Upack program package for crystal structure prediction: Force fields and crystal structure generation for small carbohydrate molecules

• Published in: Journal of computational chemistry 1999-06, Vol.20 (8), p.799-812
• Main Authors: van Eijck, Bouke P., Kroon, Jan
• Format: Article
• Language: English
• Subjects: carbohydrates; crystal structure prediction; force fields; polymorphism
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/(SICI)1096-987X(199906)20:8<799::AID-JCC6>3.0.CO;2-Z

The Upack 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, Unitat, was derived from Gromos87 by adjusting some parameters to obtain a better geometric description of these crystal structures. This united‐atom force field and the all‐atom Opls 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