ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Computational Chemistry and Molecular Modeling  (24)
  • Navier-Stokes equations  (1)
  • Structure refinement  (1)
Collection
Keywords
Publisher
Years
  • 1
    Electronic Resource
    Electronic Resource
    The hydration shell of myoglobin (1992)
    Springer
    European biophysics journal 21 (1992), S. 313-320 
    Details
    ISSN: 1432-1017
    Keywords: Monte Carlo ; Crystal water ; Structure refinement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The space in the unit cell of a metmyoglobin crystal not occupied by myoglobin atoms was filled with water using Monte Carlo calculations. Independent calculations with different amounts of water have been performed. Structure factors were calculated using the water coordinates thus obtained and the known coordinates of the myoglobin atoms. A comparison with experimental structure factors showed that both the low and the high resolution regime could be well reproduced with 814 Monte Carlo water molecules per unit cell with a B-value of 50 Å2. The Monte Carlo water molecules yield a smaller standard R-value (0.166) than using a homogeneous electron density for the simulation of the crystal water (R = 0.212). A reciprocal space refinement of the water and the protein coordinates has been performed. Monte Carlo calculations can be used to obtain information for crystallographically invisible parts of the unit cell and yield better coordinates for the visible part in the refinement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00188343
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation of flow past a plate (1986)
    Springer
    Journal of scientific computing 1 (1986), S. 145-150 
    Details
    ISSN: 1573-7691
    Keywords: Molecular dynamics ; Navier-Stokes equations ; separated flow
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract Molecular dynamics simulations with a soft-sphere potential have been carried out to model two dimensional fluid flow obstructed by a plate. At fluid velocities large enough to obtain adequate signal to noise resolution, two counter-circulating vortices are observed behind the obstruction. The stationary state length scale of these vortices is found to be roughly proportional to the average velocity in the system, as predicted by the hydrodynamic theory.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01061390
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Parallelism in quantum chemistry: Hydrogen bond study in DNA base pairs as an example (1984)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 26 (1984), S. 601-618 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present results on the energetics of the hydrogen bridges for the Guanine-Cytosine pair obtained in a DNA fragment consisting of three stacked base pairs in the B-DNA conformation. The wave function computations on the 87 atom system are all-electron ab initio SCF-MO computations obtained with a basis set of 1032 primitive gaussian functions contracted to 315. Even if the results are only preliminary, one can tentatively advance conclusions relative to the molecular field effect of stacked base-pairs on the potential energy surface for a hydrogen bond. These computations have been performed with a modified version of our molecular program, which uses an IBM 4341 host and six to ten attached array processors (FPS-164) in parallel. The strategy to convert the program from sequential to parallel is briefly outlined and comparisons with our parallel system are made with a present-day “vector” super-computer. From these studies, we conclude that if one adopts the “parallel” approach presented and tested here, much larger chemical systems than previously are now amenable to all-electron ab initio computations.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560260854
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Nonadditivity of interaction in water trimers (1980)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 17 (1980), S. 377-398 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The energy of (H2O)3 has been calculated for 29 geometrical configurations of the trimer using the SCF LCAO MO method and extended as well as minimal basis sets of Gaussian functions. For two configurations two intermediate basis sets have also been tested. The results show the nonadditive component of the interaction energy to be small. They also indicate that fairly reliable results for the trimer can be obtained using minimal basis sets and the counterpoise method to eliminate the basis set superposition error. The nonadditive contribution to the interaction energy is shown to be mainly due to the long-range induction interaction.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560170302
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    Electronic correlation contribution to the three-body potentials for water trimers (1983)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 23 (1983), S. 1803-1806 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A number of trimers of water molecules have been computed with an extended basis set in the Hartree-Fock and in the direct CI approximations. It has been verified that the three-body interaction energy can be calculated within the Hartree-Fock method. Therefore, the correlation corrections to the Hartree-Fock level are essentially additive and do not contribute significantly to three-body effects.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560230509
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 6
    Electronic Resource
    Electronic Resource
    Supercomputing and supercomputers for science and engineering in general and for chemistry and biosciences in particularThis paper, presented at the conference, was partially published in Biological and Artificial Intelligence Systems, edited by E. Clementi and S. Chin, Eds. (ESCOM Science Publishers B.V., Leiden, The Netherlands, 1988). (1989)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 3-89 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We start by pointing out relationships between production of information, global simulation, and supercomputing, thus placing our research activities in today's society context. Then we detail the evolution in hardware and software for 1CAP, our experimental supercomputer, which we claim to be especially well suited for supercomputing in science and engineering. A preliminary discussion of 1CAP/3090 (our latest experimental effort) is included. Many examples from different disciplines are provided to verify our assertions. We “prove” our point by presenting an example of global supercomputing. Starting with 3 nuclei and 10 electrons, building up to a single water molecule, then to a few hundred, we learn, for example, about Raman, infrared, and neutron scattering; we then move up to a few hundred thousand molecules to analyze particle flow and obstructions; finally we experiment, but only preliminarily, with a few million particles to learn more on nonequilibrium dynamics as in the Rayleigh-Benard systems. In this way, quantum mechanics is overlapped with statistical mechanics and expanded into microdynamics. The entire paper is finally reanalyzed from a different perspective, presenting rather systematically, even if most briefly, our ideas on “modern” computational chemistry, where quantum mechanics is as much needed as fluid dynamics and graphics. In this section the main computational techniques are analyzed in terms of computer programs and their associated flow diagrams to solve the basic equations using parallel supercomputers.
