Pseudosymmetric layers in high-<i>Z</i>′ and <i>P</i>1 structures of organic molecules

Brock, Carolyn Pratt

doi:10.1039/d0ce00302f

Cited by 10 publications

(12 citation statements)

References 32 publications

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“…The label alt layers was used for the 51 structures in which there are obvious layers that differ in composition, approximate symmetry, packing and/or orientation (Figs. 4 and 5; see also Brock, 2020). The term hybrid packing was applied to the 78 structures in which different parts of the molecule pack with different approximate symmetry (Fig.…”

Section: Categoriesmentioning

confidence: 99%

“…4 and 5). Eleven of the 51 were described previously (Brock, 2020). The others were either added to the CSD later, had been missed or had been excluded because of hydrogen bonds between the layers.…”

Section: Some Structures Are Composed Of Different Layers That Alternatementioning

confidence: 99%

“…The aim of the project was to determine the prevalence of true approximate symmetry in P1, Z > 1 structures. Previous studies of Z 0 > 4 and of layered structures (Brock, 2016(Brock, , 2020 had identified approximate symmetry in many of them. No previous study of P1 structures has reported a careful look at symmetry other than approximate inversion.…”

Section: Introductionmentioning

confidence: 99%

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Pervasive approximate periodic symmetry in organic P1 structures

Brock

2022

Acta Crystallogr B Struct Sci Cryst Eng Mater

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The goal of this project was to identify the prevalence of approximate symmetry in organic P1 structures. In the November 2019 version of the Cambridge Structural Database (CSD), there are 2592 organic, P1, R ≤ 0.050 structures; complete, unique entries are available for 1407 Z = Z′ > 1 and 1049 Z = Z′ = 1 structures. All the Z > 1 structures can have approximate symmetry; the Z = 1 structures were scanned to find those composed of molecules or ions that might lie on a special position and those that have two or more large molecules or ions that are very similar. The number of Z = 1 structures so identified was 285, of which 49 were grouped with the Z > 1 structures because Z effective > 1. The packing in each of the 1407 + 285 = 1692 structures was investigated. The 144 that should almost certainly have been described in a smaller or higher-symmetry unit cell were removed from the list; 120 of the 144 are composed of achiral or racemic material. (About half of the Z = 1 and 89% of the Z > 1 structures are composed of enantiopure material.) Approximate periodic symmetry was found in 86% of the 1337 remaining Z > 1 structures and in 72% of the 211 remaining Z = 1 structures. About a third of the enantiomerically pure structures mimic inversion symmetry; 38% have approximate rotational symmetry. For the structures of achiral and racemic material, distorted glide or mirror symmetry is more common than is distorted inversion symmetry. Approximate rotational and glide symmetry was found to be periodic in two dimensions considerably more often than in three. In 4% of the structures, different layer types alternate or layers are related by approximate local rotations, as well as by small translations. In 5% of the structures, different parts of the molecule are segregated into two-dimensional regions that have different approximate symmetries. More than a third of the structures that are a distorted version of a higher-symmetry structure were determined at T ≥ 288 K.

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Section: Categoriesmentioning

confidence: 99%

Section: Some Structures Are Composed Of Different Layers That Alternatementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Pervasive approximate periodic symmetry in organic P1 structures

Brock

2022

Acta Crystallogr B Struct Sci Cryst Eng Mater

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“…The so-called high- Z ′ ( Z ′ > 4) structures of molecular compounds are rare, and there have been several studies in recent years discussing the origins of such structures. − Often a simple translational pseudosymmetry is featured in these crystal structures . This raises a question as to why the particular compound has crystallized as a high- Z ′ rather than as an ordinary Z ′ = 1 structure with a smaller unit cell.…”

Section: Introductionmentioning

confidence: 99%

Toward Understanding High-Z′ Organic Molecular Crystals through the Superspace Method: The Example of Glycyl-l-valine

Rekis

Schönleber

Noohinejad

et al. 2021

Crystal Growth & Design

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The high-Z′ (Z′ = 7) structure of glycyl-l-valine has been redetermined at 298 K, using synchrotron radiation and exploiting the superspace approach. The analysis of the diffraction data reveals that the structure can be described as a commensurately modulated crystal structure with superspace group P212121(0σ20)000 and modulation wave vector q = (0, 2/7, 0). A new Z′ = 1 phase has been discovered for this compound at 323 K that is related to the known Z′ = 7 phase. The origin of the modulated phase has been explored by analyzing intermolecular interactions and molecular conformations in terms of t-plots and through a comparison to (1) the newly discovered high-temperature phase, (2) a hypothetical Z′ = 1 structure at 298 K, and (3) a similar Z′ = 1 structure of the related compound glycyl-l-leucine. The results show that the conformational flexibility of the glycyl-l-valine molecule ensures optimization of the hydrogen-bond network which causes the modulation and thus a high Z′ value of the supercell. This study highlights the elegance and convenience of the superspace approach to explain the occurrence of at least part of the rarely occurring high-Z′ structures of molecular compounds.

