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CHEMISTRY (590 journals)            First | 1 2 3 4 5 6 | Last

European Journal of Histochemistry     Open Access   (Followers: 2)
European Journal of Medicinal Chemistry     Hybrid Journal   (Followers: 13)
European Online Journal of Natural and Social Sciences     Open Access   (Followers: 14)
Faraday Discussions     Full-text available via subscription   (Followers: 2)
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Fluid Phase Equilibria     Hybrid Journal   (Followers: 4)
Fluorescent Materials     Open Access   (Followers: 1)
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Foundations of Chemistry     Hybrid Journal   (Followers: 3)
Frontiers in Chemistry     Open Access   (Followers: 1)
Frontiers of Chemical Science and Engineering     Hybrid Journal   (Followers: 1)
Frontiers of Chemistry in China     Hybrid Journal   (Followers: 2)
Fullerenes, Nanotubes and Carbon Nanostructures     Hybrid Journal   (Followers: 4)
Fundamentals of Interface and Colloid Science     Full-text available via subscription   (Followers: 6)
Future Medicinal Chemistry     Full-text available via subscription   (Followers: 4)
Gels     Open Access  
Geochemical Transactions     Open Access   (Followers: 2)
GFF     Hybrid Journal  
Global Journal of Chemistry     Open Access   (Followers: 1)
Glycobiology Insights     Open Access   (Followers: 1)
Graphene     Open Access   (Followers: 10)
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Green and Sustainable Chemistry     Open Access   (Followers: 4)
Green Chemistry Letters and Reviews     Open Access   (Followers: 4)
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Handbook of Exploration and Environmental Geochemistry     Full-text available via subscription   (Followers: 1)
Handbook of Exploration Geochemistry     Full-text available via subscription  
Handbook of Surface Science     Full-text available via subscription   (Followers: 3)
Handbook of Vapor Pressure     Full-text available via subscription  
Helvetica Chimica Acta     Hybrid Journal   (Followers: 11)
Heritage Science     Open Access   (Followers: 4)
Heteroatom Chemistry     Hybrid Journal   (Followers: 2)
High Energy Chemistry     Hybrid Journal  
Hungarian Journal of Industry and Chemistry     Open Access  
Hydrogels     Open Access  
Indian Chemical Engineer     Hybrid Journal   (Followers: 3)
Indian Journal of Chemical Technology (IJCT)     Open Access   (Followers: 11)
Indian Journal of Chemistry - Section B (IJC-B)     Open Access   (Followers: 6)
Indian Journal of Natural Products and Resources (IJNPR)     Open Access   (Followers: 3)
Indonesian Journal of Chemical Science     Open Access  
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Industrial Chemistry Library     Full-text available via subscription   (Followers: 5)
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Inorganica Chimica Acta     Hybrid Journal   (Followers: 5)
Instrumentation Science & Technology     Hybrid Journal   (Followers: 4)
International Archives of Science and Technology     Open Access  
International Journal for Ion Mobility Spectrometry     Hybrid Journal   (Followers: 1)
International Journal of Adhesion and Adhesives     Hybrid Journal   (Followers: 14)
International Journal of Advanced Chemistry     Open Access  
International Journal of Analytical Mass Spectrometry and Chromatography     Open Access   (Followers: 5)
International Journal of Bioassays     Open Access   (Followers: 5)
International Journal of Biological and Chemical Sciences     Open Access   (Followers: 5)
International Journal of Biological Chemistry     Open Access   (Followers: 4)
International Journal of Biomedical Nanoscience and Nanotechnology     Hybrid Journal   (Followers: 6)
International Journal of Carbohydrate Chemistry     Open Access   (Followers: 7)
International Journal of Chemical and Analytical Science     Full-text available via subscription   (Followers: 4)
International Journal of Chemical and Life Sciences     Open Access   (Followers: 4)
International Journal of Chemical Kinetics     Hybrid Journal   (Followers: 5)
International Journal of Chemical Technology     Open Access   (Followers: 4)
International Journal of Chemistry     Open Access   (Followers: 9)
International Journal of Chemoinformatics and Chemical Engineering     Full-text available via subscription   (Followers: 2)
International Journal of Corrosion     Open Access   (Followers: 12)
International Journal of High Throughput Screening     Open Access   (Followers: 2)
International Journal of Materials and Chemistry     Open Access   (Followers: 5)
International Journal of Medicinal Chemistry     Open Access   (Followers: 8)
