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  • 1995-1999
  • 1985-1989  (226)
  • 1985  (226)
  • Computational Chemistry and Molecular Modeling  (226)
  • 101
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 28 (1985), S. 691-701 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A multiconfigurational variation of moments (MCM) is presented to determine correlated orbital energies. Appropriate multiconfigurational one-particle operators are introduced starting for closed-shell systems from the restricted Hartree-Fock (RHF) scheme and for open-shell system from the unrestricted Hartree-Fock (UHF) scheme. The advantage of these operators is the linear form of the correlation energy in the configuration interaction (CI) coefficients. They obey HF analogous pseudoeigenvalue equations and are therefore a generalization of the HF operator. In principle, the scheme can be extended to a multiconfiguration self-consistent field (MCSCF) procedure for moments. In contrast to the SCF formalism they allow an orbital description of degeneracy and quasidegeneracy of the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital. With these operators, funnels of thermally forbidden Woodward-Hoffman reactions, as well as dissociations, can be described in a physically meaningful fashion by orbitalcorrelation diagrams.
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  • 102
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 28 (1985), S. 233-237 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electron density at the pyridine nitrogen atom and the π-electron density of the pyridine ring were calculated by the CNDO/2-MO method assuming standard bond lengths and angles. The indices were found to correlate with the pKa values of pyridine derivatives and with the electronic substituent constants of the Hammett type. The correlations were best for four-substituted pyridines, making the routine CNDO/2-MO calculations useful for studies of quantitative relations between structure and biological activity of the compounds.
    Additional Material: 1 Tab.
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  • 103
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 28 (1985), S. 269-286 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: We adapt the use of the Lie algebra su (n) we proposed in former papers to a system made up of two subsystems (respectively, nA and nB states). We show how reduced density operators, correlation problems, and overall and reduced evolution equations, may be made precise with this formalism.
    Notes: L'usage de l'algèbre de Lie su (n), proposé dans les articles précédents, est adapté a l'étude d'un système formé de deux sous-systèmes, respectivement à nA et nB états. On montre comment diverses notions (opérateurs-densités réduits, problèmes de corrélation, équations d'évolution globales et réduites) peuvent être précisées grâce au formalisme introduit.
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  • 104
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 28 (1985), S. 703-713 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A formalism was developed in the multiconfigurational variation of moments (MCM) framework, which yields physically meaningful orbital energies for occupied and virtual orbitals starting from self-consistent field (SCF) calculations. This is possible through a skillful distribution of the correlation energy on the orbital energies. The application of this method is demonstrated by SINDO1 calculations on the dissociation of H2 and the following symmetry-forbidden reactions: (1) torsion of ethylene; (2) ring opening of (a) cyclobutene, and (b) cyclopropyl cation; (3) cycloreversion of 1, 1-dicyano-2-methoxycyclobutane. The allowed reactions corresponding to 2a and 2b are investigated in the SCF scheme. The energy hypersurfaces are calculated for all reactions and the MO correlation diagrams are presented and discussed.
    Additional Material: 11 Ill.
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  • 105
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 28 (1985), S. 421-428 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have analyzed the dependence of the serotonin receptor binding affinity on the electronic and steric reactivity indexes for a group of 5-substituted tryptamines. The approaches employed are a new nonempirical Quantitative Structure - Activity relationship approach and multiple regression analyses. The results suggest that the variation of the receptor binding affinity in 5-substituted tryptamines is related to the variation of the net charge of two atoms and to the steric bulk of the N-substituent. A receptor model is proposed.
    Additional Material: 4 Ill.
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  • 106
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 28 (1985), S. 757-771 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the framework of the additive SIBFA 2 procedure, the intermolecular interaction energy is computed as a sum of five terms: ΔE = EMTP + Erep + Epol + ECT + Edisp. In order to assess the accuracy of the procedure to compute cation-ligand interactions, the interaction of alkali (Na+, K+) and alkaline-earth (Mg2+, Ca2+) cations with two representative ligands H2O and HCOO- has been studied and the results compared with those of ab initio SCF extended basis set computations. The additive procedure reproduces very satisfactorily the results of ab initio computations as concerns the numerical values of the interaction energies and the equilibrium cation-ligand distances, as well as the evolution of the energy components. A detailed study of these components at different distances helps, in particular, to delineate the relative weights of the charge-transfer and polarization contributions within the second-order energy.
    Additional Material: 1 Ill.
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  • 107
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 27 (1985), S. 105-105 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 108
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 27 (1985), S. 135-144 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: PCILO computations have been carried out on the conformation of p-dimethylaminobenzylidene-p-nitroaniline [I(m)], p-nitrobenzylidene-p-dimethylaminoaniline [I(n)] and the corresponding stilbene [II(a)] and azobenzene [II(b)] derivatives. The aniline rings in Im and In are found to be twisted out of the plane containing the central atoms by 60° and 30°, respectively. The two phenyl rings in case of II(a) are twisted out of plane in opposite directions by 30° each. II(b) was found to be planar. The results have been compared with the earlier experimental findings and used as a possible explanation for the visible absorption spectra of the four molecules.
    Additional Material: 5 Ill.
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  • 109
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we present numerical calculations of close-coupling equations to study vibrational predissociation of the T-shaped He…I2(B) van der Waals molecule. In the region of high vibrational excitation of the I2 subunit, the vibrational predissociation rates are related to the widths of the resulting resonances for the He-I2(B) collision. We apply a reasonable approximation to calculate the necessary background S matrix, i.e., the S matrix in absence of resonances. The rates of perpendicular vibrational predissociation, as a function of the initial I2 vibrational quantum number v1, show a maximum at v1 = 58 almost in agreement with the experimental data. However, an oscillatory and very interesting behavior of the rates in the region 60 ≤ v1 ≤ 65 is found.
    Additional Material: 2 Ill.
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  • 110
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    International Journal of Quantum Chemistry 27 (1985), S. 231-232 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 111
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    International Journal of Quantum Chemistry 27 (1985), S. 145-157 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The orthogonalized direct diagonalization (ODD) method is used to predict the valence-shell ionization spectra for the series of hydrocarbons ethane (C2H6), ethylene (C2H4), and acetylene (C2H2) within an EOM/propagator formalism. Both (a) third-order and (b) higher-order (with h5 terms in the excitation operator manifold) calculations are presented in order to illustrate the effect of the extended operator manifold on the predicted valence-shell spectra. It is shown that the major effect of the h5 manifold is concentrated in its “occupied” part. Along with a general shifting of the main lines for outer valence ionizations to lower values (together with a slight reduction in pole strength), it is found that the effect of the h5 manifold in the inner valence region is dependent on the system being studied.
    Additional Material: 3 Ill.
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  • 112
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    International Journal of Quantum Chemistry 27 (1985), S. 181-194 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio SCF MO calculations at the STO-3G level have been carried out on CH2OHOPO3-H and CH2OHOPO32-, which have been considered as model systems for the Cl-phosphate moiety of sugars. The results predict higher anomeric energy for the phosphate moiety at Cl atom of pyranosides. Also a trans arrangement of the exocyclic O - P bond is preferred rather than a gauche arrangement, thus exhibiting a reverse exo-anomeric effect. A complete potential energy map has been constructed for CH3OPO3-H, a model system for C6-phosphate moiety. It is seen that the bond angle optimization brings down the relative energies of various conformations. The effect of the phosphate group on the preferred conformation of phosphate containing polysaccharides is also discussed.
    Additional Material: 5 Ill.
