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U pack program package for crystal structure prediction: Force fields and crystal structure generation for small carbohydrate molecules
Author(s) -
van Eijck Bouke P.,
Kroon Jan
Publication year - 1999
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199906)20:8<799::aid-jcc6>3.0.co;2-z
Subject(s) - force field (fiction) , crystal structure prediction , crystal structure , crystal (programming language) , atom (system on chip) , molecule , chemistry , crystallography , opls , field (mathematics) , hydrogen atom , hydrogen bond , computational chemistry , physics , computer science , mathematics , group (periodic table) , quantum mechanics , pure mathematics , organic chemistry , programming language , embedded system
The U pack program package for crystal structure generation was used to build hypothetical crystal structures for 32 pyranoses and 24 polyalcohols. A subset of these was used to compare six force fields in their ability to reproduce the experimentally observed structures, preferably with low energies and high rankings with respect to the structure with lowest energy. One of these force fields, U nitat , was derived from G romos 87 by adjusting some parameters to obtain a better geometric description of these crystal structures. This united‐atom force field and the all‐atom O pls force field performed best, and were used in the crystal structure generation for the full set of compounds. For these carbohydrates, hundreds of hypothetical polymorphic structures are generated in an energy window of about 25 kJ/mol. On average, the experimental structures had reasonable energies and rankings. These lists are good starting points for more sophisticated calculations, and can be used for structure determination by powder diffraction methods. In a few cases, serious doubt was raised concerning the hydrogen‐bond network reported in the literature, for which more plausible alternatives appear to exist. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 799–812, 1999