurs from either the N1 of the heterocyclic ring or N17 of the amide substitution. This process is followed by a fast proton removal resulting in the formation of stable allylic and/or benzylic radicals which then undergo further oxidation to the 2-oxo-1,2-dihydropyrimidin-5-carboxamides (DHPMs). © 2011 American Chemical Society.
Monatshefte fur Chemie (00269247)141(11)pp. 1203-1212
Density functional theory at B3LYP/6-31++G(d,p) level was applied to study structural, electronic, and bonding characteristics of some 3,4- dihydropyrimidin-2(1H)-ones substituted at C4 position (DHPMs) of pharmaceutical interest. Results of this study show that in these DHPMs the six-membered ring adopts a pseudo-boat conformation with a pseudo-axial orientation of the C4 substituent, and the heights of the C4 and N4 atoms from the boat plane depend on the type and position of the substituent on the aryl ring. Thermochemical analysis of these DHPMs and their corresponding oxidation products shows that the enthalpy of the oxidation reaction depends on the nature of the substituent at the C4 position, falling in a range of 25 kJ/mol for all compounds. © 2010 Springer-Verlag.
Memarian, H.R.,
Farhadi, A.,
Sabzyan, H.,
Soleymani m., M. Journal of Photochemistry and Photobiology A: Chemistry (18732666)209(2-3)pp. 95-103
A variety of Biginelli 5-acetyl-3,4-dihydropyrimidin-2(1H)-ones are efficiently oxidized to their corresponding pyrimidin-2(1H)-one derivatives upon UV irradiation under argon atmosphere in chloroform solution. The nature of the additional substituent on the phenyl ring located on C-4 of the heterocyclic ring influences the rate of reaction. An electron-transfer induced photoreaction is proposed based on the formation of HCl and CH2Cl2. © 2009 Elsevier B.V.
Ultrasonics Sonochemistry (13504177)17(3)pp. 579-586
In this study, various 5-acetyl-3,4-dihydropyrimidin-2(1H)-ones were synthesized and the dehydrogenation of these compounds by potassium peroxydisulfate in aqueous acetonitrile under thermal and sono-thermal conditions were investigated. Whereas the effect of the nature of 4-substituent influences the rate of reaction, the application of sonic waves decreases drastically the time of thermal reaction. © 2009 Elsevier B.V. All rights reserved.
Chemical Physics (03010104)362(3)pp. 120-129
A detailed study of the gas flow in carbon nanotubes (CNT) and carbon nanotube junctions (CNTJ) can open the way towards the study of the reaction mixture flow in prospective nano-reactors. In this work, flow of the pure and mixed CO/CO2 gases through some selected CNTs and three types of CNT1-J-CNT2 CNTJs, (12,12)-J-(3,8), (12,8)-J-(8,12) and (8,8)-J-(13,0), are studied using molecular dynamic simulations. Results of this study show that regardless of the diameter and helicity type of the CNT1 and CNT2, when the flow starts with the molecules in the CNT1, the number density of molecules in the CNT2 is higher than that in the CNT1. Projected radial distribution of the molecules are calculated and analyzed in terms of the molecule-molecule and molecule-wall interactions. The well-structured projected radial distribution results show that the CNT radius and helicity as well as the type of molecules determine the lateral distribution of the gas molecules along the flow. © 2009 Elsevier B.V. All rights reserved.
Journal Of The Iranian Chemical Society (1735207X)6(3)pp. 489-503
Magnetic interaction was included in the simulation of the evolution of the electron wave-packet of the hydrogen molecular ion H2+ in femtosecond intense pulsed laser fields applied along the molecular axis. This evolution was followed by solving 2-D time-dependent Schrödinger equation at some fixed inter-nuclear separations. Magnetic interaction effects at non-relativistic intensities induced a phase shift in the time evolution of the electron wave-packet, and an excess z-component angular momentum as compared with the results obtained in the absence of magnetic interaction. Furthermore, the H2+ electron WP displacement showed a drift and wiggling in the propagation direction which was different from that observed under pure electric field of the laser pulse. The local fluxes at different points of the 2-D space borders and the time-dependent induced angular momentum are calculated and analyzed.
