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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1017-1029 
    ISSN: 0192-8651
    Keywords: pseudospectral ; parallel ; Hartree-Fock ; gradient ; scalable ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present an outline of the parallel implementation of our pseudospectral electronic structure program, Jaguar, including the algorithm and timings for the Hartree-Fock and analytic gradient portions of the program. We also present the parallel algorithm and timings for our Lanczos eigenvector refinement code and demonstrate that its performance is superior to the ScaLAPACK diagonalization routines. The overall efficiency of our code increases as the size of the calculation is increased, demonstrating actual as well as theoretical scalability. For our largest test system, alanine pentapeptide [818 basis functions in the cc-pVTZ(-f) basis set], our Fock matrix assembly procedure has an efficiency of nearly 90% on a 16-processor SP2 partition. The SCF portion for this case (including eigenvector refinement) has an overall efficiency of 87% on a partition of 8 processors and 74% on a partition of 16 processors. Finally, our parallel gradient calculations have a parallel efficiency of 84% on 8 processors for porphine (430 basis functions).   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1017-1029, 1998
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1030-1038 
    ISSN: 0192-8651
    Keywords: pseudospectral ; parallel ; localized Møller-Plesset, scalable ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have developed a parallel version of our pseudospectral localized Møller-Plesset electronic structure code. We present timings for molecules up to 1010 basis functions and parallel speedup for molecules in the range of 260-658 basis functions. We demonstrate that the code is scalable; that is, a larger number of nodes can be efficiently utilized as the size of the molecule increases. By taking advantage of the available distributed memory and disk space of a scalable parallel computer, the parallel code can calculate LMP2 energies of molecules too large to be done on workstations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1030-1038, 1998
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1217-1228 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is presented for the refinement of reduced-model structures of proteins. A simulated annealing minimization is carried out in which the trial moves consist of the replacement of three-residue segments from a presorted library. The segments in the library are screened independently by their net end-to-end rotations so as to reproduce a distribution of conformations in the library similar to those in the ensemble. A general form of a look-up table contact potential is used to evaluate the free energy. This algorithm has been implemented on a parallel connection machine, on which a large number of molecules can be simultaneously simulated. The calculation of the pairwise distance matrix is distributed across the nodes of the machine to achieve an increase in performance and a reduction in the memory required on each node to store the potential table. The results of the refinement are shown for the test case of myoglobin, and the parallel performance is compared to that of a serial version of the algorithm. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1570-1590 
    ISSN: 0192-8651
    Keywords: dielectric continuum ; Poisson-Boltzmann equation ; finite element ; mesh generation ; grid generation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present an automatic three-dimensional mesh generation system for the solution of the Poisson-Boltzmann equation using a finite element discretization. The different algorithms presented allow the construction of a tetrahedral mesh using a predetermined spatial distribution of vertices adapted to the geometry of the dielectric continuum solvent model. A constrained mesh generation strategy, based on Bowyer's algorithm, is used to construct the tetrahedral elements incrementally and embed the Richards surface of the molecule into the mesh as a set of triangular faces. A direct mesh construction algorithm is then used to refine the existing mesh in the neighborhood of the dielectric interface. This will allow an accurate calculation of the induced polarization charge to be carried out while maintaining a sparse grid structure in the rest of the computational space. The inclusion of an ionic boundary at some finite distance from the dielectric interface can be automatically achieved as the grid point distribution outside the solute molecule is constructed using a set of surfaces topologically equivalent to this boundary. The meshes obtained by applying the algorithm to real molecular geometries are described.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1570-1590, 1997
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1591-1608 
    ISSN: 0192-8651
    Keywords: dielectric continuum ; Poisson-Boltzmann equation ; finite element ; electrostatics ; solvation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The automatic three-dimensional mesh generation system for molecular geometries developed in our laboratory is used to solve the Poisson-Boltzmann equation numerically using a finite element method. For a number of different systems, the results are found to be in good agreement with those obtained in finite difference calculations using the DelPhi program as well as with those from boundary element calculations using our triangulated molecular surface. The overall scaling of the method is found to be approximately linear in the number of atoms in the system. The finite element mesh structure can be exploited to compute the gradient of the polarization energy in 10-20% of the time required to solve the equation itself. The resulting timings for the larger systems considered indicate that energies and gradients can be obtained in about half the time required for a finite difference solution to the equation. The development of a multilevel version of the algorithm as well as future applications to structure optimization using molecular mechanics force fields are also discussed.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1591-1608, 1997
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1863-1874 
    ISSN: 0192-8651
    Keywords: electronic structure ; transition metals ; pseudospectral methods ; Hartree-Fock theory ; density functional theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have developed a parameterization enabling ab initio electronic structure calculation via the PS-GVB program on transition-metal-containing systems using two standard effective core potential basis sets. Results are compared with Gaussian-92 for a wide range of complexes, and superior performance is demonstrated with regard to computational efficiency for single-point energies and geometry optimization. Additionally, the initial guess strategy in PS-GVB is shown to provide considerably more reliable convergence to the ground state.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1863-1874, 1997
    Additional Material: 9 Tab.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 0894-3230
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: To probe regioselectivity in Meisenheimer complexation, the reaction of two picryl halides (PiX where X = F, Cl) with a series of aryloxide nucleophiles (phenoxide, 2,4,6-trimethylphenoxide and 2,6-di-t-butylphenoxide) were monitored by 1H NMR spectroscopy in dimethyl sulphoxide at ambient temperature and in acetonitrile-dimethoxyethane(MeCN-DME) at low temperature (-40°C). The reactions of both picryl halides with the ambident (oxygen versus carbon) nucleophile, phenoxide ion (PhO-), and 2,4,6-trimethylphenoxide (mesitoxide, MesO-) leads to clean SNAr displacement of X via the oxygen site of the nucleophile to form the respective aryl picryl ethers, i.e. phenyl picryl ether (3a) and mesityl picryl ether (3b). Meisenheimer complex formation at C-1 or C-3 was not detected in these systems. With 2,-6-di-t-butylphenoxide (2,6-DTBPhO-), where oxygen attachment of the aryloxide is precluded by the bulky ortho t-butyl groups, para-carbon attachment was found to occur at C-1 to give picryl 2,6-di-t-butylphenol (3d) in competition with C-attack at C-3 to give the respective carbon-bonded Meisenheimer complexes [X = Cl (4) and X = F (5)]. For both picryl halides, the ratio of 3d, the product of C-1 attack, to the product of C-3 attack, 4 or 5, was roughly 7:1. These findings are considered with regard to the nucleofugality of the halide, X, steric hindrance (F-strain) to attack by the aryloxides at the various positions and stereoelectronic stabilization of C-1 adducts afforded by n → σ* donation.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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