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  • 2005-2009
  • 1990-1994  (766)
  • 1985-1989  (529)
  • 1920-1924
  • Biochemistry  (1.295)
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  • 201
    Digitale Medien
    Digitale Medien
    Analytical density-dependent representation of Hartree - Fock atomic potentials (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 410-421 
    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 procedure to represent atomic electron charge densities [L. Fernandez Pacios, J. Phys. Chem., 95, 10653 (1991); J. Phys. Chem., 96, 7294 (1992)] is here generalized to obtain simple analytical functions for potential energy contributions. Based upon suitable functions to describe atomic electron densities in a physically meaningful form, the procedure is developed to define density-dependent analytical expressions for the electrostatic (classical) and exchange (quantum) potentials by means of proper approximate functionals. Calculations of correlation energies by using various density-functional approaches are also performed. The whole scheme is used to represent Hartree-Fock limit atomic wave functions by Clementi-Roetti. This way, a set of analytically simple, nonbasis set-dependent functions are defined with the aim to be further implemented in energy decomposition schemes for molecular interactions studies using atomic instead of electronic building blocks. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140405
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  • 202
    Digitale Medien
    Digitale Medien
    A molecular mechanics study of alkyl peroxides (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 755-768 
    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: Studies have been carried out on alkyl peroxides with MM3 that have led to a parameter set that allows the calculation of geometries, energies, vibrational frequencies, and heats of formation for alkyl hydroperoxides (R—O—O—H) and dialkyl peroxides (R1—O—O—R2). The results obtained are in agreement with the available experimental and theoretical data. A similar, although less good, parameter set has been developed for MM2. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140702
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  • 203
    Digitale Medien
    Digitale Medien
    Ab initio SCF and Møller - plesset studies on hexafluorides of selenium and tellurium (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1234-1239 
    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: SCF and Møller-Plesset calculations were done for the systems AB6 (TeF6 and SeF6) and AB6E (TeF2-6 and SeF2-6) to determine their relative stabilities and geometric structures. The SCF calculations show that both TeF2-6 (as expected) and SeF2-6 (despite a small central atom) possess nonoctahedral shapes. However, at the Møller-Plesset level only the TeF2-6 ion, studied with a large valence basis set, retains nonoctahedral geometry. The calculated structural parameters of the ion in C3v symmetry (the bond lengths are 2.212 and 1.975 Å and the bond angles are 104.9 and 83.4 °) differ considerably from the octahedral values (2.101 Å and 90.0°), yet the corresponding total energy is only about 1 kcal/mol smaller. The results show significant dependence of the computational predictions on the basis sets used and indicate the need to include electron correlation effects in the studies devoted to establishing the stereochemical activity of the lone electron pair. © John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141012
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  • 204
    Digitale Medien
    Digitale Medien
    New approach to the rapid semiempirical calculation of molecular electrostatic potentials based on the am1 wave function: Comparison with ab initio hf/6-31g* resultsThis work was presented in part at the 205th National Meeting of the American Chemical Society, Denver, CO, March 28-April 2, 1993. (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1101-1111 
    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 new approach to the computation of molecular electrostatic potentials based on the AM1 wave function is described. In contrast to the prevailing philosophy, but consistent with the underlying NDDO approximation, no deorthogonalization of the wave function is carried out. The integrals required for the computation of the electronic contributions to the molecular electrostatic potential are evaluated in a manner similar to that of the AM1 core-electron attraction integrals, while the nuclear contributions are computed using a new semiempirical function - ZA(SASA, SpSp)[1 + exp[ - ωA(RAi - δA)]] - where the atomic parameters ωA and δA are obtained by calibration against the results of ab initio HF/6-31G* calculations. Isopotential contour maps for guanine and cytosine obtained with the new method are qualitatively almost indistinguishable from their HF/6-31G* counterparts, while quantitative comparisons for the minima for a wide range of molecules are reproduced with an rms error of 5.2 kcal mol-1. The locations of the “lone-pair” minima for a wide range of heterosubstituted organic molecules generally fall within 0.02 Å of the corresponding HF/6-31G* minima while those in the π-regions of unsaturated molecules are generally within 0.2 Å. Because of the rapid integral evaluation, the fully semiempirical method described here is extremely economical. For example, for the guanine-cytosine base pair it is 〉500 times faster than calculations in which the complete integral matrix is computed analytically from the deorthogonalized AM1 wave function. © John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140911
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  • 205
    Digitale Medien
    Digitale Medien
    Ab initio models for multiple-hydrogen exchange: Comparison of cyclic four- and six-center systems (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1149-1163 
    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: High-level ab initio calculations {QCISD(T)/6-311 +G**//MP2(fu)/6-31 +G**, with corrections for higher polarization [evaluated at MP2/6-311 +G(3df,2p)] and ΔZPE//MP2(fu)/6-31 +G**, i.e., comparable to Gaussian-2 theory} indicate concerted mechanisms for double- and triple-hydrogen exchange reactions in HF and HCl dimers and trimers, in mixed dimers and trimers containing one NH3, and in mixed dimers of HF, HCl, and NH3 with formic acid. All these reactions proceed via cyclic four- or six-center transition structures, the latter being generally more favorable. Calculated activation barriers (ΔHd̊ at 0 K, kcal/mol) are 42.3 for (HF)2, 20.3 for (HF)3, 41.2 for (HCl)2, 25.6 for (HCl)3, 36.0 for NH3-HF, 10.6 for NH3(HF)2, 19.9 for NH3-HCl, 2.3 for NH3(HCl)2, 9.7 for HCO2H-HF, 7.0 for HCO2H-HCl, and 11.3, for HCO2H-NH3. The barriers are lower for the more ionic systems and when more ion pair character is present. © John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141005
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  • 206
    Digitale Medien
    Digitale Medien
    Shape groups of the electronic isodensity surfaces for small molecules: Shapes of 10-electron hydrides (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1172-1183 
    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: An algorithm for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented in the form of a comprehensive package of computer programs, GSHAPE, and applied to a series of 10-electron hydrides to critically evaluate the methodology. Attention is paid to the effects of nuclear geometry and the size of basis on the molecular shape. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend on two continuous parameters: a density value defining the density contour and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is calculated at the ab initio level using basis sets ranging from STO-3G to 6-31G**. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visualization of the results is one option of our program using Application Visualization Software (AVS). For a given molecule, in a given nuclear geometry, the technique provides a 2-D shape map, displaying the distribution of the shape gruops as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, a variety of 2-D shape maps are discussed. © John Wiley & Sons, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141007
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  • 207
    Digitale Medien
    Digitale Medien
    Ab initio molecular orbital studies for compounds of magnesium (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1523-1533 
    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: Using a 6-311G** basis set with estimation of correlation energy at the MP2 level, structural and energetic data for 40 molecular species containing magnesium have been calculated. For about half the species studied, further energetic data were obtained using Pople's G2 method. Enthalpy changes at 298.15 K were obtained for isogyric reactions and standard enthalpies of formation were derived from these. Comparison of the standard enthalpies of formation with the sparse literature data suggests the MP2/6-311G** standard enthalpies of formation are accurate to ± 15 kJ mol-1 and the corresponding G2 enthalpies accurate to ± 10 kJ mol-1. The calculated ΔH0f [MgN, g] revealed a gross error in the currently accepted value for this function. It is intended that these results will be used to parameterize the semiempirical molecular orbital package, MOPAC, for the element magnesium. © John Wiley & Sons, Inc.
    Zusätzliches Material: 13 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141215
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  • 208
    Digitale Medien
    Digitale Medien
    “Full numerical” diatomic matrix elements: Simplified shooting method (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1519-1522 
    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 problem of diatomic matrix elements Mnn′ = 〈Ψn|Q|Ψn′〉 related to the anharmonic oscillator is considered for standard operators Q of the form x = r - re (r is the radial variable), powers of x, or exponentials, or combinations of such operators; the quantum numbers (n, n′) may be equal or not. A “full numerical” method to determine Mnn′ is presented for any type of the potential U, analytic like that of Morse or numerical like the RKR potential. This numerical method is a simplified version of the standard Cooley shooting method (CSM). The present simplified shooting method (SSM): (1) shoots in one direction only (instead of two); (2) avoids starting problems and matching problems; (3) determines the “end” point automatically (without prior guesses); and (4) reduces thus the number of grid points effectively needed. Examples for analytic (Morse) and RKR potentials are presented. The numerical application to a standard example used by Delgado-Barrio et al. [J. Comp. Chem., 7, 208 (1986)] using the CSM, and by Kobeissi et al. [J. Comp. Chem., 10, 358 (1989)] using the highly accurate “Canonical Functions” method, shows that when the SSM and CSM are used with the same integrator and the same mesh size the relative discrepancy ΔMnn′(between computed and exact M) is averaged for several (n, n′) to 5.4 × 10-4 for the CSM and to 8.5 × 10-6 for the present SSM. This improvement in accuracy is supplemented by a reduction in computer time consumption. © John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141214
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  • 209
    Digitale Medien
    Digitale Medien
    Theoretical investigation into the potential of halogenated methanes to undergo reductive metabolism (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1575-1579 
    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 density-functional theory (DFT)-based computational chemistry software package DMol was used to provide insight into the reductive potentials of a series of halomethanes. It is known that certain members of this series are readily reduced in vivo via catalysis by cytochrome P450. DMol was used to calculate the electron affinities of these molecules to be used as measures of their reduction potentials. Our results are consistent with experimental electrochemical reduction potentials and indicate that electron affinity is dependent upon the number and type of halogens present in the molecule. Calculated bond lengths and angles also compared favorably with experimental results and estimates derived from other ab initio methods of calculation. Concurrent with this study was the observation of a linear empirical relationship between electron affinity and the lowest unoccupied molecular orbital energy. It is possible that these values could be used as indicators of reductive potentials and ultimately of metabolic rates for use in PB-PK models designed to predict the dose associated with the toxicity of molecules of this and other classes. © John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141220
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  • 210
    Digitale Medien
    Digitale Medien
    Calculation of the interaction energy in a localized representation for a trimer (Ne3) system (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1136-1141 
    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 studied the transferability of the localized orbitals (LOs) of interacting Ne atoms using several basis sets. Both at SCF and at MP2 and MP3 levels, the contributions of the LOs have been calculated and discussed for the Ne2 and Ne3 systems. It was shown that for the LOs the transferability is satisfied to a good extent and due to the transferability the interaction energy at the correlated level can be calculated by using only the LOs of the supermolecule. The basis set superposition error (BSSE) is simply extracted from the intramolecular parts of the correlation energy. The two- and three-body interaction energies have been investigated for the studied systems. © John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141003
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  • 211
    Digitale Medien
    Digitale Medien
    Divide-and-conquer, pattern matching, and relaxation methods in interpretation of 2-D NMR spectra of polypeptides (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1164-1171 
    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: One task in the interpretation of the 2-D nuclear magnetic resonance (NMR) spectrum is to assign its signal patterns to their corresponding amino acids in proteins or polypeptides. To carry out this task of interpretation, one requires sufficient chemical knowledge and expertise to reason from a set of highly noisy data. We present a system called RUBIDIUM (a Rule-Based Identification in 2-D NMR Spectrum) to formulate the expertise and automate the process of interpretation. Given a protein or polypeptide with a known amino acid sequence and the 2-D NMR spectra (both COSY and NOESY), RUBIDIUM yields plausible assignments of lines that account for most signals observed in the spectrum and conform to prior chemical knowledge. Rules of pattern matching are used to detect plausible signal patterns. The expertise of the sequence-specific assignment task is formulated to assign a signal pattern to amino acids. To cope with ambiguities and noise, RUBIDIUM adopts various low-level data preprocessing techniques, the strategy of divide and conquer, and the relaxation technique to decrease the complexity and recover from overconstrained conditions. The polypeptides oxytocin and vasopressin are used to illustrate the performance of RUBIDIUM. © John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141006
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  • 212
    Digitale Medien
    Digitale Medien
    LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1212-1233 
    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 central goal in molecular dynamics simulations is increasing the integration time-step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevin/implicit-Euler scheme. Here, we present a modified Langevin/implicit-Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time-steps. However, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is solved by implicit numerical integration. In this way, the high-frequency and fast-varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time-step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane demonstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes. © John Wiley & Sons, Inc.