Iranian Journal of Science and Technology, Transaction A: Science (10286276)33(1)pp. 87-102
Time-dependent Schrödinger equation for a 1-D model of hydrogen molecular ion H2+ in intense laser field linearly polarized along the molecular axis is solved. Ionization rates are calculated for different initial states. The evolution of electronic wavefunction at fixed inter-nuclear separations are simulated and analyzed. The results obtained for the ground state of this 1-D model of H2+ show appreciable qualitative agreement with the results obtained previously in the 2-D and 3-D studies. The Ponderomotive energy effect on the beginning of ionization in different initial states is observed. The above threshold ionization has a large contribution in the ionization of electrons, except for the ground state and at equilibrium inter-nuclear separation. The ionization rates show that at some inter-nuclear separations larger than 4.0 au, resonance enhancement ionization by some higher excited states occur. At inter-nuclear separations shorter than 4.0 au, the ground state does not show any resonance with higher excited states. © Shiraz University.
Zeitschrift fur Naturforschung - Section B Journal of Chemical Sciences (09320776)64(5)pp. 532-540
A new facile cost-effective method for the oxidation of acetyl and carboethoxy derivatives of 3,4dihydropyrimidin-2(1H)-ones (DHPMs) by using potassium peroxydisulfate in water as solvent under microwave irradiation has been developed. Whereas the presence of the acetyl group instead of the carboethoxy group in position 5 decreases the rate of oxidation, the nature of the additional subtituent (electron-donating or electron-withdrawing group) and its location on the phenyl ring (ortho-, meta- or para-position) attached to C-4 of the dihydropyrimidinone ring influence the rate of reaction. Increase in the rate of the reaction compared with that of the reaction under reflux condition is the advantage of the use of microwave irradiation for this oxidation method.
Journal of Electroanalytical Chemistry (15726657)633(1)pp. 259-263
A new method is established for the electrochemical detection of zirconium ion (Zr(IV)) based on electrochemical impedance spectroscopy transduction method, and hydroxamated gold surface recognition system. The method successfully served for the detection of Zr(IV) with a wide dynamic range of 1.0 × 10-9 to 5.0 × 10-5 mol L-1, and a detection limit in nmol L-1 scale. Construction of the calibration curve by "one-impedance for one-concentration" method developed here helped us to save the experimental time by saving the data acquisition time by a factor of ∼20, and further, eliminating data approximation and parameter extraction times. © 2009 Elsevier B.V. All rights reserved.
Iranian Journal of Medical Hypotheses and Ideas (17359104)3(1)
Nanoscience and Nanotechnology has enabled us to produce new atomic, molecular and cluster structures with desired properties in systematic and controlled approaches. Nanoelectronics (or Molecular Electronics) circuits which is based on molecular and quantum mechanical concepts and phenomena, can be used to design an intelligent system for the detection and prognosis of the initial electrical signals of the nervous and epileptic seizures. The design of the required power source based on the electrical currents of the nervous system and the location of the installation site are the most important features of the design and application of such an intelligent system. In the design of the molecular components needed for the nanoelectronic circuits of this system, physcochemical theoretical and computational techniques can be used. For the optimal design and performance of this prognosis system, environmental effects such as local electric and magnetic fields, and biochemical environments, should be taken into account.In this article, the idea of the design of an intelligent nanoelectronic system for the detection, prognosis and possible control of epileptic attacks is presented. The phases of the design, application and performance analysis of this system include; 1) Detailed clinical analysis of the epileptic electrical signals prior, during and after the attack. 2) Feasibility study of the simulation of the nervous system and the perturbative effects of the epileptic seizure on it using in vivo nanoprobes. 3) Feasibility study of the usage of electric signals of the nerves of other organs having less complexity compared to brain for faster and more accurate prognosis. 4) Design of an in vivo nanoelectronic circuit for the detection and prognosis of the initial signals of epileptic seizures. 5) Feasibility study of the design and production of nanoelectrodes implantable in the skull for the reduction or extinction of the perturbative nervous signals in order to minimize the effects of epileptic seizure.
