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  • 1995-1999  (1,577)
  • Theoretical, Physical and Computational Chemistry  (1,576)
  • Nuclear reactions
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Space science reviews 84 (1998), S. 199-206 
    ISSN: 1572-9672
    Keywords: Nuclear reactions ; Nucleosynthesis ; Abundances ; Stars:Evolution ; Interior ; Rotation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We first recall the observational and theoretical facts that constitute the so-called 3He problem. We then review the chemical anomalies that could be related to the destruction of 3He in red giants stars. We show how a simple consistent mechanism can lead to the destruction of 3He in low mass stars and simultaneously account for the low 12C/13C ratios and low lithium abundances observed in giant stars of different populations. This process should both naturally account for the recent measurements of 3He/H in galactic HII regions and allow for high values of 3He observed in some planetary nebulae. We propose a simple statistical estimation of the fraction of stars that may be affected by this process.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 189-197 
    ISSN: 0020-7608
    Keywords: atomic Hartree-Fock ; augmented Fourier basis ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a scheme for Hartree-Fock and related calculations on atoms using a Fourier basis augmented by an exponential function. All multiple sums in the variational energy expression are written as single sums over combinations of multiplications and convolutions. The computational cost of the method is thus practically linear in the number of basis functions. The results compare favorably with the most precise published results of numerical grid methods and variational calculations.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 189-197, 1998
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 205-217 
    ISSN: 0020-7608
    Keywords: potential energy surface ; transition structure ; nonrigid molecule ; symmetry group ; reaction path ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The symmetry group of a nonrigid molecule is related to that of the transition structure that is related to the rearrangement process which contributes to the “nonrigidity” of the molecular system. The resulting permutation/rotation/reflection groups for nonrigid molecules can be much larger in order than the usual Longuet-Higgins permutation/inversion group. A few examples are presented to illustrate the definition of the symmetry group for nonrigid molecules.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 205-217, 1998
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 219-239 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We review some recent developments of high-order response theory and illustrate the utility of this theory for a selection of nonlinear properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 219-239, 1998
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 253-267 
    ISSN: 0020-7608
    Keywords: DFT ; carbonyloxyl radicals ; CASPT2 ; chemical reactions ; isomerizations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the lowest electronic states of HCOO· in C2v and Cs symmetries were optimized employing density functional theory (DFT) methods with extended basis sets including up to f- (on C and O) and d- (on H) polarization functions. Generalized gradient functionals (BLYP) and adiabatically connected functionals (B3LYP and B3PW91) were employed for studying HCOO·, as well as the isomer HOCO· (trans), the dissociation limit H·+CO2, and the transition state for the decomposition. At the best DFT levels employed, the ground state of HCOO· is 2A1 (in C2v) with equal C—O bond lengths, while the low-lying 2B2 state is only about 4 kJ/mol above (without inclusion of zero-point energies). The broken-symmetry 2A′ state (with unequal C—O bond lengths, i.e., Cs symmetry) is predicted to be about 13 kJ/mol above the 2A1 state and to be a transition state for the isomerization HCOO· (2A1)→HOCO· (2A′), with the trans-HOCO· isomer about 55 kJ/mol more stable. These facts agree closely with the most recent CASPT2/ANO calculations on this system. Therefore, it is concluded that some DFT models can be used safely for the study of larger radicals of the same type (despite several drawbacks discussed at length in this study). B3PW91, using several basis sets, is subsequently applied to the study of the possible reaction mechanisms of acetyloxyl radical, which exhibits a much more complicated path than formyloxyl, due to the presence of the methyl group. The optimum structures of isomers with coplanar or perpendicular CH and CO bonds were obtained for CH3COO· and two saddle points identified on the path of decomposition into CH3· and CO2. On the other side, saddle points for isomerization into CH3OCO· and CH2COOH· were also located, and the decomposition of the former to CH3O·+CO investigated. Finally, the structure of the benzoyloxyl radical (C6H5COO·) and its possible decomposition products were investigated along the same lines.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 253-267, 1998
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 283-290 
    ISSN: 0020-7608
    Keywords: LiB ; spectroscopic constants ; excited states ; VBSCF ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The common correspondence between molecular orbital theory and resonance theory in the description of the electronic structure of a molecule is used to select valence bond (VB) structures constructing wave functions of the low-lying states of LiB and LiB+. The spectroscopic parameters of the low-lying states of LiB and LiB are determined by using the valence bond self-consistent field (VBSCF) method. For comparison, multconfiguration SCF (MCSCF) calculations for LiB are also carried out. If the overlap-enhanced orbitals are employed, a compact VB wave function can correctly describe bond making and bond breaking in the entire dissociation process for the low-lying electronic states of LiB. All calculations locate the ground state as 3Π. The VB calculation with 14 VB structures at the level of the basis set DH(s, p) predicts an excellent dissociation energy of 1.16 eV and vibrational frequency of 527 cm-1 for the ground state, which is in good agreement with previous high-level calculations with a large basis set. The effect of the basis set on the numerical quality of the VBSCF calculation is investigated. It is important for improving accuracy of the VB calculation to enlarge the basis set, although the VB treatment including more VB structures with a relatively small basis set needed in the nonorthogonal VB calculation can reasonably describe dissociation behavior for systems with few electrons. The chemical bonds in the ground state 3Π and the excited state (1)3Σ- have ionicities of 63.4 and 65.1%, respectively, while chemical bond in the first excited state 1Σ+ is mainly covalent. Other several low-lying states are also investigated by the VB and MCSCF methods.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 283-290, 1998
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 303-312 
    ISSN: 0020-7608
    Keywords: bithiophene ; internal rotation ; DFT calculations ; MP2 calculations ; Fourier-fitted torsional potentials ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The internal rotation of 2,2′-bithiophene was investigated within the density functional theory (DFT) approach. Fully optimized DFT torsional potentials are compared with Møller-Plesset (MP2) results which predict a fourfold potential with s-cis- and s-trans-gauche minima. DFT calculations fail in describing the energetics of the internal rotation because they favor planar vs. perpendicular conformers. Gradient-corrected functionals provide torsional potentials where the gauche minima have almost vanished and the s-cis↔s-trans interconversion barriers are twice as high as the barriers obtained at the MP2 level. The use of local functionals augments the shortcomings of the DFT approach. The gauche minima completely disappear and the rotational barriers are now about three times higher than the MP2 barriers. As an efficient computational approach, we suggest having geometries optimized at the DFT level and conformational energies evaluated via single-point MP2 calculations. The fitting of MP2//DFT energies to truncated Fourier expansions allows one to predict the torsional angles and the relative energies of the critical points of the rotational potential with an accuracy similar to that afforded by MP2 calculations including full geometry optimization.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 303-312, 1998
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 321-329 
    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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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 341-350 
    ISSN: 0020-7608
    Keywords: alumina ; periodic SCF ; surface potential ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic structure of the (001) and (110) α-alumina surfaces was determined by periodic Hartree-Fock method in statically relaxed geometries. Both (001) and (110) surfaces generate specific surface states into the energy gap. Significant influence of charge-transfer effect on the surface-adsorbate potential is possible in both cases studied. The inclusion of the exponential part to the standard potential forms was suggested for the description of the interaction potential in such cases.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 341-350, 1998