    Zusätzliches Material: 13 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141011
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  • 213
    Digitale Medien
    Digitale Medien
    Masthead (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140101
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  • 214
    Digitale Medien
    Digitale Medien
    Editorial (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1-1 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140102
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  • 215
    Digitale Medien
    Digitale Medien
    MNDO parameters for helium: Optimization, tests, and application to endohedral fullerene - helium complexes (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 37-44 
    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: MNDO parameters for helium are derived from an optimization that employs only atomic and diatomic reference data. Comparisons with published high-level ab initio results indicate that MNDO correctly predicts the existence of covalently bonded helium compounds and normally reproduces the geometries of these small charged molecules reasonably well. Endohedral fullerene-helium complexes and the transition states for their formation are studied for C60, C60, and C602+. The calculated barriers are discussed and compared with those for the passage of helium through C6H6, C6H6+, and C6H62+. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140108
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  • 216
    Digitale Medien
    Digitale Medien
    Comparison of computational methods applied to oxazole, thiazole, and other heterocyclic compounds (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 75-88 
    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 variety of computational methods, including the semiempirical techniques AM1, PM3, and MNDO, and the thermochemical basis sets of Benson and Stine, was used to calculate and compare heats of formation (ΔHf°) data for optimized geometries of a variety of aromatic and nonaromatic heterocycles. Detailed analyses, including 6-31G* and MP2/6-31G* ab initio calculations, were performed for the oxazole and thiazole heterocycles. The results indicate a scatter among the methods sensitive to the nature of the heterocycle. This was in particular evident in the oxazole molecule, where AM1 gave a singularly high value of ΔHf° consistent with longer calculated bond lengths, particularly about the oxygen atom. Aromatic stabilization energy appears to be addressed differently among the employed methods. Implications of this contrast applied to calculation of macromolecular systems containing heterocyclic units are discussed.
    Zusätzliches Material: 10 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140112
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  • 217
    Digitale Medien
    Digitale Medien
    Molecular conformations from distance matrices (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 114-120 
    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: Two algorithms are introduced that show exceptional promise in finding molecular conformations using distance geometry on nuclear magnetic resonance data. The first algorithm is a gradient version of the majorization algorithm from multidimensional scaling. The main contribution is a large decrease in CPU time. The second algorithm is an iterative algorithm between possible conformations obtained from the first algorithm and permissible data points near the configuration. These ideas are similar to alternating least squares or alternating projections on convex sets. The iterations significantly improve the conformation from the first algorithm when applied to the small peptide E. coli STh enterotoxin. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140115
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  • 218
    Digitale Medien
    Digitale Medien
    Parallelization strategies for molecular simulation using the Monte Carlo algorithm (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 127-137 
    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 describe the development of Metropolis Monte Carlo algorithms for a general network of multiple instruction multiple data (MIMD) parallel processors. The implementation of farm, event, and systolic parallel algorithms on transputer-based computers is detailed and their relative performance discussed. Although the emphasis is on methodology, the application of such parallel algorithms will be important for addressing computational problems such as the determination of free energy differences in complex biologically important molecular systems. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 11 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140202
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  • 219
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    Ab initio study of the ground and excited states of HCP and its isomer HPC (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 186-194 
    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 potential energy surface of HCP converting to HPC in its ground electronic state has been investigated with ab initio methods at levels up to MP2/6-311G**//MP4/6-311G** as well as TZV + + ** CASSCF. All geometries are fully optimized and compare favorably to previous theoretical and experimental values. The HCP molecule is predicted to be 85.4 kcal/mol lower in energy than its linear isomer at the-MP2/6-31G*//MP2/6-31G* level. The energy barrier for hydrogen rearrangement is found to be merely 2.3 kcal from the HPC end. CASSCF studies were initiated to clarify the low barrier and lent support to a flat surface as HPC converts to stable, linear HCP at the TZV + + ** level. CASSCF also predicts that HPC is unstable with respect to bending. Harmonic vibrational frequencies for HCP results in 5% accuracy or better. A bent triplet is found to be the lowest excited state using the CASSCF method. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140206
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  • 220
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    Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 206-215 
    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: Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested in Monte Carlo statistical mechanics simulations for the pure liquids of toluene, m-cresol, anisole, aniline, and benzonitrile at 25°C at 1 atm. The merged potential functions yielded acceptable thermodynamic results for the liquids except in the case of aniline, for which the error in the heat of vaporization was 12%. This was remedied by enhancing the polarity of the model to be more consistent with the observed dipole moment of aniline. Overall, the average errors in computed heats of vaporization and densities were then 2 and 1%, respectively. The structures of the liquids were characterized through energy and radial distribution functions. For m-cresol and aniline, the molecules participate in averages of 1.6 and 1.4 hydrogen bonds, respectively. Condensed phase effects on the torsional energies for anisole, m-cresol, and aniline were found to be small; m-cresol has a slightly enhanced tendency to be nonplanar in the liquid than in the gas phase, while anisole shows the opposite pattern. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 15 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140208
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  • 221
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    Fast generation of molecular surfaces from 3D data fields with an enhanced “marching cube” algorithm (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 246-250 
    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: An improved version of the “marching cubes” algorithm [W. Lorensen and H. Cline, Comp. Graph. 21, (1987)] for the generation of isosurfaces from 3D data fields is presented and applied to molecular surfaces. The new algorithm avoids inconsistent pattern definitions of the original one, which lead to artificial gaps. The advantage of a logarithmic interpolation procedure, in particular for data fields typically occurring in molecular science, is demonstrated. An example is the generation of molecular surfaces based upon electron density data. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 10 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140212
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  • 222
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    Digitale Medien
    Rapid empirical calculation of the first (n or π) ionization potential of organic molecules (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 138-154 
    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 first ionization potential of an organic molecule containing electrons in nonbonding or π-type molecular orbitals can rapidly be calculated using parameters describing physical and chemical effects. These parameters include effective polarizability, resonance stabilization of a cation, π- and σ-charges, and electronegativity and are directly calculated from the structure of the compound. Correlation analyses with the first ionization potentials were carried out on various data sets classified into five groups to cover a wide range of organic molecules. The equations thus obtained were integrated into a system that automatically calculates the ionization potential of an organic compound from a connection table as obtained by a graphic input program. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140203
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  • 223
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    Digitale Medien
    Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 195-205 
    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: Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested by computing free energies of hydration for toluene, p-xylene, phenol, anisole, benzonitrile, p-cresol, hydroquinone, and p-dicyanobenzene. The calculations featured Monte Carlo simulations at 25°C and 1 atm with statistical perturbation theory. The average difference between the computed results and experimental data for the absolute free energies of hydration is 0.5 kcal/mol. The AM1-SM2 method is also found to perform well in predicting the free energies of hydration for the substituted benzenes. In addition, the Monte Carlo simulations provided details on the hydration of the substituted benzenes, in particular for the solute-water hydrogen bonding. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 13 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140207
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  • 224
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    Use of effective core potentials for ab initio calculations on molecular siloxanes and silicates (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 216-225 
    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 series of ab initio electronic structure calculations have been performed on the (H3Si)2O molecule using a range of basis sets. The accuracy of these calculations was evaluated by comparison with several experimental measurements. These calculations support earlier results indicating that polarization functions on the bridging oxygen atom are usually required to obtain a bent geometry for the Si-O-Si linkage in disiloxane. It was found that ab initio calculations utilizing effective core potentials and a double-ζ valence description augmented with polarization functions (CEP-31G*) provide results comparable in quality to those obtained using the all-electron 6-31G* basis set. To demonstrate the general utility of these effective core potential basis sets for theoretical studies of molecular silicates, calculations were performed on the (HO)3SiOSi(OH)3 molecule. The results obtained are in excellent agreement with previous experimental and ab initio calculations using all-electron basis sets. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140209
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  • 225
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    Further comments on the lack of homoaromaticity in triquinacene (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 251-251 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140213
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  • 226
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    Digitale Medien
    Observations concerning the treatment of long-range interactions in molecular dynamics simulations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 278-284 
    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: Molecular dynamics simulations of pure water employing two different empirical water models have been used to study the effects of different methods for truncation of long-range interactions in molecular mechanics calculations. As has been observed previously in integral equation studies, “shifting” these interactions on an atom-by-atom basis was found to produce artificial structuring in the water and affect diffusion rates. In cases where some form of short-range truncation must be used, the ST2 switching function applied on a group-by-group basis was found to be the most realistic procedure. If atom-based shifting must be employed, a cutoff distance greater than or equal to 12.0 Å was found to be required to produce realistic results. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140304
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  • 227
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    Is tetrahedral H42+ a minimum? Anomalous behavior of popular basis sets with the standard p exponents on hydrogen (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 285-294 
    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 nature of the tetrahedral H42+ stationary point (minimum or triply degenerate saddle) depends remarkably upon the theoretical level employed. Harmonic vibrational analyses with, e.g., the 6-31G** (and 6-31 + +G**) and Dunning's [4s2p1d;2s1p] [D95(d,p)] basis sets using the standard p exponent suggest (erroneously) that the Td geometry is a minimum at both the HF and MP2 levels. This is not the case at definitive higher levels. The C3H42+ structure with an apical H is another example of the failure of the calculations with the 6-31G**, 6-311G**, and D95(d,p) basis sets. Even at MP2/6-31G** and MP2/ cc-pVDZ levels, the C3v structure has no negative eigenvalues of the Hessian. Actually, this form is a second-order saddle point as shown by the MP2/6-31G** calculation with the optimized exponent. The D4h methane dication structure is also an example of the misleading performance of the 6-31G** basis set. In all these cases, energy-optimized hydrogen p exponents give the correct results, i.e., those found with more extended treatments. Optimized values of the hydrogen polarization function exponents eliminate these defects in 6-31G** calculations. Species with higher coordinate hydrogens may also be calculated reliably by using more than one set of p functions on hydrogen [e.g., the 6-31G(d,2p) basis set]. Not all cases are critical. A survey of examples, also including some boron compounds, provides calibration. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140305