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  • 113
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    International Journal of Quantum Chemistry 27 (1985), S. 235-244 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Internal rotation energy levels for phenol, fluoracetaldehyde, and difluoracetaldehyde are estimated with two methods: first, by means of the reduced inertia moment formula introduced by Pitzer; second, with use of an internal axis system and by taking into account the influence of the overall rotation through the inertia factor. Two methods have been used to estimate potential barriers (CNDO/2 and PCILO). Results are related to the asymmetry of the tops. Theoretical far IR spectra for the three molecules are calculated. In the case of phenol, good agreement is found with experimental data.
    Additional Material: 7 Tab.
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  • 114
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    International Journal of Quantum Chemistry 27 (1985), S. 281-292 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio Hartree-Fock calculations are performed on hydrates of the F- and Cl- ions using 6-31G, 6-31G**, and 6-21G basis sets. Geometries and binding energies are obtained. An estimate of the correlation energy is provided by an MP2/6-31G (Møller-Plesset second-order perturbation) calculation. Comparisons are made between the Cl-(SO2) and the Cl-(H2O) complexes.
    Additional Material: 4 Ill.
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  • 115
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    International Journal of Quantum Chemistry 27 (1985), S. 375-379 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The two-dimensional (2D) energy of the hydrogen molecule is carried out by the Heitler-London method. The 2D integrals (which are more localized compared to 3D ones) are performed in the light of the 3D Slater integrals. A discussion of such 2D systems is briefly outlined for doped semiconductors.
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  • 116
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    International Journal of Quantum Chemistry 27 (1985), S. 407-416 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic energy band of the molecular crystal NMP-TCNQ is calculated by means of the EHMO/LCAO-MO-CO method. In the calculation, both NMP and TCNQ are treated as quasi-one-dimensional columns, respectively. The results demonstrate that (i) the positions of the electronic energy bands of a molecular crystal are determined by that of the corresponding molecular orbitals of the respective isolated molecules; (ii) the widths of energy bands are determined by the interaction between the molecular orbitals of adjacent molecules in the crystal. These facts support the conclusion which we have given in the previous articles. The relationship between the structure of energy bands of the crystal NMP-TCNQ and its electrical conductivity at room temperature is discussed and compared with the crystal TTF-TCNQ. The differences of electrical conductivities of both crystals can be explained by the formula given by Fröhlich and Sewell.
    Additional Material: 5 Ill.
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  • 117
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    International Journal of Quantum Chemistry 27 (1985), S. 465-473 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electronic structures of the π-π type complexes of pyridine with boron trihalides have been studied by means of IEHMO calculation. The results indicate that BX3(X = F, Cl, Br, I) tends to react with C5H5N in a planar configurations against the plane of C5H5N. The most stable configurations of complexes are at 60° of orientation angle ϕ for X = Cl, Br, I, but at 0° for X = F. A linear relationship between In Eb, the logarithm of rotation potential barriers, and the radii of halogen atoms r0 has been observed, and has been deduced from Morse potential function. In the complex, the donating properties of BX3 have an increase from X = F to I, and BF3 functions as an acceptor, but the others as donors. It has been shown that every energy level of the complex is corresponding to that of the donor or the acceptor, which we have discussed by the perturbation theory. The bonds between D and A appear essentially as π-π type but not pure.
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  • 118
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    International Journal of Quantum Chemistry 27 (1985), S. 501-525 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new set of generators of the operator algebra over the electronic Fock space is introduced. It is shown that with this set of generators the “basis” Lie algebra can be associated and that the operator algebra of the Fock space is the homomorphic image of the corresponding universal enveloping algebra. The algebraic structure revealed is used for deriving the reduction formulas for the elements of the simplest spin tensor operators between the Gelfand states.
    Additional Material: 9 Tab.
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  • 119
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    International Journal of Quantum Chemistry 27 (1985), S. 699-707 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An extended pairing scheme is presented which ensures the fulfillment of pairing conditions not only between the sets of occupied orbitals for spin α and for spin β, but also between their orthogonal complements, i.e., the sets of virtual orbitals for spin α and spin β, as well as between occupied orbitals for spin α and virtual orbitals for spin β and between virtual orbitals for spin α and occupied orbitals for spin β. It is shown that the extended pairing properties are suggested by some aspects of the construction of alternant molecular orbitals. The algorithm for singular value decomposition of rectangular matrices is proposed for use in practical implementations of the (extended) pairing scheme.
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  • 120
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    International Journal of Quantum Chemistry 27 (1985), S. 691-697 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conventional partition functions of models with quadratically dependent energy spectra (e.g., translation in a box or free internal rotation), which are widely used in literature, exhibit an incorrect limit behavior in the region of low temperatures and/or small values of the characterizing molecular parameter. In particular, this leads to the absurd value  - ∞ for the contribution of these motions to the entropy term at these limit conditions. This incorrect behavior appears to be due to the replacement of rigorous summation by integration in conventional derivation of these partition functions. The derived improved practical formulas with the correct limit behavior indicate that it will be necessary to carry out quite substantial numerical corrections in the case of many reactivity characteristics reported in the literature. Particularly, the improved formulas should be applied with (small) molecular complexes at the typical temperatures of their observation, e.g., van der Waals molecules with free internal rotation. Simultaneously discussed is the possibility of application of the functional relation valid for a rigorous partition function of the considered type of energy spectrum. The reasoning in the case of the translational partition function indicates that, in principle, it can depend on the vessel shape. Possible consequences for thermodynamics of the ideal gas are analyzed.
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  • 121
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    International Journal of Quantum Chemistry 27 (1985), S. 803-804 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 122
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    International Journal of Quantum Chemistry 28 (1985), S. 27-37 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ground-state energies of He, Be, and Ne isoelectronic series have been calculated. The Dirac-Hartree-Fock energy values have been corrected by adding Breit, vacuum polarization, self-energy, nuclear mass, and electron correlation corrections. The resulting energies are compared with the experimental values. As a result, an estimate of the correlation-relativistic cross-term energy is obtained. The effect, for large-Z atoms, proves to be quite substantial.
    Additional Material: 2 Ill.
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  • 123
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    International Journal of Quantum Chemistry 28 (1985), S. 103-108 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Wilson, Jankowski, and Paldus have recently applied nondegenerate many-body perturbation theory (MBPT) to simple models, in which the degree of quasidegeneracy could be varied continuously, and concluded that the nondegenerate theory was applicable even near degeneracy. The error in their results changes, however, considerably with geometry, leading to an incorrect potential surface. An extension of their calculations shows convergence even at exact degeneracy (square planar H4). It is shown here that the apparently good convergence is due to the suppression of the large (infinite at exact degeneracy) component of the perturbation energy in low order by the way the Hamiltonian is partitioned. This component will, however, resurface at higher orders, leading to slow convergence or even divergence. The low-order sum of the perturbation series is not very meaningful, depends strongly on details of the zero-order Hamiltonian, and yields, in general, incorrect potential surfaces. Multireference MBPT eliminates these problems.
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  • 124
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    International Journal of Quantum Chemistry 28 (1985), S. 163-180 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Extensive ab initio molecular-orbital calculations were carried out on trifluoromethylamine (TFM) to elucidate changes in geometry and electronic structure upon fluorination. The calculations show that the decomposition of CF3NH2 is slightly endoenergetic, and the heats of atomization of CF3NH2 and CH3NH2 show decreased stability of the species upon fluorination. Characteristic of CF3NH2 is a highly polar, strong, short CN bond. More limited calculations were carried out on CF3OH and CH3OH, and the electronic structure of CF3OH is found to be generally similar to that of CF3NH2. The reduced basicity of the fluorinated amine cannot be ascribed to the inductive effect; the enhanced acidity of the fluorinated alcohol reflects the weakening of the OH bond. No evidence leads to a confirmation of the existence of nitrogen-fluorine hyperconjugation in the fluorinated amine.