International Journal of Minerals, Metallurgy, and Materials     Hybrid Journal   (Followers: 11)
International Journal of Molecular Imaging     Open Access   (Followers: 1)
International Journal of Molecular Sciences     Open Access   (Followers: 1)
International Journal of Nano Dimension     Open Access   (Followers: 2)
International Journal of Nonferrous Metallurgy     Open Access   (Followers: 2)
International Journal of Photochemistry     Open Access   (Followers: 1)
International Journal of Photoenergy     Open Access   (Followers: 2)
International Journal of Physical Sciences     Open Access  
International Journal of Spray and Combustion Dynamics     Full-text available via subscription   (Followers: 7)
International Journal of Tryptophan Research     Open Access   (Followers: 1)
International Letters of Chemistry, Physics and Astronomy     Open Access  
Iranian Polymer Journal     Hybrid Journal   (Followers: 5)
Israel Journal of Chemistry     Full-text available via subscription   (Followers: 2)
JBIC Journal of Biological Inorganic Chemistry     Hybrid Journal   (Followers: 4)
JCP : BioChemical Physics     Hybrid Journal   (Followers: 2)
JOT Journal für Oberflächentechnik     Hybrid Journal  
JOT-International Surface Technology     Hybrid Journal   (Followers: 2)
Journal of Chromatography & Separation Techniques     Open Access   (Followers: 10)
Journal of Thermodynamics & Catalysis     Open Access   (Followers: 4)
Journal of Adhesion     Hybrid Journal   (Followers: 7)
Journal of Adhesion Science and Technology     Hybrid Journal   (Followers: 7)
Journal of Advanced Oxidation Technologies     Full-text available via subscription   (Followers: 1)
Journal of Advances in Chemistry     Open Access   (Followers: 5)
Journal of Agricultural and Food Chemistry     Full-text available via subscription   (Followers: 19)
Journal of Agricultural Chemistry and Environment     Open Access  
Journal of Amino Acids     Open Access   (Followers: 3)
Journal of Analytical Methods in Chemistry     Open Access  
Journal of Analytical Sciences, Methods and Instrumentation     Open Access   (Followers: 1)
Journal of AOAC International     Full-text available via subscription   (Followers: 8)

  First | 1 2 3 4 5 6 | Last

Journal Cover   Journal of Theoretical and Computational Chemistry
  [SJR: 0.364]   [H-I: 17]   [8 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0219-6336 - ISSN (Online) 1793-6888
   Published by World Scientific Homepage  [120 journals]
  • Theoretical insight into the interplay between lithium and
           halogen–hydride bonds: An ab initio study
    • Authors: Morteza Vatanparast, Mohammad Taghi Taghizadeh, Elahe Parvini
      Abstract: Journal of Theoretical and Computational Chemistry, Volume 14, Issue 06, September 2015.
      Quantum chemical calculations have been performed to analyze the intermolecular interactions in the ternary NCLi⋯NCX⋯HMgY complexes (X = F, Cl, Br; Y = H, F, Cl, Br, Li). A cooperative effect is observed between the lithium and halogen–hydride bonds in these complexes. The cooperative energy ranges from -1.81 kJ/mol to -5.21 kJ/mol, -3.59 kJ/mol to -9.86 kJ/mol and -4.77 kJ/mol to -14.27 kJ/mol for X = F, Cl and Br, respectively (at MP2/6-311++G(d,p) level). The geometrical and interaction energies analysis reveal that the lithium bond has a greater enhancing effect on the halogen–hydride bond. The results of many-body analysis indicate that two- and three-body interaction energies have a positive contribution to the total interaction energy. The electronic characteristics of the complexes have been analyzed through molecular electrostatic potential (MEP), atoms in molecules (AIM), electron localization function (ELF) and natural bond orbital (NBO) methodologies. • Cooperativity effect between lithium and halogen–hydride bonds was investigated. • The cooperative energy ranges from −1.81 to −14.27 kJ/mol. • Molecular electrostatic potential is used to rationalize the cooperativity effect.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-01T06:55:42Z
      DOI: 10.1142/S0219633615500467
  • DFT Calculations on polarizabilities and hyperpolarizabilities for the
           neutral and anionic yttrium oxide clusters
    • Authors: Ambigapathy Suvitha, Natarajan Sathiyamoorthy Venkataramanan