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 359-365 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A theoretical analysis of γ-Al2O3 (110) surface hydroxylation based on ab initio Hartree-Fock embedded cluster calculations was carried out. Both tetrahedral and octahedral Al sites were considered. These sites were modeled by a series of clusters of increasing size: Al8O3, Al12O5, and Al16O8, embedded in an array of point charges. The adsorption of water was found to be dissociative or nondissociative depending on the cluster size, although the mechanism clearly converges toward dissociation for the more reliable models in agreement with the experiment. This dependence can be explained in light of the basicity modification of surface oxide ions induced by the environment as well as by surface relaxation. Comparison of chemisorption energies suggests that the preferred site for hydroxylation is a low coordination tetrahedral aluminum.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 359-365, 1998
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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 375-378 
    ISSN: 0020-7608
    Keywords: electronic structure ; catalytic properties ; Wangh-type anion ; heteropoly compounds ; DV-Xα method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic structure of Waugh anion (NiMo9O32)6- has been calculated by the DV-Xα method. The electronic structure and catalytic behavior of the Waugh anion are discussed. At the same time, the difference in electronic structure and relationship in catalytic behavior between Waugh and Keggin anions are compared.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 375-378, 1998
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 395-405 
    ISSN: 0020-7608
    Keywords: intramolecular H bonds ; gas-phase stability ; continuum solvent ; solvation free energy ; point charge model ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational properties of bilirubin present a considerable interest from the medical and biological points of view, because of the toxic pigment peculiar solubility features. Therefore, ab initio geometry optimizations at the 3-21G/SCF level were carried out on a few model-built structures of bilirubin, after substituting the methyl groups on the heteroaromatic rings with H atoms. The structures obtained show a varied network of H bonds, ranging from 0 to 6 H bonds for the lowest-energy conformer in vacuo. This conformer assumes a “ridge-tile” shape previously found in both MM/MD simulations [D. A. Lightner et al., J. Am. Chem. Soc. 114, 10123 (1992)] and semiempirical calculations [W. H. Shelver et al., Int. J. Quantum Chem. 44, 141 (1992)], but at the ab initio level, its computed H-bond geometrical parameters are fairly consistent with the X-ray observed ones. The relative stability of all the structures is compared in vacuo and in aqueous solution using the polarizable continuum model (PCM) of the solvent, whose stabilizing effect, however, is not sufficient to fill the large energy gap between the less lipophilic conformers and the most stable one in vacuo, in agreement with previous CD measurements. The energetic cost imposed to the solvent effect by each intramolecular H bond is almost constant if the other structural features do not change appreciably. The trend of the purely electrostatic results obtained employing a partial charge model of bilirubin is analogous to that produced by its polarized ab initio charge distribution.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 395-405, 1998
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  • 13
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 429-440 
    ISSN: 0020-7608
    Keywords: symmetric group ; class-sums ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An algorithm for the evaluation of products of arbitrary conjugacy class-sums in the symmetric group is conjectured. This algorithm generalizes a procedure presented sometime ago, which deals with products in which at least one of the class-sums involved consists of a single cycle (and an appropriate number of fixed points). Let the support size of a conjugacy class be the number of indices that are not fixed points. The algorithm proposed implies that the coefficient of the class-sum C in the product of the class-sums A and B is given in terms of a well-defined enumeration problem within the symmetric group Sp, where p is the smallest of the support sizes of A, B, and C.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 429-440, 1998
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 441-474 
    ISSN: 0020-7608
    Keywords: quantum fluid dynamics ; atom-laser interaction ; femtosecond dynamics ; density functional theory ; high harmonic generation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comprehensive, nonperturbative, time-dependent quantum mechanical (TDQM) approach is proposed for studying the dynamics of a helium atom under an intense, ultrashort (femtoseconds) laser pulse. The method combines quantum fluid dynamics (QFD) and density functional theory. It solves a single generalized nonlinear Schrödinger equation of motion (EOM), involving time and three space variables, which is obtained from two QFD equations, namely, a continuity equation and an Euler-type equation. A highly accurate finite difference scheme along with a stability analysis is presented for numerically solving the EOM. Starting from the ground-state Hartree-Fock density for He at t=0, the EOM yields the time-dependent (TD) electron density, effective potential surface, difference density, difference effective potential, ground-state probability, 〈r〉, magnetic susceptibility, polarizability, flux, etc. By a Fourier transformation of the TD dipole moment along the linearly polarized-field direction, the power and rate spectra for photoemission are calculated. Eleven mechanistic routes for photoemission are identified, which include high harmonic generation as well as many other spectral transitions involving ionized, singly excited, doubly excited (autoionizing), and continuum He states, based on the evolution of the system up to a particular time. Intimate connections between photoionization and photoemission are clearly observed through computer visualizations. Apart from being consistent with current experimental and theoretical results, the present results offer certain predictions on spectral transitions which are open to experimental verification.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 441-474, 1998
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 491-501 
    ISSN: 0020-7608
    Keywords: positron-molecule complex ; positron affinity ; full variational molecular orbital method ; nuclear wave function ; orbital relaxation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Optimal Gaussian-type orbital (GTO) basis sets of positron and electron in positron-molecule complexes are proposed by using the full variational treatment of molecular orbital (FVMO) method. The analytical expression for the energy gradient with respect to parameters of positronic and electronic GTO such as the orbital exponents, the orbital centers, and the linear combination of atomic orbital (LCAO) coefficients, is derived. Wave functions obtained by the FVMO method include the effect of electronic or positronic orbital relaxation explicitly and satisfy the virial and Hellmann-Feynman theorems completely. We have demonstrated the optimization of each orbital exponent in various positron-atomic and anion systems, and estimated the positron affinity (PA) as the difference between their energies. Our PA obtained with small basis set is in good agreement with the numerical Hartree-Fock result. We have calculated the OH- and [OH-; e+] species as the positron-molecular system by the FVMO method. This result shows that the positronic basis set not only becomes more diffuse but also moves toward the oxygen atom. Moreover, we have applied this method to determine both the nuclear and electronic wave functions of LiH and LiD molecules simultaneously, and obtained the isotopic effect directly.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 491-501, 1998
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  • 16
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 503-513 
    ISSN: 0020-7608