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  • 125
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    International Journal of Quantum Chemistry 28 (1985), S. 213-232 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The formalism developed in the first two papers of this series is applied to the investigation of a new weak-field model. This crystal-field model lies on the use of a symmetry-adapted weak-field basis and an effective Hamiltonian involving in a symmetrical way both spin- and orbit-dependent contributions. Some general properties of this Hamiltonian are studied and complete calculation of its matrix elements is conducted in a symmetry-adapted weak-field basis in the case of an arbitrary configuration nlN in any symmetry. The case of a configuration ndN in octahedral symmetry is fully explored. In this case, the proposed weak-field model is restricted to a 12-parameter model which accounts for isotropic and anisotropic Coulomb interactions, isotropic and anisotropic spin-orbit interactions, and crystal-field interactions. A comparison between this 12-parameter weak-field model and the 14-parameter strong-field model is established. Equivalence between the latter two models requires two constraint relations to be satisfied for some strong-field parameters. These two relations are examined with various viewpoints.
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  • 126
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    International Journal of Quantum Chemistry 28 (1985), S. 287-295 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The potential energy of a homonuclear X4 molecule is an invariant of the atom permutation group S4 acting on the internal coordinates of X4. It is shown by means of invariant theory that six algebraically independent invariants and five additional invariants are required to express the general invariant function for this group. Explicit expressions for these 11 invariants are given.
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  • 127
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    International Journal of Quantum Chemistry 28 (1985), S. 349-373 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: General formulas have been derived for molecular integrals arising in the use of the identity derived by Harriman for describing the Fermi-contact interaction in a molecule. Computational aspects are discussed and numerical examples are shown for several sets of the usual Cartesian Gaussian-type orbitals.
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  • 128
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    International Journal of Quantum Chemistry 28 (1985), S. 335-348 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A unitary group reformulation of electron propagator theory is used to derive the second-order and 2p - h Tamm-Dancoff self-energy approximations for open-shell applications. A highest weight representation of the reference state is chosen in order to facilitate matrix element evaluation, but two special cases precluded by this choice are also discussed. Detailed numerical calculations are described for the lithium atom, oxygen molecule, and the amidogen radical.
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  • 129
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    International Journal of Quantum Chemistry 28 (1985) 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 130
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    International Journal of Quantum Chemistry 28 (1985) 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 131
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    International Journal of Quantum Chemistry 28 (1985), S. 181-202 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The well known one-to-one correspondence between the eigenstates of the total spin for a system of spin-½ particles and irreducible representations of the symmetric group with up to two rows in the Young shape is the basis of interesting formal developments in quantum chemistry and in the theory of magnetism. As an explicit manifestation of this correspondence the class operators of the symmetric group are demonstrated to be expressible in terms of the total spin operator. This correspondence does not hold for higher elementary spins. The extension to arbitrary spin is investigated using Schrödinger's generalization of the Dirac identity, which expresses the transpositions in terms of two-particle spin operators. It is shown that additional operators, which for σ = ½ reduce to the total spin operator, are needed for a complete classification. Some aspects of the formalism are developed in detail for σ = 1. In this case a classification identical with that provided by the irreducible representations of the symmetric group is obtained in terms of the eigenstates of two commuting operators, one of which is the total spin operator.
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  • 132
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    International Journal of Quantum Chemistry 28 (1985), S. 239-244 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Based on the literature values, the pK1 and pK2 for pyrazine and its six methyl derivatives, the correlation with electron density on the nitrogen atoms N1 and N4 was found. The effect of methyl group was proved to be additive. The total electron density, π-electron density, and dipole moments for compounds under study were determined by the CNDO/2-MO method.
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  • 133
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    International Journal of Quantum Chemistry 28 (1985), S. 297-309 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An ab initio investigation of the potential energy hypersurfaces of the Na+/H2 system is presented. The calculations have been performed on SCF level and with the inclusion of correlation effects by means of the CEPA-PNO, IEPA-PNO, and PNO-CI methods. The basis set consists of gaussian lobes (12s, 8p, d) on Na and (8s, p) on H. The distance of the Na nucleus to the midpoint of H2 was varied between 0.0 and 10 bohrs, whereas the region of H—H distances considered was 0.5 to 10 bohrs. The angular dependence of the hypersurface was investigated as well. The system Na+/H2 has an absolute energy minimum for C2v geometry at R equal approximately 5.0 bohrs and rHH = 1.40 bohrs.
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  • 134
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    International Journal of Quantum Chemistry 28 (1985), S. 311-314 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The maximum entropy procedure (MEP) of Jaynes has been extended to the case involving constraints in complementary spaces. It has been rigorously shown that the sum of information entropies in position and momentum spaces is invariant to uniform scaling of the electron coordinates. A new MEP procedure requires that this sum of entropies must be maximized subject to the known constraints in both spaces. A specific application of this maximization procedure for synthesizing atomic-electron densities in coordinate and momentum spaces has been outlined.
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  • 135
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    International Journal of Quantum Chemistry 28 (1985), S. 641-648 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hybrid orbitals of tetrahedral oxy-ions containing some d character have been calculated by maximum overlap method. The d characters of hybrid orbitals increase in the order of SiO44-, PO43-, SO42-, ClO4-, and decrease in order of GeO44-, AsO43-, SeO42-, BrO4-. The bond strengths are also obtained for these ions. The hybrid Orbital of VO43-, CrO42-, and MnO4- are of the type d3s as the result of calculation.
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  • 136
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    International Journal of Quantum Chemistry 28 (1985), S. 663-663 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 137
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    International Journal of Quantum Chemistry 28 (1985), S. 665-686 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper serves a twofold purpose. First, Löwdin's inner projection in both nonperturbative and perturbative forms is applied to the quartic anharmonic oscillator. Inner projection with perturbation theory yields rational approximations to Brillouin-Wigner-type perturbation expansions. These lower bounds are compared with [N - 1, N] Padé approximants to the Rayleigh-Schrödinger perturbation series for this problem. These Padés are also expressible as the even convergents, w2N, of a Stieltjes-type continued fraction. The latter representation has certain advantages with respect to its Padé counterpart. Inner projection without perturbation theory provides significantly better results than the perturbative version. The application of inner projection techniques to a perturbed hydrogen atom is not straightforward. The usual problems associated with the continuum spectrum of hydrogen are present. By means of a nonunitary “tilting” transformation associated with the Lie group SO(4, 2), these problems may be bypassed. In the SO(4, 2)-reformulated eigenvalue problem, a reinterpretation of the basic variables, as developed by Silverstone and Moats, yields a new Hamiltonian that permits direct use of the inner projection method. This method has been applied to the ground state of the hydrogen atom in a magnetic field, using both four- and eight-dimensional basis manifolds. This represents the first application of inner projection to this problem.
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  • 138
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    International Journal of Quantum Chemistry 28 (1985), S. 741-756 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A comparative study of quasirelativistic equations used in atomic structure calculations has been performed. A uniform derivation of all the equations is presented, and some of their specific features are discussed in detail. Electron density distributions, orbital energies, and expectation values of rn obtained with different methods are compared with the ones resulting from the Schrödinger and Dirac equations. The most accurate are found to be the equations of Wood and Boring and of Barthelat, Pelissier, and Durand. (They reproduce almost exactly the Dirac electron densities and expectation values.) The simplest, though least accurate, equation is proposed by us. It gives the relativistic energy corrections with about 6% accuracy and retains exactly the form of the nonrelativistic Schródinger equation. Consequently, its application in analytical SCF-CI calculations does not require any additional integral calculation.