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      The electronic properties, polarizabilities, first and second hyperpolarizabilities of YOn clusters of n = 1–12 were studied using the quantum chemical method. The vertical ionization potential (VIP) values for the anionic clusters increase monotonically with the cluster size. Among the neutral clusters YO3 and YO8 have the least chemical hardness values, where in anionic clusters with size n < 4 possesses the least chemical hardness. Anionic clusters have more electrons attracting tendency than the neutral clusters. The computed static mean polarizability of neutral yttrium oxides has positive values but is close to zero. The incorporation of oxygen atom quenches the polarizability of yttrium. The computed polarizability anisotropy of neutral clusters shows an oscillatory effect both at static and at dynamic conditions. The first hyperpolarizability for many YOn clusters are close to zero. The existence of high symmetry in these clusters reduces the first hyperpolarizability values which was supported by the small dipole moments. The computed γ values for the static neutral and anionic clusters show only a small variation. The decrease in the polarizability and second hyperpolarizability with size can be interpreted in terms of the electronic delocalization and chemical bonding in the clusters.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-28T02:29:56Z
      DOI: 10.1142/S0219633615500492
  • Theoretical design of
           benzo[1,2-b:3,4-b[math]:5,6-b[math]]tristhianaphthene and its derivatives
           as high performance organic semiconductors
    • Authors: Jun Yin, Kadali Chaitanya, Xue-Hai Ju
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      In order to probe the effects of substituents (F and CN) attached to benzo[1,2-b:3,4-[math]:5,6-[math]]tristhianaphthene (BTTP) on their charge carrier transport properties, we investigated the characteristics of molecular structures and charge transport properties of BTTP and its derivatives (BTTP1, BTTP2, BTTP3, BTTP4, and BTTP5). Six crystal structures were predicted by the Monte Carlo-simulated annealing method with the embedded electrostatic potential charges method. Even a subtle change of geometrical structures may result in a great change of the reorganization energy. With increasing numbers of substituted fluorine atoms, the reorganization energy of the BTTP derivative increases, which is disadvantageous to the electron transport. In contrast, the attachment of the electron-withdrawing cyano groups to BTTP decreases the reorganization energy and raises the electron affinity, which is beneficial to electron injection and charge carrier stabilization. The introduction of cyano groups also results in an enhancement of [math]–[math] interaction and leads to an increase in the transfer integrals. Among the six compounds, the novel compound BTTP4 has the largest electron mobility (1.154[math]cm[math]) on account of its larger transfer integral and smaller reorganization energy, indicating that BTTP4 is a promising high-performance n-type organic semiconductor and worth to synthesize. The analysis of angular-resolution anisotropic mobilities for the BTTP and BTTP4 shows that it is helpful to control the orientations of the conducting channels for a better charge transport efficiency. This work provides a rational strategy for the design of high-performance n-type organic semiconductors from molecule to crystal structure.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-13T09:30:04Z
      DOI: 10.1142/S0219633615500583
  • Comparison of the selectivity of [M(12-Crown-4)][math] (M=Li[math],
           Na[math], K[math]) complexes for halide anions and some neutral molecules;
           a computational study
    • Authors: Faranak Dastineh, Sadegh Salehzadeh, Mehdi Bayat, Yazdan Maghsoud
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      A theoretical study on the selectivity of a series of [M(12C4)][math] (M = Li[math], Na[math], K[math], 12C4 = 12-crown-4) complexes for F[math], Cl[math] and Br[math] anions and a number of neutral molecules (CH3CN, CH3OH, NH3, H2O, py, and 12C4) is reported. At first, it was shown that in the gas phase among all studied halide anions and neutral molecules, halides have much more bonding interaction with all [M(12C4)][math] cations. Calculated interaction energies of above anions and [M(12C4)][math] cations decrease from F[math] to Br[math]. Also the interaction energy of halide anions with [M(12C4)][math] complexes, decreases from [Li(12C4)][math] to [K(12C4)][math]. The electron decomposition analysis showed that the bond between [M(12C4)][math] complexes and both the neutral and anion guests is mainly electrostatic in nature. Then the selectivity of [M(12C4)][math] complexes for studied anions and neutral molecules are compared in methanol, acetone, acetonitrile, and nitromethane solutions. It was shown that both the desolvation process of reactants and the strength of host–guest interactions have significant effect on the selectivities. Thus the selectivity of [Li(12C4)][math] cation for NH3 and H2O neutral molecules in solution, in contrast to the gas phase, is higher than that for bromide anion. The results of calculations showed that all [M(12C4)][math] complexes, specially [Li(12C4)][math], have high selectivity for F[math] over other halide anions and neutral molecules.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-12T02:12:10Z
