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    Calculating the acidity of silica supported alkyl sulfonic acids considering the matrix effect: A DFT study

    , Article Phosphorus, Sulfur and Silicon and the Related Elements ; Vol. 189, Issue. 6 , 2014 , Pages 849-857 ; ISSN: 10426507 Vafaeezadeh, M ; Fattahi, A ; Sharif University of Technology
    Abstract
    (Equation present) Density functional theory (DFT) was used to investigate the acidity of the various silica alkyl sulfonic acids. In this regard, cluster models with various alkyl spacer lengths were selected to mimic the surface of silica gel. The effects of distance from the surface and the role of hydrogen bond (H-bond) on the ΔHacidity values of these catalysts were investigated. DFT calculations revealed that a notable gap of ΔH acidity values exists between the structures considering lateral hydrogen bonding with the surface of the silica HB structure and the structures with omitted surface interactions (non-HB structures). Natural bonding orbital (NBO) and quantum theory of atoms in... 

    Structural relevance of N2O2-donor naphthodiaza-crown macrocyclic ligands to selective fluorescence signaling behavior towards aliphatic tertiary amines

    , Article Journal of Photochemistry and Photobiology A: Chemistry ; Volume 314 , 2016 , Pages 42-51 ; 10106030 (ISSN) Ghanbari, B ; Zarepour Jevinani, M ; Sharif University of Technology
    Elsevier  2016
    Abstract
    A series of N2O2-donor naphthodiaza-crown macrocyclic ligands, L1-L5, were synthesized and characterized by IR, 1H and 13C NMR spectroscopy, mass spectrometry as well as microanalysis. Preliminary observations employing UV-vis spectrophotometry of L3 in ethanol revealed that triethylamine (TEA) has a significant blue-shift effect on the entire of the spectra. Then, the detection of aliphatic and aromatic amines by L3 were followed by monitoring of fluorescence quenching of the resulting adducts in terms of their binding with L1-L5. Both steady-state and time-resolved spectroscopic measurements in the... 

    Evaluation of hydrogen bonds formation in the selected rare sugars based on 6-31G* and 6–311 + + G(d,p) basis sets

    , Article Journal of Molecular Modeling ; Volume 27, Issue 11 , 2021 ; 16102940 (ISSN) Mosapour Kotena, Z ; Razi, M ; Ahmadi, S ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2021
    Abstract
    Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including gulose, allose, altrose, and talose, are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C2-4 atoms. The basis sets effect in evaluation of the possibility intramolecular hydrogen bonding (H-bonds) in the selected rare sugars was studied from 6-31G* to 6–311 ++ G(d,p) basis sets using DFT, AIM, and NBO methods. The results show that the selected rare sugars are more stable at 6–311 ++ G(d,p) basis sets compared to 6-31G* because their electronic energies were reduced... 

    Theoretical study of protic solvents hydrogen bonding effect, on the reaction of cyclopentadiene and vinyl acetate; apart from the bulk properties

    , Article Journal of Molecular Structure: THEOCHEM ; Volume 909, Issues 1–3 , September , 2009 , Pages 86–90 Irani, M ; Haqgu, M ; Gholami, M. R. (Mohammad Reza) ; Sharif University of Technology
    Abstract
    Ab initio, DFT, Monte Carlo statistical mechanics and atom in molecule methods have been applied to investigate the hydrogen bonding effect of protic solvents, apart from the bulk properties, on the reaction of cyclopentadiene and vinyl acetate. The results show that methanol accelerates the rate of the reaction more than water. DFT calculations demonstrate that the interaction of the carbonyl group oxygen atom with solvent molecules in transition state is stronger and more effective than the ether-type oxygen atom. Also, when the solvent molecule is near the oxygen of the carbonyl group the rate of reaction is larger than when it is near the ether-type oxygen. In addition, methanol... 

    Conformational aspects of glutathione tripeptide: Electron density topological & natural bond orbital analyses

    , Article Structural Chemistry ; Volume 24, Issue 1 , 2013 , Pages 147-158 ; 10400400 (ISSN) Aliakbar Tehrani, Z ; Fattahi, A ; Sharif University of Technology
    2013
    Abstract
    Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density Δ2 ρ(r) from Bader's atom in molecules theory. Charge transfer energies based on... 

