Playing around with <i>MP</i>, a tool for the analysis of pseudosymmetry: recurrent appearance of local pseudo-space groups in the asymmetric unit of <i>Z</i>′ = 4 structures

Baggio, Ricardo

doi:10.1107/s2053229620001904

Cited by 6 publications

(1 citation statement)

References 53 publications

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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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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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Identifying and characterizing translationally modulated molecular crystal structures

Brock

Taylor

2020

Acta Crystallogr Sect B

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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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Pervasive approximate periodic symmetry in organic P1 structures

Brock

2022

Acta Crystallogr Sect B

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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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Playing around with MP, a tool for the analysis of pseudosymmetry: recurrent appearance of local pseudo-space groups in the asymmetric unit of Z′ = 4 structures

Cited by 6 publications

References 53 publications

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

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

Identifying and characterizing translationally modulated molecular crystal structures

Pervasive approximate periodic symmetry in organic P1 structures

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