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  • Biochemistry  (150)
  • Wiley-Blackwell  (150)
  • Annual Reviews
  • Oxford University Press
  • Periodicals Archive Online (PAO)
  • 1980-1984  (150)
  • 1935-1939
  • 1984  (87)
  • 1981  (63)
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  • 1980-1984  (150)
  • 1935-1939
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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 58-62 
    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 and very rapid method for the calculation of electrostatic isopotential maps is proposed. The potential is composed of transferable bond fragments. According to chemical evidence, σ-, lone-pair, and π-bond contributions are considered. The computational work is proportional to the first power of the number of bond orbitals; therefore very large systems, such as enzymes or DNA, can be handled also. Transferability of bond orbital characteristics such as polarity, s character, and orientation is discussed. Though the absolute value of the potential is overestimated, trends obtained with STO-3G calculations are reflected correctly.
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  • 2
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 87-95 
    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 carboxylat anion, involved in the structure of numerous compounds of biological interest, participates in a number of intermolecular interactions involving water, cations, and other cellular constituents. A set of ab initio SCF computations have been carried out with an extended polarized basis set on HCOO-, its molecular electrostatic potential, and its interaction with Li+, Na+, K+, and H2O. The results are compared with those of a minimal good quality basis set. An evaluation of the basis set superposition error is made in the two basis as well as that of the contribution of the dispersion energy to the hydration. The analogies and differences in the nucleophilic character of the formate and the phosphate groups are discussed.
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  • 3
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 73-82 
    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 effect of the basis set superposition error (BSSE) on the calculated electronic structure of a molecular stacking complex is analyzed with the counterpoise correction method. The complex between para-hydroxyaniline (PHA) and formamidinium cation (FAM) is calculated ab initio with the STO-3G and Whitman-Hornback minimal bases, and with two split valence basis sets: 4-31G and STO-3G(D). When the counterpoise correction is applied, the charge redistribution in the PHA/FAM complex calculated with all four basis sets suggests that the complex is electrostatic in nature and that the main polarization is from the PHA toward FAM. The FAM cation is polarized away from the intermolecular region, thus causing further increase in the electrostatic interaction. This picture is not evident with the STO-3G related bases if the counterpoise correction is not applied. Thus, the BSSE in the charge redistribution is shown to be particularly large in the STO-3G basis and in the diffuse, split valence, STO-3G(D). Both these basis sets suffer from an inappropriate description of the core region. Where there is an improved description of the electron density in the core region, as in the calculations with the energy-optimized Whitman-Hornback basis and with the 4-31G basis, the counterpoise correction has only a very small effect on the charge redistribution. After the counterpoise correction is applied, the two minimal basis sets yield nearly identical charge redistribution results, as do the two split valence bases. It is therefore suggested that basis sets used in the calculation of molecular complexes might be classifiable according to criteria such as the degree of contraction and the quality of the description of angular polarization. This would help in the comparative evaluation of results obtained with different bases since minimal basis sets (or split valence bases) would become directly identifiable as groups yielding qualitatively similar results.
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  • 4
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981) 
    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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  • 5
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 149-156 
    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 geometry and energy of tetra-tert-butylethylene have been determined by the molecular mechanics method. A twisting of the double bond by 45.5° was found. The ground state of the molecule should be a singlet. The calculated strain energy is higher than those of tri-tert-butylmethane and tetra-iso-propylethylene, but the possibility of synthesis of the compound is not excluded.
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  • 6
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981) 
    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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  • 7
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 244-250 
    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 set of programs has been developed to calculate molecular spin-orbit interaction with Gaussian-type wavefunctions in connection with the popular GAUSSIAN 76 program. The spin-orbit contributions to the fine structure of O2 (X3∑g-), NH (X3∑-), and CH2 (X3B1) are evaluated with the standard STO-3G and 6-31G basis sets; for NH the influence of bond functions added to the latter basis set is also investigated. The results are compared to values previously obtained with other types of basis sets.
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 273-277 
    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 semianalytic method is presented for computing the concentration distribution in enzyme-substrate fast reaction systems. By means of this method, not only can much computation work be saved but a semianalytic expression for the concentration distribution will be obtained. This expression is very useful for analysis and discussion of the kinetic characteristics of this kind of reaction system.
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  • 9
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 251-260 
    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 and SCF-CI calculations have been performed to investigate substituent effects on ground- and excited-state properties of 4-R-pyrimidines, and to compare these with substituent effects in 2- and 4-R-pyridines, with R including the π donating and σ withdrawing groups CH3, NH2, OH, F, and C2H3 and the σ and π electron-withdrawing groups CHO and CN. Substitution leads to significant changes in the internal angles of the pyrimidine ring, which are independent of the nature of the substituent. The geometry of the pyrimidine ring is more sensitive to substitution in the 4 position than the pyridine ring geometry is to substitution in either the 2 or the 4 position. The isodesmic reaction energies for substituent transfer from the 4 position of pyrimidine to the 2 or 4 position of pyridine indicate that all R groups except CN have a relative stabilizing effect in pyrimidine. The presence of a π donating group leads to an increase in the n→π* transition energy of 4-R-pyrimidines, while the π withdrawing group CN leads to a decrease in the transition energy relative to pyrimidine. Orbital energy differences and virtual excitation energies tend to correlate with n→π* transition energies of 4-R-pyrimidines with saturated R groups, but such correlations are masked by π conjugation, n orbital interaction, and configurational mixing when the unsaturated groups C2H3, CHO, and CN are present. The electronic effects of a π donating group are stronger when the group is bonded to pyrimidine than to pyridine, but those of a π withdrawing group are weaker when the group is bonded to pyrimidine.
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  • 10
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    Journal of Computational Chemistry 2 (1981), S. 376-383 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum chemical calculations of polymers and solids, especially on an ab initio level, represent a large computational task and therefore necessitate efficient computing methods. This is particularly true for the oscillatory integrals appearing in such calculations. For these integrals efficient integration methods based both on the Chebyshev series and the spline representation of the nonoscillatory part of the integrand are considered; they are found far superior compared with more standard integration rules. In two- and three-dimensional systems, directions with maximum oscillatory behavior can be selected along which these new efficient integration techniques can be used advantageously. The ideas are illustrated by Hückel crystal orbital (HCO) bond orders for the polyacetylene chain and the graphite layer. In the latter example, also, a method for the integration of oscillatory integrands with a singularity is given.
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  • 11
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 402-409 
    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 Monte Carlo algorithm, capable of simulating numerically the time and space dependence of chemical concentrations in a reacting system, is presented. This method is used to study the phenomenon of trigger waves in the Oregonator model of the Belousov-Zhabotinskii reaction, including the diffusion of species X and Y in one dimension. The results show that a small disturbance in a homogeneous mixture can grow into a chemical (trigger) wave propagating in space at constant velocity. The dependence of this velocity on several factors is studied, namely, initial concentrations, the diffusion of Y, and the stoichiometry of the autocatalytic step of the model. A comparison of the Monte Carlo results with a previous simulation also is discussed.
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  • 12
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 416-421 
    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 with the STO-3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water-water interactions and nonadditivity effects are also significant.
