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The intramolecular cation-π interaction of some aryl amines and its drastic influence on the basicity of them: AIM and NBO analysis
, Article Computational and Theoretical Chemistry ; Vol. 1036 , May , 2014 , pp. 51-60 ; ISSN: 2210271X ; Fattahi, A ; Hashemi, M. M ; Sharif University of Technology
Abstract
In this study, drastic influence of the intramolecular cation-π interaction on the basicity of selected amines has been considered. The optimized minimum energy geometries of different studied amines and their protonated structures were determined by using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. Geometry optimizations indicate that the most stable structures of protonated amines are stabilized by intramolecular cation-π interaction. The proton affinity (PA) of selected amines is controlled by the strength of intramolecular cation-π interaction of ammonium with aromatic ring. These cation-π interactions strongly influence the basicity of amines. Natural bond orbital (NBO)...
Theoretical investigation on the structure and properties of alumazine⋯m complexes (M = Li+, Na+, K+, Be2+, Mg2+, and Ca2+)
, Article Journal of Theoretical and Computational Chemistry ; Volume 12, Issue 5 , August , 2013 ; 02196336 (ISSN) ; Sharif University of Technology
2013
Abstract
The nature of alumazine⋯M (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical...
Thermochemical properties of some vinyl chloride-induced DNA lesions: Detailed view from NBO & AIM analysis
, Article Structural Chemistry ; Volume 23, Issue 6 , 2012 , Pages 1987-2001 ; 10400400 (ISSN) ; Torabifard, H ; Fattahi, A ; Sharif University of Technology
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) ; 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...
Theoretical study of borazine: cation-π (Be 2+, Mg 2+, and Ca 2+) interaction
, Article Structural Chemistry ; 2012 , Pages 1-7 ; 10400400 (ISSN) ; Sharif University of Technology
2012
Abstract
The geometries of the complexes of Be 2+, Mg 2+, and Ca 2+ metal cations with borazine ring were studied. The complexes were optimized at the B3LYP level and the 6-311++G(d,p) basis set. Then, the interaction energies corrected by basis set super position error were calculated in the same level. The results show that interaction energy is strongly dependent on the charge-to-size ratio of the cation. Therefore, Be 2+ cation has the most interaction energy value with respect to Mg 2+ and Ca 2+ metal cations. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to...
Design and synthesis of new family of ionic liquids based on 2-iminium-1,3-dithiolanes: A combined theoretical and experimental effort
, Article Journal of Molecular Structure ; Vol. 1056-1057, issue. 1 , January , 2014 , p. 56-62 ; Shakourian-Fard, M ; Farvardin, M. V ; Raeesi, M ; Hashemi, M. M ; Behzadi, H ; Sharif University of Technology
Abstract
An efficient method for synthesis of 2-iminium-1,3-dithiolane as a new family of ionic liquids with reaction of dithiocarbamates with methyl triflouromethanesulfonate was described. Theoretical study on the synthesized ionic liquids was also performed by quantum chemistry calculation. Geometry optimization on the ion pairs was carried out with the B3LYP/6-311++G(d,p) level of theory. The interaction energies were calculated, and corrected by the basis set superposition error (BSSE) calculated by the counterpoise method. The results of natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses indicate that the interactions occur via hydrogen bonding between oxygen...
Molecular structure and character of bonding of mono and divalent metal cations (Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and cu +) with guanosine: AIM and NBO analysis
, Article Structural Chemistry ; Volume 23, Issue 3 , June , 2012 , Pages 613-626 ; 10400400 (ISSN) ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
2012
Abstract
The B3LYP/6-311++G (d,p) density functional approach was used to study the gas-phase metal affinities of Guanosine (ribonucleoside) for the Li +, Na +, K +, Mg 2+, Ca 2+, Zn 2+, and Cu + cations. In this study we determine coordination geometries, binding strength, absolute metal ion affinities, and free energies for the most stable products. We have also compared the results for Guanosine, with our previously reported results for 20-Deoxyguanosine. Based on the results, it is obvious that MIA is strongly dependent on the charge-to-size ratio of the cation. Guanosine interacts more strongly with Zn 2+ than do with Mg 2+, Ca 2+, and Cu? and therefore stronger interactions lead to higher MIA....
Influence of the water molecules (n 5 1-6) on the interaction between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue
, Article Structural Chemistry ; Volume 23, Issue 3 , 2012 , Pages 857-865 ; 10400400 (ISSN) ; Nasiri, M ; Fattahi, A ; Vafaeezadeh, M ; Sharif University of Technology
2012
Abstract
Influence of the addition of water molecules (n = 1-6) on the interaction energy between Li +, Na +, K + cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d, p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation-π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation-π interaction indicates that there is a correlation between the...
Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2'-deoxythymidine with different anions
, Article Structural Chemistry ; Volume 23, Issue 1 , July , 2012 , Pages 17-28 ; 10400400 (ISSN) ; Fattahi, A ; Sharif University of Technology
2012
Abstract
Hydrogen bonding interactions between thymine nucleobase and 2'-deoxythymidine nucleoside (dT) with some biological anions such as F - (fluoride), Cl - (chloride), OH - (hydroxide), and NO 3 - (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory...
Theoretical Investigation of Hydrogen Bonding Effects on Interaction of Metal Nanoclusters with Histidine, Oxidation of Olefins by MnO4– & Acidity Enhancement of Alcohols
, Ph.D. Dissertation Sharif University of Technology ; Fattahi, Alireza (Supervisor) ; Mahmoodi Hashemi, Mohammad (Supervisor) ; Jamshidi, Zahra (Supervisor)
Abstract
This thesis is divided into three parts: In part I, interactions of neutral and anionic forms of histidine with coinage metal nano clusters M3 (M = Au, Ag and Cu) are investigated. Results demonstrate that nonconventional M…H-O hydrogen bonds and M-X bonds (X = N, O) play stabilization roles in interactions of histidine and metal nano clusters. Presence of negative charge in ligand leads to increase of binding energy of complexes. In the next step, the effects of coinage metal nano clusters on the gas-phase acidity of weak organic acid (histidine) have been explored. The acidity of isolated histidine is compared with the acidity of its Au3–, Ag3– and Cu3–complexed species. Moreover, pKa...
Interaction of cations with 2′-deoxythymidine nucleoside and analysis of the nature and strength of cation bonds
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 2 , JAN , 2012 , Pages 153-161 ; 08943230 (ISSN) ; Fattahi, A ; Jamshidi, Z ; Sharif University of Technology
2012
Abstract
Binding of Mg 2+, Ca 2+, Zn 2+, and Cu + metal ions with 2′-deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6-311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri-coordinated · (O2, O4′, O5′). Among the four types of cations, Zn 2+ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N-glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate...
Influence of Intramolecular Hydrogen Bonding on Ability of Leaving Group in SN2 Reactions
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Alireza (Supervisor)
Abstract
Many of the significant reactions in chemistry and biology are related to bimolecular nucleophilic substitution (SN2) reactions which have been studied first by Hughes and Ingold in the 1930s. Afterward, many organic chemists have continued this work. Up to now, numerous experimental kinetic and theoretical researches have studied the mechanism of these reactions. Since most SN2 reactions occur in solution, a large number of these studies have been devoted to the solvent effects. One of these effects that has been examined extremely is H-bonding via protic solvents that lowers the energy of an anionic nucleophile relative to the transition state, in which the charge is more diffuse, and...
Theoretical Investigation of Hydrogen Bonding Effects on Interaction of Metal Nanoclusters with Biomolecules & Acidity Enhancement of Alcohols
, Ph.D. Dissertation Sharif University of Technology ; Fattahi, Alireza (Supervisor) ; Mahmoodi Hashemi, Mohammad (Supervisor) ; Jamshidi, Zahra (Co-Advisor)
Abstract
This thesis is divided into three parts: In part I, conformational properties of neutral, anionic, cationic and zwitterionic forms of glutathione tripeptide were investigated by means of DFT-B3LYP method with 6-31+G (d,p) basis set. Results show that glutathione is a very flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond and its charge. Conformation of each amino acid in glutathione tripeptide depends on its orientation within the peptide sequence in addition to the conformation of other amino acids within the chain. Investigation of intramolecular hydrogen bonds in these conformers by means of AIM analysis demonstrates...
Theoretical Investigation of Hydrogen Bonding Effects on Acidity Enhancement of Alkyl sulfonic Acids and Hydroxy Alkyl Sulfonic Acids in Gas and Solution Phase
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Ali Reza (Supervisor) ; Hormozi-Nezhad, Mohammad Reza (Supervisor)
Abstract
Hydrogen bonding is an important weak interaction encountered in gas, liquid, as well as solid phases. The hydrogen bond plays a very vital role in many life processes and is one of the most frequently used terms in chemistry and biology.