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  • 228
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    Digitale Medien
    Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 295-311 
    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: In a previous aqueous protein dynamics study, we compared the rms deviation relative to the crystal structure for distance-dependent and constant dielectric models with and without a nonbonded cutoff. The structures obtained from a constant dielectric simulation with a cutoff were substantially different from the structures obtained from a distance-dependent dielectric simulation, with and without cutoff, and a constant dielectric model without a cutoff. In fact, structures from the distance-dependent dielectric simulations were insensitive to the nonbonded cutoff and in good agreement with the structures generated from the constant dielectric simulation without a cutoff. In addition, the solute-solvent temperature differential and solvent evaporation artifacts, characteristic of the constant dielectric simulation with a cutoff, were not present for the distance-dependent dielectric simulations. In this current work, we explore whether this dielectric-dependent cutoff-sensitive behavior for a constant dielectric model arises from the discontinuities in the forces at the nonbonded cutoff or from neglecting the structure-stabilizing interactions beyond the nonbonded cutoff. We also examine the origin of the dielectric-dependent artifacts, and its potential influence on the structural disparity. Several protocols for protein dynamics simulations are compared using both constant and distance-dependent dielectric models, including implementation of a switching function and a nonbonded cutoff and two different temperature coupling algorithms. We show that the distance-dependent dielectric model conserves energy in the SPASMS molecular mechanics and dynamics software for the time steps and nonbonded cutoffs commonly used in macromolecule simulations. Although the switching function simulation also conserved energy over a range of commonly used cutoffs, the constant dielectric model with a switching function yielded conformational results more similar to a constant dielectric simulation without a switching function than to a constant dielectric model without a nonbonded cutoff. Therefore, the conformational disparity between the dielectric models arises from neglecting important structure-stabilizing interactions beyond the cutoff, rather than differences in energy conservation. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140306
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  • 229
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    Digitale Medien
    Fitting of nonlinear regressions by orthogonalized power series (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 363-370 
    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 outline a procedure that resolves ambiguities in fitting nonlinear data by power series. As is well known, the coefficients in the regression equations depend upon the truncation of the power series. We outline the procedure in which the coefficients of the regression using a power expansion are independent of the degree of the polynomials used. This is achieved by considering mutual regression of descriptors and using residuals as novel variables. The derived regression equations show unusual numerical stability, i.e., the coefficients of the regression equations are constant and independent of the truncation of the power series. The process is illustrated in an example to show all details and facilitate duplicating the process for interested readers. The method described here complements recently outlined procedures for construction of orthogonal descriptors for use in multivariate regression analysis. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140311
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  • 230
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    Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 392-400 
    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: Semiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl-mercaptans (Cys-46, Cys-176), an imidazole (His-67), and a water. An imidazole (His-51) hydrogen bonded to a hydroxy-acetate (Ser-48) forms the remote base. AM1 calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His-51) via hydrogen-bonded hydroxy-acetate (Ser-48), creating a proton relay system; and (2) the rate-limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD+), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc-bound OH- and by direct deprotonation of zinc-bound ethanol by imidazole via hydroxyacetate (Ser-48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner-sphere-pentacoordinated complex to the active site zincion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our results. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140403
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  • 231
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    Supplementary d and f functions in molecular wave functions: Optimum and nonoptimum exponents (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 54-66 
    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: Energy optimization calculations have been carried out to determine the variability of optimum p, d, and f polarization function exponents in molecules containing first- and second-row elements and in normal valency and hypercoordinate species. Optimum exponents were determined for single sets of higher-order functions at both Hartree-Fock and correlated (Moller-Plesset) levels of theory using the Dunning-Hay double zeta and the McLean-Chandler triple zeta basis sets. More detailed calculations were used to test the response to nonoptimum d and f function exponents of the total energy, the optimum geometry, and harmonic stretching frequencies. The variability in optimum exponents and the size of the energy penalties incurred by adopting nonoptimum values reduces the utility of standard exponents for p, d, and f polarization functions. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140110
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  • 232
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    Digitale Medien
    Ability of the PM3 quantum-mechanical method to model intermolecular hydrogen bonding between neutral molecules (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 89-104 
    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: The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-1 suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-1 imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 Å for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-1. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and O predict that donor strength follows the order F 〉 O 〉 N and acceptor strength follows the order N 〉 O 〉 F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H---N bond to be the strongest and the N-H---F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140113
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  • 233
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    Digitale Medien
    Multigrid solution of the Poisson - Boltzmann equation (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 105-113 
    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 multigrid method is presented for the numerical solution of the linearized Poisson-Boltzmann equation arising in molecular biophysics. The equation is discretized with the finite volume method, and the numerical solution of the discrete equations is accomplished with multiple grid techniques originally developed for twodimensional interface problems occurring in reactor physics. A detailed analysis of the resulting method is presented for several computer architectures, including comparisons to diagonally scaled CG, ICCG, vectorized ICCG and MICCG, and to SOR provided with an optimal relaxation parameter. Our results indicate that the multigrid method is superior to the preconditioned CG methods and SOR and that the advantage of multigrid grows with the problem size. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140114
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  • 234
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    Digitale Medien
    Benzene is not very rigid (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 121-125 
    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 concept of molecular kurtosis as a dynamic molecular shape descriptor is introduced and used to compare the relative flexibilities of benzene and cyclohexane. For small torsional deformations (〈15°) the potential energy surfaces are similar, indicating both molecules are flexible. Using molecular kurtosis, the stiffness of benzene and cyclohexane are compared from gas-phase stochastic dynamics simulations and validated by distributions found in the Cambridge Structural Database. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140116
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  • 235
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    Digitale Medien
    Ab initio calculations on phosphorus compounds. II. Effects of disubstitution on ligand apicophilicity in phosphoranes (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 522-529 
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    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Geometry optimizations at the HF/3-21G(*) and HF/6-31G* levels of ab initio theory have been carried out for various isomers of model disubstituted phosphoranes PH3XY(X, Y=OH, CH3, NH2, and SH). Reasonable agreement was obtained between the optimized geometries and available crystal structure data for analogous compounds. The isomers were further characterized by frequency calculations. The MP2/6-31G*//6-31G* + ZPE energy data reveal that the interactions between the ligands are relatively small (0-4 kcal mol-1) for the most stable conformations of the isomers. Hence, for these conformations the apicophilicities (based upon monosubstituted phosphoranes) are approximately additive. The less stable PH3XY conformations are in general transition states or higher-order saddle points, and their interligand interactions are larger in magnitude (up to 10 kcal mol-1); the results with these conformations suggest that apicophilicities may not be as additive for some highly substituted phosphoranes. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140504
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  • 236
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    Substrate specificity of cytochrome P450cam for L- and D- norcamphor as studied by molecular dynamics simulations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 541-548 
    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: In our earlier molecular dynamics simulations, we found that there was a discrepancy between the predicted and experimental product ratios when norcamphor is hydroxylated by cytochrome P450cam. The experimental results suggest that there is a nearly equimolar ratio between the 5- and 6-hydroxynorcamphor (45% 5-, 47% 6-, and 8% 3-hydroxynorcamphor) [W.M. Atkins and S.J. Sligar, J. Am. Chem. Soc., 109, 3754 (1987)]. Our previous simulations predicted predominately from 68-88% 5-hydroxynorcamphor [M.B. Bass et al., Prot. Struct. Funct. Genet., 13, 26 (1992); M.B. Bass et al., Proc. Natl. Acad. Sci. U.S.A., submitted]. One possible explanation for this discrepancy is that the simulations were performed using D-norcamphor while the experiments were conducted with racemic norcamphor. The suggestion that norcamphor is the D-isomer was based upon the similarity with the native substrate D-camphor. Indeed, the reported crystallographic structure for norcamphor-bound P450cam models norcamphor as the D-isomer. Unfortunately, the two stereomers have never been separated. The simulations presented here model the L-isomer of norcamphor. Three simulations each of the L- and D-isomers of norcamphor bound to cytochrome P450cam were compared to account for the effects due to substrate orientation and the assignment of random velocities. The results presented here show that the L-isomer of norcamphor is predicted to give rise to predominately 6-hydroxynorcamphor, while the D-isomer gives rise to mainly 5-hydroxynorcamphor. From this data, we infer that racemic norcamphor will give rise to nonracemic 5- and 6-hydroxynorcamphors after oxidation by cytochrome P450cam. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140506
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  • 237
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    Digitale Medien
    FORTRAN routine to compute Born-Oppenheimer potential energy curves directly from spectroscopic data (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 579-586 
    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 computer program that calculates Born-Oppenheimer potential energy curves of diatomic molecules directly from spectroscopic data is presented. Rather than performing the usual preliminary fitting of the experimental data to a single polynomial in the variable (v + 1/2), where v is the vibrational quantum number, the program contains an accurate built-in interpolation routine by which each experimental input point belongs to its own polynomial. The program is tested on the ground state of the H2 molecule and results are compared with the most accurate ab initio calculations available. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140511
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  • 238
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    Digitale Medien
    Molecular interaction potential: A new tool for the theoretical study of molecular reactivity (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 587-602 
    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 new methodology to compute molecular interaction potentials (MIPs) is developed and tested. The calculation of the MIP is based upon the generalization of the rigorous quantum mechanical molecular electrostatic potential (MEP) and further addition of a classical repulsion-dispersion term. As a result, the MIP is able to represent not only with high accuracy electrostatic interactions but also represent in a suitable way steric effects. The analysis of the results obtained for different molecules demonstrates the superiority of the MIP with regard to the standard MEP to describe nonbonded interactions, in particular hydrogen bonds. The comparison of results calculated at the ab initio I 6-31G* and semiempirical AM1 levels points out the suitability of semiempirical calculations to qualitatively reproduce the most relevant reactive features of the molecules. Finally, possible applications of the MIP in different fields are discussed. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140512