    Keywords: ring currents ; conjugated molecules ; Pariser-Parr-Pople model ; valence bond method ; correction vector technique ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied magnetism and aromaticity of polycyclic ring systems by analyzing ring currents for different circulations in these molecules. The technique employed for calculating ring currents uses correction vectors which implicitly includes all the eigenstates of the Hamiltonian in the space of the chosen configurations. We have employed the Pariser-Parr-Pople Hamiltonian and have carried out full configuration interaction (CI) calculations for small systems and approximate CI calculations for large systems. The systems studied include polyacenes, nonaromatic ring systems including the C60 fragments pyracylene, fluoranthene, and corannulene, and heteroatomic systems with upto two six-membered rings. We find that in polyacenes, the aromaticity of the extreme phenyl rings reduces with increasing number of phenyl rings in the system, and it saturates at ≈⅔ the benzene value. In systems containing nonaromatic rings, we find paramagnetic or diamagnetic behavior for different circulations depending upon the number of atoms in the chosen ring cycle, in agreement with the 4n+2 rule. In corannulene, the largest fragment of C60 we have studied, the five-membered ring is weakly diamagnetic while the six-membered ring is more diamagnetic, although much less than in isolated benzene. The ring structures with heteroatoms studied are pyridine, pyrimidine, and its isomers, s-triazine, quinoline and its isomer, and quinazoline and its isomers. All these have similar ring currents as in their purely carbon counterparts, although ions of these molecules show interesting behavior.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 503-513, 1998
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  • 17
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1137-1143 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The computed molecular surface electrostatic potentials of a group of anticonvulsants of various chemical types were investigated with the objective of identifying common features that may be related to their activities. The calculations were carried out with the density functional B3P86/6-31G* procedure, using HF/STO-3G*-optimized geometries. Analysis of several statistically based properties of the surface potentials indicates that the negative regions are of primary importance and that an optimum intermediate level of local polarity, or internal charge separation, is required.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1137-1143, 1998
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  • 18
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    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1159-1168 
    ISSN: 0020-7608
    Keywords: nitrogenase ; nitrogen fixation ; INDO ; DFT ; PM3tm ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We follow the initial activation of the nitrogen molecule at the FeMo cofactor of nitrogenase and subsequently model the hydrogenation of N2 up to the fourth protonation step using the intermediate neglect of differential overlap quantum-chemical model. The results obtained favor a reaction mechanism going through hydrazido intermediates on the 4-Fe surfaces, externally to the FeMo cofactor. Calculations using density functional theory on smaller model systems also support the suggested mechanism over other possible schemes that involve early release of the first molecule of ammonia as a product of the enzymatic reaction. We also demonstrate that dielectric stabilization due to the protein around the cofactor could lower markedly the barrier for the product release as an ammonium ion.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1159-1168, 1998
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  • 19
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    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1145-1157 
    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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  • 20
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1169-1175 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: RHF/6-31G* investigations of 4-, 5-, and 6-ethyl(Et)-indole-3-acetic acid (IAA) yielded 11 symmetry-unique local minima with syn-periplanar orientation of the —COOH group for each of these compounds. The global minima are of C1 symmetry in all cases. Comparison with earlier results shows that ethylation or chlorination in position 5 or 6 introduces only minor changes on the orientation of the acetic acid side group, with no effect on the reaction paths related to this group. For 4-Et-IAA, the deviations from unsubstituted IAA are larger but preserve the pattern of reaction paths that is present in unsubstituted IAA, which is in contrast to 4-Cl-IAA, where local minima and reaction paths are completely different.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1169-1175, 1998
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  • 21
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 1185-1194 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The integrated molecular transform (FTm) is a unitary numerical index of structure that is capable of uniquely representing different molecular structure conformations with the exception of enantiomers. Other molecular indices have been derived from FTm as well as from the normalized molecular moment (Mn), for example, the analogous electronic and charge transforms (FTe and FTc) and moments (Me and Mc). In this study, each of these indices was calculated for up to 10 sampled conformations of each of the C1-C10 normal alkanes as they were subjected to a standard annealing process. Statistical analyses of the resulting data in the individual series and subsequent box plots, permitting facile examination of those results, indicated that the respective transform indices (FTm, FTe, FTc) are unique, that is, with no statistically significantly overlap across the series. For the Mn and Me indices, the numerical values for methane overlapped those of ethane in the first instance and both ethane and propane in the second. The Mc index values overlapped in several instances in the series. Inasmuch as the noted molecular indices are based only on parameters of structural origin, these results have profound implications for the correlation and estimation of properties derived not only from a general structure representation, but also for those properties which may be dependent on specific molecular conformations. This includes the potential for indices of molecular flexibility and conformationally dependent atomic electron densities.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1185-1194, 1998
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  • 22
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    International Journal of Quantum Chemistry 70 (1998), S. 1209-1215 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report on optimal molecular connectivity descriptors for nitrogen atoms in amines for use in structure-property correlations. The descriptors represent generalized molecular connectivity indices with adjusted diagonal entries in the adjacency matrices of the corresponding molecular graphs, such that the standard error in a regression for boiling points in a set of amines is minimized. Advantages of the so-optimized descriptors for multivariate regression analysis in structure-property-activity studies are discussed.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 1209-1215, 1998
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  • 23
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    International Journal of Quantum Chemistry 70 (1998), S. 583-589 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, we used Helmholtz's theorem to construct an unambiguous exchange-correlation energy density for use in density functional theory. This energy density requires only knowledge of the density dependence of the exchange-correlation energy functional, EXC, for its calculation. We calculate this energy density for Hooke's atom in three different regimes: the high-density (or weakly correlated) limit; a moderate density, comparable to that of the He atom; and a low density, in which the system is strongly correlated. We compare the exact unambiguous energy density with approximate energy densities found from approximate energy functionals. The exchange-correlation energy can be deduced directly from the density in the highly correlated limit and a new formula for the high-density limit of the correlation energy is given.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 583-589, 1998
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  • 24
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    International Journal of Quantum Chemistry 70 (1998), S. 571-581 
    ISSN: 0020-7608
    Keywords: partitioning ; level shift ; quasi-degenerate PT ; Dyson equation ; geminals ; excited states ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For the treatment of electron correlation, one most often uses the Møller-Plesset (MP) partition which defines the zero-order Hamiltonian through the spectral resolution of the Fockian. We investigate how the MP partitioning can be improved while still using the Hartree-Fock (HF) reference state; and how the HF wave function can be substituted by a correlated one preserving the formal simplicity of the HF-based approach. To improve the MPn result, we introduce a fine tuning of energy denominators replacing the HF orbital energies with the ionization potentials obtained from the second-order Dyson equation. As this equation usually tends to close the gaps, a slight decrease of the denominators is expected, inducing an improvement of low-order correlation energies. We keep the simplicity of the MP partitioning and handle Dyson corrections as simple level shifts. Substituting doubly filled HF orbitals by strongly orthogonal geminals, one introduces a correlated reference state which is variational, size-consistent, and properly describes single-bond dissociation. This wave function, the antisymmetrized product of strongly orthogonal geminals (APSG), offers a good starting point for further corrections. We show that the use of an APSG reference state in the equation-of-motion technique leads to Tamm-Dankoff approach (TDA) equations which account for correlation effects in electronic excitation energies.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 571-581, 1998