      DOI: 10.1142/S0219633615500571
  • QM/MM description of periodic systems
    • Authors: K. Doll, T. Jacob
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-07T02:55:06Z
      DOI: 10.1142/S0219633615500546
  • In silico modeling of aspalathin and nothofagin against SGLT2
    • Authors: Wei Liu, Huanjie Wang, Fancui Meng
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Aspalathin and nothofagin are the major dihydrochalcones found in rooibos (Aspalathus linearis), which display anti-diabetic activities, but the mechanism is still unclear. In this paper, hSGLT2 (human sodium dependent glucose co-transporter 2), a target for diabetes mellitus, was built using homology modeling method. Molecular docking and dynamics simulations were carried out on aspalathin, nothofagin and SGLT2 complexes with dapagliflozin as positive control. The results show that both the binding energies and binding modes of aspalathin and nothofagin are similar to dapagliflozin, indicating that either component of rooibos may exhibit anti-diabetic effects through inhibiting SGLT2 receptor. However, the predicted permeability value of aspalathin and nothofagin is low, which may cause poor absorption, resulting in weak SGLT2 inhibition. Calculation results elucidate the possible inhibiting mechanism of aspalathin and nothofagin against SGLT2, and therefore enhance our understanding of anti-diabetic activities of rooibos.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-07T02:55:05Z
      DOI: 10.1142/S021963361550056X
  • Assessing density functionals for the prediction of thermochemistry of
           Ti–O–Cl species
    • Authors: Yingbin Ge, Douglas DePrekel, Kui-Ting Lam, Kevin Ngo, Phu Vo
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Titanium dioxide (TiO2) nanoparticles are widely used in contaminant remediation, photocatalysis and solar cell manufacturing. The low-cost production of TiO2 nanoparticles via the combustion of titanium tetrachloride (TiCl4) in oxygen is thus an important industrial process. To accurately model the flame synthesis of TiO2 nanoparticles, reliable thermodynamic data of Ti–O–Cl species are indispensable but often unavailable. We therefore carried out benchmark calculations, using the left-eigenstate completely renormalized singles, doubles and perturbative triples (CR-CC(2,3), aka CR-CCL) method with the cc-pVTZ basis set, to obtain the equilibrium structures and vibrational frequencies of selected Ti–O–Cl species; we then performed single-point CCSD(T)/aug-cc-pVLZ ([math]–5) calculations to extrapolate the CCSD(T)/CBS energies. After analyzing the experimental and calculated enthalpy of selected Ti–O–Cl species, the standard enthalpy of formation of the TiOCl2 molecule is determined to be [math]600.5[math]kJ/mol at 298[math]K. The standard enthalpy of all other Ti–O–Cl species are determined accordingly. Finally, we assessed the accuracy of 42 popular density functionals for the Ti–O–Cl species. Among these assessed functionals, the B98 functional, tightly followed by B97-1 and B3LYP, exhibits the best overall performance in the prediction of the thermochemistry of the Ti–O–Cl species.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-07T02:55:04Z
      DOI: 10.1142/S0219633615500558
  • Comprehensive modeling of the antioxidant mechanism of ebselen
    • Authors: Jun-Hao Jiang, Hui Zhou, Hui-Jie Li, Yu-Chun Wang, Mei Tian, Ya-Lin Huang, Ping Deng
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Three possible catalytic cycles for ebselen have been comprehensively modeled by theoretical calculations using density functional theory (DFT) at a mixed basis set level; the 6-31G(d) basis set for hydrocarbon fragments and the 6-31++G(d,p) basis set for other atoms. The 2 → 3 → 3′ → 3″ → 4′ → 4 → 2 cycle is the main pathway in the glutathione peroxidase (GPx) cycle (cycle A), and IM3→TS3 is the rate controlling process. The 1 → 5 → 8 → 8″ → 1 cycle is the main pathway for the oxidation cycle (cycle B), and the rate controlling step is the 8″ → 1 step. Ebselen reacts with the selenol 3 to form the diselenide 9, and this is the rate controlling step for cycle C. The extremely high energy barrier for the IM9→TS9 process indicates that cycle C is unlikely to occur in vivo. Although cycle B is favored based on the energy analysis, with a maximum energy barrier of only 26.68 kcal/mol at the mixed basis set level, it is generally unlikely to have very high concentrations of peroxides present in vivo. The results indicate that in order to improve the antioxidant activity of ebselen, it would be necessary to suitably modify the molecular structure of ebselen to reduce the energy barrier of the IM3→TS3 process.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-07T02:55:04Z
