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  • 1985-1989  (224)
  • 1930-1934
  • 1987  (224)
  • Biochemistry  (133)
  • Physical Chemistry
  • 101
    Electronic Resource
    Electronic Resource
    An algorithm for construction of the molecular distance matrix (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 170-173 
    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: A simple computer-oriented method is presented for constructing the (molecular) distance matrix. The distance matrix considered is the graph-theoretical (topological) distance matrix.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080209
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  • 102
    Electronic Resource
    Electronic Resource
    Announcement (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 186-186 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080212
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  • 103
    Electronic Resource
    Electronic Resource
    Macromolecular structure and specificity: Computer-assisted modeling and applications, Edited by Babu Venkataraghavan and Richard J. Feldmann, Annals of the New York Academy of Sciences, New York, 209 pp. Price: $48.00 (1985). (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 185-185 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080211
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  • 104
    Electronic Resource
    Electronic Resource
    Molecular mechanics and the deformation of macromolecules: The use of a very short cutoff combined with a quadratic approximation (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 174-184 
    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: An approximation to the molecular mechanical treatment of structural deformations of macromolecules is presented. The method is based on a partitioning of the conformational energy into three parts. The first part is covered by the condensed potential functions which absorb many short-range nonbonding interactions. The second part consists of a few nonbonded interactions below a very short cutoff radius of 4 Å. The third part, consisting of the vast majority of pairwise interactions, is approximated by a quadratic expression confined to a subspace of the conformational space. A detailed computational example on LH-RH, including an analysis of the errors resulting from other conventional approximation methods, is given. A comparison to the conventional cutoff approximation used in x-ray refinement delivers a speedup factor of at least two orders of magnitude.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080210
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  • 105
    Electronic Resource
    Electronic Resource
    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080401
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  • 106
    Electronic Resource
    Electronic Resource
    Introduction (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 281-281 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080402
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  • 107
    Electronic Resource
    Electronic Resource
    Converged calculations of rotational energy transfer in HF—HF collisions (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 282-290 
    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: We have performed large-scale close coupling calculations of rotational-to-rotational energy transfer in HF—HF collisions for the realistic potential energy surface of Brobjer and Murrell. We employ up to 525 angular terms in the expansion of the potential and up to 440 coupled channels in the rotational-orbital basis set. The results for zero total angular momentum are well converged for relative translational energies up to over 0.6 eV, and they show extensive rotational excitation.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080403
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  • 108
    Electronic Resource
    Electronic Resource
    Theoretical study on the mechanism of the thermal decarboxylation of acrylic and benzoic acids. Models for aqueous solution (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 158-169 
    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 mechanism of acrylic and benzoic acid decarboxylation in aqueous solution has been investigated by ab initio methods using the STO-3G and 3-21G basis sets. In those reactions, the solvent is represented successively by one and two water molecules. Their active participation as a proton relay in the chemical process is demonstrated by the large decrease in the activation energy with respect to the reaction studied in the absence of water. In the absence of any intermediate found along the reaction pathway, the proposed mechanism is the concerted process; the free acid being the species that undergoes decarboxylation via a pseudounimolecular mechanism by interaction with a chain of water molecules. At the transition state, the carboxylic hydrogen transfer to one water molecule, the reorganization of the chain of water molecules through which the proton is transferred and the cleavage of the C—C bond are much more advanced than the proton transfer from the last water molecule to the α-carbon atom of the carboxyl group.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080208
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  • 109
    Electronic Resource
    Electronic Resource
    On Madelung's constant (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 291-295 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080404
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  • 110
    Electronic Resource
    Electronic Resource
    Transition structure in a diabatic surface formalism (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 296-306 
    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 theory of an implementation of the diabatic surface model within the Heitler-London valence bond approach is described. It is shown that the HL-VB wave function can be obtained from a Van-Vleck transformation of an MC-SCF wave function which has been built from atom-localized orbitals. This wave function is built from a superposition of two diabatic components, reactantlike and productlike. The transition structure is then obtained as the minimum of the seam of intersection of the diabatic surfaces and the algorithm for performing this constrained optimization is described. Several areas of application are also discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080405
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  • 111
    Electronic Resource
    Electronic Resource
    Centrifugal distortions in molecules: An ab initio approach with application to ozone (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 307-312 
    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: Our procedure for employing analytical gradients of ab initio potential energy hypersurfaces in the description of centrifugally distorted molecules is applied for the first time to an asymmetric top, namely ozone. Both single determinantal (HF/6-31G*) and analytically fitted multiconfigurational self-consistent field surfaces were utilized. The focus of the HF/6-31G* study is upon the centrifugal distortion pathway. Quartic centrifugal spectroscopic coefficients are obtained in both cases and are in reasonable agreement with experiment.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080406
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  • 112
    Electronic Resource
    Electronic Resource
    Simulation studies of branched polymer molecules (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 333-340 
    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: Monte Carlo simulation results are presented for lattice models of uniform stars (one branch point of functionality f = 3), combs (two branch points, ƒ = 3,3) and brushes (two branch points ƒ = 3,4 and ƒ = 3,5). We estimate the critical exponent γ(ƒ), the ratio g(ƒ) = 〈SN2(ƒ)〉/〈SN2(1)〉 (where 〈SN2(ƒ)〉 is the mean-square radius of gyration of a structure having ƒ branches and N monomers), and the meansquare end-to-end branch lengths, as a function of the number and arrangement of branches. Comparisons with theoretical predictions and experimental data are made where possible, leading to a test of some predictions, and a suggestion concerning future experiments.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080409
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  • 113
    Electronic Resource
    Electronic Resource
    Coupled equations approach to multiphoton molecular processes (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 313-323 
    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: Using the dressed molecule picture of molecule radiation interactions (A.D. Bandrauk et al., J. Chem. Phys., 79, 3256; 80, 4926; 83, 2840) one can deduce multiphoton processes (absorption, scattering, nonlinear optical properties, etc.) amplitudes from coupled second-order differential equations with electronic surfaces and transition moments as input data obtainable from quantum chemical calculations. The present approach enables one to include in the calculation bound and continuum states simultaneously by the use of appropriate boundary conditions for the numerical solutions of these coupled equations. In the case of weak radiative couplings, one recovers the usual Fermi-Golden rule expressions for electronic absorption, raman scattering, etc. The method is thus quite general, bridging the weak field (traditional photochemistry) and the strong field (laser chemistry) regimes which are attainable with today's lasers. The numerical solutions of the coupled equations give us the stationary states of the molecule + radiation system, called dressed molecule. Preparation of the initial state can be mimicked in the coupled equations by an artificial channel method for processes involving a final-state dissociation. Examples of such calculations will be presented in the diatomic Cl2 for which several ab initio electronic states and transition moments were available.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080407
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  • 114
    Electronic Resource
    Electronic Resource
    Implementation and applications of Gaussian 82 on a CDC Cyber 205 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 324-332 
    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 implementation of the GAUSSIAN 82 system of quantum chemistry codes on the CDC Cyber 205 supercomputer required approximately 1 1/2 man years of effort. Idiosyncracies of the Cyber 205 architecture, operating system, and compiler in so far as they affect the conversion and operation of large quantum chemistry codes on the machine are described. While advantage has not been taken of the powerful vector processor, the high intrinsic speed of the scalar processor and the large virtual storage capacity of the Cyber 205 make it a very powerful research tool for computational chemistry. The impact of the GAUSSIAN 82/Cyber 205 combination on computational chemistry research at the University of Calgary is illustrated by brief descriptions of a range of applications from highly accurate calculations on small systems to semiempirical studies of large molecular aggregates. Complete geometry optimizations and harmonic frequency analyses, for the most part, have become routine.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080408
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  • 115
    Electronic Resource
    Electronic Resource
    Generalized potential surfaces under inclusion of nuclear motion (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 350-357 
    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: A new method for the solution of the vibronic Schrödinger equation is presented. The proposed approach allows the preservation of the concept of potential surfaces under inclusion of nuclear motion. The dynamical interaction of electrons and nuclei is partially included in the equation determining the potential surfaces. The corresponding electronic wave functions can be used as a basis for a generalized representation. Since the variation principle is involved for the determination of the potential surfaces, the proposed representation may be considered as a generalization of the adiabatic one. As a consequence the vibrational wave equation and the calculation of radiationless transition probabilities is simplified.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080411
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  • 116
    Electronic Resource
    Electronic Resource
    Chemical applications of topology and group theory. 23. A comparison of graph-theoretical and extended Hückel methods for study of bonding in octahedral and icosahedral boranesPaper presented at the CIC Symposium on Computational and Mathematical Chemistry, Saskatoon, Saskatchewan, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 341-349 