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  • 239
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    Digitale Medien
    Are most of the stationary points in a molecular association minima? Application of Fraga's potential to benzene-benzene (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 647-654 
    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 importance of characterizing the stationary points of the intermolecular potential by means of Hessian eigenvalues is illustrated for the calculation of the benzene-benzene interaction using an atom-to-atom pair potential proposed by Fraga (FAAP). Two models, the standard one-center-per atom and another using three-centers-per atom due to Hunter and Sanders, are used to evaluate the electrostatic contributions and the results are compared. It is found in both cases that although using low-gradient thresholds allows optimization procedures to avoid many stationary points that are not true minima computing time considerations makes the usual procedure of using high-gradient thresholds [say, 10-2 kj/(mol Å)] as the most efficient. Moreover, this later procedure can be recommended because the actual minima can be characterized by means of Hessian eigenvalues even if these high-gradient thresholds are used, and further decreasing of the convergence criterion does not imply significant modifications in the geometric parameters of the minima. The possible advantages of using the three-centers-per-atom model for the calculation of molecular associations between delocalized systems are also discussed on the basis of the agreement of the benzene-benzene results with experimental and theoretical data taken from the literature. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140604
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  • 240
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    Digitale Medien
    Madelung fields from optimized point charges for ab initio cluster model calculations on ionic systems (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 680-684 
    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 simple procedure devised to obtain optimized point charges to represent the Madelung potential is reported and applied to six different crystal structures occurring in ionic systems. Their use in ab initio cluster model calculations is discussed through some selected examples and results compared with those arising from the use of the well-known Evjen method. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140608
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  • 241
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    Digitale Medien
    Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 691-698 
    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 new stochastic (Monte Carlo) procedure, termed torsional flexing, has been devised for searching the conformational space of cyclic molecules. Torsional flexing causes a local, torsion angle-biased, distortion of a ring bond in a cyclic molecule. Because torsional flexing does not cause large atomic movements, even when it is applied to several bonds simultaneously, subsequent energy minimization generally proceeds rapidly. Nevertheless, the torsional flexing method is prone to generate structures that cross energy barriers so that the structure resulting after energy minimization is frequently a different conformer of the cyclic molecule. Conformational searches on cycloheptadecane, oxobrefeldin A, cyclopenta-L-alanine, and rifamycin SV based upon torsional flexing indicated that torsional flexing is among the best methods yet devised for searching the conformational space of flexible cyclic molecules. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140610
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  • 242
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    Digitale Medien
    Beyond the MNDO model: Methodical considerations and numerical results (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 775-789 
    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: It is suggested to improve the MNDO model by the explicit inclusion of valence-shell orthogonalization corrections, penetration integrals, and effective core potentials (ECPs) in the one-center part of the core Hamiltonian matrix. Guided by analytic formulas and numerical ab initio results, the orthogonalization corrections are expressed in terms of the resonance integrals that are represented by a new empirical parametric function. All two-center Coulomb interactions and ECP integrals are evaluated analytically in a Gaussian basis followed by a uniform Klopman-Ohno scaling. One particular implementation of the proposed NDDO SCF approach is described and parameterized for the elements H, C, N, O, and F. In a statistical evaluation of ground-state properties, this implementation shows slight but consistent improvements over MNDO, AM1, and PM3. Significant improvements are found for excited states, transition states, and strong hydrogen bonds. Possible further enhancements of the current implementation are discussed. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140704
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  • 243
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    Implementation of the direct SCF and RPA methods on loosely coupled networks of workstations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 818-830 
    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 use of a cluster of workstations as an alternative supercomputer resource is demonstrated using the ab initio direct SCF and RPA code DISCO. DISCO was implemented using several different mechanisms to achieve the requisite parallelization. The various parallel software mechanisms are characterized based upon several different criteria, including portability, ease of use, and relative efficiency. The application of direct SCF and RPA techniques to study the static polarizability of paranitroaniline is described. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140708
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  • 244
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    Digitale Medien
    Masthead (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140801
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  • 245
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    Digitale Medien
    Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 881-894 
    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 report a theoretical study of the stretching of chemical bonds and its implications on the force-field parametrization. Computations were performed at the SCF and MCSCF levels by using minimal, split-valence, and large extended and polarized basis sets. The stretching energy profiles were determined considering up to 25 perturbed geometries of 11 different bonds (6 singles, 2 doubles, and 3 triples). The energy profiles and stretching parameters are compared with the experimental data compiled in the most popular force fields. MCSCF stretching energy profiles are mainly anharmonic and can be only roughly reproduced by quadratic equations. The use of Allinger's MM2 quasiharmonic expression appears as the best choice because it fits with reasonable accuracy a large percentage of the stretching profile without increasing the complexity of the formalism and of the parametrization procedure. MCSCF computations are needed to obtain reliable stretching force parameters. In this respect, MCSCF calculations considering as active space only the bonded and nonbonded orbitals of the perturbed bond seems to be the best strategy to obtain good results at a minimum computational cost, especially if small split-valence basis sets like the 3-21G are used. Results obtained at this level of sophistication are completely comparable to stretching parameters compiled on empirical force fields. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140802
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  • 246
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    Digitale Medien
    Analysis of the core-repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 895-898 
    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 AM1 and PM3 potential energy surfaces of cyclopentane have been compared and the energy difference between two (boat and chair) cyclohexane conformers analyzed. The effects of reparameterization and different core-repulsion functions (CRFs) have been studied. The H—H, C—H, and C—C CRF energy contributions have been calculated separately. The results show that the CRF energy corrections stabilize the correct (MM2 and ab initio) geometries. The PM3 equilibrium geometry of cyclopentane is closer to the MM2 and ab initio results than the AM1 geometry. It is known that above 190 pm the AM1 H—H CRF curve is smooth and negative but the PM3 H—H CRF curve has a trough and a shoulder. It has been shown that this latter oscillation is not damped by other parameters. As a result, the H—H PM3 energy gradient curve is different from the quasilinear AM1 and ab initio gradient curves. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140803
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  • 247
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    Digitale Medien
    Masthead (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140601
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  • 248
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    Digitale Medien
    Treatment of hydrogen bonding in SINDO1 (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 639-646 
    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: For the treatment of hydrogen bonding in SINDO1, 2p orbitals are introduced on hydrogen. The optimization of the orbital exponent together with the generation of approximate formulas for the core attraction integrals is sufficient to obtain good geometries and binding energies in hydrogen bonded systems. The method is applied to the dimers (H2O)2, (NH3)2, (HF)2, (HCOOH)2, (HCN)2, (H2S)2, and (HCI)2, mixed dimers NH3 · H2O and H2O · HCN, and cyclic polymers (HF)n(n = 3, 4, 6). © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140603
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  • 249
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    Digitale Medien
    Techniques for the compression of sequences of integer numbers and real numbers with fixed absolute precision (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 673-679 
    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: Algorithms to reduce the space needed to store information either in memory or magnetic media are presented. These algorithms were designed to pack and unpack two common kinds of data types: sequences of sets of integers that change in a regular fashion and real numbers of fixed absolute precision. One typical application of these techniques is in the storage of electron repulsion integrals in ab initio calculations, where the indices of the basis functions are a good example of data of the first type and the integrals of the second type. In this case, savings in storage space of 50% or more can be obtained with reasonable accuracies in the energies. FORTRAN subroutines are presented for packing/unpacking indices and integrals both in the IBM and IEEE 754 64-bit floating point formats. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140607
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  • 250
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    Digitale Medien
    Relative basicities of carboxylate lone pairs in aqueous solution (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 685-690 
    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: Relative basicities of the lone pairs of the acetate ion have been determined using ab initio calculations for the gas phase and Monte Carlo simulations for the aqueous phase. The syn lone pair is found to be more basic by only 1.25 pKa units. This small difference is the result of a large intrinsic preference for the syn conformer of the conjugate acid in the gas phase, offset by an almost equally large preferential solvation of the anti conformer in the aqueous phase. The better solvation of the anti conformer is due to stronger solute-solvent interactions. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140609
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  • 251
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    Digitale Medien
    Application of parallel processing techniques to improving the efficiency of MM2 molecular mechanics calculations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 977-985 
    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 application of parallel processing techniques to molecular mechanics calculations is evaluated. Using the standard molecular mechanics package, MM2, four different parallel versions of the program are implemented in a four-processor computing environment. A set of 529 test structures is used to compare the efficiency of the parallel versions of MM2 to a standard serial version of the program. Statistics describing execution times and program execution cycles are gathered and analyzed. The effects of parallel processing overhead and computer system load are explored, and the practical utility of parallel processing in molecular mechanics is estimated. The results of these parallelization experiments indicate that for geometry optimizations requiring significant amounts of computing time an improvement in program execution speed approaching 50% is realizable. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140813
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  • 252
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    Digitale Medien
    AMBER force-field parameters for guanosine triphosphate and its imido and methylene analogs (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 995-1005 
    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: Parameters were derived for guanosine triphosphate (GTP) and GTP analogs suitable for the AMBER force field. Electrostatically derived net atomic charges and force parameters were extracted from MNDO semiempirical calculations. The later parameters came from fitting MNDO and AMBER atom-atom forces in a manner that is extensible to other compounds that lack sufficient vibrational spectral data. The geometric parameters for these compounds were obtained from model compounds in the Cambridge crystallographic data base. Dynamic simulations of Na4 GTP and Na2 Mg GTP of 140 and 100 ps, respectively, indicated a strong preference for a syn C2′ exo conformation in solution. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140815
