Analytic second derivative of molecular energy with respect to all parameters for floating Gaussi... more Analytic second derivative of molecular energy with respect to all parameters for floating Gaussian type orbitals were proposed for the first time in our group.1 In the present study, further simplification and application has been made and the viability of the method was demonstrated by writing a program and computing the analytic force constant of H 2, LiH and BH molecules. It is shown that this method is efficient both in accuracy and saving in computational time.
There has been much attention on unconventional hydrogen bond in literature, particularly on inte... more There has been much attention on unconventional hydrogen bond in literature, particularly on intermolecular dihydrogen bond. But there is less attention on intra-molecular dihydrogen bond. In this research, we have tried to find some rules in these types of interactions. ...
Based on the linear combination of atomic orbital-molecular orbital by the natural bond orbitals ... more Based on the linear combination of atomic orbital-molecular orbital by the natural bond orbitals (NBO) theory, the attractive donor-acceptor superposition interaction between filled (Lewis-type) and vacant (non-Lewis-type) orbitals provide a general mechanism for quantal energy lowering. This interaction has a direct impact on the quantity of the second-order stabilization energy. Therefore, the valence non-Lewis density (VNLD) index, the electron density of unoccupied valence nonbonding and antibonding orbitals, is introduced as an approach to describe and measure aromaticity. This index is based on the frontier orbital concept. To investigate the validity of the proposed aromaticity index, we selected several test sets of organic and inorganic molecules such as different ring sizes in cyclic and heterocyclic hydrocarbons, and all-metal and semimetal clusters, and compared our findings with previous aromaticity analysis. According to the results, VNLD values are well correlated and anticipated the order of aromaticity with the formerly introduced criteria. Furthermore, VNLD reveals that the rings with π-sextet electrons localized in a ring are more aromatic than the other rings, thus, it is in line with Clar's rule. Our proposed aromaticity index has advantages such as, easy to obtain from NBO analysis, and does not require reference molecules which made it more applicable for realizing the aromaticity order in many organic and inorganic compounds.
This review is dedicated to my PhD supervisor Professor J. W. Linnett, to Professor N. C. Handy w... more This review is dedicated to my PhD supervisor Professor J. W. Linnett, to Professor N. C. Handy who taught me Configuration Interaction (CI) during my postdoctoral period, and to Professor M. J. S. Dewar, who taught me theoretical physical organic chemistry.
The interactions of pure (Au(k), Ag(k), and Cu(k); k = 1-3) and binary alloy (Au(n)Ag(m) and Au(n... more The interactions of pure (Au(k), Ag(k), and Cu(k); k = 1-3) and binary alloy (Au(n)Ag(m) and Au(n)Cu(m); m + n = k <or= 3) metal clusters with hydrogen sulfide (H(2)S) have been investigated by using density functional theory (BP86, B3LYP, and CAM-B3LYP) and ab initio methods (MP2 and CCSD(T)), with a focus on the nature of metal-sulfur bonds. Binding energy calculations indicate that for pure metal clusters, the tendency of metal to interact with H(2)S has the order of Au > Cu > Ag. In binary alloy clusters, alloying Au(k) with copper and silver decreases the attraction of Au toward H(2)S, while alloying Ag(k) and Cu(k) by gold increases the attraction of Ag and Cu toward H(2)S, significantly. Dissociation energy values for isolated metal clusters specify the more favorable formation of binary alloy clusters (Au(n)Ag(m) and Au(n)Cu(m)) over pure ones. The nature of M-S bonds (M = Au, Ag, and Cu) is also interpreted by means of the quantum theory of atoms in molecules (QTAI...