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  • 139
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    Journal of Computational Chemistry 6 (1985), S. 9-12 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Part of the reaction between 2H-pyran-2-ones and organomagnesium compounds has been investigated by means of MNDO and ab initio calculations. Criteria for the mechanism of reaction are provided by the stereoselectivity observed and calculations are consistent with this stereoselectivity. Conformations of the reaction intermediates are given.
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  • 140
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    Journal of Computational Chemistry 6 (1985), S. 28-38 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The values of log10 P (partition coefficient, in octanol/water) were calculated for about 200 organic molecules of diverse structures and functionalities. The method involves a simple procedure and appears accurate enough for semiquantitative applications. Further, this method of calculating log10 P values was shown to be successful in providing a better quantitative structure activity relationship (QSAR) than the Hansch-type approach in the study of inhibitory activity of substituted phenols on Bacillus Subtilis spore germination.
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  • 141
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program SURVIB is described for calculating vibrational anharmonicity constants for polyatomic molecules. The program requires as input a grid of calculated energies in the vicinity of a stationary point. This grid is fit, in a least squares sense, to a polynomial function of the internal coordinates. This analytic representation of the energy surface is employed in a normal mode analysis, and the energy is reexpanded as a polynominal function of the normal mode coordinates (expressed as vectors in the mass-weighted atomic Cartesian coordinate space). The resulting coefficients are used in a second-order perturbation theory analysis to obtain the vibrational anharmonicity constants. Also reported is an application of this program to formaldehyde employing ab initio, RHF, MP2, MP3, and RHF-CI calculations. The spectroscopic constants obtained for H2CO are in good agreement with experimentally derived values recently reported by Reisner.
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  • 142
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    Journal of Computational Chemistry 6 (1985), S. 56-60 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: α↑HF and α↓HF are derived for use in spin polarized Hartree-Fock-Slater programs. They are assumed to depend only on the number of up and down spin electrons in the atom. The calculated eigenvalues show a slight improvement only for carbon, nitrogen, and oxygen.
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  • 143
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    Journal of Computational Chemistry 6 (1985), S. 189-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MO calculations have been performed for neutral and cationic C2H2F2 structures. Olefinic and carbene structures are investigated for the neutral isomers, while olefinic, carbene, and fluoronium-type cations are found. Stability orders and rotational barriers are discussed in terms of orbital and Coulomb interaction. Contrary to previous studies, the higher stability of the geminal isomers is interpreted to be caused by Coulomb attraction.
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  • 144
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    Journal of Computational Chemistry 6 (1985), S. 469-477 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Local pseudopotential calculations have been performed for the ground state of disilane as well as for the lowest singlet and triplet states of disilene and silylsilylene. Comparison with all-electron calculations shows good agreement for geometries and relative stabilities.
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  • 145
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    Journal of Computational Chemistry 6 (1985), S. 462-468 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The maximization of the exchange interaction between the canonical Hartree-Fock virtual and occupied orbitals leads to a transformed set of virtual orbitals which are well suited as one-electron functions for CI calculations. The procedure, generally known for a long time is seldom applied, despite its simplicity and very low computational demand. However, it is found to be particularly useful in the case of multireference CI, since an improved energy is obtained with a considerable shortening of the CI expansion. Moreover, in the final CI wave function, several configurations appear with considerable weight, thus allowing an easy choice of additional configurations to be inserted in the definition of a new zero-order wave function. The efficiency of the computational procedure is discussed for the case of a Li6 cluster of D3h symmetry and for the NaCO and PdCO complexes. Results are reported for the relative stability of four different geometrical arrangements of the Li6 cluster.
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  • 146
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    Journal of Computational Chemistry 6 (1985) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 147
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    Journal of Computational Chemistry 6 (1985), S. 486-491 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The hydrogen atom transfer reaction between substituted methanes (substituents; H, F, CH3, OH, and CN) and methyl radicals was studied by 4-31G (UHF) calculations using the MINDO/3 geometries. The transition state structures and energy barriers were determined, and variations of the transition state and of the reactivity due to the change of substituent were analyzed based on the potential energy surface characteristics. It was concluded that the reaction is of the SH2 type with a backside attack, and transition state variations are controlled by the vector sum of the component parallel to (Hammond rule) and one perpendicular to the reaction coordinate (anti-Hammond rule). It was also concluded that the most important factor influencing the reactivity is bond dissociation energy effect directly related to the spin transfer of the radical species, and the polar effect need not be overemphasized.
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  • 148
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    Journal of Computational Chemistry 6 (1985), S. 514-519 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Reequilibration processes are often encountered within solids and they have long been described mathematically. However, computation of reequilibration data over entire processes is often difficult. An algorithm has been developed specifically for this purpose. It allows a fast and efficient computation of reequilibration parameters. Anisotropic diffusion can, moreover, be taken into account.
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  • 149
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    Journal of Computational Chemistry 6 (1985), S. 533-537 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The compact orbital and auxiliary basis sets for LCAO-LSD calculations introduced in Part I are tested in molecular calculations on Cr2 and Ni4. The present results for spectroscopic constants and valence orbital energies obtained using medium size orbital expansions with a double-zeta representation for valence orbitals are in very good agreement with those previously calculated with very extended sets. Since the computational time of the present calculations is reduced severalfold compared with the extended basis set calculations, the present basis sets allow increased efficiency of the LCAO-LSD calculations and allow the method to be extended to larger systems.
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  • 150
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    Journal of Computational Chemistry 6 (1985), S. 552-561 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The basic notions and definitions, necessary for the better understanding of Part I of this series, are presented. The mathematical proof is given for sufficiency of the various HOC procedures for vertex canonical numbering and graph orbit finding.
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  • 151
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    Journal of Computational Chemistry 6 (1985), S. 570-580 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometries of ten isomers of dimethyl cyclohexane were determined by ab initio gradient geometry refinement with the 4-21G basis set. It is found that many intramolecular interactions are clearly manifested by correlated structural trends, and that they are consistent with strain energies calculated by employing previously defined ab initio group equivalents. Specifically, non-bonded interactions are found between two adjacent methyl groups in some of the forms, and between axial methyl groups and adjacent axial C—H bonds in others. Unperturbed axial C—H and C—C bonds are consistently longer than equatorial bonds. In general, C—H bonds which are involved in non-bonded repulsive interactions are shortened, i.e., strengthened, and the corresponding H—C—C angles are large, compared to non-interacting parameters.
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  • 152
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    Journal of Computational Chemistry 6 (1985), S. 592-597 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometrical parameters for benzene, fluorobenzene, and cyanobenzene have been calculated using the 6-31G*(5D) and 6-31G** basis sets, and, in addition, the 6-31 + G*(5D) basis set in the case of fluorobenzene. Compared to previous results obtained using the 6-31G basis set there are minor changes in the magnitude of the bond lengths and angles in the ring, but the relative values remain unaltered. The values for the ipso angles in fluorobenzene and cyanobenzene are again somewhat less than those reported from microwave and/or electron diffraction studies. The distortion of the ring is characterized as either an elongation or a flattening with respect to the F-C1⃛C4 and N≡C—C1≡C4 axes, and the shape is characterized as either a broadening or a narrowing across the ring just below the F and Cn group, i.e., an increase or a decrease in the C2⃛C6 internuclear distance, relative of the C3⃛C5 distance.