    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 graph-theory derived model for the bonding topology in the globally delocalized polyhedral boranes B6H62- and B12H122- is evaluated by comparison of the energies of the core molecular orbitals with those obtained by the 1962 LCAO-MO extended Hückel calculations of Hoffmann and Lipscomb. Of particular interest is how well the complete graphs K6 and K12 used in the graph-theory derived model approximate the bonding topologies of the unique internal orbitals (radial orbitals) of the octahedron and icosahedron, respectively. In the case of the B6H62- octahedron the single positive eigenvalue of the K6 graph corresponds to the results from the extended Hückel calculations. In addition, the parameters from the latter calculations indicate a ratio of 0.625 for the overlap of the unique internal orbitals of the trans atom pairs relative to cis atom pairs as compared with unity implied by an unweighted K6 graph. In the case of the B12H122- icosahedron the graph-theory derived model is far less satisfactory since the single positive eigenvalue of the K12 graph disagrees with the four bonding core molecular orbitals (an A1g and three triply degenerate T1u molecular orbitals) found by the extended Hückel calculations after removing the effect of the mixing of core and surface bonding orbitals corresponding to the same irreducible representations. However, this core-surface orbital mixing raises the energy of the triply degenerate T1u core molecular orbitals to antibonding levels so that the graph-theory derived model fortuitiously gives correct skeletal electron counts for the regular icosahedron despite this fundamental error.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080410
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  • 117
    Electronic Resource
    Electronic Resource
    Analysis of the π-electronic structure of infinitely large networks. I. Some remarks on the characteristic polynomial and density of states of large polycyclic aromatic hydrocarbons (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 358-366 
    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: General expressions of the characteristic polynomials of various series of cyclic and linear polymers of polycyclic aromatic hydrocarbons are presented, i.e., polyacene, zigzag-polyacene, 1,4-dimethylbenzene polymer, polyperylene, etc. The densities of states of cyclic and linear polymers with the same repetitive units are shown. In some cases the allowed region of the energy levels of these polymers is found not to be the same. Several related problems are discussed.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080412
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  • 118
    Electronic Resource
    Electronic Resource
    Linear notations and molecular graph similarity (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 367-374 
    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: Two simple linear notation systems are suggested to encode molecular structure including stereochemical elements. Both systems give rise to a unique numbering of the molecular graph, and thus also lead to a unique linear notation. Both linear notation systems are extremely compact and require only standard chemical symbols. A string comparison technique is developed to measure the similarity of two molecular linear notations. This procedure allows one to define a molecular similarity index with values that range from zero to unity, the zero value characterizing complete dissimilarity and the value of unity denoting identity. The notation and similarity index procedures are applied to several small molecular structures.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080413
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  • 119
    Electronic Resource
    Electronic Resource
    The density amplitude ρ½ and the potential which generates it (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 375-379 
    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 square root of the density ρ½ satisfies a Schrödinger equation with an effective local potential V(r). The form of this potential is obtained for (a) the ground state of the Be atom, (b) neutral atoms in the limit of very large atomic number from the statistical theory, and (c) almost spherical molecules XH4, again in the limit of many electrons. Some comments are made on the possibility of relativistic generalization of this method.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080414
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  • 120
    Electronic Resource
    Electronic Resource
    Character tables and symmetry eigenvectors for two C3v rotor molecular systems (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 380-388 
    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 character tables of the Altmann groups for the double internal rotation of C3v rotor molecules of different symmetries were determined. These symmetries were those of para-xylene, trans-1,2-dimethylcyclopropane, cis-N-methylethylidenimine, dimethylamine, and a dimethylated asymmetrical molecule. From these character tables, the symmetry eigenvectors, which block diagonalize the Hamiltonian matrix, were deduced. The symmetry eigenvectors were derived with the help of a small computer.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080415
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  • 121
    Electronic Resource
    Electronic Resource
    Computational studies of 1,2-dithiete and dithioglyoxal (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 389-396 
    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: Ab initio calculations are reported on the energies, geometries, vibrational frequencies, and ionization potentials of the H2C2S2 isomers: 1,2-dithiete, cis-dithioglyoxal, and trans-dithioglyoxal. In contrast to most earlier computations, the results of this work indicate that 1,2-dithiete and cis-dithioglyoxal lie close in energy (within 3 kcal/mol) with the dithial more stable. Trans-dithioglyoxal is found to be 4.1 kcal/mol more stable than the cis isomer and faces a barrier to internal rotation of 5.5 kcal/mol. The predicted rotational constants for 1,2-dithiete agree within ∼0.05 GHz with the experimentally observed values thus lending credence to the predictions for cis-dithioglyoxal (Ae 14.30683, Be 2.46324, Ce 2.10143 GHz). Vibrational frequencies are given as potential aids to the identification of these molecules. 6-31G* ΔSCF calculations predict that at low energies (8 to 13 eV) the photoelectron spectra of 1,2-dithiete, cis-dithioglyoxal and trans-dithioglyoxal should be similar.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080416
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  • 122
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    Electronic Resource
    PERTURB: A special-purpose algebraic manipulation program for classical perturbation theory (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 397-411 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Classical perturbation theory provides a particularly promising route to EBK quantization of nonseparable systems. However, the number of terms generated when implementing perturbation theory for systems with more than two degrees of freedom can prove too large for general purpose symbolic manipulators to handle. We describe PERTURB, a specialized algebraic manipulation program written in C for quantization of multidimensional systems. A review of operator based classical perturbation theory is given, and the relationship between this type of perturbation theory and quantum mechanical Van Vleck perturbation theory discussed. The relative performance of the Dragt-Finn and Lie transform algorithms is assessed.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080417
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  • 123
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    Electronic Resource
    Time step error in diffusion Monte Carlo simulations: An empirical study (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 412-419 
    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: Diffusion Monte Carlo (DMC) is a random walk computational method for solving the ground-state Schrödinger equation for atoms or molecules. One obtains a biased simulated energy which is used to estimate the exact energy, where the bias increases with the time step used in the simulation. We present six new DMC algorithms, all of which have the same theoretical justification. Yet, when applied to the LiH and H2 molecules, the algorithms give results with markedly different error. Furthermore, algorithms which exhibit a small error when applied to one molecule show significantly greater error for the other. The explanation for these results relates to sampling of configuration space in the neighborhood of the nuclei. We investigate this issue hoping that our results will aid in the design of more efficient DMC algorithms.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080418
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  • 124
    Electronic Resource
    Electronic Resource
    Computational aspects of master equation transformation in terms of moments (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 420-427 
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    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 master equation describing the temporal evolution of a gaseous system in contact with a heat bath can be transformed into a system of linear, constant-coefficient, first-order differential equations of moments of the population distribution. While it has the advantage that populations are obtained directly from observables (moments), this system of equations is not too well-conditioned and unless precautions are taken, unsurmountable numerical problems appear. These are principally associated with manipulations (inversion and taking the exponential of a matrix) involving slightly modified Vandermonde matrices whose elements span a very wide range of orders of magnitude. This article discusses ways to avoid these pitfalls which consist principally of a suitable matrix normalization.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080419
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  • 125
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    Electronic Resource
    Discrete models of growth and dynamical percolation in chemistry (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 428-435 
    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: Space-time lattice (cellular automaton) models of pattern formation and growth are described. Suitable local rules for automation evolution represent the spreading of wave fronts of activity in an excitable medium. A random distribution of seeds produces expanding rings that fuse and are annihilated. The seeding density, pA, is used as a scaling parameter to give unique, reduced dynamics in an arbitrary dimension d. For d = 2, in this (continuum) picture, the rings fuse globally (percolate) at a critical instant, t̂c = 0.45. For the unscaled time evolution, dynamical percolation is examined in the pA × t plane. A swath of these percolating states is found. On the “explosion” boundary of this swath the percolation cluster just forms; on the “implosion” boundary it breaks up. Using a small-sample method the fractal dimension of the critical (boundary) cluster is estimated to be 1.9 (±0.01). Also percolation for continuously emitting seeds, which produce “discs” of activity, is related to ring evolution.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080420
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    Open-shell coupled-cluster method: Electron affinities of Li and Na (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 448-453 
    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 open-shell coupled-cluster method and the diagrams needed for its implementation are described. The method is applied to the electron affinities of Li and Na, which are calculated in two ways: as the ionization potential of the anions or as the energy of adding the second electron to the cations. The two schemes give essentially the same results, in very good agreement (〈0.02 eV) with experiment. Three-body effects are negligible.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080423
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    The application of strictly localized geminals to the description of chemical bonds (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 436-441 
    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: A theory is developed in which closed-shell molecules are viewed as systems of weakly interacting chemical bonds. Composite-particle creation operators obtained by an appropriate quasiparticle transformation are used to create the wave function of two-electron bonds. These quasiparticles are bosons, since they are composed of two electrons, but the total many-electron wave function is properly antisymmetric. The internal structure of the quasi-Bose-particles is affected by inductive interbond interactions. Delocalization and dispersion interactions between different bonds are neglected, thus the approach corresponds to a first-order many-body PT (Perturbation Theory) with a correlated, but fully localized, reference state. The whole formalism is developed ab initio. The nonorthogonality problem is handled by a biorthogonal formulation. To illustrate the effectiveness of the model, numerical calculations are reported.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080421
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    The MMP2 calculational method (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 581-603 
    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 molecular mechanics (MMP2) program and procedures for the treatment of conjugated hydrocarbons, and some of the results which they can achieve are described. The program is an updated version of the similar MMP1 program, but contains some differences. It is based on an SCF π system calculation, rather than on the VESCF method used earlier. All parameters are compatible with those in the MM2 program. Hence it is possible to calculate heats of formation, resonance energies, and structures for conjugated hydrocarbons in a way that is consistent with the calculations on non-conjugated molecules. The overall results as far as structure and energy are somewhat better than they were with the MMP1 program.