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  • 13
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    Journal of Computational Chemistry 2 (1981), S. 422-432 
    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 with the STO-3G basis set have been performed to investigate substituent effects on the structures and stabilization energies of water:4-R-pyrimidine complexes, with R including CH3, NH2, OH, F, C2H3, CHO, and CN. Except for the cyclic water:4-aminopyrimidine complex hydrogen bonded at N3, these complexes have open structures stabilized by a nearly linear hydrogen bond formed through a nitrogen lone pair of electrons. When hydrogen bonding occurs at N3, the complexes may have planar or perpendicular conformations depending on the substituent, but when hydrogen bonding occurs at N1, the perpendicular is generally slightly preferred, and there is essentially free rotation of the 4-R-pyrimidine. Primary substituent effects alter the electronic environment at the nitrogens, and tend to make N3 a poorer site for hydrogen bonding than N1, primarily because of a stronger π electron-withdrawing effect at N3. However, the relative stabilities of complexes hydrogen bonded at N1 and N3 are also influenced by secondary substituent effects, which may be significant in stabilizing complexes bonded at N3. Substitutent effects on the structures and stabilization energies of the water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyridine complexes. Configuration interaction calculations indicate that although absorption of energy by the pyrimidine ring destabilizes the water:4-R-pyrimidine complexes, these may still remain bound in the excited n → π* state. This is in contrast to the fate of open water:2-R-pyridine and water:4-R-pyridine complexes, which dissociate in this state.
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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 460-469 
    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 conformational behavior of the C-terminal neurotensin pentapeptide, Arg-Pro-Tyr-Ile-Leu OH [NT(9-13)], was investigated using empirical energy calculations. A special aim was to display the specific contribution of each residue to induce conformations able to interact with biological receptors. Restrictions were then introduced in intramolecular interactions involving the Arg side chain and the terminal COOH group. The stablest conformations include in the order of decreasing stability: a distorted helical form for the C-terminal tetrapeptide, a (Pro2-Tyr3) β turn I, an α helix, an extended form, and a (Tyr2-Ile3) β turn III, which are energetically rather close (ΔE 〈 3 kcal/mol). The NT(9-13) peptide appears then as a rather flexible molcule with a noteworthy ability of adaptation to a substrate. Extended forms would be in agreement with a zipper model of interactions with receptors, whereas folded forms involving helices and β, γ turns would support a lock and key model. The specific contribution of side chains, specially those of Tyr and Arg residues as well as the key position of the Pro residue emerge clearly from this study.
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  • 15
    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 crystal orbital calculations have been performed on regular polyethylene chains applying basis sets of minimal and double-zeta quality. Relative stabilities of periodic all-trans, all-gauche, and alternating trans-gauche conformers have been evaluated, including extensive geometry optimization. Potential curves for a simultaneous rotation around C—C single bonds from the all-trans to the all-gauche conformation have been computed applying the rigid-rotor approximation, the flexible-rotor approximation, and an additional reoptimization of C—C distances. A rigid-rotor potential curve from the all-trans to the alternating trans-gauche conformation has been computed as well. Results obtained are compared with ab initio calculations on butane and pentane and with semiempirical and empirical force-field studies on polyethylene.
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  • 16
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    Journal of Computational Chemistry 5 (1984), S. 64-71 
    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 degrees of conformational freedom of poly L-D β-helical chain are analyzed consistent with the helical parameters of gramicidin A structure. From conformational energy calculations, “helical librations” that can be sustained by this structure are described and the energy of libration as a function of the cavity size is presented. Two different modes of conformational change are identified corresponding to librations of all L-D-peptide units or all D-L-peptide units while retaining the helical parameters. Such helical librations are considered relative to conformational perturbations due to the presence of an ion in the channel.
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  • 17
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    Journal of Computational Chemistry 5 (1984), S. 84-88 
    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 use of symmetry coordinates (SC) in geometry optimization is discussed. A computer program incorporating the use of sc, together with analytical calculation of the gradient and quadratic acceleration, is described. Also reported are careful test results on a series of small molecules and typical results with a long series of molecules up to quite large size (40-60 atoms).
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  • 18
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    Journal of Computational Chemistry 5 (1984), S. 89-103 
    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 technique to generate electrostatic contours on a steric surface is presented and applied to the presentation of molecules that interact with DNA. A set of electrostatic points at predetermined values along with their derivatives are obtained on the steric contours as they are generated. The steric contours are generated in a set of parallel planes. Points with given electrostatic values are then connected between and within the contours mathematically with a Taylor's expansion and two rules: the first to tentatively line up points that can be connected, and the second to check to insure that the remaining points can be connected. This method insures that contours will not cross by requiring that a possible connection of two points leaves an even number of remaining points for each electrostatic value in isolated regions of unused points bounded by points that have already been connected. The hidden line algorithm used previously to draw molecules in a space-filling model within the context of steric contours is applied to the complete problem of the presentation of a molecule bound to DNA with steric contours in parallel planes, and with electrostatic contours drawn on this steric surface.
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  • 19
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    Journal of Computational Chemistry 5 (1984), S. 115-121 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Analysis of a Gaussian potential function suitable for modeling degenerate bending vibrations in weakly bound molecular complexes is presented. Approximate eigenvalues and eigenvectors are obtained by application of perturbation theory. Comparison to the “exact” eigenvalues obtained via a numerical solution shows that the first- and higher-order perturbation corrections are consistent with variational principles.
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  • 20
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    Journal of Computational Chemistry 5 (1984), S. 170-174 
    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 algorithm is described for generating atomic Cartesian coordinates of conformations of macrocyclic molecules possessing exact rotational or rotation-reflection symmetries. A fragment representing the asymmetric unit of the molecule is suitably oriented in space, and then a symmetry operator is applied to generate the initial coordinates of the molecule. An empirical force field of interatomic interactions is used to generate equilibrium conformations. Results of calculations performed on two cyclic polylactones and one crown ether using this approach are given. They reveal that symmetric conformations of these molecules are often preferred. Since the latter conformations are probably responsible for the specialized properties of these molecules, this method should facilitate doing theoretical studies on these kinds of compounds.
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  • 21
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    Journal of Computational Chemistry 5 (1984), S. 182-185 
    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 principles of a new method, the method of zero determinants, are described which can be used for the determination of the number of exponentials in accurate, multiexponential decay curves, as well as for the smoothing of multiexponential experimental data. It is based on the idea that the determinant of an overdetermined data matrix for accurate data is zero. The method is not limited by mathematical approximations, and thus uncovers the decay curve hidden in the data set.
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  • 22
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    Journal of Computational Chemistry 5 (1984), S. 197-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Group equivalents which are useful for converting energies derived from ab initio calculations into enthalpies of formation have been obtained. They allow ΔHf to be estimated from 6-31G* energies with an uncertainty on the order of ±2 kcal/mol.
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  • 23
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    Journal of Computational Chemistry 5 (1984), S. 207-215 
    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 effect of different exponents, Slater, Burns, Clementi, and Best Limited Molecular Orbital (BLMO) on the approximate one-electron property expectation values from minimum basis-set calculations is reported for Roothaan-Hartree-Fock (RHF), neglect of diatomic differential overlap (NDDO), and maximum overlap method (MOM) calculations on FH, CO, and LiH.
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  • 24
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    Journal of Computational Chemistry 5 (1984), S. 225-229 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Changes of electronic charge distribution following the lowest singlet n-π* transitions of benzaldehyde, benzamide, benzoic acid, the phthalaldehydes, pyridine, and the diazines have been examined using the CNDO-S/CI method. A Singlet n-π* transition is found as a general rule to direct electronic charges to the para position of the atom in the ring that carries the lone pair or to which the substituent carrying the lone pair is attached.
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  • 25
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    Journal of Computational Chemistry 5 (1984), S. 261-262 
    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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  • 26
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    Journal of Computational Chemistry 5 (1984), S. 241-247 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous investigators have shown that statistical mechanical averages for configuration-dependent physical properties of long unperturbed polyoxyethylene chains are sensitive to the gauche-trans energy difference for rotation about C—C bonds. Agreement between theory and experiment could be obtained only by significant adjustment of this energy away from values predicted by semiempirical conformational energy computations. The present work examines the success of MM2 in evaluating conformational properties of long unperturbed polyoxyethylene chains. Calculations are performed which identify the rotational isomers, and their energies, for the indicated bonds in CH3OCH2CH2O—CH2—CH2—OCH2CH2OCH3. These energies are used to assign statistical weights utilized in the configuration partition function for a rotational isomeric state chain with symmetric threefold interdependent rotations. The customary generator matrix scheme is employed to evaluate the mean-square unperturbed end-to-end distance, mean-square unperturbed dipole moment, and their temperature coefficients. Contrary to computational schemes employed previously, MM2 is found to provide an estimate of the gauche-trans energy difference for rotation about C—C which is in harmony with the known dimensions and dipole moments of the unperturbed polymer. MM2 also provides good estimates for most of the other parameters required in the rotational isomeric state treatment. A notable exception is provided by the gauche-trans energy difference for rotation about the C—O bond. This energy difference is overestimated by MM2.
