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Chemical Database
A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data. Types of chemical databases Bioactivity database Bioactivity databases correlate structures or other chemical information to bioactivity results taken from bioassays in literature, patents, and screening programs. Chemical structures Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D structural formulae). While these are ideal visual representations for the chemist, they are unsuitable for computational use and especially for search and storage. Small molecules (also called ligands in drug design applications), are usually represented using lists of atoms and their connections. Large molecules such as proteins are however more compactly represented using the sequences of their amino acid buildin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligands
In coordination chemistry, a ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electron pairs, often through Lewis bases. The nature of metal–ligand bonding can range from covalent to ionic. Furthermore, the metal–ligand bond order can range from one to three. Ligands are viewed as Lewis bases, although rare cases are known to involve Lewis acidic "ligands". Metals and metalloids are bound to ligands in almost all circumstances, although gaseous "naked" metal ions can be generated in a high vacuum. Ligands in a complex dictate the reactivity of the central atom, including ligand substitution rates, the reactivity of the ligands themselves, and redox. Ligand selection requires critical consideration in many practical areas, including bioinorganic and medicinal chemistry, homogeneous catalysis, and environmental chemis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vapor–liquid Equilibrium
In thermodynamics and chemical engineering, the vapor–liquid equilibrium (VLE) describes the distribution of a chemical species between the vapor phase and a liquid phase. The concentration of a vapor in contact with its liquid, especially at equilibrium, is often expressed in terms of vapor pressure, which will be a partial pressure (a part of the total gas pressure) if any other gas(es) are present with the vapor. The equilibrium vapor pressure of a liquid is in general strongly dependent on temperature. At vapor–liquid equilibrium, a liquid with individual components in certain concentrations will have an equilibrium vapor in which the concentrations or partial pressures of the vapor components have certain values depending on all of the liquid component concentrations and the temperature. The converse is also true: if a vapor with components at certain concentrations or partial pressures is in vapor–liquid equilibrium with its liquid, then the component concentration ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phase Equilibria
In thermodynamics, the phase rule is a general principle governing "pVT" systems, whose thermodynamic states are completely described by the variables pressure (), volume () and temperature (), in thermodynamic equilibrium. If is the number of degrees of freedom, is the number of components and is the number of phases, then :F = C - P + 2 It was derived by American physicist Josiah Willard Gibbs in his landmark paper titled ''On the Equilibrium of Heterogeneous Substances'', published in parts between 1875 and 1878. The rule assumes the components do not react with each other. The number of degrees of freedom is the number of independent intensive variables, i.e. the largest number of thermodynamic parameters such as temperature or pressure that can be varied simultaneously and arbitrarily without determining one another. An example of one-component system is a system involving one pure chemical, while two-component systems, such as mixtures of water and ethanol, have two che ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reaction Mechanism
In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs. A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases. The conjectured mechanism is chosen because it is thermodynamically feasible, and has experimental support in isolated intermediates (see next section) or other quantitative and qualitative characteristics of the reaction. It also describes each reactive intermediate, activated complex, and transition state, and which bonds are broken (and in what order), and which bonds are formed (and in what order). A complete mechanism must also explain the reason for the reactants and catalyst used, the stereochemistry observed in reactants and products, all products formed and the amount of each. The electron or arrow pushing method is often used in i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not consid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionized, for example by bombarding it with a beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragments) are then separated accordin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NMR Spectra Database
A nuclear magnetic resonance spectra database is an electronic repository of information concerning Nuclear magnetic resonance (NMR) spectra. Such repositories can be downloaded as self-contained data sets or used online. The form in which the data is stored varies, ranging from line lists that can be graphically displayed to raw free induction decay (FID) data. Data is usually annotated in a way that correlates the spectral data with the related molecular structure. Data format Line list The form in which most NMR is described in literature papers. It is common for databases to display line lists graphically in a manner that is similar to how processed spectra might appear. These line list however lack first and higher order splitting, satellites from low abundance isotopes like carbon or platinum, as well as the information concerning line width and other informative aspects of line shape. The advantage of a line list is that it requires a minimal amount of memory. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cambridge Structural Database
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 compound, organic, metalorganic, 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 crystallography, crystallographers and chemists from around the world, are freely accessible (as deposited by authors) on the Internet via the CSD's parent organization's website (CCDC, Repository). The CSD is overseen by the not-for-profit incorporated company called the Cambridge Crystallographic Data Centre, CCDC. The CSD is a widely ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystallographic Databases
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. (Molecules need to crystallize into solids so that their regularly repeating arrangements can be taken advantage of in X-ray, neutron, and electron diffraction based crystallography.) Crystal structures of crystalline material are typically determined from X-ray or neutron single-crystal diffraction data and stored in crystal structure databases. They are routinely identified by comparing reflection intensities and lattice spacings from X-ray powder diffraction data with entries in powder-diffraction fingerprinting databases. Crystal structures o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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