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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 42 (1992), S. 1209-1235 
    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 molecular dynamics simulation for liquid water at room temperature is reported. A sample of 1000 water molecules has been analyzed with the Nieser-Corongiu-Clementi polarizable potential, to which is added vibrational flexibility. The sample was contained in a cubic box subject to periodic boundary conditions, a cutoff radius of 15.54 Å was used in evaluating energies and forces, the long-range interactions were taken into account with the reaction field method, and the integration of the equation of motion has been performed using a sixth-order Gear predictor-corrector algorithm. The simulation, after 35 ps of equilibration time, has been carried out for 10.4 ps with a time step of 1.25 × 10-16 s. The trajectories and velocities, collected in the production phase of the simulation, have been used to compute the geometry of the water molecule within the liquid, thermodynamical quantities, the pair correlation functions, the Dore neutron pair correlation function, X-ray and neutron scattering structure functions, translational, rotational, orientational autocorrelation functions and their Fourier transforms, mean square displacements, diffusion coefficients, and NMR relaxation times. A detailed study on the spectral density is presented, and good agreement is found with the most recent infrared, Raman, and neutron scattering laboratory data. All the simulated properties so far analyzed are in good agreement with experimental data, and, with confidence, we can assess that our ab initio polarizable potential with inclusion of vibrations is the most reliable water potential in today's literature for the description of water.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 615-625 
    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 effects of the solvent on the tautomeric equilibria of cytosine and uracil are studied using Onsager's reaction field model in the framework of density functional theory. In this model, the solute molecule is placed in a spherical cavity of radius ao immersed in a continuous medium with a dielectric constant e, treating the solute-solvent electrostatic interactions at the dipole level. The cavity radius is evaluated by determining the molecular volume with a quantum mechanical approach. The solvent effect brings significant changes in the geometrical parameters of some cytosine tautomers, but only very small changes to those of the uracil tautomers. Our results are in good agreement with available experimental results and confirm that the polarization of the solute by the continuum has important effects on the absolute and relative solvation energies. Frequency shifts and intensity variations in the infrared spectra due to the presence of the solvent are also presented. © 1995 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 45 (1993), S. 511-544 
    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 shall start with very small systems like H2 and H3, computed with very accurate methods (Hylleraas-CI) or atomic systems up to Zn with accurate methods (CI), then move to more complex ones, like C60, but now with somewhat less accurate methods, specifically Hartree-Fock with density functionals, the latter for the correlation energy but not for the exchange energy. For even more complex tasks like geometry optimization of C60, we have resorted to even simpler and parametrized methods, like local density functionals. Then, we could use quantum mechanics either to provide interaction potentials for classical molecular dynamics or to directly solve dynamical systems, in a quantum molecular dynamics approximation. Having demonstrated that we can use the computational output from small systems as input to larger ones, we discuss in detail a new model for liquid water, which is borne out entirely from ab initio methods and nicely links spectroscopic, thermodynamics, and other physicochemical data. Concerning time scales, we use classical molecular dynamics to determine friction coefficients, and with these we perform stochastic dynamic simulations. The use of simulation results from smaller systems to provide inputs for larger system simulations is the “global simulation” approach, which, today, with the easily available computers, is becoming more and more feasible. Projections on simulations in the 1996-1998 period are discussed, new computational areas are outlined, and a N4 complexity algorithm is compared to density functional approaches. © 1993 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 673-679 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 15
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 1017-1024 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of cyclolinopeptide A [c-(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val)], a naturally occurring peptide with remarkable cytoprotective activity, has been investigated by means of molecular dynamics simulations in various molecular environments. Structural and dynamical properties have been analyzed and compared with those experimentally determined. A detailed analysis of hydrogen bonds is reported.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 16
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 763-777 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report on a computer experiment in which, using Monte Carlo techniques, we considered a three-turn (30-base-pairs) B-DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B-DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B-DNA strands are fully analyzed and described in detail. A model for base-pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism are discussed.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 17
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
    Additional Material: 21 Ill.
    Type of Medium: Electronic Resource
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  • 18
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Monte Carlo simulations are reported for a system of 447 water molecules enclosing a B-DNA double-helix fragment with 12 base pairs and the corresponding sugar and phosphate units. From a detailed analysis on the interaction energies and probability distributions (at a simulated temperature of 300 K), the water molecules can be partitioned into clusters strongly interacting with (1) the phosphates, (2) the sugars, (3) the sugars and the bases, and (4) the base pairs. In addition, transgroove and interphosphate filament of hydrogen-bonded water molecules have been detected. From simulations performed with variable numbers of water molecules, a theoretical isotherm has been obtained, with the characteristic sigmoidal shape, known from absorption-desorption experiments on related systems. The expected main features for the structure of water molecules solvating B-DNA with Na+ counterions are briefly discussed at the end of the paper.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
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  • 19
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 42 (1992), S. 1353-1381 
    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 new self-consistent set of ab initio analytical pair potential to predict specific nonbonded interactions of protein with nucleic acid, of protein with protein, and of nucleic acid with nucleic acid. The purpose of this study is to represent the interaction between biological molecules with an accuracy equivalent to the ab initio molecular orbital calculations, which are used as reference data to obtain the pair potentials. Atoms in nucleic acids and proteins are classified according to their chemical environments. An “effective charge,” a modification of a charge obtained from the Mulliken population analysis, is introduced and used to represent the electrostatic energy. More than 30,000 SCF interaction energies have been calculated to provide the reference data for the fitting procedure that we have adopted in the parameterization of the potentials. The standard deviation is 1.61 kcal/mol for interaction energies spanning the range from about -220 kcal/mol to +20 kcal/mol. Molecular dynamics simulations, using the above new set of force field, have been performed successfully for the systems where adequate treatments of specific interactions are required: The stability of α-helix of C-peptide and the interaction of spermine with oligonucleotide are examined as preliminary examples.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 20
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 59 (1996), S. 263-269 
    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: Two different approaches were used to explain the distribution of water coordinates in the crystallographically invisible part of the unit cell. Monte Carlo calculations were done starting from different initial water structures. Extended Monte Carlo calculations using equal initial structures were also used to obtain two further water structures. The differences between the Monte Carlo water structures were used to calculate the mean-square displacements of the water molecules. Monte Carlo calculations starting from different structures lead to a mean-square displacement of 0.58 Å2, whereas extended Monte Carlo moves using the same initial structure only show a mean-square displacement of 0.17 Å2. The mean-square displacement of 0.58 Å2 can be used to explain the experimental data. © 1996 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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