    Additional Material: 14 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080504
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    Fast vector-scalar-multiply-and-add subroutines for VAX computers (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 618-624 
    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: We describe a set of simple VAX assembly language, Fortran-callable subroutines for performing vectorscalar-multiply-and-add operations which can increase processing speed by more than 10%. The routines are simple enough that they may be translated readily for use on other machines.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080506
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    Algorithm for rapid calculation of Hessian of conformational energy function of proteins by supercomputer (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 625-635 
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    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 improved algorithm is presented for rapid calculation of the hessian matrix for the conformational energy of a protein as a function of only dihedral angles. The speed of the calculation, which is about one order faster than by the previous method, is achieved by two considerations. First, the algorithm is designed to take advantage of the supercomputer pipeline architecture. Second, long-range, nonbonded interactions are cut off and long-range electrostatic interactions are approximated by dipole-dipole interactions in order to reduce the number of pairwise interactions that have to be computed. The results of benchmark tests of the program are given as applied for four globular proteins of different sizes.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080507
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    Strategies for vectorizing the sparse matrix vector product on the CRAY XMP, CRAY 2, and CYBER 205 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 636-644 
    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: Large randomly sparse matrix vector products are important in a number of applications in computational chemistry, such as matrix diagonalization and the solution of simultaneous equations. Vectorization of this process is considered for the CRAY XMP, CRAY 2, and CYBER 205, using a matrix of dimension of 20 000 with from 1% to 6% nonzeros. Efficient SCATTER/GATHER capabilities add coding flexibility and yield significant improvements in performance. For the CYBER 205, it is shown that minor changes in the IO can reduce the CPU time by a factor of 50. Similar changes in the CRAY codes make a far smaller improvement.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080508
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    A specific inhibitor design approach by means of molecular dynamics calculation for porcine pancreatic elastase (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 645-650 
    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: A 27-picosecond (ps) molecular dynamics calculation has been carried out for the 1:2 enzyme-ligand complex between porcine pancreatic elastase (PPE) and acetyl-alanine-proline-alanine (APA). A data analysis has been carried out using a total of 450 structures. During the simulation, the root-mean-square fluctuations (RMSF) increased compared with the x-ray data. Some differences of the hydrogen bond arrangement in the MD average structures are found especially for SER 195, suggesting the fluctuations of the ligand molecules. The radius of gyration decreased a little during the simulation. Although intermolecular hydrogen bonds between two substrates (APA1 and APA2) has not been found by a 1.65-Å high-resolution x-ray diffraction study, the MD calculation showed the intermolecular hydrogen bond between them to be 3.2 Å. The extended active site of PPE is so wide compared with the size of a tripeptide that such a hydrogen-bound hexapeptide can be more specific than tripeptides, which is consistent with the kinetic data previously reported.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080509
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    Molecular valence calculations on cyclohexasulfur, cycloheptasulfur, and cyclooctasulfur (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 658-662 
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    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 theoretical study of homocyclic sulfur species S6, S7, and S8 was carried out using a molecular valence method involving stepwise approximations for orthogonality and core-valence interactions. The valence shell orbitals are described at the minimal basis level. The geometries of the molecules are predicted well as compared with other theoretical studies and the experimental values. The slight overestimation of the SS bond length is typical to the nonpolarized basis sets. The energies of the valence orbitals are well in accord with the conventional all-electron ab initio results. The trend in the stabilities of the three molecules is discussed. The present method provides an attractive possibility to study homocyclic and heterocyclic systems involving heavier chalcogens with no increase of the computing time.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080511
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    Basis sets for molecular interactions. 1. Construction and tests on (HF)2 and (H2O)2 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 663-673 
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    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 superposition error (BSSE) remains one of the major difficulties besetting current ab initio calculations of molecular interactions. Despite the widespread notion that lowering of the BSSE to negligible magnitude requires extremely large basis sets, we show that simple modifications of basis sets of only moderate size (e.g., 6-31G**) can accomplish the same end at much reduced computational expense. These modifications include reoptimization of the orbital exponents within the framework of the relevant molecules, plus addition of a single diffuse shell of sp orbitals on nonhydrogen centers. Subsequent addition of a second set of d-functions further lowers the SCF BSSE, bringing it below 0.1 kcal/mol for both (HF)2 and (H2O)2. It is notable that addition of the latter d-functions without prior reoptimization of the valence orbitals produces the opposite effect of an increase in the BSSE. Although the MP2 BSSE is also substantially decreased by the above modifications, it appears difficult to reduce this quantity below about 0.4 kcal/mol.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080512
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    Basis sets for molecular interactions. 2. Application to H3N—HF, H3N—HOH, H2O—HF, (NH3)2, and H3CH—OH2 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 674-682 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Modifications of the standard 6-31G** basis set as recommended in the accompanying paper are found to markedly lower the basis set superposition error (BSSE) in the title complexes, in contrast to enlargement to a triple-ζ scheme or by addition of a diffuse sp shell or a second set of d-functions without prior optimization, all of which lead to BSSE increase. After appropriate correction for correlation and superposition effects, all basis sets (with the exception of the standard 6-31G** and 6-311G** with their very large BSSE) predict the cyclic geometry of NH3 dimer to be more stable than the linear arrangement. Correlation and BSSE can shift the equilibrium intermolecular distance in H3CH-OH2 by up to 0.4 Å. Failure to correct for superposition error leads to a drastic exaggeration of both the SCF and MP2 components of the interaction energy in this complex. Much better estimates are furnished by our recommended basis sets with their smaller superposition errors.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080513
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    Molecular orbital theory of the properties of inorganic and organometallic compounds 5. Extended basis sets for first-row transition metals (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 861-879 
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    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 series of efficient split-valence basis sets for first-row transition metals, termed 3-21G, has been constructed based on previously-formulated minimal expansions of Huzinaga, in which each atomic orbital has been represented by a sum of three gaussians. The original Huzinaga expansions for s- and p-type orbitals (except those for 1s) have been fit by least squares to new three-gaussian combinations in which the two sets of orbitals (of the same n quantum number) share gaussian exponents. The Huzinaga three-gaussian expansions for ls and 3d atomic orbitals have been employed without alteration. The valence description of the 3-21G basis sets comprises 3d-, 4s- and 4p-type functions, each of which has been split into two- and one-gaussian parts. 4p functions, while not populated in the ground state of the free atoms, are believed to be important to the description of the bonding in molecules. The performance of the 3-21G basis sets is examined with regard to the calculation of equilibrium geometries and normalmode vibrational frequencies for a variety of inorganic and organometallic compounds containing first-row transition metals. Calculated equilibrium structures, while generally superior to those obtained at STO-3G, are not as good as those for compounds containing main-group elements only. The calculations generally underestimate the lengths of double bonds between transition metals and main-group elements, and overestimate the lengths of single linkages. Calculated normal-mode vibrational frequencies for metal-containing systems are less uniform than in those for main-group compounds.
    Additional Material: 10 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080614
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    Molecular orbital theory of the properties of inorganic and organometallic compounds. 6. Extended basis sets for second-row transition metals (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 880-893 
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    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 series of efficient split-valence basis sets for second-row transitions metals, termed 3-21G, has been constructed based on previously formulated minimal expansions of Huzinaga, and in a manner analogous to the previous development of 3-21G basis sets for first-row metals. The Huzinaga three Gaussian expansions for s- and p-type orbitals of given n quantum number have been fit by least squares to new three Gaussian combinations in which the two sets of functions share the same Gaussian exponents. The original three Gaussian expansions for 1s, 3d, and 4d atomic orbitals have been employed as is. The valence description comprises 4d- 5s- and 5p-type functions, each of which has been split into two and one Gaussian parts. 5p functions, while not populated in the ground state of the free atom, are believed to be important in the description of the bonding in molecules.The performance of the 3-21G basis sets is examined with regard to the calculation of equilibrium geometries and normal-mode vibrational frequencies for a variety of simple inorganic and organometallic compounds incorporating second-row transition metals.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080615
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    Topology of conical intersections and Jahn-Teller crossing: Application to the standard model for XY4 molecules in T2 ground statesPresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 850-860 
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    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 topological understanding of a potential function requires a knowledge of its critical points and indices. These concepts are mathematically meaningless if the potential function is not twice continuously differentiable. When conical intersections or Jahn-Teller crossings are encountered, the adiabatic potential, defined as the lowest eigenvalue of a Hamiltonian, can be smoothed everywhere. Moreover, the limiting properties of the smoothed critical points for vanishing values of a smoothing parameter lead to a unambiguous definition of a pseudo critical point of the limiting potential. Therefore, Morse theory is readily applicable to the ground state potential function in spite of the first order discontinuities. The regularization procedure is formally and numerically applied to the simplest Hamiltonian matrix of order 3 describing the Jahn-Teller effect of XY4 molecules in the T2 ground states. Various kinds of pseudo-critical points are encountered and are shown to satisfy the Morse theory.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080613
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    Application of SINDO1 to sulphur compounds (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1004-1015 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SINDO1 calculations are presented for ground state geometries, heats of formation, ionization potentials and dipole moments. These calculations are based on a new parametrization of SINDO1 for second-row elements which features inclusion of 3d orbitals and zero point energies. The comparison shows an improvement over MNDO, especially for hypervalent sulphur compounds.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080709
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    Application of SINDO1 to chlorine and sodium compounds (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1040-1050 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SINDO1 calculations are presented for ground state geometries, heats of formation, ionization potentials and dipole moments of chlorine and sodium compounds. These calculations are based on a new parametrization of SINDO1 for second-row elements which features inclusion of 3d orbitals and zero point energies. The comparison shows a substantial improvement over MNDO in geometries and heats of formation of hypervalent compounds and ionization potentials, whereas other properties are of similar quality.
