scholarly journals dSNAP: a computer program to cluster and classify Cambridge Structural Database searches

2005 ◽  
Vol 38 (5) ◽  
pp. 833-841 ◽  
Author(s):  
Gordon Barr ◽  
Wei Dong ◽  
Christopher J. Gilmore ◽  
Andrew Parkin ◽  
Chick C. Wilson
Keyword(s):  
Cluster Analysis ◽  
Data Processing ◽  
Computer Program ◽  
Classification Scheme ◽  
Multivariate Data ◽  
Distance Matrix ◽  
Cambridge Structural Database ◽  
Levels Of Detail ◽  
Structural Database ◽  
Visualization Tools

A computer program that automatically classifies and clusters structural fragments extracted from mining the Cambridge Structural Database is described. The methodology is based on cluster analysis and multivariate data processing of distance matrix information describing the extracted fragments. Coupled with the calculations is a set of visualization tools that enable the user to view and verify the proposed classification scheme, and further explore it in varying levels of detail. Two examples are presented: the first is based on a simple difluoroalkene fragment and the second, more complex, on a chiral vicinal dialcohol,R1(OH)CHCH(OH)R2.

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.

Searching for stereoisomerism in crystallographic databases: algorithm, analysis and chiral curiosities

2017 ◽  
Vol 73 (3) ◽  
pp. 453-465 ◽  
Author(s):  
E. Grothe ◽  
H. Meekes ◽  
R. de Gelder
Keyword(s):  
Computer Program ◽  
Crystallographic Data ◽  
Cambridge Structural Database ◽  
Algorithm Analysis ◽  
Automated Identification ◽  
Crystallographic Databases ◽  
Multiple Structures ◽  
Ring Structures ◽  
Structural Database

The automated identification of chiral centres in molecular residues is a non-trivial task. Current tools that allow the user to analyze crystallographic data entries do not identify chiral centres in some of the more complex ring structures, or lack the possibility to determine and compare the chirality of multiple structures. This article presents an approach to identify asymmetric C atoms, which is based on the atomic walk count algorithm presented by Rücker & Rücker [(1993),J. Chem. Inf. Comput. Sci.33, 683–695]. The algorithm, which we implemented in a computer program namedChiChi, is able to compare isomeric residues based on the chiral centres that were identified. This allows for discrimination between enantiomers, diastereomers and constitutional isomers that are present in crystallographic databases.ChiChiwas used to process 254 354 organic entries from the Cambridge Structural Database (CSD). A thorough analysis of stereoisomerism in the CSD is presented accompanied by a collection of chiral curiosities that illustrate the strength and versatility of this approach.

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.

Using cluster analysis to study transition-metal geometries: four-coordinate complexes with two salicylaldiminato or related ligands

2007 ◽  
Vol 63 (4) ◽  
pp. 612-620 ◽  
Author(s):  
Andrew Parkin ◽  
Gordon Barr ◽  
Anna Collins ◽  
Wei Dong ◽  
Christopher J. Gilmore ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Transition Metal ◽  
Metal Complexes ◽  
Prior Knowledge ◽  
Transition Metal Complexes ◽  
Cambridge Structural Database ◽  
Metal Coordination ◽  
Coordination Geometry ◽  
Geometric Similarity ◽  
Structural Database

Cluster analysis is shown to be an effective method to analyse and classify metal coordination geometry in a very large number of four-coordinate bis-salicylaldimato (or bis-β-iminoketonate) transition-metal complexes available in the Cambridge Structural Database. The methods described require no prior knowledge of chemistry to be input; retrieved structures are automatically clustered into groups based purely on the geometric similarity of the fragments and these groupings can then be interpreted by the structural chemist.

