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  • 1995-1999  (3,212)
  • Chemical Engineering  (1,635)
  • 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
    Additional Material: 7 Ill.
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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
    Electronic Resource
    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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    Electronic Resource
    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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    Electronic Resource
    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
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    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
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  • 47
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    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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    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
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  • 49
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    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
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  • 50
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    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
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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
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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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    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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    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
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  • 56
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    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
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  • 58
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    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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    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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    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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  • 64
    ISSN: 0192-8651
    Keywords: gas-phase proton affinity and basicity ; density functional computations ; protonation of DNA acid bases ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Gradient-corrected density functional computations with triple-zeta-type basis sets were performed to determine the preferred protonation site and the absolute gas-phase proton affinities of the most stable tautomer of the DNA bases thymine (T), cytosine (C), adenine (A), and guanine (G). Charge distribution, bond orders, and molecular electrostatic potentials were considered to rationalize the obtained results. The vibrational frequencies and the contribution of the zero-point energies were also computed. Significant geometrical changes in bond lengths and angles near the protonation sites were found. At 298 K, proton affinities values of 208.8 (T), 229.1 (C), 225.8 (A), and 230.3 (G) kcal/mol were obtained in agreement with experimental results.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 989-1000, 1998
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  • 65
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    Journal of Computational Chemistry 19 (1998), S. 1001-1016 
    ISSN: 0192-8651
    Keywords: ab initio ; molecular mechanics ; hydrogen bond ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Extensive calculations on hydrogen bonded systems were carried out using the improved MM3 directional hydrogen bond potential. The resulting total function was reoptimized. Comparisons of the hydrogen bonding potential function from ab initio calculations (MP2/6-31G**); the original MM3(89); and the reoptimized MM3 force field MM3(96), for a variety of C, N, O, and Cl systems including the formamide dimer and formamide-water complex, are described herein. Hydrogen bonding is shown to be a far more complicated and ubiquitous phenomenon than is generally recognized.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1001-1016, 1998
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  • 66
    ISSN: 0192-8651
    Keywords: cryptophanes ; molecular dynamics ; free energy perturbation ; preorganization ; binding selectivity ; solvent effects ; molecular recognition ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantitative assessment of the “best fit” between neutral molecules and the cavity of a “rigid” neutral receptor is a challenging task in supramolecular chemistry, drug design, and biology. We investigate this question by molecular dynamics and free-energy perturbation simulations performed on the macrocyclic ligand cryptophane-E (L) and its L·S complexes with three tetrahedral guests (S=CH2Cl2, CHCl3, and CCl4) in the gas phase and in chloroform solution. The van der Waals interactions are shown to play a crucial role in the calculated complexation selectivity. Calculations using Lennard-Jones 6-12 potentials and “standard” OPLS R*Cl and εCl parameters for the Cl atoms of S lead to a preference for CCl4, in contrast to the selectivities observed experimentally in solution (CHCl3 〉 CH2Cl2 〉 CCl4). Based on systematic investigations of the relative free energies of binding of CHCl3/S, we derive a set of R*Cl and εCl van der Waals parameters that account for experimental binding data. Although the complexes are of the van der Waals type, their electrostatic representation is also crucial for correct calculation of relative stabilities. Thus, the recognition of the “best guest” stems from a subtle balance of distance and time-dependent, cumulative noncovalent interactions between atoms of S and of L, which require an accurate representation. In addition, even in a weakly polar solvent, like chloroform, solvation effects are shown to modulate the recognition of the neutral substrates.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 820-832, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1017-1029 
    ISSN: 0192-8651
    Keywords: pseudospectral ; parallel ; Hartree-Fock ; gradient ; scalable ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present an outline of the parallel implementation of our pseudospectral electronic structure program, Jaguar, including the algorithm and timings for the Hartree-Fock and analytic gradient portions of the program. We also present the parallel algorithm and timings for our Lanczos eigenvector refinement code and demonstrate that its performance is superior to the ScaLAPACK diagonalization routines. The overall efficiency of our code increases as the size of the calculation is increased, demonstrating actual as well as theoretical scalability. For our largest test system, alanine pentapeptide [818 basis functions in the cc-pVTZ(-f) basis set], our Fock matrix assembly procedure has an efficiency of nearly 90% on a 16-processor SP2 partition. The SCF portion for this case (including eigenvector refinement) has an overall efficiency of 87% on a partition of 8 processors and 74% on a partition of 16 processors. Finally, our parallel gradient calculations have a parallel efficiency of 84% on 8 processors for porphine (430 basis functions).   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1017-1029, 1998