    Additional Material: 12 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080712
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080801
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    Refined ab initio 6-31G split-valence basis set optimization of the molecular structures of biphenyl in twisted, planar, and perpendicular conformations (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1057-1065 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Improved full ab initio optimizations of the molecular structure of biphenyl in twisted minimum energy, coplanar, and perpendicular conformations by use of Poles's GAUSSIAN 82 program have been performed in the 6-31G basis set. These lead to geometries and energies of much higher reliability than our earlier STO-3G results. The torsional angle Φmin obtained now is 45.41° in close agreement with the recent experimental value of 44.4° ± 1.2°. Calculated CC distances may be converted to experimental ED rg-values by means of independently determined linear regression correlations with very high statistical confidence, although they agree better with experimental x ray data for coplanar biphenyl without this correction. Calculated intramolecular angles are very similar for both STO-3G and 6-31G basis sets. The calculated torsional energy barrier towards Φ = 90° (ΔE90) is 6.76 kJ/mol in close agreement with the experimental-31G value of 6.5 ± 2.0 kJ/mol. For coplanar biphenyl with D2h-symmetry the calculated torsional energy barrier ΔE0 is 13.26 kJ/mol which is surprisingly much higher than the experimental value of 6.0 ± 2.1 kJ/mol. This discrepancy could not be resolved by optimizations assumed for two kinds of distortions of planarity of orthohydrogens from the molecular plane of the coplanar carbon atoms. But for the twisted minimum energy conformation asymmetric bending of ortho-H atoms lead to a torsional angle Φmin = 44.74° together with a dihedral angle towards ortho-H of 1.22°, and consequently even to an increase of torsional energy barriers to ΔE0 = 13.51 and ΔE90 = 6.91 kJ/mol.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080714
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    Application of the MuMATH computer algebra system to sets of first order kinetic equations of significance in chemistry (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 442-447 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Analytical solutions to systems of first order differential equations have long been available; however, they become so involved that they are seldom used. Numerical simulations are preferred in practice, although they produce bulky output that is difficult to interpret. Even worse, they are occasionally seriously in error owing to “stiffness” in the equations, intrinsic instability, or other pathological behavior. Computer algebra systems can handle the complicated manipulations that make the analytical solutions of first order kinetic systems inconvenient and can serve as a check on numerical simulations. We show applications of the small MuMATH(R) computer algebra package to a variety of first-order process, including relaxation kinetics and the analysis of stability of steady states in nonlinear kinetic systems.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080422
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    Numerical calculation of eigenvalues for the Schrödinger equation. III (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 459-461 
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    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 recently developed method for calculation of eigenvalues is applied to a four coupled oscillator system previously used to test more approximate methods. Analysis is presented to show how the present method scales for systems of two, three, and four coupled oscillator systems.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080425
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    On the SCF calculation of excited states: Singlet states in the two-electron problem (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 454-458 
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    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 determining SCF wave functions for excited electronic states is examined for singlet states of two-electron systems using a Lowdin natural orbital transformation of the full CI wave function. This analysis facilitates the comparison of various SCF methods with one another. The distribution of the full CI states among the natural orbital MCSCF states is obtained for the S states of helium using a modest Gaussian basis set. For SCF methods that are not equivalent to the full CI wave functions, it is shown that the Hartree-Fock plus all single excitation wave functions are equivalent to that of Hartree-Fock plus one single excitation. It is further shown that these wave functions are equivalent to the perfect pair or TCSCF wave functions in which the CI expansion coefficients are restricted to have opposite signs. The case of the natural orbital MCSCF wave function for two orbitals is examined in greater detail. It is shown that the first excited state must always be found on the lower natural orbital MCSCF CI root, thus precluding the use of the Hylleras-Undeim-MacDonald (HUM) theorem in locating this state. It is finally demonstrated that the solution obtained by applying the HUM theorem (minimizing the upper MCSCF CI root with respect to orbital mixing parameters) is an artifact of the MCSCF method and does not correspond to any of the full CI states.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080424
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    The modeling of chemical phenomena using topological indices (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 470-480 
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    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 class of graph invariants known today as topological indices are being increasingly realized by chemists and others to be powerful tools in the description of chemical phenomena. Topological indices generally characterize both the size and shape of chemical species; in recent years a number of such indices have been put forward that sensitively reflect the amount of branching present in molecules. Chemists are thus able to model accurately the chemical behavior of an extensive range of chemical substances in all three thermodynamic states. In discussing the manifold applications of topological indices to the description of physicochemical properties, we present a survey of the progress to date in this area and point out some of the advantages and drawbacks of using topological indices.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080427
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    The shape of molecular charge distributions: Group theory without symmetry (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 462-469 
    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: A group theoretical framework is proposed for a detailed characterization of the shapes of electronic charge distributions of general, asymmetric molecules. The proposed shape groups are the homology and cohomology groups of charge density contour surfaces. These shape groups depend on two real parameters, the charge density value a for the contour and a curvature parameter b. The two-parameter family of various homology groups and cohomology groups of charge density contour surfaces is independent of the symmetry properties of the molecules and gives a concise description of the dominant shape characteristics. For any fixed parameter value b these groups may change only at specific charge density values, characteristic to the given molecule. On the other hand, for a fixed-charge density contour the group changes induced by a change in the curvature parameter b provide a description of the fine details of the shape of the electron density. The changes in the structure of these groups follow strict algebraic relations, that provide a quantitative measure for shape-similarity between various molecules. The two-parameter shape group method is an extension of an earlier method proposed for biochemical applications.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080426
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  • 148
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    Bond critical points in the electronic structures of the main group diatomic hydrides of lithium through bromine (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 489-498 
    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 bond critical points and associated electronic properties of the diatomic hydrides of the twenty-one main group elements from lithium to bromine have been calculated with large basis sets. As part of a systematic study of the polarity of chemical bonds, the position of the bond critical point, the charge density at the bond critical point, the Laplacian of the charge density at the bond critical point, and the molecular dipole moment of each molecule have been calculated. Particular attention has been paid to the effect of bond length elongation and contraction on the electronic properties. Variation of the bond length reveals that with atoms of low electronegativity, the bond critical point of AH tends to follow atom A, whereas with atoms of high electronegativity, the bond critical point tends to follow the hydrogen atom as the bond lengthens. Furthermore, it is shown that some properties of the diatomic hydrides vary monotonically within each row of the periodic table, while others effect a classification according to the character of the bond.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080429
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  • 149
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    Theoretical study of the addition of hydrogen halides to olefins: A comparison between (HCl)2 and (HF)2 additions to ethylene (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 481-488 
    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 addition of HCl and (HCl)2 to ethylene is theoretically studied by means of ab initio SCF techniques using the 3-21G basis set. A statistical thermodynamics analysis is also carried out. When a comparison is made with the HF and (HF)2 additions to ethylene, the general fact of the catalytic action of the second HX molecule in the (HX)2 complex is revealed. The behavior of HF, however, is very different from that of HCl, since in the former case the driving force in the termolecular transition state is the bonding between fluorine and carbon, while in the latter case the driving force is the bonding between carbon and hydrogen, as generally accepted for electrophilic reactions. The use of density plots of the transition states on the plane of the cycle allows us to conclude that, while both HF and HCl termolecular transition states are hexacyclic, the bimolecular transition state of the HCl addition is bicentric and not tetracentric as previously reported.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080428
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  • 150
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    Quasiperiodization in classical hyperchaos (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 510-515 
    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: A 1D gas with maximal chaos in the sense of Sinai is considered. An idea originally proposed by Gibbs (that particle indistinguishability imposes a well-defined symmetry having nontrivial quantitative implications) is investigated in the light of this example. A new quantitative implication of the Gibbs paradox, quasiperiodization, is found to apply to the present system.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080431
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  • 151
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    Some methods and applications of electron density distribution analysis (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 499-509 
    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: Accurate and efficient integration of the electron density function over arbitrary regions has been previously achieved by exploiting a separation of variables. Recently, a computer program has been written that calculates ρ, \documentclass{article}\pagestyle{empty}\begin{document}$ \buildrel{\rightharpoonup}\over{\nabla} $\end{document}ρ, and ∇2ρ in an expeditious fashion, taking advantage of the separation of variables in the electron density function. Accurate integrations of ∇2ρ over arbitrary regions can also be accomplished. The structure of the program is suited especially to vector processors. As a result of the efficiencies of these programs, functions of the electron density, such as the density itself, the surrounding electrostatic potential, ∇ρ, and ∇2ρ have been calculated in three dimensions. Results of calculations for nitrated cubanes are presented illustrating how the effects of the nitro groups are manifested in the electron density and associated properties.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080430
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    An algorithm for geometry optimization without analytical gradients (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 563-574 
    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: A numerical algorithm for locating both minima and transition states designed for use in the ab initio program package GAUSSIAN 82 is presented. It is based on the RFO method of Simons and coworkers and is effectively the numerical version of an analytical algorithm (OPT = EF) previously published in this journal. The algorithm is designed to make maximum use of external second derivative information obtained from prior optimizations at lower levels of theory. It can be used with any wave function for which an energy can be calculated and is about two to three times faster than the default DFP algorithm (OPT = FP) supplied with GAUSSIAN 82.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080502
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    An objective computer-oriented method for the calculation of formation constants from the formation function. A weighted least-squares curve fitting (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 575-580 
    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: A computer program has been developed that calculates, using the weighted least-squares technique, the overall formation constants, Bi, of mononuclear complexes, the standard deviations of Bi, SDVi, and an estimate of goodness of fit, Goodness-of-Fit Parameter (GOFP), given a set of average ligand numbers, VNj, the corresponding free ligand concentrations, VAj, and an error parameter P. The formation function used is ∑(VNj - i) · (Bi) · (VAj)i = 0 where i ranges from O to n with a maximum of 10 and j ranges from O to l with a maximum of 40. The Bi and (Bi - SDVi) must be positive and GOFP must be either unity or as close to unity as possible. An option is available that allows the computation of P, if it is not provided, so that GOFP is equal or very close to unity. The method has been applied to the formation of the complexes Cadmium-Imidazole, Cobalt(II)-Bis(2-Quinaldylphenyl Ketone), Copper-Ammonia, Silver-4-Aminobutan-1-ol Nitrate, and Copper(II)-Bis(2-Quinaldylphenyl Ketone). The results are quite satisfactory and reliable as compared with other computational techniques. Input data and results for the five complexes mentioned are shown.
