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  • Biochemistry  (519)
  • Wiley-Blackwell  (519)
  • Copernicus
  • 2020-2024
  • 1985-1989  (519)
  • 1
    Electronic Resource
    Electronic Resource
    Basis set quality versus size II. Approximate GTO wave functions for second row transition metal atoms (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 495-502 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis sets ranging in size from (16, 10, 7) to (20, 14, 11) have been derived for the atoms Y-Cd. Separate sets represent the energy optimized wave functions for each of the s2dn, s1dn+1, and s0dn+2 configurations. The energies from the largest sets are within 3 mhartrees of the values obtained in numerical Hartree-Fock calculations. Reasonable Hartree-Fock s2dn- s1dn+1 and s2dn- s0dn+2 excitation energies may be obtained either using the largest basis sets, or using d-orbitals optimized for the s0dn+2 configurations. The basis sets are slightly unbalanced in favor of the s-functions and in disfavor of the d-functions, but various alternative basis sets may be derived by combining parts of the five parent sets. The convergence of radial expectation values is discussed.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100407
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  • 2
    Electronic Resource
    Electronic Resource
    A method for fitting a smooth ribbon to curved DNA (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 529-551 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for fitting a smooth ribbon representation of DNA structures is proposed. Following a review of the relevant definitions for classical linear helical DNA and generalizations to curving helices, a parameterization of smooth ribbons is given, which leads to tractable expressions. In addition it suggests a new way to define twist, tilt, and roll for a base step that is free of the ambiguities caused by noncommutativity of finite rotations. A least squares fitting criterion for ribbons is then proposed. In some cases the optimal ribbon with respect to this criterion is not unique. This problem is analyzed, and the circumstances in which it can occur are specified. To resolve the nonuniqueness problem, a variational description of the optimal ribbon is proposed, namely the ribbon of lowest elastic energy achieving a specified level of fit with respect to the least squares criterion. The appropriate level of fit is decided using distances of backbone atoms from fitted ribbon axes. Theoretical tests of the fitting methodology are presented, and as a sample application a smooth ribbon is fit to an existing experimental structure.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100411
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  • 3
    Electronic Resource
    Electronic Resource
    Masthead (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100501
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  • 4
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    Theoretical studies in molecular recognition: Rebek's cleftThis article is dedicated to Lou Allinger on the occasion of his 60th birthday and in honor of his many contributions to computational chemistry. (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 595-602 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular recognition in Rebek's cleft was studied with the MM2 force field. A new computational protocol was used to determine the free energies of substrate binding to this topologically unique model receptor. The energies and structural features of substrate-receptor complexes reveal that molecular recognition involves ammonium ion binding to the interior of the cleft and aromatic π-stacking on the exterior of the cleft.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100502
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  • 5
    Electronic Resource
    Electronic Resource
    A molecular mechanics (MM2) study of Furan, Thiophene, and related compounds (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 635-647 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular mechanics calculations reported earlier for nitrogen heterocycles have now been extended to include the title compounds, and related molecules. It is in general possible to calculate these structures with an accuracy that compares favorably with experiment.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100506
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  • 6
    Electronic Resource
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    Announcement (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 748-748 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100515
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  • 7
    Electronic Resource
    Electronic Resource
    Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability-directed search procedure (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 798-816 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure that finds the most probable conformational states of a protein chain is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. The conformation of the entire chain is represented by a sequence of single-residue conformational states; the distinct conformations in this representation are called “chain-states.” The first article in this series described a procedure that computes tripeptide conformational probabilities from the amino acid sequence using pattern recognition techniques. The procedure described in this article uses the tripeptide probabilities to estimate the probabilities of the chain-states. The chain-state probability estimator is a product of conditional and marginal probabilities (obtained from the tripeptide probabilities), with a penalty factor to eliminate conformations containing α-helices and ∊-strands of excessive length. The probability estimator considers short-range conformational information, medium-range sequence information and some simple long-range information (through the restrictions on helix and strand lengths). Energy minimization calculations can be carried out in the region of conformational space corresponding to a particular chain-state. By selecting the most probable chain-states, the search can be focused on the most probable, or “important,” regions of the conformational space. These energy calculations are described in the third article of the series. The complete procedure described by the three articles is called PRISM, for pattern recognition-based importance sampling minimization.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100604
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  • 8
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    Pattern recognition in the prediction of protein structure. III. An importance-sampling minimization procedure (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 817-831 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure that generates random conformations of a protein chain, and then applies energy minimization to find the structure of lowest energy, is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. Each state corresponds to a rectangular region in the φ, ψ map. The conformation of an entire chain is then represented by a sequence of single-residue conformational states. The distinct “chain-states” in this representation correspond to multidimensional rectangular regions in the conformational space of the whole protein. A set of highly-probable chain-states can be predicted from the amino acid sequence using the pattern recognition procedure developed in the first two articles of this series. The importance-sampling minimization procedure of the present article is then used to explore the regions of conformational space corresponding to each of these chain-states. The importance-sampling procedure generates a number of random conformations within a particular multidimensional rectangular region, sampling most densely from the most probable, or “important,” sections of the φ, ψ map. All values of φ and ψ are allowed, but the less-probable values are sampled less often. To achieve this, the random values of φ and Φ are generated from bivariate gaussian distributions that are determined from known X-ray structures. Separate gaussian distributions are used for proline residues in the α and ∊ states, for glycine residues in the α, ∊, α*, and ∊* states, and for ordinary residues involved in 29 different tripeptide conformations. Energy minimization is then applied to the randomly-generated structures to optimize interactions and to improve packing. The final energy values are used to select the best structures. The importance-sampling minimization procedure is tested on the avian pancreatic polypeptide, using chain-states predicted from the amino acid sequence. The conformation having the lowest energy is very similar to the X-ray conformation.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100605
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  • 9
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    Analytical energy derivatives and normal modes in force fields employing lone-pair pseudoatoms (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 856-860 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas are derived for analytical first and second energy derivatives with respect to nuclear coordinates in molecular mechanics force fields employing lone-pair pseudoatoms. These derivatives may further be used for the calculation of normal modes and vibrational frequencies while properly accounting for the presence of pseudoatoms. The equations are applied using the MM2 force field to calculate the vibrational spectrum of methanol to illustrate the applicability of the method. The results are compared to both experiment and a numerical approximation in which small masses are assigned to the lone-pair pseudoatoms.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100608
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  • 10
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    Long-Range proton-proton coupling constants. I. Propanic coupling involving a methyl group 4JMeH (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 887-895 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An equation is formulated on the basis of theoretical INDO/FPT calculations which describes the angular dependence of the propanic long-range coupling constant 4JMeH in substituted HCCCH3 fragments. This equation is a truncated Fourier series in the torsion angle φ, HCCMe, which takes into account the dependence of the Fourier coefficients on the bond angle θ, CCMe. The substituent effects are assumed to be additive. Some parameters in the equation may be obtained from the 4JMeH couplings in propane and neopentane derivatives. The calculated effect upon 4JMeH of changes in the bond angle θ is significant and it seems to be in part the cause of some effects which have been attributed to conformational dependence.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100705
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  • 11
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    Molecular mechanics of peroxides. II. Cyclic compounds (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 911-920 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformations of various cyclic peroxides have been determined using a molecular mechanics force field developed by the authors and previously applied to linear peroxides. Comparison of the results with those of experimental and ab initio studies shows that this force field may be employed without correction for cyclic compounds.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100708
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  • 12
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    Coupled cluster method with first-order correlation orbitals versus multireference configuration interaction method. Accurate calculations for HF, H2O, and NH3 (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 928-934 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article shows that with our Hylleras-functional based method1 for generating correlation orbitals, we can determine electronic structures for small polyatomic systems very accurately. The procedure is ab initio, uses conventional Gaussian basis sets, and solves the electronic Schrödinger equation with the coupled cluster method. A comparison is made with MRCI results obtained in equivalent basis sets for the HF, H2O, and NH3 molecules.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100710
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  • 13
    Electronic Resource
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    Masthead (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100801
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  • 14