    Additional Material: 33 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560350103
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 7
    Electronic Resource
    Electronic Resource
    Dirac-Fock self-consistent field method for closed-shell molecules with kinetic balance and finite nuclear size (1991)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 39 (1991), S. 487-517 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a general method of implementing the kinetic balance condition within the Dirac-Fock (DF) self-consistent field (SCF) formalism for closed-shell molecular structure. We review the steps leading to the derivation of DF SCF equations for closed-shell molecules, particularly as formulated by Matsuoka et al. In the present approach, the large component of the molecular spinors are expanded in terms of atomic basis spinors of spherical-type Gaussian functions, with the small component related to the large component by the kinetic balance condition. It is shown that imposing the kinetic balance condition on geometric Gaussian-type basis functions allows us to obtain the Fock matrix elements, involving both the large and the small components, form the standard nonrelativistic Cartesian-type matrix elements. By using properties of orthogonal polynomials, the solid spherical harmonics are expressed in Cartesian form, thus providing a general basis for transformation of one- and two-electron-matrix elements, obtained from a Cartesian Gaussian-type basis, to a spherical Gaussian-type basis. The advantages of using kinetically balanced geometric Gaussian-type basis functions in molecular DF calculations including finite-size nucleus effects are emphasized. For the sake of completeness, we have added in an appendix corrections to the nuclear attraction matrix elements for the finite-size nucleus already derived by Matsuoka.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560390322
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 8
    Electronic Resource
    Electronic Resource
    Interaction of methane molecules (1980)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 17 (1980), S. 429-448 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Potential-energy curves for CH4·CH4 have been calculated using the SCF LCAO MO method. Six different mutual orientations of the molecules have been considered and several basis sets have been employed. An analytical potential has been fitted to the computed energy values and used in a Monte Carlo calculation to yield a spherically averaged CH4·CH4 potential. The potential, if corrected for dispersion interaction, agrees fairly well with that derived from thermophysical data. At short distances it disagrees with the potentials derived from scattering experiments which, however, are also incompatible with the experimental potential for large distances.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560170305
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 9
    Electronic Resource
    Electronic Resource
    Theoretical study of some Van der Waals molecules (1980)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 17 (1980), S. 775-798 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Van der Waals molecules Ar · HF, Ar · H2O, and Ar · HCl have been analyzed with potential surfaces obtained by SCF energies corrected for the basis set superposition error and by including dispersion forces. The computed properties for these Van der Waals molecules are in good agreement with recent experimental observations.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560170417
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 10
    Electronic Resource
    Electronic Resource
    Preliminary attempt to follow the enthalpy of an enzymatic reaction by ab initio computations: Catalytic action of papain (1978)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 14 (1978), S. 815-838 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new theoretical approach to study the enthalpy variations occurring during an enzymatic reaction is presented. The structural modifications of the enzyme-substrate complex along the reaction path are distinguished as macro- and microdeformations. Macrodeformations, which concern primarily the approach of the substrate to the enzyme and the release of the reaction products and arise from nonbonded interactions, are treated with an empirical method for computing the energy of a macromolecule. Microdeformations, which are local displacements driven by variations of the electronic structure and its energy and involve only a limited portion of the complex, are treated with the ab initio SCF-LCAO-MO method. The reaction path is idealized as a sequence of major steps: at each step, first the empirical program REFINE is used to calculate the geometry of the system for that step, then the energy of an appropriate subsystem is computed ab initio with the program IBMOL, using the geometry provided by REFINE and applying small concerted atomic displacements. Thus along the entire reaction path one can obtain an energy profile computed with the ab initio method and compatible with the structure of the whole complex. This approach was applied here to the first steps of the reaction of proteolysis catalyzed by papain. The formation of an ion pair ImH+ …S- between the side chains of residues His-159 and Cys-25 was examined in detail. The results show that the instability of the ion pair decreases by ˜ 11.5 kcal/mol when the interactions with residues Asn-175 and Ala- 160 are taken into account; the instability is further decreased by ˜2 kcal/mol after a partial geometry optimization. The energies of the noncovalent enzyme-substrate complex and of the tetrahedral intermediate were computed, considering N-methyl acetamide (NMA) as model substrate and representing papain with the residues Cys-25, His-159, Gln-19, and Ala-160. The interaction energy of the noncovalent complex is -3.8 kcal/mol, compared to the value of +7.4 kcal/mol for the CH3S- -NMA complex. The tetrahedral intermediate is found to be less stable than the noncovalent complex by 27 and 38.5 kcal/mol, respectively, for the papain-NMA and the CH3S- -NMA systems. While these rather large energy differences are possibly due to the incorrect geometry of the tetrahedral intermediate and optimization of the structure is required, it appears that the interactions with the various protein residues represent a very important stabilization factor, which lowers the onthalpy variations during the reaction.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560140613
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...