Ashrafi a.r., A.R.,
Hamadanian m., M.,
Tavangar, Z.,
Sabzyan, H. Digest Journal of Nanomaterials and Biostructures (18423582)4(2)pp. 319-322
A Euclidean graph associated with a molecule is defined by a weighted graph with adjacency matrix M = [dij], where for i≠j, dij is the Euclidean distance between the nuclei i and j. In this matrix dii can be taken as zero if all the nuclei are equivalent. Otherwise, one may introduce different weights for distinct nuclei. In this article, the automorphism group symmetry of a capped nanotube is computed.
Journal Of Molecular Modeling (16102940)14(11)pp. 1023-1033
An organic molecule, designed in this study, is proposed as a candidate molecular switch and characterized using the B3LYP/6-31G* computational method. Structural and electronic properties of this molecular switch (M) and its singly charged (M+ and M-) species in their lowest and the first higher spin states are calculated and analyzed. Molecular volume and electronic spatial extent (ESE) of this nanoswitch undergo negligibly small changes (<2%) upon charging. Furthermore, the small difference between the calculated dipole moments of the M+ and M- species shows that switching between negative and positive poles does not significantly affect the charge transfer performance of this molecular switch. Natural bond orbital (NBO) and spin density distributions are also calculated and analyzed. A preliminary study on the response of the proposed molecular switch to the external electric field approves its function as a multi-pole nanoswitch controlled by a bias voltage. © Springer-Verlag 2008.
Journal of the Chinese Chemical Society (00094536)55(5)pp. 962-970
Dissolution of some industrially relevant atomic and diatomic species (Ar, Ne, H, O, H2, N2 and O2) in the 5 x 5 2-D hexagonal and square helium lattices, as the model of the liquid helium cryogen, has been studied using ab initio MP2/6-31++G computations. Structural, electronic and thermochemical properties have been calculated and analyzed for these solution lattices. Results of these calculations show that dissolution of Ar, Ne, H and H2 species is more favored at higher temperatures. A reverse trend is observed for the dissolution of O, N2 and O 2 species. Astaggered orientation is preferred by all diatomic species in both lattices. Results of this study also show that breakage of the O2 molecule becomes slightly easier in the 2-D helium lattices as compared with that of the H2 molecule. Effect of the cavity geometry and size, and position of the solute in the lattice have also been studied. Analysis of the results shows that the range of the interaction between the solute and solvent atoms is only one helium layer.
Chemical Physics (03010104)352(1-3)pp. 297-305
Contributions of the vibrational motions to the NMR shielding constants are calculated and studied theoretically for the isolated H2, HF and H2O molecules in the gas phase. Intramolecular potential energy surfaces (PES) and their corresponding wave functions have been calculated using B3LYP/6-311++G** method. Shielding constant surfaces for the 1H, 17O and 19F nuclei in these molecules have been calculated over their PES's using CSGT method. Distribution of the shielding constants and their corresponding averages are calculated for each vibrational state. Combination effects of the populated vibrational levels (and different vibrational modes in the case of H2O molecule) to the NMR shielding constants are also evaluated. From the results obtained for H2O, it can be concluded that for polyatomic molecules different vibrational modes may have opposite effects on the nuclear shielding constants and thus may partially cancel vibrational contributions to shielding constants. The zero-point vibrational contributions to the NMR shielding constant of the nuclei of the HF and H2O molecules calculated via our approach are comparable with those reported by Ruud et al. [K. Ruud, P.-O. Åstrand, P.R. Taylor, J. Chem. Phys. 112 (2000) 2668, K. Ruud, P.-O. Åstrand, P.R. Taylor, J. Am. Chem. Soc. 123 (2001) 4826]. © 2008 Elsevier B.V. All rights reserved.
PHYSICAL REVIEW A (10502947)76(6)
In response to the preceding Comment, results of our research show that rate is not necessarily linearly time-dependent and it is possible to define and calculate instantaneous ionization rate. We show that a negative ionization rate and the quiver motion in strong laser field are not necessarily correlated and may occur independently. Furthermore, a negative ionization rate is not identical to recombination. Details of the instantaneous ionization rate and photoelectron kinetic energy release are calculated and analyzed for the evolution of the electron wave packet of H-2(+) in a 25-cycle ultrashort intense linearly polarized laser pulse of I=1.0 x 1014 W/cm(2) intensity and lambda=1064 nm wavelength with a sin(2)-shaped envelope.