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    Computational strategies for the optimization of equilibrium geometries and transition-state structures at the semiempirical level (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 939-950 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several improvements have been made to the gradient algorithms commonly used to optimize equilibrium and transition-state geometries at the semiempirical level. A gradient algorithm derived from a combination of a variable metric method (Davidon-Fletcher-Powell/Broyden-Fletcher-Goldfarb-Shanno) and Pulay's direct inversion in the iterative subspace method for geometry optimization (GDIIS) is compared with the variable metric method combined with an accurate linear search algorithm. The latter method is used routinely in the standard semiempirical program packages, MNDO, MOPAC, and AMPAC. The combined variable metric and GDIIS algorithm is also compared with GDIIS which uses a static metric. The performance of these algorithms is examined for a wide range of systems with respect to both choice of coordinate system (for cyclic molecules) and guess for the initial Hessian. The results show that the GDIIS method is up to ca. 40% more efficient than the variable metric combined with accurate line search algorithm: however, the exact savings vary depending on the coordinate system and initial Hessian. For noncyclic systems, variable-metric GDIIS is usually equal or superior to static-metric GDIIS, and consistently performs ca. 30% more efficiently than the variable metric combined with accurate line search algorithm. For the optimization of cyclic molecules, an improved estimate of the initial Hessian has increased the efficiency by at least a factor of two. Greater efficiencies (usually 〉40%) are also obtained when static-metric GDIIS is used to refine the geometry after the initial application of a transition-state search based on the variable metric combined with line search algorithm. On the basis of these results, we recommend several changes to the algorithms as currently implemented in the standard semiempirical program packages.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100712
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  • 15
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    Molecular symmetry and ab initio calculations. I. Symmetry-matrix and symmetry-supermatrix (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 957-962 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article the matrix elements can be grouped into classes by means of the molecular symmetry. By introducing the concepts of symmetry-matrix and symmetry-supermatrix and determining their operation rules, the storage of the supermatrix can be asymptotically reduced by a factor of ca. g2 (g is the order of the molecular symmetry group) and the calculation of Fock matrix during each SCF cycle can be reduced proportionally. Besides, by using the DIIS method combined with the symmetry-matrices, the convergence behavior for highly symmetric molecules can be improved.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100714
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  • 16
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    The dynamics of gallamine: A potent neuromuscular blocker. A determination by quantum mechanics and molecular dynamics (i) in vacuo studies (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 975-981 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100803
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  • 17
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    Validation of the general purpose tripos 5.2 force field (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 982-1012 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular mechanics force field implemented in the Sybyl program is described along with a statistical evaluation of its efficiency on a variety of compounds by analysis of internal coordinates and thermodynamic barriers. The goal of the force field is to provide good quality geometries and relative energies for a large variety of organic molecules by energy minimization. Performance in protein modeling was tested by minimizations starting from crystallographic coordinates for three cyclic hexapeptides in the crystal lattice with rms movements of 0.019 angstroms, 2.06 degrees, and 6.82 degrees for bond lengths, angles, and torsions, respectively, and an rms movement of 0.16 angstroms for heavy atoms. Isolated crambin was also analyzed with rms movements of 0.025 angstroms, 2.97 degrees, and 13.0 degrees for bond lengths, angles, and torsions respectively, and an rms movement of 0.42 angstroms for heavy atoms. Accuracy in calculating thermodynamic barriers was tested for 17 energy differences between conformers, 12 stereoisomers, and 15 torsional barriers. The rms errors were 0.8, 1.7, and 1.13 kcal/mol, respectively, for the three tests. Performance in general purpose applications was assessed by minimizing 76 diverse complex organic crystal structures, with and without randomization by coordinate truncation, with rms movements of 0.025 angstroms, 2.50 degrees, and 9.54 degrees for bond lengths, angles and torsions respectively, and an average rms movement of 0.192 angstroms for heavy atoms.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100804
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  • 18
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    A theoretical study of solvation energies of FCH2COO-, FCH2COOH, and F2CHCOO- (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 1031-1037 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A continuum and a discrete-continuum models are used to determine the solvation energies of FCH2COO-, FCH2COOH, and F2CHCOO-. For the anions, the continuum model provides results closer to the experiment, while for the acid, the addition of one water molecule improves the continuum-only energy.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540100807
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  • 19
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    Basis sets for molecular interactions. 1. Construction and tests on (HF)2 and (H2O)2 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 663-673 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis set superposition error (BSSE) remains one of the major difficulties besetting current ab initio calculations of molecular interactions. Despite the widespread notion that lowering of the BSSE to negligible magnitude requires extremely large basis sets, we show that simple modifications of basis sets of only moderate size (e.g., 6-31G**) can accomplish the same end at much reduced computational expense. These modifications include reoptimization of the orbital exponents within the framework of the relevant molecules, plus addition of a single diffuse shell of sp orbitals on nonhydrogen centers. Subsequent addition of a second set of d-functions further lowers the SCF BSSE, bringing it below 0.1 kcal/mol for both (HF)2 and (H2O)2. It is notable that addition of the latter d-functions without prior reoptimization of the valence orbitals produces the opposite effect of an increase in the BSSE. Although the MP2 BSSE is also substantially decreased by the above modifications, it appears difficult to reduce this quantity below about 0.4 kcal/mol.
    Additional Material: 6 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540080512
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  • 20
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    Basis sets for molecular interactions. 2. Application to H3N—HF, H3N—HOH, H2O—HF, (NH3)2, and H3CH—OH2 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 674-682 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Modifications of the standard 6-31G** basis set as recommended in the accompanying paper are found to markedly lower the basis set superposition error (BSSE) in the title complexes, in contrast to enlargement to a triple-ζ scheme or by addition of a diffuse sp shell or a second set of d-functions without prior optimization, all of which lead to BSSE increase. After appropriate correction for correlation and superposition effects, all basis sets (with the exception of the standard 6-31G** and 6-311G** with their very large BSSE) predict the cyclic geometry of NH3 dimer to be more stable than the linear arrangement. Correlation and BSSE can shift the equilibrium intermolecular distance in H3CH-OH2 by up to 0.4 Å. Failure to correct for superposition error leads to a drastic exaggeration of both the SCF and MP2 components of the interaction energy in this complex. Much better estimates are furnished by our recommended basis sets with their smaller superposition errors.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080513
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  • 21
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    Two approaches to the calculation of molecular resonance states: Solution of scattering equations and matrix diagonalizationPresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 683-699 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have analyzed two approaches to reproduce the resonance expansion of the scattering matrix appropriate for the calculation of molecular resonance states. The first is based on the resonance theory of Siegert-Humblet-Rosenfeld (SHR) and the second on the Fano-Feshbach formalism. The direct method of calculating the resonance expansion characteristics, devised on the basis of the SHR theory, makes it possible to obtain the energies and partial widths (detailed decay rate constants) of resonances. The Fano-Feshbach formalism, on the other hand, elucidates the resonance state as a concept and facilitates the interpretation of calculation results. The use of computational methods is illustrated by the study of the decay of a model triatomic system and of gas-phase nucleophilic substitution reactions. Used in the latter case is the division of all degrees of freedom of the reacting system into the adiabatic and dynamic ones along with an algorithm of inclusion of the restricted dynamical treatment in the calculation of reaction rate constants.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080514
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  • 22
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    The inverse problem of isomer enumerationPresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 700-717 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The present article addresses the problem of identifying the structure of a parent compound through its chemical fingerprints such as the various numbers of isomeric substitution patterns, along the lines of Kekulé when he arrived at his benzene formula. In a pioneering paper (1929), Lunn and Senior laid out the conceptual framework for the permutation group description of substitution isomerism. It remained, however, for Pólya's celebrated contribution (1937) to initiate the actual mathematical realization of their vision. Pólya supplied the tools for solving the isomer enumeration problem: given a (symmetrical) parent compound, enumerate its spectrum of substitution patterns. The converse problem, though ranked the more interesting one by Lunn & Senior, hardly received any mathematical attention. The present article offers a complete and effective solution.
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    Molecular graphs as topological objects in spacePresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 718-726 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Stereochemistry deals primarily with distinctions based on rigid geometry, e.g., bond angles and lengths. But some chemical species have molecular graphs (such as knots, catenanes, and nonplanar graphs K5 and K3.3) that reside in space in a topologically nontrivial way. For such molecules there is hope of using topological methods to gain chemical information. Viewing a molecular graph as a topological object in space makes it unrealistically flexible; but if one proves that a certain graph is “topologically chiral” or that two graphs are “topological diastereomers,” then one has ruled out interconversion under any physical conditions for which the molecular graph still makes sense. In this paper, we consider several kinds of topological questions one might ask about graphs in space, methology and results available, and specific topological properties of various molecules.
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    Hartree Fock instabilities of sulfur-nitrogen ring systems: S2N2Presented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 727-735 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Hartree-Fock instablities of S2N2 are reported and compared with those of S3N3- and S4N42+. These unsaturated sulfur nitrogen planar rings are π electron rich and although the symmetry adapted HF solutions are singlet stable at the experimental bond lengths they become unstable with only a very modest increase in bond length. The broken symmetry solutions for S2N3, S3N3-, and S4N42+ are of planar C2v type with one of the nitrogens stripped of its π electrons, producing a π hole.