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  • 68
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    Journal of Computational Chemistry 19 (1998), S. 308-318 
    ISSN: 0192-8651
    Keywords: tellurium tetrachloride ; ab initio calculations ; density functional theory ; vibrational analysis ; scaled quantum mechanical method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Vibrational analysis of tellurium tetrachloride, TeCl4, was performed with Hartree-Fock (HF), MP2, and generalized gradient approximation density functional theory (DFT) methods supplemented with polarized double-zeta split valence (DZVP) basis sets and relativistic effective core potentials (RECP) of Hay and Wadt. The molecular geometry is best reproduced at the HF and MP2/RECP+DZVP [polarized Hay and Wadt RECP for Te and 6-31G(d) basis set for Cl] levels of theory. The DFT methods gave rise to poorer results, especially those using Becke's 1988 exchange functional. Generally, the vibrational frequencies calculated by the MP2 and B3-type DFT methods with the all electron and RECP+DZVP basis sets as well as at the HF/RECP level were in satisfactory accord with the experimental data. The agreement was good enough to assist the assignment of the measured vibrational spectra. The best agreement with the experimental vibrational frequencies was achieved with the scaled HF/RECP force field. Consistent results were obtained for the unobserved A2 (ν4) fundamental, where the results of the best methods were within 4 cm-1. The best force fields were obtained with the following methods: Becke3-Lee-Yang-Parr and Becke3-Perdew/all electron basis, MP2 and Becke3-Perdew/RECP+DZVP, and HF/RECP. The methods using RECPs are advantageous for large-scale computations. The RECP basis set effectively compensates the errors of the HF method for TeCl4; however, it provides poor results with correlated methods.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 308-318, 1998
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  • 69
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    Journal of Computational Chemistry 19 (1998), S. 947-960 
    ISSN: 0192-8651
    Keywords: olefin polymerization ; Ziegler-Natta catalysis ; quantum chemical methods ; ethylene ; TiH2CH3+ ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Insertion of ethylene into the Ti-methyl bond in TiH2CH+3 is chosen as a model reaction for investigating the performance of a range of contemporary quantum chemical models in polymerization studies. Basis set effects are investigated at the self-consistent-field level, covering Hartree-Fock, pure DFT, and hybrid DFT. In agreement with findings in part I of this study, the basis set sensitivity of ethylene is shown to introduce a bias in computed energetics, amounting to 2-3 kcal/mol when DZP bases are used to compute the overall heat of monomer insertion. The geometry of stationary points relevant to the insertion reaction is determined using hybrid density functional theory. Based on these structures, the energy profile of the insertion reaction is computed using a range of popular quantum chemical approximations. The methods include Hartree-Fock and Møller-Plesset (MP) perturbation theory up through the fourth order in spin-restricted, spin-unrestricted, and spin-projected formalisms. Furthermore, configuration-interaction-based methods are included, of which the top level method is singly and doubly excited coupled clusters with a perturbative estimate of the contribution from triply excited configurations added [CCSD(T)]. The performance of the methods just mentioned, as well as three pure density functional and three hybrid density functional methods, are compared with respect to “best” relative energies, defined through extrapolation of CCSD(T) correlation energies according to the PCI scheme of Siegbahn and coworkers. Even though the MP series show poor convergence, spin-projected MP2, as well as two pure DFT methods (BPW91, BP86) and PCI-78 based on the MCPF method, show similar and very good agreement with best relative energies for the insertion reaction.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 947-960, 1998
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    Journal of Computational Chemistry 19 (1998), S. 363-367 
    ISSN: 0192-8651
    Keywords: solution structuring ; radial distribution functions ; available volume ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The traditional method of analyzing solution structuring properties of solutes using atom-atom radial distribution functions (rdfs) can give rise to misleading interpretations when the volume occupied by the solute is ignored. It is shown by using the examples of O(4) in α- and β-D-allose that a more reliable interpretation of rdfs can be obtained by normalising the rdf using the available volume, rather than the traditional volume of a spherical shell.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 363-367, 1998
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    Journal of Computational Chemistry 19 (1998), S. 368-376 
    ISSN: 0192-8651
    Keywords: general coupling operator ; coupling operator ; wave functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We comment on the convergence of the general coupling operator for all types of one-configuration or multiconfigurational wave functions that still preserve the one-configuration structure for the energy expression. The choice on the best arbitrary real and antisymmetric parameters inherent in the coupling operator methodology is discussed, giving a theoretical reason. Another type of coupling operator is defined, presented, and analyzed. Finally, we give some numerical examples related to the low-lying electronic states of a cluster model for K2NiF4 solid.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 368-376, 1998
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    Journal of Computational Chemistry 19 (1998), S. 396-403 
    ISSN: 0192-8651