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  • 253
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    Digitale Medien
    Ab initio study of hydrogen bonding in the phenol-water system (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1027-1035 
    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: Three hydrogen-bonded minima on the phenol-water, C6H5OH - H2O, potential energy surface were located with 3-21G and 6-31G** basis sets at both Hartree-Fock and MP2 levels of theory. MP2 binding energies were computed using large “correlation consistent” basis sets that included extra diffuse functions on all atoms. An estimate of the effect of expanding the basis set to the triple-zeta level (multiple f functions on carbon and oxygen and multiple d functions on hydrogen) was derived from calculations on a related prototype system. The best estimates of the electronic binding energies for the three minima are -7.8, -5.0, and -2.0 kcal/mol. The consequences of uncertainties in the geometries and limitations in the level of correlation recovery are analyzed. It is suggested that our best estimates will likely underestimate the complete basis set, full CI values by 0.1-0.3 kcal/mol. Vibrational normal modes were determined for all three minima, including an MP2/6-31G** analysis for the most strongly bound complex. Computational strategies for larger phenol-water complexes are discussed. © John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140904
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  • 254
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    Digitale Medien
    Chiral force constants: Recommendations for the presentation of internal coordinate force constants (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 751-752 
    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: Some force constants associated with the internal coordinates that sense handedness or chirality can have opposite signs in the enantiomers of chiral molecules. Examples of such force constants include interaction force constants between a torsional and stretching or bending internal coordinates. The sign reversal for these force constants in the enantiomers of chiral molecules or in opposite-handed molecular segments is best recognized by labeling them as chiral force constants. Recognition of chiral force constants suggests that certain guidelines are to be followed in the presentation of internal coordinate force constants. © 1993 by John Wiley & Sons, Inc. © John Wiley & Sons, Inc.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140617
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  • 255
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    Digitale Medien
    A critical comparison of search algorithms applied to the optimization of protein side-chain conformations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 790-798 
    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: Three different optimization algorithms are applied to solving the problem of finding the best side-chain conformations with a test set of 14 globular proteins having known crystallographic conformations. It is shown that simulated annealing, simple and modified genetic algorithms, and a heuristic combinatorial approach achieve similar optimal solutions, with the exception of simulated annealing applied to the largest proteins. The efficiency of the different algorithms, however, shows wide variations. General conclusions are drawn concerning the optimal approach to such problems. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140705
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  • 256
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    Hydrolytic degradation of α-substituted polyglycolic acids: A semiempirical computational study (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 809-817 
    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 two-step hydrolyses of substituted polyglycolic acids are modeled by the semiempirical MNDO Hamiltonian using small molecule analogs to determine the effect of the alkyl substituents on the reaction and activation enthalpies. Reaction enthalpies remain reasonably constant up to three carbons, before becoming less exothermic for large alkyl substituents. Activation enthalpies show patterns that can be explained by steric effects. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140707
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  • 257
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    Digitale Medien
    Lattice representations of globular proteins: How good are they? (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1194-1202 
    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: Using a number of different lattice models of proteins, the problems introduced by the discretization of a protein backbone are discussed and examples of the most typical errors arising in low coordination number lattices presented. The geometric properties of different lattices used in the literature are compiled, and for all of them the resulting α-carbon models of proteins are described in detail and compared to the original structures obtained from experiment. © John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141009
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  • 258
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    Theoretical investigations on thallium halides: Relativistic and electron correlation effects in T1X and T1X3 compounds (X=F, C1, Br, and I) (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 913-921 
    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: Relativistic and electron correlation effects in thallium halides TlX and TlX3 (X=F, Cl, Br, and I) are investigated by extensive ab initio configuration interaction calculations. Spin-orbit coupling is included at the Hartree-Fock level for the diatomic TlBr and TlI. At the best level of treatment of electron correlation (quadratic configuration interaction), the calculated molecular properties are in good agreement with experimental results, i.e., for the diatomic thallium halides deviations from experimental values are 〈0.06 Å for bond distances, 〈0.14 mdyn/Å for force constants, 〈35 kJ/mol for dissociation energies, and 〈0.3 D for dipole moments. The convergence of the Møller-Plesset series up to the fourth order is discussed. Two alternative structures of TlI3 are compared. At the Møller-Plesset level of theory, the trigonal planar structure with thallium in the oxidation state + 3 is the preferred gas phase arrangement compared with the bent arrangement containing a linear I3- unit and thallium in the oxidation state + 1, the difference being ca. 95 kJ/mol. Vibrational frequencies are predicted for all trigonal planar thallium(III) halides. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140806
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  • 259
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    Computational convergence of electronic structure calculations of transition metal ligand complexes (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 961-969 
    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: Calculations of binding energies and optimum geometries of compounds of the series M(H2O)+ with M = Sc to Zn have been carried out and compared with gas-phase experimental data and with the Rosi and Bauschlicher MCPF calculations. Hartree-Fock calculations and correlated calculations at MP2, MP4, and QCISD(T) levels were used to test the dependence of the results upon the level of correlation. A test of basis set dependence was also carried out, using parallel calculations on four basis sets ranging in size from a small DZ set to a TZ contraction. Correlation levels above MP2 and elaboration of the metal d-function basis set to (4d/3d) size or greater were both necessary for convergence with the most uniformly reliable results obtained from QCISD(T) calculations on a basis set with a (6d/4d) contraction for the d-function space. However, MP2 or higher-level calculations with a contracted four or five d function set [(5d/3d) or (4d/3d)] are capable of yielding results on binding energies and geometries close to the current gas-phase experimental uncertainty on electrostatically bound transition metal complexes. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140811
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  • 260
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    Evaluation of one-electron integrals for arbitrary operators V(r) over Cartesian Gaussians: Application to inverse-square distance and Yukawa operators (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 986-994 
    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 procedure is presented for generating one-electron integrals over any arbitrary potential operator that is a function of radial distance only. The procedure outlines that for a nucleus centered at point C integrals over Cartesian Gaussians can be written as linear combinations of 1-D integrals. These Cartesian Gaussian functions are expressed in a compact form involving easily computed auxiliary functions. It is well known that integrals over the Coulomb operator can be expressed in terms of Fn(T) integrals, where \documentclass{article}\pagestyle{empty}\begin{document}$$ F_n \left(T \right) = \int_0^1 {u^{2n} e^{ - Tu^2 } {\rm d}u} $$\end{document} By means of a substitution for Fn(T) by other simple functions, algorithms that form integrals over an arbitrary function can be generated. Formation of such integrals is accomplished with minor editing of existing code based on the McMurchie-Davidson formalism. Further, the method is applied using the inverse-square distance and Yukawa potential operators V(r) over Cartesian Gaussian functions. Thus, the proposed methodology covers a large class of one-electron integrals necessary for theoretical studies of molecular systems by ab initio calculations. Finally, by virtue of the procedure's recursive nature it provides us with an efficient scheme of computing the proposed class of one-electron integrals. © 1993 John Wiley & Sons, Inc.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140814
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  • 261
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    Assessment of methods used for predicting lipophilicity: Application to nucleosides and nucleoside bases (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1019-1026 
    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: Estimating log P (logarithm of “1-octanol to water” partition coefficients) as a measure of lipophilicity for organic compounds is of considerable importance in drug discovery. Several methods have been developed for this purpose, each with its own drawbacks and advantages. In this article, a systematic comparison of three well-documented and fully computerized methods has been attempted for a set of nucleosides and bases. The first method (BLOGP) is based on overall molecular properties derived from a molecular orbital calculation to predict log P. The second method (CLOGP) uses fragmental lipophilicity constants with correction factors and treats log P as an additive-constitutive property. The third method (ALOGP) is based on an additivity scheme of atomic lipophilicity constants, with the constitutive factor governed by an elaborate list of atom types. However, none of these methods take into account conformational flexibility or intramolecular hydrogen bonding, which can cause substantial discrepancy between observations and predictions. A comparison of predictions from each of these methods indicates that the atomic contribution method (ALOGP with r = 0.842 and SD = 0.51) is better than other methods (with r = 0.395 and SD = 1.2 for BLOGP and r = 0.713 and SD = 0.93 for CLOGP) for this class of compounds. Our overall assessment is that we do not have, as yet, a highly reliable, fully computerized log P prediction method applicable to flexible heterocycles such as nucleoside analogs. © John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140903
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    Quantification of substituent and ligand size by the use of solid angles (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1042-1049 
    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 new, generalized, method for measuring the steric size of ligands and substituents has been developed. The method is based on the solid angle concept, the solid angle being generated by the pairwise addition of spheres (atoms). The problem of overlapping spheres (atoms) has been solved analytically and the algorithm provided permits evaluation of the steric space occupied by any combination of spheres (atoms). A range of solid angles for commonly encountered ligands and substituents has been determined and compared to literature values for linear cone angles. © John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140906
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  • 263
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    Digitale Medien
    New combining rules for rare gas van der waals parameters (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1077-1084 
    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: New combining rules are proposed for the well depth, ∊, and interaction distance, σ, describing nonbonded interatomic forces for rare gas pair interactions. Concepts underlying current combining rules applied in simulations of macromolecular and polymer systems are shown to be incompatible with experimental data on the rare gases. The current combining rules are compared with the new results using the experimental data. Mathematical properties of combining rules are considered, and it is shown how to reduce combining rule formulas from a two-parameter to a single-parameter problem. It is also shown how to graphically analyze combining rules against experimental data. We demonstrate using this analysis technique that the rare gas potentials do not obey a single combining rule for the ∊ parameter but do follow a single combining rule for the σ parameter. Finally, we demonstrate that a combining rule using both ∊ and ω can be used to predict the ∊ parameters for the mixed rare gas pairs. © John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140909
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  • 264
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    Digitale Medien
    Partitioning the motion in molecular dynamics simulations into characteristic modes of motion (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1259-1271 
