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  • Biochemistry  (25)
  • Wiley-Blackwell  (25)
  • American Chemical Society
  • Blackwell Publishing Ltd
  • 2005-2009
  • 1985-1989  (25)
  • 1945-1949
  • 1988  (25)
  • 1
    Electronic Resource
    Electronic Resource
    A molecular mechanics-NMR pseudoenergy approach to the solution conformation of glycolipids (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 133-147 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present here a protocol for the determination of oligosaccharide solution conformation from a combination of molecular mechanics calculations and NMR distance constraints treated as pseudoenergies. As an illustration of our methodology we have chosen the determination of the solution conformation of the tetrasaccharide headgroup of the glycolipid globoside. In order to test the ability of our methodology to avoid becoming trapped in local minima, we have chosen three starting structures, well displaced from one another in conformational space. The structures obtained upon convergence of the calculations with distance constraint pseudoenergies were quite similar to one another. For two of the three glycosidic linkages in globoside, the results from the calculations were virtually identical for each of the three starting structures. We also apply our protocol to a model which allows for the existence of multiple conformers in an effort to explore the possibility of conformational flexibility in the oligosaccharide headgroup of globoside.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090206
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  • 2
    Electronic Resource
    Electronic Resource
    Hydration of Fe+: A Monte Carlo simulation of water clusters and of a dilute aqueous solution (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 819-826 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo statistical thermodynamic computer simulations are reported for several clusters Fe+ (H2O)n at different temperatures and for a dilute aqueous solution of Fe+ at 298 K. The energy of each configuration has been calculated in the pairwise additivity approximation using the MCY potential for the water-water interaction and an ab initio analytical potential built by us for the Fe+-H2O interaction. Energy and structural analysis of the generated configurations lead to the prediction of a coordination number of six for the first hydration shell of the Fe+ ion, both in clusters and in dilute solution. Finally, the variation in the distance to the Fe+ ion of the energy and orientation of water molecules in the solution are discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090804
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  • 3
    Electronic Resource
    Electronic Resource
    Doublet instability and the molecular structure of AlO2A contribution from the “Grup Química Quàntica de Catalunya, Institut de'Estudis Catalans.” (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 836-843 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The possible Cs, C2v, and C∞v structures of AlO2 corresponding to the two lowest electronic states which dissociate into the neutral Al(2P) and O2(3Σg-) fragments have been investigated at the ab initio self-consistent field (SCF) and CI levels using nonempirical pseudopotentials. The most stable structure corresponds to a C2v symmetry in the 2A2 electronic state. However, this structure presents the three-center three-electron Hartree-Fock instability and CASSCF calculations were necessary to unequivocally characterize it as true minimum. Moreover, only another stable structure, of C2v geometry, was found to be a minimum, corresponding to a low-lying excited state of 2A1 symmetry. The optimized C∞v structures were not minima on the corresponding potential energy surfaces and no evidence of any stable Cs structure was found. Calculating values are compared with the different experimental data obtained from the reaction of Al and O2 in frozen gas inert matrices.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090806
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  • 4
    Electronic Resource
    Electronic Resource
    Determination of the water geometry in violuric acid monohydrate with a Monte Carlo simulation (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 11-17 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The positions and orientations of water molecules in violuric acid crystals have been determined with the Metropolis Monte Carlo method. The interaction potentials between water and violuric acid needed in the simulation have been developed using ab initio calculations corrected for the basis set superposition error with the C.P. technique and fitted to atom-atom pairwise potentials. The agreement between experimental data and simulation results is good, proving that the interaction potentials can be used with confidence.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090103
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  • 5
    Electronic Resource
    Electronic Resource
    A conformational study of a biologically active conjugated syn-oxime (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 67-74 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conjugated system (E)-tiglaldoxime is the simplest example of a perillartine analog which exhibits sweetness with a taste potency greater than sucrose with almost no bitter aftertaste. In previous studies, the structure of this biologically active compound has been assumed to be planar with the C=C double bond trans to the C=N bond of the oxime moiety. In this article a conformational analysis of this molecule is reported. The results indicate that, although the trans conformer of the planar molecule is indeed the global minimum, other conformers lie within a few kilocalories of this minimum. Hence, other accessible conformations may be available for interaction with the receptor and, therefore, may be biologically active. The structural parameters obtained for this conjugated syn-oxime are nearly identical to those of (E)-acetaldoxime. This fact has implications for the transferability of these parameters to the more complicated perillartine analogs.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090109
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  • 6
