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  • 1
    Electronic Resource
    Electronic Resource
    Molecular mechanics assessment of the configurational statistics of polyoxyethylene (1984)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 241-247 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous investigators have shown that statistical mechanical averages for configuration-dependent physical properties of long unperturbed polyoxyethylene chains are sensitive to the gauche-trans energy difference for rotation about C—C bonds. Agreement between theory and experiment could be obtained only by significant adjustment of this energy away from values predicted by semiempirical conformational energy computations. The present work examines the success of MM2 in evaluating conformational properties of long unperturbed polyoxyethylene chains. Calculations are performed which identify the rotational isomers, and their energies, for the indicated bonds in CH3OCH2CH2O—CH2—CH2—OCH2CH2OCH3. These energies are used to assign statistical weights utilized in the configuration partition function for a rotational isomeric state chain with symmetric threefold interdependent rotations. The customary generator matrix scheme is employed to evaluate the mean-square unperturbed end-to-end distance, mean-square unperturbed dipole moment, and their temperature coefficients. Contrary to computational schemes employed previously, MM2 is found to provide an estimate of the gauche-trans energy difference for rotation about C—C which is in harmony with the known dimensions and dipole moments of the unperturbed polymer. MM2 also provides good estimates for most of the other parameters required in the rotational isomeric state treatment. A notable exception is provided by the gauche-trans energy difference for rotation about the C—O bond. This energy difference is overestimated by MM2.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540050306
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  • 2
    Electronic Resource
    Electronic Resource
    On searching neighbors in computer simulations of macromolecular systems (1984)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 272-279 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Various algorithms for evaluating nonbonded interactions in molecular dynamics (MD) simulations of macromolecular systems are considered, and a combination of two techniques using a space grid for finding neighbor atoms is proposed. The application of grid search techniques to nonrectangular periodic systems is discussed. Finally, the computing time required by different algorithms is compared on a Cray-1 vector processing computer as well as on a CDC Cyber 170/760 sequential computer. Neighbor list techniques turn out to be faster than the grid search techniques for the systems considered here. However, storage requirements may exclude the use of neighbor list techniques for large systems. Finally, MD of complex macromolecular systems turned out to be about 4-14 times faster on a Cray-1 than on a Cyber 170/760.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540050311
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  • 3
    Electronic Resource
    Electronic Resource
    Critical comparison of the ab initio and spectroscopic methyl-C—H bond length difference in acetyl compounds, CH3C(=O) XArticle no. 35 in the series Ab Initio Studies of Structural Features Not Easily Amenable to Experiment. (1984)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 517-522 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In order to provide additional data for the relative lengths of methyl-C—H bond distances in acetyl derivatives, which are difficult to determine accurately by the conventional tools of structural chemistry, the geometries of CH3COH, CH3COF, CH3COCH3, CH3COOH, and CH3CONH2 were determined by ab initio SCF gradient optimization at the 5-31G** level and compared with previous 4-21G results. For acetaldehyde 6-311G4* calculations were also performed and the correlated methyl-C—H stretching potential energy functions were determined. It is found that the calculated differences between the in-plane and out-of-plane methyl-C—H bonds are practically independent of the computational scheme. The calculated results are in contrast to relative bond lengths obtained by some vibrational overtone spectroscopic studies, but are in perfect agreement with C—H bond length differences determined from isolated C—H stretching frequencies of partially deuterated compounds. The reliability of the latter, and other spectroscopic data concerning the assignment of the methyl-C—H vibrations are critically analyzed. On the basis of the available evidence we conclude: (1) the methyl groups of the CH3C(=O)X systems here discussed contain one strong (in-plane) and two weak (out-of-plane) C—H bonds; (2) intensities of C—H local mode spectra do not provide a reliable basis for assignment to individual bonds.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540050603
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  • 4
    Electronic Resource
    Electronic Resource