    Keywords: Monte-Carlo simulation ; catalytic processes ; stochastic kinetic model ; solid surfaces ; graphic representation ; catalysis by metal ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Monte-Carlo model for the simulation of alkene hydrogenation on metallic catalysts has been developed and implemented in Fortran language. We describe the model employed for ethylene hydrogenation on platinum and show the flow chart of the program. Computational characteristics such as number of necessary calculations to reach steady state, running times on different platforms, and effect of the size of the catalyst matrix, are presented. Good correlation between simulated and experimental data was observed. A subroutine allows for visual observation of the reaction. This approach is very useful for obtaining a personal impression of the important factors governing the reaction. By using this example the advantages of Monte-Carlo simulation to test the level of understanding of catalytic phenomena are discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 396-403, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1130-1140 
    ISSN: 0192-8651
    Keywords: asymmetrization effects ; electron donor-acceptor ; materials for nonlinear optics ; population analysis ; dipole alignment ; structural effects of conjugation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Asymmetric donor-acceptor-substituted π-conjugated systems with low dipole moments and structural components that favor parallel alignment of neighboring molecules are potential molecular organic materials with nonlinear optical properties for which near prefect dipole parallel alignment is possible. The asymmetrical 4-methoxysubstituted acetophenone azines with the substituents fluorine (1), chlorine (2), bromine (3), cyano (4), and nitro (5) in the 4′-position have been studied in this context, and for 2 and 3 the dipole parallel alignment has indeed been accomplished in crystals of the pure material. In the present study, the effects of asymmetrization on the structure and the electronic structures of the ground states of 1-5 have been explored at the RHF/6-31G* level. The properties of the optimized structures of the azines 1-5, a comparative analysis of asymmetrical and symmetrical azines, and natural population analyses, all show no significant evidence for conjugation over the azine bridge. The concept of azine spacers as “conjugation stoppers” is useful and the dipole moments of asymmetrical azines are relatively small. The analysis suggests that the charge transfer between the donor and acceptor contributes to the dipole moment much less than is generally assumed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1130-1140, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1141-1145 
    ISSN: 0192-8651
    Keywords: internal rotation ; ethane ; energy pathways ; broken symmetry ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Computational studies of the minimum energy pathway for internal rotation of a methyl group are often made by constraining one dihedral angle at a sequence of values and optimizing all other parameters. When this is done, the methyl group adopts an asymmetric configuration at intermediate values of the torsion angle, with unequal bond lengths, bond angles, and torsion angles, even though the moiety against which it is rotating is another methyl group. The potential surface leading to this phenomenon is investigated using Hartree-Fock SCF calculations at the 6-31G* and 6-311G** levels and the detailed structural behavior of the methyl group during the course of the internal rotation is examined. It is shown that the nature of the constraint governs the resulting deformation of the methyl group symmetry.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1141-1145, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1370-1386 
    ISSN: 0192-8651
    Keywords: acyl halides ; MM3 ; ab initio calculations ; conformational analysis ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new molecular mechanics (MM3) force field has been developed based on various experimental data as well as ab initio calculations. Computer-generated molecular structures and energy values were compared with experimentally determined data. The acyl halides studied were formyl halides, acetyl halides, propionyl halides, n-butyryl halides, 2-methylpropionyl halides, and 2,2-dimethylpropionyl halides. The rms deviations were 0.005 Å and 1.06° for bond lengths and bond angles, respectively. MM3 was in good overall agreement with the available structural, conformational, and thermodynamic data.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1370-1386, 1998
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    Journal of Computational Chemistry 19 (1998), S. 488-503 
    ISSN: 0192-8651
    Keywords: density functional theory ; electron density ; shell structure ; Fukui function ; atomic hardnesses ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An approximation to the Fukui function in atoms recently proposed in the form of a gradient correction to the local density approximation expression is here investigated. The spatial behavior of this function is analyzed, focusing on the gradient correction term. Physical information on the shell structure of atoms is shown to be conveyed by the radial distribution of that term. The analytically modeled densities (AMD) procedure is also implemented, and global atomic hardnesses are calculated with Hartree-Fock and AMD representations of atomic electron densities.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 488-503, 1998
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    Journal of Computational Chemistry 19 (1998), S. 430-458 
    ISSN: 0192-8651
    Keywords: force fields ; amides ; conformations ; ab initio ; quantum chemistry ; molecular mechanics ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: As the field of biomolecular structure advances, there is an ever-growing need for accurate modeling of molecular energy surfaces to simulate and predict the properties of these important systems. To address this need, a second generation amide force field for use in simulations of small organics as well as proteins and peptides has been derived. The critical question of what accuracy can be expected from calculations in general, and with this class II force field in particular, is addressed for structural, dynamic, and energetic properties. The force field is derived from a recent methodology we have developed that involves the systematic use of quantum mechanical observables. Systematic ab initio calculations were carried out for numerous configurations of 17 amide and related compounds. Relative energies and first and second derivatives of the energy of 638 structures of these compounds resulted in 140,970 ab initio quantum mechanical observables. The class II peptide quantum mechanical force field (QMFF), containing 732 force constants and reference values, was parameterized against these observables. A major objective of this work is to help establish the role of anharmonicity and coupling in improving the accuracy of molecular force fields, as these terms have not yet become an agreed upon standard in the ever more extensive simulations being used to probe biomolecular properties. This has been addressed by deriving a class I harmonic diagonal force field (HDFF), which was fit to the same energy surface as the QMFF, thus providing an opportunity to quantify the effects of these coupling and anharmonic contributions. Both force field representations are assessed in terms of their ability to fit the observables. They have also been tested by calculating the properties of 11 stationary states of these amide molecules. Optimized structures, vibrational frequencies, and conformational energies obtained from the quantum calculations and from both the QMFF and the HDFF are compared. Several strained and derivatized compounds including urea, formylformamide, and butyrolactam are included in these tests to assess the range of applicability (transferability) of the force fields. It was found that the class II coupled anharmonic force field reproduced the structures, energies, and vibrational frequencies significantly more faithfully than the class I harmonic diagonal force field. An important measure, rms energy deviation, was found to be 1.06 kcal/mol with the class II force field, and 2.30 kcal/mol with the harmonic diagonal force field. These deviations represent the error in relative configurational energy differences for strained and distorted structures calculated with the force fields compared with quantum mechanics. This provides a measure of the accuracy that might be expected in applications where strain may be important such as calculating the energy of a system as it approaches a (rotational) barrier, in ligand binding to a protein, or effects of introducing substituents into a molecule that may induce strain. Similar results were found for structural properties. Protein dynamics is becoming of ever-increasing interest, and, to simulate dynamic properties accurately, the dynamic behavior of model compounds needs to be well accounted for. To this end, the ability of the class I and class II force fields to reproduce the vibrational frequencies obtained from the quantum energy surface was assessed. An rms deviation of 43 cm-1 was achieved with the coupled anharmonic force field, as compared to 105 cm-1 with the harmonic diagonal force field. Thus, the analysis presented here of the class II force field for the amide functional group demonstrates that the incorporation of anharmonicity and coupling terms in the force field significantly improves the accuracy and transferability with regard to the simulation of structural, energetic, and dynamic properties of amides.    © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 430-458, 1998
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    Journal of Computational Chemistry 19 (1998), S. 504-511 
    ISSN: 0192-8651
    Keywords: geometry optimization ; natural internal coordinates ; connectivity ; graph theory ; ring systems ; intermolecular interactions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple, customizable connectivity scheme is rigorously defined in which pairs of atoms are classified into three categories. The tools of graph theory are used to analyze the molecular graph and to efficiently find rings and ring assemblies through a combination of pruning and homeomorphic reduction. The definition of natural internal coordinates is extended in a nonredundant fashion for the various cases of weakly interacting components and for fused ring systems. The ring system coordinates were tested and found to be superior to Z-matrix coordinates.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 504-511, 1998
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  • 79
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    Journal of Computational Chemistry 19 (1998), S. 512-523 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; force field ; transition metal compounds ; coordinated ligands ; organic backbone ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new molecular mechanics force field has been developed that takes into account the fact that, upon coordination to a transition metal ion, the redistribution of electron density leads to small but significant structural changes in the organic backbone of the ligand. Structural studies indicate that the perturbation by coordination to a metal ion extends to the α-carbon atom of the donor, the perturbation is roughly independent of the metal center for M2+ and M3+ and negligible for M+, and the perturbation of the Cα(SINGLE BOND)Cα′ bond is roughly independent of the donor atom. New parameter sets for oxalates, imidazoles, and pyrazoles are also presented. The refined parameters have been validated with a large number of monodentate, multidentate, and macrocyclic ligands.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 512-523, 1998
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    Journal of Computational Chemistry 19 (1998), S. 524-534 
    ISSN: 0192-8651
    Keywords: ab initio conformational analysis ; cyclooctane molecule ; potential energy surface ; Hartree-Fock theory ; Møller-Plesset theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surface (PES) for the cyclooctane molecule was comprehensively investigated at the Hartree-Fock (HF) level of theory employing the 3-21G, 6-31G, and 6-31G* basis sets. Six distinct true minimum energy structures (named B, BB, BC, CROWN, TBC, and TCC1), characterized through harmonic frequency analysis, were located on the multidimensional PES. Two transition state structures were also located on the PES for the cyclooctane molecule. Electron correlation effects were accounted for using the Møller-Plesset second-order perturbation theory (MP2) approach. The predicted global minimum energy structure on the ab initio PES for the cyclooctane molecule is the BC conformer. A gas phase electron diffraction study at 300 K suggested a conformational mixture while an NMR study in solution at 161.5 K predicted the BC conformer as the predominant form. The equilibrium constants reported in the present study, which were evaluated from the ab initio calculated total Gibbs free energy change values, were in good agreement with both experimental investigations. The ab initio results showed that the low temperature condition significantly favored the BC conformer while above room temperature both BC and CROWN structures can coexist.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 524-534, 1998
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    Journal of Computational Chemistry 19 (1998), S. 593-609 
    ISSN: 0192-8651