    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: Molecular dynamics (MD) simulations result in a comprehensive description of molecular motion. However, to gain insight into the dynamic behavior of molecules it is important to be able to identify different types of motions and characterize them. We have developed a novel technique aimed at characterizing the motion of the system using digital signal processing techniques. The amplitudes and phases of the Fourier transform of the atomic fluctuations are used to define the characteristic modes of motion in the MD trajectory. This yields a pictorial description of the oscillatory motions in a manor analogous to normal-mode (NM) analysis. The validity of this method has been tested on small molecules such as water, acetamide, and a blocked polyalanine in a helical conformation. The NMs obtained by diagonalizing the mass-weighted second derivative matrix were combined to generate “NM trajectories” that served as well-characterized test cases. Distinct characteristic modes can be extracted from both NM and MD trajectories. The modes extracted from the NM trajectories were identical to the original NMs. The modes extracted from the MD trajectories were in most cases highly correlated to the corresponding NM. However, intermixing of some of the modes occurred, particularly when conformational changes took place. This technique is flexible and can be applied to the molecular system as a whole or to a subset of atoms of interest. Fourier transform calculations are fast and therefore the analysis stage is not demanding in computational resources. Anharmonicity is included explicitly in the simulations and solvent can be included as well. © John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141102
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  • 265
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    Critical reevaluation of proximity effects in the barton oxidation and related intramolecular reactionsTaken from S. Vijayakumar, PhD Thesis, University of Toledo, Toledo, Oh, 1992. (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1313-1319 
    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 limiting factor to account for the increased rate of intramolecular reactions between functional groups as opposed to their intermolecular counterparts can and has been explained both by proximity effects and by activation energy. Neither explanation has emerged as the single most important reason in all or even the majority of cases studied. We have therefore reexamined the spatiotemporal hypothesis of Menger and the transition-state energy approach of Houk on a consistent set of compounds subjected to the Barton oxidation or related reactions in an effort to more clearly define the reasons for the proximity effect. For the 26 structures studied, neither hypothesis provides a consistent, quantitative explanation although the transitionstate energy hypothesis offered the most promise. © John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141107
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  • 266
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    Digitale Medien
    Constrained optimization in cartesian coordinates (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1339-1346 
    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: Modifications are made to a previously published algorithm for constrained optimization in Cartesian coordinates (J. Comp. Chem., 13, 240, 1992) to incorporate both fixed and dummy atoms. Standard distance and angle constraints can now be specified with respect to dummy atoms, greatly extending the range of constraints that can be handled. Fixed atoms can be eliminated from the optimization space and so there is no need to calculate their gradients resulting in potentially significant savings of CPU time in ab initio computations. Several examples illustrate the range and versatility of the modified algorithm. © John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141111
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  • 267
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    Digitale Medien
    Analysis of the genetic algorithm method of molecular conformation determination (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1385-1395 
    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: Many important problems in chemistry require knowledge of the 3-D conformation of a molecule. A commonly used computational approach is to search for a variety of low-energy conformations. Here, we study the behavior of the genetic algorithm (GA) method as a global search technique for finding these low-energy conformations. Our test molecule is cyclic hexaglycine. The goal of this study is to determine how to best utilize GAs to find low-energy populations of conformations given a fixed amount of CPU time. Two measures are presented that help monitor the improvement in the GA populations and their loss of diversity. Different hybrid methods that combine coarse GA global search with local gradient minimization are evaluated. We present several specific recommendations about trade-offs when choosing GA parameters such as population size, number of generations, rate of interaction between subpopulations, and combinations of GA and gradient minimization. In particular, our results illustrate why approaches that emphasize convergence of the GA can actually decrease its effectiveness as a global conformation search method. © John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141115
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  • 268
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    Digitale Medien
    Conformational searching methods for small molecules. II. Genetic algorithm approach (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1407-1414 
    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 demonstrate the use of a genetic algorithm (GA) search procedure for finding low-energy conformations of small to medium organic molecules (1-12 rotatable bonds). GAS are in a class of biologically motivated optimization methods that evolve a population of individuals where individuals who are more “fit” have a higher probability of surviving into subsequent generations. Here, an individual is a conformation of a given molecule and the fitness is the molecule's conformational energy. In the course of a simulated evolution, the population produces conformations having increasingly lower energy. We test the GA method on a suite of 72 molecules and compare the performance against the CSEARCH algorithm in Sybyl. For molecules with more than eight rotatable bonds, the GA method is more efficient computationally and as the number of rotatable bonds increases the relative efficiency of the GA method grows. The GA method also found energies equal to or lower than the energy of the relaxed crystal structure in the large majority of cases. © John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141117
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  • 269
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    Digitale Medien
    Electric dipole polarity of diatomic molecules (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1440-1445 
    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 restricted SCF (single-configuration SCF) and MCSCF (multiconfiguration SCF) calculations are performed to compute the ground-state electric dipole moments of four pairs of diatomic molecules - (1) CO and BF; (2) SiO and AlF; (3) CS and BCl; and (4) SiS and AlCl - at a number of internuclear distances on both sides of the equilibrium position. Near Hartree-Fock accuracy is obtained in the SCF calculations. All eight molecules have a range of internuclear distance in which electric dipole moments are of the polarity of A-B+. The shapes of computed electric dipole moment functions are discussed in the language of the molecular orbital method and in relationship to electronegativities of atoms. The present study gives us deeper understanding of electron transfer inside molecules and consequently of the apparent contradiction between electronegativity and the dipole polarity of some molecules. © John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141205
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  • 270
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    Bulk properties from finite cluster calculations. VIII. Benchmark calculations of the efficiency of extrapolation methods for the HF and MP2 energies of polyacenes (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1468-1481 
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    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 total energies per unit cell of both the undistorted and the Peierls-distorted polyacene polymers are computed from the respective HF/6-311G** and MP2/6-311G** finite-cluster data using 40 different extrapolation schemes. The benchmark calculations, which aim at assessing the efficiency of extrapolation methods, clearly show that the best procedure for obtaining rapidly converging bulk properties should involve computation of the energy differences, followed by rational extrapolation techniques such Wynn's p algorithm or its iteration, both with the interpolation points xn = (n + 1)2, and closely related extrapolation methods, or Wynn's ε algorithm and its close relative, Aitken's iterated Δ2 algorithm. © John Wiley & Sons, Inc.
    Zusätzliches Material: 20 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141209
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  • 271
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    Digitale Medien
    Comparison of atomic charges derived via different procedures (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1504-1518 
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    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 were obtained from ab initio molecular orbital calculations using a variety of procedures to compare them and assess their utility. Two procedures based on the molecular orbitals were examined, the Mulliken population analysis and the Weinhold-Reed Natural Population Analysis. Two procedures using the charge density distribution were included; the Hirshfeld procedure and Bader's Atoms in Molecules method. Charges also were derived by fitting the electrostatic potential (CHELPG) and making use of the atomic polar tensors (GAPT). The procedures were first examined for basis set independence, and then applied to a group of hydrocarbons. The dipole moments for these molecules were computed from the various atomic charges and compared to the total SCF dipole moments. This was followed by an examination of a series of substituted methanes, simple hydrides, and a group of typical organic compounds such as carbonyl derivatives, nitriles, and nitro compounds. In some cases, the ability of the charges to reproduce electrostatic potentials was examined. © John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141213
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    Evaluation of AM1-calculated radical cation ion-neutral complexes (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1561-1574 
    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: AM1 semiempirical molecular orbital calculations are reported for 20 ion-neutral complexes, including hydrogen-bonded complexes, presumably involved in the gas-phase unimolecular decomposition of simple organic radical cations. The systems investigated are [C2H4O2]·+, [C2H5NO]·+, [C2H6O]·+, [C2H6O2]·+, [C3H6O]·+, [C3H6O2]·+, [C3H8O]·+, and [C3H8O2]·+. The AM1 results are compared with ab initio molecular orbital calculations at different levels of theory up to MP3/6-31G(d, p)//SCF/6-31G(d) + ZPVE and the available experimental data. AM1 fails to predict some local minima and the equilibrium geometries calculated for several complexes are found to be qualitatively different from those predicted by the ab initio calculations. However, reasonable agreement is generally found for the stabilization energies of the complexes toward dissociation into their loosely bound components. © John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141219
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    Use of molecular dynamics simulations with ab initio SCF calculations for the determination of the deuterium quadrupole coupling constant in liquid water and bond lengths in ice (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1553-1560 
    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 deuterium quadrupole coupling constant and asymmetry parameter in heavy water were determined using ab initio SCF calculations. Snapshots from a molecular dynamics simulation were used to give liquid water cluster configurations and the influence of simulation parameters on the quadrupole coupling constant was investigated. The electronic potential model and the number of molecules in the molecular dynamics simulation and the pressure of the system were found to have only a small influence on the quadrupole coupling constant. The average value of the quadrupole coupling constant at room temperature, corrected for the known deficiency of the ab initio calculation in the gas phase, yields a quadrupole coupling constant of 253 kHz, in perfect agreement with the most recent experiments. The oxygen - deuterium bond lengths in ice Ih, ice II, and ice IX were determined using experimental quadrupole coupling constants and a model equation. An averaged bond length of 98.9 pm was obtained for the Ih form, which is approximately 2 pm shorter than that determined by neutron diffraction studies, whereas the bond lengths for the four deuterium sites in ice II and the three sites in ice IX are in fair agreement with experiment. © John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141218
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    Conformational analysis of HIV protease inhibitors. I. Rotation of the amide group adjacent to the P′1 decahydroisoquinoline ring system in ro 31-8959 and related systems (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1446-1453 
    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: Pipecolic acid derivatives have proven to be effective P′1 groups in a series of highly potent inhibitors of the enzyme HIV protease. One such inhibitor, Ro 31-8959, contains the saturated bicyclic ring system decahydroisoquinoline (DIQ) in the P′1 position. The binding orientation of Ro 31-8959 is known from X-ray crystallography. However, the bound conformation of the S-hydroxy diastereomer has not been studied, and for this molecule there are at least two different possible binding conformations. Specifically, the N-alkyl substituents may be equatorial or axial and the 3-carboxamide may be rotated into several different orientations. To gain a better understanding of the relative energies of these various conformations, ab initio molecular orbital calculations have been carried out on a series of pipecolic acid and DIQ derivatives. The results indicate that the lowest-energy N-equatorial rotamer is always at least 3 kcal/mol more stable than the lowest-energy N-axial rotamer. The presence of the second ring, as in the DIQ system, considerably raises the equatorial-axial difference to nearly 7 kcal/mol. Also, the preferred rotation angle of the amide group is different for the N-equatorial and N-axial cases. When the molecular dynamics-averaged conformation of the bound S-hydroxy inhibitor is considered, the energy difference between the N-equatorial and N-axial conformers drops to 4-5 kcal/mol. The preferred amide rotations in these systems are compared to those found in proline-containing peptides. Finally, some observations are made with respect to the large conformational energy penalty necessary for binding Ro 31-8959. © John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141206