    Additional Material: 5 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540080503
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    Configurational specificity of stacking interactions in DNA base pairs: A computational analysis (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 604-617 
    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: A theoretical study of stacking patterns of various hydrogen-bonded base pair complexes has been undertaken. Modified Rayleigh-Schrodinger perturbation theory for intermediate range interactions, has been employed to evaluate the stacking interactions using multicentered-multipole expansion method. Net atomic charge and corresponding dipole components located at each of the atomic centers have been computed by CNDO/2 method. An analysis of the intermolecular forces involved in the stable formation of the various base pair complexes, has been presented and the results have been discussed in the light of experimental as well as other theoretical observations. The possibility of relative preference of the left-handed configuration for alternating sequences has been quantitatively explored.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080505
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    Theoretical studies on the acid hydrolysis of methyl carbamatePart 45 in the series, Determination of Reactivity by MO Theory. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 794-800 
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    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 mechanism of the A2 acid hydrolysis of methyl carbamate was investigated using MNDO method. The reaction was found to proceed in two steps: (1) the rate-determining nucleophilic attack of water on the carbonyl carbon of the N-protonated tautomer involving the tetrahedral TS; and (2) the fast subsequent proton abstraction by the leaving group, NH3, to form products. The mechanism is similar to that involved in the A2 hydrolysis of acetamide. Effects of substituents, R1, R2, and R3 in R1OCONR2R3, on rates can be predicted by the changes in electron densities on alkoxy oxygen and N, in complete agreement with the experimental results. We concluded that there is no need for invoking two different mechanisms for amides and carbamates since a common mechanism can easily accommodate all the experimental results.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080607
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    Improvement of the hydrogen bonding correction to MNDO for calculations of biochemical interest (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 835-849 
    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: Recent suggestions for correcting H—Acceptor interactions within MNDO, together with results of crystallographic analysis, were used to modify this SCF semiempirical calculation for multiple hydrogen bonded associations. Thermodynamic profiles for model systems of biochemical interest such as H2O—H2O, hydration of neutral and charged molecules, dimerizations and proton transfers show the advantages of this method. Its treatment of charges, bonding, geometries, energetics and vibrational frequencies is shown to be comparable to ab initio calculations with various basis sets. However, basic MNDO deficiencies and criteria applied for H-bonding result in some too high barriers for proton transfers.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080612
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    Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 826-834 
    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 build-up procedure for predicting low-energy conformations of polypeptides has been extended to cover the case of peptides in aqueous solutions. The revised procedure consists of five steps to be applied to each stage of the build-up. I. All low-energy minima of each of the two fragments to be joined are combined as starting points for energy minimization of the enlarged fragment, and those minima of the enlarged fragment within a certain upper bound of the lowest energy are retained. II. Whenever one of the combinations in Step I leads to an atomic overlap, the minimization is started again using a pseudoenergy function which remains finite everywhere and becomes equal to the standard energy function when no atoms overlap. III. The minima generated in Steps I and II are culled by ignoring side-chain conformations and retaining only those minima whose backbone conformations differ significantly. IV. The rotameric states of the side chains are optimized, by testing their energy of interaction with the rest of the molecule, and subjecting the whole molecule to a further round of energy minimization if the test indicates that this would reduce the energy. V. The energies of all minima are recomputed with inclusion of a term for solvation and with a smaller upper bound as the criterion for retention. The original build-up procedure consisted of Steps I and III only. Examples are presented showing the effectiveness of the new Steps II and IV in locating low-energy minima, and the problems that remain to be solved, chiefly concerning Step V, are discussed.
    Additional Material: 2 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540080611
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    Computer enumeration of polyhexes using the compact naming approach (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 906-915 
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    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 enumeration of polyhexes can be easily carried out by utilizing a compact name (CN) approach to code chemical structures. The Fortran program performing generation of benzenoid hydrocarbons with 1-10 rings is presented. The computed structures are divided into various classes according to their cata- or peri- as well and non- or radicaloid character. Use of the additive nodal increments (ANI) approach leads to algorithm producing representative samples of the polyhexes' sets which can be applicable in testing of various topological formulae.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080617
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    On color polynomials of Fibonacci graphs (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 956-959 
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    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 recursion exists among the coefficients of the color polynomials of some of the families of graphs considered in recent work of Balasubramanian and Ramaraj. Such families of graphs have been called Fibonacci graphs. Application to king patterns of lattices is given. The method described here applies only to the so called Fibonacci graphs.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080704
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    Fast matrix multiplication (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 960-964 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several implementations of matrix multiplication (MMUL) in Fortran and VAX assembly language are discussed. On a VAX-11/780 computer, the most efficient MMUL is achieved through vector-scalar-multiply-and-add (VSMA) operations, rather than by means of dot products. We also discuss optimal MMUL algorithms for use in virtual memory machines when the data overflow the working set.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080705
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    Voronoi binding site models (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 943-955 
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    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 frequently occurring problem in drug design and enzymology is that the binding constants for several compounds to the same site are known, but the geometry and energetic interactions of the site are not. This paper presents in detail a novel approach to the problem which accurately but compactly represents the allowed conformation space of each ligand, accurately depicts their three-dimensional structures, and realistically allows each ligand to adopt the conformation and positioning in the site which is most favorable energetically. The investigator supplies only the ligand structures and observed binding free energies, along with a proposed site geometry. With no further assumptions about how the ligands bind and what parts of the ligands are important in determining the binding, the algorithm fits the observed binding energies without leaving outliers, predicts exactly how each of the given ligands binds in the site, and predicts the strength and mode of binding of new compounds, regardless of chemical similarity to the original set of ligands. The method is illustrated by devising a simple site that accounts for the binding of five polychlorinated biphenyls to thyroxine binding prealbumin. This model then predicts the binding energies correctly for an additional six biphenyls, and fails on one compound.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080703
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    A note on the efficient and accurate computation of the phase functions φ and χ in semiclassical approximations (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 965-971 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Efficient and accurate algorithms for the computation of two so-called phase functions which arise in semiclassical approximations are presented together with results from checks on their accuracy.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080706
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    Monte Carlo study of the aqueous hydration of dimethylphosphate conformations (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 917-942 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo computer simulations were performed on dilute aqueous solutions of the dimethylphosphate anion and the sodium dimethylphosphate ion pair, with the two phosphodiester torsional angles in the gauche-gauche, gauche-trans, and trans-trans conformations. The structural and energetic aspects of the aqueous hydration of each molecule were analyzed in terms of quasi component distribution functions based on the proximity criterion and partitioned into ionic, hydrophilic, and hydrophobic contributions to facilitate an understanding of the hydration pattern and conformational trends in these multifunctional solutes. Special attention was also paid to methodological issues affecting hydration, such as statistical uncertainty in the determined hydration indices, choice of partial atomic charges for the solute atoms, and solute-water interaction potentials adopted in the simulations. The results showed that gauche-trans and gauche-gauche forms are equally favorable for the dimethylphosphate anion with the trans extended form destabilized by hydration. The sodium dimethylphosphate ion pair hydration energetically favors the trans-trans conformation.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080702
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    Determination of an empirical energy function for protein conformational analysis by energy embedding (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 972-981 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is quite easy to propose an empirical potential for conformational analysis such that given crystal structures lie near local minima. What is much more difficult, is to devise a function such that the native structure lies near a relatively deep local minimum, at least in some neighborhood of the native in conformation space. An algorithm is presented for finding such a potential acting on proteins where each amino acid residue is represented by a single point. When the given structure is either an α-helical, β-strand, or hairpin bend segment of pancreatic trypsin inhibitor, the resulting potential function in each case possesses a deep minimum within 0.10 Å of the native conformation. The improved energy embedding algorithm locates a marginally better minimum in each case only 0.1-1.3 Å away from the respective native state. In other words, this potential function guides a conformational search toward structures very close to the native over a wide range of conformation space.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080707
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    Gaussian basis sets for the fifth row elements, Mo-Cd, and the sixth row elements W-RN (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 982-1003 
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    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 17 s-type, 12 p-type, and 8 d-type functions, for the fifth row elements, Mo—Cd, and 19 s-type, 14 p-type (16 p-type), 10 d-type and 5 f-type functions for the sixth row elements, W—Rn, are presented. The basis sets are of double zeta quality, and are optimized to .002 a.u. in the energy. The energies are compared with D.Z. STO basis sets.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080708
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    Benzene-benzene (phenyl-phenyl) interactions in MM2/MMP2 molecular mechanics calculations (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1139-1145 
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    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/MMP2 force-field gives an incorrect description of benzene-benzene interactions. This deficiency may be overcome by the addition of electrostatic interactions. Using point charges of -0.15 on carbon and +0.15 on hydrogen, a good agreement between benzene dimer potentials calculated by MMP2 and ab initio SCF CI potentials is obtained. The influence of the addition of point charges on calculated structures and conformational energies has been studied. Examples are given in which the addition of electrostatic interactions between phenyl groups substantially improves calculated conformational energies.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080811
