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  • Theoretical, Physical and Computational Chemistry  (28)
  • Wiley-Blackwell  (28)
  • 1
    Electronic Resource
    Electronic Resource
    Ab initio conformational analysis of cyclooctane molecule (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 524-534 
    Details
    ISSN: 0192-8651
    Keywords: ab initio conformational analysis ; cyclooctane molecule ; potential energy surface ; Hartree-Fock theory ; Møller-Plesset theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surface (PES) for the cyclooctane molecule was comprehensively investigated at the Hartree-Fock (HF) level of theory employing the 3-21G, 6-31G, and 6-31G* basis sets. Six distinct true minimum energy structures (named B, BB, BC, CROWN, TBC, and TCC1), characterized through harmonic frequency analysis, were located on the multidimensional PES. Two transition state structures were also located on the PES for the cyclooctane molecule. Electron correlation effects were accounted for using the Møller-Plesset second-order perturbation theory (MP2) approach. The predicted global minimum energy structure on the ab initio PES for the cyclooctane molecule is the BC conformer. A gas phase electron diffraction study at 300 K suggested a conformational mixture while an NMR study in solution at 161.5 K predicted the BC conformer as the predominant form. The equilibrium constants reported in the present study, which were evaluated from the ab initio calculated total Gibbs free energy change values, were in good agreement with both experimental investigations. The ab initio results showed that the low temperature condition significantly favored the BC conformer while above room temperature both BC and CROWN structures can coexist.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 524-534, 1998
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  • 2
    Electronic Resource
    Electronic Resource
    A chemometric analysis of ab initio vibrational frequencies and infrared intensities of methyl fluoride (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 167-177 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Factorial design and principal component analyses are applied to CH3F infrared frequencies and intensities calculated from ab initio wave functions. In the factorial analysis, the quantitative effects of changing from a 6-31G to a 6-311G basis, of including polarization and diffuse orbitals, and of correcting for electron correlation using the second-order Møller-Plesset procedure are determined for all frequencies and intensities. The most significant main effect observed for the frequencies corresponds to the shift from Hartree-Fock to MP2 calculations, which tends to lower all frequency values by approximately 100 cm-1. For the intensities, the main effects are larger for the CF stretching and the CH3 asymmetric stretching modes. Interaction effects between two or more of the four factors are found to be of minor importance, except for the interaction between correlation and polarization. The principal component analysis indicates that wave functions with polarization and diffuse orbitals at the second-order Møller-Plesset level provide the best estimates for the harmonic frequencies, but not for the intensities. For the frequencies, the first principal component distinguishes between MP2 and Hartree-Fock calculations, while the second component separates the wave functions with polarization orbitals from those without these orbitals. For the intensities, the separation is similar but less well defined. This analysis also shows that wave function optimization to calculate accurate intensities is more difficult than an optimization for frequencies. © 1996 by John Wiley & Sons, Inc.
