A simple graphical method to pinpoint local pseudosymmetries in<i>Z</i>′ &gt; 1 cases

Baggio, Ricardo

doi:10.1107/s2053229619007861

Cited by 15 publications

(6 citation statements)

References 49 publications

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“…A number of excellent approaches to the observation and examination of molecular similarity and pseudosymmetry in crystal structures have been developed. These include the molecule-overlay options in MATCH (Collins et al, 2006), XP (Sheldrick, 2008), and Mercury (Macrae et al, 2020), the atomic-pair mid-point analysis (Baggio, 2019(Baggio, , 2020, and the identification and characterization of translationally modulated structures (Brock & Taylor, 2020). We became interested in Z 0 > 1 structures as we attempted to explore the hypothesis that there is often a direct relationship between the matrix relating pairs of independent molecules in twinned crystals having Z 0 > 1 and the twin law (Foxman & Young, 2018;Young & Foxman, 2020).…”

Section: Resultsmentioning

confidence: 99%

cis-Bis(L-DOPA-κ² N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry

et al. 2021

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The crystal structure of the cis isomer of cis-bis(L-DOPA-κ2 N,O)copper(II) monohydrate (L-DOPA is 3,4-dihydroxy-L-phenylalanine) (CuLD), [Cu(C9H10NO4)2]·H2O, is a singular example of a structurally characterized, homoleptic, crystalline metal L-DOPA complex. CuLD crystallizes in the space group P21, with Z′ = 2. The two independent molecules are square planar, and are interconnected by a linear hydrogen-bonded chain containing 12 independent hydrogen bonds. The copper ions in both molecules have weak apical intermolecular Cu...O interactions [2.739 (2) and 2.973 (2) Å] with catechol –OH groups. A survey of the Cambridge Structural Database suggested that cis and trans isomers of Cu(NH2–C–CO2)2 amino acid complexes are equally likely to occur. 12 strong O—H...O and N—H...O hydrogen bonds stabilize an unusual linear arrangement of the Cu complexes. The Cu...Cu′ distances along the chain are nearly equal [5.0739 (3) and 5.1107 (3) Å] and the Cu...Cu′...Cu angles are nearly linear [176.75 (1)°]. The MATCH procedure available in the Oxford University Crystals for Windows package was used to carry out a detailed analysis of the relationship between the two independent molecules. MATCH has some particular advantages in studying the details of pseudosymmetry, which include: (i) no atomic-order requirements; (ii) the pseudosymmetry matrix is readily available, which allows quick insight into the symmetry elements involved and their location; and (iii) the differences between molecular centroids, as well as between all atomic positions and torsion angles, are listed. A tutorial presentation is designed to attract new users to the technique. In the present case, a search for a pseudosymmetric relationship between the two independent molecules showed that they are related by a pseudo-42 axis along the crystallographic c direction. A detailed analysis shows that the pseudo-42 symmetry is disrupted by torsions about the CH2—C(ipso) bonds, and that there is no supergroup that can be used to describe the crystal structure.

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Section: Resultsmentioning

confidence: 99%

cis-Bis(L-DOPA-κ² N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry

et al. 2021

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“…Approximate symmetry is pervasive in structures with Z 0 ! 4 (Brock, 2016;Baggio, 2019Baggio, , 2020; this work) but until now there has been no program that identifies approximate symmetry both automatically and reliably. (PLATON spots overlooked symmetry well but that is a less complicated task.…”

Section: Discussionmentioning

confidence: 99%

Identifying and characterizing translationally modulated molecular crystal structures