Journal of Fluorine Chemistry (00221139)128(6)pp. 668-673
Structural and electronic properties of oligomers including dimer, trimer and tetramer of fluoromethylpyrroles (FMPs), NC4H4-CHnF3-n with n = 0, 1, 2, 3, and their radical cations have been studied using DFT-B3LYP method with 6-31G(d, p) basis set. FMPs are proposed in this research as candidate monomers for conducting polymers with modified characteristics compared to polypyrrole and polymethylpyrrole. A preliminary study using a set of ab initio computations (HF) with medium basis set was carried out on di-, tri- and tetramer in order to investigate the stability of configuration of polymer chains for FMPs. The B3LYP/6-31G** optimized geometry and stereochemistry show that the selectivity of branching of the propagating polymer chain is affected by the characteristics of the substitutions of monomer and, therefore, the growth pattern of the polymer chain can be predicted upon characterization of different centers of the monomers. Also, the results of this study, including quinoid coefficients, orbital energy spacing, charge- and spin-density distributions and electric dipole moment vectors show that conducting polymers consisted of trifluoromethyl pyrrole (Py-CF3), compared with the other FMPs, are the most favorable to be used as monomers for conducting polymer structural and electronic properties. © 2007 Elsevier B.V. All rights reserved.
Physical Review A - Atomic, Molecular, and Optical Physics (10502947)74(4)
Component instantaneous ionization rate (IIR) is introduced and the approach of its calculation is formulated. The component IIR's and the overall (time-averaged) component ionization rates are calculated for H2+ at different values of internuclear distance in a linearly polarized laser field with I=1.0× 1014 W/cm2 intensity and λ=1064 nm wavelength by direct numerical solution of the fixed-nuclei full dimensional time-dependent Schrödinger equation. The exact overall component ionization rates calculated by time-averaging of the component IIR are compared with those calculated approximately via the virtual detector (VD) method. Details of the time-dependent behavior of the outgoing and incoming electron wave packets of the H2+ system in intense laser field at subfemtosecond time scale are studied based on the calculated component IIR. It is shown clearly that the positive (outgoing electron wave packet) signals of the IIR and its z component are strong and sharp but the negative (returning electron wave packet) signals of the IIR are smooth and weak. The structure of the ρ component of the IIR has smooth structure. Relation between the R -dependent ionization rate and duration of the ramp of the laser pulse is studied and it is explicitly shown that for internuclear distance R<5.6, when the laser pulse is turned on without a ramp, the first peak of R -dependent ionization rates moves towards the peak of the lower time-dependent Floquet quasienergy state (QES). © 2006 The American Physical Society.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (01661280)731(1-3)pp. 239-239
Physical Review A - Atomic, Molecular, and Optical Physics (10502947)71(6)
Ionization rates of the hydrogen molecular ion H-2(+) under linearly polarized pulse of intense laser fields are simulated by direct solution of the fixed-nuclei time-dependent Schrodinger equation for the Ti:sapphire laser lines lambda=790 and 800 nm at high intensities starting from just above the Coulomb explosion threshold (i.e., 6.0x10(13), 1.0x10(14), 3.2x10(14), and 1.4x10(15) W cm(-2)). Results obtained in this research exhibit a high degree of complexity for the R-dependent enhanced ionization rates for the H-2(+) system in these intense laser fields. The R-dependent ionization peaks move towards small internuclear distances and their structure becomes simpler and smoother with the increase in the intensity of the laser pulse, i.e., with the decrease in the Keldysh parameter. Results obtained in this research are comparable to and even more reliable than the results of other theoretical calculations reported recently and successfully simulate the experimental ionization data.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (01661280)713(1-3)pp. 43-49
Quantum mechanical ab initio and density functional theory methods have been used to describe electrical and thermochemical properties of all fluoropyrroles and their anions and cations. The study of electrical properties was based on the values of orbital energy spacings including HUMO-LUMO gap (HLG) and electronic spatial extent (ESE) calculated at DFT-B3LYP/6-31G** level of theory. Results of this computational study are compatible with the assumptions that electron transport occurs through the lowest unoccupied molecular orbital. and that the conduction barrier is determined by the molecular electrochemical potential. This study also shows that molecules become polarized and eventually charged as the applied external potential increases. Also. thermochemical properties of fluoropymoles have been calculated at room temperature (298.15 K) and at 373.15 K. Preliminary study on some representative fluoropyrroles has been carried out using U/RHF. MP2 and DFT-B3LYP methods with a variety of basis sets. However, only B3LYP/6-31G** calculations gave satisfactory results. Details of the computational techniques and geometry optimization procedures and some other characteristics of these compounds have been reported in [H. Sabzyan, A. Omrani, J. Phys. Chem. A. 107 (2003) 6476]. (C) 2004 Elsevier B.V. All rights reserved.
