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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 58-62 
    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 simple and very rapid method for the calculation of electrostatic isopotential maps is proposed. The potential is composed of transferable bond fragments. According to chemical evidence, σ-, lone-pair, and π-bond contributions are considered. The computational work is proportional to the first power of the number of bond orbitals; therefore very large systems, such as enzymes or DNA, can be handled also. Transferability of bond orbital characteristics such as polarity, s character, and orientation is discussed. Though the absolute value of the potential is overestimated, trends obtained with STO-3G calculations are reflected correctly.
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  • 2
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 87-95 
    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 carboxylat anion, involved in the structure of numerous compounds of biological interest, participates in a number of intermolecular interactions involving water, cations, and other cellular constituents. A set of ab initio SCF computations have been carried out with an extended polarized basis set on HCOO-, its molecular electrostatic potential, and its interaction with Li+, Na+, K+, and H2O. The results are compared with those of a minimal good quality basis set. An evaluation of the basis set superposition error is made in the two basis as well as that of the contribution of the dispersion energy to the hydration. The analogies and differences in the nucleophilic character of the formate and the phosphate groups are discussed.
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  • 3
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 73-82 
    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 effect of the basis set superposition error (BSSE) on the calculated electronic structure of a molecular stacking complex is analyzed with the counterpoise correction method. The complex between para-hydroxyaniline (PHA) and formamidinium cation (FAM) is calculated ab initio with the STO-3G and Whitman-Hornback minimal bases, and with two split valence basis sets: 4-31G and STO-3G(D). When the counterpoise correction is applied, the charge redistribution in the PHA/FAM complex calculated with all four basis sets suggests that the complex is electrostatic in nature and that the main polarization is from the PHA toward FAM. The FAM cation is polarized away from the intermolecular region, thus causing further increase in the electrostatic interaction. This picture is not evident with the STO-3G related bases if the counterpoise correction is not applied. Thus, the BSSE in the charge redistribution is shown to be particularly large in the STO-3G basis and in the diffuse, split valence, STO-3G(D). Both these basis sets suffer from an inappropriate description of the core region. Where there is an improved description of the electron density in the core region, as in the calculations with the energy-optimized Whitman-Hornback basis and with the 4-31G basis, the counterpoise correction has only a very small effect on the charge redistribution. After the counterpoise correction is applied, the two minimal basis sets yield nearly identical charge redistribution results, as do the two split valence bases. It is therefore suggested that basis sets used in the calculation of molecular complexes might be classifiable according to criteria such as the degree of contraction and the quality of the description of angular polarization. This would help in the comparative evaluation of results obtained with different bases since minimal basis sets (or split valence bases) would become directly identifiable as groups yielding qualitatively similar results.
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  • 4
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 5
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 149-156 
    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 geometry and energy of tetra-tert-butylethylene have been determined by the molecular mechanics method. A twisting of the double bond by 45.5° was found. The ground state of the molecule should be a singlet. The calculated strain energy is higher than those of tri-tert-butylmethane and tetra-iso-propylethylene, but the possibility of synthesis of the compound is not excluded.
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  • 6
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 7
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 244-250 
    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 set of programs has been developed to calculate molecular spin-orbit interaction with Gaussian-type wavefunctions in connection with the popular GAUSSIAN 76 program. The spin-orbit contributions to the fine structure of O2 (X3∑g-), NH (X3∑-), and CH2 (X3B1) are evaluated with the standard STO-3G and 6-31G basis sets; for NH the influence of bond functions added to the latter basis set is also investigated. The results are compared to values previously obtained with other types of basis sets.
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 273-277 
    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 semianalytic method is presented for computing the concentration distribution in enzyme-substrate fast reaction systems. By means of this method, not only can much computation work be saved but a semianalytic expression for the concentration distribution will be obtained. This expression is very useful for analysis and discussion of the kinetic characteristics of this kind of reaction system.
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  • 9
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 251-260 
    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 and SCF-CI calculations have been performed to investigate substituent effects on ground- and excited-state properties of 4-R-pyrimidines, and to compare these with substituent effects in 2- and 4-R-pyridines, with R including the π donating and σ withdrawing groups CH3, NH2, OH, F, and C2H3 and the σ and π electron-withdrawing groups CHO and CN. Substitution leads to significant changes in the internal angles of the pyrimidine ring, which are independent of the nature of the substituent. The geometry of the pyrimidine ring is more sensitive to substitution in the 4 position than the pyridine ring geometry is to substitution in either the 2 or the 4 position. The isodesmic reaction energies for substituent transfer from the 4 position of pyrimidine to the 2 or 4 position of pyridine indicate that all R groups except CN have a relative stabilizing effect in pyrimidine. The presence of a π donating group leads to an increase in the n→π* transition energy of 4-R-pyrimidines, while the π withdrawing group CN leads to a decrease in the transition energy relative to pyrimidine. Orbital energy differences and virtual excitation energies tend to correlate with n→π* transition energies of 4-R-pyrimidines with saturated R groups, but such correlations are masked by π conjugation, n orbital interaction, and configurational mixing when the unsaturated groups C2H3, CHO, and CN are present. The electronic effects of a π donating group are stronger when the group is bonded to pyrimidine than to pyridine, but those of a π withdrawing group are weaker when the group is bonded to pyrimidine.
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  • 10
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    Journal of Computational Chemistry 2 (1981), S. 376-383 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum chemical calculations of polymers and solids, especially on an ab initio level, represent a large computational task and therefore necessitate efficient computing methods. This is particularly true for the oscillatory integrals appearing in such calculations. For these integrals efficient integration methods based both on the Chebyshev series and the spline representation of the nonoscillatory part of the integrand are considered; they are found far superior compared with more standard integration rules. In two- and three-dimensional systems, directions with maximum oscillatory behavior can be selected along which these new efficient integration techniques can be used advantageously. The ideas are illustrated by Hückel crystal orbital (HCO) bond orders for the polyacetylene chain and the graphite layer. In the latter example, also, a method for the integration of oscillatory integrands with a singularity is given.
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  • 11
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 402-409 
    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 Monte Carlo algorithm, capable of simulating numerically the time and space dependence of chemical concentrations in a reacting system, is presented. This method is used to study the phenomenon of trigger waves in the Oregonator model of the Belousov-Zhabotinskii reaction, including the diffusion of species X and Y in one dimension. The results show that a small disturbance in a homogeneous mixture can grow into a chemical (trigger) wave propagating in space at constant velocity. The dependence of this velocity on several factors is studied, namely, initial concentrations, the diffusion of Y, and the stoichiometry of the autocatalytic step of the model. A comparison of the Monte Carlo results with a previous simulation also is discussed.
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  • 12
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 416-421 
    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 the STO-3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water-water interactions and nonadditivity effects are also significant.
