The Cambridge Crystallographic Data Centre (CCDC) is a non-profit organisation based in Cambridge, England. Its primary[ citation needed ] activity is the compilation and maintenance of the Cambridge Structural Database, a database of small molecule crystal structures. They also perform analysis on the database for the benefit of the scientific community, and write and distribute computer software to allow others to do the same.
In 1962, Dr. Olga Kennard OBE FRS set up a chemical crystallography group within the Department of Chemistry, University of Cambridge. In 1965 she founded the CCDC and established the associated Cambridge Structural Database. At that time, there were only about 3,000 published X-ray structures, and the work involved converting these into a machine-readable form. [1] Kennard invited Frank Allen to join the group, which he did in 1970, becoming Scientific Director and then Executive Director before retiring in 2008.[ citation needed ]
In 1992, the CCDC moved into its own building adjacent to the Cambridge chemistry department. This new headquarters was designed by the Danish architect Professor Erik Christian Sørensen and won The Sunday Times Building of the Year Award in 1993. [2]
The CCDC still retains very close links as a University Partner Institution that trains students for postgraduate research degrees but from 1987 became an independent company. By 2019 the database had grown to over a million structures. [2]
The staff at the CCDC curate the database of small-molecule organic and metal-organic crystal structures and make these available for download by the public. They also create and maintain a suite of cheminformatics software that may be used to apply the data to applications in the life sciences, including crystal engineering and materials science. [1] [3] [4]
CCDC developed programs such as ConQuest and Mercury [5] that run under Windows and various types of Unix, including Linux. ConQuest is a search interface to the Cambridge Structural Database (CSD).[ citation needed ] Mercury is a crystal structure visualizer tool, of which later versions released in 2015 and later provide the functionality to generate 3D prints. [6]
Crystallography is the branch of science devoted to the study of molecular and crystalline structure and properties. The word crystallography is derived from the Ancient Greek word κρύσταλλος, and γράφειν. In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming 2014 the International Year of Crystallography.
X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract in specific directions. By measuring the angles and intensities of the X-ray diffraction, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal and the positions of the atoms, as well as their chemical bonds, crystallographic disorder, and other information.
The covalent radius, rcov, is a measure of the size of an atom that forms part of one covalent bond. It is usually measured either in picometres (pm) or angstroms (Å), with 1 Å = 100 pm.
A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together and can be represented using structural formulae and by molecular models; complete electronic structure descriptions include specifying the occupation of a molecule's molecular orbitals. Structure determination can be applied to a range of targets from very simple molecules to very complex ones.
Olga Kennard, Lady Burgen was a Hungarian-born British scientist who specialised in crystallography. She was the founder of the Cambridge Crystallographic Data Centre.
The Cambridge Structural Database (CSD) is both a repository and a validated and curated resource for the three-dimensional structural data of molecules generally containing at least carbon and hydrogen, comprising a wide range of organic, metal-organic and organometallic molecules. The specific entries are complementary to the other crystallographic databases such as the Protein Data Bank (PDB), Inorganic Crystal Structure Database and International Centre for Diffraction Data. The data, typically obtained by X-ray crystallography and less frequently by electron diffraction or neutron diffraction, and submitted by crystallographers and chemists from around the world, are freely accessible on the Internet via the CSD's parent organization's website. The CSD is overseen by the not-for-profit incorporated company called the Cambridge Crystallographic Data Centre, CCDC.
A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal..
Nuclear magnetic resonance crystallography is a method which utilizes primarily NMR spectroscopy to determine the structure of solid materials on the atomic scale. Thus, solid-state NMR spectroscopy would be used primarily, possibly supplemented by quantum chemistry calculations, powder diffraction etc. If suitable crystals can be grown, any crystallographic method would generally be preferred to determine the crystal structure comprising in case of organic compounds the molecular structures and molecular packing. The main interest in NMR crystallography is in microcrystalline materials which are amenable to this method but not to X-ray, neutron and electron diffraction. This is largely because interactions of comparably short range are measured in NMR crystallography.