      DOI: 10.1142/S0219633615500534
  • Halogen and solvent effects on the conformational, vibrational and
           electronic properties of 1,4-diformylpiperazine: A combined experimental
           and DFT study
    • Authors: Cemal Parlak, Mahir Tursun, Chandraju Sadolalu Chidan Kumar, Duygu Bilge, Nadide Kazanci, Lydia Rhyman, Ponnadurai Ramasami
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      The molecular structure and properties of 1,4-diformylpiperazine (1,4-dfp, C6H10N2O2) were investigated by Fourier transform infrared (FT-IR) spectroscopy, Raman spectroscopy and density functional theory (DFT). The Becke-3-Lee–Yang–Parr (B3LYP) functional was used with the 6-31++G(d,p) basis set. Total energy distribution (TED) analysis of normal modes was performed to identify characteristic frequencies by the scaled quantum mechanical (SQM) method. Halogeno-analogs of 1,4-dfp were studied to understand the halogen effect. Computations were focused on five conformational isomers of the compounds in the gas phase and in solutions. The computed and experimental frequencies of the C=O stretching vibration of 1,4-dfp were correlated with the empirical solvent parameters such as the Kirkwood–Bauer–Magat (KBM) equation, the solvent acceptor number (AN), Swain parameters and linear solvation energy relationships (LSER). The electronic properties of the compounds were also examined. The findings from the present work may be useful to understand systems involving the halogens and conformational changes analogous to the compounds investigated.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-01T02:38:58Z
      DOI: 10.1142/S0219633615500509
  • Theoretical study of the structure, spectroscopic properties and
           anti-cancer activity of tetrahydrochromeno[4,3-b]quinolines
    • Authors: Ahmed Taki Eddine Ardjani, Sidi Mohamed Mekelleche
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      In the present work, a theoretical study of the geometrical structures and spectroscopic (IR, 1H and 13C NMR, UV-visible) properties, and anti-cancer activity of cis-fused tetrahydrochromeno[4,3-b]quinolines have been performed. The equilibrium geometries have been optimized at the B3LYP/6-31G(d) computational level and the present study puts in evidence the stability preference of the cis stereoisomers in comparison with the trans ones as expected experimentally. The vibrational frequencies and IR spectra were calculated at the same level of theory and compared to experimental FT-IR spectra and the spectral peaks have been assigned on the basis of potential energy distribution results. UV-visible absorption bands were calculated using the TD-DFT/B3LYP/6-31G(d) method. The 13C nuclear magnetic resonance chemical shifts and the coupling constants were calculated at the B3LYP level using the gauge independent atomic orbital (GIAO) method in chloroform solvent. The 1H chemical shifts were calculated using the recently proposed WP04/6-31G(d) DFT functional. The visualization of the molecular electrostatic potential (MEP) surfaces and the docking simulation show that the absence of the methyl group at 2-position of tetrahydrochromeno[4,3-b]quinoline moiety is responsible of the potential anti-cancer activity of this compound.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-01T02:38:57Z
      DOI: 10.1142/S0219633615500522
  • Modeling reactivation of the phosphorylated human butyrylcholinesterase by
           QM(DFTB)/MM calculations
    • Authors: Anna Kulakova, Sofya Lushchekina, Bella Grigorenko, Alexander Nemukhin
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Human butyrylcholinesterase (BChE) is a bioscavenger that protects the enzyme which is critical for the central nerve system, acetylcholinesterase, from poisoning by organophosphorus agents. Elucidating the details of the hydrolysis reaction mechanism is important to understand how the phosphorylated BChE can be reactivated. Application of the QM(DFTB)/MM(AMBER) method to construct the minimum energy pathways for the hydrolysis reaction of the diethylphosphorylated BChE allowed us to suggest a mechanism of reactivation of the wild-type and the G117H mutated enzyme. Unlike previous approaches assuming that either His438 or His117 serves as a general base in the catalysis, in our proposal the Glu197 residue is responsible for activation of the nucleophilic water molecule (Wat) leading to the chemical transformations that restore the catalytic Ser198 residue in BChE. In agreement with the experimental data, it is shown that the G117H mutation facilitates the reactivation of the inhibited enzyme.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-10-01T02:38:57Z