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    Rotational barrier in phosphatriafulvene: An MCSCF study (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 3-7 
    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: As probed by ab initio calculations at SCF and MCSCF levels, the rotational barrier of the PC double bond in the title compound is similar in magnitude to the corresponding one in methylenephosphane. The transition state for rotation is dipolaric in nature. On this basis, a combination of electron releasing and electron accepting substituents reduces the magnitude of the rotational barrier in phosphatriafulvene. It is supported by experimental investigations. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140103
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  • 276
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    An electron repulsion integral compression algorithm (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 8-12 
    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 data compression algorithm for packing/unpacking floating point numbers is presented. The method has been used to compress large volumes of data commonly generated in ab initio quantum mechanical calculations. To retain an accuracy of 10-6 Hartree on the final energy, the required file space needed is approximately half its original size whereas the CPU time required to solve the Hartree-Fock self-consistent field equations increases with 30-60%. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140104
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  • 277
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    Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 263-277 
    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: Combining the modified Urey-Bradley-Shimanouchi intramolecular potential energy function with an appropriate intermolecular energy function, normal coordinate calculations have been performed for both α and β anomers of glucose and for some deuterated analogs in the crystalline state. The overall agreement between the observed and calculated frequencies leads to an average error on the order of 3 and 5 cm-1 for α and β glucose, respectively. In both cases, it is shown that the intermolecular potential energy terms are essential to reproduce perfectly the whole spectra, in particular for the hydroxyl stretching region, the anomeric and crystalline spectral regions, and the low-frequency range. Moreover, the intermolecular interactions have a nonnegligible influence on the value of the intramolecular force constants. But, the potential energy distribution of vibrational modes are in accord with previous works performed for an isolated molecule. It is also important to point out that approximately the same set of force constants has been used for both molecules, differences existing only for the atoms involved in the anomeric configuration. Likewise, different charge distributions have been calculated and tested with different value of the dielectric constant. Charges determined by the AM1 quantum mechanical procedure with a value of 3 for the dielectric constant have the merit to reproduce quite well the whole spectra and in particular the frequency range below 200 cm-1. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140303
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  • 278
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    Stochastic searches for lactone and cycloalkene conformers (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 330-348 
    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 stochastic search method coupled to MM3(92) has been used to locate as many conformers as possible for 6- to 11-membered ring lactones, trans-cycloalkenes, and cis-cycloalkenes. A comparison was carried out between the conformers of lactones and cycloalkenes of the same ring size for each force field. These comparisons were carried out by means of (1) conformational distances, defined as the rms deviation between the dihedral angles of the conformers being compared, and (2), substitution, in which a lactone was transformed into an olefin and vice versa, trying to keep as much as possible the initial geometry, followed by reoptimization. It is found that cycloalkenes and lactones share many common characteristics. The thermodynamic information provided by MM3 was used to study the dependence of conformer population upon (1) temperature and (2) total number of conformers. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140308
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  • 279
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    Conformational dependence of the electrostatic potential-derived charges of dopamine: Ramifications in molecular mechanics force field calculations in the gas phase and in aqueous solution (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 353-362 
    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 electrostatic potential-derived charges for the catecholamine neurotransmitter dopamine were calculated at the STO-3G and 6-31G* basis sets for six different molecular conformations. The degree of variance of the charges with changing conformations was examined. The 6-31G* basis set produced charges that were more sensitive to changes in conformation than those derived from the STO-3G electrostatic potentials. The implication of the charge variations in molecular mechanics calculations was also investigated. The molecular mechanics results in the gas phase exhibited a variance depending upon the charge set used. The force field calculations varied much less when aqueous solvation was included in the calculations through a continuum model. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140310
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  • 280
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    Digitale Medien
    Masthead (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140401
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  • 281
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    Reconsideration of solvent effects calculated by semiempirical quantum chemical methods (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 371-377 
    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: AM1 and PM3 semiempirical calculations are reported for the solvent effects on the tautomeric equilibria of 2-pyridone/2-hydroxypyridine and 4-pyridone/4-hydroxypyridine in the gas phase and solution. The solvent effects on the tautomeric equilibria were investigated by self-consistent reaction field (SCRF) theory implemented in the AMPAC and MOPAC program in two different ways: one in which all the solvent relaxation is included in the quantum mechanics and the total energy must be corrected for the solvent change in energy, method A; and a second in which the quantum mechanics directly includes this term, method B. The calculated (AM1, method A) tautomeric equilibrium constants (log K1) for 2-pyridone in the gas phase, cyclohexane, chloroform, and acetonitrile are -0.3, 0.3, 0.8, and 1.3, respectively, in good agreement with the experimental data (-0.4, 0.24, 0.78, and 2.17, respectively). For 4-pyridone/4-hydroxypyridine differences between calculated log K1 for the gas phase, chloroform and acetonitrile (-6.0, -2.6, and -1.2, respectively) and experimental data (〈 -1, 0.11, and 0.66, respectively) are larger but the experimental values are also less certain. The experimental acetonitrile data are disturbed by specific interactions. An extension of the SCRF for aqueous solutions is reviewed. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140312
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  • 282
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    Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and ab initio calculations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 379-391 
    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 conformational features of a large number of hydroperoxides ROOH and peroxides ROOR′, where R and R′ are alkyl groups of different and increasing size and phenyl rings, including ortho substituted derivatives, were obtained from molecular mechanics calculations by employing a standard package. For the molecules of small molecular size, comparison was carried out with the results of ab initio calculations. Heats of formation were also obtained from molecular mechanics for hydroperoxides and peroxides: The values are, in general, overestimated. For the molecules containing the CF3 group, the calculated values are subject to large errors and heats of formation were obtained from ab initio total energies in the “atom equivalents” scheme. To estimate the homolytic dissociation energies of the different bonds in the peroxide molecules, heats of formation of R·, ·OR, and ·OOR radicals were employed and several of them had to be calculated. Different approaches were employed - molecular mechanics calculations, ab initio energies within the atom equivalent and isodesmic reaction schemes, and Benson's group additivity rule; values consistent within the different calculation methods were chosen for estimating dissociation energies. The bond dissociation energies indicate different trends in these molecules as a function of the nature of the R and R′ groups and the possible electronic effects operating in these molecules are discussed. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140402
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  • 283
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    Comparison of a posteriori and a priori BSSE correction schemes for SCF intermolecular energiesPresented in part at the VIIth International Congress on Quantum Chemistry, Menton, France, July 1991. (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 401-409 
    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 systematic SCF study has been undertaken to compare the conventional a posteriori Boys-Bernardi BSSE correction scheme with our recent CHA/F method in which BSSE is excluded in a priori manner. Potential curves have been obtained for nine simple hydrogen-bonded systems by using nine different basis sets for each. It is concluded that the difference between the a posteriori BB and the a priori CHA schemes diminishes much faster when the basis set improves than BSSE disappears from the uncorrected SCF results. This fact gives an additional confidence in the CHA results, permitting one to draw the explicit conclusion that, at the SCF level of theory, the a priori CHA/F scheme can be considered the ultimate solution of the BSSE problem for weakly bonded systems. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140404
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  • 284
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    Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR-derived conformations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 438-444 
    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: Conformational analysis of bradykinin (BK), a nonapeptide of the sequence RPPGFSPFR, was accomplished using annealed molecular dynamics (AMD) at 1000 K in BIOGRAF 2.2. One hundred anneal cycles produced 100 conformations over approximately 2000 ps. These conformations were compared to structures derived by nuclear magnetic resonance (NMR) methods for similar shape and energy. Energy minimization of relevant conformations using both BIOGRAF 2.2 and AMBER 3.0a revealed that the AMD-determined conformations are in the same energy range as the NMR-determined structures. Also, the shape of the relevant conformations appeared similar, suggesting that AMD is a good tool for the conformational analysis of small peptide ligands. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140407
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  • 285
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    Improved solutions to the one-center McMurchie - Davidson tree search problem (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 452-454 
    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 present an improvement to Johnson, Gill, and Pople's results for reducing the cost of using the McMurchie-Davidson RNLM recurrence relation for one-center integrals. Recursive replacement of singly referenced and single-term auxiliary integrals results in floating point operation (FLOP) savings of up to 11% and explicit auxiliary integral calculation reductions of up to 76% with respect to the full list and up to 46% with respect to FLOP-reduced lists with no replacement. The programs are written in the string-manipulation language Convert; one of the programs automatically generates a FORTRAN subroutine given an integral list. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140409
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  • 286
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    Yammp: Development of a molecular mechanics program using the modular programming method (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 455-470 
    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: Molecular mechanics is a fast developing discipline with new methods and potential fields appearing every year. A versatile molecular mechanics program supports many methods and potential fields that make it unavoidably large. There are problems writing and maintaining large programs with traditional methods because of data and other dependencies. Modular programming provides a solution. A program is developed as a collection of highly independent modules containing only related data structures and procedures. These entities are isolated in the module and access to them is provided through a well-defined and controlled interface. The high degree of independence circumscribes programming errors. Most of all, it reduces the cost of revising the program as only a small part of the program needs to be read and understood for each revision. We implemented a molecular mechanics program, yammp, using the modular programming method. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140410
