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.

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.

Pseudosymmetric layers in high-Z′ and P1 structures of organic molecules

CrystEngComm ◽  
2020 ◽  
Vol 22 (43) ◽  
pp. 7371-7379 ◽  
Author(s):  
Carolyn Pratt Brock
Keyword(s):  
Organic Molecules ◽  
Cambridge Structural Database ◽  
Approximate Symmetry ◽  
Different Types ◽  
Structural Database

Layers having obvious approximate symmetry higher than that of the overall 3-D crystal are present in 20–25% of the Z′ > 4 and P1 organic structures archived in the Cambridge Structural Database. In some structures different types of layers alternate.

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.

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.

scholarly journals Enabling efficient exploration of metal–organic frameworks in the Cambridge Structural Database

CrystEngComm ◽  
2020 ◽  
Vol 22 (43) ◽  
pp. 7152-7161 ◽  
Author(s):  
Aurelia Li ◽  
Rocio Bueno-Perez ◽  
Seth Wiggin ◽  
David Fairen-Jimenez
Keyword(s):  
Metal Organic Frameworks ◽  
Cambridge Structural Database ◽  
Metal Organic ◽  
Structural Database ◽  
Efficient Exploration

A tutorial review for mining the ever growing number of metal–organic frameworks data in the Cambridge Structural Database, for MOF scientists of all backgrounds.

scholarly journals Development of a Cambridge Structural Database Subset: A Collection of Metal–Organic Frameworks for Past, Present, and Future

2017 ◽  
Vol 29 (7) ◽  
pp. 2618-2625 ◽  
Author(s):  
Peyman Z. Moghadam ◽  
Aurelia Li ◽  
Seth B. Wiggin ◽  
Andi Tao ◽  
Andrew G. P. Maloney ◽  
...  
Keyword(s):  
Metal Organic Frameworks ◽  
Cambridge Structural Database ◽  
Metal Organic ◽  
Structural Database

scholarly journals Estudio DFT de las Propiedades Electrónicas y Reactividad Química en el Cluster de Cobre Hexaquis (mu2-Benzoato- O,O')-hexa-cobre(I)

2018 ◽  
Vol 28 (1) ◽  
Author(s):  
Jean Pierre Chavez Serrano ◽  
José Miguel Díaz R ◽  
Rocio Lizeth Valentín Carhuancho
Keyword(s):  
Metal Organic Frameworks ◽  
Cambridge Structural Database ◽  
Metal Organic ◽  
Structural Database ◽  
La Red

Los MOFs (Metal-Organic Frameworks), son una nueva clase de materiales híbridos microporosos definidos como redes extendidas, conformados por iones metálicos unidos mediante enlaces covalentes coordinados con ligandos orgánicos polifuncionales, formando estructuras en 1D, 2D y 3D. Este estudio computacional evalúa las propiedades electrónicas y reactividad química de una sección de la red metal-orgánico (MOFs) para el cobre con ligandos carboxilato (benzoato) reportado en la Cambridge Structural Database (CSD) denominado clúster de cobre hexaquis (m2-Benzoato-O,O')-hexacobre(I), con el fin de explicar el comportamiento de los sitios activos presentes en su estructura. El cálculo se realizó con el programa Q-Chem 4.0, el cual es utilizado para predicciones precisas de estructuras moleculares, reactividades y espectros vibratorios, electrónicos y de RMN, utilizando la interfaz gráfica de Spartan 14 versión 1.1.4 y el funcional de densidad hibrido B3LYP y la función base 6-31G*.

Patterns of soft C—H...O hydrogen bonding in diaryl sulfones

2001 ◽  
Vol 57 (2) ◽  
pp. 190-200 ◽  
Author(s):  
Christopher Glidewell ◽  
William T. A. Harrison ◽  
John N. Low ◽  
Jamie G. Sime ◽  
James L. Wardell
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Cambridge Structural Database ◽  
Two Dimensional ◽  
One Dimensional ◽  
Different Types ◽  
Structural Database

In bis(4-tolyl) sulfone, C14H14O2S (1), 2,5,4′-trimethyldiphenyl sulfone, C15H16O2S (2), and 4-chlorodiphenyl sulfone, C12H9ClO2S (3), the molecules are linked by soft C—H...O hydrogen bonds into three different types of one-dimensional aggregate: simple chains in (1), molecular ladders in (2) and chains of fused rings in (3). In each of 3,4-dimethyl-4′-chlorodiphenyl sulfone, C14H13ClO2S (4), and 2,5-dimethyldiphenyl sulfone, C14H14O2S (5), the C—H...O hydrogen bonds link the molecules into two different types of two-dimensional sheet, based on a (4,4) net in (4) and a (3,6) net in (5). The patterns of soft C—H...O hydrogen bonds in (1)—(5) are compared with those in other diaryl sulfones, mainly retrieved from the Cambridge Structural Database, whose substitution patterns preclude the formation of hard hydrogen bonds. Observed aggregation modes range from the formation of no C—H...O hydrogen bonds at all, via finite (zero-dimensional) arrays through one-, two- and three-dimensional systems.

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