      DOI: 10.1142/S0219633615500510
  • QM study of complexation between natural bilirubin and poly-terthiophene
           carboxylic acid–Mn(II) as a biosensor: Temperature and interferences
    • Authors: Mina Ghiasi, Masoumeh Molaei, Mansour Zahedi
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Bilirubin is an insoluble yellow pigment produced from heme catabolism and serves as a diagnostic marker of liver and blood disorders. Here, a systematic study of several interactions and arrangements between different forms of natural bilirubin and poly-5, 2′-5′, 2′′-terthiophene-3-carboxylic acid/Mn(II)2 complex, PTTCA–Mn(II)2, as a biosensor of bilirubin has been investigated extensively. The PTTCA–Mn(II)2 biosensor detects natural bilirubin through the mediated electron transfer by the Mn2+. Initially, density functional theory (DFT) using B3LYP and different basis sets including 6-31G* and 6-311G** has been employed to calculate the details of electronic structure and electronic energies of natural biliverdin and δ-, β- and γ-bilirubin. Next, the interaction of the PTTCA–Mn(II)2 biosensor, being in three possible spin states, with δ-, β- and γ-natural bilirubin with 1:1 and 1:2 stoichiometry using UB3LYP/6-31G* method has been investigated. Natural population analysis (NPA) calculations have been used to derive more suitable interaction sites of bilirubin with Mn2+ ions in PTTCA–Mn(II)2 biosensor. Investigation of different manganese complexes with bilirubin shows that the most stable complex is high spin state (total electron spin S = 5/2) rather than intermediate and low spin states with 1:2 stoichiometry. Also, the temperature effect and interferences from other biological compounds such as ascorbic acid, L-glutamic acid, uric acid, creatine, glucose and dopamine have been investigated. The nature of the interaction between manganese metal cations and natural bilirubin is also discussed employing NPA, molecular orbital (MO) analysis and Bader's Atoms in Molecule (AIM) theory.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-09-17T06:03:21Z
      DOI: 10.1142/S0219633615500480
  • DFT study and topological analysis of the bonding in DNA Hoogsteen-type
           base pairs
    • Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      The purpose of our work is to characterize and present a theoretical comparative study of a variety of compounds based on DNA base pairs linked with some transition metal ions in gas phase: C–M–G (Cytosine–metal–Guanine) where M = Ag(I), Zn(II), Cd(II) and A–M–T (Adenine–metal–Thyminate) where M = Co(II), Ru(I), Ni(I), Y(II), Zn(I), Cd(I), Cu(II). Geometry optimization and frequency calculations were carried out at DFT/ZORA/BLYP-D/TZ2P level. M–N and M–O bonds were investigated with the quantum chemical topology (QCT): Quantum theory of atoms in molecules (QTAIM) and electron localization functions (ELF). The hydrogen bonds: N10–H…O7 for A–M–T complexes and N7–H…O10 for C–M–T ones were visualized and discussed, QTAIM and ELF prove the existence of O7–H…N10 hydrogen bond for some A–M–T systems, since the bond critical point (BCP) of N7–H having ∇2ρ(r) < 0, so it has a covalent character confirming the existence of a tautomer process of these complexes. Bonding energy E(bond), Pauli repulsion E(Pauli), electrostatic E(elect), and orbital E(orb) interactions were represented and compared together. Hirschfeld's charges showed the existence of charge transfer process in the bridge moieties. It seems that, in contrast to natural base pairs that are stabilized by hydrogen bonding, Hoogsteen-type base pairs are held together by coordinative bond with metal ions.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-09-15T04:04:44Z
      DOI: 10.1142/S0219633615500479
  • Pseudo Jahn–Teller origin of twisting in 3,6-pyridazinedione
           derivatives; N2C4H2Y2Z2(Y = O, S, Se, Z = H, F, Cl, Br) compounds
    • Authors: Ali Reza Ilkhani