The roadblock on the way to perform the quantum mechanical calculation as the “SCF or DFT” method... more The roadblock on the way to perform the quantum mechanical calculation as the “SCF or DFT” method for some molecules such as drugs, biological molecules, and so on is that these molecules are too large to study. They need a computer with a large amount of system memory and a very fast CPU. Therefore, we are looking for an entirely quantum-mechanical procedure to study the electronic properties of a large molecule with considerable saving computational time and acceptable accuracy. This procedure is based on searching for the active parts of a molecule, which are essentially HOMO and LUMO parts and their surroundings, and is called truncated molecule (TM) in this manuscript. To this end, at first, this procedure is inspected for Mn-complex, due to the availability of its experimental UV spectra. The calculation of the UV spectrum for TM part of Mn-complex shows λmax = 355.64 nm, while experimental UV spectra is λmax = 334.31 nm, and the corresponding theoretical value for the original molecule reveals λmax = 346.99 nm. The CPU time for the original molecule is 448,045 s that is reduced to 101,555 s for TM with acceptable accuracy (the CPU ratio is 4.41). Furthermore, this procedure is also tested for one of the sequences of A-chain of insulin, Docetaxel (drug molecule), and Taxol (drug molecule); the acceptable resemblance between UV spectra of the original and TM molecule is obtained. The computational time is reduced with a ratio of 3.59, 2.44, and 1.69, respectively.
In this study, electronic structures of ground state of pure vanadium sub-nano clusters, Vn (n=2-... more In this study, electronic structures of ground state of pure vanadium sub-nano clusters, Vn (n=2-5), and their interactions with small ligands for example CO and triplet O2 molecules are investigated by using density functional theory (DFT) calibration at the mPWPW91/QZVP level of theory. The favorable orientations of these ligands in interaction with pure vanadium sub-nano clusters were determined. Multiplicities of these pure clusters are triple, doublet, singlet and doublet for dimer, trimer, tetramer and pentamer, respectively. While the CO molecule is associatively adsorbed on vanadium clusters, triplet O2 is dissociated over adsorption. Primary and secondary hyper-conjugation concepts have been employed to show stabilization of vanadium oxide complexes. Natural bond orbital (NBO) and natural resonance theory (NRT) analysis revealed that trimer, tetramer and pentamer clusters are relatively delocalized and have some resonance structures.
This article gives you proof that bimetallic transition metal clusters with the difference in ele... more This article gives you proof that bimetallic transition metal clusters with the difference in electronegativity are better catalysts than monoatomic one. To prove this fact, a study of ethylene adsorption on bimetallic clusters vanadium-nickel VnNim (2≤n+m≤6) has been demonstrated. Our result shows that hardness has a quite good linear correlation with the non-Lewis of VnNi (n=1-5) cluster (R2=0.99). This finding is important, because this is the first time in literature that presents an orbital explanation for hardness. It is possible to see the results of both nickel doped in vanadium cluster and also vanadium doped in nickel cluster. The maximum interaction for these species is for one nickel substituted alloy, VnNi (n=1-5). This finding corresponds to the lowest energy gap between HOMO of bimetallic clusters and LUMO of ethylene, according to Fukui equation of reactivity. A successful demonstration has been performed by extrapolation of theoretical results to predict the best mi...
Abstract This research has been carried out to study and find a rather general description for a ... more Abstract This research has been carried out to study and find a rather general description for a lone pair orbital in molecules. Since the orbital parameters must be manageable in advance, and also the correct geometry of the molecule (bond angle and bond length) is dependent upon the appropriate lone pair description, the FSGO method including optimization has been used to obtain orbital parameters and nuclear coordinates corresponding to minimum energy. Three molecules (NH 3 , H 2 O, and the CH 2 singlet) have been selected to test the proposed description of lone pairs. The results obtained for the bond angle for these molecules are 107.9,104.1,102.2° respectively.
... Isomeric u and A Radicals from Carboxylic Acids and Amides Michael J. S. Dewar,* Ali H. Pakia... more ... Isomeric u and A Radicals from Carboxylic Acids and Amides Michael J. S. Dewar,* Ali H. Pakiari, and Adriana B. Pierinil Department of Chemistry The University of Texas at Austin, Austin, Texas 7871 2 Received August 10, 1981 ... (4) (a) Day, JC; Katsaros, M. G.; Kocher, W. D ...
