Mercury: visualization and analysis of crystal structures
01 Jun 2006-Journal of Applied Crystallography (International Union of Crystallography (IUCr))-Vol. 39, Iss: 3, pp 453-457
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.
Abstract: Since its original release, the popular crystal structure visualization program Mercury has undergone continuous further development. Comparisons between crystal structures are facilitated by the ability to display multiple structures simultaneously and to overlay them. Improvements have been made to many aspects of the visual display, including the addition of depth cueing, and highly customizable lighting and background effects. Textual and numeric data associated with structures can be shown in tables or spreadsheets, the latter opening up new ways of interacting with the visual display. Atomic displacement ellipsoids, calculated powder diffraction patterns and predicted morphologies can now be shown. Some limited molecular-editing capabilities have been added. The object-oriented nature of the C++ libraries underlying Mercury makes it easy to re-use the code in other applications, and this has facilitated three-dimensional visualization in several other programs produced by the Cambridge Crystallographic Data Centre.
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TL;DR: 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.
7,879 citations
Cites background from "Mercury: visualization and analysis..."
...The most recent Mercury publication (Macrae et al., 2006) described the features added since the release of the original program....
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TL;DR: The creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures, are described.
Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.
6,313 citations
Cites methods from "Mercury: visualization and analysis..."
...This uses many of the visualization and menu options available in the CSD-System program Mercury (Macrae et al., 2006)....
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TL;DR: An overview of Mercury 4.0, an analysis, design and prediction platform that acts as a hub for the entire Cambridge Structural Database software suite, is presented.
Abstract: The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.
2,075 citations
Cites background from "Mercury: visualization and analysis..."
...…become established as a prominent crystal structure visualizer with a free-to-access version available for any researcher and many thousands of citations of its first two versions [at the time of writing 4608 for Mercury 1.0 (Macrae et al., 2006) and 5459 for Mercury 2.0 (Macrae et al., 2008)]....
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TL;DR: Th Thin CuSCN films can replace organic hole-transporting layers that limit thermal stability of devices and demonstrate PSCs that achieve stabilized efficiencies exceeding 20% with copper(I) thiocyanate (CuSCN) as the hole extraction layer.
Abstract: Perovskite solar cells (PSCs) with efficiencies greater than 20% have been realized only with expensive organic hole-transporting materials. We demonstrate PSCs that achieve stabilized efficiencies exceeding 20% with copper(I) thiocyanate (CuSCN) as the hole extraction layer. A fast solvent removal method enabled the creation of compact, highly conformal CuSCN layers that facilitate rapid carrier extraction and collection. The PSCs showed high thermal stability under long-term heating, although their operational stability was poor. This instability originated from potential-induced degradation of the CuSCN/Au contact. The addition of a conductive reduced graphene oxide spacer layer between CuSCN and gold allowed PSCs to retain >95% of their initial efficiency after aging at a maximum power point for 1000 hours under full solar intensity at 60°C. Under both continuous full-sun illumination and thermal stress, CuSCN-based devices surpassed the stability of spiro-OMeTAD–based PSCs.
1,210 citations
TL;DR: The origins of the CCDC are traced, the growth of the CSD and its extensive associated software system are described, and its impact and value are summarized as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development.
Abstract: The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal–organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700 000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40 000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC’s funding model in relation to open access and open data paradigms.
974 citations
References
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TL;DR: Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences.
Abstract: The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution mat...
799 citations
"Mercury: visualization and analysis..." refers methods in this paper
...Since several of the file formats do not carry bond-type information, an algorithm has been implemented for deducing bond types from three-dimensional atomic coordinate information (Bruno et al., 2004)....
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224 citations
102 citations
"Mercury: visualization and analysis..." refers background in this paper
...9(a) shows a segment of code for finding hydrogen bonds in the crystal structure of benzamide (Penfold & White, 1959), Fig....
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TL;DR: A number of conventions for the parameterization of atomic anisotropic displacements are used in the literature and in crystallographic programs as discussed by the authors, with a special emphasis on their application in macromolecular crystallography.
Abstract: A number of conventions for the parameterization of atomic anisotropic displacements are used in the literature and in crystallographic programs. Here we summarize the commonly used conventions, with a special emphasis on their application in macromolecular crystallography. We then describe a new software toolbox for the handling of the various parameterizations of atomic anisotropic displacements and their interconversion. All algorithms are integrated into the freely available Computational Crystallography Toolbox.
51 citations
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01 Jun 2004
37 citations
"Mercury: visualization and analysis..." refers methods in this paper
...8), which was implemented following published methodology (Bennema & Meekes, 2004)....
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