Physical chemistry
Mahdi Rezaei Sameti; Fateme Ataeifar
Volume 6, Issue 3, pp. 218-324, Serial No. 20 , July 2018, , Pages 280-292
Abstract
In this research, the effects of HCN adsorption on the surface of the pristine, Ge, P, and GeP doped boron nitride nanotube (BNNTs) are investigated by using density function theory at the B3LYP/6–31G(d, p) level of theory. At the first step, we consider different configurations for adsorbing HCN ...
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In this research, the effects of HCN adsorption on the surface of the pristine, Ge, P, and GeP doped boron nitride nanotube (BNNTs) are investigated by using density function theory at the B3LYP/6–31G(d, p) level of theory. At the first step, we consider different configurations for adsorbing HCN molecule on the surface of BNNTs. The optimized models are used to calculate the structural, electrical, NQR parameters and quantum descriptors such as global hardness, global softness, electrophilicity, gap energy, Fermi level energy, electronic chemical potential, and electronegativity of BNNTs/HCN complex. Inspection of results demonstrates that with doping Ge impurity the sensivity of BNNTs for adsorbing HCN molecule increase significantly from original values. The adsorption of HCN molecule on the surface of Ge-doped is more stable and favourable than other those models. With adsorbing of HCN gas and doping of Ge and GeP the NQR, quantum molecular descriptors and molecular orbital energies of the nanotube alter significantly from original state. On the other hand the electrophilicity index of E model is more than those other models.
Physical chemistry
Fatemeh Elmi; Nasser Hadipour
Volume 5, Issue 4, pp. 364-493, Serial No. 17 , October 2017, , Pages 372-380
Abstract
A fragment of Histidine rich protein II (HRP II 215-236) was investigated by 14N and 17O electric field gradient, EFG, tensor calculations using DFT. This study is intended to explore the differences between 310-helix and α-helix of HRPII both in the gas phase and in solution. To achieve the aims, ...
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A fragment of Histidine rich protein II (HRP II 215-236) was investigated by 14N and 17O electric field gradient, EFG, tensor calculations using DFT. This study is intended to explore the differences between 310-helix and α-helix of HRPII both in the gas phase and in solution. To achieve the aims, the 17O and 14N NQR parameters of a fragment of HRPII (215-236) for both structures are calculated. Due to the side chain arrangements of the 310-helix, this conformation contains several hydrogen bonding contacts in comparison to the α-helix form. The resultant 14N and 17O s of peptide bonds of HRPII are affected by these contacts. Both in the gas phase and in solution, the differences in 14N s of backbone are within the uncertainties identical between two conformers but not for NH groups of backbone that the related amino acids participate in intramolecular hydrogen bond formation with side chain. In this case, the differences in 14N of backbone are avg.= 0.36 in gas phase and avg.= 0.43MHz in solution. However, differences in 17O parameters of the backbone C=O are distinguishable between two conformers, regardless of in gas phase and in solution, with and without influencing of the intramolecular hydrogen bond. These differences reveal how hydrogen bond interactions affect EFG tensors at the sites of oxygen and nitrogen nuclei.
Organic chemistry
Ali Ramazani; Masoome Sheikhi Sheikhi; Ali Souldozi; Sang Woo Joo; Hooriye Yahyaei
Volume 5, Issue 4, pp. 364-493, Serial No. 17 , October 2017, , Pages 449-470
Abstract
Dimethyl (z)-2-[(2-methyl-5-oxo-1-cyclopentyl)oxy]-2-butenedioate has been synthesized using one-pot three component reaction between N-isocyaniminotriphenylphosphorane (Ph3PNNC), 3-methylcyclopentene-1,2-dione and dimethyl acetylenedicarboxylate. Also, optimized geometry and nuclear magnetic resonance ...
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Dimethyl (z)-2-[(2-methyl-5-oxo-1-cyclopentyl)oxy]-2-butenedioate has been synthesized using one-pot three component reaction between N-isocyaniminotriphenylphosphorane (Ph3PNNC), 3-methylcyclopentene-1,2-dione and dimethyl acetylenedicarboxylate. Also, optimized geometry and nuclear magnetic resonance ( NMR ) of the title compound are evaluated using HF and B3LYP methods and 6-311+G(d) basis set. Moreover, the 1H and 13C NMR chemical shift values of the molecule are calculated and compared with experimental results. Frontier molecular orbitals (FMOs), total density of states (DOS), electronic properties, natural charges, NMR parameters and NBO analysis for product were calculated by theoretical calculations. Finally, molecular electrostatic potential (MEP) surface is obtained for understanding the active regions of molecule.