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  • 13
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    Journal of Computational Chemistry 2 (1981), S. 422-432 
    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 the STO-3G basis set have been performed to investigate substituent effects on the structures and stabilization energies of water:4-R-pyrimidine complexes, with R including CH3, NH2, OH, F, C2H3, CHO, and CN. Except for the cyclic water:4-aminopyrimidine complex hydrogen bonded at N3, these complexes have open structures stabilized by a nearly linear hydrogen bond formed through a nitrogen lone pair of electrons. When hydrogen bonding occurs at N3, the complexes may have planar or perpendicular conformations depending on the substituent, but when hydrogen bonding occurs at N1, the perpendicular is generally slightly preferred, and there is essentially free rotation of the 4-R-pyrimidine. Primary substituent effects alter the electronic environment at the nitrogens, and tend to make N3 a poorer site for hydrogen bonding than N1, primarily because of a stronger π electron-withdrawing effect at N3. However, the relative stabilities of complexes hydrogen bonded at N1 and N3 are also influenced by secondary substituent effects, which may be significant in stabilizing complexes bonded at N3. Substitutent effects on the structures and stabilization energies of the water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyridine complexes. Configuration interaction calculations indicate that although absorption of energy by the pyrimidine ring destabilizes the water:4-R-pyrimidine complexes, these may still remain bound in the excited n → π* state. This is in contrast to the fate of open water:2-R-pyridine and water:4-R-pyridine complexes, which dissociate in this state.
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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 460-469 
    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 conformational behavior of the C-terminal neurotensin pentapeptide, Arg-Pro-Tyr-Ile-Leu OH [NT(9-13)], was investigated using empirical energy calculations. A special aim was to display the specific contribution of each residue to induce conformations able to interact with biological receptors. Restrictions were then introduced in intramolecular interactions involving the Arg side chain and the terminal COOH group. The stablest conformations include in the order of decreasing stability: a distorted helical form for the C-terminal tetrapeptide, a (Pro2-Tyr3) β turn I, an α helix, an extended form, and a (Tyr2-Ile3) β turn III, which are energetically rather close (ΔE 〈 3 kcal/mol). The NT(9-13) peptide appears then as a rather flexible molcule with a noteworthy ability of adaptation to a substrate. Extended forms would be in agreement with a zipper model of interactions with receptors, whereas folded forms involving helices and β, γ turns would support a lock and key model. The specific contribution of side chains, specially those of Tyr and Arg residues as well as the key position of the Pro residue emerge clearly from this study.
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  • 15
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    Journal of Computational Chemistry 4 (1983), S. 181-186 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Gaussian basis sets, consisting of 15 s-type, 11 p-type, and 6 d-type functions, for the fourth-row main group elements, In-Xe, are presented. In order to compare these basis sets with larger ones, calculations have been performed in I2 and TeO2.
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  • 16
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    Journal of Computational Chemistry 4 (1983), S. 283-293 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Energetics and geometries for the hydrated gaseous halide anions have been computed from a simple model in which the molecular dipole of water was composed of two parts, one due to a lone pair on oxygen (60%) and the rest to formal charges on the nuclei. The calculations were made for both the symmetric and nonsymmetric structures. A variety of structures were used to compute potential energies and distances with up to six water molecules. The total energy consisted of a sum of electrostatic, polarization, dispersion, and repulsion terms. Various sets of repulsive potential parameters, ranging from those determined from molecular beam experiments to those determined using experimental ion-water distances or energies, have been employed to compute repulsive interaction energies. It was found that the range parameters play a significant role in deciding the magnitudes of the distances and energies, as the latter are most sensitive to them. It was also shown that with a simple correlation scheme the consistency of the experimental energies and distances can be tested separately without using repulsive potential parameters from other sources. It also suggests that a range of parameters can be used to compute repulsion energies. Despite the fact that the model is greatly simplified, the agreement of both the predicted ion-oxygen distances and energies with both experiment and other calculations is excellent. A detailed analysis of our calculation suggests that the negative ion clusters with one to three water molecules contain symmetric orientation of water molecules, while those with more than three may contain asymmetric orientations of water molecules or a mixture of both. From the log-log plots of hydration energies versus (R + radius of water molecule), we have proposed empirical expressions of the type ΔEn-1,n = 10·0x (R + 1.38)-y with both Pauling's and Ladd's radii for univalent ions with which stepwise hydration energies of the latter can be predicted if we know thier radii. The values predicted for the alkali cations are in excellent agreement with the experimental and theoretical values, indicating the consistency of the simple model.
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  • 17
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    Journal of Computational Chemistry 4 (1983), S. 345-349 
    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 tautomerism of the uracil-4-hydroxyuracil system is examined with the 3-21G basis set and full geometry optimization using gradient techniques. Single-point calculations at the 6-31G level were also done and the results compared with the 2-pyridone-2-hydroxypyridine system. The best ΔE(taut) obtained in this work is 74.1 kJ/mol.
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  • 18
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    Journal of Computational Chemistry 4 (1983) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 19
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    Journal of Computational Chemistry 4 (1983), S. 1-8 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations of the equilibrium geometries have been carried out on nine possible isomers of MH2N2, where M = C or Si, and compared with the results of MNDO calculations. The results for the carbon compounds are in good agreement with available experimental data, but in the case of the silicon compounds, the molecules are predicted to be unstable with respect to decomposition to SiH2 and N2. The inclusion of electron correlation at the MP3 level does not alter the order of the relative stabilities, although the importance of the correlation contribution varies substantially between the different isomers.
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  • 20
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    Journal of Computational Chemistry 4 (1983), S. 23-32 
    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 computer-oriented algorithm is developed for enumerating and generating all rigorously planar benzenoid hydrocarbons. An additional algorithm is also developed for identification and enumeration of carcinogenic bay regions. The results are reported for undisrupted benzenoid structures up to ten fused rings. The reported numbers of isomeric benzenoids do not agree with the results in the literature, because other authors included in their considerations some polyhexes which are not strictly planar structures (e.g., helicenes) or which represent rings of hexagons (e.g., circulenes). The reported results for enumeration of bay regions fully agree with those of Balasubramanian et al.
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  • 21
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    Journal of Computational Chemistry 4 (1983), S. 58-67 
    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 low-cost microcomputer and package of assembly language routines has been developed to emulate the structure and performance of a large analog computer. The advantages of the analog computer, as implemented in this scheme, include (1) a significant reduction in the programming effort involved in modeling complex dynamic systems and (2) the control of the simulation and model parameters in a completely interactive and flexible manner. The symbolic nomenclature and schematic representations involving devices, such as integrators, comparators, multipliers, and function generators, offers a powerful alternative to the more conventional numerical methods, that is, to provide very simply the solutions to large systems of differential equations. This approach invariably leads the user to a more thorough understanding of the dynamic character of the system. The technique is illustrated using a chemical kinetics example involving the simulation of laser-induced fluorescence. The results of this work have provided an assessment of a systematic error that occurs when using induced resonance fluorescence to measure OH concentrations in the troposphere of the earth.
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  • 22
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    Journal of Computational Chemistry 4 (1983), S. 104-109 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Approximate minimum energy reaction paths have been calculated for two thioketone-enethiol tautomeric systems using an ab initio SCF-MO method. The calculations indicate nearly equal stabil ties of the isolated tautomers in both systems and an energy barrier of ca. 85 kcal/mol for their interconversion. This barrier is expected to be significantly lower in solution as a result of solvent-solute interactions.
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  • 23
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    Journal of Computational Chemistry 4 (1983), S. 114-122 
    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 MM2 molecular mechanics force field, as modified for halogens, is able to predict the structures, dipole moments, and energies of the isomers of benzene hexachloride. For benzene tetrachloride and naphthalene tetrachloride the field exaggerates the stability of conformers with axial chlorine, but gives satisfactory results if the field is modified to allow for interaction between electronegative substituents and the π electrons.