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    MNDO Calculations on [n]metacyclophanes (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1154-1169 
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    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 on [n]metacyclophanes and a variety of related compounds are reported. An analysis of the strain, imposed by the oligomethylene bridge, and its distribution over the distorted benzene ring and the oligomethylene bridge is presented. The effect of strain and bending of the benzene ring on aromatic delocalization is investigated by a comparison of ΔHof of the bent benzene systems with that of a correspondingly bent, but localized 1,3,5-cyclohexatriene. The results indicate that, even in the case of the highly bent [4]metacyclophane (1a), localization is unfavorable by about 10 kcal/mol.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080813
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    Benzene, aromatic rings, van der Waals molecules, and crystals of aromatic molecules in molecular mechanics (MM3) (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1146-1153 
    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: Benzene has been studied with the MM3 force field, first as a monomer, then as a van der Waals dimer, then in the crystal. The non-bonded aromatic portion of the MM3 force field has been derived to fit reasonably well the known properties for the above. The force field includes dipoles of 0.6 and 0.9 D for Csp2—H and Csp2—Csp3 bonds, respectively. The benzene dimer is calculated to have a lower energy when perpendicular, than when eclipsed face to face. The crystal of benzene has a herringbone pattern with correct cell constants and heat of sublimation, while hexamethylbenzene as the dimer and in the crystal has a skewed-stack of pancakes type structure, as observed.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080812
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    An investigation of the relative stabilities of the isomers of CF2N2: Comparison of ab initio and MNDO calculations (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1170-1178 
    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: Ab initio SCF calculations at the HF/3-21G level and semi-empirical MNDO calculations have been used to locate the stationary points on the CF2N2 energy surface. Perfluorodiazomethane is predicted to be most stable isomer, but perfluorodiazirine is predicted to lie only ca 41 kJ higher in energy at the SCF level. There are significant differences between the ab initio and MNDO results for the ordering of some of the isomers. Frequency calculations give results in good agreement with the limited experimental data on these molecules.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080814
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  • 170
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    Ab initio program for treatment of related molecules. II. Integral transformation in extended systems (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1179-1190 
    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: An integral transformation procedure is reported as a part of an ab initio program (named SYCETY) developed recently for spatially extended molecules. It is shown that all advantages of the program SYCETY can be kept. The procedure is especially suitable to transform the integrals to a localized basis set. By using the MBPT with localized basis the most important part of the correlation can be calculated even for large (spatially extended) systems.
    Additional Material: 9 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080815
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  • 171
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    The Hylleraas-CI method in molecular calculations: Two-electron integrals (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1191-1198 
    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 the Hylleraas-CI method, first proposed by Sims and Hagstrom, correlation factors of the type rijv are included into the configurations of a CI expansion. The computation of the matrix elements requires the evaluation of different two-, three-, and four-electron integrals. In this article we present formulas for the two-electron integrals over Cartesian Gaussian functions, the most used basis functions in molecular calculations. Most of the integrals have been calculated analytically in closed form (some of them in terms of the incomplete Gamma function), but in one case a numerical integration is required, although the interval for the integration is finite and the integrand well-behaved. We have also reported on partial and preliminary computations for the H2 molecule using our four-center general formulas; a basis set of s- and p-type functions yielded at R = 1.4001 Å an energy of - 1.174380 a.u. to be compared with Kolos and Wolniewicz value of - 1.174475.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080816
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  • 172
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    Announcement (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1232-1232 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080819
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  • 173
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    Innate degree of freedom of a graph (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 516-521 
    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: For a Kekulé structure we consider the smallest number of placements of double bonds such that the full Kekulé structure on the given parent graph is fully determined. These numbers for each Kekulé structure of the parent graph sum to a novel structural invariant F, called the degree of freedom of the graph. Some qualitative characteristics are identified, and it is noted that apparently it behaves differently from a couple of other invariants related to Kekulé structures.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080432
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  • 174
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    Graph generators (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 522-535 
    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: We consider the construction of highly symmetrical vertex transitive graphs. Some such graphs represent the degenerate rearrangements in which a molecule or an ion is formed by breaking and making bonds so that the final and the initial skeleton is identical. The approach is closely related to Cayley's graphs for selected groups. We restrict the choice of generators to symmetric matrices. Successive multiplications of such matrices generate other permutation matrices of the same dimension, each new matrix representing a new vertex for a transitive graph under the construction. In particular we restrict our discussion to matrices of dimension 3 and 4 and proceed to construct systematically all transitive graphs using 4 × 4 symmetric matrices as generators.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080433
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  • 175
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    Stereotopological indices for a family of chemical graphs (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 536-548 
    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: We describe a mathematical method that can be employed to define stereotopological indices of placements of certain graphs in space. These indices are applied to successfully distinguish between configurations in a chemically interesting family of knotted and/or linked four-valent oriented graphs in space. The methods are fundamentally algebraic and combinatorial in nature and are most readily understood in the context of calculations and the study of several key examples that are presented.
    Additional Material: 31 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080434
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  • 176
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    Molecular dynamics simulation of the 1:1 enzyme-ligand complex between porcine pancreatic elastase and acetyl-alanine-proline-alanine (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 801-809 
    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: A 31.5 picosecond (ps) MD calculation has been completed for the 1:1 enzyme-ligand complex between porcine pancreatic elastase (PPE) and acetyl-alanine-proline-alanine (APA). The 1:2 complex studied crystallographically at product saturation conditions precludes the study of a 1:1 complex (PPE and APA1); this objective has been achieved by computational methods described here. The acetyl group of the ligand was found to occupy two neighboring sites, one within the primary specificity site and the other out into solution. The primary change of the ligand structure is ψ1 torsion angle being 171.5°. Supported by an interactive graphic display, the dynamical fluctuations of a smaller ligand compared with the width of the active site as PPE were observed by the MD simulation, although the complex has not been detected by any spectroscopic method.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080608
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  • 177
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    Towards a valence-orbital/bond-orbital description of biochemical H-bonds from ab initio calculationsWork partially presented at the International Symposium on Applications of Mathematical Concepts to Chemistry, Dubrovnik, Yugoslavia, September 2-5, 1985. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 816-825 
    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: We have studied the system NH3…H+…HN=CH-CH=CH2, which is a model for an enzymatic site characterized by an important pi-electron contribution, with the aim of contributing to the molecular orbital theory of H-bridge formation and proton transfer. Ab initio canonical orbitals from STO-3G and 4.31G bases have been determined for various geometrical configurations, and analyzed in terms of Mulliken's Modified Valence Atomic Orbitals obtained by suitable contraction. Also, the orbital correlation diagram has been obtained and discussed. At least two sigma MO's can be considered specific of the H-bond: they involve the expected hybrids giving rise to stereoelectronic effects associated with the lone pairs of the two heavy atoms. Population analysis suggests that the bridge hydrogen changes its population very little during its motion along the bridge, although its in situ atomic orbital does not change: this means that it acts essentially as a relay center in charge transfer between the two moieties of the H-bonded complex. As expected on intuitive grounds, charge transfer involves essentially the sigma cores.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080610
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  • 178
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    Atomic charges derived from electrostatic potentials: A detailed study (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 894-905 
    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: A new algorithm for fitting atomic charges to molecular electrostatic potentials is presented. This method is non-iterative and rapid compared to previous work. Results from a variety of gaussian basis sets, including STO-3G, 3-21G and 6-31G*, are presented. Charges for a representative collection of molecules, comprising both first and second row atoms and anions are tabulated. The effects of using experimental and optimized geometries are explored. Charges derived from these fits are found to adequately reproduce SCF dipole moments. A small split valence representation, 3-21G, appears to yield consistently good results in a reasonable amount of time.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080616
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  • 179
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    Announcement (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 916-916 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080618
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  • 180
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080701
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  • 181
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    Calculation of enthalpies of hydrogenation of hydrocarbons (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1131-1138 
    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: Sets of hydrogen molecule equivalents have been developed which permit the calculation of hydrogenation of different types of carbon-carbon bonds from ab initio total energies (3-21G and 6-31G* basis sets, and, to a more limited extent, for MP2/6-31G* data) of reactants and products. The calculated enthalpies of hydrogenation are in good agreement with experiment for unstrained molecules, with average errors on the order of 2 kcal/mol. The 6-31G* equivalents allow the enthalpies for strained molecules to be calculated accurately, but the 3-21G equivalents do not. The equivalents for both basis sets have been tested by calculating the enthalpies of hydrogenation of carbon-carbon bonds in nitrogen- and oxygen-containing organic molecules, free radicals, and classical carbocations. The results are in good agreement with experiment in most cases.