    Graph theoretical classification and coding of chemical reactions with a linear mechanism (1982)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 95-111 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Linear mechanisms of catalytic and noncatalytic chemical reactions which are theoretically feasible have been classified and coded using a detailed procedure for the unique numbering of cycles, edges, and vertices in the kinetic graphs. The following classification criteria are used in a hierarchical order: number of cycles and vertices, mutual connectivity of the cycles, manner of linking any pair of cycles, number of elements linking two cycles, mutual position of two cycles joined to a third one, orientation of edges, and presence of pendant vertices. All the types and classes of mechanisms are presented for reactions having up to five and four routes, respectively.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540030115
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  • 5
    Electronic Resource
    Electronic Resource
    Application of an ion-fitted pseudopotential to HF, H2O, NH3, BeO, and HCl in a Gaussian lobe basisFrom the thesis of T. T. Nguyen. (1984)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 640-649 
    Details
    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 core potentials for atoms of atomic numer 1-18 fitted to ion spectra by Chang, Habitz, Pittel, and Schwarz have been extended to the molecular case in a Gaussian lobe basis by using a six-Gaussian (6G-POT) representation for the exponential factors of the atomic core potentials. In a (9s/5p/1d) basis the 6G-POT one-electron energies, dipole moments, and Mulliken charges are improved over a one-Gaussian potential form for HF, NH3, and H2O; BeO also yields good agreement within 2.6% of the experimental bond length. For HCl, the core potential shows larger errors in the dipole moment (7%) and one-electron eigenvalues (2%), but a 75% saving in computer time is realized for HCl compared with only about 35% for first-row systems using the 6G-POT core potentials. Analytical expressions are given to extend the 6G-POT method up to s, p, d, f, and g valence shells.
    Additional Material: 9 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540050618
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  • 6
    Electronic Resource
    Electronic Resource
    On the gearing of methyl groups in hexamethylbenzene (1980)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 76-80 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical force field calculations were performed on hexamethylbenzene to elucidate the internal motions of the methyl groups. When the benzene ring is constrained to be planar (as in solid-phase studies), the methyl groups undergo a geared, disrotatory motion. When this constraint is relaxed, results are force field dependent. Calculated barriers are in good agreement with experimentally determined values.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540010110
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  • 7
    Electronic Resource
    Electronic Resource
    Spherically symmetric axial Gaussian lobe 3d and 4f orbitals (1982)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 130-134 
    Details
    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 axial Gaussian lobe orbital (AGLO) representations of 3d and 4f orbitals proposed by LeRouzo and Silvi have been angularly optimized to ensure spherical symmetry of filled 3d and 4f shells. The functions have been tested on the hydrogen atom in the presence of high quality s and p basis sets and found to provide excellent minimal Gaussian representations of polarization functions. Exact orbital degeneracy is not obtained within each shell, however. Tabulated values are given to allow arbitrary scaling of the 3d and 4f lobe mimic orbitals.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540030203
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  • 8
    Electronic Resource
    Electronic Resource
    MINDO/3 Calculation of carbocation heats of formation (1982)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 208-213 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation calculated by MINDO/3 are reported for 42 carbocations for which experimental heats of formation have been published. Errors associated with these calculations can be large, with an overall range of ±13 kcal/mol. Correction of systematic errors in the MINDO/3 calculations by means of hydrocarbon models and isodesmic relationships results in a reduction in the range of errors to ±8 kcal/mol. Comparison with experimental heats of reaction of hydride transfer equilibria minimizes experimental errors and gives an average absolute error of 2 kcal/mol with a range of ±3 kcal/mol.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540030211
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  • 9
    Electronic Resource
    Electronic Resource
    A study by molecular mechanics of the geometric isomers of benzene hexachloride, benzene tetrachloride, and naphthalene tetrachloride (1983)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 4 (1983), S. 114-122 
    Details
    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.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540040116
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  • 10
    Electronic Resource
    Electronic Resource
    Ab initio study of catalyzed and uncatalyzed amide bond formation as a model for peptide bond formation: Ammonia-Glycine reactions (1983)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 4 (1983), S. 449-460 
    Details
    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.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540040402
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