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  • 25
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    International Journal of Quantum Chemistry 70 (1998), S. 557-570 
    ISSN: 0020-7608
    Keywords: electron correlation ; reduced density matrices ; N-representability ; cumulants ; particle-hole duality ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Through the 3,5-contracted Schrödinger equation (3,5-CSchE) quantum energies and 3-particle reduced density matrices (3-RDMs) are determined directly without wave functions. Since the 3,5-CSchE involves the 5-RDM, its solution is indeterminate without N-representability conditions. However, the indeterminacy of the 3,5-CSchE may be removed through a reconstruction strategy for building the 4- and 5-RDMs from the 3-RDM. We present a systematic procedure for obtaining corrections for Valdemoro's reconstruction functionals from two complementary approaches, the particle-hole duality and the theory of cumulants. With the cumulants we are able to demonstrate that we have obtained all terms in the reconstruction functionals which may be written as antisymmetric products of the lower rdms. The cumulants allow us to understand the reconstruction functionals in terms of a renormalized many-body perturbation theory. The reconstruction functionals also lead to a natural generalization of Wick's theorem for evaluating expectation values of fermionic annihilation and creation operators with respect to correlated reference states. Previous work [Phys. Rev. A 57, 4219 (1998)] has explored the determination of correlation energy and 2-RDMs through the 2,4-CSchE, also known as the density equation. Because the reconstruction functionals employed with the 3,5-CSchE depend only on the antisymmetric products of lower RDMs in constrast to those used with the 2,4-CSchE, the 3,5-CSchE method presented here does not require the solution of systems of linear equations during reconstruction or the storage of the reconstructed RDMs. Application of the 3,5-CSchE technique to a quasi-spin model generates ground-state energies and 2-RDMs similar in accuracy to single-double configuration interaction (SDCI). We employ a simple iterative procedure for the solution of the 3,5-CSchE without traditional diagonalization. The CSchE techniques offer an approximate solution of the N-representability problem and a new approach to electron correlation.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 557-570, 1998
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  • 26
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    International Journal of Quantum Chemistry 70 (1998), S. 623-626 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The leaky aquifer function W(x, y) is an incomplete Bessel function which has had application in hydrology and more recently in electronic-structure calculations. This article presents an expansion which improves the efficiency of the calculation of W in the only part of its range not treated adequately by previously published methods, namely, the regime where x and y are both larger than unity but one is much larger than the other.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 623-626, 1998
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  • 27
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    International Journal of Quantum Chemistry 70 (1998), S. 613-622 
    ISSN: 0020-7608
    Keywords: excitation energies ; dynamic correlation effects ; perturbation theory ; MBPT ; multireference perturbation theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present the formalism for the treatment of several states of the same symmetry in basis-set reduction (BSR), a form of second-order Brillouin-Wigner multireference perturbation theory, which incorporates the first-order correction of the primary-space wave function with respect to its orthogonal complement. We benchmark this method for some valence and some Rydberg excitations of four small molecules (O2, CO, ethene, and ozone). In direct comparison with the underlying MR-SDCI benchmark results, we find an average accuracy of 0.2 eV or better for the excitation energies of the molecules considered and demonstrate the stability of the method with increasing size of the basis set and primary space. We argue that the configuration-based approach in BSR allows an accurate description of dynamical correlation effects with minimal primary space wave functions, containing far fewer configurations than are required for a CASSCF-based perturbative treatment of the molecules.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 613-622, 1998
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  • 28
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    International Journal of Quantum Chemistry 70 (1998), S. 651-658 
    ISSN: 0020-7608
    Keywords: electron propagator ; propagator theory ; Brueckner orbitals ; anions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vertical electron detachment energies of F- and OH- have presented difficulties for perturbative electron propagator methods. A recently derived, nondiagonal, renormalized approximation and two additional improvements are studied here. These improvements are replacement of the Hartree-Fock reference determinant by a determinant of approximate Brueckner orbitals generated by a coupled-cluster doubles calculation and retention of correlation terms in the 2hp-2hp block of the superoperator Hamiltonian matrix. Agreement with experiment is significantly better with these methods. When Hartree-Fock orbitals are used, electron detachment energies are underestimated, but approximate Brueckner orbitals lead to overestimates.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 651-658, 1998
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  • 29
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    International Journal of Quantum Chemistry 70 (1998), S. 681-691 
    ISSN: 0020-7608
    Keywords: excited states ; Kato's theorem ; adiabatic connection ; optimized potential method ; KLI approximation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Density functional theory for a single excited state is presented using Kato's theorem and the concept of adiabatic connection. The degenerate case is also detailed. The optimized potential method is generalized. The generalized Krieger, Li, and Iafrate (KLI) approximation is derived.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 681-691, 1998
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  • 30
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    International Journal of Quantum Chemistry 70 (1998), S. 693-701 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small nickel clusters up to the tetramer are investigated within the framework of the local spin density functional theory. Several competitive states are studied for the dimer. Both the geometry and the spin state are optimized for several starting symmetries in the case of the trimer and the tetramer. Moreover, all those calculations are followed by a vibrational analysis in order to discriminate between real minima and saddle points on the potential energy surface. It is found that Jahn-Teller deformations play an important role in determining transition-metal cluster geometries. Equilibrium geometries, electronic configurations, binding energies, magnetic moments, and harmonic frequencies are reported in this work.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 693-701, 1998
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  • 31
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    International Journal of Quantum Chemistry 70 (1998), S. 711-727 
    ISSN: 0020-7608
    Keywords: density matrix response functions ; N-scaling ; time-dependent Hartree-Fock ; nonlinear response ; bosonization ; carotenoids ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The response of the single-electron density matrix of a many-electron system to an external field is calculated using the time-dependent Hartree-Fock (TDHF) technique. A procedure for inverting the resulting nonlinear response functions to obtain an effective quantum multilevel system that has the same response is developed. The number of effective states is gradually increased as higher-order nonlinearities are computed. The complete set of intrastate and interstate density matrices and excited-state energies can be calculated. A favorable N-scaling of computational effort with size can be obtained making use of the localization of the optical transitions in real space.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 711-727, 1998
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  • 32
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Static second hyperpolarizabilities were calculated for molecules including tetrahydrofuran homologs by ab initio molecular orbital methods at the Hartree-Fock and various correlation levels. Substitution of the heteroatom with a heavier atom is found to be effective for increase of the second hyperpolarizability of these homologs. Comparison between the present results and previous results for furan homologs shows that π-conjugation is not effective for the increase of second hyperpolarizability of the molecules when the heteroatom is heavier.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 737-743, 1998