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  • 153
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    Journal of Computational Chemistry 6 (1985), S. 610-613 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Within the model of anisotropic rotational diffusion, the quantitative treatment of dipolar and quadrupolar spin-lattice relaxation provides valuable information about molecular structures and molecular associations. When quadrupolar relaxation is involved, the title program calculates: (1) the electric field gradient tensor (EFGT) which is diagonalized; (2) the assymetry parameter, the components of the principal axes of the EFGT in the molecular frame of reference and the quadrupole coupling constant; and (3) the rotational diffusion constants which are iteratively determined from the experimental quadrupolar relaxation times. Analogously, for dipolar relaxation ISHTAR calculates the tensor of inertia, the diagonalization of which leads to diffusion constants and free rotor correlation times and the rotational diffusion constants from the experimental spectral densities.
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  • 154
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    Journal of Computational Chemistry 6 (1985), S. 625-633 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Infrared spectra were obtained for the series of 2,X-dimethylheptanes (X = 2,3,4,5,6) and were interpreted with the aid of normal coordinate calculations. 2,2-DMH exists as two conformers, with the Cs conformer being the only one present in the crystalline solid. 2,3-DMH exists in at least three conformations, all of C1 symmetry. Ambiguities in spectral data indicate that more conformations are present. Two C1 conformations of 2,4-DMH were shown to be present, but an unassigned band may indicate the presence of a third conformer. The presence of at least four conformers, all of C1 symmetry, was shown to be necessary to explain the spectrum of 2,5-DMH. Finally, 2,6-DMH was shown to exist as three conformers, of symmetries Cs, C2, and C1. Vibrational assignments were made for all the probable conformers of all five compounds.
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  • 155
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    Journal of Computational Chemistry 6 (1985), S. 647-651 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Inner projections of the polarization propagator (IPPP) are used to study several features of the throughspace transmission of 31P-31P coupling constants. Cis-1,2-diphosphinoethylene is chosen as a model compound. INDO ground state wave functions are used, including two different second-row parameterizations. Results obtained with a phosphorus spd basis set are also presented. It is found that the overlap of phosphorus lone-pairs constitute an efficient coupling pathway. Results are discussed in terms of experimental values for similar compounds taken from the literature. Theoretical predictions are in line with experimental trends.
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  • 156
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    Journal of Computational Chemistry 6 (1985), S. 76-77 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 157
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 158
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    Journal of Computational Chemistry 6 (1985), S. 79-87 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Transition states for the two probable pathways for the gas-phase hydrolysis of hydrogen isocyanate have been determined using the MINDO/3 method. Activation barriers obtained showed that the one-step mechanism is preferred to the two-step mechanism involving an intermediate. It was shown that the reaction of polymeric water has lower activation barrier than the reaction of monomeric water. Energy and charge decomposition analysis showed that in the former less energy is required in the deformation of molecules for the transition state (TS) formation due to the cyclic flow of electronic charges in the TS.
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  • 159
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    Journal of Computational Chemistry 6 (1985), S. 108-115 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General definitions of valence, degree of bonding between pairs of atoms, and atomic anisotropy and reactivity are given. They can be applied to closed- or open-shell molecular wave functions (in the semiempirical, quasi or full ab initio SCF levels), as well as to GVB ones. The properties and usefulness of the definitions are discussed as well as their relation to former empirical notions. Examples of their application are also reported.
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  • 160
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    Journal of Computational Chemistry 6 (1985), S. 116-121 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Third-order Møller-Plesset perturbation theory (MP3) with a 6-31G** basis set was applied to study the relative stabilities of H+(X)2 conformations (X = CO and N2) and their clustering energies. The effect of both basis set extensions and electron correlation is not negligible on the relative stabilities of the H+(CO)2 clusters. The most stable conformation of H+(CO)2 is found to be a C∞v structure in which a carbon atom of CO bonds to the proton of H+(CO), whereas that of H+(N2)2 is a symmetry D∞h structure. The second lowest energy conformations of H+(CO)2 and H+(N2)2 lie within 2 kcal/mol above the energies of the most stable structures. Clustering energies computed using MP3 method with the 6-31G** basis set are in good agreement with the experimental findings of Hiraoka, Saluja, and Kebarle. The low-lying singlet conformations of H+(X)3 (X = CO and N2) have been studied by the use of the Hartree-Fock MO method with the 6-31G** basis set and second-order Møller-Plesset perturbation theory with a 4-31G basis set. The most stable structure is a T-shaped structure in which a carbon atom of CO (or a nitrogen atom of N2) attacks the proton of the most stable conformation of H+(X)2 clusters.
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    Journal of Computational Chemistry 6 (1985), S. 122-141 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program in Pascal is developed for computing the matching polynomials of graphs and lattices. This program is based on the recursive relation for matching polynomials outlined by Hosoya [Bull. Chem. Soc. Jpn., 44, 2332 (1971)], Gutman and Hosoya [Theor. Chim. Acta, 48, 279 (1978)], and others. The graph whose matching polynomial is of interest is reduced recursively until the graph reduces to several trees. The characteristic polynomial of a tree is the same as the matching polynomial. The characteristic polynomials of resulting trees are computed using the computer program based on Frame's method developed by Balasubramanian [Theor. Chim. Acta, 65, 49 (1984)]; J. Comput. Chem., 5, 387 (1984). The resulting polynomials are then assembled to compute the matching polynomial of the initial graph. The program is especially useful in generating the matching polynomials of graphs containing a large number of vertices. The matching polynomials thus generated are potentially useful in several applications such as lattice statistics (dimer covering problem), aromaticity, valence bond methods (enumeration of perfect matchings) in the calculation of grand canonical partition functions, in the computation of thermodynamic properties of saturated hydrocarbons, and in chemical documentation.
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  • 162
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    Journal of Computational Chemistry 6 (1985), S. 148-155 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have carried out a series of molecular mechanics calculations on the alkali ion complexes of valinomycin. For the ions Na+, K+, Rb+, and Cs+ we have found three-fold rotationally symmetric conformations as the lowest energy structures, while for Li+ a markedly asymmetric configuration is preferred. The relative free energies of the complexes show that Li+ is by far the poorest binding partner in solution, followed by Na+, which is in turn far poorer than any of the three larger ions. The binding selectivity derives from the slower variation of the complexation free energy with ionic size than the ionic solvation free energy, so that the ionophore is unable to compete with the solvent for the smaller ions. Our calculated strain energies suggest that valinomycin's failure to form complexes with the smaller ions in solution is due partially to the rigidity of the ionophore structure, which prevents the central cavity from contracting to accommodate them. Certain geometric criteria indicate that K+ provides the best fit to the binding site, although there is some inconsistency between the energetic and geometric criteria of binding ability.
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  • 163
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    Journal of Computational Chemistry 6 (1985), S. 168-172 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The protonation energies of alkylated derivatives of NH3 and OH2 are calculated at the Hartree-Fock level with the split-valence 4-31G basis set. The methyl, dimethyl, and ethyl amines are studied; oxygen bases include methanol, dimethylether, and ethanol. The geometries of each molecule and its protonated analog are fully optimized. It is found that protonation leads to significant changes in the molecular structures. In particular, the bonds to the N and O atoms are substantially elongated, especially when the other atom involved is C rather than H. The calculated absolute proton affinities are somewhat larger than the experimental values. However, the differences in protonation energies of the various molecules relative to one another agree quantitatively with experiment. Replacement of one H atom of the base by a methyl group induces an increase in proton affinity of some 10 kcal/mol. If a second methyl group is added to the N or O atom, a further increment of about 70% this amount is noted. On the other hand, placement of the second C atom on the first methyl group (to form an ethyl substituent) leads to a smaller increase (∼30%). The magnitudes of these alkyl substituent effects are somewhat larger for the oxygen bases than for the amines.
