Mining the Cambridge Structural Database for Matched Molecular Crystal Structures: A Systematic Exploration of Isostructurality

2017 ◽  
Vol 17 (6) ◽  
pp. 3192-3203 ◽  
Author(s):  
Ilenia Giangreco ◽  
Jason C. Cole ◽  
Elizabeth Thomas
Keyword(s):  
Crystal Structures ◽  
Molecular Crystal ◽  
Cambridge Structural Database ◽  
Systematic Exploration ◽  
Structural Database

scholarly journals Identifying and characterizing translationally modulated molecular crystal structures

2020 ◽  
Vol 76 (4) ◽  
pp. 630-642 ◽  
Author(s):  
Carolyn Pratt Brock ◽  
Robin Taylor
Keyword(s):  
Crystal Structures ◽  
Quality Indicators ◽  
Conformational Changes ◽  
Molecular Crystal ◽  
Unit Cell ◽  
Cambridge Structural Database ◽  
Modulated Structure ◽  
Structural Database ◽  
Independent Molecules ◽  
Different Parts

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.

Stacking interactions of resonance-assisted hydrogen-bridged rings and C6-aromatic rings

2020 ◽  
Vol 22 (24) ◽  
pp. 13721-13728 ◽  
Author(s):  
Jelena P. Blagojević Filipović ◽  
Michael B. Hall ◽  
Snežana D. Zarić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Aromatic Rings ◽  
Structural Database

Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings have been studied by analyzing crystal structures in the Cambridge Structural Database and performing quantum chemical calculations.

GRX: a program to search the CSD for functional group exchanges

2005 ◽  
Vol 38 (4) ◽  
pp. 694-696 ◽  
Author(s):  
Jacco van de Streek ◽  
Sam Motherwell
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Functional Group ◽  
Cambridge Structural Database ◽  
Structural Database

In order to establish the effect of exchanging one functional group by another on the crystal structure, one would like to be able to search the Cambridge Structural Database for all pairs of crystal structures where this substitution has been made. A program calledGRX(group exchange) was written for that purpose.

scholarly journals The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

2017 ◽  
Vol 73 (3) ◽  
pp. 240-245 ◽  
Author(s):  
Colin R. Groom ◽  
Jason C. Cole
Keyword(s):  
Drug Discovery ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structural Chemistry ◽  
Cambridge Structural Database ◽  
Complement Protein ◽  
Ligand Discovery ◽  
Structural Database ◽  
Core Part

Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility.

Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

2015 ◽  
Vol 71 (10) ◽  
pp. 921-928 ◽  
Author(s):  
Kulsoom Kamal ◽  
Hardesh K. Maurya ◽  
Atul Gupta ◽  
Prema G. Vasudev
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Cambridge Structural Database ◽  
Database Analysis ◽  
Molecular Conformations ◽  
Keto Esters ◽  
Organic Molecular Crystals ◽  
Structural Database

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013).RSC Adv.3, 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014).Angew. Chem. Int. Ed.53, 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple-bond]C interaction (X = F, Cl, Br or I),viz.the N...Xdistance and the C—X...N and C—N...Xangles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

scholarly journals The Cambridge Structural Database in chemical education: analysis of hydrogen-bonded networks in salts of hexaaqua metal ions with organic counter-ions

2020 ◽  
Vol 53 (6) ◽  
pp. 1593-1602
Author(s):  
Massimo Moret
Keyword(s):  
Metal Ions ◽  
Crystal Structures ◽  
Structure Analysis ◽  
Structural Information ◽  
Crystal Structure Analysis ◽  
Molecular Structures ◽  
Intramolecular Interactions ◽  
Cambridge Structural Database ◽  
Counter Ions ◽  
Structural Database

This paper describes a laboratory course that introduces basic crystallographic data analysis to chemistry students encountering for the first time the world of crystals and crystal structures. The aim of the course is to provide students with direct contact with crystal structures and hands-on experience in structure analysis. To this end, a set of appropriately simple inorganic molecular structures was selected, consisting of salts of hexaaqua metal ions with organic counter-ions. By exploiting the crystallographic tools available in the Cambridge Structural Database program Mercury, students learn how to visualize and analyse a set of atomic coordinates. In this way they learn how to extract bonding and structural information concerning intramolecular interactions in both salt components. Intermolecular interactions are next analysed by looking closely at supramolecular motifs and packing patterns generated by hydrogen bonds. This pragmatic approach turned out to be effective and extremely useful for summarizing many chemical concepts learned by students during a bachelor degree course in chemistry. The experience provides at the same time some basic capabilities for properly managing crystal structure analysis.

The Cambridge Structural Database: a quarter of a million crystal structures and rising

2002 ◽  
Vol 58 (3) ◽  
pp. 380-388 ◽  
Author(s):  
Frank H. Allen
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structure Data ◽  
Crystal Structure Data ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
Chemical Information ◽  
Structural Database ◽  
Statistical Survey

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.

Isostructurality in one and two dimensions: isostructurality of polymorphs

2004 ◽  
Vol 60 (5) ◽  
pp. 547-558 ◽  
Author(s):  
László Fábián ◽  
Alajos Kálmán
Keyword(s):  
Crystal Structures ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Cambridge Structural Database ◽  
Two Dimensional ◽  
Structural Database ◽  
Specific Packing ◽  
Packing Interactions

A set of polymorphic crystal structures was retrieved from the Cambridge Structural Database in order to estimate the frequency of isostructurality among polymorphs. Altogether, 50 structures, the polymorphs of 22 compounds, were investigated. It was found that one-, two- or three-dimensional isostructurality is exhibited by approximately half of the compounds analyzed. Among the isostructural polymorphs, the frequency of one-, two- and three-dimensional isostructurality is similar. From the examples, it appears that three-dimensional isostructurality is connected to the gradual ordering of crystal structures, while one- and two-dimensional isostructurality can often be related to specific packing interactions. The possibility of many similar interactions seems to decrease the probability of the occurrence of isostructural polymorphs. Conformational polymorphs do not exhibit isostructurality.

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