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New additions to quasiracemic materials have been developed by cocrystallizing a ternary component – hydrogen oxalate – with pairs of amino acid quasienantiomers where at least one of the side-chain R groups contains a sulfur atom. Of the eight quasiracemates investigated, six exhibit crystal packing that drastically deviates from the expected centrosymmetric alignment present in the racemic counterparts and the extant database of quasiracemic materials. These structures were quantitatively assessed for conformational similarity (CCDC-Mercury structure overlay) and the degree of inversion symmetry (Avnir's Continuous Symmetry Measures) for each quasienantiomeric pair. Despite the variance in quasienantiomeric components, these structures exhibit a high degree of isostructurality where the principal components assemble by a complex blend of common N + –H⋯O and O–H⋯O − interactions. These charge-assisted hydrogen-bonded networks form thermodynamically favored crystal packing that promotes cocrystallization of a structurally diverse set of quasienantiomeric components.
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Progressive alignment of crystals: reproducible and efficient assessment of crystal structure similarity
During in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis ( e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals ( PAC ) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration ( R g ) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters ( i.e. to minimize R g ) or prioritized reduced RMSD ( i.e. via possibly elongated clusters with relatively larger R g ). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK . However, the lower R g values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.
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- Award ID(s):
- 1751688
- PAR ID:
- 10403343
- Date Published:
- Journal Name:
- Journal of Applied Crystallography
- Volume:
- 55
- Issue:
- 6
- ISSN:
- 1600-5767
- Page Range / eLocation ID:
- 1528 to 1537
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1107/S1600576722009670