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  • 27
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    Journal of Computational Chemistry 5 (1984), S. 272-279 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Various algorithms for evaluating nonbonded interactions in molecular dynamics (MD) simulations of macromolecular systems are considered, and a combination of two techniques using a space grid for finding neighbor atoms is proposed. The application of grid search techniques to nonrectangular periodic systems is discussed. Finally, the computing time required by different algorithms is compared on a Cray-1 vector processing computer as well as on a CDC Cyber 170/760 sequential computer. Neighbor list techniques turn out to be faster than the grid search techniques for the systems considered here. However, storage requirements may exclude the use of neighbor list techniques for large systems. Finally, MD of complex macromolecular systems turned out to be about 4-14 times faster on a Cray-1 than on a Cyber 170/760.
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  • 28
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    Journal of Computational Chemistry 5 (1984), S. 280-287 
    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 is described which evaluates the second-order Møller-Plesset energy using the integral list formed by HONDO 5. In this program use may be made of full molecular symmetry for most common point groups, even if they contain two-dimensional representations. The algorithm for the integral transformation may also be applied to other methods beyond Hartree-Fock. Some numerical results and timings are presented.
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  • 29
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    Journal of Computational Chemistry 5 (1984), S. 571-575 
    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 conformational analysis was applied to the study of the variation of heats of formation (HOF) and geometrical parameters of small-ring propellanes. As expected, the calculated HOF is the smallest for [4,4,4] propellane I and the largest for [2,2,2]propellane X. In spite of the different trends exhibited by the strain energy components, the calculated HOF values may be reproduced within a simple additivity scheme. The calculated bridgehead-bridgehead bond length is the longest for [2,2,2]propellane (1.655 Å), lowers with increasing molecular size, and is equal to 1.558 Å for [4,4,4]propellane. In agreement with experimental findings the latter value is significantly larger than the standard value of 1.54 Å typical for unstrained hydrocarbons. Other calculated geometrical parameters as well as HOF values cannot be compared with experimental and/or theoretical results since there is a lack of reliable experimental data. Surprisingly, [2,2,2]propellane was found to be more flexible than the less strained bicyclo[2,2,2]octane.
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  • 30
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    Journal of Computational Chemistry 5 (1984), S. 581-588 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three newly defined information theoretic topological indices, namely “degree complexity (Id),” “graph vertex complexity (HV),” and “graph distance complexity (HD)” along with three other information indices have been used to study their discriminating power of 45 trees and 19 monocyclic graphs. It is found that the newly defined indices have satisfactory discriminating power while HD has been found to be the only index to discriminate all the graphs studied.
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  • 31
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    Journal of Computational Chemistry 5 (1984), S. 589-597 
    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 formula for the first derivative of the MCSCF energy with respect to a nuclear coordinate is reviewed. The efficient utilization of symmetry in programs employing symmetry-adapted basis functions is described: Advantages that are also obtained for higher derivatives and for gradients of nonself-consistent wave functions are briefly discussed. Using CASSCF wave functions, the method is applied to the question of nonlinearity in the heavy atom chain of propadienone (CH2CCO).
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  • 32
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    Journal of Computational Chemistry 5 (1984), S. 606-611 
    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 transition states involved in the hetero-Diels-Alder reactions of acrylaldehyde-ethylene and butadiene-formaldehyde systems were characterized using an efficient method of locating a saddle point on the energy surface of two coordinates calculated with MINDO/3 method. It has been shown that parallel transition and rotation of the conjugate coordinate frame lead to the reaction and orthogonal coordinate system on the hyperbolic paraboloid energy surface. It was concluded that the method we adopted is similar to the “X-method” but is much simpler to apply to real reaction systems.
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  • 33
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    Journal of Computational Chemistry 2 (1981), S. 1-6 
    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 barriers on the MINDO/3 reaction paths for π and σ approaches to concerted cycloaddition of methylene to s-cis-1,3-butadiene are analyzed by a new energy decomposition scheme and compared to the results of published extended Hückel calculations. The relatively small (6 kcal) preference for the σ approach is essentially based on next-nearest-neighbor (1,3) resonance interactions, which are stabilizing in the σ but destabilizing in the π approach. Both routes are characterized by large distortion energies (mainly disrotation at the diene termini in the case of the π approach) and nonbonded repulsions. The excessive magnitude of both of these effects ultimately derives from the weak pericyclic binding which prevails at initial diene geometries, especially the pericyclic topology involving the methylene LUMO. Although previous work has emphasized the contribution of closed-shell repulsions to the barrier, no such effect is explicitly included in MINDO. The closed-shell repulsions to which the extended Hückel barrier has been solely attributed are shown to involve next-nearest-neighbor (antiaromatic) resonance interactions.
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  • 34
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    Journal of Computational Chemistry 2 (1981), S. 14-19 
    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 empirical potential, EPEN, has been used to establish the structures of isolated hydrogen-bonded clusters in methanol. The most stable configuration of the dimer is found to have a trans near-linear form, whereas the most stable forms of the trimer and tetramer are cyclic. Charge interactions in the tetramer make it the most stable, in terms of energy per hydrogen bond, of these three species. These results are in conformity with various types of experiment. Other species of dimer, trimer, and tetramer, corresponding to local energy minima, have also been identified.
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  • 35
    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 C=O bond length and fC=O,C=O, the corresponding harmonic stretching force constant, are calculated ab initio using the 4-31G basis set (augmented by polarization functions on the sulfur and chlorine) with full geometry optimization for the monosubstituted carbonyl compounds RCHO, where R = H, CHO, CH=CH2, CO2H, CH=CHOH, OH, OC(=O)OH, OOH, S—H, Li, F, Cl, and NH2. Straight-line relationships are found in plots of ln[fC=O,C=O] vs. ln[rC=O] for the series of compounds in which carbon atoms and oxygen atoms are bonded directly to the carbonyl carbon, in accordance with the empirical expression f = C′/rn. The slopes and intercepts give n = 7.62 and 6.47, C′ = 62.6 and 48.6, for the lines with carbon and oxygen as the atom bonded directly to the carbonyl carbon, respectively. The point for formaldehyde lies very close to the C line, whereas the points for SH, Li, F, Cl, and NH2 lie closer to the O line.
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  • 36
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    Journal of Computational Chemistry 2 (1981), S. 161-167 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parameters for sulfoxides used in force field MM1 were modified to be incorporated into force field MM2. The conformations of ten alkyl sulfoxides were then calculated using MM2 with these new parameters. The alkyl groups used were methyl, ethyl, isopropyl, and t-butyl. It was found that of the many possible conformations for these compounds, only one or two stable conformers exist, and that the number of these conformers agrees with the number of reported S—O stretching frequencies in almost every case. No apparent correlation between the vibration frequency and the molecular structure was found.
