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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
    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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  • 3
    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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  • 4
    Electronic Resource
    Electronic Resource
    Ab initio determination of the proton affinities of small neutral and anionic moleculesThis work is dedicated to Professor John Pople in honor of his contributions to computational chemistry and his 60th birthday. (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 321-333 
    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 proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anions is proposed and applied to CH3-, NH2-, OH-, and CN-.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070309
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  • 5
    Electronic Resource
    Electronic Resource
    Chemical shift bond derivatives for molecules containing first-row atoms (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 546-559 
    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 primary and secondary first and second derivatives of the NMR isotropic chemical shift with respect to bond length modification have been calculated in the gauge invariant atomic orbital (GIAO) perturbed Hartree-Fock approach for some 177 first-row nuclei in 63 molecules using the mixed basis heavy:6-311G(d)/hydrogen:4-31. The shift derivative with respect to multiple bond length changes correlates linearly with the shift itself while changes involving single bonds behave differently. Agreement between experimental derivatives and those calculated theoretically is good but the calculations show that second derivatives as well as both types of secondary effects cannot always be neglected. The correlation between the shift derivative and the isotropic shift indicates an exponential variation of the chemical shift with bond length near the vicinity of the equilibrium structure for multiple bonds.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120504
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  • 6
    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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  • 7
    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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  • 8
    Electronic Resource
    Electronic Resource
    Locally dense basis sets for chemical shift calculations (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 648-659 
    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: Calculations of chemical shifts have been carried out using “locally dense” basis sets for the resonant atom of interest, and smaller, attenuated sets on other atoms in the molecule. For carbon, calculations involving a 6-311G(d) triply split valence set with polarization on the resonant atom and 3-21G atomic bases on other heavy atoms result in good agreement with experiment, and are virtually identical to those found employing the larger basis on all atoms. For species such as nitrogen, oxygen, and fluorine where standard balanced basis sets do not agree well with experiment, use of attenuated sets fail as well. The use of locally dense basis sets permits calculations previously impractical, and the successful application to carbon suggests that the chemical shift is most dependent on the local basis set, and less so on whether or not a balanced or unbalanced calculation is being carried out.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100507
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  • 9
    Electronic Resource
    Electronic Resource
    Polypentapeptide of elastin: Damping of internal chain dynamics on extension (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 850-855 
    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: Molecular dynamics simulations out to 100 ps have been carried out at 300 K in vacuo on the repeating pentapeptide, (VPGVG), of the elastin fiber. The structure employed in the simulation is a β-spiral (helical structure) with 2.7 pentamers per turn and with a 9.45 Å rise per turn and 21.6 Å rise per turn in the relaxed and extended states, respectively. Large amplitude backbone torsion angle fluctuations are observed in the relaxed state, and significant damping is observed upon extension, particularly in the suspended segments of the β-spiral structure. Accordingly the entropy change an extension was computed and found to be a substantial -1.1 entropy units per residue. The various energy components are compared for relaxed and extended states and the relevance of the results to the molecular mechanism of entropic elasticity is discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100607
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  • 10
    Electronic Resource
    Electronic Resource
    Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1153-1163 
    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 this article the adaptation of the Empirical Conformational Energy Program for Peptides (ECEPP/3) and two conformational search methods [viz., the Monte Carlo minimization (MCM) method and the electrostatically driven Monte Carlo (EDMC) method] to the Kendall Square Research KSR1 computer is described. The MCM and EDMC methods were developed to surmount the multiple-minima problem in protein folding. Parallelization of these codes led to substantial speedups (expressed as the ratio between the mean time per energy evaluation in one processor and the mean time per energy evaluation in a set of processors) over the serial versions of these codes. A comparison of the performance of these algorithms on the KSR1 and on the IBM ES9000 computers is presented. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540160909
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