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  • 24
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    Journal of Computational Chemistry 4 (1983), S. 124-124 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 25
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    Journal of Computational Chemistry 4 (1983), S. 127-135 
    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 relativistic effective core potential (REP) has been generated for the uranium atom and used in self-consistent-field calculations of the A states of UH, UF, and their ions. Energy curves were calculated at the base configuration level which ensures the dissociating atoms are described by Hartree-Fock wavefunctions. The electronic bonding of these molecules is found to be similar to that of comparable alkaline-earth hydrides and fluorides. The uranium 6p, 6d, and 5f orbitals retain their atomic character but the orbitals extend into the bonding region and are distorted by overlap repulsion and electrostatic effects. Nonetheless, the atomic energetic coupling determines that low energy states will have the maximum spin multiplicity and maximum orbital angular momentum projection consonant with the charge-transfer bonding.
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  • 26
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    Journal of Computational Chemistry 4 (1983), S. 154-157 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Following an earlier proposal to evaluate electron repulsion integrals over Gaussian basis functions by a numerical quadrature based on a set of orthogonal polynomials (Rys polynomials), \documentclass{article}\pagestyle{empty}\begin{document} $$ (\eta \eta \parallel \eta \eta) = 2(\rho/\pi)^{1/2} \sum\limits_{\alpha = 1, N} I_x(u_{\alpha})I_{y}(u_{\alpha}) I_z(u_{\alpha})W_{\alpha} $$ \end{document} a computational procedure is outlined for efficient evaluation of the two-dimensional integrals Ix, Iy, and Iz. Compact recurrence formulas for the integrals make the method particularly fitted to handle high-angular-momentum basis functions. The technique has been implemented in the HONDO molecular orbital program.
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  • 27
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    Journal of Computational Chemistry 4 (1983), S. 175-180 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: CNDO/Force and compliance constant methods were applied to define general quadratic potential functions for F2CO and HCOF. A satisfactory set of compliants was obtained by suitably scaling down the stretching and stretch-stretch elements of the initial force constant matrix, evaluated by the CNDO/force approach, followed by fitting the compliants to available experimental data.
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    Journal of Computational Chemistry 4 (1983), S. 218-225 
    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 the determination of the vibration-rotation eigenvalue in diatomic molecules is considered. An eigenvalue equation totally independent from the eigenfunction is written for any potential, analytical or numerical. This equation uses uniquely the vibration-rotation canonical functions; its resolution is reduced to that of a simple and classical numerical problem. Examples of numerical applications for analytical (Morse) and numerical potentials are presented. It is shown that the vibrational eigenvalues deduced from the eigenvalue equation are within 10-6 cm-1 of the exact values. Comparison with conventional methods are presented and discussed.
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  • 29
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Symmetry methods employed in the ab initio polyatomic program HONDO are extended to the coupled perturbed Hartree-Fock (CPHF) formalism, a key step in the analytical computation of energy first derivatives for configuration interaction (CI) wavefunctions, and energy second derivatives for Hartree-Fock (HF) wavefunctions. One possible computational strategy is to construct Fock-like matrices for each nuclear coordinate in which the one- and two-electron integrals of the usual Fock matrix are replaced by the integral first derivatives. “Skeleton” matrices are constructed from the unique blocks of electron-repulsion integral derivatives. The correct matrices are generated by applying a symmetrization operator. The analysis is valid for many wavefunctions, including closed- or open-shell spin-restricted and spin-unrestricted HF wavefunctions. To illustrate the method, we compare the computer time required for setting up the coupled perturbed HF equations for eclipsed ethane using D3h symmetry point group and various subgroups of D3h. Computational times are roughly inversely proportional to the order of the point group.
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  • 30
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    Journal of Computational Chemistry 4 (1983), S. 276-282 
    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 scheme is presented that enables photographic representation of the (two-dimensional) surfaces of (three-dimensional) molecular orbitals and electron density functions. The algorithm has been implemented by a program which is completely general and computationally efficient.
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  • 31
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    Journal of Computational Chemistry 4 (1983), S. 308-312 
    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 force field has been developed, on the basis of available experimental and partial retention of diatomic differential overlap (PRDDO) data, to permit molecular mechanics calculations on azoxyalkanes. The calculated structures and enthalpies of formation are in fair agreement with experimental results. The calculated enthalpies of formation and strain energies are compared with the corresponding quantities for analogous azoalkanes.
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  • 32
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    Journal of Computational Chemistry 4 (1983), S. 337-344 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Interchange and many-body perturbation theory are applied to the calculation of the radiative lifetime of the 3B1 state of SO2. The radiative lifetime of 3B1 SO2 is predicted to be 7.6 msec, in excellent agreement with the experimental collision-free phosphorescence lifetime. As a separate calculation, interchange perturbation theory is used to determine the radiative lifetime of the 1A1 state of CH2.
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  • 33
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    Journal of Computational Chemistry 4 (1983), S. 333-336 
    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 nearest-neighbor exclusion model for intercalation was studied using an energetical approach. It was shown that creation of the intercalation site in the exclusion model corresponds to the same energetical destabilization of the structure as in the standard model of intercalation. The stability of the intercalation complex formed in the case of the exclusion model is lower by 68 kcal/mol as compared with the standard model, but geometrical structures of both complexes are very similar. The electrostatic molecular potential method was also used to further characterize the intercalation site formed within both models of intercalation.
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  • 34
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    Journal of Computational Chemistry 4 (1983), S. 350-361 
    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 major relativistic effects are included into the model potential (MP) method of Bonifacic and Huzinaga. The effects are incorporated on the level of Cowan and Griffin's relativistic Hartree-Fock (RHF) method. The model potential parameters are determined using the results of nonrelativistic Hartree-Fock (NHF) and RHF calculations. A new scheme of selection of the basis functions for use in atomic and molecular MP calculations is proposed. To obtain agreement with the Hartree-Fock calculations on AgH and Ag2, the 4p shell has to be included explicitly in the MP calculations. The explicit treatment of the 4p electrons and the resulting reduction of the core size are necessary in order to overcome difficulties with approximate representation of the large 4p-4d core-valence interactions on the MP level.
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  • 35
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    Journal of Computational Chemistry 4 (1983), S. 399-403 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parameters have been derived so as to enable the inclusion of deuterium in the MM2 molecular mechanics force field. Several compounds were studied and the results are compared with experiment. The results are never qualitatively wrong, but the accuracy ranges from excellent to only fair. They are quite good for hydrocarbons, but less so for ketones.
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  • 36
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    Journal of Computational Chemistry 4 (1983), S. 404-409 
    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 radical cations H3PPH3+⋅, H3PSH2+⋅, H3PClH+·, and HClClH+· have been studied by ab initio molecular-orbital theory. An increasing tendency to adopt trigonal bipyramidal (TBP) gemoetries is observed for the phosphorus radicals with sulfur and chlorine ligands. The three-electron bond dissociation energies are calculated to be between 7 and 31 kcal mol-1. The dependence of these bond energies on the ionization potentials for the neutral hydrides is illustrated, and the deformation of phosphorus σ* radicals towards TBP structures is discussed.
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  • 37
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    Journal of Computational Chemistry 4 (1983), S. 428-437 
    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 computer method for the calculation of the pseudorotational parameters in five-membered rings from vicinal proton spin-spin coupling constants is described. Some typical problems met in practice are discussed. Applications of the program in the conformational analysis of some substituted cyclopentanes are presented.