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  • 37
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    Journal of Computational Chemistry 2 (1981), S. 182-187 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Harmonic force fields have been calculated for the planar hydrogen-bonded ring conformer of β-hydroxyacrolein, cCc, which is the most stable, and the chain conformer, cCt, generated by 180° rotation of O—H about the C—O bond axis. The equilibrium structure obtained using the 4-31 G basis set with full geometry optimization was employed in each case. Selected force constants for the bonds directly concerned in the formation of the ring from the chain structure, and the increments in going from the one to the other, are compared with the values for the corresponding conformers of performic and formic acids. As the ring size increases from four in trans-formic acid, to five in cis-cis-performic acid and to six in the cCc conformer of β-hydroxyacrolein there is a successive increase in the mechanical strength of the hydrogen-bridging unit. The energy changes for the chain → ring conversion do not follow this progression: performic acid is out of order. But, since a force constant is a localized bond property, whereas the energy changes are determined not only by interactions specific to the hydrogendonor and hydrogen-acceptor groups but also by interactions involving more distant parts of the molecule, the force constants for the bonds directly concerned in the formation of the hydrogen bridge provide a less ambiguous basis for comparing the strength of the intramolecular hydrogen bonding.
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  • 38
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    Journal of Computational Chemistry 2 (1981), S. 188-199 
    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 with the STO-3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water-uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N1—H and O2, N3—H and O2, and N3—H and O4. Open structures form at O4, N1—H, and N3—H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N1—H and the cyclic one at N1—H and O2. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N3—H and a cyclic structure at N3—H and O4. The third cyclic structure at N3—H and O2 collapses to the “wobble” dimer at N3—H and O4. The two “wobble” dimers are significantly more stable than the open dimer formed at O4, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N1—H than N3—H, owing to a more favorable molecular dipole moment alignment when association occurs through H1. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water-uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.
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  • 39
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    Journal of Computational Chemistry 2 (1981), S. 287-303 
    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 computer program we have been developing to build models of molecules and calculate their interactions using empirical energy approaches. The program is sufficiently flexible and general to allow modeling of small molecules, as well as polymers. As an illustration, we present applications of the program to study the conformation of actinomycin D. In particular, we study the rotational isomerism about the D-Val-, L-Pro, and L-Pro-Sar amide bonds as well as comparing the energy and structure of the Sobell model and the x-ray structure of actinomycin D.
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  • 40
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    Journal of Computational Chemistry 2 (1981), S. 304-323 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrostatic potentials and Mulliken net atomic charges were calculated from STO-3G, 6-31G, and 6-31G** SCF-MO wavefunctions for hydrogen fluoride, water, ammonia, methane, acetylene, ethylene, carbon dioxide, formaldehyde, methanol, formamide, formic acid, acetonitrile, diborane, and carbonate ion. In each case optimized net atomic charges (potential-derived charges) were also obtained by fitting the electrostatic potentials calculated directly from the wavefunctions in a shell enveloping the molecules outside of their van der Waals surfaces. The electrostatic potentials calculated from the potential-derived charge distributions were then compared with the defined quantum mechanical electrostatic potentials and with the electrostatic potentials of the Mulliken charge distributions.
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  • 41
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    Journal of Computational Chemistry 2 (1981), S. 356-360 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: At high levels of ab initio theory (6-31G*//4-31G), the most stable C4H42+ isomer is indicated to be the nonplanar cyclobutadiene dication (1a); the planar form, 1b, is indicated to be 7.5 kcal/mol less stable. The second most stable C4H42+ isomer, the methylenecyclopropene dication, is indicated to prefer the perpendicular (2a) over the planar (2b) arrangement by 7 kcal/mol. The “anti van't Hoff” cyclo-(HB)2C=CH2 system (4), isoelectronic with 2, also prefers the perpendicular conformation (4a), and retains the C=C double bond. The linear butatriene dication (3) is the least stable C4H42+ species investigated. The perpendicular (D2d) arrangement (3a), permitting double allyl cationlike conjugation, is preferred over the planar D2h form (3b) by 26 kcal/mol. The heat of formation of the most stable form of C4H42+, 1a, is estimated to be 623-640 kcal/mol. This species should be thermodynamically stable toward dissociation into smaller charged fragments.
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  • 42
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New estimates of Hartree-Fock limit energies (ERHF) for selected AH and AHn hydrides, diatomic and linear polyatomic molecules have been made utilizing ESCF values recently reported in the literature for HF, N2, CO, NH3, and CH4 which are very close to the respective limits. These new values have been used to investigate the applicability of Ermler and Kern's procedure for estimating ERHF: i.e., a factor f is first evaluated from data for reference molecules, where f = ERHF/ESCF, which is then used with ESCF values for other molecules to obtain their ERHF values. f has been evaluated for three groups of reference molecules—HF, H2O, NH3, CH4, N2, and CO; CH4, C2H2, C2H4, and C2H6; and C2H2, HCN, and N2—utilizing ESCF data in the literature for many Gaussian-type orbital (GTO) basis sets together with some new values calculated at the (9,5,1) to (13,8,2) levels. Trends in the variation of f within each group of reference molecules from one basis set to another, and the trends in f from one group of reference molecules to another, are discussed in detail. To minimize the influence of these effects in an ERHF estimate it is recommended that the f value should be derived from reference molecules which possess a similar combination of structural features, i.e., bonded hydrogen, single, double, or triple bonds, and the number of lone-pair electrons. Further calculations show that an f value based on data for closed-shell molecules is not applicable to open-shell species.
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  • 43
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    Journal of Computational Chemistry 2 (1981), S. 53-57 
    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 charge distributions along the CH bonds of methane, ethylene, and acetylene have been obtained by numerical integration of 6-31G** wavefunctions. Several criteria for assigning electron populations to carbon and hydrogen lead to negative charge on H for methane and ethylene and a positive charge on H for acetylene. These results are contrasted with the charges derived from the μCHeff obtained from infrared intensity measurements. The difference between the results from infrared intensities and from the electron density calculations has been shown to result from incomplete orbital following in the molecular deformation and the creation of a “bent-bond” moment. Its magnitude has been estimated.
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  • 44
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    Journal of Computational Chemistry 2 (1981), S. 83-86 
    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 modified integral package for evaluation of two-electron integrals over Gaussian basis functions is described. Modifications are implemented in the MOLECULE program system and are especially suited for the study of large molecules and molecular complexes.
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  • 45
    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 Gaussian-type basis sets for molecular calculations are usually prepared by an atomic SCF program in which spherical coordinates are used. On the other hand, many molecular SCF and CI programs are written by using the Cartesian coordinates and as a result six-membered d-type functions (x2, y2, z2, xy, yz, zx)e-γr2 are often used. They contain one additional 3s function which does not exist in the atomic calculation. Therefore, we shall have an incorrect, deeper molecular binding energy, unless we readjust the atomic total energy by adding the 3s orbital to the original basis set. Some examples are shown in the case of Cu2 molecule, where we have found that the correction is quite appreciable, which was overlooked in previous work.
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  • 46
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    Journal of Computational Chemistry 2 (1981), S. 108-125 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Compact contracted Gaussian basis sets introduced in the preceding article are tested for ab initio molecular calculations on molecules containing third-row atoms (Na through Cl). It is found that the effect of splitting valence orbitals is essential for these molecules and addition of polarization functions to split basis sets can yield computed geometries, spectroscopic constants, and atomization energies in close agreement with the result of near Hartree-Fock calculations.
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  • 47
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    Journal of Computational Chemistry 2 (1981), S. 157-160 
    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 is presented for the calculation of partition coefficients of solutes in water lipid systems. Log P values are calculated based on the charge densities of the atoms as determined by quantum mechanical methods. In this article, the results have been obtained from charge densities calculated by two methods: MINDO/3 and Hückel-type calculation based primarily on topology. Results are favorably compared with those obtained by fragment analysis.
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  • 48
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    Journal of Computational Chemistry 2 (1981), S. 177-181 
    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 empirical potential EPEN/2 has been used to establish the structures of isolated hydrogen-bonding ammonia clusters. The most stable forms of the dimer have a linear or near-linear structure. The trimer has a closed structure with zero dipole moment. Two stable tetramer forms were found: one with a closed structure and zero dipole moment in agreement with experimental findings, and one with a pyramidal structure with nonzero dipole moment which may be an artifact of the EPEN/2 potential. The relation of the dimer structures to the limited available experimental information is discussed.