The Journal of Applied Crystallography is a peer-reviewed scientific journal published by Wiley-Blackwell on behalf of the International Union of Crystallography. It was established in 1968 with André Guinier as the founding editor. The journal covers the application of crystallography and crystallographic techniques. William Parrish (1914–1991) chaired the committee that started the journal.
The Crystallography Open Database (COD) is a database of crystal structures. Unlike similar crystallographic databases, the database is entirely open-access, with registered users able to contribute published and unpublished structures of small molecules and small to medium-sized unit cell crystals to the database. As of May 2016, the database has more than 360,000 entries. The database has various contributors, and contains Crystallographic Information Files as defined by the International Union of Crystallography (IUCr). There are currently five sites worldwide that mirror this database. The 3D structures of compounds can be converted to input files for 3D printers.
Frank Harmsworth Allen FRSC CChem (1944–2014) was an internationally recognised crystallographer.
Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and macOS. Main application areas in MOE include structure-based design, fragment-based design, ligand-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, structural biology and bioinformatics, protein and antibody modeling, molecular modeling and simulations, virtual screening, cheminformatics & QSAR. The Scientific Vector Language (SVL) is the built-in command, scripting and application development language of MOE.
Margaret Cairns Etter, known informally as Peggy Etter, was an American chemist who contributed to the development of solid state chemistry for crystalline organic compounds. She is known for her work characterizing and classifying contacts by hydrogen bonds in organic compounds. Her "enlightened imagination, innovative creativity, and unfailing enthusiasm" is recognised as having a "transformative effect" in many areas of organic chemistry.
Dorothy June Sutor was a New Zealand-born crystallographer who spent most of her research career in England. She was one of the first scientists to establish that hydrogen bonds could form to hydrogen atoms bonded to carbon atoms. She later worked in the laboratory of Kathleen Lonsdale on the characterisation and prevention of urinary calculi.
This is a timeline of crystallography.
Mercury is a freeware developed by the Cambridge Crystallographic Data Centre, originally designed as a crystal structure visualization tool. Mercury helps three dimensional visualization of crystal structure and assists in drawing and analysis of crystal packing and intermolecular interactions. Current version Mercury can read "cif", ".mol", ".mol2", ".pdb", ".res", ".sd" and ".xyz" types of files. Mercury has its own file format with filename extension ".mryx".
CrystalExplorer (CE) is a freeware designed to analysis the crystal structure with *.cif file format.
Alexander Frank Wells, or A. F. Wells, was a British chemist and crystallographer. He is known for his work on structural inorganic chemistry, which includes the description and classification of structural motifs, such as the polyhedral coordination environments, in crystals obtained from X-ray crystallography. His work is summarized in a classic reference book, Structural inorganic chemistry, first appeared in 1945 and has since gone through five editions. In addition, his work on crystal structures in terms of nets have been important and inspirational for the field of metal-organic frameworks and related materials.
Susan Reutzel-Edens is an American chemist who is the Head of Science at the Cambridge Crystallographic Data Centre. Her work considers solid state chemistry and pharmaceuticals. She is interested in crystal structure predictions. She serves on the editorial boards of CrystEngComm and Crystal Growth & Design.
Monolayer protected clusters (MPCs) are one type of nanoparticles or clusters of atoms. A single MPC contains three main parts: metallic core, protective ligand layer and metal-ligand interface between, each defined by their distinctive chemical and structural environments. The main part of a MPC is a metallic core, which can consist of a single metal or it can be a mixture of metals. Bare metal particles tend to be reactive. They usually react with environment or with other particles making larger structures. Ligand layer is used to protect them, so that the particle size is preserved. Ligands are usually some organic molecules and they are bound to metallic core via some linking atoms such as sulfur or phosphorus forming thiol and phosphine ligands. However, there are alkynyl and carbene protected MPCs, where carbon is directly bound to metal atoms. Ligand layer can consist of a single type of ligands, like in the case of thiolate-protected gold clusters, or it can contain several different molecules. Even though the ligand layer is usually used to passivate a nanoparticle, it is not a passive part of the MPCs. For example, ligands can be functionalized to work in specific applications such as binding to surfaces or acting as a carrier for other molecules. Ligand layer also contributes to the total electronic structure of the particle, which furthermore affects the superatomic nature of the particle.
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