Journal of Physics B: Atomic, Molecular and Optical Physics (09534075)37(20)pp. 4143-4157
Ionization of the hydrogen molecular ion under linearly polarized intense laser fields is simulated by direct solution of the fixed-nuclei time-dependent Schrödinger equation for X = 790 nm and 1 = 1 × 1014 W cm-2. Different adaptive grids used in this study produced very similar results. The results are in agreement with, and thus support, the results of recent calculations carried out by other researchers. Detailed structure of the ionization rates is presented which has not been reported so far in the literature. The use of the virtual detector method resulted in more details of the ionization rates of the hydrogen ion molecule and hydrogen atom. This method especially allowed a simultaneous detection of the parallel and perpendicular components of the ionization rates.
Khosravi-darani, K.,
Sabzyan, H.,
Zeini-isfahani, A.,
Parsafar, G. Iranian Journal Of Chemistry And Chemical Engineering (10219986)23(2)pp. 45-53
In this work, a more accurate prediction of liquid evaporation flux has been achieved. The statistical rate theory approach, which is recently introduced by Ward and Fang and exact estimation of vapor pressure in the layer adjacent to the liquid-vapor interface have been used for prediction of this flux. Firstly, the existence of an equilibrium layer adjacent to the liquid-vapor interface is considered and the vapor pressure in this layer and its thickness calculated. Subsequently, by using the Fick's second law, an appropriate vapor pressure expression for the pressure of equilibrium layer is derived and by this expression and the statistical rate theory approach, evaporation flux is predicted more accurately than the previous work. Finally, some novel steady state evaporations are simulated and the effects of both liquid and vapor temperature and the effect of the length of the evaporation chamber on the evaporation flux are investigated.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (01661280)678(1-3)pp. 67-76
Intermolecular potential energy surface for the F2-F2 system has been obtained using MP2/6-31G* computations for 20,724 different geometries with F-F bond length left relaxed to be optimized. Counterpoise correction has been used to eliminate the basis set superposition error. Characteristics of the potential energy curves such as well-depth, position of the potential minimum, well-width and hard-sphere collision diameter have been studied in detail. Molecular volume, vibrational harmonic frequencies and thermochemical stabilities (compared to the two isolated F2 monomers) corresponding to the optimized structures of the F2-F 2 complex have also been calculated and studied. © 2004 Elsevier B.V. All rights reserved.
Chemical Physics (03010104)301(1)pp. 141-152
Structural and thermochemical properties of one-dimensional (1D) Li N (N=2-20) lithium lattices have been studied using DFT-B3LYP/6-31G* method. From the optimized structures of 1D lithium lattices, it is understood that lattices with odd and even number of lithium atoms have different structural, bonding and electrical characteristics. Electric charge distribution over the lithium atoms of these 1D lattices has been studied and compared with their binding patterns. Diagonal elements of the electrical polarizability tensor and HOMO-LUMO gap (HLG) have also been calculated in order to study comparative electrical conductivity of these lithium nanowires. A comparative study of the ground state electronic energy and electric polarizability and HLG has also been carried out on the positive and negative ions and higher spin multiplicity of these lattices. In this research, electron-phonon interaction which is the dominant source of electrical resistance for single-crystals is not considered in the analysis of the electric conductivity of these 1D lithium lattices. © 2004 Elsevier B.V. All rights reserved.
Journal of Chemical Physics (10897690)120(9)pp. 4306-4315
Proton nuclear magnetic resonance spin-lattice relaxation time measurements were conducted at 500 MHz proton Larmor frequency on two hydrogen-argon gas mixtures. Relaxation times were also calculated using quantum mechanical close-coupled computations. The differences found between the experimental and theoretical results indicate that the short-range anisotropy of the potential surface is too weak. It was shown that the reciprocal regime possess much higher sensitivity to changes in the anisotropic component of the intermolecular potential energy surface.
