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  • Biochemistry  (140)
  • Wiley-Blackwell  (140)
  • American Chemical Society (ACS)
  • De Gruyter
  • 1990-1994  (140)
  • 1994  (140)
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Verlag/Herausgeber
  • Wiley-Blackwell  (140)
  • American Chemical Society (ACS)
  • De Gruyter
Erscheinungszeitraum
  • 1990-1994  (140)
Jahr
  • 1
    Digitale Medien
    Digitale Medien
    Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 12-22 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 6 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150103
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  • 2
    Digitale Medien
    Digitale Medien
    Newton-Raphson optimization of the explicitly correlated Gaussian functions for calculations of the ground state of the helium atom (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 54-60 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150107
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  • 3
    Digitale Medien
    Digitale Medien
    General parameterization of a reaction field theory combined with the boundary element method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 90-104 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent-dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150111
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  • 4
    Digitale Medien
    Digitale Medien
    Conformation and reactivity of α-oxo-ketenes: Ab initio and semiempirical (AM1, PM3) calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 132-143 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150203
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  • 5
    Digitale Medien
    Digitale Medien
    Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 200-207 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150210
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  • 6
    Digitale Medien
    Digitale Medien
    A ring-bracing approach to computer-assisted ligand design (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 233-240 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be ‘braced’ using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150213
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  • 7
    Digitale Medien
    Digitale Medien
    Force field calculations (MM3) on glyoxal, quinones, and related compounds (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 251-268 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150302
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  • 8
    Digitale Medien
    Digitale Medien
    A comparative study of effective core potential and full-electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 313-321 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Effective core potential (ECP) and full-electron (FE) calculations for MoS4-2, MoO4-2, and MoOCl4 compounds were analyzed. Geometry parameters, binding energies, charge distributions, and topological properties of the electronic density were studied for Mo—L bonds (L = S, O, Cl). Results clearly indicate that those approaches that include valence plus 4s and 4p electrons (ECP2 methods) are able to reproduce the topological properties of Mo—L bonds, charge distributions, and geometries with respect to those obtained by FE methods. ECP methods that consider only the 4d and 5s valence electrons (ECP1) fail in the calculation of molecular properties. The use of 5p functions in ECP1 approaches produces a negative Mulliken charge on Mo. Bader's charges give more consistent results than Mulliken's ones. A new parameter for measuring the degree of ionicity is proposed. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150306
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  • 9
    Digitale Medien
    Digitale Medien
    Ab initio study of low-lying electronic states of the PF2 radical (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 346-350 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low-lying electronic states X2B1, 2A1, 2B2, and 2A2 of the PF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X2B1 state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the 2A1 → X2B1 and 2A2 → X2B1 transitions, and radiative lifetimes for the 2A1 and 2A2 states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150309
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  • 10
    Digitale Medien
    Digitale Medien
    Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 351-373 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero-sum ethane-to-ethane′ perturbation ΔΔGaq(CH3—methyl—X → X—methyl—CH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO—NH → CH=CH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL-) in a potential of mean force calculation ΔGMeOH(SAL- · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 11 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150310
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