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

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.