Analytic second derivative of molecular energy with respect to all parameters for floating Gaussi... more Analytic second derivative of molecular energy with respect to all parameters for floating Gaussian type orbitals were proposed for the first time in our group.1 In the present study, further simplification and application has been made and the viability of the method was demonstrated by writing a program and computing the analytic force constant of H 2, LiH and BH molecules. It is shown that this method is efficient both in accuracy and saving in computational time.
There has been much attention on unconventional hydrogen bond in literature, particularly on inte... more There has been much attention on unconventional hydrogen bond in literature, particularly on intermolecular dihydrogen bond. But there is less attention on intra-molecular dihydrogen bond. In this research, we have tried to find some rules in these types of interactions. ...
Based on the linear combination of atomic orbital-molecular orbital by the natural bond orbitals ... more Based on the linear combination of atomic orbital-molecular orbital by the natural bond orbitals (NBO) theory, the attractive donor-acceptor superposition interaction between filled (Lewis-type) and vacant (non-Lewis-type) orbitals provide a general mechanism for quantal energy lowering. This interaction has a direct impact on the quantity of the second-order stabilization energy. Therefore, the valence non-Lewis density (VNLD) index, the electron density of unoccupied valence nonbonding and antibonding orbitals, is introduced as an approach to describe and measure aromaticity. This index is based on the frontier orbital concept. To investigate the validity of the proposed aromaticity index, we selected several test sets of organic and inorganic molecules such as different ring sizes in cyclic and heterocyclic hydrocarbons, and all-metal and semimetal clusters, and compared our findings with previous aromaticity analysis. According to the results, VNLD values are well correlated and anticipated the order of aromaticity with the formerly introduced criteria. Furthermore, VNLD reveals that the rings with π-sextet electrons localized in a ring are more aromatic than the other rings, thus, it is in line with Clar's rule. Our proposed aromaticity index has advantages such as, easy to obtain from NBO analysis, and does not require reference molecules which made it more applicable for realizing the aromaticity order in many organic and inorganic compounds.
This review is dedicated to my PhD supervisor Professor J. W. Linnett, to Professor N. C. Handy w... more This review is dedicated to my PhD supervisor Professor J. W. Linnett, to Professor N. C. Handy who taught me Configuration Interaction (CI) during my postdoctoral period, and to Professor M. J. S. Dewar, who taught me theoretical physical organic chemistry.
The interactions of pure (Au(k), Ag(k), and Cu(k); k = 1-3) and binary alloy (Au(n)Ag(m) and Au(n... more The interactions of pure (Au(k), Ag(k), and Cu(k); k = 1-3) and binary alloy (Au(n)Ag(m) and Au(n)Cu(m); m + n = k <or= 3) metal clusters with hydrogen sulfide (H(2)S) have been investigated by using density functional theory (BP86, B3LYP, and CAM-B3LYP) and ab initio methods (MP2 and CCSD(T)), with a focus on the nature of metal-sulfur bonds. Binding energy calculations indicate that for pure metal clusters, the tendency of metal to interact with H(2)S has the order of Au > Cu > Ag. In binary alloy clusters, alloying Au(k) with copper and silver decreases the attraction of Au toward H(2)S, while alloying Ag(k) and Cu(k) by gold increases the attraction of Ag and Cu toward H(2)S, significantly. Dissociation energy values for isolated metal clusters specify the more favorable formation of binary alloy clusters (Au(n)Ag(m) and Au(n)Cu(m)) over pure ones. The nature of M-S bonds (M = Au, Ag, and Cu) is also interpreted by means of the quantum theory of atoms in molecules (QTAI...
