Searching the Cambridge Structural Database for the `best' representative of each unique polymorph

2006 ◽  
Vol 62 (4) ◽  
pp. 567-579 ◽  
Author(s):  
Jacco van de Streek
Keyword(s):  
Crystal Structure ◽  
Computer Program ◽  
Crystal Structures ◽  
Cambridge Structural Database ◽  
Structural Database

A computer program has been written that removes suspicious crystal structures from the Cambridge Structural Database and clusters the remaining crystal structures as polymorphs or redeterminations. For every set of redeterminations, one crystal structure is selected to be the best representative of that polymorph. The results, 243 355 well determined crystal structures grouped by unique polymorph, are presented and analysed.

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.

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.

scholarly journals Generation of crystal structures using known crystal structures as analogues

2016 ◽  
Vol 72 (4) ◽  
pp. 530-541 ◽  
Author(s):  
Jason C. Cole ◽  
Colin R. Groom ◽  
Murray G. Read ◽  
Ilenia Giangreco ◽  
Patrick McCabe ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Single Component ◽  
Cambridge Structural Database ◽  
Shape Similarity ◽  
Interaction Potentials ◽  
Structural Database ◽  
The Many

This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean bysimilarin both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach.

First global analysis of the GSK database of small molecule crystal structures

CrystEngComm ◽  
2021 ◽  
Author(s):  
Leen N. Kalash ◽  
Jason C. Cole ◽  
Royston C. B. Copley ◽  
Colin M. Edge ◽  
Alexandru A. Moldovan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Crystal Structures ◽  
Small Molecule ◽  
Global Analysis ◽  
Structural Features ◽  
Cambridge Structural Database ◽  
Structure Database ◽  
Structural Database ◽  
Crystal Structure Database

Analysis of the molecular and structural features of the GSK crystal structure database and Cambridge Structural Database leads to improved reliability in hydrogen bond propensity models for pharmaceutical polymorphs.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications

2014 ◽  
Vol 70 (1) ◽  
pp. 91-105 ◽  
Author(s):  
Peter T. A. Galek ◽  
James A. Chisholm ◽  
Elna Pidcock ◽  
Peter A. Wood
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Stability ◽  
Statistical Models ◽  
Cambridge Structural Database ◽  
Acceptor Atom ◽  
Coordination Behaviour ◽  
Structural Database

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

New software for searching the Cambridge Structural Database and visualizing crystal structures

2002 ◽  
Vol 58 (3) ◽  
pp. 389-397 ◽  
Author(s):  
Ian J. Bruno ◽  
Jason C. Cole ◽  
Paul R. Edgington ◽  
Magnus Kessler ◽  
Clare F. Macrae ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
High Performance ◽  
Cambridge Structural Database ◽  
Search Interface ◽  
Intermolecular Contacts ◽  
Structural Database

Two new programs have been developed for searching the Cambridge Structural Database (CSD) and visualizing database entries: ConQuest and Mercury. The former is a new search interface to the CSD, the latter is a high-performance crystal-structure visualizer with extensive facilities for exploring networks of intermolecular contacts. Particular emphasis has been placed on making the programs as intuitive as possible. Both ConQuest and Mercury run under Windows and various types of Unix, including Linux.

Utilizing organic and organometallic structural data in powder diffraction

2014 ◽  
Vol 29 (S2) ◽  
pp. S19-S30 ◽  
Author(s):  
Jason C. Cole ◽  
Elena A. Kabova ◽  
Kenneth Shankland
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
Powder Diffraction Data ◽  
Racemic Form ◽  
Structure Solution ◽  
Structural Database

The Cambridge Structural Database (CSD) is a database of small molecule organic and organometallic crystal structures elucidated using X-Ray and neutron crystallography. The CSD is distributed alongside a system of software (the Cambridge Structural Database System) to academic and industrial users. The system contains a number of applications (in particular DASH, ConQuest, and Mogul) that can be used to aid crystallographers in the solution and refinement of crystal structures from powder diffraction data, and in the interpretation of crystal structure models (in particular, Mercury). This publication uses a racemic form of ornidazole (Z′ = 3) to illustrate the efficacy of DASH in the crystal structure solution from powder diffraction data. Furthermore, numerous features in Mogul and Mercury that aid crystal structure solution and interpretation of crystallographic data are revised. Finally, a review of a new method for using database-derived geometric information directly in structural solution is presented.

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.

Cluster analyses of metal-organic fragments using the dSNAP software

2009 ◽  
Vol 65 (6) ◽  
pp. 707-714
Author(s):  
Anna Collins ◽  
Chick C. Wilson ◽  
Christopher J. Gilmore
Keyword(s):  
Metal Complex ◽  
Computer Program ◽  
Cambridge Structural Database ◽  
Clustering Method ◽  
Cluster Analyses ◽  
Organic Systems ◽  
Different Types ◽  
Metal Organic ◽  
Structural Database

The dSNAP computer program has been used to classify searches of the Cambridge Structural Database for two ligands: —O—CH2—CH2—O— and N(CH2CH2O—)3 commonly found in metal-organic systems. The clustering method used is based on total geometries (i.e. all the lengths and angles involving all the atoms in the search fragment, whether bonded or not) and proved capable of distinguishing in a wholly automatic, objective way between different types of metal complex purely on the basis of the geometry of the ligand and the relative positions of the O atoms to the metals.

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