    Additional Material: 9 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080810
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  • 182
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    A force field for allenes and for nonlinear acetylenes within the MM2 approximation (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1225-1231 
    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: Geometries and heats of formation for allenes may now be calculated with an extended version of MM2. The torsional barriers about bonds in an acetylenic unit are much more complicated than originally thought, if the unit is nonlinear. Ab initio calculations have been used to show just what these torsional barriers are, and the MM2 force field has been adapted to this information.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080818
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  • 183
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    Masthead (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987) 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550191001
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  • 184
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    Data on the thermochemistry of azoalkanes (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 929-942 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rate constant of the primary decomposition step was determined for four symmetrical and four unsymmetrical azoalkanes. From the experimental activation energies and some literature enthalpy data, the following enthalpies of formation of radicals and group contributions were calculated: ΔHƒ (CH3N2) = 51.5 ± 1.8 kcal mol-1, ΔHƒ (C2H5N2) = 44.8 ± 2.5 kcal mol-1, ΔHƒ (2-C3H7N2) = 37.9 ± 2.2 kcal mol-1, [NA-(C)] = 27.6 ± 3.7 kcal mol-1, [NA-(ṄA) (C)] = 61.2 ± 3.1 kcal mol-1.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550191005
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  • 185
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    Masthead (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987) 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550191101
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  • 186
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    Disproportionation reactions between alkyl and fluoroalkyl radicals. IV. Pentafluoroethyl and ethyl radicals (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 963-973 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new determination of the disproportionation/combination ratio for C2F5 and C2H5 radicals gives a value of Δ(C2F5, C2H5) = 0.24 ± 0.02, independent of temperature. The cross-combination ratio for the two radicals was found to increase with temperature and the significance of this is discussed in evaluating Δ.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550191103
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  • 187
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    The gas phase reactions of hydroxyl radicals with a series of aliphatic alcohols over the temperature range 240-440 K (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 1015-1023 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Absolute rate constants were determined for the gas phase reactions of OH radicals with a series of aliphatic alcohols using the flash photolysis resonance fluorescence technique. Experiments were performed over the temperature range 240-440 K at total pressures (using Ar diluent gas) between 25-50 Torr. The kinetic data for methanol (k1), ethanol (k2), and 2-propanol (k3) were used to derive the Arrhenius expressions \documentclass{article}\pagestyle{empty}\begin{document}$$ k_1 = (4.8 \pm 1.2) \times 10^{ - 12} \exp [- (480 \pm 70)/T]\,{\rm cm}^3\, {\rm molecule}^{ - 1} {\rm s}^{ - 1} $$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$ k_2 = (7.4 \pm 3.2) \times 10^{ - 12} \exp [- (240 \pm 110)/T]{\rm cm}^3 {\rm molecule}^{ - 1} {\rm s}^{ - 1} $$\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$$ k_3 = (5.8 \pm 1.9) \times 10^{ - 12} \exp [- (30 \pm 90)/T]\,{\rm cm}^3\, {\rm molecule}^{ - 1} {\rm s}^{ - 1} $$\end{document} At 296 K, the measured rate constants (in units of 10-13 cm3 molecule-1 s-1) were: k1 = (8.61 ± 0.47), k2 = (33.3 ± 2.3), and k3 = (58.1 ± 3.4). Room temperature rate constants for the OH reactions with several other aliphatic alcohols were also measured. These were (in the above units): 1-propanol, (53.4 ± 2.9); 1-butanol, (83.1 ± 6.3) and 1-pentanol, (108 ± 11). The results are discussed in terms of the mechanisms for these reactions and are compared to previous literature data.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550191106
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  • 188
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    Masthead (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987) 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550191201
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  • 189
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    Gas phase thermolysis of cyanomethyl t-butyl sulfide and cyanomethyl t-butyl ether (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 1053-1062 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The pyrolyses of cyanomethyl t-butyl sulfide and its oxygen homologue have been studied in a stirred-flow system over the temperature range 490-540°C and pressures between 5 and 14 Torr. In both cases, isobutene is formed as product in over 97% yield. Hydrogen sulfide is obtained in about half the amount of isobutene in the pyrolysis of the sulfide. Hydrogen cyanide is formed in the pyrolysis of the ether. The first-order rate coefficients for the consumption of the reactants followed the Arrhenius equations Cyanomethyl t-butyl sulfide: \documentclass{article}\pagestyle{empty}\begin{document}$$ k({\rm s}^{ - 1}) = 10^{12.63 \pm 0.23} \exp (- 201.7 \pm 3.5)\,{\rm kj}/{\rm mol }\,RT $$\end{document} Cyanomethyl t-butyl ether: \documentclass{article}\pagestyle{empty}\begin{document}$$ k({\rm s}^{ - 1}) = 10^{11.27 \pm 0.30} \exp (- 186 \pm 5)\,{\rm kj}/{\rm mol }\,RT $$\end{document}A molecular mechanism involving polar four-centered cyclic transition states is proposed for both reactions, with the CN group stabilizing the partial negative charge developed at the S and O atoms.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550191202
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  • 190
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    Kinetics of the gas-phase reactions of Cl atoms with chloroethenes at 298 ± 2 K and atmospheric pressure (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 1097-1105 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using a relative rate technique, rate constants have been determined for the gas-phase reactions of Cl atoms with the cholorethenes and ethane at 298 ± 2 K and 735 torr total pressure of air. Using a rate constant of 1.97 × 10-10 cm3 molecule-1 s-1 for the reaction of Cl atoms with n-butane, the following rate constants (in units of 10-11 cm3 molecule-1 s-1) were obtained: vinyl chloride, 12.7 ± 0.2; 1,1-dichloroethene, 14.0 ± 0.2; cis-1,2-dichloroethene, 9.65 ± 0.10; trans-1,2-dichloroethene, 9.58 ± 0.18; trichloroethene, 8.08 ± 0.10; tetrachloroethene, 4.13 ± 0.23; and ethane, 6.17 ± 0.08 (where the indicated error limits do not include the uncertainties in the rate constant for n-butane). A small amount of cis-trans isomerization was observed for the reactions involving the cis- and trans-1,2-dichloroethenes. These data are compared and discussed with the available literature data.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550191206
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  • 191
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    The pyrolysis of acetylene-styrene mixtures between 450 and 550°C (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 659-678 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The pyrolysis of acetylene-styrene mixtures has been studied from 450-550°C in a quartz reaction vessel in the absence and presence of O2 or NO. The rates of disappearance of reactants and formation of adducts are first-order in each reactant. The major product is polymer, with the adducts accounting for about 2.5% and 6.2% of the styrene removed at 450 and 550°C, respectively. The acetylene-to-styrene removal ratio is about 27 independent of temperature. The adducts formed are methyl indene and 1,2-dihydronaphthalene. These are about half-suppressed in the presence of O2 or NO. The rate coefficients for reactant removal and adduct formation are: \documentclass{article}\pagestyle{empty}\begin{document}$$ \log \{ k\{ {\rm C}_{\rm 2} {\rm H}_{\rm 2} \},M^{ - 1} {\rm s}^{ - 1} \} = 7.53 \pm 0.10 - (90.6 \pm 1.5)/2.3RT $$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$ \log \{ k\{ {\rm C}_{\rm 8} {\rm H}_{\rm 8} \},M^{ - 1} {\rm s}^{ - 1} \} = 6.63 \pm 0.60 - (98.5 \pm 8.8)/2.3{\rm }\,RT $$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$ \log \{ k\{ {\rm C}_{{\rm 10}} {\rm H}_{{\rm 10}} \},M^{ - 1} {\rm s}^{ - 1} \} = 8.27 \pm 0.66 - (143.3 \pm 9.8)/2.3RT $$\end{document} where the activation energies are in kJ/mol and the uncertainties are one standard deviation. As the reaction proceeds, the methyl indene and 1,2-dihydronaphthalene decompose, and indene and naphthalene are formed. In addition, an unidentified isomer of naphthalene is produced as an initial minor product, and it also decomposes as the reaction proceeds.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550190708
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    Masthead (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987) 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550190101
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  • 193
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    Bond dissociation energies and radical heats of formation in CH3Cl, CH2Cl2, CH3Br, CH2Br2, CH2FCl, and CHFCl2 (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 15-24 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An analysis of thermochemical and kinetic data on the bromination of the halomethanes CH4-nXn (X = F, Cl, Br; n = 1-3), the two chlorofluoromethanes, CH2FCl and CHFCl2, and CH4, shows that the recently reported heats of formation of the radicals CH2Cl, CHCl2, CHBr2, and CFCl2, and the C—H bond dissociation energies in the matching halomethanes are not compatible with the activation energies for the corresponding reverse reactions. From the observed trends in CH4 and the other halomethanes, the following revised ΔH°f,298 (R) values have been derived: ΔH°f(CH2Cl) = 29.1 ± 1.0, ΔH°f(CHCl2) = 23.5 ± 1.2, ΔHf(CH2Br) = 40.4 ± 1.0, ΔH°f(CHBr2) = 45.0 ± 2.2, and ΔH°f(CFCl2) = -21.3 ± 2.4 kcal mol-1. The previously unavailable radical heat of formation, ΔH°f(CHFCl) = -14.5 ± 2.4 kcal mol-1 has also been deduced. These values are used with the heats of formation of the parent compounds from the literature to evaluate C—H and C—X bond dissociation energies in CH3Cl, CH2Cl2, CH3Br, CH2Br2, CH2FCl, and CHFCl2.