Chemical Physics (03010104)306(1-3)pp. 105-113
Structural, electronic, thermochemical and electrical properties of mono-, di- and trihalomethylpyrroles (HMPys), NC 4H 4-CH nX 3 - n; X = F, Cl, Br; n = 0, 1, 2, 3, and their radical cations have been studied using DFT-B3LYP method with 6-31G(d,p) basis set. Vibrational frequencies and NMR shielding constants of these compounds have also been calculated and analyzed. HMPys are proposed in this research as candidate monomers for conducting polymers with modified characteristics compared to polypyrrole and polymethylpyrrole. Stability of HMPy radical cations have been studied in detail and compared with available experimental data, including oxidation potentials. Results of the present study show that bromomethylpyrroles have the highest thermochemical stability and have higher characteristics for electropolymerization compared to fluoro- and chloromethylpyrroles. Stability of HMPys increases with increasing number of substituted halogen atoms. © 2004 Elsevier B.V. All rights reserved.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (01661280)712(1-3)pp. 109-115
A question has been raised on the possible difference between the two electric polarizability tensor elements perpendicular to the molecular axis of OCS molecule, possibly, due to the significant difference between O=C and C=S pi-bonds, predicted by both the VB and localized MO theories. In other words, the VB and localized MO pictures for this molecule has been criticized. This question has been addressed by examining electronic characteristics as well as the degeneracy of the bending vibrational modes of this molecule at different ab initio RHF, CIS, MP4, and DFT-B3LYP levels of theory. The results showed that no isolated molecular orbitals corresponding to the individual O=C and C=S pi-bonds exist in this molecule. It is also found that electronic characteristics of this molecule have a cylindrical symmetry with respect to the molecular axis, as is expected from the symmetry of its total Hamiltonian reflected in the HF, post-HF and DFT-KS orbitals. Deficiency of classical VB theory is suggested to be cured by introducing a new type of resonance in which different resonance structures differ only in the orientation of the set of atomic valence orbitals, which are correlated by a C-n operation, without any differences in the bond orders and cross-populations between the participating atoms. (C) 2004 Elsevier B.V. All rights reserved.
Journal of Physical Chemistry A (15205215)107(33)pp. 6476-6482
Electronic, structural, and spectroscopic properties of the ground-state neutral and singly ionized mono-, di-, tri-, and tetrafluoropyrroles are studied using ab initio and density functional theory quantum mechanical methods. The effects of the number and position of the substituents on the electrochemical properties of the pyrrole ring have been studied. Using the optimized structures obtained for these molecules and their cations, IR and NMR spectra have been calculated and analyzed. The results of this study, including charge- and spin-density distribution analyses, show that among all of these compounds 3-fluoropyrrole and 3,4-difluoropyrrole have the most suitable conditions for electropolymerization.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (01661280)626(1-3)pp. 143-158
Structural, thermochemical stability, electrical and molecular orbital properties of (CO)n cyclic oligomers of CO (oxocarbons) have been calculated using RHF and DFT-B3LYP levels of theory with 6-31G*basis set. Contributions of these compounds in the macroscopic properties of solid CO have been investigated. Atoms in molecule (AIM) and NBO analyses have been carried out to study in detail the nature of the C-C bonds in these molecules. Population analysis has been used to search for any possible aromaticity in the rings of these cyclic oxocarbons. AIM and population analysis showed that ring bonds in the (CO)3 molecule have an aromatic character significantly more than those in other molecules do. The results of this study showed that (CO)n cyclic oligomers do not contribute significantly to the physicochemical properties of CO in the solid phase due to being thermodynamically instable at standard pressure and temperature. © 2003 Elsevier Science B.V. All rights reserved.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (01661280)663(1-3)pp. 149-157
