Color Differences Highlight Concomitant Polymorphism of Chalcones

Hall, Charlie L.; Guo, Rui; Potticary, Jason; Cremeens, Matthew E.; Warren, Stephen D.; Andrusenko, Iryna; Gemmi, Mauro; Zwijnenburg, Martijn A.; Sparkes, Hazel A.; Pridmore, Natalie E.; Price, Sarah L.; Hall, Simon R.

doi:10.1021/acs.cgd.0c00285

Cited by 13 publications

(12 citation statements)

References 73 publications

(110 reference statements)

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“…However, the PBE functional, which was the best that could be used, is known to suffer from delocalization error. [15] This affects the modelling of the N atom conformation and stability of polymorphs of 5-methyl-2-[(2-nitrophenyl)-amino]-3-thiophenecarbonitrile (ROY) [16] and dimethylamino-nitrochalcone [17] so our calculations are likely to have inaccurate amine geometries as well as cell volumes (Figure S4). The experimental au26 structure was only slightly higher (less than 1.2 kJ mol À 1 Figure 5, Table S2) in energy than bd74 (which has the same layer structure and polar ribbons) and fc35 (which has non-polar ribbons).…”

Section: Resultsmentioning

confidence: 99%

The Crystal Structure of 5‐Aminouracil and the Ambiguity of Alternative Polymorphs

Watts

Price

et al. 2021

Israel Journal of Chemistry

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The nucleobase derivative 5-aminouracil (AUr, C 4 H 5 N 3 O 2 ) is of interest for its biological activity, yet the solid state structure of this compound has remained elusive owing to its propensity to crystallize as aggregates of microcrystalline particles. Here we report the first single-crystal structure of AUr determined from synchrotron x-ray diffraction data. An early crystal structure prediction effort, which assumed that AUr was rigid in the isolated molecule optimized conformation, provided several poor matches to the simu-lated PXRD pattern. Revisiting these crystal structures, by periodic electronic level modelling (PBE-TS optimization) gave more realistic relative lattice energies, but a good match to the experimental powder pattern required using the experimental cell parameters. PXRD and Raman spectroscopy suggest that phase impurities may be present in the bulk crystallization product, though the identity of alternative polymorphs could not be confirmed on the basis of the data available.

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Section: Resultsmentioning

confidence: 99%

The Crystal Structure of 5‐Aminouracil and the Ambiguity of Alternative Polymorphs

Watts

Price

et al. 2021

Israel Journal of Chemistry

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“…Chalcones are a class of natural products widely used in medicinal chemistry. For instance, the (E)-3′-dimethylamino-nitrochalcone has demonstrated concomitant polymorphism, easily detectable by the different colors associated to each form [97].…”

Section: The Special Cases: Concomitant Vanishing (Or Disappearing) and Intergrowth Polymorphismmentioning

confidence: 99%

Polymorphism and Supramolecular Isomerism: The Impasse of Coordination Polymers

Sánchez-Férez¹,

Pons²

2022

Crystallization and Applications

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The chapter presented hereafter, outlines the narrow link between chemistry and crystallography that impelled the identification of polymorphism and provided a priceless grounding to understand structure-properties relationship. It was initially conceived for organic substances but actually embraced by metal–organic products, especially in the study of coordination polymers. All of the technologic advances have provided profound insights on the control of crystal structures formation revealing that any applied stimulus over a substance can undergo a structural transformation. This has led to the implementation of several methodologies in the industrial and academic segment shedding light on the source of hitherto, not well understood results.

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“…The bright colors of fruits and vegetables are due in part to the flavonoids, derived from chalcones. Some chalcone derivatives are polymorphic, with different colors exhibited by different polymorphs, 52 arising from the packing differences. Chalcones are also used as fluorescent probes in imaging, such as a library of dialkyaminochalcones, 53 many of which showed high fluorescence in DMSO, and a sharp structure–activity relationship in cellular cytotoxicity.…”

Section: Introductionmentioning

confidence: 99%

Packing Preferences of Chalcones: A Model Conjugated Pharmaceutical Scaffold

Price

2022

Crystal Growth & Design

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We sought the crystal packing preferences of the chalcone scaffold by analyzing 232 single-component crystal structures of chalcones with a small (six or fewer non-hydrogen atoms) substituent on either or both rings, including the unsubstituted molecule. This covers 216 molecules, as some are polymorphic, and 277 independent molecular conformations, as 16% of the crystal structures have more than one symmetry independent molecule. Quantum mechanical conformational profiles of the unsubstituted molecule and the almost 5000 crystal structures within 20 kJ mol –1 of the global minimum generated in a crystal structure prediction (CSP) study have been used to complement this analysis. Although π conjugation would be expected to favor a planar molecule, there are a significant number of crystal structures containing nonplanar molecules with an approximately 50° angle between the aromatic rings. The relative orientations of the molecules in the inversion-related dimers and translation-related dimers in the experimental crystal structures show the same trends as in the CSP-generated structures for the unsubstituted molecule, allowing for the substituent making the side-to-side distances larger. There is no type of dimer geometry associated with particularly favorable lattice energies for the chalcone core. Less than a third of the experimental structures show a face-to-face contact associated with π···π stacking. Analysis of the experimental crystal structures with XPac and Mercury finds various pairs of isostructural crystals, but the largest isostructural set had only 15 structures, with all substituents (mainly halogens) in the para position. The most common one-dimensional motif, found in half of the experimental crystal structures, is a translation-related side-to-side packing, which can be adopted by all the observed conformations. This close-packed motif can be adopted by chalcones with a particularly wide variety of substituents as the substituents are at the periphery. Thus, although the crystal structures of the substituted chalcones show thermodynamically plausible packings of the chalcone scaffold, there is little evidence for any crystal engineering principle of preferred chalcone scaffold packing beyond close packing of the specific molecule.

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Color Differences Highlight Concomitant Polymorphism of Chalcones

Cited by 13 publications

References 73 publications

The Crystal Structure of 5‐Aminouracil and the Ambiguity of Alternative Polymorphs

The Crystal Structure of 5‐Aminouracil and the Ambiguity of Alternative Polymorphs

Polymorphism and Supramolecular Isomerism: The Impasse of Coordination Polymers

Packing Preferences of Chalcones: A Model Conjugated Pharmaceutical Scaffold

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