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      3,6-pyridazinedione and two of its derivatives where oxygen atoms of the molecule are substituted by two sulfur or selenium (N2C4Y2H4) were studied with the goal of answering the following question: "Which N2C4Y2H4 compounds are unstable in their planar configuration?" Additionally, the origin of the twisting instability of 3,6-pyridazinedione planar configuration and three of its 1,2-dihalo derivatives (N2C4H2O2Z2) were rationalized by employing the pseudo Jahn–Teller effect (PJTE) to explain the difference between N2C4H2O2Z2 structures in series. Therefore, the structures of six 3,6-pyridazinediones (N2C4H2Y2Z2) were optimized in both equilibrium and planar configurations, and their vibrational frequencies were calculated. Then the adiabatic potential energy surface (APES) profiles along the a2 distortion coordinates were calculated. Based on the calculation results, N2C4S2H4 and N22C4Se2H4 compounds were stable in the planar structure; but, due to the vibronic coupling interaction between the 1A1 ground state and the first excited state 1A2, the twisting instability occurred in planar N2C4H2O2Z2 series. The (1A1 + 1A2) ⊗ a2 problem was found to be the reason of the breaking symmetry phenomena in all the four N2C4H2O2Z2 in series from unstable planar configuration (highest-symmetry C2v) to the stable twisted geometry with C2 symmetry. Finally, the vibronic coupling constants of the PJTE of the compounds in series were estimated by fitting the secular equation roots along the normal coordinates of distortion.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-08-12T03:26:43Z
      DOI: 10.1142/S0219633615500455
  • Structural, QTAIM, thermodynamic properties, bonding, aromaticity and NMR
           analyses of cation–π interactions of mono and divalent metal
           cations (Li+, Na+, K+, Be2+, Mg2+, and Ca2+) with substituted pyrazine
    • Authors: Maryam Zaboli, Heidar Raissi
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Theoretical investigation of 42 cation-π complexes formed by the alkali metal (Li+, Na+, K+), alkaline-earth cations (Be2+, Mg2+, Ca2+) and π-system of the pyrazine and its derivatives have been performed at density functional theory (DFT) (B3LYP functional) and MP2 methods with 6-311++G** basis set in the gas phase and the polarized continuum model (PCM)-water solvation. The following substituents have been taken into consideration: Br, Cl, CH3, OH, OCH3 and SH. The interactions present in these complexes have been investigated by means of the natural bond orbital (NBO) and the Bader's quantum theory of atoms in molecules (QTAIMs) approaches. The effects of the interactions on NMR data have been probed using the GIAO-based method to extend investigation of the studied compounds. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies show that charge transfer occurs within each complex. Vibrational frequencies and physical properties such as dipole moment, chemical potential, chemical hardness and chemical electrophilicity of these compounds have been systematically explored. The aromaticity of aromatic rings has been measured using several well-established indices of aromaticity such as nucleus-independent chemical shift, harmonic oscillator models of the aromaticity, para-delocalization index, average two-center indices, aromatic fluctuation index and π-fluctuation aromatic index.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-08-12T03:26:43Z
      DOI: 10.1142/S0219633615500443
  • Ab initio and DFT studies on the structures, binding energies and nature
    • Authors: Masoud Hatami, Mehdi Bayat, Hassan Keypour, Sadegh Salehzadeh
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      A comprehensive theoretical study on the structure and stability of linear and triangular isomers of anionic clusters of zinc, cadmium and mercury [math] and their binding with one and two alkali metal cations (X+ = Li+, Na+, K+) has been investigated at the density functional (BP86 and B3LYP) and ab initio (MP2, MP4 and coupled cluster single and double (CCSD)) methods. The results showed that in all cases, the triangular geometry with D3h symmetry is more stable than linear one. The calculated values of interaction energies (IE) between [math] anions and two X+ cations, Wiberg bond indices (WBI) and the electron densities at bond critical points (BCP), ρ(BCP), for Y–X bonds show that among all complexes investigated here at all levels of theory Zn3Li2 and Hg3K2 have the largest and the smallest values of IE, WBI and ρ(BCP), respectively. The natural charges of the atoms and WBI involved in the bonding as well as the global value of the charge transfer ΔQ from [math] to X+ cation in X2Y3 clusters, evaluated through natural population analysis, confirmed that covalent contribution in Y–X bond formation increases from K+ to Li+. Also the energy decomposition analyses (EDA) were used to detect the nature of interaction in the complexes. The results confirmed that the contribution of electrostatic interactions in present complexes is almost more than 70%.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-08-05T02:59:51Z
      DOI: 10.1142/S0219633615500431
  • Application of counter propagation artificial neural network for
           classification and genetic diversity assessment of some Pseudomonas