    Theoretical study of protic solvents hydrogen bonding effect, on the reaction of cyclopentadiene and vinyl acetate; apart from the bulk properties

    , Article Journal of Molecular Structure: THEOCHEM ; Volume 909, Issue 1-3 , 2009 , Pages 86-90 ; 01661280 (ISSN) Irani, M ; Haqgu, M ; Gholami, M. R ; Sharif University of Technology
    2009
    Abstract
    Ab initio, DFT, Monte Carlo statistical mechanics and atom in molecule methods have been applied to investigate the hydrogen bonding effect of protic solvents, apart from the bulk properties, on the reaction of cyclopentadiene and vinyl acetate. The results show that methanol accelerates the rate of the reaction more than water. DFT calculations demonstrate that the interaction of the carbonyl group oxygen atom with solvent molecules in transition state is stronger and more effective than the ether-type oxygen atom. Also, when the solvent molecule is near the oxygen of the carbonyl group the rate of reaction is larger than when it is near the ether-type oxygen. In addition, methanol... 

    Neutral intramolecular hydrogen-bonded bases

    , Article Croatica Chemica Acta ; Volume 82, Issue 1 , 2009 , Pages 41-45 ; 00111643 (ISSN) Tian, Z ; Fattahi, A ; Lis, L ; Kass, S. R ; Sharif University of Technology
    2009
    Abstract
    B3LYP/aug-cc-pVDZ computations were carried out on polyamines with up to seven amino groups. The gas-phase proton affinities of these compounds are 219.6 (1-BuNH2), 238.6 (H2NCH2CH2CH 2CH2NH2), 252.8 [(H2NCH 2CH2CH2)2CHNH2], 261.3 [(H2NCH2CH2CH2) 3CNH 2 (1)], and 288.5 kcal mol-1 [(H2NCH 2CH2CH(NH2)CH2CH2) 3CNH2]. These results indicate that the tetraamine is near the top of the basicity scale and the heptaamine is more basic than any neutral organic compound which has been measured to date. A gas-phase equilibrium acidity determination between 1 and DBU also was carried out, and PA(1) = 256.2 ± 2.1 kcal mol-1 was obtained. This demonstrates that multiple intramolecular hydrogen bonds can... 

    Influence of remote intramolecular hydrogen bonding on the acidity of hydroxy-1,4-benzoquinonederivatives: A DFT study

    , Article Journal of Physical Organic Chemistry ; Volume 32, Issue 4 , 2019 ; 08943230 (ISSN) Bayat, A ; Fattahi, A ; Sharif University of Technology
    John Wiley and Sons Ltd  2019
    Abstract
    In this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy-1,4-benzoquinone derivatives have been investigated ab initio by employing density functional theory (DFT) methods. The computational studies were performed for both gas and solution (H 2 O, DMSO, and MeCN solutions) phases. Our results indicated that remote hydrogen bonding could play an important role in increasing the acidity of hydroxy-1,4-benzoquinone. Noncovalent interaction reduced density gradient (NCI-RDG) methods were used to visualize the attractive and repulsive interactions in the studied acids and their conjugate bases. Natural bond orbital (NBO) analysis was performed to confirm... 

    Synthesis and crystal structure of bis (tetrabutylammonium)(4,4′- azodi(phenylcyanamide)) salt • [(n-Bu)4N] 2[azodicyd2-] • H2O

    , Article Journal of Chemical Crystallography ; Volume 38, Issue 4 , 2008 , Pages 311-314 ; 10741542 (ISSN) Boghaei, D. M ; Behzadian Asl, F ; Khavasi, H. R ; Sharif University of Technology
    2008
    Abstract
    The chemical preparation and crystal structure for a 4,4′- azodi(phenylcyanamide) salt) in the solid state are reported. This compound crystallizes in the triclinic space group P with the following unit cell parameters: a = 9.759(3) Å, b = 11.237(4) Å, c = 11.919(4) Å, α = 95.54(3)°, β = 98.50(3)°, γ = 109.39(2)°, Z = 1 and V = 1204.4(7) Å3. The 4,4′-azodi(phenylcyanamide) dianion, azodicyd2-, is approximately planar, with the cyanamide groups (-N=C=N) in an anti conformation relative to each other and the azo group (-N=N-) adopting the more thermodynamically stable trans conformation. The crystal X-ray analysis shows that there are one azo molecule cation, two tetrabutylammonium cations and... 

    Hydrogen bonding effects on acidity enhancement of barbiturates and their metabolites in gas and solution phase, a DFT study

    , Article Computational and Theoretical Chemistry ; Volume 1196 , 2021 ; 2210271X (ISSN) Daneshfar, M ; Fattahi, A ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    Density functional theory method and B3LYP/6-31+G(d) level of theory were used to predict the acidity of barbiturates and their corresponding metabolites in the gas and solution phase (H2O). Polarized continuum model was applied to calculate pKa values of barbiturates and metabolites. A comparison between acidity of barbiturates and metabolites in the gas and solution phase indicates that the acidity strength of barbiturates enhances with the increase of intramolecular hydrogen bonds in metabolites. This acidity can increase to 9.47 kcal/mol in gas phase and 2.73 pKa units in solution phase for a typical metabolite of barbiturate due to the effect of intramolecular hydrogen bonds. Also,... 