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    URL: http://dx.doi.org/10.1002/jcc.540080601
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    Ab-initioMRD-CI calculations on a C—NO2 decomposition pathway of nitrobenzenePresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 736-743 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To study molecular decomposition pathways it is necessary to use ab initio multireference determinant-configuration interaction or MCSCF (multiconfiguration SCF) calculations. The MRD-CI (multireference double excitation-configuration interaction technique of Buenker and Peyerimhoff) calculations on the decomposition pathway of nitrobenzene were carried out using all of the occupied molecular orbitals in the region of the bond being dissociated, plus all of the virtual orbitals. An effective CI Hamiltonian was used into which were folded the effects of all of the occupied molecular orbitals from which excitations were not allowed. So far we have investigated the lowest 1A1, 3A1, 1A2, 3A2, 1B1, 3B1, 1B2, 3B2 states and are investigating the higher states. Our results show a wealth of structure in the potential energy surfaces for the various electronic states of nitrobenzene as a function of distance. A number of the states are predissociative and change dominant configuration one or more times along these potential energy surfaces.
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    Hamiltonian dynamics of chemical reactions. Consecutive first-order reactions and reactions possessing one autocatalytic intermediatePresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 744-751 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A recently proposed Hamiltonian approach to phenomenological chemical kinetics [T. Georgian and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 10, 331 (1983); T. Georgian, J.M. Halpin, and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 11, 347 (1984)] is applied to all consecutive first-order, single-step reactions, and to all reactions possessing one autocatalytic intermediate. The reaction Hamiltonians presented are shown to be consistent with the phenomenological rate equations and the relationship between reaction form and the form of the reaction potential is discussed. In particular, we show: (1) that the interaction between consecutive reactions manifests itself as a coupling term in the reaction potential, a term which may be eliminated via transition to “normal reaction coordinates” for the chemical system; and (2) that coupled sets of autocatalytic reactions give rise to coupling terms in the reaction Hamiltonian which are characteristic of the reaction mechanism.
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    Column design. 3. Theoretical studies of a chiral stationary phase used in column chromatography (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 753-760 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational features of a chiral stationary phase used in column chromatography are discussed. The syn forms invoked in chiral recognition models are consistent with MNDO and MM2 calculations. It is speculated that the inherent flexibility of the syn form makes these phases effective templates for analyte binding.
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    Ab initio study of the He(1S)-Li2(X̃, 1∑g+) interaction by the SCF and MP2 methods (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 761-771 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio electronic structure calculations have been carried out for the He(1S)-Li2 (X̃, 1∑g+) interaction both by the single-configuration SCF and correlated second-order MP2 methods using an extended basis set. From these calculations, an estimate of the isotropic (V0) and first two anisotropic (V2 and V4) terms of the He-Li2 potential surface has been obtained. An assessment of the leading induced-dipole-induced-dipole dispersion energy is presented from the MP2 energies. Where possible, a comparison is made with previous unpublished ab initio calculations by Staemmler and Stahl using the CEPA method.
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    CNDO Force constants for glucose (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 772-777 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force constants for both anomers of glucose are evaluated using CNDO/Force method.
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    Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 778-787 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms for a finer description of cavities in continuous media and for a more efficient selection of sampling points on the cavity surface are described. Applications to the evaluation of solute surface and volume and to the calculation of the solute-solvent electrostatic interaction energy, as well as of the cavitation energy are shown as examples.
    Additional Material: 8 Ill.
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    A study of basis set effects on structures and electronic structures of phosphine oxide and fluorophosphine oxide (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 788-793 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A variety of basis sets have been used for geometric and electronic structure studies. Electronic effects were measured using integrated spatial electron populations (ISEP). The two largest basis sets used, 6-31G* and DZ+P, give significantly different results. Use of two d-orbital sets (6-31G*[dd]) or decontraction of the 2sp shell on phosphorus has little further effect. d-Orbitals on oxygen are required for consistent electronic structure results, and d-orbitals on fluorine have a small but significant effect. Use of diffuse functions, required for anions, is not recommended with small basis sets on neutral molecules. Large negative charges (≈-1.5) on oxygen are given by all of the larger basis sets by the ISEP procedure and indicate that the PO bond in these compounds is largely semi-polar. The best simple symbolic representation of phosphine oxide is H3P+—0-, rather than H3P=0.
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    Theoretical studies on the acid hydrolysis of methyl carbamatePart 45 in the series, Determination of Reactivity by MO Theory. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 794-800 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The mechanism of the A2 acid hydrolysis of methyl carbamate was investigated using MNDO method. The reaction was found to proceed in two steps: (1) the rate-determining nucleophilic attack of water on the carbonyl carbon of the N-protonated tautomer involving the tetrahedral TS; and (2) the fast subsequent proton abstraction by the leaving group, NH3, to form products. The mechanism is similar to that involved in the A2 hydrolysis of acetamide. Effects of substituents, R1, R2, and R3 in R1OCONR2R3, on rates can be predicted by the changes in electron densities on alkoxy oxygen and N, in complete agreement with the experimental results. We concluded that there is no need for invoking two different mechanisms for amides and carbamates since a common mechanism can easily accommodate all the experimental results.
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    Announcement (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 916-916 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    URL: http://dx.doi.org/10.1002/jcc.540080618
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080701
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    Computer enumeration of polyhexes using the compact naming approach (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 906-915 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The enumeration of polyhexes can be easily carried out by utilizing a compact name (CN) approach to code chemical structures. The Fortran program performing generation of benzenoid hydrocarbons with 1-10 rings is presented. The computed structures are divided into various classes according to their cata- or peri- as well and non- or radicaloid character. Use of the additive nodal increments (ANI) approach leads to algorithm producing representative samples of the polyhexes' sets which can be applicable in testing of various topological formulae.
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    An efficient newton-like method for molecular mechanics energy minimization of large molecules (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1016-1024 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Techniques from numerical analysis and crystallographic refinement have been combined to produce a variant of the Truncated Newton nonlinear optimization procedure. The new algorithm shows particular promise for potential energy minimization of large molecular systems. Usual implementations of Newton's method require storage space proportional to the number of atoms squared (i.e., O(N2)) and computer time of O(N3). Our suggested implementation of the Truncated Newton technique requires storage of less than O(N1.5) and CPU time of less than O(N2) for structures containing several hundred to a few thousand atoms. The algorithm exhibits quadratic convergence near the minimum and is also very tolerant of poor initial structures. A comparison with existing optimization procedures is detailed for cyclohexane, arachidonic acid, and the small protein crambin. In particular, a structure for crambin (662 atoms) has been refined to an RMS gradient of 3.6 × 10-6 kcal/mol/Å per atom on the MM2 potential energy surface. Several suggestions are made which may lead to further improvement of the new method.
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    Systematic drug receptor mapping: A new approach to the analysis of conformational energy calculations of flexible molecules with application to dopaminergic and adrenergic agonists (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1075-1083 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The computer program PRODIS is used to find low energy conformations of flexible molecules by searching the potential energy surface(s) of one or more torsion angles via rigid rotation. The n-dimensional grid of energy versus torsion angles is then converted to a Boltzman probability distribution, with the probability being represented not as a function of torsion angle, but rather a distance between two atoms. These atoms are chosen by comparison with a known, active analogue in which certain atoms have previously been determined as requirements for drug activity. PRODIS produces a list of low energy conformations, their corresponding interatomic distances and the Boltzman probability for each distance ±0.125, as well as the total probability for each conformation. The user also specifies a target interatomic distance and range (usually derived from a more rigid analogue) for which PRODIS lists all conformations and their Boltzman probability that meet this distance.
    Additional Material: 6 Ill.
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    Masthead (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988) 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    URL: http://dx.doi.org/10.1002/jcc.540090101
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    Determination of the water geometry in violuric acid monohydrate with a Monte Carlo simulation (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 11-17 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The positions and orientations of water molecules in violuric acid crystals have been determined with the Metropolis Monte Carlo method. The interaction potentials between water and violuric acid needed in the simulation have been developed using ab initio calculations corrected for the basis set superposition error with the C.P. technique and fitted to atom-atom pairwise potentials. The agreement between experimental data and simulation results is good, proving that the interaction potentials can be used with confidence.
