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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 97 (1993), S. 12093-12099 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 6690-6694 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A novel way has been developed for using the umbrella potential method of calculating the potential of mean force using molecular dynamics. During a simulation, the umbrella potential is improved periodically, taking into account all results obtained previously. The method was tested by the determination of the potential of mean force for the central dihedral angle in glycol (as a molecule in vacuo and in solutions in water and in CCl4). Advantages over other methods are that a relatively small amount of manual intervention is necessary and that an intermediate result after a small simulation time is already a complete, although crude estimate of the potential of mean force. A robust method to estimate the error in obtained energy differences between conformations and in the parameters of the potential of mean force (PMF) is also supplied.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 3639-3646 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Different methods to calculate the potential of mean force using molecular dynamics have been used to estimate the difference in free energy between the gauche and trans conformations of the 1,2-ethanediol (glycol) molecule dissolved in water and in carbon tetrachloride. Results indicate that even in this simple model study simulations of many picoseconds are needed to obtain acceptably low estimated standard deviations. The calculated trans/gauche ratio in aqueous solution is larger than the observed one. Assuming that the solvent effects are more reliable than the intramolecular force field we used the observed ratio to predict an abundance of about 3% trans to be present in CCl4 solution. Details of the results for this solvent agree well with infrared spectra.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 535-542 
    ISSN: 1600-5740
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The UPACK program for crystal structure prediction was extended to allow the possibility of more than one molecule in the asymmetric unit. A search method was developed where the essential parameters (including torsional angles of hydroxyl groups) take random values. Energy minimization and clustering then lead to a list of hypothetical structures. In a test for six hexapyranoses this random search method was found to be approximately equally as efficient as the previously used systematic grid search method for one independent molecule. As a second test, the generation of structures with more than one independent molecule was performed for ethanol. A multitude of possible structures was found, the experimental one (two independent molecules in space group Pc) always being present. However, for \alpha-D-mannose (two independent molecules with five unknown hydroxyl torsional parameters each) the number of hypothetical structures was so large that the experimental structure was never encountered. Finally, a crystal structure generation for hydrates of pyranoses and polyalcohols was carried out. When the total number of unknown parameters was less than 20, the experimental structure was encountered. As usual, the empirical energies were not adequate to select that structure from the list of possible ones. Even then, the procedure proved to be valuable in identifying the most probable hydrogen-bonded network in cases where hydrogen positions in the experimental crystal structure were missing.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 745-745 
    ISSN: 1600-5740
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the paper by van Eijck & Kroon (2000) the fifth and sixth sentences in the third paragraph of §2.1 are incorrect. The correct paragraph is here reprinted in full. Table 6 also contains errors and thus is also reprinted below.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1600-5740
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A collaborative workshop was held in May 1999 at the Cambridge Crystallographic Data Centre to test how well currently available methods of crystal structure prediction perform when given only the atomic connectivity for an organic compound. A blind test was conducted on a selection of four compounds and a wide range of methodologies representing the principal computer programs currently available were used. There were 11 participants who were allowed to propose at most three structures for each compound. No program gave consistently reliable results. However, seven proposed structures were close to an experimental one and were classified as `correct'. One compound occurred in two polymorphs, but only one form was predicted correctly among the calculated structures. The basic problem with lattice energy based methods of crystal structure prediction is that many structures are found within a few kJ mol−1 of the global minimum. The fine detail of the force-field methodology and parametrization influences the energy ranking within each method. Nevertheless, present methods may be useful in providing a set of structures as possible polymorphs for a given molecular structure.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 459-474 
    ISSN: 0192-8651
    Keywords: crystal structure prediction ; distributed multipoles ; molecular dynamics ; symmetry constraints ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Possible crystal structures of acetic acid were generated, considering eight space groups and assuming one molecule in the asymmetric unit. Our grid-search method was compared with a Monte Carlo approach as implemented in the Biosym/MSI Polymorph Predictor. This revealed no sampling deficiencies. A large number of possible crystal structures were found (∼100 within only 5 kJ/mol), including the experimental structure. Energy minimizations were done with a united-atoms force field (GROMOS), an all-atoms force field (AMBER), and a potential that describes the electrostatic interactions with distributed multipoles (DMA). In all cases, the experimental structure had a low lattice energy. The number of hypothetical crystal structures was reduced considerably by removing space-group symmetry constraints, or by a primitive molecular dynamics shake-up. Nevertheless, sufficient structures of equal or lower energy compared with the experimental structure remained to suggest that other factors need to be considered for genuine structure prediction.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 459-474, 1998
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1036-1042 
    ISSN: 0192-8651
    Keywords: crystal structure prediction ; fast clustering ; equivalent structures ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Most methods of crystal structure prediction generate many trial structures. Because these may differ in choice of unit cell, it is not always immediately obvious whether or not two such structures are equivalent. A method to answer this question is described for the case where the asymmetric unit contains one molecule in a general position, defined by the rotation and translation of that molecule with respect to some reference geometry. In the comparison of two structures, the rotation needed to transform one orientation into the other is determined first. Then it is checked whether this rotation corresponds to a transformation that is compatible with the imposed space group symmetry. A final test compares the cell lengths, the cell angles, and the molecular centers of gravity after the transformation of one structure into the other. The method is implemented for triclinic, monoclinic, and orthorhombic systems and is found to be very fast in tests on hypothetical crystal structures of acetic acid. © 1997 John Wiley & Sons, Inc. J Comput Chem 18:1036-1042, 1997
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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