    • Authors: Mahsa Izadiyan, S. Mohsen Taghavi, Parisa Izadiyan
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Members of the genus Pseudomonas bacterium are of great interest because of their importance in plant disease. In this study, DNA fingerprints of 60 strains of Pseudomonas bacteria including three species of Pseudomonas syringae (Pseudomonas syringae pv. syringae (Pss) and Pseudomonas syringae pv. Lachrymans (Psl)), Pseudomonassavastanoi (Psa) and Pseudomonas tolaasii (Pt) were used for developing a robust predictive classification model. The DNA fingerprints were obtained by repetitive polymerase chain reaction (Rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindromes (REP), and BOXAIR primers. The classification results of counter propagation artificial neural network (CP-ANN) modeling indicated that a combination of Rep-PCR fingerprinting and chemometrics analysis can be used as an effective and powerful methodology to differentiate species of Pseudomonas and pathovars of P. syringae strains based on a predictive model.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-07-28T03:23:03Z
      DOI: 10.1142/S021963361550042X
  • Modulation of the optical properties of D-π-A type azobenzene
           derivatives by changing the π-conjugated backbones: A theoretical
    • Authors: Zeyu Liu, Xiufen Yan, Long Li, Guohua Wu
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      The optical properties of two series of azobenzene derivatives were modulated by backbone modifications with the density functional theory (DFT) calculations. Compared to the short-chain molecule, the chromophore with an elongated π-bridge exhibits a greater extent of charge transfer during one-photon excitation and hence possesses a larger molecular first hyperpolarizability (β0). Meanwhile, an evident red-shift in the maximum absorption was observed after extension of the π-conjugated backbone. The tendency of the static β0 value derived from the two-state model is consistent with the result of the calculation at M06-2X/6–311++G(d,p) level by means of analytical derivative method. The dynamic perturbations were revealed to cause the obvious enhancement of the first hyperpolarizability. The more closer the foundational wavelength to two times the value of the maximum absorption in one-photon transition, the larger βRHS value is observed for the chromophore. The nonlinear optical (NLO) properties augment with the introduction of the THF solvents by comparing the gas-phase values. With increasing the length of conjugated bridge, the dynamic βRHS value increases more rapidly in THF solution than in vacuum.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-07-28T03:23:02Z
      DOI: 10.1142/S0219633615500418
  • Understanding the quantitative structure–activity relationship of
           acetylcholinesterase inhibitors for the treatment of Alzheimer's disease
    • Authors: Anuradha Sharma, Poonam Piplani
      Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print.
      Alzheimer's disease (AD) is the most common cause of dementia in old aged people and clinically used drugs for treatment are associated with side effects. Thus, there is a current demand for the discovery and development of new potential molecules. However, the recent advances in drug therapy have challenged the predominance of the disease. In this manuscript, an attempt has been made to develop the 2D and 3D quantitative structure–activity relationship (QSAR) models for a series of rutaecarpine, quinazolines and 7,8-dehydrorutaecarpine derivatives to obtain insights to Acetylcholinesterase (AChE) inhibition. Five different QSAR models have been generated and validated using a set of 52 compounds comprising of varying scaffolds with IC50 values ranging from 11,000 nM to 0.6 nM. These AChE-specific prediction models (M1–M5) adequately reflect the structure–activity relationship of the existing AChE inhibitors. Out of all developed models, QSAR model generated using ADME properties has been found to be the best with satisfactory statistical significance (regression (r2) of 0.9309 and regression adjusted coefficient of variation [math] of 0.9194). The QSAR models highlight the importance of aromatic moiety as their presence in the structure influence the biological activity. Additional insights on the compounds show that acyclic amines attached to side chain have lower activity than cyclic amines. The QSAR models pinpointing structural basis for the AChEIs suggest new guidelines for the design of novel molecules.
      Citation: Journal of Theoretical and Computational Chemistry
      PubDate: 2015-07-16T02:35:02Z
      DOI: 10.1142/S0219633615500406
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