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  • 33
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    International Journal of Quantum Chemistry 70 (1998), S. 745-750 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (CH3)2NC6H4NC6H4O is a merocyanine dye that exists in resonance between the two extreme conformations of a keto and an eno form. The keto form is more stable in the gas phase and the eno form is believed to be more stable in solution. We show that the keto form can prevail in nonpolar solvents, but in polar solvents like chloroform, the eno form should be dominant. Analysis is made of the solvent effects in the low-lying absorption transition and its consequence in the first dipole hyperpolarizability. We show by explicit calculations that the hyperpolarizability of the eno form is one order of magnitude greater than in the keto form. We then contend that this structure dependence may also lead to very large changes of the hyperpolarizability of similar molecules and polymers in solvents.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 745-750, 1998
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  • 34
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    International Journal of Quantum Chemistry 70 (1998), S. 771-778 
    ISSN: 0020-7608
    Keywords: electric field effects ; hyperfine interactions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A recently published theory of electric field effects on electron spin resonance hyperfine couplings [Phys. Ref. Lett. 79, 379, (1997)] is extended to nuclear quadrupole coupling. With the use of the ab initio coupled Hartree-Fock approach and augmented Sadlej basis set, results are obtained for the first-order corrections to the isotropic and anisotropic parts of hyperfine coupling tensor and the electronic part of the electric field gradient tensor for 17O and 2H nuclei in OH radical. The first-order coefficients exhibit a number of interesting features. The calculated results, in general, appear to be insensitive to the bond-centered polarization functions used in the calculation.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 771-778, 1998
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  • 35
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    International Journal of Quantum Chemistry 70 (1998), S. 779-788 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ground-state density amplitude {ρ(r)}1/2 for atoms and molecules satisfies a Schrödinger equation in which the customary one-body potential energy V(r) of density functional theory is supplemented by the addition of the Pauli potential Vp(r). Since neither the exchange-correlation potential Vxc or Vp are presently known as functionals of the electron density ρ(r), approximations are currently unavoidable. Here, widespread use is made of semiclassical approximations, within a self-consistent field framework both with and without magnetic fields. The importance of low-order gradient quantities ∇2ρ/ρ and (∇ρ/ρ)2 is one focal point, while a generalized low-density approximation is another. New relativistic differential equations are given. Then, the arguments are generalized to embrace the so-called Slater sum P(r, β) : β=(kβT)-1, of statistical mechanics, generated by the one-body potential V(r). This is a generalized partition function, and differential equations are set up for this quantity P(r, β) with and without external fields. Finally, some potentially fruitful directions for treating cylindrically symmetric inhomogeneous electron liquids are outlined, following the very recent work of Amovilli and March. These include modeling the Slater sum along the electric field direction for the Stark effect in a hydrogenlike atom.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 779-788, 1998
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  • 36
    ISSN: 0020-7608
    Keywords: pulsed magnetic field ; Zeeman effect ; quadruple metal bonds ; octachlorodirhenate ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A procedure is given for the analysis of optical absorption data acquired in the hostile environment of a pulsed 1000-Tesla magnet.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 797-804, 1998
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  • 37
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    International Journal of Quantum Chemistry 70 (1998), S. 825-830 
    ISSN: 0020-7608
    Keywords: molybdenum ; phase stability ; relativity ; Douglas-Kroll ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The body-centered cubic-face-centered cubic (bcc-fcc) structural phase stability of molybdenum (Mo) is studied as a function of volume with both nonrelativistic and scalar-relativistic linear combinations of Gaussian-type orbitals-fitting functions (LCGTO-FF) calculations. It is demonstrated that relativity has a significant, albeit small effect, on the bcc-fcc structural energy difference, which increases with pressure. The scalar-relativistic structural energy difference curve is shown to be in excellent agreement with an earlier scalar-relativistic calculation using the full-potential linear muffin-tin orbital (FP-LMTO) method, clearly demonstrating the ability of the scalar-relativistic LCGTO-FF method to resolve an extremely subtle relativistic effect. It is argued that relativity will tend to delay pressure-induced structural phase transitions that are triggered by electron band reordering.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 825-830, 1998
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  • 38
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    International Journal of Quantum Chemistry 70 (1998), S. 831-853 
    ISSN: 0020-7608
    Keywords: Liquid water ; H-bond pattern ; orientational defect ; water cluster ; “dangling” bond ; ab initio HF/6-311(d, p) calculation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fifteen different structures of the water hexamer found ab initio within the 6-311G(d, p) basis set in the interval of 1.75 kcal/mol above the global minimum represent an unprecedented wide range of conformational plasticity of liquid water. The present work also provides the first ab initio demonstration of the existence of pentacoordinated water clusters of an orientational defect type and elaborates their properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 831-853, 1998
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  • 39
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    International Journal of Quantum Chemistry 70 (1998), S. 863-875 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 3-substituted-2-methoxybenzoic acid system exhibits resonance-stabilized intramolecular hydrogen bonding between the 2-methoxy oxygen and the adjacent carboxylic acid. This intramolecular hydrogen bond can be disrupted by adding another substituent with variable size on the neighboring 3-position of the ring. To relieve steric strain, the system must sacrifice hydrogen bonding and/or resonance stabilization. Full-energy optimizations have been done at HF/D95V (valence double-zeta Dunning-Huzinaga), HF/6-31G* (Pople), HF/D95 (full double-zeta Dunning-Huzinaga), HF/D95V(d, p), and HF/6-31+G(d, p). Further single-point calculations were done at MP2/D95V, MP2/6-31G*, MP2/D95, MP2/D95V(d, p), and MP2/6-31+G(d, p). The thermal populations of various conformational states including the hydrogen-bonding conformation are presented. The computational results were compared with the experimental thermal population of hydrogen bonding determined by nuclear magnetic resonance (NMR) and infrared (IR) spectroscopies. Results indicate that polarization of the second-row elements in intramolecular hydrogen bonding and perturbation-theory calculations that correct for electron correlations are very important for intramolecular hydrogen bonding. Adding polarization and diffuse functions to the hydrogens, while useful, are quite costly for these systems and do not seem to be as important.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 863-875, 1998
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  • 40
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    International Journal of Quantum Chemistry 70 (1998), S. 887-896 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We compare two systematic approaches to the calculation of reaction rates in liquid solutions: the separable equilibrium solvation (SES) approximation and the equilibrium solvation path (ESP) approximation. These approaches are tested for two reactions, ClCH3+NH3→Cl-+H3CNH3+ (R1) and NH4+…N′H3→NH3…N′H4+ (R2), both in aqueous solution. The first reaction illustrates the importance of variational optimization of the transition state, and the second illustrates the importance of tunneling. Free energies of solvation are calculated by the Solvation Model 5. All calculations are carried out by the new AMSOLRATE program, which is an interface of the AMSOL and POLYRATE programs.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 887-896, 1998
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  • 41
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    International Journal of Quantum Chemistry 70 (1998), S. 909-917 