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“…Approximate symmetry relating independent molecules is often associated with approximate symmetry that is periodic in at least two dimensions (Brock, 2020), but O'Brien et al point out that the approximate 4 2 axis does not lead to any supergroup description. In a three-dimensional supergroup including a 4 2 axis the crystallographic 2 1 axis along b would have to be accompanied by an at least approximate 2 1 axis along a, but along a there is no symmetry of any kind other than translation (Fig.…”

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Approximate symmetry in the third reported structure of a metal complex of L-DOPA

Brock¹

2021

Acta Crystallogr C

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The 2021 article 'cis-Bis(l-DOPA-2 N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry' by O'Brien et al. (2021) is notable for two reasons. First, it reports only the third crystal structure of a metal complex containing the medicinally important ligand l-DOPA (3,4-dihydroxy-lphenylalanine). Second, the article includes a tutorial on finding approximate symmetry relationships between molecules that are chemically equivalent but crystallographically independent. Identification of approximate symmetry in molecular crystals is not yet a solved problem; rather, it is an area of considerable recent activity. Rekis (2020) proposed a method for finding approximate inversion centers; Brock & Taylor (2020) described software for finding approximate translations; Brock (2020) identified layers that have higher approximate symmetry than does the whole crystal; Baggio (2019, 2020) outlined a general method that can be used to find approximate symmetry of all types and applied it to a large number of Z 0 = 4 structures.l-DOPA is a major drug that has been used for more than 50 years to treat the motor symptoms of Parkinson's disease; global sales of its various forms are measured in the billions of USD. It is then very surprising to find that the Cambridge Structural Database (CSD; Groom et al., 2016) contains only two structures (FETTON and FETVEF;Suzuki et al., 1998) in which l-DOPA is coordinated to a metal, and two more (XOYXUH and XOYXUH01; Shemchuk et al., 2019) in which it is part of an ionic cocrystal (with LiCl).There are numerous structures in the CSD of metal complexes containing the naturally occurring amino acids tyrosine (Tyr; 4-hydroxy-l-phenylalanine) and phenylalanine (Phe) that are the biological precursors of l-DOPA. In almost all of those structures the amino acid coordinates through both its amino and carboxylate groups. The CSD version of May 2021 includes 61 different R 0.075 structures of metal complexes of Tyr and 83 of Phe; there are, however, only two structures of any precision of l-DOPA complexes. Given its medical significance and market value it seems certain that many attempts have been made to grow diffraction-quality crystals of metal complexes of l-DOPA, but if so, then most of those attempts failed. It would seem that the addition of the second hydroxy substituent on the phenyl ring must be determining, but why? O'Brien et al. note that they had difficulty finding a crystal that diffracted well. Shemchuk et al. (2019) mention the low quality of the data for XOYXUH; their structure of the polymorph XOYXUH01 was determined from powder data. The R factors for FETTON and FETVEF (0.073 and 0.079, respectively; Suzuki et al., 1998) are surprisingly high. The small number of l-DOPA structures with metals and the problems with data quality suggest that some feature of l-DOPA interferes with crystal packing. Looking at the hydrogen-bonding tendencies of vicinal hydroxy groups located on phenyl rings might be a way to approach the problem.The re...

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Pseudosymmetric layers in high-Z′ and P1 structures of organic molecules

Abstract: Layers having obvious approximate symmetry higher than that of the overall 3-D crystal are present in 20–25% of the Z′ > 4 and P1 organic structures archived in the Cambridge Structural Database. In some structures different types of layers alternate.

Cited by 10 publications

References 32 publications

Pervasive approximate periodic symmetry in organic P1 structures

Pervasive approximate periodic symmetry in organic P1 structures

Toward Understanding High-Z′ Organic Molecular Crystals through the Superspace Method: The Example of Glycyl-l-valine

Approximate symmetry in the third reported structure of a metal complex of L-DOPA

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