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  • 1995-1999
  • 1985-1989  (133)
  • 1880-1889
  • 1987  (133)
  • Biochemistry  (133)
  • 101
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080431
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  • 102
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080430
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  • 103
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080502
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  • 104
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080503
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  • 105
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080505
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  • 106
    Electronic Resource
    Electronic Resource
    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 
    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 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080607
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  • 107
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080612
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  • 108
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080611
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  • 109
    Electronic Resource
    Electronic Resource
    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 
    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 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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  • 110
    Electronic Resource
    Electronic Resource
    On color polynomials of Fibonacci graphs (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 956-959 
    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 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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  • 111
    Electronic Resource
    Electronic Resource
    Fast matrix multiplication (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 960-964 
    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: 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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  • 112
    Electronic Resource
    Electronic Resource
    Voronoi binding site models (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 943-955 
    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 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080703
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  • 113
    Electronic Resource
    Electronic Resource
    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 
    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: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080706
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  • 114
    Electronic Resource
    Electronic Resource
    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 
    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 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080702
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  • 115
    Electronic Resource
    Electronic Resource
    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 
    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: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080707
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  • 116
    Electronic Resource
    Electronic Resource
    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 
    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: 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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  • 117
    Electronic Resource
    Electronic Resource
    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 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2/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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  • 118
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    Electronic Resource
    MNDO Calculations on [n]metacyclophanes (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1154-1169 
    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: 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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  • 119
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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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  • 120
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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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  • 121
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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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  • 122
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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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  • 123
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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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  • 124
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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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  • 125
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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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  • 126
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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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  • 127
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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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  • 128
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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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  • 129
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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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  • 130
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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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  • 131
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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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  • 132
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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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  • 133
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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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