    ISSN: 0020-7608
    Keywords: charge transfer ; α-particles ; alkali atoms ; MO expansion ; close coupling ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cross sections for single-electron capture by α-particles from ground state K and Rb were calculated in the low-to-intermediate energy region by employing the molecular expansion method in the framework of impact parameter formulation. The colliding partners are treated as a pseudo-one-electron system and the technique of the pseudopotential is used to account for their mutual interactions. The molecular wave function of the quasimolecule formed during the collision is expanded in terms of basis sets of atomic orbitals on two centers. The resulting coupled equations are solved semiclassically where a straight-line trajectory describes the relative motion of the two nuclei. The effect of electron translation is also suitably incorporated. The calculated cross sections, both total and partial, are presented and compared with the available experimental measurements.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 909-917, 1998
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  • 42
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Kramers' restricted Hartree-Fock (KRHF) and second-order Møller-Plesset perturbation (KRMP2) methods using relativistic effective core potentials (RECP) with spin-orbit operators and two-component spinors are extended to the unrestricted forms, KUHF and KUMP2. As in the conventional unrestricted methods, the KUHF and KUMP2 methods are capable of qualitatively describing the bond breaking for a single bond. As a result, it is possible to estimate spin-orbit effects along the dissociation curve at the HF and MP2 levels of theory as is demonstrated by the test calculations on the ground states of HI and CH3I. Since the energy lowering due to spin-orbit interactions is larger for the I atom than for the closed-shell molecules, dissociation energies are reduced and bond lengths are slightly elongated by the inclusion of the spin-orbit interactions.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 91-98, 1998
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  • 43
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    International Journal of Quantum Chemistry 66 (1998), S. 107-108 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 44
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    International Journal of Quantum Chemistry 66 (1998), S. 1-7 
    ISSN: 0020-7608
    Keywords: Symmetry ; projection operator ; VB wave function ; transition energy ; chemical bonds ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method constructing symmetry-adapted bonded Young tableau bases is proposed, based on the symmetry properties of bonded tableaus and the projection operator associated with a point group. Several examples including the ground states and π excited states of O3-, O3, O3+, and C3- are shown for instruction to construct the symmetrized valence bond (VB) wave function. Excitation energies of transitions from the ground states to π excited states of O3-, C3H5, and C3- are calculated with an optimized symmetrized valence bond wave function in the σ-π separation approximation. Good agreement between the VB and experimental excitation energies is observed. The bonding features of the ground state and the first π excited singlet and triplet states for S3 are discussed according to bonding populations from VB calculations. Both the singlet-biradical and the dipole structures have significant contributions to the ground state X 1A1 of S3, while the excited state 1 1B2 is essentially composed of the dipole structures, and the 1 3B2 excited state is comprised from a triplet-biradical structure.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 1-7, 1998
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  • 45
    ISSN: 0020-7608
    Keywords: keto/enol and imine/enamine tautomerizations ; intramolecular hydrogen shift ; transition structures ; comparison of several calculation methods ; asynchronous process ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The transition structures associated with the possible intramolecular tautomerization for acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems as models of keto/enol and imine/enamine interconversion processes, respectively, were characterized. The relative stabilities of the tautomers and the associated barrier heights were calculated. Ab initio analytical gradients and second derivatives at the HF level of theory and 3-21G, 6-31G, 6-31G**, 6-31++G**, and 6-311++G** basis-set, DFT (BP86/6-311++G** and BLYP/6-311++G**), and semiempirical (AM1 and PM3) procedures were used to identify the stationary points. Correlation effects were estimated using the perturbational approach at MP2/6-31G**, MP2/6-311++G**, and MP2/6-311++G (3df,2p) levels. The geometry, electronic structure, harmonic vibrational frequencies, and transition vector associated with the transition structures as well as the relative stabilities of different isomers and barrier heights were analyzed. The dependence of these properties upon theoretical methods is analyzed and discussed. The transition structures are four-membered rings and the corresponding transition vectors are associated to collective fluctuations. The 1,3 intramolecular hydrogen migration is much more advanced than are the hybridization changes on donor and acceptor centers at the transition structure. The corresponding barrier heights can be related to the change of bond orders and acid/base properties of these centers. A comparison of the results obtained with different methods renders that the nature of the transition structure seems to be a rather robust entity.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 9-24, 1998
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  • 46
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 25-30 
    ISSN: 0020-7608
    Keywords: Hylleraas-CI ; P states of 4He ; variance minimization ; upper and lower bounds ; perturbation theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Extensive Hylleraas-CI calculations for the lowest Po states of 4He were performed. The dependence of the variational energy values Eκ on the mass parameter κ given by κ=mHe2+/me- is discussed. Furthermore, lower bounds to Eκ were calculated using variance minimization.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 25-30, 1998
    Additional Material: 1 Ill.
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  • 47
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 31-45 
    ISSN: 0020-7608
    Keywords: magnetic susceptibility ; magnetic shielding tensor ; gauge invariance ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A transformation of the transverse Coulomb vector potential was implemented to calculate molecular magnetic properties via the random-phase approximation (RPA) within the framework of a “longitudinal gauge.” In this gauge, the diamagnetic contribution to magnetic susceptibility is a tensor with equal diagonal components as in atoms, irrespective of molecular symmetry, whereas diagonal and average diamagnetic contributions to the nuclear magnetic shielding are the same as in the Coulomb gauge. Near-Hartree-Fock magnetic susceptibility and nuclear magnetic shielding tensors were evaluated for a set of small molecules, HF, H2O, NH3, and CH4, employing extended Gaussian basis sets. The peculiar features of the longitudinal gauge, and the fulfillment of a series of sum rules involving the virial operator, which must be satisfied to guarantee gauge invariance of total magnetic tensors, were exploited to check the degree of convergence of theoretical values and to estimate the corresponding Hartree-Fock limit for the properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 31-45, 1998
    Additional Material: 15 Tab.
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  • 48
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 66 (1998), S. 47-68 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Three-dimensional crystal structures of the charge-transfer complexes of tetrathiafulvalene (TTF) with tetracyanoquinodimethane (TCNQ), (N,N′-dicyanbenzoquinondiimine (DCNQI), and N,N′-dicyan-2,5-dimethyl-1,4-benzoquinondiimine (2,5-Me2-DCNQI) were studied within the ab initio Hartree-Fock crystal orbital approximation using the CRYSTAL92 routine package. A qualitative agreement with the experimental data was achieved, and a definite border between one-electron and many-electron effects in the specific physical properties of the crystals under study was drawn. The calculations led to the tentative conclusion that the true chemical reaction corresponding to the charge transfer in such systems is a two-step transfer of two electrons from the donor's HOMO to the acceptor's LUMO and not only single-electron transfer, as usually believed. Then, whether the system is conductive or semiconductive depends upon the degree of the charge transfer (one, two, or no electrons, respectively). But the final degree of the charge transfer and the density of states on the Fermi level should be determined by many-electron effects. The theoretical approach used in this work seems to be of crucial importance in designing organic crystals with specific physical properties.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 47-68, 1998
    Additional Material: 18 Ill.
