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  • Biochemistry  (749)
  • Wiley-Blackwell  (749)
  • American Institute of Physics
  • Blackwell Publishing Ltd
  • 1990-1994  (749)
  • 1975-1979
Collection
Keywords
Publisher
  • Wiley-Blackwell  (749)
  • American Institute of Physics
  • Blackwell Publishing Ltd
  • Springer  (8)
Years
Year
  • 1
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    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.540110101
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  • 2
    Electronic Resource
    Electronic Resource
    SCF, MP2, and CEPA-1 calculations on the OH ‥ O hydrogen bonded complexes (H2O)2 and (H2O-H2CO) (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1-18 
    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: Counterpoise corrected ab initio calculations are reported for (H2O)2 and H2O-H2CO. Geometry searches were done in the moment-optimized basis DZP' at the SCF, MP2, and CEPA-1 levels of theory, followed by more accurate single-point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are -4.7 ±0.3 kcal/mol for a near-linear (H2O)2 structure and -4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH2 structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C2h) and bifurcated (C2v) transition structures for (H2O)2 are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA-1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110102
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  • 3
    Electronic Resource
    Electronic Resource
    A data compression method applicable to first-order convergent iterative procedures (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 45-57 
    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 data compression method is presented that is generally applicable to first-order convergent iterative procedures that employ subspace expansions or extrapolations based on successive correction vectors. This method is based on the truncation of insignificant information in successive correction vectors. Although the correction vectors themselves may be severely truncated with the proposed approach, the final solution vector may be represented to arbitrary accuracy. A feature of the proposed method is that more slowly convergent iterative procedures allow the correction vectors to be more severely truncated without affecting the overall convergence rate. The method is implemented and applied to the iterative Davidson diagonalization method. If the compressed representation of the expansion vectors can be held in main computer memory, then a significant reduction in the I/O requirements is achieved.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110105
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  • 4
    Electronic Resource
    Electronic Resource
    Partial optimization of large molecules and clusters (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 67-75 
    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: By examining the displacement coordinate metric three modes of constrained optimization for large molecules and clusters are suggested. The first method corresponds to a conventional optimization using internal coordinates. The second mode has applications with respect to both internal and cartesian coordinates. The final mode is particularly interesting because it can result in computational savings. A mixture of both internal and cartesian coordinates is specified where these coordinates are usually a subset of the molecules or clusters total coordinate set. In the optimization only a subset of the energy derivatives need be evaluated reducing the computational effort associated with the gradient calculation.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110108
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  • 5
    Electronic Resource
    Electronic Resource
    Calculation of the nonlinear optical properties of molecules (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 82-87 
    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 finite-field method for the calculation of polarizabilities and hyperpolarizabilities is developed based on both an energy expansion and a dipole moment expansion. This procedure is implemented in the MOPAC semiempirical program. Values and components of the dipole moment (μ), polarizability (α), first hyperpolarizability (β), and second hyperpolarizability (γ) are calculated as an extension of the usual MOPAC run. Applications to benzene and substituted benzenes are shown as test cases utilizing both MNDO and AM1 Hamiltonians.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110110
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  • 6
    Electronic Resource
    Electronic Resource
    Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 121-151 
    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 has been developed for global energy minimization of surface loops of proteins in the presence of a fixed core. The ECEPP potential function has been modified to allow more accurate representations of hydrogen bond interactions and intrinsic torsional energies. A computationally efficient representation of hydration free energy has been introduced. A local minimization procedure has been developed that uses a cutoff distance, minimization with respect to subsets of degrees of freedom, analytical second derivatives, and distance constraints between rigid segments to achieve efficiency in applications to surface loops. Efficient procedures have been developed for deforming segments of the initial backbone structure and for removing overlaps. Global energy minimization of a surface loop is accomplished by generating a sequence (or a trajectory) of local minima, the component steps of which are generated by searching collections of local minima obtained by deforming seven-residue segments of the surface loop. The search at each component step consists of the following calculations: (1) A large collection of backbone structures is generated by deforming a seven-residue segment of the initial backbone structure. (2) A collection of low-energy backbone structures is generated by applying local energy minimization to the resulting collection of backbone structures (interactions involving side chains that will be searched in this component step are not included in the energy). (3) One low-energy side-chain structure is generated for each of the resulting low-energy backbone structures. (4) A collection of low-energy local minima is generated by applying local energy minimization to the resulting collection of structures. (5) The local minimum with the lowest energy is retained as the next point of the trajectory. Applications of our global search procedure to surface segments of bovine pancreatic trypsin inhibitor (BPTI) and bovine trypsin suggest that component-step searches are reasonably complete. The computational efficiency of component-step searches is such that trajectories consisting of about 10 component steps are feasible using an FPS-5200 array processor. Our procedure for global energy minimization of surface loops is being used to identify and correct problems with the potential function and to calculate protein structure using a combination of sequence homology and global energy minimization.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110115
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  • 7
    Electronic Resource
    Electronic Resource
    Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 416-430 
    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 systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first-order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO-3G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split-valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6-31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110403
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  • 8
    Electronic Resource
    Electronic Resource
    Dynamics of peptides with fixed geometry: Kinetic energy terms and potential energy derivatives as functions of dihedral angles (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 487-492 
    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: Expressions are derived for computing the kinetic energy of a peptide with fixed geometry, in terms of dihedral angles as generalized coordinates; other expressions required for the solution of Lagrange's equations are also presented. The peptide is regarded as held stationary at one end. We also outline the computations that are needed in calculating the components of the third derivative of a potential energy function that consists of a sum of pairwise interatomic interactions.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110407
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  • 9
    Electronic Resource
    Electronic Resource
    Combined application of pair potentials and the MM2 force field for the modeling of ionophores (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 819-828 
    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: Complexes of alkali and alkaline earth cations with organic compounds are modeled by describing ionligand interaction energies with pair potentials and intraligand as well as interligand energies with the MM2 potential. New pair potentials for the interaction of Li+, Na+, K+, Mg2+, and Ca2+ ions are derived on the basis of 30,000 ab initio interaction energy values with 70 selected model ligand molecules. Various problems of the combination of these two basically different potentials are discussed. An application for the K+ complex of 18-crown-6 is presented. For more flexible ligands the introduction of three-body correction terms of the pair potentials seems necessary.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110705
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  • 10
    Electronic Resource
    Electronic Resource
    Electronic structure and photoelectron spectra of Sb2 and Sb4 from local-spin-density calculations. Model potential for Sb (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 924-929 
    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 geometry, electronic structure, and photoelectron spectra of Sb2 and Sb4 have been investigated employing the LCGTO-MP-LSD method. For both molecules the geometrical and spectroscopic constants computed using the VWN potential are in very good agreement with the available experimental data. The HeI photoelectron spectra were computed with different potentials (Xα, GL, HL, BH, and VWN). The calculated spectra are in excellent agreement with the experimental ones and the use of the VWN potential gives the most accurate results. The reliable results for molecules complement those for the Sb atom and show that the proposed LSD Model Potential is able to give an accurate description of the structural and spectroscopic properties of the title molecules.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110804
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