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    Acetylcholine in water: Ab-initio potential and Monte Carlo simulation (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 1-10 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF-LCAO-MO computations using a minimal basis set have been carried out on the acetylcholine ion in different conformations. The rotational barrier around the C9-C8-O1-C2 dihedral angle (τ1) has been also calculated: the curve presents a broad minimum. SCF calculations have been carried out on the system Ach-water at 468 different separations and/or orientations; the interaction energies were then fitted to a pair potential function used in Monte Carlo (MC) simulations of Ach water solution. The rdfs indicate a global first hydration shell with about 38 waters. Details about the hydration shell are presented. The overall MC results indicate that for the Ach ion in water solution at room temperature relative free rotation is possible around τ1, and that Ach is well represented as a large positively charged hydrated globe with a small mobile tail free of strong interactions with the surrounding water molecules.
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    Molecular mechanics and molecular shape. V.For Part IV, see Ref. 1. on the computation of the bare surface area of molecules (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 18-24 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article examines the numerical estimation of molecular surface areas within the model of overlapping atomic spheres. One has the choice of either basing the estimate on all elements that contribute to the surface, or of ignoring systematically some elements in the interatomic clefts. It is argued that the second choice, even though more approximate, implicitly improves on the model and is to be preferred. Since surface areas are not measurable, the demonstration is unavoidably roundabout, relying mostly on correlation analysis. Among the regressors occur two compounded parameters. One, ratio of the surface area of the equivalent sphere to the surface area, is interpreted as a measure of molecular globularity. It reflects the molecular axis-ratio and surface convolution. The other, ratio of the surface area to the volume, is interpreted as a measure of the global congestion of a chemical residue. Together with a measure of the local congestion at the point of attachment, it affects the steric hindrance that a residue offers. The relation between the surface area and the number of valence electrons is also discussed.
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    Integral data compression for FPS 64-BIT processors: Improved I/O and reduced storage (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 148-157 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Compression of two-electron integral data is used to reduce integral storage and I/O requirements with FPS M64 Series (formerly FPS-X64) processors. Schemes are developed and implemented in assembly language to compress floating-point values to a fixed-point accuracy, and unsigned integer numbers. The floating-point scheme stores only the significant bits of the mantissa and a short, biased exponent. The unsigned integers are packed into fixed-length fields just long enough to hold the largest value. The packing procedures are tested on FPS-164 and FPS-264 processors (since renamed M64/145 and M64/60 by FPS) and incorporated into HONDO to compress two-electron integral files. Reduction factors of 0.2-0.4 are obtained for floating-point compression and 0.3-0.5 for index packing, with typical overall factors around one-third. The advantages of improved I/O and storage efficiency are accompanied by a small increase in processor time to perform the packing and unpacking. Timing changes for HONDO are presented, and both packing schemes dramatically reduce SCF elapsed times with FPS-264 processors. It is concluded that compression effectively extends external storage capacities, improves I/O efficiency, and can reduce the elapsed time of I/O bound calculations.
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    Construction of the best set of four orthonormal 2s-2p hybrid orbitals by least-squares methods (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 356-361 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A least-squares procedure for the construction of four 2s-2p hybrid orbital direction vectors that deviate least from four given bond vectors emanating from a tetravalent atom is described. The procedure is used as a tool for the interpretation of structural data from X-ray diffraction, electron diffraction, and microwave experiments.
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    Characteristics of the Watson-Crick type hydrogen-bonded DNA base pairs: An ab initio molecular orbital study (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 362-368 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Characteristics of the Watson-Crick-type hydrogen-bonded base pairs, thymine-adenine and cytosineguanine, are presented. These were established using an ab initio molecular orbital method. Base-base interactions are revealed to have dominant roles in the structures of nucleic acids and also in their functions. The most stable conformations in Watson-Crick-type base pairs are almost in accord with the structure observed in fiber X-ray diffraction study. Explanations are given of the origin of the sequencedependent local structures which differ from one base pair to the next, as observed in single-crystal X-ray analyses. In the case of the thymine-adenine base pair, it is shown that various geometrical parameters having almost the same stability are available. According to the propeller twist, the instability is not large enough for a base pair to be twisted readily.
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    AM1 calculations of rotation around essential single bonds and preferred conformations in conjugated molecules (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 369-377 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Equilibrium twist angles, rotational barriers around essential single bonds, and preferred conformations for over 60 conjugated organic molecules were calculated using the semiempirical AM1 (Austin model 1) method. Comparison with ab initio and experimental data shows that AM1 can be applied quite successfully to conformational problems of this type. Relatively large errors are, however, found for compounds in which lone pair-hydrogen and especially lone pair-lone pair interactions are decisive for their conformational behavior. AM1-calculated rotational barriers in conjugated molecules, however, are found to be much too low. Moreover, AM1 does not seem to even correctly reproduce the trend of rotational barriers within a series of structurally related compounds. E/Z energy differences obtained by AM1 are also frequently considerably too low. In contrast to rotational barriers, their trends and thus conformational preferences, however, are quite satisfactorily calculated by this method. Ionization potentials obtained by AM1 are too high by about 0.5 eV. However, trends are quite well predicted.
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    The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 343-355 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general algorithm is described which exhaustively searches conformational space using an internal coordinate tree search. Using only geometrical operations and a set of criteria for eliminating chemically unreasonable structures, the algorithm generates starting geometries for optimization by molecular mechanics. An implementation of this algorithm is exceedingly fast and finds all known minima, as well as several new ones, for four test alkanes. This method makes feasible global conformational searches for molecules with up to 109 conformational possibilities.
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    URL: http://dx.doi.org/10.1002/jcc.540090409
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    Automatic classification of chemical structure databases using a highly parallel array processor (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 378-386 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article describes the use of the ICL Distributed Array Processor (DAP) for the automatic classification of chemical structure databases using the Jarvis-Patrick clustering method. This method is based upon the calculation of a table containing the nearest neighbors for each of the molecules in the database which is to be clustered. These nearest neighbors can be identified very efficiently using the DAP since it allows up to 4096 molecules to be compared with a specified molecule in parallel. Experiments with files of 4096 and 8192 structures from the Fine Chemicals Database show that clustering with the DAP is up to 6.7 times as fast as using a highly efficient, inverted file algorithm on an IBM 3083 mainframe.
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    URL: http://dx.doi.org/10.1002/jcc.540090413
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    A method for calculating atomic charges in large molecules (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 399-405 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple electronegativity method is used to calculate atomic charges for molecules of interest to biochemistry. These include purines, pyrimidines, and amino acids. Results are compared to those obtained from other theoretical methods (ab initio and semiempirical) as well as to nuclear magnetic resonance (NMR) data. Correlation is fair with CNDO results but very good for ab initio, DelRe, and other electronegativity methods. Good correlation was also achieved with NMR data. It is shown that a correction factor may be required in some cases and that important resonance effects need to be taken into account. Because of the small amount of calculational effort involved, these results suggest that this method could be quite useful in this field.
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    URL: http://dx.doi.org/10.1002/jcc.540090415
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    Numerical sensitivity of trajectories across conformational energy hypersurfaces from geometry optimized molecular orbital calculations: AM1, MNDO, and MINDO/3 (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 387-398 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The monocyclic β-lactam [[4(S)-methyl-2-oxo-1-azetidinyl]thia]acetic acid was studied by the semiempirical molecular orbital methods AM1, MNDO, and MINDO/3. Using the reaction coordinate option in the program MOPAC on VAX and Cray X-MP computers, the potential energy curve was calculated for rotation of the C2-N1-S-C torsional angle in the conformationally flexible side chain while optimizing all other geometrical variables in the molecule. The trajectory taken during geometry optimization was found to be sensitive to the computer, the program version, the convergence criteria, and the degree of code optimization used in the calculation. In order to reduce the likelihood of spurious results, conformational or reaction energy hypersurfaces need to be calculated with the more precise SCF convergence and minimization criteria available in programs for MINDO/3, MNDO, and AM1 calculations. The nitrogen in the model β-lactam antibiotic is predicted to invert periodically as the dihedral angle to the exocyclic N-substituent sweeps through 360°.
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    URL: http://dx.doi.org/10.1002/jcc.540090414
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    Efficient calculation of electrically based intermolecular potentials of weakly bonded clusters (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 476-487 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrical interactions between molecules are important effects in weak and long-range attractions. With quantum mechanical techniques now capable of yielding values of all multipole polarizabilities, hyperpolariabilities, and beyond, exhaustive treatment of electrical interaction is no longer out of the question. An efficient computational strategy is presented for the evaluation of electrical interaction energies to any desired level for small, medium, and large (ca. 100 molecules) clusters. With incorporation of repulsive, hard-wall potentials, global surfaces may be examined. Example calculations are presented.