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  • 38
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    Journal of Computational Chemistry 4 (1983), S. 449-460 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: As a model reaction for peptide and bond formation, the SN2 reactions between glycine and ammonia have been studied with and without amine catalysis: \documentclass{article}\pagestyle{empty}\begin{document}$${\rm NH}_3 + {\rm NH}_2 {\rm CH}_2 {\rm COOH} + ({\rm NH}_3 ) \to {\rm NH}_2 {\rm CH}_2 {\rm CONH}_2 + {\rm H}_2 {\rm O} + ({\rm NH}_3 )$$\end{document} using ab initio molecular-orbital methods. For each of the catalyzed and uncatalyzed reactions, two reaction mechanisms have been examined: a two-step and a concerted mechanism. The stationary points of each reaction, including intermediate and transition states, have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of the reaction. The calculations demonstrate that a second ammonia molecule catalyzes amide bond formation, and that the two-step mechanism is more favorable than the concerted one for the catalyzed reaction, while for the uncatalyzed reaction both mechanisms are competitive.
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  • 39
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis-set balance parameters, defined in terms of various projections of an abstract force vector in the space spanned by the logarithms of orbital exponents, are evaluated for a sample of 100 Gaussian basis sets. These basis sets are taken from a random Gaussian distribution of bases, centered on the best energy, fully variational uniform quality (UQ) atomic orbital (AO) basis sets. With each basis geometry optimization has been carried out for model molecule dimethyl sulfoxide, the wavefunction of which molecule is exceptionally sensitive to basis-set errors. Correlations between the balance of basis sets and calculated molecular properties are analyzed.
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  • 40
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    Journal of Computational Chemistry 4 (1983), S. 513-523 
    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 molecular orbital theory has been used to probe the effect of the substituent X on the structures, strain energies, stabilization energies, inversion barriers, and proton affinities of carbanions CH3CX CH3- and cis-C3H4X-, where X = H, F, CN, and NC. All geometries have been optimized with a 3-21G basis set, and the parent anions (X = H) were also optimized with the same basis set with a diffuse function added (i.e. the 3-21 + G basis set). The anions, with the exception of the α-cyanoisopropyl anion, are pyramidal. The out-of-plane angle, α, for the pyramidal anions decreases in the order F 〉 H ≈ NC 〉 CN, and the barriers to inversion follow the same order with the cyclopropyl anions consistently having higher barriers than the isopropyl anions. The substituents strongly stabilize the anions with the stabilization energy following the order CN 〉 NC 〉 F. The cyano group slightly reduces the strain energy of cyclopropane, but the isocyano and fluoro substituents are weakly and strongly destabilizing, respectively. The pyramidal cyclopropyl anions are less strained than the cyclopropanes except when the substituent is a cyano group where the strain energies are reversed but are very similar. The planar anions all have higher strain energies than the cyclopropanes.
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  • 41
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    Journal of Computational Chemistry 4 (1983), S. 552-555 
    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 very simple yet effective device for reducing the number of self-consistent-field (SCF) cycles in central finite-difference calculations of molecular properties is presented. The efficiency of this is demonstrated by MINDO/2 calculations of the force constants of a variety of molecules. The device consists of using information about the wavefunction at two values of a perturbation parameter to provide an estimate of the wavefunction at a third. This estimate is then used as an initial guess in an SCF procedure. The underlying theory is discussed and applications to other problems are suggested.
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  • 42
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    Journal of Computational Chemistry 4 (1983), S. 567-577 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio computation procedure to obtain electronic transition wave numbers in solution is presented and discussed. The continuum description of the bulk solvent is adopted, and solute-solvent interaction is reduced to a closed-form interaction operator added to the solute Hamiltonian. The resulting Schrödinger equations are solved variationally. No limitations are imposed on the shape of the solvent cavity or on the level of accuracy of the ab initio procedure.
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  • 43
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    Journal of Computational Chemistry 4 (1983), S. 605-605 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 44
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    Journal of Computational Chemistry 4 (1983), S. 594-604 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Proton affinities (PA) of 80 neutral bases were calculated using the semiempirical molecular orbital procedure MNDO. These were compared with the corresponding experimental and, where available, ab initio STO-3G and 4-31G data. For the 12 bases studied which led to ions which were not hyperconjugatively stabilized, the mean absolute error between the calculated and experimental values was 7.2 kcal mol-1. However, a plot of these data revealed a clear tendency of MNDO to underestimate the PAs of the more basic molecules. Where hyperconjugative stabilization of the ion was possible, the calculated PAS were underestimated by a further 7-10 kcal mol-1 for each attached alkyl group. Calculated and observed methyl-and ethyl-cation affinities were compared for 18 bases with qualitatively similar results.
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  • 45
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    Journal of Computational Chemistry 2 (1981), S. 1-6 
    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 barriers on the MINDO/3 reaction paths for π and σ approaches to concerted cycloaddition of methylene to s-cis-1,3-butadiene are analyzed by a new energy decomposition scheme and compared to the results of published extended Hückel calculations. The relatively small (6 kcal) preference for the σ approach is essentially based on next-nearest-neighbor (1,3) resonance interactions, which are stabilizing in the σ but destabilizing in the π approach. Both routes are characterized by large distortion energies (mainly disrotation at the diene termini in the case of the π approach) and nonbonded repulsions. The excessive magnitude of both of these effects ultimately derives from the weak pericyclic binding which prevails at initial diene geometries, especially the pericyclic topology involving the methylene LUMO. Although previous work has emphasized the contribution of closed-shell repulsions to the barrier, no such effect is explicitly included in MINDO. The closed-shell repulsions to which the extended Hückel barrier has been solely attributed are shown to involve next-nearest-neighbor (antiaromatic) resonance interactions.
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  • 46
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    Journal of Computational Chemistry 2 (1981), S. 14-19 
    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 empirical potential, EPEN, has been used to establish the structures of isolated hydrogen-bonded clusters in methanol. The most stable configuration of the dimer is found to have a trans near-linear form, whereas the most stable forms of the trimer and tetramer are cyclic. Charge interactions in the tetramer make it the most stable, in terms of energy per hydrogen bond, of these three species. These results are in conformity with various types of experiment. Other species of dimer, trimer, and tetramer, corresponding to local energy minima, have also been identified.
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  • 47
    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 C=O bond length and fC=O,C=O, the corresponding harmonic stretching force constant, are calculated ab initio using the 4-31G basis set (augmented by polarization functions on the sulfur and chlorine) with full geometry optimization for the monosubstituted carbonyl compounds RCHO, where R = H, CHO, CH=CH2, CO2H, CH=CHOH, OH, OC(=O)OH, OOH, S—H, Li, F, Cl, and NH2. Straight-line relationships are found in plots of ln[fC=O,C=O] vs. ln[rC=O] for the series of compounds in which carbon atoms and oxygen atoms are bonded directly to the carbonyl carbon, in accordance with the empirical expression f = C′/rn. The slopes and intercepts give n = 7.62 and 6.47, C′ = 62.6 and 48.6, for the lines with carbon and oxygen as the atom bonded directly to the carbonyl carbon, respectively. The point for formaldehyde lies very close to the C line, whereas the points for SH, Li, F, Cl, and NH2 lie closer to the O line.