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  • 49
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF-CI calculations on uracil and water-uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C4—O group, while the second is associated with excitation of the C2—O group. In the first n → π* state, hydrogen bonds at O4 are broken, so that the open water-uracil dimer at O4 dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N3—H and a cyclic structure at N3—H and O4 in the ground state, collapses to a different “wobble” dimer at N3—H and O2 in the excited state. The third dimer, a “wobble” dimer at N1—H and O2, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O2 are broken in the second n → π* state, the three water-uracil dimers remain bound. The “wobble” dimer at N1—H and O2 changes to an excited open dimer at N1—H. The “wobble” dimer at N3—H and O4 remains intact, and the open dimer at O4 is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.
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  • 50
    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 with a minimal (STO-3G) basis set on a number of sulfur-containing molecules are used to show that Koopmans' theorem and minimal basis calculations may be a simple but adequate way of obtaining inner-shell ionization potentials and chemical shifts of large molecules. The x-ray photoelectron spectrum of (C6H5)2SNSO2C6H4CH3 is discussed with reference to an ab initio SCF minimal basis calculation on the model molecule H2SNSO2H.
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  • 51
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    Journal of Computational Chemistry 2 (1981), S. 225-230 
    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 molecular orbital (MO) calculations for two series of sulfur-oxygen compounds are reported: the S(IV) system of SO2, H2SO3, HSO3-, and SO32-, and the S(VI) system of SO3, H2SO4, HSO4-, and SO42-. Geometries about the sulfur atoms were optimized using the STO-3G* basis set; energies at these geometries were computed by the STO-3G and 44-31G basis sets both with and without five Gaussian d orbitals on S. The sulfur-oxygen bond lengths and the angles about the central atoms agree fairly well with experiment. The stabilization energy associated with the addition of the d orbitals was found to be a constant amount per bond (ca. 54 and 28 kcal mole-1 in the minimal and extended bases, respectively) in hypervalent compounds. The isomer HSO3- was predicted to be more stable than SO2(OH)-, but the reverse was true for HSO2(OH) compared to SO(OH)2. The deprotonation energies for the acids and the hydration energies for the oxides also were computed and discussed with reference to experimental data.
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  • 52
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    Journal of Computational Chemistry 2 (1981), S. 261-265 
    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 molecular orbital calculations are reported for H2S, its radical cation, and the H2SSH2+ radical cation. At the MP2/4-31G level the S—S three-electron bond is 2.85 Å long, and has a dissociation energy of 31.2 kcal mole-1. The performance of MNDO semiempirical molecular orbital theory is compared with the ab initio results.
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  • 53
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    Journal of Computational Chemistry 2 (1981), S. 266-272 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Significant improvements in calculational efficiency and capability with the self-consistent electron pairs (SCEP) method has resulted from several new computational developments. A new procedure for constructing the important internal Coulomb and exchange operators has substantially reduced the preiteration time. A general scheme for utilizing molecular symmetry has been used to advantage in reducing the number of pair functions and external operators that must be found explicitly at each iteration. A projection operator tool has been implemented and found to be quite effective at minimizing the number of iterations required at some point on a potential energy surface when an SCEP wavefunction exists for some nearby point. These and other improvements in the program construction have yielded sizable reductions in time for some representative test cases, including water and a potential energy curve for formaldehyde. The new SCEP program also performs low-order perturbation theory treatments and coupled electron pair approximation (CEPA) calculations using the same operator approach. The usefulness of the approach is demonstrated by very large scale calculations on the stability of the two interstellar glycine conformers. These calculations involve the variational treatment of 82,205 symmetry-adapted singly and doubly substituted configurations involving 225 internal electron pairs.
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  • 54
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    Journal of Computational Chemistry 2 (1981), S. 347-355 
    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 spin-orbit coupling operator is brought into a simplified form through a convenient choice of origin for the orbital angular momentum operator. The eigenvalue problem of the Hamiltonian that includes the spin-orbit (SOC) operator as a perturbation is solved by means of a linear variational procedure in the basis of the spin-pure molecular eigenstates. Test calculations on benzophenone are presented and the results are compared to experiment. We discuss the minimal size of the spin-pure variational basis needed to achieve stable results as well as the amount of single-excitation configurational mixing needed to describe the spin-pure molecular eigenstates.
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  • 55
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    Journal of Computational Chemistry 2 (1981) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 56
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    Journal of Computational Chemistry 5 (1984) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 57
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    Journal of Computational Chemistry 5 (1984), S. 24-34 
    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 problem of predicting the mode of binding of a small molecule to a receptor site on a protein. One plausible approach, given a rigid molecule and its geometry, is to search directly for the orientation in space that maximizes the degree of contact. The computation time required for such a naive procedure is proportional to n3m3, where n is the number of points in the site where binding can occur, and m is the number of atoms in the ligand. We give an alternative, combinatorial approach, in which only “contact-no-contact” criteria are considered. We relate this problem to the well-known combinatorial problem of finding cliques in a graph and show that we can use a solution to the clique problem not only to solve our original problem, but also the problem of avoiding energetically unfavorable matches. Our experience with this method indicates that the computation time required is proportional to nm2.8, with a lower constant of proportionality than that of the naive procedure.
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  • 58
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    Journal of Computational Chemistry 5 (1984), S. 35-43 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiempirical molecular orbital calculations by the MNDO method are reported for sulfur rings and chains S3 through S8, for the corresponding dications, S22+ through S82+, and for S4+. The MNDO method seems quite successful in predicting the geometries of neutral catenated sulfur molecules, even the unusual bond-length alternation and extent of coplanarity in cyclo-S7. In contrast to hydrocarbon rings, for which its prediction of strain is erratic, MNDO is consistent in its calculated strain energies in small cyclosulfur rings; unfortunately all the strain energies are overestimated by 70%. As a consequence of this error, the method must be considered unreliable in its predictions of structures for the dications Sn2+, since many of these ions could potentially exist as strained bicyclic systems. In addition, MNDO appears to have difficulty handling long, partial SS σ bonds, as are found to occur in S82+. It may be for this reason that MNDO predicts, apparently incorrectly, that the open-chain isomers of Sn2+ are more stable than are any of the cyclic forms, at least for S52+ to S82+. With respect to neutral Sn molecules, however, the MNDO predictions appear more reliable than ab initio molecular orbital (MO) calculations using small basis sets without polarization functions and without configuration interaction (CI). However, MNDO apparently underestimates by about a factor of two the strength of the three-electron π bonds present in the terminal links of sulfur diradical chains.
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  • 59
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The Floating Point Systems, Inc. Model 164 Attached Processor (FPS-164) is a high-speed, pipelined, parallel processor designed for large-scale scientific computation. Benchmark studies of operations common in quantum chemistry codes are discussed and the performance of the FPS-164 is compared with other commonly available computers. A complete system of electronic structure codes has been implemented on the FPS-164 using the Fortran-77 cross-compiler and calls to optimized vector and matrix routines. The conversion of a generalized valence bond (GVB) code illustrates the strategy adopted to adapt Fortran codes to the FPS-164. A typical production example, a large scale (GVB) and configuration interaction calculation on the vinyl radical, shows a net throughput equivalent to nearly nine VAX 11/780 computers.
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    Journal of Computational Chemistry 5 (1984), S. 104-112 
    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 discuss the implementation and computational efficiency of one approach to adjusting the Hill equation of adsorption to a set of empirical data, pointing out some aspects that seem to be valid in the general case. The approach consists basically of minimizing squares of deviations of the adsorbed amounts, which are numerically computed in terms of the empirical pressures and the parameters. Hill's equation is dealt with as a prototype of nonlinear equations seldom used by chemists because none of their variables can be set free.