![Synthesis, spectroscopic (NMR and FT-IR) and theoretical (HF and DFT) investigation of dimethyl (Z)-2-[(2-methyl-5-oxo-1-cyclopentyl)oxy]-2-butendioate](data/icc/coversheet/251502083894.png)
Physical chemistry
Mehdi Ghambarian; Zahra Azizi; Mohammad Ghashghaee
Volume 5, Issue 1, pp. 1-120, Serial No. 14 , January 2017, , Pages 28-34
Abstract
Density-functional-based and ab initio calculations were implemented at different computational levels to estimate the binding energy of Zn2+ ion adsorbed on the available sites of a silicate MEL-type adsorbent. B3LYP and MP2 were used in combination with the 6-31G*, 6-31+G*, LanL2DZ, 6-311+G*, and Def2-TZVP ...
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Density-functional-based and ab initio calculations were implemented at different computational levels to estimate the binding energy of Zn2+ ion adsorbed on the available sites of a silicate MEL-type adsorbent. B3LYP and MP2 were used in combination with the 6-31G*, 6-31+G*, LanL2DZ, 6-311+G*, and Def2-TZVP basis sets. The zinc cation was found to preferentially occupy the 6MR sites followed by the cage-like positions. Nevertheles, all of the available sites exhibited negative amounts for the Gibbs free energy and enthalpy of adsorption with the corresponding population-averaged values of –160.84 and –169.53 kcal/mol at the B3LYP/Def2-TZVP level. Overall, the B3LYP/LanL2DZ method illustrated the highest deviation from the others both in trends and absolute values of binding energy. While the absolute binding energy ranged from 131.23 to 230.79 kcal/mol over different sites, the population-averaged binding energies altered from 146.08 to 162.54 kcal/mol depending on the method employed.
Physical chemistry
Reza Fazaeli; Mohammad Solimannejad
Volume 2, Issue 4, pp. 236-325, Serial No. 5 , October 2014, , Pages 244-254
Abstract
Density functional (DFT) calculations at M05-2x/aug-cc-pVDZ level were used to analyze the interactions between dimethyl sulfoxide (DMSO) dimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the ...
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Density functional (DFT) calculations at M05-2x/aug-cc-pVDZ level were used to analyze the interactions between dimethyl sulfoxide (DMSO) dimers. The structures obtained have been analyzed with the Atoms in Molecules (AIMs) and Natural Bond Orbital (NBO) methodologies. Four minima were located on the potential energy surface of the dimers. Three types of interactions are observed, CH•••O, CH•••S hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the sulfur atom. Stabilization energies of dimers including BSSE and ZPE are in the range 27–40 kJ mol-1. The most stable conformers of dimers at DFT level is cyclic structure with antiparallel orientation of S=O groups that pairing with three C–H…O and a S…O interactions.
Physical chemistry
Morteza Vatanparast; Nabi Javadi; Rasoul Pourtaghavi Talemi; Elahe Parvini
Volume 2, Issue 4, pp. 236-325, Serial No. 5 , October 2014, , Pages 316-325
Abstract
The character of the intermolecular interactions in Cl2-HX (X =F, Cl and Br) complexes has been investigated by means of the second-order Möller–Plesset perturbation theory (MP2) and the density functional theory (DFT) calculations. The results show that there are two types of lowest interaction ...
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The character of the intermolecular interactions in Cl2-HX (X =F, Cl and Br) complexes has been investigated by means of the second-order Möller–Plesset perturbation theory (MP2) and the density functional theory (DFT) calculations. The results show that there are two types of lowest interaction potential equilibrium structures in the interactions between Cl2 and HX: X∙∙∙Cl type geometry and hydrogen-bonded geometry. The calculated interaction energies show that the X∙∙∙Cl type structures are more stable than the corresponding hydrogen-bonded structures. The nature of the intermolecular interactions has been also investigated by natural bond orbital (NBO) and atoms in molecules (AIM). The AIM analysis reveals that both types of intermolecular interactions are “closed-shell” noncovalent interactions.
Physical chemistry
Reza Behjatmanesh; Negin Safaeian
Volume 2, Issue 2, pp. 82-163, Serial No. 3 , April 2014, , Pages 147-156
Abstract
: In this work, different levels of theory containing HF, B3LYP, and MP2 with different basis sets such as 6-31G, 6-31G*, 6-311G, 6-311+G, 6-31+G*, 6-31+G are used to predict relative acidity constants of some aniline derivatives. Three different kinds of radii containing UAHF, Bondi, and Pauling are ...
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: In this work, different levels of theory containing HF, B3LYP, and MP2 with different basis sets such as 6-31G, 6-31G*, 6-311G, 6-311+G, 6-31+G*, 6-31+G are used to predict relative acidity constants of some aniline derivatives. Three different kinds of radii containing UAHF, Bondi, and Pauling are used to study how cavity forms change acidity constants. In all cases, DPCM model is used to simulate solvation Gibbs free energy. Furthermore, one similar level and basis set has been linked to IEFPCM and DPCM models to compare the results. To relate gas-phase Gibbs free energy to the solution Gibbs free energy, a simple thermodynamic cycle is used. Results show that quantum chemical calculations are robust techniques for estimating acidity constants.
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