    Cooperativity effects of intramolecular OH...O interactions on pK a values of polyolalkyl sulfonic acids in the gas phase and solution: A density functional theory study

    , Article Journal of Physical Organic Chemistry ; Vol. 27, issue. 7 , 2014 , p. 604-612 Najdian, A ; Shakourian-Fard, M ; Fattahi, A ; Sharif University of Technology
    Abstract
    Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution (H2O, DMSO, and CH 3CN) phase. Polarized continuum model was applied to calculate pKa values of alkyl sulfonic acids and polyolalkyl sulfonic acids. A comparison between acidity of alkyl sulfonic acids and polyolalkyl sulfonic acids in the gas and solution phase indicates that the acidity strength of polyolalkyl sulfonic acids enhances with the increase of the cooperativity effect of intramolecular hydrogen bonds in polyolalkyl sulfonic acids. Natural bond orbital and quantum theory of atoms in molecules... 

    Interactions of glutathione tripeptide with gold cluster: Influence of intramolecular hydrogen bond on complexation behavior

    , Article Journal of Physical Chemistry A ; Volume 116, Issue 17 , 2012 , Pages 4338-4347 ; 10895639 (ISSN) Tehrani, Z. A ; Jamshidi, Z ; Javan, M. J ; Fattahi, A ; Sharif University of Technology
    2012
    Abstract
    Understanding the nature of the interaction between metal nanoparticles and biomolecules has been important in the development and design of sensors. In this paper, structural, electronic, and bonding properties of the neutral and anionic forms of glutathione tripeptide (GSH) complexes with a Au 3 cluster were studied using the DFT-B3LYP with 6-31+G**-LANL2DZ mixed basis set. Binding of glutathione with the gold cluster is governed by two different kinds of interactions: Auâ€"X (X = N, O, and S) anchoring bond and Au··•·•H-X nonconventional hydrogen bonding. The influence of the intramolecular hydrogen bonding of glutathione on the interaction of this peptide with the gold cluster has been... 

    Acidity enhancement of α-carbon of beta diketones via hydroxyl substituents: A density functional theory study

    , Article Journal of Physical Organic Chemistry ; Volume 34, Issue 3 , 2021 ; 08943230 (ISSN) Rahimi, M ; Fattahi, A ; Sharif University of Technology
    John Wiley and Sons Ltd  2021
    Abstract
    Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd  

    Synthesis and characterization of a new group of Exo-coordinating o2n2-donor macrocycles

    , Article Australian Journal of Chemistry ; Volume 69, Issue 3 , 2016 , Pages 273-278 ; 00049425 (ISSN) Ghanbari, B ; Safarkoopayeh, B ; Kia, R ; Raithby, P.R ; Sharif University of Technology
    CSIRO  2016
    Abstract
    The reaction of 15-18 membered benzodiazacrown ethers with salicylaldehyde afforded n-membered O2N2-donor macrocyclic ligands mounted with 1,3-diazacyclohexane subrings (1-4) in high yields. The products were characterized by FT-IR, 1H, 13C NMR spectroscopy, elemental analyses, and single crystal X-ray studies. The solid state structures revealed strong intramolecular hydrogen bonding between the pendant phenolic group and the tertiary nitrogen of the corresponding macroring  

    CO2 separation by supported liquid membranes synthesized with natural deep eutectic solvents

    , Article Environmental Science and Pollution Research ; Volume 28, Issue 26 , 2021 , Pages 33994-34008 ; 09441344 (ISSN) Saeed, U ; Khan, A. L ; Gilani, M. A ; Aslam, M ; Khan, A. U ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2021
    Abstract
    Betaine-based natural deep eutectic solvents (NADESs), a new class of green solvents, were immobilized into a porous polyvinylidene fluoride (PVDF) support and evaluated for the separation of CO2 from CO2/N2 and CO2/CH4 mixtures. Two types of NADESs were synthesized by mixing betaine (hydrogen bond acceptor-HBA) with malic acid and tartaric acid (hydrogen bond donors-HBD) respectively. FTIR and Raman spectroscopy were studied to confirm the synthesis and purity of the NADESs. The thermal strength of the NADESs was investigated using thermogravimetric analysis. The gas permeation results of the fabricated NADES-based-supported liquid membranes (NADES-SLMs) showed that the permeability of CO2... 

