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

Bouke P van Eijck1, Jan Kroon1

  • 1Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Journal of Computational Chemistry
|May 27, 2022
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Summary

This study used computational methods to generate hypothetical crystal structures for pyranoses and polyalcohols. The united-atom Unitat and all-atom Opls force fields accurately reproduced experimental carbohydrate structures.

Keywords:
carbohydratescrystal structure predictionforce fieldspolymorphism

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Area of Science:

  • Computational chemistry
  • Crystallography
  • Carbohydrate chemistry

Background:

  • Accurate crystal structure prediction is crucial for understanding molecular behavior.
  • Force fields play a key role in the accuracy of molecular simulations and structure generation.
  • Existing force fields may require refinement for specific classes of compounds like carbohydrates.

Purpose of the Study:

  • To generate hypothetical crystal structures for pyranoses and polyalcohols using the Upack program.
  • To evaluate and compare the performance of six different force fields in reproducing experimentally observed crystal structures.
  • To identify optimal force fields for subsequent crystal structure generation of carbohydrates.

Main Methods:

  • Utilized the Upack program package for hypothetical crystal structure generation.
  • Compared six force fields on a subset of pyranoses and polyalcohols for reproducing experimental structures.
  • Refined the Unitat force field from Gromos87 for improved geometric description.
  • Applied the best-performing united-atom (Unitat) and all-atom (Opls) force fields for full compound set generation.

Main Results:

  • Generated hundreds of hypothetical polymorphic structures for carbohydrates within a 25 kJ/mol energy window.
  • Experimental structures generally exhibited reasonable energies and rankings among generated structures.
  • The Unitat and Opls force fields demonstrated superior performance in reproducing known crystal structures.
  • Identified potential inaccuracies in literature-reported hydrogen-bond networks, proposing plausible alternatives.

Conclusions:

  • The developed force fields and generated structures serve as valuable starting points for advanced computational studies.
  • The generated crystal structure data can aid in structure determination via powder diffraction methods.
  • Computational approaches can challenge and refine existing knowledge regarding molecular interactions, such as hydrogen bonding in carbohydrates.