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  • 3
    Electronic Resource
    Electronic Resource
    Cloppa RPA-AM1 analysis of the anisotropy of NMR 1J(XY) coupling tensors in Me3XY compounds (X = 13C, 29Si, 119Sn, 207Pb; Y = 19F, 35Cl) (1997)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 61 (1997), S. 823-833 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this work, the CLOPPA approach is extended to allow the bond-contribution analysis of the anisotropic part, ΔJ, of the indirect nuclear spin-spin coupling tensor, J. As an example this method is applied to study the role played by the X-Y bond, its antibonding orbital, and the Y lone pairs in determining the Fermi contact-spin dipolar cross contribution to Δ1J(XY) in compounds of type Me3X(SINGLE BOND)Y (X = C, Si, Sn, Pb; Y = F, Cl). That contribution is found to be the main one, except for × = Pb, in this series of compounds. Calculations are carried out using semiempirical AM1 ground-state wave functions. © 1997 John Wiley & Sons, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    Theoretical studies on local anesthetics: Procaine, lidocaine, tetracaine, bupivacaine, and dibucaine - neutral and monoprotonated (1997)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 61 (1997), S. 959-980 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molecular basis of the pharmacological action of tertiary amine local anesthetics (LA) is still unclear. However, there is experimental evidence that the LA penetrates into the axon as a neutral form and acts in the charged form from the intracellular phase. In this work we report quantum chemical semiempirical results for the neutral and monoprotonated forms of procaine, lidocaine, tetracaine, bupivacaine, and dibucaine. All geometries have been fully optimized with the AM1 Hamiltonian. Solvent effects were included at the self-consistent reaction field (SCRF) approximation. We have found that the most stable conformers of positively charged LA agents are all characterized by intramolecular H-bond formation involving the protonated amine groups. INDO/S-CIS calculations have revealed that the gas-phase absorption spectra of LAs result from the superposition of the spectra of the ring π system and the carbonyl, in a large extent perturbed by intramolecular charge transfer (CT). For all studied LAs, the benzene B2u bands are very weak and the benzene B1u bands gain intensity due to symmetry breaking. Formation of intramolecular H bond strongly affects the carbonyl CT bands. On the other hand, the spectrum of dibucaine is dominated by the quinoline π system. © 1997 John Wiley & Sons, Inc.
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  • 5
    Electronic Resource
    Electronic Resource
    Ab initio study on the reaction 2NH2→NH+NH3 (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 321-329 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The geometries of the reactant, products, and transition state of the title reaction were optimized at the UHF and UMP2 levels with the double and triple zeta basis sets as well as polarization functions by using the energy-gradient method. The potential-energy barrier for this reaction is 3.73 kcal/mol at the UMP-SAC4 level of theory. The intrinsic reaction coordinate (IRC) was performed at the UMP2/6-311G** level. The changes of the geometry and the bound vibrational modes along the IRC were analyzed. To obtain a more reliable potential-energy curve for the study of the reaction dynamics, the UMP2 energy profile was refined along the IRC with the UQCISD(T) and UMP-SAC4 levels of theory. The theoretical rate constants calculated by the conventional and the variational transition-state theories at the UMP-SAC4 level agree approximately with the experimental values in the high-temperature range from 2000 to 3000 K and are not affected by the variation and quantum effects.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 321-329, 1997
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  • 6
    Electronic Resource
    Electronic Resource
    Phytochrome structure: A new methodological approach (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1145-1157 
    Details
    ISSN: 0020-7608
    Keywords: phytochrome ; absorption spectra ; semiempirical ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Higher plants use the protein phytochrome as a photosensor. In physiological temperatures phytochrome exists in two forms: Pr and Pfr. The chromophore of phytochrome is an open-chain tetrapyrrole. On the pathway from Pr to Pfr four intermediates (Lumi-R, Meta-Ra, Meta-Rb, and Meta-Rc) can be distinguished, while only two (Lumi-F and Meta-F) can be seen on the way back from Pfr to Pr. We have used the x-ray structure of the C-Phycocyanin protein Fremyella diplosiphon bacteria as a template to build a model (∼200 atoms) that includes only the chromophore and five amino acids of the phytochrome (Arg316-Cys321-His322-Leu323-Gln324) around it. Using the existing experimental evidences, we have proposed a three-dimensional (3D) structure for Pr, Pfr, and intermediates and a mechanism for the photoisomerization as well. Structures were fully optimized using AM1 (Unichem package on a Cray J90-NACAD). Using the INDO/S method of Zerner and co-workers, we calculated the absorption spectra of the model compounds and compared them with the experimental data. The oscillator strength ratio is an indicator of the chomophore conformation in biliproteins. The calculated spectra reproduces well the spectra of the phytochrome (Pr, Pfr, and intermediates) except for the lower energy band. This result is attributed to the small number of amino acids in the models. The calculated ratios (fVIS/fUV-fosc of visible band over fosc of UV band and f2/f1-fosc of second absorption band over fosc of first absorption band) for the models match very well the experimental ratios obtained for the phytochrome (Pr, Pfr, and intermediates). This supports the proposed mechanism for the photoisomerization process.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1145-1157, 1998
