Journal ArticleDOI
Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures
Clare F. Macrae,Ian J. Bruno,James A. Chisholm,Paul R. Edgington,Patrick McCabe,Elna Pidcock,Lucia Rodriguez-Monge,Robin Taylor,Jacco van de Streek,Peter A. Wood +9 more
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TLDR
Mercury as discussed by the authors is a crystal structure visualization tool that allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns, as well as the ability to perform packing similarity calculations between structures containing the same compound.Abstract:
The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.read more
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Journal ArticleDOI
Validation of ligands in macromolecular structures determined by X-ray crystallography
Oliver S. Smart,Vladimír Horský,Swanand Gore,Radka Svobodová Vařeková,Veronika Bendová,Gerard J. Kleywegt,Sameer Velankar +6 more
TL;DR: Better metrics are required to be able to assess small-molecule ligands in macromolecular structures in Worldwide Protein Data Bank validation reports, including ligand electron-density fit outliers.
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Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs
TL;DR: The Cambridge Structural Database now contains more than 3500 entries for α-amino acids alone as mentioned in this paper, with a classification of amino acid structures, describes essential structural elements, especially hydrogen bonding preferences and coordination to metal ions, and considers recent investigations on phase transitions as the result of extreme temperatures or pressure.
Journal ArticleDOI
New cobalt(II) and nickel(II) complexes of benzyl carbazate Schiff bases: Syntheses, crystal structures, in vitro DNA and HSA binding studies
Palanivelu Nithya,Sannasi Helena,Jim Simpson,Malaichamy Ilanchelian,Aathi Muthusankar,Subbiah Govindarajan +5 more
TL;DR: The binding constant values indicate strong binding of metal complexes with CT-DNA and HSA, and it is shown that the cobalt and nickel complexes can quench the intrinsic fluorescence of HSA through static quenching process.
Journal ArticleDOI
The hydrogen bond between N—H or O—H and organic fluorine: favourable yes, competitive no
TL;DR: X-H...F-C interactions are more likely when the acceptor is Csp2-F or CR3F, and when the donor is C-NH2, and they occur significantly more often in structures containing tertiary alcohols or solvent molecules, or with Z' > 1, i.e. when there may be unusual packing problems.
Journal ArticleDOI
A series of compounds forming polar crystals and showing single-crystal-to-single-crystal transitions between polar phases
Roberto Centore,Mojca Jazbinsek,Angela Tuzi,Antonio Roviello,Amedeo Capobianco,Andrea Peluso +5 more
TL;DR: In this paper, the crystal structure of 4-hydroxybenzohydrazide was determined by single crystal X-ray analysis and second harmonic generation experiments were performed on powder samples, and three different crystal phases have been identified (phases I, II and III), all having the same polar space group Pna21, and the transitions from I to II and from III to II are topotactic.
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Journal ArticleDOI
Patterns in Hydrogen Bonding: Functionality and Graph Set Analysis in Crystals
TL;DR: In this article, a review of the most promising systematic approaches to resolving this enigma was initially developed by the late M. C. Etter, who applied graph theory to recognize, and then utilize, patterns of hydrogen bonding for the understanding and design of molecular crystals.
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Mercury: visualization and analysis of crystal structures
Clare F. Macrae,Paul R. Edgington,Patrick McCabe,Elna Pidcock,Greg P. Shields,Robin Taylor,Matthew Towler,Jacco van de Streek +7 more
TL;DR: Mercury as discussed by the authors is a crystal structure visualization program that allows to display multiple structures simultaneously and overlay them, which can be used for comparison between crystal structures and to overlay them in a table or spreadsheets.
Journal ArticleDOI
Retrieval of Crystallographically-Derived Molecular Geometry Information
Ian J. Bruno,Jason C. Cole,Magnus Kessler,Jie Luo,W. D. Sam Motherwell,Lucy H. Purkis,Barry Smith,Robin Taylor,Richard I. Cooper,Stephanie E. Harris,A. Guy Orpen +10 more
TL;DR: Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences.
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IsoStar: A library of information about nonbonded interactions
TL;DR: Crystallographic and theoretical data on intermolecular nonbonded interactions have been gathered together in a computerised library (’IsoStar‘) and show that there is great variability in the geometrical preferences of different types of hydrogen bonds.
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COMPACK: a program for identifying crystal structure similarity using distances
TL;DR: In this article, the relative position and orientation of molecules are captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information, and can be used to determine whether two crystal structures are the same to within specified tolerances.