    Electronic Resource
    Electronic Resource
    A molecular mechanics study of neutral molecule complexation with crown ethers (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 111-124 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics methods are applied to the study of neutral molecule complexation with crown ethers. Protocols for the development of parameters necessary to describe these molecule-molecule interactions are presented. Application of these methods to the study of 1:1 and 2:1 (guest:host) complexation between acetonitrile (1), nitromethane (2), malononitrile (3) and dimethylsulfone (4) reveals positive cooperativity in formation of the 2:1 complexes in isolation.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090204
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  • 7
    Electronic Resource
    Electronic Resource
    Integral data compression for FPS 64-BIT processors: Improved I/O and reduced storage (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 148-157 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Compression of two-electron integral data is used to reduce integral storage and I/O requirements with FPS M64 Series (formerly FPS-X64) processors. Schemes are developed and implemented in assembly language to compress floating-point values to a fixed-point accuracy, and unsigned integer numbers. The floating-point scheme stores only the significant bits of the mantissa and a short, biased exponent. The unsigned integers are packed into fixed-length fields just long enough to hold the largest value. The packing procedures are tested on FPS-164 and FPS-264 processors (since renamed M64/145 and M64/60 by FPS) and incorporated into HONDO to compress two-electron integral files. Reduction factors of 0.2-0.4 are obtained for floating-point compression and 0.3-0.5 for index packing, with typical overall factors around one-third. The advantages of improved I/O and storage efficiency are accompanied by a small increase in processor time to perform the packing and unpacking. Timing changes for HONDO are presented, and both packing schemes dramatically reduce SCF elapsed times with FPS-264 processors. It is concluded that compression effectively extends external storage capacities, improves I/O efficiency, and can reduce the elapsed time of I/O bound calculations.
    Additional Material: 7 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090207
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  • 8
    Electronic Resource
    Electronic Resource
    The rigorous computation of the molecular electric potential (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 171-187 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is presented for the rigorous computation of the electric potential of molecules of arbitrary shape, under the assumption of continuous linear dielectric media. The computational technique involves finding the distribution of induced polarization charge on the molecular surface, and proceeds by an application of the method of boundary elements. The surface, which separates the molecular interior (of low dielectric constant) from the highly polar solvent, is given a piece-wise analytic representation as a collection of curvilinear elements. Given a set of internal fixed charges, the distribution of polarization-charge is found as a continuous function over the surface elements, and the electric potential (including all polarization effects) is then easily computed at any point. The method is applied to a spherical interface, and to several small molecules of biological interest, including a hexapeptide. The resulting potentials show good convergence in all cases. The future application of the method to macromolecules is discussed.
    Additional Material: 14 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090209
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  • 9
    Electronic Resource
    Electronic Resource
    Charge calculations in molecular mechanics. V. Silicon compounds and π bonding (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 244-256 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A previously published scheme for the calculation of partial atomic charges has been extended to include silicon, and has been parameterized for a range of Si—X bonds (X=C,H,O,F,Cl,Br). For the silicon-halogen and silicon-oxygen bonds, a comparison is made between charges calculated with and without the inclusion of π-bonding. An extensive data set consisting of experimental geometries and dipole moments for the silicon compounds considered is presented and this leads to the selection of standard Si—X bond lengths. The calculated dipole moments for the above compounds are in good agreement with those obtained experimentally only when the π charges are included. A comparison has also been made between the partial charges from this scheme and those obtained from computational methods using the Mulliken population analysis. There is considerable disagreement between the methods. Finally, the implications of the charges and structural data are considered in terms of application to zeolite systems.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090308
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  • 10
    Electronic Resource
    Electronic Resource
    Ab initio studies of the ground-state potential energy surface of formamide (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 600-603 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations employing a standard double-zeta basis set augmented with various polarization functions have been used to investigate the lowest energy region of the ground-state potential energy surface of the formamide molecule. Hartree-Fock calculations with only d polarization functions on the nonhydrogen atoms located two stable minima, that with geometry distorted from planarity having slightly lower energy; only one stable minimum with planar structure is found when p polarization functions on the hydrogens are included. In contrast optimizations, which account approximately for the correlation energy using second-order Møller-Plesset perturbation theory consistently favor a single slightly nonplanar minimum energy geometry.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540090604
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