The structure of 1,2,4,4,6-pentaphenyl-1,4-dihydropyridine

1990 ◽  
Vol 55 (8) ◽  
pp. 2059-2065 ◽  
Author(s):  
Jaroslav Vojtěchovský ◽  
Jindřich Hašek ◽  
Jiří Ječný ◽  
Karel Huml
Keyword(s):  
Title Compound ◽  
Cambridge Structural Database ◽  
Boat Conformation ◽  
Planar Conformation ◽  
Structural Database ◽  
Independent Molecules ◽  
Dihydropyridine Ring

Title compound is triclinic, Mr = 461.60; P1, a = 9.158(1), b = 16.062(3), c = 19.472(3) Å, α = 110.69(1)°, β = 89.70(1)°, γ = 103.17(1)°, V = 2 600(1) Å3, Z = 4, Do = 1.15(3), Dc = 1.179(1) Mg m-3, λ(CuKα) = 1.5418 Å, μ = 0.509 mm-1, F(000) = 976 K, R = 0.040 for 8 059 unique observed reflections. Both symmetrically independent molecules show a different geometry of the 1,4-dihydropyridine ring: either the boat conformation with apexes C(sp3), N and boat angles 14.7(3)° and 10.3(2)° respectively, or the planar conformation. The conformation has been compared with similar dihydropyridines obtained from Cambridge Structural Database.

scholarly journals Targeted classification of metal–organic frameworks in the Cambridge structural database (CSD)

2020 ◽  
Vol 11 (32) ◽  
pp. 8373-8387 ◽  
Author(s):  
Peyman Z. Moghadam ◽  
Aurelia Li ◽  
Xiao-Wei Liu ◽  
Rocio Bueno-Perez ◽  
Shu-Dong Wang ◽  
...  
Keyword(s):  
Surface Chemistry ◽  
Specific Surface ◽  
Large Scale ◽  
Metal Cluster ◽  
Metal Organic Frameworks ◽  
Cambridge Structural Database ◽  
Metal Organic ◽  
Structural Database

Large-scale targeted exploration of metal–organic frameworks (MOFs) with characteristics such as specific surface chemistry or metal-cluster family has not been investigated so far.

Applications of the Cambridge Structural Database to molecular inorganic chemistry

2002 ◽  
Vol 58 (3) ◽  
pp. 398-406 ◽  
Author(s):  
A. Guy Orpen
Keyword(s):  
Inorganic Chemistry ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
High Quality ◽  
Computational Data ◽  
Inorganic Complexes ◽  
Fundamental Research ◽  
Structural Database ◽  
Structure Correlation ◽  
Molecular Dimensions

Applications of the data in the Cambridge Structural Database (CSD) to knowledge acquisition and fundamental research in molecular inorganic chemistry are reviewed. Various classes of application are identified, including the derivation of typical molecular dimensions and their variability and transferability, the derivation and testing of theories of molecular structure and bonding, the identification of reaction paths and related conformational analyses based on the structure correlation hypothesis, and the identification of common and presumably energetically favourable intermolecular interactions. In many of these areas, the availability of plentiful structural data from the CSD is set against the emergence of high-quality computational data on the geometry and energy of inorganic complexes.

Spacer conformation in biologically active molecules

2004 ◽  
Vol 76 (5) ◽  
pp. 959-964 ◽  
Author(s):  
J. Karolak-Wojciechowska ◽  
A. Fruzinski
Keyword(s):  
Statistical Data ◽  
Population Analysis ◽  
Cambridge Structural Database ◽  
Biologically Active ◽  
Aliphatic Chain ◽  
X Ray ◽  
Flexible Spacer ◽  
Conformational Preferences ◽  
Structural Database ◽  
The One

Based on our contemporary studies on the structures of biologically active molecules, we focus our attention on the aliphatic chain and its conformation. That flexible spacer definitely influenced the balanced position of all pharmacophoric points in molecules of biological ligands. The one atomic linker and two or three atomic spacers with one heteroatom X =O, S, CH2, NH have been taken into account. The conformational preferences clearly depend on the heteroatom X. In the discussion, we utilize our own X-ray data, computation chemistry methods, population analysis, and statistical data from the Cambridge Structural Database (CSD).

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