Brock

Taylor

2020

Acta Crystallogr B Struct Sci Cryst Eng Mater

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Most structural (i.e. displacive) modulations make molecules independent that had been related by translation in a phase having a smaller or centered unit cell. In the modulated structure the independent molecules are differentiated by small translations, rotations, and/or conformational changes but an approximate translational relationship is normally retained. A program has been written to identify such pseudotranslations because they can be difficult to find by eye and because they combine with each other and with lattice translations in ways that can be confusing. To characterize the pseudotranslations the program calculates their fractional translational, orientational, and conformational components as well as several quality indicators. While many pseudotranslations are obvious, others are borderline; setting tolerances for identifying a pseudotranslation proved difficult. Defaults were chosen to reproduce experience-based judgment but they can be varied in the program input. The program was run for organic and for metallo-organic structures with R ≤ 0.075 in the 2019 release of the Cambridge Structural Database. The frequency of pseudotranslations increases with Z′ and is approximately 50% for Z′ > 4. Some structures were found in which an identified pseudotranslation cannot correspond to a modulation. These include structures in which some but not all of the molecules are related by pseudotranslations and structures in which pseudotranslations in different parts of the unit cell have different directions.

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“…Conversely, in form β, the three molecules have very similar conformations. As recently suggested by Clegg, Brock and Baggio, [59][60][61][62] the pseudosymmetry between non-crystallografically equivalent molecules was checked. In the case of form α (crystallized in P21/c space group) by observing the two coplanar molecules in Figure 3a it is possible to notice that, although they are not generated from each other by a space group operation, most of the atoms are related by a local 2-fold axis perpendicular to the plane where the two molecule lies (or by an inversion center in the plane in the case of the smaller disorder component).…”

Section: Raman and Ir Spectroscopic Characterizationmentioning

confidence: 99%

Polymorphism and solid state peculiarities in imidazo[1,5-a]pyridine core deriving compounds: An analysis of energetic and structural driving forces

Priola

Conterosito

Volpi

et al. 2022

Journal of Molecular Structure

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The polymorphism and solid-state peculiarities of imidazo [1,5-a]pyridine derivatives have been investigated by a theoretical and experimental approach to shed light on the structural and energetic features of this family. Four couples of polymorphs and an ionic crystal form have been reported and analysed. Hirshfeld Surface and Energy Frameworks have been used to better understand the crystal packing features, in comparison with literature structures. The collection of all these characterizations made possible to analyse the differences between the polymorphs, the main energetic component dominating the crystal packing, and the effect of the different substitution on the central molecular skeleton on packing disposition. The assignment of vibrational spectra for the imidazo[1,5a]pyridine core has been performed for the first time. Although the discussed polymorphs are very different in their crystal packing, from the energetic point of view they present a strong similarity. In all cases, the main interactions are π‧‧‧π stacking and C-H‧‧‧π to the aromatic rings, with some tendency to the formation of C-H‧‧‧N contacts to the central imidazo [1,5a]pyridine nitrogen. The main energetic component is the dispersive one, with some contribution from the electrostatic component, and this situation is not modified by the presence of differing substituents. When hydrogen bond are present, the crystal packing is strongly modified and, energetically, the electrostatic component can overcome the dispersive on.

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A simple graphical method to pinpoint local pseudosymmetries inZ′ > 1 cases

Cited by 15 publications

References 49 publications

cis-Bis(L-DOPA-κ² N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry

cis-Bis(L-DOPA-κ² N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry

Identifying and characterizing translationally modulated molecular crystal structures

Polymorphism and solid state peculiarities in imidazo[1,5-a]pyridine core deriving compounds: An analysis of energetic and structural driving forces

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A simple graphical method to pinpoint local pseudosymmetries inZ′ > 1 cases

Cited by 15 publications

References 49 publications

cis-Bis(L-DOPA-κ2 N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry

cis-Bis(L-DOPA-κ2 N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry

Identifying and characterizing translationally modulated molecular crystal structures

Polymorphism and solid state peculiarities in imidazo[1,5-a]pyridine core deriving compounds: An analysis of energetic and structural driving forces

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Product

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cis-Bis(L-DOPA-κ² N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry

cis-Bis(L-DOPA-κ² N,O)copper(II) monohydrate: synthesis, crystal structure, and approaches to the analysis of pseudosymmetry