Ali Pakiari - Academia.edu (original) (raw)

Papers by Ali Pakiari

International Journal of Modern Physics C, 2002

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.

Journal of Molecular Structure: THEOCHEM, 2004

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. ...

Journal of Molecular Graphics and Modelling, 2021

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.

Structural Chemistry, 2015

Electronic and geometrical structures of small Cobalt cluster (Co n , n = 2-5), which were used a... more Electronic and geometrical structures of small Cobalt cluster (Co n , n = 2-5), which were used as building block in Cobalt cluster compounds, were fully investigated in this article. Since small Cobalt clusters as a nanoparticle have many applications in scientific works and technology, it is essential for understanding their relatively accurate electronic structure. The most stable symmetrically and electronically structure confirmed by frequency test for studied clusters is as follows: 5-et (quintet) Co 2 is of course linear, and its HOMOs described by degenerate d xy orbitals in b-spin part located on both atoms; 8-et (octet) Co 3 is almost scalene triangle and its HOMO in s-orbital of a-spin part located on Co (1) ; 11-et Co 4 is rhombus, d xz orbital of bspin part located on Co (2) is its HOMO part. 12-et Co 5 is pyramidal with HOMO in p x orbital located on Co (5) in bspin part, which show very low (0.06) occupation number. This large depletion of electron in HOMO occupation of Co 5 explains high chemical reactivity of this species. Density functional theory, DFT, was used through software Gaussian 09. Xc-correlation functional was chosen among the many recommended xc-functionals for transition metal in the literature by calibration procedure in such a way that the results can match with experimental values. So suitable xc-functional B3P86 and 6-311??G* basis set were found. Natural bond orbital, NBO, has also been used for analysis.

Journal of Molecular Graphics and Modelling, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Journal of Molecular Graphics and Modelling, 2019

In the present work, the p and p *-electronic nature of substitution constants (s) of the twenty-... more In the present work, the p and p *-electronic nature of substitution constants (s) of the twenty-two monosubstituted benzene derivatives (MSBDs) are estimated in terms of the para-delocalization index (PDI) and total non-Lewis structure (TNLS), respectively. Since these compounds are aromatic, the other descriptors of aromaticity such as nuclear independent chemical shifts and aromatic stabilization energy have been examined. Because of no considerable variation for the p and p *-electron delocalization in the ring systems, a very weak correlation has been demonstrated between all aromaticity indices. Also, none of these descriptors has a linear correlation with the values of s for both electron-donating groups (EDGs) and electron-withdrawing groups (EWGs) in a simultaneous relationship. We now propose the usage of the dipole moments values of molecules, considering their directions, by multiplying the PDI and TNLS values as probes to interpret s values for benzene and MSBDs since the dipole moment can affect the p and p *-electron delocalization. It is interesting to note that there is a remarkable linear correlation between our suggested probes, ±mPDI and ±mTNLS, and s p , s m , and s þ =s À for EDGs and EWGs in simultaneous linear relationships. Also, these probes have a relative relationship with Kirkwood and Westheimer equation. Additionally, the regression coefficient between ±mPDI and ±mTNLS is 0.989.

Chemical Modelling

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.

Computational and Theoretical Chemistry, 2016

In this study, electronic structures of ground state of pure vanadium sub-nano clusters, V n (n =... more In this study, electronic structures of ground state of pure vanadium sub-nano clusters, V n (n = 2-5), and their interactions with small ligands, CO and triplet O 2 molecules, are investigated 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 O 2 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) analyses revealed that trimer, tetramer and pentamer clusters are relatively delocalized and have some resonance structures.

The journal of physical chemistry. A, Jan 2, 2010

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...

Journal of the Iranian Chemical Society, 2010

Adenosine 5 '-triphosphate (ATP) and Guanine 5 '-triphosphate (GTP), which are highly significant... more Adenosine 5 '-triphosphate (ATP) and Guanine 5 '-triphosphate (GTP), which are highly significant species for biological system as sources of energy, along with two other compounds, ribose 5 '-triphosphate (RTP) and triposphate (TP), have been investigated theoretically. The capability of releasing terminal phosphoric acid and existent intramolecular bonds in their structure have been studied in gas phase. Due to the presence of hydrogen bonds in the above molecules, several inner and stable rings have been formed by atoms in molecules. The Quantum Theory of Atoms in Molecules (QTAIM) has been used in order to discover the intramolecular interactions properties in terms of charge densities. We have also demonstrated that the release of terminal phosphoric acid in ATP and GTP are both facilitated in the presence of ribose and base in comparison with TP and RTP. Our calculations have been done using density functional procedure.

Journal of Molecular Modeling, 2021

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.

Journal of Molecular Graphics and Modelling, 2018

This article provides some evidence on higher catalytic activity of bimetallic transition metal c... more This article provides some evidence on higher catalytic activity of bimetallic transition metal clusters, with a difference in electronegativity, compared to the monoatomic clusters. In this respect, adsorption of ethylene on bimetallic clusters of vanadium-nickel V n Ni m (2 ≤ n + m ≤ 6) is investigated. Our results show that hardness has a quite good linear correlation with the non-Lewis MO of V n Ni (n = 1-5) cluster (R 2 = 0.99). This finding is of particular importance, because, for the first time in literature, it presents an orbital description for hardness. The optimized structure of pure and nickel-doped vanadium clusters and pure and vanadium-doped nickel clusters are studied for up to six atoms. The maximum interaction belongs to nickel substituted alloy, V n Ni (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 mixing of two metals revealing that V 8 Ni is the best cluster if it is sable experimentally. We have also demonstrated that the larger bimetallic cluster has more conductivity and reactivity which is the demonstration of nano character.

Journal of Molecular Structure: THEOCHEM, 2003

In this research, we will introduce non-Walsh type B and extra five driving forces in molecular g... more In this research, we will introduce non-Walsh type B and extra five driving forces in molecular geometry determination, and demonstrate them in this paper. The question first came to our mind when we considered that CH 3 radical has planar structure, but SiH 3 radical is in bent form, while both molecules have an electron on central atom from Lewis structure viewpoint, and they must have bent structure according to Walsh rule. We will show three contrasts in current theory; there are many molecules which do not follow Lewis valence theory and Walsh rule, and also they have spin multiplicity, but they do not show torsion in molecule. Therefore, we are looking for some types of existing interactions between different molecular orbitals in particular type of category of molecules: AX 3 , AH 2 X and AHX 2 in the form of radical, cation and anions, where A is C, Si, Ge, N or P atom, and X is F, Cl or Br atom. In spite of studying one category of compound in this article, a generalized method for investigation of these types of interactions will be presented, which can be used in other similar cases. We will demonstrate the reasons for such molecules having particular geometry, which are caused by some interactions such as lone pair of X-atom with radical electron on A-atom, lone pair of X and s-bond, hybridization of electrons on central atom, back bonding and spin multipilicity. B3lyp with 6-311G** basis set have been applied to our calculations, and atom in molecule (AIM), natural bond orbital (NBO), are also used for the results analysis.

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.

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

Computational and Theoretical Chemistry

J Am Chem Soc, 1982

... 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 ...