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  • 49
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 94-101 
    ISSN: 0192-8651
    Keywords: Dunham method ; rovibrational energy levels ; rovibrational Schrödinger equation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A numerical algorithm of the Dunham method for the solution of the rovibrational Schrödinger equation is proposed. It uses a new quasi-Hermitian method of constructing the optimal approximate polynomial for the tabularly defined potential curve of a diatomic molecule obtained from an ab initio calculation. In this method the optimal polynomial approximates the potential curve and its derivatives, but it uses only information about the potential curve for its construction. This property of the new method arises from analysis of a spectral representation of the optimal polynomial to determine how well it approximates the potential curve and its derivatives. Appropriate derivatives of the potential curve, needed in the Dunham method, are calculated by recurrence relations. Comparison with the finite-difference method shows that the precision of both methods is similar, while the Dunham method is hundreds of times faster.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 94-101, 1998
    Additional Material: 6 Tab.
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  • 50
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. v 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: No abstract.
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  • 51
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    Journal of Computational Chemistry 19 (1998), S. 123-128 
    ISSN: 0192-8651
    Keywords: gas phase structures ; conformational properties ; gas electron diffraction ; theoretical calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical calculations in combination with experimental gas phase structure research can be performed in two ways. The first is to support and improve experimental analyses by including additional data from theoretical calculations. This is to the advantage of the experiment. The second way is a comparison of geometric structures and conformational properties obtained with different theoretical methods with the experimental result. This comparison indicates which theoretical method or methods are suitable for a specific compound. This approach is to the advantage of the theory.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 123-128, 1998
    Additional Material: 2 Ill.
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  • 52
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    Journal of Computational Chemistry 19 (1998), S. 113-122 
    ISSN: 0192-8651
    Keywords: density-functional theory ; 51V ; chemical shift calculations ; mechanism of ethylene polymerization ; barriers for ethylene insertion ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Employing gradient-corrected levels of density-functional theory (DFT), medium-sized basis sets, and optimized geometries, chemical shifts are calculated for [VOClnF3-n] (n=0-3), VF5, [VO(OCH2CH2)3N], [V(CO)6]-, [V(CO)5(N2)]-, as well as for the model compounds [VO(OMe)nMe3-n] (n=0-3) and their AlH3 adducts. Experimental trends in δ(51V) are well reproduced with DFT-based methods; for example, the slopes of the δ(51V)calc vs. δ(51V)expt linear regression lines are 0.92 and 1.03 at the GIAO-BP86 and GIAO-B3LYP levels, respectively. Ethylene polymerization observed with [V(O⋅⋅⋅AlX3)(OR)nR′3-n] (X, R, R′=bulky alkyl, aryl, or silyl groups) is shown for model systems (X=H, R=R′=Me) to proceed by insertion of the olefin into a V - C bond via a transition state with approximate square-pyramidal coordination about vanadium. For the tri- and dialkyl derivatives (n=0, 1), similar activation barriers of ca. 19 kcal/mol are computed (BP86 level including zero-point energies), whereas that of the monoalkyl species (n=2) is predicted to be much higher, ca. 30 kcal/mol. The relevance of these results for the apparent relationship between δ(51V) and catalytic activities is discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 113-122, 1998
    Additional Material: 6 Ill.
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  • 53
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    Journal of Computational Chemistry 19 (1998), S. 139-143 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The reactivity of the fullerenes is primarily a function of their strain, as measured by the pyramidalization angle or curvature of the conjugated carbon atoms. A consideration of the orientation of the π-orbitals shows that η2-complexation reactions lead to reaction products with the fullerenes that are very similar to those obtained from unstrained alkenes. Furthermore, a large amount of strain energy is released in this reaction, so it is clear just why this reaction is important in fullerene chemistry. On the other hand, it is shown that the π-orbitals of C60 are poorly oriented for overlap with an exohedral metal atom centered over the five- or six-membered rings, but well disposed for overlap with an endohedral metal atom centered under the five- or six-membered rings.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 139-143, 1998
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  • 54
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 129-138 
    ISSN: 0192-8651
    Keywords: ab initio ; formimidol ; H-bond ; energy barrier ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The central C atom of the OCCCO skeleton of the malonaldehyde molecule is replaced by N, and the effects upon the intramolecular H-bond and the proton transfer are monitored by ab initio calculations in the ground and excited electronic states. The H-bond is weakened in the singlet and triplet states arising from n→π* excitation in both molecules, which is accompanied by a heightened barrier to proton transfer.3ππ* behaves in the same manner, but the singlet ππ* state has a stronger H-bond and lower barrier. Replacement of the central C atom by N strengthens the intramolecular H-bond. Although the proton transfer barrier in the ground state of formimidol is lower than in malonaldehyde, the barriers in all four excited states are higher in the N-analog. The latter substitution also dampens the effect of the n→π* excitation upon the H-bond and increases the excitation energies of the various states, particularly ππ*.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 129-138, 1998
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  • 55
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 144-153 
    ISSN: 0192-8651
    Keywords: molecular dynamics simulations ; clay mineral adsorption ; clay mineral parameter development ; trichloroethene adsorption on clay minerals ; organic chlorine electrostatic charges ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The adsorption of trichloroethene, C2HCl3, on clay mineral surfaces in the presence of water has been modeled as an example describing a general program that uses molecular dynamics simulations to study the sorption of organic materials at the clay mineral/aqueous solution interface. Surfaces of the clay minerals kaolinite and pyrophyllite were hydrated at different water levels corresponding to partial and complete monolayers of water. In agreement with experimental trends, water was found to outcompete C2HCl3 for clay surface sites. The simulations suggest that at least three distinct mechanisms coexist for C2HCl3 on clay minerals in the environment. The most stable interaction of C2HCl3 with clay surfaces is by full molecular contact, coplanar with the basal surface. This kind of interaction is suppressed by increasing water loads. A second less stable and more reversible interaction involves adsorption through single-atom contact between one Cl atom and the surface. In a third mechanism, adsorbed C2HCl3 never contacts the clay directly but sorbs onto the first water layer. To test the efficacy of existing force field parameters of organic compounds in solid state simulations, molecular dynamics simulations of several representative organic crystals were also performed and compared with the experimental crystal structures. These investigations show that, in general, in condensed-phase studies, parameter evaluations are realistic only when thermal motion effects are included in the simulations. For chlorohydrocarbons in particular, further explorations are needed of atomic point charge assignments.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 144-153, 1998
    Additional Material: 5 Ill.