    Keywords: natural resonance theory ; resonance theory ; natural bond orbitals ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a new quantum-mechanical resonance theory based on the first-order reduced density matrix and its representation in terms of natural bond orbitals (NBOs). This “natural” resonance theory (NRT) departs in important respects from the classical Pauling-Wheland formulation, yet it leads to quantitative resonance weights that are in qualitative accord with conventional resonance theory and chemical intuition. The NRT variational functional leads to an optimal resonance-weighted approximation to the full density matrix, combining the “single reference” limit of weak delocalization (incorporating diagonal population changes only) with the full “multireference” limit of strong delocalization (incorporating off-diagonal couplings between resonance structures. The NRT variational functional yields an error measure that serves as an intrinsic criterion of accuracy of the resonance-theoretic description. The NRT program structure, algorithms, and numerical characteristics are described in supplementary material, and detailed chemical applications are presented in two companion papers.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 593-609, 1998
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    Journal of Computational Chemistry 19 (1998), S. 610-627 
    ISSN: 0192-8651
    Keywords: natural resonance theory ; resonance theory ; valency ; bond order ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Resonance weights derived from the Natural Resonance Theory (NRT), introduced in the preceding paper are used to calculate “natural bond order,” “natural atomic valency,” and other atomic and bond indices reflecting the resonance composition of the wave function. These indices are found to give significantly better agreement with observed properties (empirical valency, bond lengths) than do corresponding MO-based indices. A characteristic feature of the NRT treatment is the description of bond polarity by a “bond ionicity” index (resonance-averaged NBO polarization ratio), which replaces the “covalent-ionic resonance” of Pauling-Wheland theory and explicity exhibits the complementary relationship of covalency and electrovalency that underlies empirical assignments of atomic valency. We present ab initio NRT applications to prototype saturated and unsaturated molecules methylamine, butadiene), polar compounds (fluoromethanes), and open-shell species: (hydroxymethyl radical) to demonstrate the numerical stability, convergence, and chemical reasonableness of the NRT bond indices in comparison to other measures of valency and bond order in current usage.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 610-627, 1998
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    Journal of Computational Chemistry 19 (1998), S. 685-694 
    ISSN: 0192-8651
    Keywords: molecular dynamics ; domain decomposition algorithm ; parallel computers ; pair list for molecular dynamics code on SIMD machines ; array processor elaborator (APE) ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In recent years several implementations of molecular dynamics (MD) codes have been reported on multiple instruction multiple data (MIMD) machines. However, very few implementations of MD codes on single instruction multiple data (SIMD) machines have been reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD codes for SIMD machines, such that, generally, the full connectivity computation has been used. We present an algorithm, the global cut-off algorithm (GCA), which permits the use of pair lists on SIMD machines. GCA is based on a probabilistic approach and requires the cut-off condition to be simultaneously verified on all nodes of the machine. The MD code used was taken from the GROMOS package; only the routines involved in the pair lists and in the computation of nonbonded interactions were rewritten for a parallel architecture. The remaining calculations were performed on the host computer. The algorithm has been tested on Quadrics computers for configurations of 32, 128, and 512 processors and for systems of 4000, 8000, 15,000, and 30,000 particles. Quadrics was developed by Istituto Nazionale di Fisica Nucleare (INFN) and marketed by Alenia Spazio.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 685-694, 1998
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    Journal of Computational Chemistry 19 (1998), S. 716-725 
    ISSN: 0192-8651
    Keywords: NMR ; boron nitride ; solid state ; theoretical chemistry ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hydrogen-saturated cut-outs of hexagonal boron nitride have been used to model the solid state. Model compounds have been geometry optimized by means of density functional theory, whereas chemical shift calculations have been carried out at the coupled-perturbed Hartree-Fock level of theory employing gauge-including atomic orbital (GIAO) basis sets. The reliability of results has been tested against experimental values for chemical shifts in stable molecules with similar structural elements. With increasing cluster size, viz. a vanishing influence of the saturating hydrogens on the innermost nitrogen atoms, we find a convergence of 15N chemical shifts. A classification scheme for the chemical environment of a nitrogen atom has been set up according to its bonding graph including the second coordination sphere. For a given connectivity, chemical shifts vary within a few parts per million, thus enabling us to predict a 15N-NMR chemical shift of -285 ± 5 ppm for solid α-boron nitride.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 716-725, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1515-1525 
    ISSN: 0192-8651
    Keywords: cation-π ; development ; CHARMm22.0 ; correction term ; force field ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The modeling of voltage-gated ion-channel proteins is a continuing challenge for force-field calculations because of the diverse range of interactions involved. In particular, current force fields are not parameterized for either ion-amino acid or amino acid-electric field interactions. To address the parameterization of ion-amino acid interactions, we have tested the use of empirical correction terms, derived from ab initio calculations of single amino acids (representing the peptide backbone) interacting with K+ ions. Having demonstrated the utility of such an approach, we then extended the application to the amino acid side chains. The calculation of the interaction of K+ with serine, cysteine, methionine, lysine, arginine, aspartate, histidine (uncharged), tyrosine, tryptophan, and phenylalanine, both completes the parameterization of the molecular environments contained in the amino acids, and allows specific comment on these ion-functional group interactions. The cation-π interactions were of particular interest, given recent proposals in the literature and the fear that force fields would not be able to treat such interactions. We present a comprehensive comparison of the ab initio (DFT [BLYP], 6-311 G**) and force field (CHARMm22.0) assessments of these interactions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1515-1525, 1998
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  • 86
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    Journal of Computational Chemistry 19 (1998), S. 1526-1533 
    ISSN: 0192-8651