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    Journal of Computational Chemistry 5 (1984), S. 113-113 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 62
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    Journal of Computational Chemistry 5 (1984), S. 129-145 
    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 present an approach for deriving net atomic charges from ab initio quantum mechanical calculations using a least squares fit of the quantum mechanically calculated electrostatic potential to that of the partial charge model. Our computational approach is similar to those presented by Momany [J. Phys. Chem., 82, 592 (1978)], Smit, Derissen, and van Duijneveldt [Mol. Phys., 37, 521 (1979)], and Cox and Williams [J. Comput. Chem., 2, 304 (1981)], but differs in the approach to choosing the positions for evaluating the potential. In this article, we present applications to the molecules H2O, CH3OH, (CH3)2O, H2CO, NH3, (CH3O)2PO2-, deoxyribose, ribose, adenine, 9-CH3 adenine, thymine, 1-CH3 thymine, guanine, 9-CH3 guanine, cytosine, 1-CH3 cytosine, uracil, and 1-CH3 uracil. We also address the question of inclusion of “lone pairs,” their location and charge.
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  • 63
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: A collection of programs which aid in the use of group theory has been developed for the Apple II. The programs automate much of the tedious algebra necessary to generate character tables and representation matrices from the properties of the operators chosen to generate the group. At the same time, the presentation of intermediate results provides a schematic guide to the procedures by which groups are constructed. The choice of generators is not limited to the reflections, rotations, and inversions, which are the familiar features of chemical group theory. Any generator representable as a permutation may be treated; thus general permutation groups and Longuet-Higgins groups may be studied. As an illustration we describe the states of beryllium borohydride, which require a form of Longuet-Higgins group theory.
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  • 64
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    Notes: The geometries of several conformations of ethyl and isopropyl formate were optimized by the ab initio gradient method on the 4-21G level. The calculations are in agreemnt with the existence of two conformers of ethyl formate of nearly equal energy. The COCC torsional angle in one is anti (180°) and in the other is gauche (about 80°). The equilibrium configuration of the isopropyl group in the formate is found to be unsymmetrical, with a COCH torsional angle of about 40°. A second minimum of torsional energy, at COCH = 180°, is 1.2 kcal/mol less stable than the unsymmetrical form. The calculations demonstrate the tranferability of internal rotational-potential parameters and of conformationally dependent geometrical trends between ethyl and isopropyl formate. There is good agreement between the calculated results and empirical potential-energy functions and rotational constants determined from microwave spectroscopy.
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  • 65
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    Journal of Computational Chemistry 5 (1984), S. 200-206 
    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 conformational characteristics of allylamine were investigated by the ab initio STO-3G basis set. The results indicate that the molecule exists in a number of stable conformations through rotations about the CC—NH and CC—CN bonds. The TE (trans-CCNLP, LP representing lone-pair electrons, and eclipsed-CCCH) is the most stable, while TC (trans-CCNLP and cis-CCCN), GE (gauche-CCNLP and eclipsed-CCCH), G′C(gauche′-CCNLP and cis-CCCN), and G′E (gauche′-CCNLP and eclipsed-CCCH) conformations are less stable, respectively, by 0.41, 0.67, 0.92, and 1.14 kcal mol-1. These results are in general consistent with previous experimental results. Rationale for the conformational characteristics and order of stabilities are explored.
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    Journal of Computational Chemistry 5 (1984) 
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    Journal of Computational Chemistry 5 (1984), S. 217-224 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MINDO/3 calculations were performed on the potential energy profile involved in the equilibrium \documentclass{article}\pagestyle{empty}\begin{document}$$ \begin{array}{l} {\rm crotonic acid \rightleftharpoons isocrotonic acid \rightleftharpoons but-3-enoic acid} \\ {\rm (III)\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(II)\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(I)} \\ {\rm } \,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\to {\rm propene + CO}_{\rm 2} \\ \end{array} $$\end{document}Optimized structures of stable molecules and transition states have been determined; thermodynamic stabilities of pure acids and barriers indicated that the equilibrium can be set up from any acids. It was argued that direct decarboxylation is only conceivable from (I), since in this process a 1, 5-hydrogen shift is involved, whereas a higher barrier process of 1, 3-hydrogen shift is required in direct decarboxylations from other acids. Direct interconversion of (I) and (III) was found to be unfavorable due to a high barrier involved.
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    Journal of Computational Chemistry 5 (1984), S. 252-260 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas are given for convergence-accelerated lattice sums over all intermolecular Coulomb, London, and repulsive interactions. Their implementation in the consistent force field is described. Optimum values of convergence constant and summation limit are found for r-12, r-9, and r-1 interaction terms. Energy minimization in all degrees of freedom, also intramolecular, for crystals of Ar, KCl, and C2H6 is reported.
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    Journal of Computational Chemistry 5 (1984), S. 263-271 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of correlation energy on the relative stability of different structures and dissociation products of complex lithium beryllohydrides has been investigated. The adequacy of the method employed (third-order Möller-Plesset perturbation theory) and the basis set dependence have been assessed. Trends of the correlation energy according to the molecular structure have been discussed, and the validity of an additive scheme based on electron pair contributions has been tested.
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    Journal of Computational Chemistry 5 (1984), S. 326-335 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The tendency of C—O bond lengths to change as a function of the torsional angles at an acetal carbon has been included in a new version of the molecular mechanics program MM2(82), based on the observed behavior of molecules of this class as indicated by ab initio calculations and experimental structural data. The experimental geometries and energies are reasonably well reproduced.
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    Notes: We have used energy minimization calculations to study a number of conformations of uncomplexed valinomycin. In certain cases, x-ray diffraction atomic coordinates were used directly as input coordinates, while in other cases, conformations were found by altering the x-ray coordinates prior to minimization. Five calculated conformations are reported along with their relative energies. The conformation found theoretically to be the most stable is in agreement with earlier, cruder calculations, but does not correspond to the predominant conformation observed in nonpolar solvents. A possible rationale is presented.
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    Journal of Computational Chemistry 5 (1984), S. 353-357 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of determining the amount of reactant present in the steady state of a reaction-diffusion problem with pth order reaction kinetics and slab geometry can be achieved by solving the boundary value problem \documentclass{article}\pagestyle{empty}\begin{document}$$ \begin{array}{l} u''(x) = \phi ^2 u^p (x),\,\,\,\,\,\,\,\,\,\,\,\,{\rm 0 〈 }x{\rm 〈 1} \\\\ u'(0) = 0{\rm }\,\,\,\,\,\,\,\,\,\,\,\,u(1) = 1 \\ \end{array} $$\end{document} where u is a normalized (dimensionless) concentration, and φ is the Thiele modulus. By considering the related nonlinear eigenvalue problem \documentclass{article}\pagestyle{empty}\begin{document}$$ \begin{array}{l} y''(x) = \lambda y^p (x),\,\,\,\,\,\,\,\,\,\,\,\,{\rm 0 〈 }x{\rm 〈 1, }\,\,\,\,\,\,\,p{\rm 〈 0} \\\\ y'(0) = 0,{\rm }\,\,\,\,\,\,\,\,\,\,\,\,y(1) - y'(1) = 0 \\ \end{array} $$\end{document} and constructing a sequence of functions that converges monotonically to y(x), solutions of the original boundary value problem are obtained for the negative exponent case.
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    Journal of Computational Chemistry 5 (1984) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 5 (1984), S. 427-440 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The force constants and compliance constants of methyl, silyl, and germyl fluoride, chloride, bromide, and iodide have been calculated by the iterative consistency method. Using the force fields so obtained, centrifugal distortion constants, Coriolis coupling constants, and mean amplitudes of vibration have been computed and compared with experimental data, where available.