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  • 7
    Electronic Resource
    Electronic Resource
    Theoretical calculation of carbon clusters (1997)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 65 (1997), S. 867-875 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Structural parameters and energy have been calculated for C1-3 and C9 clusters using density functional theory through the deMon program. The C1-3 clusters were fully optimized using deMon; different basis sets were tested in order to choose the suitable one to be used in the C9 clusters. In the case of C2 the results were compared with experimental values. DZVP2 basis was selected because it always gave the closest value to the experimental data. The C9 carbon clusters were designed in relation to C(100) diamond surface. The energies of the nonrelaxed and relaxed surfaces with and without hydrogen were calculated. In the same way CH3-relaxed and CH2-relaxed species were calculated. The diamond growth mechanism proposed in the literature was evaluated by an energy analysis. The C(SINGLE BOND)CH3 distance is reported.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 867-875, 1997
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  • 8
    Electronic Resource
    Electronic Resource
    Reaction path for the insertion reaction of SnCl2 into the Pt(SINGLE BOND)Cl bond: An ab initio study (1997)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 65 (1997), S. 643-650 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reaction pathway for the insertion reaction of SnCl2 into the Pt(SINGLE BOND)Cl bond on the cis-Pt(Cl)2(PH3)2 compound was investigated at the ab initio MO level of theory. The optimized structure obtained for the transition state indicates that this reaction proceeds through a three-center transition state, and the formed intermediate cis-Pt(Cl)(PH3)2(SnCl3) easily isomerizes to the trans-Pt(Cl)(PH3)2(SnCl3) compound. The nature of the bonds was investigated with the charge decomposition analysis (CDA) method and this method indicates that the SnCl3 group is a stronger trans director than is the PH3 group.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 643-650, 1997
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  • 9
    Electronic Resource
    Electronic Resource
    A semiempirical study on leupeptin: An inhibitor of cysteine proteases (1997)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 65 (1997), S. 1125-1134 
    Details
    ISSN: 0020-7608
    Keywords: leupeptin ; papain ; semiempirical ; cysteine protease ; active center ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this work, we modeled leupeptin (Ac.Leu.Leu.Arg.CHO), a natural inhibitor of proteases, and the active site of papain, a cysteine protease, using as a template the crystal structure of a leupeptin-papain complex recently obtained by Schroder and co-workers [FEBS Lett. 135(1), 38 (1993)] and including 11 amino acids relevant to the proteolytic activity of the enzyme. Our results show that the AM1 fully optimized leupeptin is more stable than is the leupeptin crystal structure by about 6.0 kcal/mol. Our results show also that in the modeled active center of papain the S - H⋅⋅⋅N structure is favored. When the aldehyde is included in the calculation, however, proton transfer occurs with a strengthening of the S-⋅⋅⋅HIm+⋅⋅⋅O(DOUBLE BOND)C (Asn175) catalytic triad. The AM1 method reproduces fairly well the interactions between the enzyme and the host molecule.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 1125-1134, 1997
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  • 10
    Electronic Resource
    Electronic Resource
    Relevant space within the spin-adapted reduced Hamiltonian theory. I. Study of the BH molecule (1997)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 65 (1997), S. 97-105 
    Details
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The algorithm for evaluating the elements of the spin-adapted reduced Hamiltonian (2-SRH) involves the whole basis set of molecular orbitals. However, under a specific condition, its eigenvectors are very sparse. These two properties lead us here to propose a projection of the 2-SRH matrix, which is equivalent to an effective truncation which facilitates considerably the applicability of the SRH method. The criteria for performing this truncation, amounting to the determination of a relevant space are discussed. The results obtained for the BH molecule are analyzed here.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 97-105, 1997
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