    Keywords: geometry optimization ; spin-orbit effect ; two-component calculation ; effective core potential with one-electron spin-orbit operator ; photoelectron spectra ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have implemented geometry optimization using an analytic gradient to a two-component Kramers' restricted Hartree-Fock (KRHF) method for polyatomic molecules with closed-shell configurations. The KRHF method is a Hartree-Fock method based on relativistic effective core potentials with effective spin-orbit operators. The derivatives of spin-orbit integrals are obtained by numerical differentiation. Geometries for the various forms of polyatomic hydrides containing row 6 p-block elements are optimized with and without spin-orbit interactions. The structural changes due to spin-orbit interactions are small, but show definite trends, which correlate well with the p1/2 spinor population. Atomization energies are reduced significantly by incorporating spin-orbit interactions for all molecules considered. The KRHF calculations of several methylhalides demonstrate that the spinor energies from the KRHF method can be useful for the interpretation of experimental photoelectron spectra of molecules exhibiting spin-orbit splittings.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1526-1533, 1998
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  • 87
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    Journal of Computational Chemistry 19 (1998), S. 893-901 
    ISSN: 0192-8651
    Keywords: Poisson-Boltzmann ; electrostatics ; Kirkwood ; Loeb ; multigrid ; multivalent ions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new multi-multigrid method is presented for solving the modified Poisson-Boltzmann equation based on the Kirkwood Hierarchy of equations, with Loeb's closure, on a three-dimensional grid. The results are compared with standard Poisson-Boltzmann calculations, which are known to underestimate the local concentration of counterions near charged parts of molecules, mainly due to neglect of fluctuations in the ionic concentrations. In the present study, the Kirkwood hierarchy of equations is discretized with the finite volume method and solved using multigrid techniques. The new possibility for solution of the three-dimensional modified Poisson-Boltzmann equation, for the first time within a model including a dielectric discontinuity, and within reasonable computational time, enables the calculation of higher valence ion distributions around arbitrarily shaped biological macromolecules.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 893-901, 1998
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  • 88
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    Journal of Computational Chemistry 19 (1998), S. 923-934 
    ISSN: 0192-8651
    Keywords: molecular integral ; electron repulsion integral ; rapid algorithm ; accompanying coordinate expansion method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general algorithm for rapidly computing the electron repulsion integral (ERI) is derived for the ACE-b3k3 formula, which has been derived previously. [K. Ishida, Int. J. Quantum Chem., 59, 209 (1996)]. A computer program code that is universal for all types of Gaussian-type orbitals (GTOs) up to h-type can be constructed by the use of this general algorithm. It is confirmed that the ACE-b3k3 algorithm is numerically very stable even for higher order GTOs. It is found that, in a floating-point-operation (FLOP) count assessment, the ACE-b3k3 algorithm is the fastest among all methods available in the literature for (dd|dd), (ff|ff), (gg|gg), and (hh|hh) ERIs when the degree of contraction of the GTO is high.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 923-934, 1998
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  • 89
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    Journal of Computational Chemistry 19 (1998), S. 961-976 
    ISSN: 0192-8651
    Keywords: piperidine ; ab initio methods ; natural bond orbital analysis ; hyperconjugation ; puckering coordinates ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A detailed conformational analysis was performed on the chair forms of piperidine, N-methylpiperidine, and some methylated derivatives using Hartree-Fock (HF) and MP2 ab initio methods with several basis sets (from 3-21G to 6-311++G**), and the most widely used semiempirical approaches (MNDO, AM1, and PM3). It was found that the use of polarized basis sets at the HF level is adequate enough for the prediction of conformational preferences in the axial/equatorial equilibrium of the N-R group in piperidines. On the other hand, the inclusion of electron correlation becomes necessary for predicting the axial/equatorial energy differences of the equilibria of the methyl group. Semiempirical methods are not recommended, because AM1 and PM3 predict opposite stabilities to those obtained experimentally and MNDO ring geometries are systematically too flat. The origin of the conformational stabilities was interpreted in terms of the natural bond orbital analysis of the HF/6-31G** wave functions. The equatorial preferences in the N-H equilibria is mainly due to lower Lewis energies, although delocalization of the nitrogen lone pair is favored in N-H axial forms. N-Methylation increases the equatorial M-Me preferences, because the Lewis energy of axial N-Me forms increases due to larger 1,3-diaxial interactions. Geometrical trends associated with the delocalization of the nitrogen lone pair and with interactions between the introduced N-R and C-Me groups were discussed and related to the degree of planarity of the six-membered ring by means of the puckering coordinates defined by Pople and Cremer.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 961-976, 1998
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  • 90
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    Journal of Computational Chemistry 19 (1998), S. 1053-1063 
    ISSN: 0192-8651
    Keywords: Gaussian ; massively parallel ; performance ; Cray T3E ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Gaussian-94 is the series of electronic structure programs. It is an integrated system to model a broad range of molecular systems under a variety of conditions, performing its calculations from the basic laws of quantum chemistry. This new version includes methods and algorithms for scalable massively parallel systems such as the Cray T3E supercomputer. In this study, we discuss the performance of Gaussian using large number of processors. In particular, we analyze the scalability of methods such as Hartree-Fock and density functional theory (DFT), including first and second derivatives. In addition, we explore scalability for CIS, MP2, and MCSCF calculations. Scalability and speedups were investigated for most of the examples with up to 64 process elements. A single-point energy calculation (B3-LYP/6-311++G3df,3p) was tested with up to 512 process elements.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1053-1063, 1998