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  • 75
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The structures and conformational energies of several conformations of propanoic acid, 2-methylpropanoic acid, and butanoic acid were determined by geometrically unconstrained ab initio gradient geometry refinement on the 4-21G level. The O=C—C—C torsional potentials of propanoic acid and butanoic acid are found to be practically identical. There are energy minima at 0° and 120°, and maxima in the 60° region and at 180°. In 2-methylpropanoic acid there are energy minima at H—C—C=O dihedral angles of 0° and 120°, and maxima at 60° and 180°. The exact positions of the maxima and minima of the H—C—C=O torsional potential of 2-methylpropanoic acid are found to be predictable from propanoic acid rotational-potential parameters. Some conformationally dependent, local geometry trends are discussed.
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    Journal of Computational Chemistry 5 (1984), S. 457-465 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Fortran-77 computer program has been written which calculates the rotation-torsion profile of a vibronic transition using an asymmetric top/free internal rotor Hamiltonian. The program is applicable to any molecule that is composed of a frame portion of C2v symmetry a free rotor portion of C3v symmetry. Rotation-torsion bands of A-, B-, and C-type contours may be calculated within an assumed Boltzmann distribution of rotation-torsion level populations or within a specified non-Boltzmann distribution of torsional level populations.
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    Journal of Computational Chemistry 5 (1984), S. 500-505 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The organization of a computer code to compute transition moments between states described in different orbital basis sets (a nonorthogonal transition moment) is described. The code is organized to minimize redundant work and allow efficient threshold checking. Three sample calculations are presented.
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    Journal of Computational Chemistry 5 (1984), S. 523-527 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A numerical procedure is described and tested for the determination of solvent sites in a crystal hydrate from computer simulation results. The method does not require the computation of density distributions.
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  • 79
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: In order to provide additional data for the relative lengths of methyl-C—H bond distances in acetyl derivatives, which are difficult to determine accurately by the conventional tools of structural chemistry, the geometries of CH3COH, CH3COF, CH3COCH3, CH3COOH, and CH3CONH2 were determined by ab initio SCF gradient optimization at the 5-31G** level and compared with previous 4-21G results. For acetaldehyde 6-311G4* calculations were also performed and the correlated methyl-C—H stretching potential energy functions were determined. It is found that the calculated differences between the in-plane and out-of-plane methyl-C—H bonds are practically independent of the computational scheme. The calculated results are in contrast to relative bond lengths obtained by some vibrational overtone spectroscopic studies, but are in perfect agreement with C—H bond length differences determined from isolated C—H stretching frequencies of partially deuterated compounds. The reliability of the latter, and other spectroscopic data concerning the assignment of the methyl-C—H vibrations are critically analyzed. On the basis of the available evidence we conclude: (1) the methyl groups of the CH3C(=O)X systems here discussed contain one strong (in-plane) and two weak (out-of-plane) C—H bonds; (2) intensities of C—H local mode spectra do not provide a reliable basis for assignment to individual bonds.
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    Journal of Computational Chemistry 5 (1984), S. 555-561 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A generalization of the quantum chemical definition of valence of atoms in molecules is suggested. Valence is considered as expectation value of diatomic parts of density operators. It appears as a sum of contributions from occupied orbitals of all atomic pairs that contain the reference atom. This definition is applicable on self-consistent-field (SCF) and configuration interaction (CI) level in any atomic orbitals (AO) basis. Its usefulness is demonstrated in an application to special molecules. Photoelectron spectroscopy and reactivity is discussed in this context.
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    Journal of Computational Chemistry 5 (1984), S. 299-306 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanical calculations for hetero-substituted hydrocarbons present certain difficulties that are not encountered in dealing with hydrocarbons. Ways are proposed to overcome such difficulties, sometimes by two-step or iterative computation. The following topics are considered: fitting the force field by using data from studies in solution; ways to estimate atomic charges or, alternatively, bond moments; ways to account for field effects upon atomic charges and bond moments.
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  • 82
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: It is shown that a Lagrange multiplier method to constrain one or several internal coordinates, or averages and combinations of these, is easily implemented in a molecular mechanics computer program that uses Newton-Raphson (NR) minimization. Results are given for constraints on nonbonded distances and torsion angles. When a potential energy surface is to be explored, it is much better to constrain the average of three torsion angles around a bond than to constrain a single torsion angle. Certain conversions can only be achieved when averages of torsion angles around different bonds are constrained. Combinations of constraints have been applied to evaluate differences between calculated and observed geometries and to obtain transition states for relatively large molecules from results for smaller molecules at relatively low costs. The efficieny of the combination of the Lagrange multiplier method and NR minimization in terms of computing time can be rated as good.
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    Journal of Computational Chemistry 5 (1984), S. 343-348 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical calculations by the combined empirical force-field (EFF)-extended Hückel molecular orbital (EHMO) approach confirm that octalene and benzo-|c|-octalene present π-bond fixation with a common single bond between the cyclooctatetraene and cyclooctatriene fragments, whereas the structure of dibenzo-|c, j|-octalene is characterized by a central double bond. The dynamic behavior of these compounds is discussed and the interconversion energy barriers are calculated; the inversion of the cyclooctatriene ring is faster than that of the cyclooctatetraene ring in octalene, but it is slower in benzo-|c|-octalene.
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  • 84
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    Journal of Computational Chemistry 5 (1984), S. 349-352 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas fully exploiting the periodicity symmetry of the electron density of polymers are deduced. They are shown to lead to efficient algorithms for the evaluation of Coulomb and exchange interactions in those systems.
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  • 85
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    Journal of Computational Chemistry 5 (1984), S. 363-373 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimized monopole expansions for the subunits of the nucleic acids are developed by a reparametrizatio of the Hückel-Del Re procedure designed to reproduce closely the electrostatic properties obtained with precise overlap multipole expansions. It is shown that satisfactory values of both potential and field may be obtained for different DNA conformations and for a transfer RNA. The charge redistribution occuring between the subunits upon forming the nucleic acids is also investigated by ab initio calculations and accounted for in developing the new parametrization.
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  • 86
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    Journal of Computational Chemistry 5 (1984), S. 381-386 
    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 nitrogen protonation energies of the imino bases HN=CHR, where R is H, CH3, NH2, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree-Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree-Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree-Fock nitrogen protonation energies of the imino bases HN=CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O=CHR.
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  • 87
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    Journal of Computational Chemistry 5 (1984), S. 395-410 
    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 geometry and energy of 2-aza-1,3-butadiene and 2,3-diaza-1,3-butadiene have been calculated using the 6-31G* basis set as a function of the CNCC and CNNC dihedral angles, respectively. With the 2-aza derivative potential minima are located at 0° (trans) and at about 130° for a gauche structure approximately 9.5 kJ mol-1 less stable than the trans. Potential maxima are at about 75° giving a gauche barrier height of approximately 19 kJ mol-1 relative to the trans structure, and at 180° (cis) giving a barrier height of approximately 14.5 kJ mol-1 relative to the 130° gauche structure. With the 2,3-diaza derivative the gauche barrier has disappeared and there are a series of gauche structures in the region 70°-100° of almost equal energy 12.5-15 kJ mol-1 less stable than the trans. In addition the cis barrier is much greater, nearly 70 kJ mol-1 relative to the trans structure. Inclusion of electron correlation, accounting for about 50% of the correlation energy, produces no significant changes in the shape of the potential energy curves. There are systematic and progressive changes in almost all the geometrical parameters as the =CH— groups in butadiene are replaced by =N—. The outward tilt and compression within the methylene groups show adverse steric interactions to be operative in the cis structures. The values of Vnn indicate that gauche structures of both the 2-aza and the 2,3-diaza derivatives near the cis structure are more compact (as with butadiene), and gauche structures of the 2-aza derivative near the trans structure are less compact (as with butadiene). Originating in the changes in bond lengths and bond angles, rotation-independent nuclear-nuclear interactions again play an important role.