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  • 48
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    Journal of Computational Chemistry 2 (1981), S. 161-167 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parameters for sulfoxides used in force field MM1 were modified to be incorporated into force field MM2. The conformations of ten alkyl sulfoxides were then calculated using MM2 with these new parameters. The alkyl groups used were methyl, ethyl, isopropyl, and t-butyl. It was found that of the many possible conformations for these compounds, only one or two stable conformers exist, and that the number of these conformers agrees with the number of reported S—O stretching frequencies in almost every case. No apparent correlation between the vibration frequency and the molecular structure was found.
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  • 49
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    Journal of Computational Chemistry 2 (1981), S. 182-187 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Harmonic force fields have been calculated for the planar hydrogen-bonded ring conformer of β-hydroxyacrolein, cCc, which is the most stable, and the chain conformer, cCt, generated by 180° rotation of O—H about the C—O bond axis. The equilibrium structure obtained using the 4-31 G basis set with full geometry optimization was employed in each case. Selected force constants for the bonds directly concerned in the formation of the ring from the chain structure, and the increments in going from the one to the other, are compared with the values for the corresponding conformers of performic and formic acids. As the ring size increases from four in trans-formic acid, to five in cis-cis-performic acid and to six in the cCc conformer of β-hydroxyacrolein there is a successive increase in the mechanical strength of the hydrogen-bridging unit. The energy changes for the chain → ring conversion do not follow this progression: performic acid is out of order. But, since a force constant is a localized bond property, whereas the energy changes are determined not only by interactions specific to the hydrogendonor and hydrogen-acceptor groups but also by interactions involving more distant parts of the molecule, the force constants for the bonds directly concerned in the formation of the hydrogen bridge provide a less ambiguous basis for comparing the strength of the intramolecular hydrogen bonding.
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  • 50
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    Journal of Computational Chemistry 2 (1981), S. 188-199 
    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 SCF calculations with the STO-3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water-uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N1—H and O2, N3—H and O2, and N3—H and O4. Open structures form at O4, N1—H, and N3—H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N1—H and the cyclic one at N1—H and O2. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N3—H and a cyclic structure at N3—H and O4. The third cyclic structure at N3—H and O2 collapses to the “wobble” dimer at N3—H and O4. The two “wobble” dimers are significantly more stable than the open dimer formed at O4, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N1—H than N3—H, owing to a more favorable molecular dipole moment alignment when association occurs through H1. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water-uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.
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    Journal of Computational Chemistry 2 (1981), S. 287-303 
    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 computer program we have been developing to build models of molecules and calculate their interactions using empirical energy approaches. The program is sufficiently flexible and general to allow modeling of small molecules, as well as polymers. As an illustration, we present applications of the program to study the conformation of actinomycin D. In particular, we study the rotational isomerism about the D-Val-, L-Pro, and L-Pro-Sar amide bonds as well as comparing the energy and structure of the Sobell model and the x-ray structure of actinomycin D.
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  • 52
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    Journal of Computational Chemistry 2 (1981), S. 304-323 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrostatic potentials and Mulliken net atomic charges were calculated from STO-3G, 6-31G, and 6-31G** SCF-MO wavefunctions for hydrogen fluoride, water, ammonia, methane, acetylene, ethylene, carbon dioxide, formaldehyde, methanol, formamide, formic acid, acetonitrile, diborane, and carbonate ion. In each case optimized net atomic charges (potential-derived charges) were also obtained by fitting the electrostatic potentials calculated directly from the wavefunctions in a shell enveloping the molecules outside of their van der Waals surfaces. The electrostatic potentials calculated from the potential-derived charge distributions were then compared with the defined quantum mechanical electrostatic potentials and with the electrostatic potentials of the Mulliken charge distributions.
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  • 53
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    Journal of Computational Chemistry 2 (1981), S. 356-360 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: At high levels of ab initio theory (6-31G*//4-31G), the most stable C4H42+ isomer is indicated to be the nonplanar cyclobutadiene dication (1a); the planar form, 1b, is indicated to be 7.5 kcal/mol less stable. The second most stable C4H42+ isomer, the methylenecyclopropene dication, is indicated to prefer the perpendicular (2a) over the planar (2b) arrangement by 7 kcal/mol. The “anti van't Hoff” cyclo-(HB)2C=CH2 system (4), isoelectronic with 2, also prefers the perpendicular conformation (4a), and retains the C=C double bond. The linear butatriene dication (3) is the least stable C4H42+ species investigated. The perpendicular (D2d) arrangement (3a), permitting double allyl cationlike conjugation, is preferred over the planar D2h form (3b) by 26 kcal/mol. The heat of formation of the most stable form of C4H42+, 1a, is estimated to be 623-640 kcal/mol. This species should be thermodynamically stable toward dissociation into smaller charged fragments.
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  • 54
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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: New estimates of Hartree-Fock limit energies (ERHF) for selected AH and AHn hydrides, diatomic and linear polyatomic molecules have been made utilizing ESCF values recently reported in the literature for HF, N2, CO, NH3, and CH4 which are very close to the respective limits. These new values have been used to investigate the applicability of Ermler and Kern's procedure for estimating ERHF: i.e., a factor f is first evaluated from data for reference molecules, where f = ERHF/ESCF, which is then used with ESCF values for other molecules to obtain their ERHF values. f has been evaluated for three groups of reference molecules—HF, H2O, NH3, CH4, N2, and CO; CH4, C2H2, C2H4, and C2H6; and C2H2, HCN, and N2—utilizing ESCF data in the literature for many Gaussian-type orbital (GTO) basis sets together with some new values calculated at the (9,5,1) to (13,8,2) levels. Trends in the variation of f within each group of reference molecules from one basis set to another, and the trends in f from one group of reference molecules to another, are discussed in detail. To minimize the influence of these effects in an ERHF estimate it is recommended that the f value should be derived from reference molecules which possess a similar combination of structural features, i.e., bonded hydrogen, single, double, or triple bonds, and the number of lone-pair electrons. Further calculations show that an f value based on data for closed-shell molecules is not applicable to open-shell species.
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  • 55
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    Journal of Computational Chemistry 2 (1981), S. 53-57 
    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 charge distributions along the CH bonds of methane, ethylene, and acetylene have been obtained by numerical integration of 6-31G** wavefunctions. Several criteria for assigning electron populations to carbon and hydrogen lead to negative charge on H for methane and ethylene and a positive charge on H for acetylene. These results are contrasted with the charges derived from the μCHeff obtained from infrared intensity measurements. The difference between the results from infrared intensities and from the electron density calculations has been shown to result from incomplete orbital following in the molecular deformation and the creation of a “bent-bond” moment. Its magnitude has been estimated.
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  • 56
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    Journal of Computational Chemistry 2 (1981), S. 83-86 
    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 modified integral package for evaluation of two-electron integrals over Gaussian basis functions is described. Modifications are implemented in the MOLECULE program system and are especially suited for the study of large molecules and molecular complexes.
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  • 57
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Gaussian-type basis sets for molecular calculations are usually prepared by an atomic SCF program in which spherical coordinates are used. On the other hand, many molecular SCF and CI programs are written by using the Cartesian coordinates and as a result six-membered d-type functions (x2, y2, z2, xy, yz, zx)e-γr2 are often used. They contain one additional 3s function which does not exist in the atomic calculation. Therefore, we shall have an incorrect, deeper molecular binding energy, unless we readjust the atomic total energy by adding the 3s orbital to the original basis set. Some examples are shown in the case of Cu2 molecule, where we have found that the correction is quite appreciable, which was overlooked in previous work.