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  • 164
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    Journal of Computational Chemistry 6 (1985), S. 182-188 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The lowest potential energy surfaces of NO3 have been investigated using CASSCF and contracted CI methods, to determine if NO3 is an intermediate in the oxidation of nitric oxide. This reaction is observed to be termolecular where an intermediate is almost certainly formed. The calculations, which were performed in C2v symmetry, show that the form of NO3 which has a near D3h geometry should not be possible to reach from ground state NO and O2. The energy of this isomer of NO3 is calculated to be 25 kcal/mol higher in energy than separated NO and O2. Furthermore, NO + O2 is separated from NO3 by very high barriers. The C2v constrained barrier is as high as 145 kcal/mol, which makes it very unlikely that NO3 could be formed even along less symmetric pathways. The origin of the barriers are analyzed, and it is shown that a special type of mechanism is involved for the state with the lowest barrier. In this mechanism, which was observed recently also for NiH2, the occupation in each symmetry changes only by one unit in each step of the reaction. The only isomer of NO3 which could be formed is a weak van der Waals complex with a very long bond distance of 6.5 a.u. N2O2 does, however, in this respect seem to be a more likely intermediate with its shorter bond distance of 4.5 a.u. Calculations around the D3h equilibrium further show that 2B2 is the ground state of this isomer of NO3 with 2A2 and 2B1 slightly higher in energy.
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  • 165
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    Journal of Computational Chemistry 6 (1985), S. 88-92 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: If numerical configuration selection procedures are used in MRDCI calculations, the full MRDCI energy may be estimated by adding energy corrections obtained by perturbation theory. Accurate results may then be obtained by including all selected CFs in the zero-order function instead of only the reference CFs.
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  • 166
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    Journal of Computational Chemistry 6 (1985), S. 93-107 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Repulsion and dispersion parameters for alkali-metal halide diatomic molecules were computed by ionic Rittner and truncated Rittner models with radial dependent repulsion terms. Experimental data on the bond energies, the equilibrium interionic distances, and the spectroscopic frequencies were employed for the purpose. The polarizabilities used were also computed from the experimental dipole moments of alkali-metal halides. The potential parameters obtained were compared with parameters from other sources and checked for consistency. The computed potential parameters of alkali-metal halide monomer molecules were used to predict the energetics and geometries for alkali-metal halide dimer molecules. The predicted values are in good agreement with experiment and other calculations indicating the consistency and reliability of the potential employed. Although the magnitude of repulsive and dispersive energy terms varies with potential functions employed, the difference between the two for a molecule is constant. The repulsive term is more sensitive than the attractive term. The uncertainty in the exponential repulsion results in an inaccurate representation of the attractive contribution. Introduction of the radial-dependent repulsion term changes the relative magnitudes of repulsive and dispersive parameters and hence the relative contribution to the total potential with monomers. But this has no significant effect on the energetics and geometries of the dimers.
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  • 167
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    Journal of Computational Chemistry 6 (1985), S. 142-147 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Localized molecular orbitals (LMOs) for several octahedral complexes are presented. Wavefunctions are calculated within the PRDDO approximations and localized by the Boys criterion. Complexes of general formula (NH3)x(CO)6-xM, M = Cr0 or Mn+ and x = 1, 2, or 3 illustrate the general trends for carbonyl complexes. Weak to moderate π-bonding results in three equivalent inner shell LMOs dominantly of metal 3s, 3p and 3d character but highly delocalized to the carbonyls. These three LMOs flank the M-CO bond axis. Other π back-bonding situations result in metal-ligand double bonds which are nonequivalent and have σ-π separability [(NH3)5(py)Mn+] and also equivalent double bonds [(NH3)5(NO)Cr+].
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  • 168
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    Journal of Computational Chemistry 6 (1985) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 169
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    Journal of Computational Chemistry 6 (1985), S. 157-167 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Sets of atom equivalents have been developed which permit the estimation of heats of formation, ΔH°f298(g), from ab initio total energies (3-21G and 6-31G* basis sets). This extends the isodesmic reaction scheme of Pople and the group equivalents of Wiberg. A variety of small inorganic and organic molecules, including fluorocarbons, free radicals, carbocations, and protonated species give excellent agreement with experiment; average errors are less than 1 kcal/mol with unstrained hydrocarbons (both basis sets), and are on the order of 2 kcal/mol for all molecules considered (6-31G*; the 3-21G basis errors, as expected, usually are somewhat higher). The results substantiate Pople's early conclusions that Hartree-Fock theory provides a generally satisfactory description of classical molecules.
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  • 170
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    Journal of Computational Chemistry 6 (1985), S. 173-181 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges obtained with a previously published charge scheme are given for amino acids and peptides. In order to do this, a method of handling charged species with the basic scheme2,3 has been developed. The charges obtained for alkylammonium ions and carboxylate ions with the scheme are presented and compared with CNDO and ab initio values. The calculated experimental dipole moments of the zwitterionic forms of glycine, alanine and β-alanine are then discussed. Finally, the atomic charges obtained for the naturally occurring amino acids are given, both in the form of the N-acetyl-N′-methyl amino acid amides, used as models for the amino acid residues in enzymes, and as the free zwitterionic amino acids. The charges obtained show a good correlation with n. m. r. chemical shifts of both carbon and hydrogen atoms.
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  • 171
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method of graphically exhibiting detailed information about a three-dimensional electron distribution function f(x,y,z) is described. Contour lines f = constant are drawn on a set of equidistant parallel planes that intersect the distribution, and a perspective view of all contours on all planes is displayed. Representative examples are given.
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  • 172
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    Journal of Computational Chemistry 6 (1985), S. 216-228 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is described to analyze observed conformations for molecular fragments with more than three torsional degrees of freedom. The method is an adaption of statistical cluster analysis to multidimensional, symmetric, periodic distributions of data points. Application to the molecular fragment M(PPh3)2 with eight torsional degrees of freedom reveals a model of conformational interconversion. The model implies gearing motion of the two PC3 fragments alternating with stepwise inversions of the helicities of the PPh3-propellers.
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  • 173
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 174
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    Journal of Computational Chemistry 6 (1985), S. 256-263 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using the previously reported ab initio interaction energies among K+, Na+, water, and Gramicidin A (GA), this report presents Monte Carlo simulations for the microscopic effect of an applied voltage (0.5 V/32 Å) on a solvated gramicidin. The reorientation of water molecules due to the applied voltage is found to be marginal for both cations. The energy contribution due to water dipoles was within 10% of the total energy contribution due to the applied voltage. Inside the channel the total energy contribution varied almost linearly along the channel axis; outside the channel the slope of the total energy contribution with respect to the channel axis decreased.
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  • 175
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    Journal of Computational Chemistry 6 (1985), S. 368-376 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The complete molecular structure of biphenyl, characterized by 12 independent parameters, has been derived by ab initio gradient techniques using a STO-3G basis set for coplanar, perpendicular, and minimum energy conformations with the constraint of planar phenyl ring units and a C2 symmetry axis along the CC interring bond. The minimum torsional angle obtained was φ = 38.63° with torsional energy barriers of 8.59 and 10.04 kJ/mol for φ = 0° and φ = 90°, respectively.