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    Ab initio vibrational analysis of three rotamers of 2-propen-1-imine, H2C=CH—HC=N—H, and methanimine, H2C=N—H (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 443-454 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The results of complete Hartree-Fock (HF)/6-31G geometry optimization and HF/6-31G//HF/6-31G force fields evaluations of three rotamers of the H2C=CH-HC—N—H molecule (s-trans-d-trans-, s-trans-d-cis- and s-cis-d-trans-2-propen-1-imine) and the H2C=N-H molecule are reported. All three conformers were found to be planar with the s-trans-d-trans conformer lowest in energy. This was corroborated by further complete optimizations of the geometries of the s-trans-d-trans and s-trans-d-cis conformers at the HF/6-31G*(5D) level as well as single-point MP4/6-31G*//HF/6-31G*(5D) calculations. The assignment of the vibrational frequencies of the propenimine rotamers and some isotopomers of methanimine are also reported. The majority of the experimental frequencies of propenimine in the gaseous phase are found to belong to the s-trans-d-trans form, but a few frequencies are attributed to the high-energy s-trans-d-cis conformer.
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    Barriers to rotation adjacent to double bonds. 4. Effect of basis set on structures, and of electron correlation on relative energies (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 488-494 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The optimized geometries for the rotamers of propanal, 2-butanone, isobutyraldehyde, methyl isopropyl ketone, and isobutyric acid obtained using the 3-21G and 6-31G* basis sets are compared, and systematic changes are noted. The relative 6-31G* energies using the 3-21G and 6-31G* geometries are generally the same within 0.1 kcal/mol. The effect of electron correlation on the relative energies is generally small. These and related data show that 6-31G* relative energies obtained using 3-21G geometries are generally satisfactory when studying rotation about C—C bonds. However, this is not the case for C—O bonds. The calculated relative energies of isomeric compounds are reproduced only with the full MP4 correction for electron correlation.
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    Basis set effects and the choice of reference geometry in ab initio calculations of vibrational spectra (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 495-504 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Tatewaki and Huzinaga's [J. Comput. Chem. 1, 205 (1980)] basis sets, constructed to minimize superposition error, were used to calculate infrared (IR) frequencies and intensities. They were found inferior to Pople bases such as 3-21G and 6-31G*. The question of whether a theoretical vibrational spectrum should be computed at experimental or theoretical bond lengths was also investigated. If the magnitude of the correlation energy increases with bond length, Hartree-Fock bond lengths are expected to be shorter than experimental, and frequencies computed there will be higher than those computed at experimental lengths. Conversely, if this magnitude decreases with R, computed lengths should be longer than experimental and should give lower computed frequencies.
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    General algorithm for calculating vibrational-librational states of a rigid molecule in an external potential. Application to benzene-water complexesThe Fortran code for the algorithm discussed will be supplied on request. (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 505-517 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general algorithm of calculating the eigenstates of a rigid molecule trapped in an external potential is reported. The wave function and the potential are expanded about a common reference configuration. The expansion coefficients of the wave function are variationally determined. Contracted basis functions may be used to restrict the number of expansion coefficients. The use of the algorithm is illustrated by calculations of intermolecular eigenstates of benzene-water complexes.
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    URL: http://dx.doi.org/10.1002/jcc.540090509
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    Electron donor-acceptor complexes: Evaluation of MNDO as a computational tool to probe intermolecular interactions (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 539-553 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Donor-acceptor pairs form EDA complexes that exist as conformational isomers exhibiting different ground-state and photochemical properties. We have sought a rapid, general, and accurate quantum mechanical computational method to generate potential energy surfaces that are representative of the donor-acceptor intermolecular interactions at the self-consistent field (SCF) level. The semiempirical molecular orbital (MO) method MNDO has been compared to ab initio methods to assess its behavior with respect to energy, dipole moment and ionization potential shifts. MNDO correctly distinguishes between repulsive and bound EDA complex states at the SCF level and produces potential curves that are smooth and free of spurious minima or cusps. MNDO curves are systematically more repulsive than those for ab initio STO-3G calculations; calculated interaction energies exhibit a mean absolute deviation of 2.90 kcal/mol. MNDO appears to provide a reliable qualitative estimate of the nondispersion portion of the interaction energy. Limitations and errors arising from minimal basis sets, single determinants, and neglect of dispersion are discussed.
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    Determination of the major solution conformation of tyrocidine A, using molecular mechanics energy minimization and NMR-derived distance and torsion angle constraints (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 522-538 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics energy calculations coupled with nuclear magnetic resonance-determined distance and torsion angle constraints have been used to determine the three-dimensional structure of tyrocidine A, a cyclic decapeptide which exists largely as a single conformation in solution. Two open-chain polyalanine models were used to represent separate halves of the peptide backbone and a combinatorial method of searching conformation space used to generate candidate structures consistent with experimental distance constraints. These structures were energy-minimized using the AMBER molecular mechanics forcefield and the resulting conformations classified by factor analysis of their Cartesian coordinates. Representative low-energy conformers of the two halves of the backbone were fused together and two candidate conformations of the completed backbone refined by further minimization using both distance and torsional constraints. Side chains were then added as their experimentally preferred rotamers and the whole molecule minimized without constraints to give the final model structure. This shows type II' and III ß turns at residues 4-5 and 9-10, respectively, coupled by twisted antiparallel strands which show hydrogen bonds between all four pairs of opposing peptide groups. The backbone conformation of residues 2-6 closely resembles that found in the crystal structure of gramicidin S.
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    URL: http://dx.doi.org/10.1002/jcc.540090511
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    Comparison of semiempirical MO methods for open-shell systems (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 702-707 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The use of AM1, MNDO, and MNDOC semiempirical MO methods for calculation of heats of formation and ionization potentials of a series of 38 radicals are described. AM1 and MNDO calculations are reported using both half-electron (HE) and Unrestricted Hartree Fock (UHF) wavefunctions. Results show the MNDOC method to give lowest overall errors, being slightly better than the HE-AM1 method. In all cases, the AM1 method shows considerable improvement over MNDO.
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    URL: http://dx.doi.org/10.1002/jcc.540090616
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    A molecular mechanics study of the Si—O bond and alkyl-silanes (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 709-718 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The standard MM2 force field and program have been modified to include Si—O groups, the force constants being derived from ab initio wavefunctions, and using partial atomic charges calculated from the empirical algorithm CHARGE2. Molecular mechanics calculations have been carried out on disiloxane, dimethoxy-dimethylsilane, methyl silyl ether, and cyclotrisiloxane, and reasonable agreement has been obtained between the observed and calculated geometries. In addition, the energies obtained using the modified force field have been tested against experimental data on alkyl silanes where energetic and structural information is available. Again good agreement is obtained. The application of the force field to extended Si—O systems will also be discussed.
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    URL: http://dx.doi.org/10.1002/jcc.540090702
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    On the computation of stationary points on potential energy hypersurfaces (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 810-818 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, a modification of a procedure proposed by Zirrilli et al. for solving nonlinear equations is presented. The method permits the computation of minima and saddle points of energy functionals. The Müller-Brown test potential and the quantum chemical description of some proton transfer reactions are given as examples.
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    URL: http://dx.doi.org/10.1002/jcc.540090803
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    Structure and properties of small silicon and aluminum clusters (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 803-809 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Small Sin and Aln clusters (n = 3-10) were studied with the semiempirical molecular orbital method (MO) method SINDO1. For each n, various structures were optimized to determine the most stable structure. To obtain good qualitative agreement with available ab initio calculations d orbitals had to be omitted from the basis set. Both silicon and aluminum tend to build three-dimensional structures rather than two- or one-dimensional structures, except for n = 3 or 4. The structure growth was studied by approaching various sites of stable structures with one or more atoms. It was found that silicon and aluminum exhibit different structure growth, and consequently, different most-stable structures. Ionization potentials, HOMO-LUMO energy differences, binding energies per atom, and average atomic valencies are presented.
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    Hydration of Fe+: A Monte Carlo simulation of water clusters and of a dilute aqueous solution (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 819-826 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo statistical thermodynamic computer simulations are reported for several clusters Fe+ (H2O)n at different temperatures and for a dilute aqueous solution of Fe+ at 298 K. The energy of each configuration has been calculated in the pairwise additivity approximation using the MCY potential for the water-water interaction and an ab initio analytical potential built by us for the Fe+-H2O interaction. Energy and structural analysis of the generated configurations lead to the prediction of a coordination number of six for the first hydration shell of the Fe+ ion, both in clusters and in dilute solution. Finally, the variation in the distance to the Fe+ ion of the energy and orientation of water molecules in the solution are discussed.