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  • 58
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    Journal of Computational Chemistry 2 (1981), S. 108-125 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Compact contracted Gaussian basis sets introduced in the preceding article are tested for ab initio molecular calculations on molecules containing third-row atoms (Na through Cl). It is found that the effect of splitting valence orbitals is essential for these molecules and addition of polarization functions to split basis sets can yield computed geometries, spectroscopic constants, and atomization energies in close agreement with the result of near Hartree-Fock calculations.
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  • 59
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    Journal of Computational Chemistry 2 (1981), S. 157-160 
    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 new method is presented for the calculation of partition coefficients of solutes in water lipid systems. Log P values are calculated based on the charge densities of the atoms as determined by quantum mechanical methods. In this article, the results have been obtained from charge densities calculated by two methods: MINDO/3 and Hückel-type calculation based primarily on topology. Results are favorably compared with those obtained by fragment analysis.
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  • 60
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    Journal of Computational Chemistry 2 (1981), S. 177-181 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The empirical potential EPEN/2 has been used to establish the structures of isolated hydrogen-bonding ammonia clusters. The most stable forms of the dimer have a linear or near-linear structure. The trimer has a closed structure with zero dipole moment. Two stable tetramer forms were found: one with a closed structure and zero dipole moment in agreement with experimental findings, and one with a pyramidal structure with nonzero dipole moment which may be an artifact of the EPEN/2 potential. The relation of the dimer structures to the limited available experimental information is discussed.
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  • 61
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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: Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF-CI calculations on uracil and water-uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C4—O group, while the second is associated with excitation of the C2—O group. In the first n → π* state, hydrogen bonds at O4 are broken, so that the open water-uracil dimer at O4 dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N3—H and a cyclic structure at N3—H and O4 in the ground state, collapses to a different “wobble” dimer at N3—H and O2 in the excited state. The third dimer, a “wobble” dimer at N1—H and O2, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O2 are broken in the second n → π* state, the three water-uracil dimers remain bound. The “wobble” dimer at N1—H and O2 changes to an excited open dimer at N1—H. The “wobble” dimer at N3—H and O4 remains intact, and the open dimer at O4 is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.
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  • 62
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Ab initio calculations with a minimal (STO-3G) basis set on a number of sulfur-containing molecules are used to show that Koopmans' theorem and minimal basis calculations may be a simple but adequate way of obtaining inner-shell ionization potentials and chemical shifts of large molecules. The x-ray photoelectron spectrum of (C6H5)2SNSO2C6H4CH3 is discussed with reference to an ab initio SCF minimal basis calculation on the model molecule H2SNSO2H.
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    Journal of Computational Chemistry 2 (1981), S. 225-230 
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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: Ab initio molecular orbital (MO) calculations for two series of sulfur-oxygen compounds are reported: the S(IV) system of SO2, H2SO3, HSO3-, and SO32-, and the S(VI) system of SO3, H2SO4, HSO4-, and SO42-. Geometries about the sulfur atoms were optimized using the STO-3G* basis set; energies at these geometries were computed by the STO-3G and 44-31G basis sets both with and without five Gaussian d orbitals on S. The sulfur-oxygen bond lengths and the angles about the central atoms agree fairly well with experiment. The stabilization energy associated with the addition of the d orbitals was found to be a constant amount per bond (ca. 54 and 28 kcal mole-1 in the minimal and extended bases, respectively) in hypervalent compounds. The isomer HSO3- was predicted to be more stable than SO2(OH)-, but the reverse was true for HSO2(OH) compared to SO(OH)2. The deprotonation energies for the acids and the hydration energies for the oxides also were computed and discussed with reference to experimental data.
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  • 64
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    Journal of Computational Chemistry 2 (1981), S. 261-265 
    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 molecular orbital calculations are reported for H2S, its radical cation, and the H2SSH2+ radical cation. At the MP2/4-31G level the S—S three-electron bond is 2.85 Å long, and has a dissociation energy of 31.2 kcal mole-1. The performance of MNDO semiempirical molecular orbital theory is compared with the ab initio results.
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  • 65
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    Journal of Computational Chemistry 2 (1981), S. 266-272 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Significant improvements in calculational efficiency and capability with the self-consistent electron pairs (SCEP) method has resulted from several new computational developments. A new procedure for constructing the important internal Coulomb and exchange operators has substantially reduced the preiteration time. A general scheme for utilizing molecular symmetry has been used to advantage in reducing the number of pair functions and external operators that must be found explicitly at each iteration. A projection operator tool has been implemented and found to be quite effective at minimizing the number of iterations required at some point on a potential energy surface when an SCEP wavefunction exists for some nearby point. These and other improvements in the program construction have yielded sizable reductions in time for some representative test cases, including water and a potential energy curve for formaldehyde. The new SCEP program also performs low-order perturbation theory treatments and coupled electron pair approximation (CEPA) calculations using the same operator approach. The usefulness of the approach is demonstrated by very large scale calculations on the stability of the two interstellar glycine conformers. These calculations involve the variational treatment of 82,205 symmetry-adapted singly and doubly substituted configurations involving 225 internal electron pairs.
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    Journal of Computational Chemistry 2 (1981), S. 347-355 
    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 spin-orbit coupling operator is brought into a simplified form through a convenient choice of origin for the orbital angular momentum operator. The eigenvalue problem of the Hamiltonian that includes the spin-orbit (SOC) operator as a perturbation is solved by means of a linear variational procedure in the basis of the spin-pure molecular eigenstates. Test calculations on benzophenone are presented and the results are compared to experiment. We discuss the minimal size of the spin-pure variational basis needed to achieve stable results as well as the amount of single-excitation configurational mixing needed to describe the spin-pure molecular eigenstates.
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    Journal of Computational Chemistry 2 (1981) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 68
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    Journal of Computational Chemistry 4 (1983), S. 9-14 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Koopmans' theorem ionization potentials have been calculated for a series of hydrides, methyls, and silyls HnX, (CH3)nX, and (SiH3)nX (X = F, Cl, n = 1; X = O, S, n = 2; X = N, P, n = 3), together with some mixed species (MH3)nXH3-n (X = N, P; M = C, Si) using ab initio SCF methods. The calculated values give excellent agreement with experimental values without the inclusion of d functions. For the chlorides, HCl, CH3Cl, and SiH3Cl, the values vary rather little over a wide range of basis sets, and are unaffected by the inclusion of d functions.
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    Journal of Computational Chemistry 4 (1983), S. 41-47 
    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 RHF energy minimization procedure based on the treatment outlined in Part I of this series of articles is presented. Test calculations performed on several closed- and open-shell systems show that the present procedure is definitely superior to the conventional SCF methods. In particular, the convergence of this procedure is ensured, the rate of convergency is high, and the computational cost of each cycle is low.
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    Journal of Computational Chemistry 4 (1983), S. 53-57 
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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: Optimum geometries of planar and 90°-twisted C2v calicene are calculated with single-configuration STO-3G and 3-21-G wavefunctions. The barrier to ring-ring rotation is computed. Bond alternation is pronounced in the planar form and decreases in the twisted form, while dipolar character increases on twisting.
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    Journal of Computational Chemistry 4 (1983), S. 48-52 
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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 effect of basis functions on molecular one-electron property expectation values calculated by approximate methods is examined using weighted and unweighted least-squares Gaussian-type orbital function expansions of Slater-type orbital functions.