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  • 91
    ISSN: 0192-8651
    Keywords: electrostatic ; potential ; PRDDO ; PESP ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The PESP (Parameterized ElectroStatic Potential) method for calculating molecular electrostatic potentials, previously parameterized for H, C, N, O, F, P, S, Cl, and Br, is extended to molecules containing Li+, Na+, Mg2+, K+, Ca2+, Zn2+, and I. For a collection of 166 molecules containing 1668 atoms with at least one metal or iodine atom, PESP achieves an average absolute deviation in electrostatic potential-derived atomic charges of 0.042e- compared with ab initio MP2/6-31G** calculations, with a correlation coefficient of 0.996. For a larger data set, consisting of 311 molecules encompassing all of the 16 elements just listed (2488 total atoms), PESP achieves an average absolute deviation of 0.040e- and a correlation coefficient of 0.995. PESP calculations are an order of magnitude faster than the simplest ab initio method (STO-3G) on large molecules, while achieving a level of accuracy that rivals much more elaborate ab initio methods.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1456-1469, 1998
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  • 92
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    Journal of Computational Chemistry 19 (1998), S. 1494-1504 
    ISSN: 0192-8651
    Keywords: continuum dielectric ; hierarchical multipole ; boundary element ; solvation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a boundary element method (BEM) for calculating the reaction field energy of a macromolecule embedded in a high-dielectric medium such as water. In a BEM calculation, the key computational task is the calculation of the induced surface charge distribution at the dielectric boundary. This is obtained by solving a system of linear equations whose dimension can run into the tens of thousands for a macromolecule. In this work, we use a fast summation hierarchical multipole method to solve for the induced surface charge densities. By careful analysis of the levels of approximation required for the various terms in the calculation, we avoid the unnecessary computation of terms that contribute negligibly to the final outcome and, consequently, achieve high computational efficiency. For a protein such as BPTI with 890 atoms, the calculation of the induced surface charge density distribution and the reaction field energy was completed in 7.9 s on an SGI workstation with an R10000 CPU.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1494-1504, 1998
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  • 93
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    Journal of Computational Chemistry 19 (1998), S. 1555-1566 
    ISSN: 0192-8651
    Keywords: molecular dynamics simulation ; semiflexible models ; macromolecules ; constraint dynamics ; helix folding ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiflexible models are often used to study macromolecules containing stable structural elements. Based on rigid body dynamics, we developed a rigid fragment constraint dynamics algorithm for the simulation of semiflexible macromolecules. Stable structural elements are treated as rigid fragments. Rigid fragment constraints, defined as combinations of distance constraints and position constraints, are introduced to limit internal molecular motion to the required mode. The constraint forces are solved separately for each rigid fragment constraint and iteratively until all constraint conditions are satisfied within a given tolerance at each time step, as is done for the bond length constraint in the SHAKE algorithm. The orientation of a rigid fragment is represented by the quaternion parameters, and both translation and rotation are solved by the leap-frog formulation. We tested the algorithm with molecular dynamics simulations of a series of peptides and a small protein. The computation cost for the constraints is roughly proportional to the size of the molecule. In the microcanonical ensemble simulation of polyvalines, the total energy was conserved satisfactorily with time steps as large as 20 fs. A helix folding simulation of a synthetic peptide was carried out to show the efficiency of the algorithm in a conformational search.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1555-1566, 1998
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  • 94
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    Journal of Computational Chemistry 19 (1998), S. 1567-1574 
    ISSN: 0192-8651
    Keywords: polycyclic conformers ; GABA rigid precursor analogs ; conformer population analysis ; comparison between ab initio, AM1, and MM2 calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy hypersurfaces for the triple inversion, from chair to boat and α to β conformations, are explored theoretically in 3-azabicyclo[3.3.1]nonan-9-one and its N-methyl derivative, by using ab initio quantum-mechanical calculations. Both compounds are precursors of rigid analogs of the potential GABAA and GABAB receptor antagonists. In contrast to results from semiempirical calculations, the chair-chair β conformers are found to be, by far, the most stable structures for both the nonmethylated and N-methylated compounds. The inversion barriers are found to be relatively low, so that the conformers could be expected to exist in thermodynamic equilibrium at room temperature. A population analysis reveals, however, that, in the ab initio approach, the molecules seem to exist practically only in the chair-chair-β conformation. The theoretical results compare well with the available experimental data.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1567-1574, 1998
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  • 95
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    Journal of Computational Chemistry 19 (1998), S. 1584-1595 
    ISSN: 0192-8651
    Keywords: semiempirical calculations ; excited states ; solvent effects ; fluorescence ; charge transfer ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several theoretical models are compared to reproduce the spectroscopic fluorescence shift of 4-(4′-N,N-dimethylaminophenyl)-3,5-dimethyl-1,7-diphenyl-bis-pyrazolo-[3,4-b;4′,3′e]-pyridine (DMA-DMPP) in different solvents. DMA-DMPP is used as a model compound because it shows a large shift in emission energy for solvents of various polarities and dual fluorescence in polar protic solvents. Although the simple Onsager model is not able to reproduce the experimental results, the self-consistent reaction field (SCRF) model with extension to excited states based on the AM1 Hamiltonian yields excellent agreement. According to the latter model, the red-shifted emission band can be related to a highly polar charge transfer state without geometrical rearrangements, whereas the normal (short wavelength) emission is attributed to emission from an excited state with increased conjugation in a flattened geometry. A supramolecular approach with six molecules of water surrounding the solute can explain satisfactorily the two distinct fluorescence bands. In protic solvents, the emitting CT state shows additional stabilization of the locally excited state with a planar conformation.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1584-1595, 1998