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  • 176
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    Journal of Computational Chemistry 6 (1985), S. 377-400 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with STO-3G and 3-21G basis sets are reported for approximately 85 pteridines of interest to the study of the reaction and inhibition mechanisms of dihydrofolate reductase. These include tautomeric, protonated, deprotonated, reduced and 6-substituted forms of the 2-amino-4-oxo- and 2,4-diamino-pteridines, many of which are not easily amenable to experimental investigation. Full geometry optimizations at the SCF/STO-3G level for 30 such pteridines have been performed. A step-wise computational protocol designed to identify the minimum level of theory necessary for reliable prediction of relative tautomer, reduction and ionization energies has been developed in an effort to minimize the cost of calculations for this reasonably large N-heterobicylic system. In general, SCF/STO-3G results were found to be inadequate while SCF/3-21G results obtained with STO-3G optimized geometries agreed with all available experimental evidence with the exception of the relative acidity of 6-methyl-7,8-dihydropterin. Correlation graphs relating experimental pKa's to the calculated ionization energies are presented: these are of potential predictive value. An analysis is given of the importance of resonance substructures, such as the guanidinium and extended-guanidinium groups, in stabilizing some preferred tautomeric and ionized forms, and in explaining the observed geometry changes.
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  • 177
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    Journal of Computational Chemistry 6 (1985), S. 432-436 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a real-time docking method using molecular graphics and high-speed calculation of the energy of interaction between a drug and a receptor. A three-dimensional tabulation of the potential is computed prior to the docking experiment, and the total interaction energy is calculated and updated on the display screen in real-time to provide immediate visual feedback to the user as the drug molecule is moved inside the receptor pocket. The “Simplex” method is then used to minimize the energy of interactions after each docking. Using this real-time method, it is now possible to examine rapidly the interactions of a large number of drugs and their analogues with receptor molecules. As an application, the interaction of thyroid hormone and its analogues with prealbumin is considered. The final interaction energies of this very rapid method compare well with those calculated by more orthodox means, while also providing visual feedback on both molecular geometry and energy.
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  • 178
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    Journal of Computational Chemistry 6 (1985), S. 455-461 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The thermal limiting high-pressure unimolecular rate constant k∞ represents, operationally, the Laplace transform of the product of microcanonical rate constant for decomposition of molecules having specified energy E [k(E)] and the density of states [N(E)]. By inversion, it is possible to recover k(E)N(E), from which one can obtain the energy dependence of k(E) and the pressure dependence of kuni, the thermal general-pressure unimolecular rate constant. This article examines numerical aspects of three methods of inversion, their reliability and dependence on sampling, i.e., on the number of available experimental data points, by comparing exact k(E) and kuni with those obtained by inversion. It turns out that the method of steepest descents is the best all-round performer.
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  • 179
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    Journal of Computational Chemistry 6 (1985), S. 478-480 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular mechanics (MMP2) description of the torsion of a methyl group attached to a conjugated system has been improved by using bond order dependent torsional force constants.
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  • 180
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    Journal of Computational Chemistry 6 (1985), S. 481-485 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A corrected Born equation, which describes the solute-dipolar solvent interaction by placing the charges of the atoms of the solute at their position in space inside a spherical cavity of the solvent, is used to calculate the solvent effect on three systems: the hydrated OH- ion, the lithiated aziridine, and the lithiated oxirane. It is found that the solvent effect stabilizes the addition of a water molecule to the OH-(H2O)3 system with the additional water acting as a proton donor. It is also found that the lithiation energy of aziridine and oxirane which are found to be 47 and 43 kcal/mol in gas-phase, respectively, decrease to 32 and 23 kcal/mol in water solution.
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  • 181
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    Journal of Computational Chemistry 6 (1985), S. 492-506 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of chance correlations in studies of structure - activity relationships using multivariate linear regression techniques is addressed. Random correlations are simulated by scrambling real potency values in data bases consisting of molecules possessing various biological properties. The statistical parameters of these correlations are compared to those obtained using the actual potency/compound data pairs and it is noted that the most noticeable differences are in the magnitude of the F values for the overall regression. Cutoff points for this parameter are suggested, which, when implemented in the recently introduced CASE method that correlates biological activity with substructural descriptors, can serve to weed out effectively the majority of meaningless correlations.
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  • 182
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    Journal of Computational Chemistry 6 (1985), S. 507-513 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SINDO1 calculations were performed to study the reactivity of molecules with a valence number derived from the density matrix. A comparison of valence numbers was made for selected examples of rotation barriers, substituted strained molecules, radical gas phase reactions, and acid-base reactions. Relations between valence, geometry, and energy changes are discussed.
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  • 183
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    Journal of Computational Chemistry 6 (1985), S. 520-532 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for preparing compact orbital and auxiliary basis sets for LCAO-LSD calculations has been developed. The method has been applied to construct basis sets for first row transition metal atoms from Sc to Zn for the 3dn-14s1 and 3dn-24s2 configurations. The properties of different expansion patterns have been tested in atomic calculations for the chromium atom.
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  • 184
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An iterative algorithm is described for finding topological equivalence, ordering, and canonical numbering of vertexes (atoms) in molecular graphs. Like the Morgan algorithm, it is based on extended connectivities but: (i) the latter are used hierarchically, i. e., the discrimination in the next iteration is carried out only for the vertices having the same extended connectivities (ranks) at the previous iteration; (ii) at equal extended connectivities, additional discrimination is introduced by the ranks of adjacent vertices; (iii) there is no “best name” search; (iv) three levels of complexity of chemical structures are distinguished and handled by different procedures.Two schemes of application of HOC procedures are presented: one directed towards a fast canonical numbering for coding systems, and another one yielding levels of topological equivalence allowing a unique topological representation of the molecule with possible applications to similarity search, structure-activity correlations, etc.
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  • 185
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A topological code is devised on the basis of the unique topological representation of the molecule described in the preceding two parts of this series.1 By adding to the topological code additional chemical information on atoms and/or bonds, as well as stereochemical information, a chemical and respectively stereochemical code (SHOC) are also constructed. The advantages of the new linear codes are that they are convention-free codes, preserving the symmetry of molecular graph, and easily implemented either manually or by means of computer programs. By concentrating all topological, chemical, and stereochemical information, our code (SHOC) is more compact and more general than the codes based on several separate lists.
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  • 186
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    Journal of Computational Chemistry 6 (1985), S. 581-586 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different schemes are explored for the calculation of the proton transfer process in the hydrogen bonded cation [CH3OH · H · NH3]+. Results from ab-initio calculations with the STO-3G, 3-21G and 4-31G basis sets, are compared in search for an efficient reliable scheme to study the potential energy curves for the proton transfer. The curve constructed from the lowest energies calculated with the frozen optimized geometries of the two possible pairs of proton donor and acceptor fragments, (i.e., CH3OH2+/NH3 and CH3OH/NH4+) is in good agreement with that obtained when all the fragments of the hydrogen bonded complex are completely optimized simultaneously.
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  • 187
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The computer implementation of the HOC procedures presented in Parts I, II and III of this series is based on the module principle. It contains a main program and seventeen subroutines in Fortran IV. The system is able to provide unique atom numbering and code for all kinds of chemical compounds in their tremendous variety of structures.
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  • 188
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    Journal of Computational Chemistry 6 (1985), S. 598-609 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The many applications of the distance matrix, D(G), and the Wiener branching index, W(G), in chemistry are briefly outlined. W(G) is defined as one half the sum of all the entries in D(G). A recursion formula is developed enabling W(G) to be evaluated for any molecule whose graph G exists in the form of a tree. This formula, which represents the first general recursion formula for trees of any kind, is valid irrespective of the valence of the vertices of G or of the degree of branching in G. Several closed expressions giving W(G) for special classes of tree molecules are derived from the general formula. One illustrative worked example is also presented. Finally, it is shown how the presence of an arbitrary number of heteroatoms in tree-like molecules can readily be accommodated within our general formula by appropriately weighting the vertices and edges of G.