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  • 72
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    Journal of Computational Chemistry 4 (1983), S. 68-72 
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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 geometry of a proposed intermediate (α-dialkylamino nitrite ester) of N-nitrosamine synthesis from nitrites is studied by ab initio SCF methods. The energy of a zwitterion is calculated and found to be high.
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  • 73
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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: MNDO has been extended to sulfur, but without inclusion of 3d AOs. Calculations are reported for heats of formation, geometries, dipole moments, and ionization energies of a variety of sulfur-containing molecules. The average discrepancy between calculated and observed heats of formation is larger than for compounds of other elements, a difference probably due, at least partly, to the lower accuracy of the thermochemical data for sulfur compounds. The calculated dipole moments agree well with experiment as do the calculated ionization energies, except for those corresponding to ionization from sulfur “lone-pair” orbitals which are too high by ca. 1 eV, probably as a result of the neglect in NDDO of interactions between inner and valence shell orbitals. As in the case of other third-period elements, the calculated heats of formation of compounds of sulfur in its higher valence states (SIV, SVI) were too positive by large amounts, due presumably to the neglect of 3d AOs.
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    Journal of Computational Chemistry 4 (1983), S. 123-123 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 150-153 
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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 standard deviation in reduced errors (SDRE) quantitatively measures the similarity between an approximate and exact wavefunction. It is the Euclidean distance between the vector of the one-electron property expectation values calculated using the approximate and exact expectation values.
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    Journal of Computational Chemistry 4 (1983), S. 170-174 
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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: Derivatives, with respect to the symmetry coordinates, of the components of the dipole polarizabilities of HF, H2O, and CH4 are calculated using the Kirkwood method and a generalization of that method. The results for the bond-stretching derivatives are in reasonable agreement with those found by finite field calculations; those for angle changes are of the correct sign, but their magnitudes are in poor agreement with the finite field ones. The results are also analyzed using a four-parameter bond polarizability model.
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    Journal of Computational Chemistry 4 (1983), S. 410-418 
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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: Quantum chemical calculations with the semiempirical molecular orbital (MO) method SINDO1 were performed on excited states of the following five- and six-membered heterocycles containing nitrogen: imidazol, pyrazol, pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine. The geometries and adiabatic excitation energies of T1, S1, S2 were calculated. We also present charges, bond orders, and dipole moments. Consequences of these results for UV spectroscopic data are discussed.
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    Journal of Computational Chemistry 4 (1983) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 461-469 
    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 calculations are presented for the head-to-head dimerized β helices for Gramicidin A transmembrane channel structures. The calculations take into account both left- and right-handed β helices, and various side-chain conformations. The energetics of the dimerization is studied by considering various docking geometries. It is concluded from these vacuum-energy calculations that the lowest energy conformation for the channel dimer is that comprised of left-handed β helices.
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  • 81
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital calculations are reported for complexes of hydroxide and methoxide anions with water and methanol. The basis set dependence of the results is carefully considered for HO- ⃛ H2O. 4-31G and 6-31G* calculations yield similar geometrical predictions; however, the 6-31G* basis set is superior for computing dissociation energies. Further extension to the 6-31G** level provides little change. The dissociation energies for the complexes range from 25 to 37 kcal/mole with hydroxide ion and methanol acting as the strongest base and acid. The difference in gas phase acidities of water and methanol is halved by the introduction of one solvent molecule.
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    Journal of Computational Chemistry 2 (1981), S. 20-29 
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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: Ab initio molecular orbital structures and energies of B2F4, B2Cl4, N2O4, and C2O42- have been calculated for both perpendicular D2d and planar D2h rotamers. The experimental trend toward greater preference for the D2d forms in going from B2F4 to B2Cl4 is reproduced. N2O4 favors the planar conformation, although the rotation barrier is overestimated at the theoretical levels used. The oxalate dianion is calculated to be more stable in the D2d conformation; the experimental planar arrangement in the solid may be due to crystal packing forces. The preferences for one conformation over another are small; analysis indicates that different effects may predominate in each case: π stabilization for B2F4, hyperconjugation for B2Cl4, lone-pair interactions for N2O4, and electrostatic repulsions for C2O42-.
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  • 83
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Means by which the Onsager theory of dielectrics may be modified in a general way to include important structurally nonspecific electrical effects exercised at or near the cavity boundary are developed and discussed. In essence they rely upon extraction of limiting numerical solutions of the Laplace equation potentials for multiple shells approximating regions of smoothly varying permittivity surrounding the dipole-containing cavity. The results of several such modifications, which usefully retain the original reaction and cavity field forms, are applied to evaluate the dielectric constants of polar solvents acting as support media for mean-space-charge attenuation of intracavity electrical interactions, and in correlation of isolated molecule and condensed phase properties of formally nonassociated solvents. For the most part such predictions and correlations are found to be improved by a wide variety of physically reasonable continuity functions. Where they are not, more rational patterns of deviations consistent with possible modes of intramolecular charge transfer and weak intermolecular association in formally nonassociated liquids are detected. Some limited comparisons with particle- and structure-dependent theories, e.g., the mean spherical model and discrete lattice formulations, also suggest that the present permittivity modifications can effectively simulate important short-range nonspecific liquid ordering effects. Various factors relating to possible adaption of the limit procedures developed to other inhomogeneous dielectric medium calculations are also briefly outlined.
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    Journal of Computational Chemistry 2 (1981), S. 363-367 
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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: SCF Hartree-Fock calculations are used to predict properties of the guanidinium fragment present in tetrodotoxin and saxitoxin, toxins known to block the sodium channels of the nerve cell membrane. The results, in terms of net atomic charges and geometries, are compared to similar calculation results obtained for the Na+-H2O complex.
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    Journal of Computational Chemistry 2 (1981), S. 384-391 
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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: With a view of using data on solutions and liquids for parameter fitting in molecular mechanical force fields, Abraham's theory of solvation is incorporated in the force field procedure. Geometries and bond moments are estimated internally, partial account being taken of bond-bond induction, and used to calculate the intramolecular electrostatic energy, dipole moment, and the dipole and quadrupole terms in the solvation energy. Three dielectric constants are used, one for the solute in the vapor, one for the solution, and one for the intramolecular space through which dipole-dipole interactions take place. Examples are given, including such where computation differs with measurement, to illustrate the performance of the scheme.
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  • 86
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    Journal of Computational Chemistry 2 (1981), S. 414-415 
    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 energy hypersurface for the system Li(H2O)4+-F(H2O)4- is investigated using the polarization model. A possible mechanism for the production of HF in this solution droplet is observed.
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  • 87
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    Journal of Computational Chemistry 2 (1981), S. 433-445 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parametrization of MNDO for aluminum and comparisons of calculated molecular properties with experimental values indicate the general usefulness of MNDO to study aluminum-containing compounds. Although results are not as good as for molecules containing only C, H, N, and O, they are nevertheless accurate enough to be useful, especially when predictive biases noted in this article are considered. Inclusion of the d orbital in the MNDO scheme may improve the aluminum results. Results for boron-containing molecules not previously reported are also reported in this article.