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  • 96
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    Journal of Computational Chemistry 19 (1998), S. 1612-1622 
    ISSN: 0192-8651
    Keywords: docking ; energy functions ; simulated annealing ; molecular dynamics ; scoring functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A good docking algorithm requires an energy function that is selective, in that it clearly differentiates correctly docked structures from misdocked ones, and that is efficient, meaning that a correctly docked structure can be identified quickly. We assess the selectivity and efficiency of a broad spectrum of energy functions, derived from systematic modifications of the CHARMM param19/toph19 energy function. In particular, we examine the effects of the dielectric constant, the solvation model, the scaling of surface charges, reduction of van der Waals repulsion, and nonbonded cutoffs. Based on an assessment of the energy functions for the docking of five different ligand-receptor complexes, we find that selective energy functions include a variety of distance-dependent dielectric models together with truncation of the nonbonded interactions at 8 Å. We evaluate the docking efficiency, the mean number of docked structures per unit of time, of the more selective energy functions, using a simulated annealing molecular dynamics protocol. The largest improvements in efficiency come from a reduction of van der Waals repulsion and a reduction of surface charges. We note that the most selective potential is quite inefficient, although a hierarchical approach can be employed to take advantage of both selective and efficient energy functions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1612-1622, 1998
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  • 97
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    Journal of Computational Chemistry 19 (1998), S. 1623-1631 
    ISSN: 0192-8651
    Keywords: docking ; genetic algorithms (GA) ; simulated annealing (SA) ; Monte Carlo (MC) ; molecular dynamics (MD) ; scoring functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We assess the efficiency of molecular dynamics (MD), Monte Carlo (MC), and genetic algorithms (GA) for docking five representative ligand-receptor complexes. All three algorithms employ a modified CHARMM-based energy function. The algorithms are also compared with an established docking algorithm, AutoDock. The receptors are kept rigid while flexibility of ligands is permitted. To test the efficiency of the algorithms, two search spaces are used: an 11-Å-radius sphere and a 2.5-Å-radius sphere, both centered on the active site. We find MD is most efficient in the case of the large search space, and GA outperforms the other methods in the small search space. We also find that MD provides structures that are, on average, lower in energy and closer to the crystallographic conformation. The GA obtains good solutions over the course of the fewest energy evaluations. However, due to the nature of the nonbonded interaction calculations, the GA requires the longest time for a single energy evaluation, which results in a decreased efficiency. The GA and MC search algorithms are implemented in the CHARMM macromolecular package.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1623-1631, 1998
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  • 98
    ISSN: 0192-8651
    Keywords: automated docking ; binding affinity ; drug design ; genetic algorithm ; flexible small molecule protein interaction ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become heritable traits (sic). We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein-ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein-ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard error of 9.11 kJ mol-1 (2.177 kcal mol-1) and was chosen as the new energy function. The new search methods and empirical free energy function are available in AUTODOCK, version 3.0.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1639-1662, 1998
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  • 99
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    Journal of Computational Chemistry 19 (1998), S. 1675-1688 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have carried out theoretical calculations to analyze molecular interactions and proton transfer mechanisms in the formate-imidazole-water system, which may be considered the simplest model of catalytic triads in serine proteases. Computations were carried out at the density functional theory level. The effect of a dielectric environment on energy surfaces is considered using a polarizable continuum model and the self-consistent reaction field approach. The role played by inertial and noninertial polarization of this environment is emphasized. Nonequilibrium solvation effects have been estimated. The results show that there are different reaction mechanisms, concerted or stepwise, that may be competitive, depending on the nature of the molecular environment.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1675-1688, 1998
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  • 100
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    Journal of Computational Chemistry 19 (1998), S. 1724-1735 
    ISSN: 0192-8651
    Keywords: reference interaction site model (RISM) theory ; salt solution ; peptide ; protein ; solvation free energy ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We developed a robust, highly efficient algorithm for solving the full reference interaction site model (RISM) equations for salt solutions near a solute molecule with many atomic sites. It was obtained as an extension of our previously reported algorithm for pure water near the solute molecule. The algorithm is a judicious hybrid of the Newton-Raphson and Picard methods. The most striking advantage is that the Jacobian matrix is just part of the input data and need not be recalculated at all. To illustrate the algorithm, we solved the full RISM equations for a dipeptide (NH2(SINGLE BOND)CHCH3(SINGLE BOND)CONH(SINGLE BOND)CHCH3(SINGLE BOND)COOH) in a 1 M NaCl solution. The extended simple point charge (SPC/E) model was employed for water molecules. Two different conformations of the dipeptide were considered. It was assumed for each conformation that the dipeptide was present either as an un-ionized form or as a zwitterion. The structure of the salt solution near the dipeptide and salt effects on the solvation free energy were also discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1724-1735, 1998
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