    Additional Material: 2 Tab.
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    URL: http://dx.doi.org/10.1002/kin.550190103
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  • 194
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    Kinetic studies on the oxidation of carbon monoxide over pure, reduced, and doped indium sesquioxides (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 1-14 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Kinetic studies on the oxidation of carbon monoxide have been carried out between 413 and 473 K at different partial pressures of carbon monoxide and oxygen by means of the static method using vacuum-activated, hydrogen-reduced, and NiO-doped In2O3 semiconductors as catalysts. A strong carbon dioxide inhibiting effect is observed. The experimental data satisfactorily fit an equation derived by assuming the controlling step to be the adsorption of gaseous oxygen on the surface of catalyst. CO and CO2 adsorb on the lattice oxygens (Oo2-), while O2 adsorbs on the oxygen vacancies (Vox) formed by vacuum-activation, H2-reduction, and NiO-doping of In2O3. When CO2 formed during the reaction is removed by means of liquid nitrogen trap, the oxidation is found to be first-order with respect to CO and to be half-order with respect to O2. The concentration of oxygen vacancy in the solid catalyst is shown to be the controlling factor for the oxidation of carbon monoxide. A possible reaction mechanism can be explained by the n-type character of In2O3 and proposed from the experimentally obtained kinetic data and conductivities.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550190102
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  • 195
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    Pulse radiolysis study of the reaction of OH radicals with C2H4 over the temperature range 343-1173 KWork performed under the auspices of the Office of Basic Energy Sciences, Division of Chemical Science, US-DOE under contract Number W-31-109-ENG-38. (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 25-34 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reaction of OH and OD radicals with ethylene in the presence of 1 atm argon and 6 Torr water vapor was studied in the temperature range 343-1173 K. The results reveal three kinetically separate temperature regions: (1) 343-563 K, where the disappearance of OH radical is dominated by the addition of OH to the double bond of ethylene; (2) 563-748 K, where concurrent reactions of addition, the reverse reaction of addition and H-atom abstraction is dominant; and (3) 748-1173 K, where H-atom abstraction is likely the main reaction. The rate for hydrogen abstraction is 2.4 × 10-11 exp[(-2104 ± 125)/T] cm3/molec-s (for OD 2.1 × 10-11 exp[(-2130 ± 172)/T] cm3/molec-s). There was no obvious pyrolysis of ethylene below 1073 K. The study of OD radical with ethylene shows a small isotope effect.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550190104
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  • 196
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    Sensitivity analysis of the two kinetic states of the Belousov-Zhabotinsky reaction (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 35-48 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A recently published kinetic model of the Belousov-Zhabotinsky reaction was studied by the feature sensitivity analysis of the slow bromide consumption and slow bromide production periods of the relaxing-type oscillatory system. The computed sensitivities allowed us to reveal the kinetic importance of the 17 individual reactions during the two, “kinetically homogeneous” states of the oscillation. Similarities and differences in the relative kinetic importances of the reaction steps were carefully studied when changing the magnitude of the rate constants (high set and low set). Of the 17 reactions examined, the attack of Ce4+ on malonic acid proved to be an essential step of the mechanism. Using the low set, there emerge more reactions which significantly affect the length of the two kinetic states.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550190105
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  • 197
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    The photochemistry of methyl cyclobutyl ketone. Part 2. Temperature dependence and the acetyl radical decomposition (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 997-1013 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Following earlier room-temperature studies, gaseous mixtures of methyl cyclobutyl ketone (MCK) diluted in argon have been photolyzed at temperatures up to 205°C. Experiments have been carried out at a variety of pressures (up to ca. 2 atm) at wavelengths of 313 nm (steady state conditions) and 308 nm (pulsed photolysis). The results are consistent with a mechanism dominated by radical-radical reactions involving acetyl, methyl, and cyclobutyl radicals. Acetyl radical processes predominate at lower temperatures while methyl radical reactions are more important at high temperatures.The results are interpreted via kinetic modelling of a mechanism in which a key role is played by the acetyl radical decomposition reaction \documentclass{article}\pagestyle{empty}\begin{document}$$ ({\rm M} +)\,{\rm CH}_{\rm 3} {\rm CO}\mathop {\longrightarrow}\limits^{\rm 3} {\rm CH}_{\rm 3} + {\rm CO\, (+ M)} $$\end{document} Values for k3 have been obtained and its temperature and pressure dependence are fitted by RRKM theory and a weak-collisional activation model to yield \documentclass{article}\pagestyle{empty}\begin{document}$$ {\rm log(}k_3 ^\infty /{\rm s}^{ - 1}) = 13.3 - 17.5{\rm\, kcal\, mol}^{{\rm - 1}} /RT\ln 10 $$\end{document} This high-pressure limiting Arrhenius equation is consistent with other studies in the same temperature range, but is difficult to reconcile with higher temperature investigations.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550191105
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    Kinetics and mechanisms of substitution at paramagnetic metal centers in organometallic complexes (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 1025-1047 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The mechanism of ligand substitution in 17- and 19-electron organometallic radicals is discussed. These species substitute ligands by an associative process some 106 to 1010 faster than analogous 18-electron complexes. When 17-electron species can be generated by bond homolysis or electron transfer reactions of 18-electron complexes, they can act as intermediates in radical chain reactions of 18-electron complexes. A 17-19 electron rule is proposed to explain transformations of organometallic radicals just as the 16-18 electron rule finds use for closed shell organometallic complexes. The origin of this rule is the favorable two-center three-electron bond that can form when an odd electron in a sterically accessible metal d-orbital interacts with an electron pair on an entering nucleophile. Besides simple substitution, these radicals can disproportionate, dimerize, and undergo insertion or atom abstraction reactions.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550191107
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  • 199
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    Rate constant for the reaction of OH radicals with dimethyl sulfide (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 1073-1082 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rate constants of the gas phase reaction of OH radicals with dimethyl sulfide (CH3SCH3) over the temperature range 260-393 K have been studied using the discharge flow-resonance fluorescence technique. The rate constants were fitted by the Arrhenius equation k = (11.8 ± 2.2) × 10-12 exp[-(236 ± 150)/T] cm3 molecule-1 s-1 with k = (5.5 ± 1.0) × 10-12 cm3 molecule-1 s-1 at 298 K. Our results are in good agreement with the lower range of values reported previously. The observation of a small positive activation energy agrees well with that reported by Hynes et al. The rate constant was not affected by the total pressure variation (0.8-3.0 torr) or by the addition of oxygen (up to 1 torr) in the flow tube.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/kin.550191204
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    Erratum (1987)
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 19 (1987), S. 1107-1107 
    Details
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Br atoms produced in a microwave discharge react abnormally rapidly with isobutane to produce HBr + t-Butyl. A VLPR study of the system at high Br atom concentration (Br ˜ 1013/cc) between 298 and 363 K permits one to separate the effects of excited atoms, Br* (2P1/2) from ground state atoms, Br (2P3/2). Rate constants for the latter agree well with bromination measurements and permit fixing ΔHƒ2980(tBu) at 9.5 ± 0.5kcal/mol in agreement with earlier work.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/kin.550191207
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