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    Molecular mechanics of peroxides. I. Parametrization and conformational analysis of linear compounds (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 851-860 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A force field has been developed for use in MM2 calculations of geometric and energy data for linear peroxides R1—O—O—R2 and tested in some of them (R1, R2 = H, Me, Et, Pri, But). The field obtained yield results that agree considerably better with experimental and ab initio data than those afforded by the only set of estimated parameters hitherto available.
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    On testing difference equations for the diatomic eigenvalue problem (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 844-850 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The determination of the vibration-rotation eigenvalues (for an electronic state of a diatomic molecule) is done using various algorithms, where the differential equation y″ + f(r)y = 0 (with given initial values yo and y′o at an origin ro) is to be integrated, that is, to be replaced by a “convenient” difference equation (DE). The best known are those of: Numerov (N), Runge-Kutta (RK), and the Taylor series expansion (TS). Each algorithm is commonly associated with an “appropriate” DE, and the conventional comparisons of algorithms and/or DE are often misleading. This work compares different DE used in the same algorithm for the same potential and with the same tests. It considers the mentioned conventional DE, and three nonconventional ones: Hajj et al. (HKN) [J. Comp. Phys., 16, 150 (1974)], Cash and Raptis (CR) [Comput. Phys. Commun., 32, 299 (1984)], and Kobeissi “integrals superposition” (IS) [J. Phys. B, 15, 693 (1982)]. A convenient test of these DE is presented and applied. It is shown that: (i) if ∊ is the average error by using Numerov DE, it is of 4∊ for RK, 2∊ for TS, ∊ × 10-3 for HKN, 4∊ × 10-4 for CR and ∊ × 10-6 for IS; (ii) if τ is the average computing time by using Numerov DE, it is of 2.9τ for RK, 3.4τ for TS, 1.5τ for HKN, 2.7τ for CR and 0.9τ for IS.
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    Doublet instability and the molecular structure of AlO2A contribution from the “Grup Química Quàntica de Catalunya, Institut de'Estudis Catalans.” (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 836-843 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The possible Cs, C2v, and C∞v structures of AlO2 corresponding to the two lowest electronic states which dissociate into the neutral Al(2P) and O2(3Σg-) fragments have been investigated at the ab initio self-consistent field (SCF) and CI levels using nonempirical pseudopotentials. The most stable structure corresponds to a C2v symmetry in the 2A2 electronic state. However, this structure presents the three-center three-electron Hartree-Fock instability and CASSCF calculations were necessary to unequivocally characterize it as true minimum. Moreover, only another stable structure, of C2v geometry, was found to be a minimum, corresponding to a low-lying excited state of 2A1 symmetry. The optimized C∞v structures were not minima on the corresponding potential energy surfaces and no evidence of any stable Cs structure was found. Calculating values are compared with the different experimental data obtained from the reaction of Al and O2 in frozen gas inert matrices.
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    The MT-MSXα(R) method: Applications to Li2, F2, and N2 molecules (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 890-892 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The multiple scattering Xα(R) method with the scaling parameter α expressed as a function of the internuclear distance is applied to the Li2, N2, and F2 molecules. Compared with the results obtained by the Xα method, the calculated Xα(R) equilibrium distances are smaller, the total energies are lower, and the dissociation energies are larger.
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    A new tool for the rapid estimation of charge distribution (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 893-904 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method has been developed which uses a rapid connectivity-based calculation to give a reasonable approximation of CNDO σ and π charges for most carbons in saturated and unsaturated hydrocarbons. In this calculation an appropriately parameterized Del Re method is used to calculate the σ charges, and if the molecule is unsaturated, these charges are used to modify the diagonal elements in a Hückel matrix, reducing the normally exaggerated π charges. The CNDO charges are obtained from “single point” calculations, using optimized geometries derived from molecular mechanics. The Del Re/Hückel method is most reliable where steric and hyperconjugative effects are absent.
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    Studies of a proposed mechanism for the reaction between 2H-pyran-2-ones and organomagnesium compounds (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 9-12 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Part of the reaction between 2H-pyran-2-ones and organomagnesium compounds has been investigated by means of MNDO and ab initio calculations. Criteria for the mechanism of reaction are provided by the stereoselectivity observed and calculations are consistent with this stereoselectivity. Conformations of the reaction intermediates are given.
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    Simple method of computing the partition coefficient (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 28-38 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The values of log10 P (partition coefficient, in octanol/water) were calculated for about 200 organic molecules of diverse structures and functionalities. The method involves a simple procedure and appears accurate enough for semiquantitative applications. Further, this method of calculating log10 P values was shown to be successful in providing a better quantitative structure activity relationship (QSAR) than the Hansch-type approach in the study of inhibitory activity of substituted phenols on Bacillus Subtilis spore germination.
    Additional Material: 5 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540060106
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    Polyatomic, anharmonic, vibrational-rotational analysis. Application to accurate ab initio results for formaldehydeWork performed under the auspices of the Office of Basic Energy Sciences, Division of Chemical Sciences, U. S. Department of Energy, under Contract W-31-109-Eng-38. (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 13-27 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program SURVIB is described for calculating vibrational anharmonicity constants for polyatomic molecules. The program requires as input a grid of calculated energies in the vicinity of a stationary point. This grid is fit, in a least squares sense, to a polynomial function of the internal coordinates. This analytic representation of the energy surface is employed in a normal mode analysis, and the energy is reexpanded as a polynominal function of the normal mode coordinates (expressed as vectors in the mass-weighted atomic Cartesian coordinate space). The resulting coefficients are used in a second-order perturbation theory analysis to obtain the vibrational anharmonicity constants. Also reported is an application of this program to formaldehyde employing ab initio, RHF, MP2, MP3, and RHF-CI calculations. The spectroscopic constants obtained for H2CO are in good agreement with experimentally derived values recently reported by Reisner.
    Additional Material: 9 Tab.
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    The α↑HF and α↓HF parameters for spin polarized Hartree-Fock-Slater calculations (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 56-60 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: α↑HF and α↓HF are derived for use in spin polarized Hartree-Fock-Slater programs. They are assumed to depend only on the number of up and down spin electrons in the atom. The calculated eigenvalues show a slight improvement only for carbon, nitrogen, and oxygen.
    Additional Material: 4 Ill.
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    Ab initio investigation of the potential energy surfaces of C2H2F2 and C2H2F2+ (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 189-199 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MO calculations have been performed for neutral and cationic C2H2F2 structures. Olefinic and carbene structures are investigated for the neutral isomers, while olefinic, carbene, and fluoronium-type cations are found. Stability orders and rotational barriers are discussed in terms of orbital and Coulomb interaction. Contrary to previous studies, the higher stability of the geminal isomers is interpreted to be caused by Coulomb attraction.
    Additional Material: 5 Ill.
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    Pseudopotential calculations on Si2H6 and Si2H4 (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 469-477 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Local pseudopotential calculations have been performed for the ground state of disilane as well as for the lowest singlet and triplet states of disilene and silylsilylene. Comparison with all-electron calculations shows good agreement for geometries and relative stabilities.
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    Usefulness of modified virtual orbitals in multireference CI procedure illustrated by calculations on lithium clusters (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 462-468 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The maximization of the exchange interaction between the canonical Hartree-Fock virtual and occupied orbitals leads to a transformed set of virtual orbitals which are well suited as one-electron functions for CI calculations. The procedure, generally known for a long time is seldom applied, despite its simplicity and very low computational demand. However, it is found to be particularly useful in the case of multireference CI, since an improved energy is obtained with a considerable shortening of the CI expansion. Moreover, in the final CI wave function, several configurations appear with considerable weight, thus allowing an easy choice of additional configurations to be inserted in the definition of a new zero-order wave function. The efficiency of the computational procedure is discussed for the case of a Li6 cluster of D3h symmetry and for the NaCO and PdCO complexes. Results are reported for the relative stability of four different geometrical arrangements of the Li6 cluster.
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    Masthead (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985) 
    Details
    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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    URL: http://dx.doi.org/10.1002/jcc.540060601
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    Theoretical studies on the hydrogen atom transfer reactionDetermination of Reactivity by MO Theory (part 36). (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 486-491 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The hydrogen atom transfer reaction between substituted methanes (substituents; H, F, CH3, OH, and CN) and methyl radicals was studied by 4-31G (UHF) calculations using the MINDO/3 geometries. The transition state structures and energy barriers were determined, and variations of the transition state and of the reactivity due to the change of substituent were analyzed based on the potential energy surface characteristics. It was concluded that the reaction is of the SH2 type with a backside attack, and transition state variations are controlled by the vector sum of the component parallel to (Hammond rule) and one perpendicular to the reaction coordinate (anti-Hammond rule). It was also concluded that the most important factor influencing the reactivity is bond dissociation energy effect directly related to the spin transfer of the radical species, and the polar effect need not be overemphasized.