    Synthesis of Metallophthalocyanine Nanoparticls and Its Application in the Oxidation of Organic Compounds,and Investigation of Hydrogen Bonding Effect on the Basicity of Amines and Orbital Interactions on Acidity Enhacment of Alcohols

    , Ph.D. Dissertation Sharif University of Technology Kheirjou, Somayyeh (Author) ; Mahmoodi Hashemi, Mohammad (Supervisor) ; Fattahi, Alireza (Supervisor)
    Abstract
    This thesis is divided into two parts: In part I, which is theoretical part, we were looking for a computational method which is extensively comparable with experimental results to determine pKa of wide variety of organic compounds. The pKa is an important property in many sciences such as chemistry, biology, and material science, since inclination of a compound to donate or accept a proton is fundamental to understanding many chemical and biochemical processes. Experimentally determined pKa values are not always available from literature sources and often estimated values are employed in their place. It is useful, therefore, to have reliable and accurate means of calculating relative and/or... 

    Thermochemical properties of some vinyl chloride-induced DNA lesions: Detailed view from NBO & AIM analysis

    , Article Structural Chemistry ; Volume 23, Issue 6 , 2012 , Pages 1987-2001 ; 10400400 (ISSN) Tehrani, Z. A ; Torabifard, H ; Fattahi, A ; Sharif University of Technology
    2012
    Abstract
    Etheno-damaged DNA adducts such as 3,N4- ethenocytosine, N 2,3-ethenoguanine, and 1,N2-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gasphase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare... 

    Can anion interaction accelerate transformation of cytosine tautomers? Detailed view form QTAIM analysis

    , Article Structural Chemistry ; Volume 23, Issue 6 , 2012 , Pages 1843-1855 ; 10400400 (ISSN) Jebeli Javan, M ; Tehrani, Z. A ; Fattahi, A ; Jamshidi, Z ; Sharif University of Technology
    Abstract
    The relative stabilities and noncovalent interactions of the six low-lying energy tautomers of cytosine nucleobase with some biological anions (such as F-, Cl-, and CN-) have been investigated in gas phase by density functional theory (DFT) method in conjunction with 6-311++G (d,p) atomic basis set. Furthermore, to systematically investigate all possible tautomerisms from cytosine induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase and in a continuum solvent using DFT calculation. We carried out geometrical optimizations with the integral equation formalism of polarizable continuum (IEF-PCM) model to account for the solvent effect, and the... 

    Influence of a β-OH substituent on SN2 reactions of fluoroethane: Intramolecular hydrogen bonding catalysis or inhibition? A theoretical study

    , Article Computational and Theoretical Chemistry ; Volume 1067 , 2015 , Pages 71-83 ; 2210271X (ISSN) Ahmadi, A. A ; Fattahi, A ; Sharif University of Technology
    Abstract
    Computational investigations on the gas phase SN2 reactions of X ions (X-=OH-,F-,Cl-,Br-, and I-) with fluoroethane and 2-fluoroethanol (β-hydroxyl ethyl fluoride) were performed by using MPW1K, M06 and CCSD(T) methods with a range of basis sets including 66-311++G**, TZVP, aug-cc-pVDZ and SDD. To better understand the nature of the corresponding intermolecular interactions, we performed natural bond orbital (NBO) analysis and Bader's quantum theory of atoms in molecules (QTAIM). In our calculations, we took into account two possible pathways for these reactions, i.e. SN2 reactions of 2-fluoroethanol. In path(i), β-hydroxyl group participates in hydrogen bonding... 

    Heterogenization of manganese porphyrin via hydrogen bond in zeolite imidazolate framework-8 matrix, a host-guest interaction, as catalytic system for olefin epoxidation

    , Article Journal of Porphyrins and Phthalocyanines ; Volume 22, Issue 11 , 2018 , Pages 972-980 ; 10884246 (ISSN) Bagherzadeh, M ; Mesbahi, E ; Sharif University of Technology
    World Scientific Publishing Co. Pte Ltd  2018
    Abstract
    A heterogenized meso-tetrakis(2,3-dihydroxyphenyl)porphyrinatomanganese(III) acetate at zeolite imidazolate framework-8 (T(2,3-OHP)PorMn@ZIF-8) is investigated for the catalytic olefin epoxidation reactions at room temperature. Heterogenization is accomplished through a non-classical hydrogen bond proposed between T(2,3-OHP)PorMn bearing O-H groups and C-H of the 2-methylimidazolate linkers in the ZIF-8 structure. The aforementioned compound is characterized by X-ray powder diffraction (XRD), atomic absorption spectroscopy (AAS), nitrogen adsorption-desorption, FT-IR spectroscopy, field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and Raman...