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  • 189
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    Journal of Computational Chemistry 6 (1985), S. 614-624 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The cellular species formed in the hydrolysis of cis-Pt(NH3)2Cl2 (DDP), namely, cis-[Pt(NH3)2XY]n+ (X, Y = Cl-, H2O, OH-; n = 0, 1, 2) have been investigated theoretically using the relativistic and nonrelativistic extended Huckel molecular orbital method. Molecular orbital (MO) results for trans-DDP and its hydrolysis products are also reported for comparison. Transition energies, molar absorption coefficients (∊), and B terms from magnetic circular dichroism (MCD) derived from theory are presented for each of the species studied. The electronic absorption and MCD spectra of all the complexes are predicted to exhibit ligand field transitions arising primarily from excitations between the occupied Pt 5d orbitals and the unoccupied Pt 5d and 6pz orbitals, respectively. The 5d → 6pz transitions are expected to yield intense absorptions in the UV spectral region. Some intensity is generated in the d → d transitions as a result of the low symmetry of these complexes. Correlation of available experimental data with theory allows spectral assignments to be made and predicted. Substituent effects in the cis- and trans-isomeric species are discussed. Finally, the applicability of the EHMO method to these systems is examined.
    Additional Material: 5 Ill.
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  • 190
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    Journal of Computational Chemistry 6 (1985), S. 634-646 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article presents a strategy to perform molecular dynamics simulations using parallel processing techniques on a parallel-distributed loosely coupled system consisting of IBM host computers (4341 and 4381) with attached scientific processors (FPS-164). This substantially enhances our ability to perform fast and more realistic large scale many-body trajectory simulations. A powerful extention of the computational range of molecular dynamics the parallel approach offers the opportunity to substantially reduce the simulation time to allow a longer simulation period to study more realistic models and larger systems. It is flexible and uses, for the most part, standard products and straightforward implementation with a broad range of applicability. The implementation of a simulation of water molecules with the inclusion of two- and three-body interactions is discussed. Some considerations in the design and implementation of parallel programs on a loosely coupled system are also presented.
    Additional Material: 5 Ill.
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  • 191
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    Journal of Computational Chemistry 6 (1985), S. 652-655 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We compare calculated total energies for 150 open-chain molecules using ab initio methodology and the PRDDO approximations. The bulk of the errors implicit in the PRDDO approximations are apparently of a one-center nature, i.e., they are due to the number and type of atoms in the molecule, and not the details of the molecular geometry. Atomic correction factors are developed which reduce the errors in the calculated total energy of PRDDO wave functions by a factor of eight relative to the ab initio reference calculations. PRDDO calculations on ring and cage compounds are shown to have additional systematic errors in the total energy.
    Additional Material: 3 Tab.
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  • 192
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    Journal of Computational Chemistry 6 (1985), S. 662-673 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Benzylic anions were studied with the semiempirical MNDO molecular orbital method. Structural changes were analyzed as metal counterions and solvents were allowed to interact with the benzylic carbon. Generally, benzylic carbanions were found to be trigonal planar but became pyramidal or bent when metals were included in the calculation.
    Additional Material: 8 Ill.
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  • 193
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    Journal of Computational Chemistry 6 (1985), S. 39-45 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hartree-Fock computations of the potential surface of Ar—H2 have been carried out and supplemented with calculations of the dispersion energy, with use of the counterpoise method to remove the basis set superposition error. The collinear and perpendicular bisector geometries are considered. The resulting potentials agree quite well with the actual experimental data.
    Additional Material: 3 Ill.
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  • 194
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    Journal of Computational Chemistry 6 (1985), S. 46-55 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Fully optimized geometries are computed at the Hartree-Fock level for formamide and methylamine with basis sets ranging up to ones that are triple-zeta plus two sets of polarization functions in the valence shell. The effect of very diffuse s and p functions is also examined. The relation of basis set size and composition to the computed amino group out-of-plane angle and to the related localized molecular orbitals is systematically investigated and compared with scattered results previously reported for other systems. It is concluded that the amino group angle is the result of a delicate balance between lone pair character of the nitrogen electrons and delocalization of these electrons into other portions of the molecule. Polarization functions in the nitrogen basis set are necessary to provide for proper description of the lone pair character, but even in methylamine the delocalization is not properly described without an extensive basis set, either polarization functions or very diffuse s and p functions, on the other heavy atoms. The effect is extreme for molecules such as formamide, aniline, and PF2NH2, where very large basis sets are required to obtain the correct out-of-plane angle.
    Additional Material: 2 Ill.
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  • 195
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    Journal of Computational Chemistry 6 (1985), S. 68-75 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The addition reactions of hydroxyl radical with imidazole and its protonated form to yield radical adducts have been investigated by ab initio SCF MO methods using STO-3G and 4-31G basis sets. Analogous radical species are of importance in radiation damage to biological systems. Of the possible radical products, the calculations indicate that the allylic species are generally favored energetically over the nonallylic forms. On an energetic basis, the results show that the allylic adducts formed by addition at the C2 and C5 positions are about equally favorable. Although the C5 species is generally identified as the experimentally observed product in aqueous media for both protonated and unprotonated imidazole, some experimental evidence exists indicating the presence of other forms. Our results suggest that this other form is the C2 adduct. The calculations also point to the protonated form of imidazole being less reactive than imidazole, which is in accord with experimental observations.
    Additional Material: 4 Ill.
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  • 196
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    Journal of Computational Chemistry 6 (1985) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 197
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    Journal of Computational Chemistry 6 (1985), S. 1-4 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is noticed that inclusion of an electrostatic term in the molecular-mechanical treatment of hydrocarbons would compel the nonbonding parameters of different force fields to become more alike than they are at present. Apart from removing the discontinuity in passing from the calculation of an unfunctionalized parent compound to the calculation of its functionalized derivatives, it is expected that the inclusion would improve results for the hydrocarbons themselves.
    Additional Material: 2 Ill.
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  • 198
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    Journal of Computational Chemistry 6 (1985), S. 5-8 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present energy component analysis calculations on alkali atom (Li,Na) hydride (H2O,NH3,H2S) interactions and compare these with corresponding (Li+ … NH3) cation … hydride interactions. In contrast to cation hydride interactions, the neutral atom-hydride interactions are shown to involve considerable contributions from all energy components.
    Additional Material: 1 Tab.
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  • 199
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy profiles were calculated for τ1, the C—C—C=O torsion, and τ2, the C—C—C—C torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4-21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ1, τ2) = (0, -60), (0, 180), (120, 180), (120, -60), and the maxima (0, 0), (180, 180), and (60, -60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a C—H bond trans to a C—C bond (C—Hs) is consistently shorter than a C—H bond (C—Ha) trans to another C—H bond. Specifically, for X—C(α) (= O)—C(β)—C(γ)—C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2-pentanone: (1) C(δ)—Hs 〈 C(δ)—Ha in all the conformers in which the δ-methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)-methyl and the ester groups, the bonding pattern is affected by a C—H⃛O=C interaction. (2) In the most stable conformers, (0, 60), C(β)—Ha 〈 C(β)—Hs, and C(γ)—Ha 〈 C(γ)—Hs, regardless of X. (3) The average C—C bonds in the τ2 = 180° conformers are consistently shorter than those with τ2 = 60° (compared at τ1 constant). In the most stable conformations (τ1 = 0°, τ2 = 60° or 180°), the bonding sequence is consistently C(α)—C(β) 〈 C(β)—C(γ) 〈 C(γ)—C(δ); whereas, when τ1 = 120°, C(α)—C(β) 〈 C(β)—C(γ) 〉 C(γ)—C(δ).
    Additional Material: 5 Ill.
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  • 200
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    Journal of Computational Chemistry 6 (1985), S. 76-76 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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