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    Computation of reequilibration data in solids (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 514-519 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Reequilibration processes are often encountered within solids and they have long been described mathematically. However, computation of reequilibration data over entire processes is often difficult. An algorithm has been developed specifically for this purpose. It allows a fast and efficient computation of reequilibration parameters. Anisotropic diffusion can, moreover, be taken into account.
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    Compact basis sets for LCAO-LSD calculations. Part II: Tests for Cr2 and Ni4 (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 533-537 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The compact orbital and auxiliary basis sets for LCAO-LSD calculations introduced in Part I are tested in molecular calculations on Cr2 and Ni4. The present results for spectroscopic constants and valence orbital energies obtained using medium size orbital expansions with a double-zeta representation for valence orbitals are in very good agreement with those previously calculated with very extended sets. Since the computational time of the present calculations is reduced severalfold compared with the extended basis set calculations, the present basis sets allow increased efficiency of the LCAO-LSD calculations and allow the method to be extended to larger systems.
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    Unique description of chemical structures on hierarchically ordered extended connectivities (HOC procedures). II. Mathematical proofs for the HOC algorithm (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 552-561 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The basic notions and definitions, necessary for the better understanding of Part I of this series, are presented. The mathematical proof is given for sufficiency of the various HOC procedures for vertex canonical numbering and graph orbit finding.
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    Molecular structures and intramolecular interactions in dimethyl cyclohexane isomers (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 570-580 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometries of ten isomers of dimethyl cyclohexane were determined by ab initio gradient geometry refinement with the 4-21G basis set. It is found that many intramolecular interactions are clearly manifested by correlated structural trends, and that they are consistent with strain energies calculated by employing previously defined ab initio group equivalents. Specifically, non-bonded interactions are found between two adjacent methyl groups in some of the forms, and between axial methyl groups and adjacent axial C—H bonds in others. Unperturbed axial C—H and C—C bonds are consistently longer than equatorial bonds. In general, C—H bonds which are involved in non-bonded repulsive interactions are shortened, i.e., strengthened, and the corresponding H—C—C angles are large, compared to non-interacting parameters.
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    The effect of including polarization functions on the geometrical parameters calculated for benzene, fluorobenzene and cyanobenzene (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 592-597 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometrical parameters for benzene, fluorobenzene, and cyanobenzene have been calculated using the 6-31G*(5D) and 6-31G** basis sets, and, in addition, the 6-31 + G*(5D) basis set in the case of fluorobenzene. Compared to previous results obtained using the 6-31G basis set there are minor changes in the magnitude of the bond lengths and angles in the ring, but the relative values remain unaltered. The values for the ipso angles in fluorobenzene and cyanobenzene are again somewhat less than those reported from microwave and/or electron diffraction studies. The distortion of the ring is characterized as either an elongation or a flattening with respect to the F-C1⃛C4 and N≡C—C1≡C4 axes, and the shape is characterized as either a broadening or a narrowing across the ring just below the F and Cn group, i.e., an increase or a decrease in the C2⃛C6 internuclear distance, relative of the C3⃛C5 distance.
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    Ishtar: An interactive system for quantitative investigation on dipolar and quadrupolar spin-lattice relaxation (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 610-613 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Within the model of anisotropic rotational diffusion, the quantitative treatment of dipolar and quadrupolar spin-lattice relaxation provides valuable information about molecular structures and molecular associations. When quadrupolar relaxation is involved, the title program calculates: (1) the electric field gradient tensor (EFGT) which is diagonalized; (2) the assymetry parameter, the components of the principal axes of the EFGT in the molecular frame of reference and the quadrupole coupling constant; and (3) the rotational diffusion constants which are iteratively determined from the experimental quadrupolar relaxation times. Analogously, for dipolar relaxation ISHTAR calculates the tensor of inertia, the diagonalization of which leads to diffusion constants and free rotor correlation times and the rotational diffusion constants from the experimental spectral densities.
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    URL: http://dx.doi.org/10.1002/jcc.540060614
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    Conformational analysis of some dimethylheptanes with the aid of normal coordinate calculations (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 625-633 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Infrared spectra were obtained for the series of 2,X-dimethylheptanes (X = 2,3,4,5,6) and were interpreted with the aid of normal coordinate calculations. 2,2-DMH exists as two conformers, with the Cs conformer being the only one present in the crystalline solid. 2,3-DMH exists in at least three conformations, all of C1 symmetry. Ambiguities in spectral data indicate that more conformations are present. Two C1 conformations of 2,4-DMH were shown to be present, but an unassigned band may indicate the presence of a third conformer. The presence of at least four conformers, all of C1 symmetry, was shown to be necessary to explain the spectrum of 2,5-DMH. Finally, 2,6-DMH was shown to exist as three conformers, of symmetries Cs, C2, and C1. Vibrational assignments were made for all the probable conformers of all five compounds.
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    The through-space transmission of 31P-31P coupling constantsPart of a Lic. Thesis (A.C.D.) presented to the University of Buenos Aires (1985). (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 647-651 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Inner projections of the polarization propagator (IPPP) are used to study several features of the throughspace transmission of 31P-31P coupling constants. Cis-1,2-diphosphinoethylene is chosen as a model compound. INDO ground state wave functions are used, including two different second-row parameterizations. Results obtained with a phosphorus spd basis set are also presented. It is found that the overlap of phosphorus lone-pairs constitute an efficient coupling pathway. Results are discussed in terms of experimental values for similar compounds taken from the literature. Theoretical predictions are in line with experimental trends.
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    Masthead (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986) 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070201
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    A method for the machine detection of near equivalence of major substructures in a molecule (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 129-139 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The use of the concept of near equivalence of substructures in a computer program concerned with organic synthesis requires a concrete definition of «nearness» and an efficient method for implementing the concept. Such a method has been devised and its use is described and examples are given.
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    A fast algorithm for the interactive docking maneuver with flexible macromolecules and probes (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 113-128 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm for the interactive docking maneuver is presented. Full attention is given to the flexibility of both substrate and macromolecule, i.e., all the fragments are allowed to move. It is assumed that any numerical quantity which depends only on the isolated macromolecule at energy minimum is disposable when approximate expressions are derived. The central idea is the concept of relevant docking coordinates which reflect the essential features of the macromolecular deformations during the docking maneuver and which substantially diminish the number of considered degrees of freedom (DF). The conformational energy is divided into two parts. The first part, represented by condensed potential functions, needs no approximations. For the second part, termed Erest, a quadratic approximation in the subspace spanned by the relevant docking coordinates is used. All the pairwise interactions between the atoms of the macromolecule are eliminated. A simple computational example using the ECEPP force field is given. Atomic coordinate computations are simplified by the introduction of virtual rotation axes for the backbone. In connection with drug design the concept of pressure pattern is defined and related to quantities appearing in the energy gradient. Extensions to substrate induced allosteric transitions are discussed.
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    Molecular mechanics and molecular shape. III. Surface area and cross-sectional areas of organic molecules (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 144-152 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A nonanalytical procedure is proposed to calculate the surface area and cross-sectional areas of molecules. Results are reviewed for about 70 species comprising alkanes, acyclic and cyclic, alkyl halides, and alcohols. By regression analysis, relationships are detected between surface areas or segment areas and physical properties. Computed cross-sectional areas are confronted with adsorption values. Four ways are proposed to define quantitatively the intuitive notion of «molecular globularity».
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    The computed force constants and vibrational spectra of toluene (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 158-164 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The complete harmonic force field and dipole moment derivatives have been computed for toluene at the Hartree-Fock level using a 4-21G basis set. The six scale factors optimized for benzene were used to scale the computed harmonic force constants of toluene. The vibrational frequencies of toluene computed from this scaled quantum mechanical force field are quite good. After a correction was made to two previously proposed spectral assignments, the mean deviation from the experimental frequencies is only 7.8 cm-1 except for the frequencies related to the methyl group. Five more scale factors for the vibrational modes of the methyl group were reoptimized. The final comparison showed an overall mean deviation of 7.5 cm-1 between the theoretical spectrum and the experimental spectrum. Computed intensities are qualitatively in agreement with experiments. They are highly useful in the investigation of questionable assignments.
