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Brock CP. Pervasive approximate periodic symmetry in organic P1 structures. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:576-588. [PMID: 35975824 DOI: 10.1107/s2052520622004929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
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 Zeffective > 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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Affiliation(s)
- Carolyn Pratt Brock
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA
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Priola E, Conterosito E, Giordana A, Volpi G, Garino C, Andreo L, Diana E, Barolo C, Milanesio M. Polymorphism and solid state peculiarities in imidazo[1,5-a]pyridine core deriving compounds: An analysis of energetic and structural driving forces. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Brock CP. Approximate symmetry in the third reported structure of a metal complex of L-DOPA. Acta Crystallogr C Struct Chem 2021; 77:441-442. [PMID: 34350840 PMCID: PMC8340035 DOI: 10.1107/s2053229621007452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022] Open
Abstract
Although l -DOPA is a major drug that has been used for more than 50 years to treat the motor symptoms of Parkinson’s disease, the Cambridge Structural Database contains only two structures in which it is coordinated to a metal. Why are there not more? The new structure is also notable for an approximate 42 axis.
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Affiliation(s)
- Carolyn Pratt Brock
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA
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Reiss GJ, Wyshusek M. The layered crystal structure of bis(theophyllinium) hexachloridostannate (IV), C14H18N8O8SnCl6. Z KRIST-NEW CRYST ST 2021. [DOI: 10.1515/ncrs-2021-0185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
C14H18N8O8SnCl6, monoclinic, P21/n (no. 14), a = 8.1810(2) Å, b = 12.6195(3) Å, c = 11.3811(2) Å, β = 90.258(2)°, Z = 2, V = 1174.97(5) Å3, R
gt(F) = 0.0266, wR
ref = 0.0620, T = 290 K.
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Affiliation(s)
- Guido J. Reiss
- Institut für Anorganische Chemie und Strukturchemie Lehrstuhl II: Material- und Strukturforschung, Heinrich–Heine–Universität Düsseldorf , Universitätsstrasse 1 , D-40225 Düsseldorf , Germany
| | - Maik Wyshusek
- Institut für Anorganische Chemie und Strukturchemie Lehrstuhl II: Material- und Strukturforschung, Heinrich–Heine–Universität Düsseldorf , Universitätsstrasse 1 , D-40225 Düsseldorf , Germany
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Brock CP, Taylor R. Identifying and characterizing translationally modulated molecular crystal structures. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:630-642. [PMID: 32831281 DOI: 10.1107/s2052520620007891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
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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Affiliation(s)
- Carolyn Pratt Brock
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, United States
| | - Robin Taylor
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, United Kingdom
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Baggio R. 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. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:258-268. [PMID: 32132284 DOI: 10.1107/s2053229620001904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/10/2020] [Indexed: 11/10/2022]
Abstract
A systematic application of the MP procedure [Baggio (2019). Acta Cryst. C75, 837-850] to a subset of Z' = 4 structures in the literature revealed a number of suggestive properties in many of the cases analysed, which allowed us to conclude that: (i) very few of those structures showed no pseudosymmetry (PS) whatsoever linking any of the possible moiety pairs in the asymmetric unit (AU), the vast majority disclosing, instead, at least two (and frequently more) molecules linked by these PS operations; (ii) on occasion, two pairs of molecules were related, each by the same PS element, enabling the resulting pair of dimers to be viewed locally as a Z' = 2 rather than a Z' = 4 case; (iii) sometimes all four moieties in the AU appeared interrelated by PS relationships, closely suggesting a distribution of symmetry operations as found in real space groups; (iv) in many cases, this resemblance was of a superior quality, leading to surprising local replicas of real space groups in the reduced realm of the AU, thus locally reducing the description to a Z' = 1 one. Through a systematic application of the MP procedure, we analyze in this article a number of these latter cases, which proved to be surprisingly common, far beyond any original expectation, and leaving open the question about the eventual reasons for the phenomenon, which would certainly merit appropriate theoretical attention.
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Affiliation(s)
- Ricardo Baggio
- Gerencia de Investigación y Aplicaciones, Centro Atómico Constituyentes, Comisin Nacional de Energía Atómica, Buenos Aires, Argentina
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Kulszewicz-Bajer I, Zagorska M, Banasiewicz M, Guńka PA, Toman P, Kozankiewicz B, Wiosna-Salyga G, Pron A. Effect of the substituent position on the electrochemical, optical and structural properties of donor–acceptor type acridone derivatives. Phys Chem Chem Phys 2020; 22:8522-8534. [DOI: 10.1039/d0cp00521e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The electrochemical and fluorescence (TADF) properties of phenoxazine derivatives of acridone are strongly isomerism-sensitive.
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Affiliation(s)
| | | | | | - Piotr A. Guńka
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw
- Poland
| | - Petr Toman
- Institute of Macromolecular Chemistry
- Academy of Sciences of the Czech Republic
- 162 06 Prague 6
- Czech Republic
| | | | | | - Adam Pron
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw
- Poland
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Garraza MS, Gimenez ME, Vega DR, Baggio R. Crystal structure and pseudosymmetry analysis of the triclinic prodrug cloxazolam (Z' = 4). ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:851-858. [PMID: 31271372 DOI: 10.1107/s2053229619008404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 11/10/2022]
Abstract
The prodrug cloxazolam [systematic name: 13-chloro-2-(2-chlorophenyl)-3-oxa-6,9-diazatricyclo[8.4.0.02,6]tetradeca-1(10),11,13-trien-8-one], C17H14Cl2N2O2, crystallizes in the triclinic space group P-1, with four chemically identical independent molecules in the asymmetric unit. However, in order to facilitate the analysis of the striking pseudosymmetry relating the four independent molecules, the structure has been analysed and reported in the nonconventional centred B-1 space-group setting. Pseudosymmetry is an eminently local property, valid only in the realm of the unit-cell boundary and not propagating to the whole crystal structure. It has been analyzed using the MP procedure described in the preceding article [Baggio (2019). Acta Cryst. C75, 837-850]. The molecules consist of a rigid core made up of three rings (five-, six- and seven-membered) and an extra six-membered ring joined to the latter group by a single C-C bond, together with a clamping intramolecular C-H...O interaction preventing free rotation and providing additional rigidity. The four molecules in the asymmetric unit pair into dimers with almost exact twofold pseudosymmetry, further linked into (001) slabs as the building bricks of the structure. Interpenetration of slabs finally leads to a three-dimensional structure of unusual compactness for an organic structure, with a Kitaigorodskii packing index of ca 0.71.
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Affiliation(s)
- María Soledad Garraza
- División Monitoreo de la Radiación Externa, Gerencia Seguridad Radiológica y Nuclear, Gerencia de Área Seguridad Nuclear y Ambiente, and, Instituto de Tecnología Nuclear Dan Beninson, UNSAM-CNEA, Buenos Aires, Argentina
| | | | - Daniel Roberto Vega
- Gerencia de Investigación y Aplicaciones, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, and, Escuela de Ciencia y Tecnología, Universidad Nacional General San Martín, Buenos Aires, Argentina
| | - Ricardo Baggio
- Gerencia de Investigación y Aplicaciones, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
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Brock CP. A new tool for finding approximate symmetry. Acta Crystallogr C Struct Chem 2019; 75:835-836. [PMID: 31271370 DOI: 10.1107/s2053229619009124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 12/27/2022] Open
Affiliation(s)
- Carolyn Pratt Brock
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA
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