Polyols or polyhydric alcohols are, strictly speaking, simply organic chemicals containing more than two hydroxyl groups. Each hydroxyl is attached to separate carbon atoms of an aliphatic skeleton.They may also contain ester, ether, amide, acrylic, metal, metalloid and other functionalities; along with hydroxyl groups. Polyols are obtained from many plant and animal sources and are synthesized by a variety of methods. Among important properties of...
Polyols or polyhydric alcohols are, strictly speaking, simply organic chemicals containing more than two hydroxyl groups. Each hydroxyl is attached to separate carbon atoms of an aliphatic skeleton.They may also contain ester, ether, amide, acrylic, metal, metalloid and other functionalities; along with hydroxyl groups. Polyols are obtained from many plant and animal sources and are synthesized by a variety of methods. Among important properties of...
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) ; 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...
Influence of H-bonds on acidity of deoxy-hexose sugars
, Article Journal of Physical Organic Chemistry ; Volume 33, Issue 10 , June , 2020 ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2020
Abstract
The unusual monosaccharaides such as deoxy-hexose sugars, including methyl-pentose and aldo-pentose, are promising and important sugars in life science. However, little research on H-bond interactions in these systems has been reported. The aldo-pentose has a proton instead of the CH2OH group on C5; conversely, methyl-pentose has a CH3 group on C5. The aim of the present study is to investigate the role and nature of intramolecular H-bonds on acidity of CH3-pentose sugars (L-fucose and L-rhamnose) and aldo-pentose sugars (D-xylose, L-lyxose, D-ribose, and L-arabinose) using B3LYP/6-311++G (d, p) level. The calculated acidity values (ΔHacid) of these Dexoy-hexose were found to be from 343 to...
Acidity enhancement of α-carbon of beta diketones via hydroxyl substituents: A density functional theory study
, Article Journal of Physical Organic Chemistry ; Volume 34, Issue 3 , 2021 ; 08943230 (ISSN) ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2021
Abstract
Density functional theory method and B3LYP/6-311++G(d,p) level of theory were used to determine the acidity of α-carbon in the hydroxyl derivatives of beta diketones in the gas phase. An investigation of acidity strength in the gas phase indicates that α-carbon of hydroxyl derivatives of beta diketones become stronger acids than the α-carbon of beta diketone itself as their conjugate bases gain more stability via both enolate and hydrogen bond formation. Natural bond orbital and quantum theory of atoms in molecules analyses also confirm the role of hydrogen bond interactions on increasing the acidity of α-carbon of hydroxyl derivatives of beta diketones. © 2020 John Wiley & Sons, Ltd
Computational insight into networking H-bonds in open and cyclic forms of galactose
, Article Journal of Molecular Structure ; Volume 1255 , 2022 ; 00222860 (ISSN) ; Fattahi, A ; Sharif University of Technology
Elsevier B.V
2022
Abstract
In this work, the intramolecular H-bonds in galactose were studied using DFT at the B3LYP/6–311++G (d,p) levels of theory, atoms in molecules (AIM), and natural bond orbital (NBO). AIM and NBO analysis revealed a cooperative network of trifurcated, bifurcated, and normal H-bonds for the conjugate bases of open galactse (O-Gal). While for the conjugate base of the cyclic form of galactose, we identified bifurcated and normal H-bonds, which may highlight a crucial feature of the biological activity of a whole class of natural sugars. The O-H…O bonds are categorized as mostly electrostatic, strong H-bonds and more favorable, whereas for multiple interactions involving C=O…H, C-H…O and C-H…H-C...
What roles do boron substitutions play in structural, tautomeric, base pairing and electronic properties of uracil? NBO & AIM analysis
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 9 , 2012 , Pages 787-796 ; 08943230 (ISSN) ; Abedin, A ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
Wiley
2012
Abstract
The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our...
Amino acid ionic liquids based on imidazolium-hydroxyl functionalized cation: New insight from molecular dynamics simulations
, Article Journal of Molecular Liquids ; Volume 279 , 2019 , Pages 51-62 ; 01677322 (ISSN) ; Sharif University of Technology
Elsevier B.V
2019
Abstract
Various thermodynamic and structural properties of amino acid ionic liquids (AAILs), comprising 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C 2 OHmim] + ) cation mixed with Glycinate [Gly], Serinate [Ser], Alaninate [Ala], and Prolinate [Pro] AA anions are explored using molecular dynamic (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis. In general, the simulated thermodynamic results are in good agreement with the reported experimental data. Structural dependence of vdW- and electrostatic energies of AAILs is [Pro] > [Ala] > [Ser] > [Gly] and [Gly] > [Ala] > [Pro] > [Ser], respectively. The similar trend of electrostatic energies is found for their interaction...