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  • 56
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 277-289 
    ISSN: 0192-8651
    Keywords: ab initio molecular orbital theory ; density functional theory ; ozone depletion problem ; halon replacement ; fire suppression mechanism ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital theory and density functional theory calculations have been carried out on the reactions of the trifluoromethyl radical with the hydroxyl and the hydrogen radicals. These reactions are key reactions that underlie a new fire extinguishing mechanism of non-bromine-containing halon replacements. The activation energies calculated by the MP2 and QCISD methods are in good agreement with the experimental values. The B3LYP, as well as MP2 and QCISD, give good results for the calculations of the heats of reactions. The GAUSSIAN-1 and GAUSSIAN-2 theory calculations present the most acxcurate results on both the activation energies and the heats of reactions. The effects of the scaling factors on the activation energies and the heats of reactions are also evaluated.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 277-289, 1998
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  • 57
    ISSN: 0192-8651
    Keywords: protein folding ; multibody interactions ; electrostatic interactions ; cumulant expansion ; potential of mean force ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Based on the dipole model of peptide groups developed in our earlier work [Liwo et al., Prot. Sci., 2, 1697 (1993)], a cumulant expansion of the average free energy of the system of freely rotating peptide-group dipoles tethered to a fixed α-carbon trace is derived. A graphical approach is presented to find all nonvanishing terms in the cumulants. In particular, analytical expressions for three- and four-body (correlation) terms in the averaged interaction potential of united peptide groups are derived. These expressions are similar to the cooperative forces in hydrogen bonding introduced by Koliński and Skolnick [J. Chem. Phys., 97, 9412 (1992)]. The cooperativity arises here naturally from the higher order terms in the power-series expansion (in the inverse of the temperature) for the average energy. Test calculations have shown that addition of the derived four-body term to the statistical united-residue potential of our earlier work [Liwo et al., J. Comput. Chem., 18, 849, 874 (1997)] greatly improves its performance in folding poly-L-alanine into an α-helix.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 259-276, 1998
    Additional Material: 9 Ill.
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  • 58
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 377-395 
    ISSN: 0192-8651
    Keywords: atomic charges ; copper complexes ; electrostatic potential charges ; molecular simulation ; rank-deficiency problems ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four methods for deriving partial atomic charges from the quantum chemical electrostatic potential (CHELP, CHELPG, Merz-Kollman, and RESP) have been compared and critically evaluated. It is shown the charges strongly depend on how and where the potential points are selected. Two alternative methods are suggested to avoid the arbitrariness in the point-selection schemes and van der Waals exclusion radii: CHELP-BOW, which also estimates the charges from the electrostatic potential, but with potential points that are Boltzmann-weighted after their occurrence in actual simulations using the energy function of the program in which the charges will be used, and CHELMO, which estimates the charges directly from the electrostatic multipole moments. Different criteria for the quality of the charges are discussed. The CHELMO method gives the best multipole moments for small and medium-sized polar systems, whereas the CHELP-BOW charges reproduce best the total interaction energy in actual simulations. Among the standard methods, the Merz-Kollman charges give the best moments and potentials, but they show an appreciable dependence on the orientation of the molecule.We have also examined the recent warning that charges derived by a least-squares fit to the electrostatic potential normally are not statistically valid. It is shown that no rank-deficiency problems are encountered for molecules with up to 84 atoms if the least-squares fit is performed using pseudoinverses calculated by singular value decomposition and if constraints are treated by elimination.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 377-395, 1998
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  • 59
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    Journal of Computational Chemistry 19 (1998), S. 418-429 
    ISSN: 0192-8651
    Keywords: Lacks-Gordon exchange functional ; Lee-Yang-Parr correlation functional ; conventional density functional ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present an analysis of the numerical performances of the exchange functional proposed by Lacks and Gordon, which we have implemented in the Gaussian series of programs. This functional has been built with the double aim of respecting most of the known scaling and asymptotic properties and of giving good numerical performances, especially as concerns noncovalent interactions. We have found that the coupling of the Lacks-Gordon exchange and Lee-Yang-Parr correlation functionals provides a reliable conventional density functional approach. The corresponding parameter-free adiabatic connection model, in which the ratio between Hartree-Fock and Lacks-Gordon exchange is determined a priori from purely theoretical considerations, allows us to obtain remarkable results for both covalent and noncovalent interactions in a satisfactory theoretical scheme, encompassing the free electron gas limit and most of the known scaling conditions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 418-429, 1998
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  • 60
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 548-573 
    ISSN: 0192-8651
    Keywords: surface loops ; structure prediction ; global energy minimization ; energy functions ; hydration free energy ; atomic multipoles ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to that seen in ab initio data. Intrinsic torsional energy is modeled as a sum over pairs of adjacent torsion angles of 2-dimensional Fourier series. Hydrophobic energy is that of a hydration shell model. The remainder of hydration free energy is obtained as the energetic effect of a continuous dielectric medium. Parameters are adjusted to reproduce the following data: a complete set of ab initio energy surfaces, meaning one for each pair of adjacent torsion angles of each blocked amino acid; experimental crystal structures and sublimation energies for nine model compounds; ab initio energies over 1014 conformations of 15 small-molecule dimers; and experimental hydration free energies for 48 model compounds. All ab initio data is at the Hartree-Fock/6-31G* level.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 548-573, 1998
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  • 61
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 585-592 
    ISSN: 0192-8651
    Keywords: semiempirical calculations ; electronic spectra ; conformational analysis ; 2,5-distyrylpyrazine laser dye ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiempirical (MNDO and PM3) molecular orbital calculations have been undertaken to study the structures of the ground and excited states of 2,5-distrylpyrazine dye to assess its activity as a laser dye. In the ground and first excited singlet states, the trans-trans structure of C2h symmetry is the most stable structure in the gas phase and in DMSO, which agrees with the experimental findings. Upon excitation, the flexibility of the molecule decreases, leading to a subsequent decrease in the radiationless deactivation pathway and this increases the fluorescence efficiency of DSP. The absorption, excitation, and emission spectra have been calculated at the MNDO level using the PM3 optimized geometries in DMSO. At this level the agreement between theory and experiment is quite good. An estimated absorption band at 377 nm (expt 380 nm) is assigned to the S0→S1 transition. The excited state absorption band at 457 nm (expt 460 nm) is assigned to the S1→S12 transition. The emission band at 458 nm (expt 460 nm) is assigned to the S′1→S′0 transition. The overlap between the emission and the excited-state absorption spectra is presumably the main reason behind the reduced laser activity of the investigated dye.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 585-592, 1998
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  • 62
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    Journal of Computational Chemistry 19 (1998), S. 658-672 
    ISSN: 0192-8651
    Keywords: full configuration interaction ; ab initio methods ; acetylene molecule ; parallel computation ; message passing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A parallel full configuration interaction (FCI) code, implemented on a distributed memory MPP computer, has been modified in order to use a direct algorithm to compute the lists of mono- and biexcitations each time they are needed. We were able to perform FCI calculations on the ground state of the acetylene molecule with two different basis sets, corresponding to more than 2.5 and 5 billion Slater determinants, respectively. The calculations were performed on a Cray-T3D and a Cray-T3E, both machines having 128 processors. Performance and comparison between the two computers are reported and discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 658-672, 1998
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  • 63
    ISSN: 0192-8651
    Keywords: solvation free energies ; GB/SA solvent model ; energy minimization calculations ; AMBER force field ; macromodel ; thermodynamic cycle perturbation (TCP) calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 769-780, 1998
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