The roadblock on the way to perform the quantum mechanical calculation as the “SCF or DFT” method... more The roadblock on the way to perform the quantum mechanical calculation as the “SCF or DFT” method for some molecules such as drugs, biological molecules, and so on is that these molecules are too large to study. They need a computer with a large amount of system memory and a very fast CPU. Therefore, we are looking for an entirely quantum-mechanical procedure to study the electronic properties of a large molecule with considerable saving computational time and acceptable accuracy. This procedure is based on searching for the active parts of a molecule, which are essentially HOMO and LUMO parts and their surroundings, and is called truncated molecule (TM) in this manuscript. To this end, at first, this procedure is inspected for Mn-complex, due to the availability of its experimental UV spectra. The calculation of the UV spectrum for TM part of Mn-complex shows λmax = 355.64 nm, while experimental UV spectra is λmax = 334.31 nm, and the corresponding theoretical value for the original molecule reveals λmax = 346.99 nm. The CPU time for the original molecule is 448,045 s that is reduced to 101,555 s for TM with acceptable accuracy (the CPU ratio is 4.41). Furthermore, this procedure is also tested for one of the sequences of A-chain of insulin, Docetaxel (drug molecule), and Taxol (drug molecule); the acceptable resemblance between UV spectra of the original and TM molecule is obtained. The computational time is reduced with a ratio of 3.59, 2.44, and 1.69, respectively.
In this study, electronic structures of ground state of pure vanadium sub-nano clusters, Vn (n=2-... more In this study, electronic structures of ground state of pure vanadium sub-nano clusters, Vn (n=2-5), and their interactions with small ligands for example CO and triplet O2 molecules are investigated by using density functional theory (DFT) calibration at the mPWPW91/QZVP level of theory. The favorable orientations of these ligands in interaction with pure vanadium sub-nano clusters were determined. Multiplicities of these pure clusters are triple, doublet, singlet and doublet for dimer, trimer, tetramer and pentamer, respectively. While the CO molecule is associatively adsorbed on vanadium clusters, triplet O2 is dissociated over adsorption. Primary and secondary hyper-conjugation concepts have been employed to show stabilization of vanadium oxide complexes. Natural bond orbital (NBO) and natural resonance theory (NRT) analysis revealed that trimer, tetramer and pentamer clusters are relatively delocalized and have some resonance structures.
This article gives you proof that bimetallic transition metal clusters with the difference in ele... more This article gives you proof that bimetallic transition metal clusters with the difference in electronegativity are better catalysts than monoatomic one. To prove this fact, a study of ethylene adsorption on bimetallic clusters vanadium-nickel VnNim (2≤n+m≤6) has been demonstrated. Our result shows that hardness has a quite good linear correlation with the non-Lewis of VnNi (n=1-5) cluster (R2=0.99). This finding is important, because this is the first time in literature that presents an orbital explanation for hardness. It is possible to see the results of both nickel doped in vanadium cluster and also vanadium doped in nickel cluster. The maximum interaction for these species is for one nickel substituted alloy, VnNi (n=1-5). This finding corresponds to the lowest energy gap between HOMO of bimetallic clusters and LUMO of ethylene, according to Fukui equation of reactivity. A successful demonstration has been performed by extrapolation of theoretical results to predict the best mi...
Abstract This research has been carried out to study and find a rather general description for a ... more Abstract This research has been carried out to study and find a rather general description for a lone pair orbital in molecules. Since the orbital parameters must be manageable in advance, and also the correct geometry of the molecule (bond angle and bond length) is dependent upon the appropriate lone pair description, the FSGO method including optimization has been used to obtain orbital parameters and nuclear coordinates corresponding to minimum energy. Three molecules (NH 3 , H 2 O, and the CH 2 singlet) have been selected to test the proposed description of lone pairs. The results obtained for the bond angle for these molecules are 107.9,104.1,102.2° respectively.
... Isomeric u and A Radicals from Carboxylic Acids and Amides Michael J. S. Dewar,* Ali H. Pakia... more ... Isomeric u and A Radicals from Carboxylic Acids and Amides Michael J. S. Dewar,* Ali H. Pakiari, and Adriana B. Pierinil Department of Chemistry The University of Texas at Austin, Austin, Texas 7871 2 Received August 10, 1981 ... (4) (a) Day, JC; Katsaros, M. G.; Kocher, W. D ...
Uploads
Papers by Ali Pakiari