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  • 88
    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 molecular orbital theory with the STO-3G basis set is used to examine both charge and energy interactions in a series of meta- and para-substituted phenylborate anions and toluenes. Comparison of the results is made with data for substituted anilinium cations. It is concluded that whereas NH3+ is a powerful σ acceptor, with essentially no π interaction, BH3- is primarily a π donor, and, to a slight extent only, a π donor. CH3 is indicated to be both a weak σ and π donor. Energies of interaction of BH3- and NH3+ with a series of substituents are an order of magnitude larger than corresponding values for CH3. Interaction energies for BH3- are of opposite sign to those for NH3+. The results may be understood qualitatively using perturbation molecular orbital (PMO) theory.
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  • 89
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    Journal of Computational Chemistry 4 (1983), S. 15-22 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SCF wavefunctions with similar extended Gaussian bases for the series HCOX with X = H, OH (syn and anti), NH2, CN, and F yield closely similar charge deformation density maps in the formyl region of all six molecules. The differences, measured by moments of partitioned atomic deformation densities, correlate almost linearly with the Hammett substituent parameters σI and σR of the several substituents X. However, systematic deviations, especially in the carbon fragment, suggest the need for modified values of the inductive parameters σI for the correlation of these molecular charge densities.
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  • 90
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    Journal of Computational Chemistry 4 (1983), S. 33-40 
    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 a new procedure for direct minimization of the RHF energy, which presents advantages over SCF methods with respect to convergence rate and computational cost. In this procedure we combine several techniques with the aim of obtaining best directions and step lengths for the iterative search for a minimum of the energy. In this article we develop the theory. Therefore, we analyze the variational function; we present a short description of the minimization techniques and we discuss in detail the way in which they are to be used. The computational aspects of the procedure will be treated in the following article.
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  • 91
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    Journal of Computational Chemistry 4 (1983), S. 73-83 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Structures XY⋅3XY⋅2XY3 of symmetry C2v (of which propane is an example) are examined and the rearrangement due to the internal rotation of the end groups XY3 studied. The isomerization graph is constructed, various forms of which are displayed and the symmetry of which has been determined. The order of the group is 72. There are nine prime (irreducible) representations (4A + E + 4G) with the following partitioning of the elements into classes: 1, 42, 62, 9, 122, 18. When the mechanism for rearrangement is generalized to include enantiomers, a duplex graph is produced with the order of the group 144 which is isomorphic to the group S2(S3,S2) (generalized wreath product of the symmetric group S2 and S3). The corresponding graph has been constructed and displayed in one of more symmetrical forms. Isomorphism of groups of order 144 is discussed and a procedure is outlined in which correspondence between distinctive combinatorial objects is established by inducing permutations of m elements from available permutations of n elements. The scheme is based on selection of suitable graph invariants in one system and their labeling as m objects which form the basis for representation of the symmetry for the other system.
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  • 92
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    Journal of Computational Chemistry 4 (1983), S. 110-113 
    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 rapid method is described for calculating the number of bonds on the shortest path between each two pairs of atoms of a molecule.
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  • 93
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    Journal of Computational Chemistry 4 (1983), S. 136-141 
    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 general method and accurate algorithm for calculating the Cartesian coordinates (xa, ya, za) from an arbitrary triple of distances r(a,i), angles, θ(a,j,k), or dihedral angles φ(a,l,m,n), specifying the position of the nucleus a relative to nuclei i,⃜, n with known Cartesian coordinates. There is a brief discussion of the requirements on the 3N-6 geometric parameters in order for them to determine the shape of an N-atomic molecule.
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  • 94
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    Journal of Computational Chemistry 4 (1983), S. 142-149 
    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 conformational preferences of the molecule 1,4-pentadien-3-one (divinylketone) have been studied by ab initio molecular orbital calculations and discussed in terms of interaction between molecular fragments. The calculations predict a molecular ground state having a fully coplanar s-cis, s-cis conformation. In addition, we find three other structures that represent local minima on the energy surface. These are a fully coplanar s-cis, s-trans form, and two nonplanar s-trans, s-trans forms having symmetries C2 and C1h, respectively. The energies of these forms relative to the ground state are 7.5, 19.2, and 35.9 kJ/mol, respectively. The coplanar s-trans, s-trans form represents a saddle point on the energy surface. All conformers and the saddle point have been completely geometry optimized by the gradient technique. For the ground state a complete in-plane harmonic force field has been evaluated.
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  • 95
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    Journal of Computational Chemistry 4 (1983), S. 158-169 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MNDO calculations of heats of formation, dipole moments, ionization potentials, and structures are reported for a wide range of compounds containing chlorine in its characteristic valence state (ClI) and one or more of the elements H, B, Be, C, N, O, and F. The calculated errors in the heats of formation and the dipole moments are not significantly greater than those previously reported for compounds containing no chlorine. First vertical ionization potentials were on average 0.95 eV too high. The ordering of higher cationic states was found to be correct, even for species such as Cl2O, Cl2, and HOCl, where ab initio-Koopmans' theorem calculations predict the incorrect ordering. The calculated energies and geometries of compounds such as CIF3 are qualitatively incorrect, probably because of the lack of 3d atomic orbitals in the orbital basis set.
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  • 96
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
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  • 97
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    Journal of Computational Chemistry 4 (1983), S. 241-251 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: STO-3G minimal basis sets for first- and second-row transition metals have been formulated and applied to the calculation of equilibrium geometries for a variety of inorganic systems, metal carbonyls, and organometallic compounds. While the overall level of agreement with experiment is not as good as that previously noted for main-group compounds, most trends and many subtle features in geometries are reproduced.
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  • 98
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    Journal of Computational Chemistry 4 (1983), S. 260-266 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular orbital computations on the sign and magnitude of the Cotton effect of (-)-α-phellandrene (a conjugated diene) and the separate twisted butadiene chromophore were performed using configuration interaction (CI) and the random phase approximation (RPA) methods with a standard minimal basis set of STO/3G orbitals. The relative contributions to the rotatory strength of (-)-α-phellandrene which arise from a twist in the diene unit, the allylic axial bond, and nonplanarity of either one or both of the C=C double bonds were determined by examining various molecular geometries. This theoretical study confirms that the allylic axial substituent/bond provides the largest contribution to the longwavelength Cotton effect. It is found that the rotatory strength arising from distortion of the planar geometry of the double bonds tends to cancel the rotatory strength arising from the sense of twist of the diene unit. The computed energies suggest that molecular geometries where the trisubstituted bond is kept planar, and where twisting is allowed about the cis double bond, may be favored over geometries where torsion is allowed about both double bonds.
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  • 99
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    Journal of Computational Chemistry 4 (1983), S. 267-275 
    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 procedure has been devised to determine the automorphism partition and the automorphism group for nondirected graphs. The general approach is to reveal the permutational symmetry by means of its systematic destruction. Symmetry decomposition pathways are created by numerically weighting specific series of vertices. Each pathway leads to a discrete ordered vector. Each pair of pathways that match reveals an element of the automorphism group. Results are presented for two molecular graphs. Further potential applications of this approach to problems of isomorphism, canonical labeling, and structural indexing are discussed.
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  • 100
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    Journal of Computational Chemistry 4 (1983), S. 302-307 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms and computer programs are developed for generating the symmetry elements of nonrigid molecules. These programs are based on the wreath product formalism for the symmetry groups of nonrigid molecules developed by the present author. Several examples are given to illustrate the procedures. Applications to weakly bound van der Waal complexes synthesized by supersonic beam expansion are also presented.
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