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  • 88
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    Journal of Computational Chemistry 5 (1984), S. 441-450 
    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 number of force fields of the molecular mechanics type have been tested for their ability to represent as an energy minimum, the observed crystal structure for three cyclic hexapeptides, cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), and cyclo-(-D-Ala-D-Ala-Gly-Gly-Gly-Gly-). The most effective force field tested was that recently proposed by Kollman and co-workers, notwithstanding its use of “united” atoms for CH, CH2, and CH3 groups. Fields proposed by Levitt, and adaptations of that of Scheraga and co-workers, were also effective. Force fields in which hydrogens bonded to electronegative atoms were not specified explicitly were less accurate in representation.
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  • 89
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    Journal of Computational Chemistry 5 (1984), S. 466-470 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Structures and relative energies were obtained for the hydrogen bonded dimers of formamide and formamidic acid using the 3-21G basis set. A double proton transfer transition state is claimed to link these two dimers. While the structure of the transition state was intermediate between those of the two dimers, the energy was only 7.6 kJ/mol greater than the less stable formamidic acid dimer. The activation energy from the formamide dimer side of the reaction was found to be 125 kJ/mol of dimer. A similar transition state was found for the amidine dimer system. The activation energy for this model reaction was found to be 66.9 kJ/mol of dimer.
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  • 90
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    Journal of Computational Chemistry 5 (1984), S. 486-499 
    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 set of procedures and guidelines are presented for the estimation of bond length, bond angle, and torsional potential constants for molecular mechanics force fields. The force field constants are ultimately derived by “subtracting” nonbonded molecular mechanics energies from corresponding molecular orbital energies using a model compound containing the chemical structure to be parameterized. Case study examples of bond length, bond angle, and torsional rotation force field parameterizations are presented. A general discussion of molecular mechanics force field parameterization strategy is included for reference and completeness. Finally, a curve-fitting program to generate force field parameters from raw data is given in Appendix I.
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  • 91
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    Journal of Computational Chemistry 5 (1984) 
    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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  • 92
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    Journal of Computational Chemistry 5 (1984), S. 528-534 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Potential energy surface for methyl fluoride dimer has been studied theoretically with ab initio molecular orbital method, using a 4-31G basis set. Dimer dissociation energies, Mulliken electronic populations, and dipole moments were obtained.
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  • 93
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    Journal of Computational Chemistry 5 (1984), S. 562-570 
    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 previously published scheme of estimating atomic charges in haloalkanes is extended to include olefines, alcohols amines, acids, ethers, and amides. In the conjugated systems the effects of mesomeric transfer of charge are explicitly included. Generally good agreement with the observed dipole moments of these compounds and their substituted derivatives is found. The atomic charges so obtained are compared with those of other semiempirical and quantum-mechanical calculations for the amide group. The charges so obtained fall within the range of values obtained by these other schemes, supporting the general validity of this approach.
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  • 94
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    Journal of Computational Chemistry 5 (1984), S. 576-580 
    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 vibration-rotation eigenvalues EvJ are sought for very high levels (up to dissociation) of a diatomic potential. The method used is the recent “eigenvalue equation” method [Kobeissi et al., J. Comput. Chem., 4, 218 (1983)] which dissociates the determination of the eigenvalue from that of the eigenfunction. A new mathematical formulation for any numerical potential is presented, which reduces the problem to the use of a single recurrent formula. A numerical application to the model potential used by Cashion [J. Chem. Phys., 39, 1872 (1963)], up to v = 23, gives results equal to the exact eigenvalues to approximately 10-14 cm-1. Another application to the model potential used by Johnson [J. Chem. Phys., 67, 4086 (1977)], up to v = 60, gives similar results.
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  • 95
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    Journal of Computational Chemistry 5 (1984), S. 535-547 
    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 ab initio self-consistent-field (SCF) algorithm taking into account all the features of the one-dimensional translational periodicity and the helical symmetry is presented. This algorithm includes the long-range correction to the Coulomb potential and is designed to calculate the band structure of periodic one-dimensional polymers (planar or helical). Its efficiency in terms of computing time and numerical accuracy is tested via applications on a (LiH)n chain, polyethylene, and four conformers of polypropylene.
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  • 96
    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 molecular orbital calculations are reported for complexes of hydroxide and methoxide anions with water and methanol. The basis set dependence of the results is carefully considered for HO- ⃛ H2O. 4-31G and 6-31G* calculations yield similar geometrical predictions; however, the 6-31G* basis set is superior for computing dissociation energies. Further extension to the 6-31G** level provides little change. The dissociation energies for the complexes range from 25 to 37 kcal/mole with hydroxide ion and methanol acting as the strongest base and acid. The difference in gas phase acidities of water and methanol is halved by the introduction of one solvent molecule.
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  • 97
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    Journal of Computational Chemistry 2 (1981), S. 20-29 
    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 molecular orbital structures and energies of B2F4, B2Cl4, N2O4, and C2O42- have been calculated for both perpendicular D2d and planar D2h rotamers. The experimental trend toward greater preference for the D2d forms in going from B2F4 to B2Cl4 is reproduced. N2O4 favors the planar conformation, although the rotation barrier is overestimated at the theoretical levels used. The oxalate dianion is calculated to be more stable in the D2d conformation; the experimental planar arrangement in the solid may be due to crystal packing forces. The preferences for one conformation over another are small; analysis indicates that different effects may predominate in each case: π stabilization for B2F4, hyperconjugation for B2Cl4, lone-pair interactions for N2O4, and electrostatic repulsions for C2O42-.
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  • 98
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Means by which the Onsager theory of dielectrics may be modified in a general way to include important structurally nonspecific electrical effects exercised at or near the cavity boundary are developed and discussed. In essence they rely upon extraction of limiting numerical solutions of the Laplace equation potentials for multiple shells approximating regions of smoothly varying permittivity surrounding the dipole-containing cavity. The results of several such modifications, which usefully retain the original reaction and cavity field forms, are applied to evaluate the dielectric constants of polar solvents acting as support media for mean-space-charge attenuation of intracavity electrical interactions, and in correlation of isolated molecule and condensed phase properties of formally nonassociated solvents. For the most part such predictions and correlations are found to be improved by a wide variety of physically reasonable continuity functions. Where they are not, more rational patterns of deviations consistent with possible modes of intramolecular charge transfer and weak intermolecular association in formally nonassociated liquids are detected. Some limited comparisons with particle- and structure-dependent theories, e.g., the mean spherical model and discrete lattice formulations, also suggest that the present permittivity modifications can effectively simulate important short-range nonspecific liquid ordering effects. Various factors relating to possible adaption of the limit procedures developed to other inhomogeneous dielectric medium calculations are also briefly outlined.
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  • 99
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    Journal of Computational Chemistry 2 (1981), S. 363-367 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SCF Hartree-Fock calculations are used to predict properties of the guanidinium fragment present in tetrodotoxin and saxitoxin, toxins known to block the sodium channels of the nerve cell membrane. The results, in terms of net atomic charges and geometries, are compared to similar calculation results obtained for the Na+-H2O complex.
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  • 100
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    Journal of Computational Chemistry 2 (1981), S. 384-391 
    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 a view of using data on solutions and liquids for parameter fitting in molecular mechanical force fields, Abraham's theory of solvation is incorporated in the force field procedure. Geometries and bond moments are estimated internally, partial account being taken of bond-bond induction, and used to calculate the intramolecular electrostatic energy, dipole moment, and the dipole and quadrupole terms in the solvation energy. Three dielectric constants are used, one for the solute in the vapor, one for the solution, and one for the intramolecular space through which dipole-dipole interactions take place. Examples are given, including such where computation differs with measurement, to illustrate the performance of the scheme.
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