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.

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.

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.

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.

scholarly journals Stabilizing the crystal structures of NaFePO4 with Li substitutions

2020 ◽  
Vol 22 (25) ◽  
pp. 13975-13980
Author(s):  
Renhai Wang ◽  
Shunqing Wu ◽  
Feng Zhang ◽  
Xin Zhao ◽  
Zijing Lin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Database ◽  
Crystal Structure Database

We build a crystal structure database for NaFePO4 by replace Li with Na in LiFePO4, and stabilize the olivine type of NaFePO4 with Li substitutions.

Concerning inorganic crystal structure types

1999 ◽  
Vol 55 (2) ◽  
pp. 147-156 ◽  
Author(s):  
G. Bergerhoff ◽  
M. Berndt ◽  
K. Brandenburg ◽  
T. Degen
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Type ◽  
Inorganic Crystal Structure Database ◽  
Full Information ◽  
Structure Database ◽  
Inorganic Crystal ◽  
The Difference ◽  
Crystal Structure Database

All representatives of an inorganic crystal structure type can be found systematically in the new database SICS (Standardized Inorganic Crystal Structures). It is derived from the Inorganic Crystal Structure Database (ICSD) by selecting the best determination of each phase. In addition, each entry is given in a standardized description and complemented by searchable descriptors \Delta, which give the difference between all structures of an isopointal set. Because of the large number of structures the full information on relationships present can only be found by means of the new database itself. Some examples are given here in printed form. The limitations and the possibilities of expansion of SICS in terms of the concept of `structure types' are demonstrated.

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.

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.

scholarly journals Geometry and conformation of cyclopropane derivatives having σ-acceptor and σ-donor substituents: a theoretical and crystal structure database study

2012 ◽  
Vol 68 (2) ◽  
pp. 182-188 ◽  
Author(s):  
Aurora J. Cruz-Cabeza ◽  
Frank H. Allen
Keyword(s):  
Crystal Structure ◽  
Bond Length ◽  
Density Functional ◽  
Crystal Structure Data ◽  
Functional Theory ◽  
Structure Information ◽  
Structure Database ◽  
Structural Database ◽  
Electron Donation ◽  
Crystal Structure Database

The structures of cyclopropane rings which carry σ-acceptor or σ-donor substituents have been studied using density-functional theory (DFT), and mean bond lengths and conformational parameters retrieved from the Cambridge Structural Database. It is confirmed that σ-acceptor substituents, e.g. halogens, generate positive ring bond-length asymmetry in which there is lengthening of the distal bond (opposite to the point of substitution), and shortening of the two vicinal bonds. This is due to withdrawal of electron density from the cyclopropane 1e′′ orbitals, which are bonding for the distal bond and antibonding for the vicinal bonds. For σ-donor substituents such as SiH3 or Si(CH3)3, the DFT and crystal structure data show negative ring bond-length asymmetry (distal bond shortened, vicinal bonds lengthened), owing to electron donation into the 4e′ ring orbital, which are also bonding for the distal bond and antibonding for the vicinal bonds. The results also show that —OH substituents induce weak positive asymmetry, but that the effects of methyl or amino substituents are either non-existent or extremely small, certainly too small to measure using crystal structure information.

scholarly journals The development and use of a crystallographic database

2016 ◽  
Vol 72 (2) ◽  
pp. 167-168 ◽  
Author(s):  
Carl Henrik Görbitz
Keyword(s):  
Crystal Structures ◽  
Small Molecule ◽  
Organometallic Compounds ◽  
Cambridge Structural Database ◽  
Acta Cryst ◽  
Individual Crystal ◽  
Data Source ◽  
Structural Database

To scientists working with small-molecule or organometallic compounds, the Cambridge Structural Database constitutes an extremely important tool for reference to individual crystal structures and as a data source for statistical investigations. The article by Groomet al.[(2016),Acta Cryst.B72, 171–179] provides updated information on the use, development and future of this database.

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