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  • 1990-1994
  • 1985-1989  (133)
  • 1987  (133)
  • Biochemistry  (133)
  • 101
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 282-290 
    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.
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  • 102
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 158-169 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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.
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  • 103
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 291-295 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 104
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 296-306 
    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.
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  • 105
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 307-312 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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.
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  • 106
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 333-340 
    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.
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  • 107
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 313-323 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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.
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  • 108
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 324-332 
    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.
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  • 109
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 350-357 
    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.
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  • 110
    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.
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  • 111
    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.
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  • 112
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 367-374 
    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.
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  • 113
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 375-379 
    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.
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  • 114
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 380-388 
    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.
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  • 115
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 389-396 
    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.
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  • 116
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 397-411 
    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.
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  • 117
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 412-419 
    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.
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  • 118
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 420-427 
    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.
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  • 119
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 428-435 
    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.
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  • 120
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 499-509 
    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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  • 121
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 562-562 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 122
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 581-603 
    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.
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  • 123
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 604-617 
    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.
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  • 124
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 618-624 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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.
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  • 125
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    Journal of Computational Chemistry 8 (1987), S. 625-635 
    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.
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  • 126
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 801-809 
    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.
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  • 127
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 956-959 
    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.
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  • 128
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 960-964 
    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.
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  • 129
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    Journal of Computational Chemistry 8 (1987), S. 1025-1039 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: With advances in computer architecture and software, Newton methods are becoming not only feasible for large-scale nonlinear optimization problems, but also reliable, fast and efficient. Truncated Newton methods, in particular, are emerging as a versatile subclass. In this article we present a truncated Newton algorithm specifically developed for potential energy minimization. The method is globally convergent with local quadratic convergence. Its key ingredients are: (1) approximation of the Newton direction far away from local minima, (2) solution of the Newton equation iteratively by the linear Conjugate Gradient method, and (3) preconditioning of the Newton equation by the analytic second-derivative components of the “local” chemical interactions: bond length, bond angle and torsional potentials. Relaxation of the required accuracy of the Newton search direction diverts the minimization search away from regions where the function is nonconvex and towards physically interesting regions. The preconditioning strategy significantly accelerates the iterative solution for the Newton search direction, and therefore reduces the computation time for each iteration. With algorithmic variations, the truncated Newton method can be formulated so that storage and computational requirements are comparable to those of the nonlinear Conjugate Gradient method. As the convergence rate of nonlinear Conjugate Gradient methods is linear and performance less predictable, the application of the truncated Newton code to potential energy functions is promising.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
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  • 130
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1084-1089 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular orbital calculation by the MINDO/3 method are reported for 50 compounds used as solvents in chemical reactions. Relationships between various parameters of electronic structure and molecular properties such as dipole moment, polarizability and Taft solvent parameters are presented. Comparison between experimental values of π* and calculated values is given.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
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  • 131
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1179-1190 
    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
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  • 132
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1191-1198 
    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
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  • 133
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    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1232-1232 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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