Molecular structure and bonding, thermochemical stability, and vibrational and NMR spectra of (NPF2)n; n = 2, 3, 4 and (NPX 2)3; X = H, Cl, Br cyclic phosphazenes have been studied employing quantum computational ab initio RHF and density functional B3LYP and B3PW91 methods using 6-31G, 6-31G* and 6-31 + G* basis sets. This study showed that these compounds have planar structure and, except for (NPH2)3, all are thermodynamically stable in the gas phase. Fluorophosphazenes (NPF2)n are found to be more stable than other phosphazenes. Furthermore, the identical values obtained for all P-N bond lengths in (NPX2)3, with X = H, F, Cl and Br, phosphazenes suggests that the π-bond system of the ring in this series of compounds has aromatic character. This is approved by high values of cross electron density between indirectly bonded atoms of the ring obtained in a population analysis carried out on these systems. © 2003 Elsevier B.V. All rights reserved.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (01661280)636(1-3)pp. 185-193
Intermolecular potential energy surface (IPS) for F2-F 2 system has been examined using RHF, MP2 and DFT-B3LYP methods. A number of basis sets from the double-zeta and triple-zeta family were used in order to evaluate the basis set effects. These effects vary with the level of theory used. Counterpoise (CP) correction has been used to show the extent of the basis set superposition error (BSSE) on the potential energy curves obtained for F2-F2 system. CP corrections revealed that B3LYP and RHF levels of theory predict a totally repulsive interaction between the two monomers of F2-F2 system. The deepest BSSE-corrected potential well have been obtained at MP2 level of theory with 6-31G* basis set. At RHF and B3LYP levels of theory the least repulsive BSSE-corrected potential have been obtained with 6-31G* basis set. Effects of basis set on the characteristics of the calculated IPS have also been analyzed based on the position of the potential minimum and its well depth as well as its corresponding hard sphere collision diameter. © 2003 Elsevier B.V. All rights reserved.
Journal of Chemical Physics (10897690)108(6)pp. 2361-2374
A combined experimental and theoretical study of the NMR spin-lattice relaxation times for the deteron of D2 in D2-Ar mixtures is presented A gas-handling system and a sample cell have been designed and successfully emploved in the experimental part of this study. Spin-lattice relaxation times for the deuteron of D2 in D2-Ar mixtures have been measured over the temperature range 180-420 K at several densities and mole fractions, and extrapolation to infinite dilution has been carried out. The quality of the results has been tested by analysis of the one-dimensional spectra. Theoretical values of the spin-lattice relaxation times associated with the D2-Ar interaction have been calculated using the XC(fit) potential energy surface obtained by Bissonnette et al. [J. Chem. Phys. 105, 2639 (1996)]. Two reliable methods have been proposed to compare the theoretical and experimental NMR spin-lattice relaxation times obtained for the equilibrium mixture of the two parity isomers of the D2-Ar system under conditions in which separate measurement of their deuteron relaxation times is not possible. The agreement between experimental and theoretical results is found to be relatively good only for higher temperatures. These results indicate that the anisotropies of the XC(fit) potential energy surface need refinement. © 1998 American Institute of Physics.
Journal of Chemical Physics (10897690)108(15)pp. 6170-6184
A combined experimental and theoretical study of the nuclear magnetic resonance (NMR) spin-lattice relaxation times for the proton and deuteron of HD in HD-Ar mixtures is presented. Spin-lattice relaxation times for the proton and deuteron of HD in HD-Ar mixtures have been measured over the temperature range 180-420 K at several densities and mole fractions, and extrapolation to infinite dilution has been carried out. Theoretical values of the spin-lattice relaxation times associated with the HD-Ar interaction have been calculated using the XC(fit) potential energy surface obtained by Bissonnette et al. [J. Chem. Phys. 105, 2639 (1996)], transformed to allow displacement of the center-of-mass of the HD molecule from its center-of-force. Both experimental and theoretical results show that the density-dependence of the deuteron relaxation times lies in the linear regime, while that of the proton lies in the non-linear regime. The experimental and theoretical results for the relaxation times of the proton are in excellent agreement. The corresponding results for the deuteron are in good agreement (within a few percent); the agreement is, however, not as good as it is for the proton. These results indicate that the transformed XC(fit) potential energy surface represents the anisotropic part of the HD-Ar interaction rather accurately. It is argued that the improved quality of the XC(fit) potential energy surface for the heteronuclear HD-Ar interaction is due to the large contribution that the isotropic part of the homonuclear potential surface makes to the anisotropic part of the heteronuclear potential surface. © 1998 American Institute of Physics.