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    Comparison of sequences as a method for evaluation of the molecular similarity (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 176-188 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: String comparison techniques were developed and applied for measuring the molecular similarity of chemical structures. The molecular structures were encoded as a sequence of numbers representing counts of paths of different lengths. The similarity index between two compounds was calculated as the difference between the gains of information derived through comparison of the corresponding molecular path sequences. Ranks between the structures of the studied data base obtained according to this similarity were used as basic data for deriving correspondences between the elements of the set of compounds. The method was applied on a group of 41 barbiturates. Correlation equations were calculated for different groups of compounds grouped according to the displayed similarity. The correlation equations and the corresponding statistics were obtained using standard computer programs. Special algorithm for computing the similarity index and the correlation matrix (outlined very briefly) was developed and implemented on VAX 11/750.
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    A minimal multiconfigurational technique (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 201-207 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A direct minimization method previously presented by the authors is applied here to biconfigurational wave functions. A very moderate increasing in the time by iteration with respect to the one-determinant calculation and good convergence properties have been found. So qualitatively correct studies on singlet systems with strong biradical character can be performed with a cost similar to that required by Hartree-Fock calculations.
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    Molecular orbital theory of the properties of inorganic and organometallic compounds 4. Extended basis sets for third-and fourth-row, main-group elementsDedicated to john pople on the occasion of his 60th birthday. (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 359-378 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two new series of efficient basis sets for third- and fourth-row, main-group elements have been developed. Split-valence 3-21G basis sets have been formulated from the minimal expansions by Huzinaga, in which each atomic orbital has been represented by a sum of three Gaussians. The original expansions for s- and p-type orbitals (except those for 1s) have been replaced by new combinations in which the two sets of orbitals (of the same n quantum number) share Gaussian exponents. The Huzinaga expansions for 1s, 3d and 4d (fourth-row elements only) have been employed without further alteration. The valence atomic functions 4s, 4p for third-row elements; 5s, 5p for fourth-row elements have been split into two and one Gaussian parts. Supplemented 3-21G(*) representations have been formed from the 3-21G basis sets by the addition of a set of single d-type Gaussian functions.The performance of 3-21G and 3-21G(*) basis sets is examined with regard to the calculation of equilibrium geometries, normal mode vibrational frequencies, reaction energies, and electric dipole moments involving a variety of normal and hypervalent compounds containing third- and fourth-row, main-group elements. The supplementary functions incorporated into the 3-21G(*) basis sets are generally found to be important, especially for the proper description of equilibrium bond lengths and electric dipole moments. 3-21G(*) representations are recommended for general use in lieu of the unsupplemented 3-21G basis sets.
    Additional Material: 12 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540070313
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    The remarkably invariant interaction energies of lithium first-row compounds with water and with ammoniaThis article is dedicated to John A. Pople in recognition of his multifaceted seminal contributions to computational chemistry in general, to this work in particular (Gaussian programs, basis sets, correlation methods, etc.), and to the theoretical study of lithium chemistry. (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 334-344 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Solvation energies of lithium first-row compounds LiX (X = H, Li, BeH, BH2, CH3, NH2, OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito (MP2/6-31 + G*//6-31G* with zero-point vibrational energy corrections at 3-21G//3-21G). The solvation energies are found to be remarkably constant: -18.0 ± 1.2 and -21.5 ± 1.3 kcal/mol for the hydrates and ammonia solvates, respectively. This independence on the nature of X is due largely to the ionic character of the LiX compounds (dipole moments 4.7-6.6 debye). The unexpectedly high solvation energies of the lithium molecule (-14.3 and -17.8 kcal/mol, respectively) are due to the polarizability of Li2. At the same level, the lithium cation has interaction energies with H2O and NH3 of -34.1 and -39.7 kcal/mol, respectively. For the hydrates of LiOH and LiF cyclic structures with hydrogen bonds and somewhat increased solvation energies also are described.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540070310
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    The evaluation of molecular electron affinitiesDedicated to Professor John A. Pople on the occasion of his 60th birthday. (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 349-358 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The performance of a variety of levels of theory in evaluating molecular electron affinities (EAs) has been systematically examined. Calculations have been carried out for six different basis sets and for nine theoretical procedures including unrestricted (UHF) and restricted (RHF) Hartree-Fock theory, Møler-Plesset perturbation theory (UMP2, UMP3, UMP4), configuration interaction (UCISD, RCISD, RCISD(Q)) and equations-of-motion (EOM) approaches. Electron affinities were evaluated for CH3, NH2, OH, F, C2H, CN, BO, N3, OCN, and NO2. Very poor results are generally obtained unless diffuse functions are included in the basis set and electron correlation is incorporated. Even with the largest basis set used in the present study (6-311 + + G(2d, 2p)), there are still residual errors greater than 0.2 eV (UMP4) or 0.6 eV (CISD) in the absolute EAs. However, better results are obtained under certain circumstances for relative EAs. The results appear to be significantly affected by spin contamination in the UHF wave-functions. For those systems for which spin contamination is small, best absolute values of the EAs generally come from the EOM and UMP2 calculations, whereas the most constant errors (thereby allowing systematic correction) are found at the UMP4, CISD, and RCISD(Q) levels. For the systems for which spin contamination is larger, best results are obtained with the CI-based procedures (CISD and RCISD(Q)). The errors in calculated EAs for the molecules with differing electronic characteristics can vary quite widely. Caution must therefore be exercised before applying schemes which rely on a constancy of errors to estimate electron affinities. The UMP procedures appear particularly suspect in this regard if spin contamination is significant. The RCISD(Q) approach is recommended under such circumstances.
    Additional Material: 16 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540070312
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    Masthead (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070401
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  • 96
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    MINDO/3 Study of the Rearrangement of 1-Methylcyclohexyl Cation to 1,2-Dimethylcyclopentyl Cation (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 417-427 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The rearrangement of the 1-methylcyclohexyl cation to the 1,2-dimethylcyclopentyl cation has been studied by MINDO/3 calculations, as an application of the branching mechanism model for cycloalkanes. Possible intermediates and transition states have been characterized by diagonalization of their Hessian matrixes. Two nonequivalent pathways, α and β scissions, are relatively close in energy. The calculated transition states are almost equivalent in energy to those found for cyclohexyl cation. Hence, the energy barriers are higher for the rearrangement of the 1-methyl than for cyclohexyl cation, because the former is less stable than the latter.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070405
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    Transport Properties of Macromolecules by Brownian Dynamics Simulation: Vectorization of Brownian Dynamics on the Cyber-205 (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 457-463 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Time consuming portions in the computation of transport properties of rigid and flexible molecules are the evaluation of subunit hydrodynamic interaction tensors Q and σ, and the procedure for satisfying subunit-subunit distance constraints. Vector algorithms to speed up these parts of the computation are given. Using these algorithms, a vector version of the Ermak-McCammon Brownian dynamics code has been developed on a Cyber-205. To demonstrate the order of speedups that can be achieved, the code was tested on a rigid “trimer” system comprising 24 spherical subunits with a fixed geometry. A speedup of about 14 times for the whole program, and of 45, 6, and 18 times for the computation of Q, σ, and for the procedure to enforce the constraints, respectively, were obtained.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070408
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  • 98
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    On the Use of Constraints in Molecular Mechanics. Rigid Group Refinement (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 476-481 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown how the refinement of groups of atoms as rigid entities can be implemented in a molecular mechanics program. The method is worked out for the Newton-Raphson scheme and eventually combined with other constraints, including the Eckart conditions. An example is also given.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070410
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    Optimization of the Generalized Valence Bond Method for Vector ProcessorsWork performed under the auspices of the Office of Basic Energy Sciences, Division of Chemical Sciences, U. S. Department of Energy, under Contract W-31-109-Eng-38. (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 500-512 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Generalized Valence Bond [GVB(pp)] multiconfiguration self-consistent field wave function optimization program has undergone substantial revision in migration from serial scalar computers (like IBM and VAX) to the FPS-164, a minisupercomputer. Many of the code optimization strategies applied to the GVB program are portable and applicable to a wide range of scientific application codes. In benchmark calculations, the optimized FPS-164 program, GVB164, is 6.5 times faster than the initial FPS-164 implementation, both programs storing the two-electron integral list on disk. GVB164 runs 30 times faster in wall time (limited by the FPS-164 disk access speed) than a reference version of GVB2P5 on the VAX 11/780. The performance of GVB164 nearly doubles again when all of the two-electron integrals can be stored in main memory.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070413
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    Open-shell coupled-cluster method: Electron affinities of Li and Na (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 448-453 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The open-shell coupled-cluster method and the diagrams needed for its implementation are described. The method is applied to the electron affinities of Li and Na, which are calculated in two ways: as the ionization potential of the anions or as the energy of adding the second electron to the cations. The two schemes give essentially the same results, in very good agreement (〈0.02 eV) with experiment. Three-body effects are negligible.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080423
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