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  • 287
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    Digitale Medien
    Masthead (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140501
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  • 288
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    Multicenter point charge model for high-quality molecular electrostatic potentials from AM1 calculations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 503-509 
    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 natural atomic orbital/point charge (NAO-PC) model based upon the AM1 wave function has been developed to calculate molecular electrostatic potentials (MEPs). Up to nine point charges (including the core charge) are used to represent heavy atoms. The positions and magnitudes of the eight charges that represent the atomic electron cloud are calculated from the natural atomic orbitals (NAOs) and their occupations. Each hybrid NAO is represented by two point charges situated at the centroid of each lobe. The positions of the centroids and the magnitudes of the charges were obtained by numerical integration of the Slater-type hybrids and the results used to set up polynomials and look-up tables that replace the integration step in the actual MEP calculation. The MEPs calculated using this method are found to be in better agreement with those obtained using RHF/6-31G* than those obtained from the AM1 wave function using Coulson charges or with MOPAC-ESP. The MEP calculations are extremely fast and have, for instance, been incorporated into an interactive graphics package. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140502
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  • 289
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    Study of localized molecular orbitals using group theory methods and its approach to the many-electron correlation problem. III. Orthogonal bonded functions (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 549-555 
    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: By using the group symmetrical localized molecular orbitals (SLMOs) as configuration-generating orbitals (CGOs) of many-electron wave functions, the symmetry adaptation of many-electron spaces is greatly simplified, and novel orthogonal bonded functions (OBFs), as complete space- and spin-adapted antisymmetrized products, are introduced. The corresponding programs for the solutions of OBFs are developed. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 6 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140507
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  • 290
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    Application of explicitly correlated Gaussian functions for calculations of the ground state of the beryllium atom (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 566-570 
    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 electronic energy of atoms and molecules may be evaluated accurately by the use of wave functions where the interelectronic distances are explicitly present. In particular, explicitly correlated Gaussian-type functions make these types of calculations feasible and computationally tractable even for more extended systems. The resulting multielectron integrals may be reduced to standard one- and two-electron integrals that are readily evaluated. Initial calculations have been made for the Be atom where all four electrons were correlated at the same time. The preliminary results show that accurate results may be obtained. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140509
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  • 291
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    Conformational analysis of 2,3,6,7-tetrahydroazepines with implications for D1-selective benzazepines (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 571-578 
    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 conformational study of the 2,3,6,7-tetrahydroazepine (THA) and closely related systems has been carried out using MM3 and CHARMm molecular mechanics, AM1 semiempirical, as well as Hartree-Fock and local density functional (LDF) ab initio methods. For THA, all methods give similar optimal geometries; however, only MM3 agrees with the Hartree-Fock calculations using a 6-31G* basis set and LDF in the rank order of energies and nature of the stationary points characterized. AM1 shows serious disagreements with those results. Tetrahydrobenzazepines and a D1 receptor agonist containing the THA nucleus were studied using CHARMm, MM3, and AM1 calculations. All methods provide similar descriptions of the geometries of the conformations accessible to these compounds. However, the same disparities in the rank order of energies are observed. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140510
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  • 292
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    MORMIN: A quasi-Newtonian energy minimizer fitting the nuclear overhauser data (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 226-236 
    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: In this article, we describe the program MORMIN, which can simultaneously minimize the mechanical energy of a given macromolecular structure, together with a weighted quadratic penalty function of the difference between the observed and computed nuclear Overhauser effect (nOe) peaks. The gradient of the nOe penalty function relatively to the proton coordinates is computed from an exact closed formula of a matrix exponential derivative. To cut CPU time, the molecular system is partitioned into nonoverlapping subsets containing the protons involved in the observed peaks. The algorithm is no longer exact, but if a 1% relative error is accepted it can be run, on a scalar computer, in about the same CPU time as needed for the calculation of the mechanical energy. We have successfully run the program in more than 1000 situations, including cases where the hybrid method failed because of the occurrence of negative eigenvalues. In some cases, the optimization of the Cartesian coordinates could be successfully extended to individual atomic diffusion times. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140210
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  • 293
    Digitale Medien
    Digitale Medien
    Masthead (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140301
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  • 294
    Digitale Medien
    Digitale Medien
    Electrostatic solvent effects on the electronic structure of ground and excited states of molecules: Applications of a cavity model based upon a finite element method (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 253-262 
    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 present investigations on the use of dielectric continuum models for the self-consistent description of electrostatic solvent effects on the ground state of a molecule and on excitation energies. The electronic structure calculations have been carried out in the framework of the INDO and INDO/S-CI method, respectively. We compare the performance of three implementations of the cavity model that all allow an arbitrary shape of the solute cavity. The procedures differ in the effort spent on the description of the charge density at the cavity surface. Two procedures in the vein of Miertus̆, Scrocco, and Tomasi (MST) rely upon point charges to model the reaction field and differ in the way the cavity surface is modeled. While one implementation divides the surface into flat triangular patches, the improved version uses curved triangles. Alternatively, we investigate a finite element method (FEM) for the calculation of the surface charge density. Applications to rod-shaped organic molecules (including their charge transfer excitations) illustrate the superiority of the improved MST formalism over the primitive one, as it exhibits faster convergence of the results with increasing node density on the cavity surface. The FEM approach, which also employs curved surface patches, leads to a further improvement as it needs less computational effort, especially in the treatment of excited states. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140302
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  • 295
    Digitale Medien
    Digitale Medien
    Comparison of the boys and Pipek-Mezey localizations in the local correlation approach and automatic virtual basis selection (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 736-740 
    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: Our implementation of Pipek-Mezey population localization is described. It is compared with other localization schemes and its use in the framework of the local correlation method is discussed. For such use, this localization is shown to be clearly superior to Boys in the case of physically well-localized systems. Our current algorithm for selection of local virtual spaces is also described. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140615
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  • 296
    Digitale Medien
    Digitale Medien
    Calculation of hydrophobic interactions from molecular dynamics, surface areas, and experimental hydrocarbon solubilities (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 741-750 
    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: Using experimental solubilities and partial pressures for hydrocarbon solution in water and molecular dynamics calculations of hydrocarbon water interaction energies, hydrocarbon-water cavity potentials are obtained and then plotted vs. accessible surface area. The data used is mainly for aliphatic hydrocarbons, but benzene is included. Molecular dynamics calculations of pairs of hydrocarbon molecules together with the cavity potential curve are then used to obtain hydrophobic interaction free energies between the hydrocarbon pairs. While the cavity potential change is related to a change in surface area for hydrocarbon systems, the hydrocarbon-water interaction energy is not, so that the hydrophobic binding energy is not. The results are in agreement with previous results by a different method (R.B. Hermann, In Seventh Jerusalem Symposium on Quantum Pharmacology, E. Bergman and B. Pullman, Eds., D. Reidel, Dordrecht, 1974, p. 441) in that there is little or no solvent-induced binding free energy between small hydrocarbon molecules in a dilute aqueous solution. It is proposed that the cavity potential vs. accessible surface area curve obtained here can be used together with OPLS parameters to calculate both hydrocarbon-water solvation free energies and hydrophobic interactions. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140616
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  • 297
    Digitale Medien
    Digitale Medien
    Linear combination of Lanczos vectors: A storage-efficient algorithm for sparse matrix eigenvector computations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 769-774 
    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 present a storage-efficient and robust algorithm for the computation of eigenvectors of large sparse symmetrical matrices using a Lanczos scheme. The algorithm is based upon a linear combination of Lanczos vectors (LCLV) with a variable iteration depth. A simple method is given to determine the iteration depth before the eigenvector computation is performed. Test calculations are reported for tight-binding models of ordered and disordered 2-D systems. The algorithm turns out to be reliable if an eigenvector residual less than 10-4 is required. We report benchmarks for various computers. Possible fields of application are discussed. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140703
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  • 298
    Digitale Medien
    Digitale Medien
    Suitability of the PM3-derived molecular electrostatic potentials (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 799-808 
    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 systematic study of the suitability of PM3-derived molecular electrostatic potentials (MEPs) is presented. Forty-six MEP minima, 81 electrostatic charges, and 17 electrostatic dipoles were determined at the PM3 level and compared with those obtained from the ab initio 6-31G* wave function, as well as from the semiempirical MNDO and AM1 wave functions. The statistical results of the comparison analysis between semiempirical and ab initio 6-31G* MEPs show that PM3 is in general reliable for the study of the MEP minima but a mediocre method as a source of electrostatic charges. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140706
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  • 299
    Digitale Medien
    Digitale Medien
    Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 831-847 
    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 conformational behavior of cellobiose (D-glc-ß(1→4)-D-glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulations in vacuo at 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic φ, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed between gt,gg, and tg conformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long-lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the 4C1 conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 13 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140709
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  • 300
    Digitale Medien
    Digitale Medien
    Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 867-878 
    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: To make improved treatments of electrostatic interactions in biomacromolecular simulations, two possibilities are considered. The first is the famous particle-particle and particle-mesh (PPPM) method developed by Hockney and Eastwood, and the second is a new one developed here in their spirit but by the use of the multipole expansion technique suggested by Ladd. It is then numerically found that the new PPPM method gives more accurate results for a two-particle system at small separation of particles. Preliminary numerical examination of the various computational methods for a single configuration of a model BPTI-water system containing about 24,000 particles indicates that both of the PPPM methods give far more accurate values with reasonable computational cost than do the conventional truncation methods. It is concluded the two PPPM methods are nearly comparable in overall performance for the many-particle systems, although the first method has the drawback that the accuracy in the total electrostatic energy is not high for configurations of charged particles randomly generated. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540140712
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