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Chemical File Format
A chemical file format is a type of data file which is used specifically to depicting molecular data. One of the most widely used is the chemical table file format, which is similar to ''Structure Data Format'' (SDF) files. They are text files that represent multiple chemical structure records and associated data fields. The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates. The Protein Data Bank Format is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another. Distinguishing formats Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format is indicated in three ways:(see ) * ''fi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Table File
Chemical table file (CT File) is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms. File formats There are several file formats in the family. The formats were created by MDL Information Systems, MDL Information Systems (MDL), which was acquired by Symyx Technologies then merged with Accelrys Corp., and now called BIOVIA, a subsidiary of Dassault Systemes of Dassault Group. CT File is an open format, BIOVIA publishes its specification. BIOVIA requires users to register to download the CTFile format specifications. Molfile An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule. The molfile consists of some header information, the Connection Table (CT) containing atom info, then bond connections and types, followed by sections for more complex i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JOELib
JOELib is computer software, a chemical expert system used mainly to interconvert chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other operating systems supporting the programming language Java. It is free and open-source software distributed under the GNU General Public License (GPL) 2.0. History JOELib and OpenBabel were derived from the OELib Cheminformatics library. Logo The project logo is just the word JOELib in the Tengwar script of J. R. R. Tolkien. The letters are grouped as JO-E-Li-b. Vowels are usually grouped together with a consonant, but two following vowels must be separated by a helper construct. Major features * Chemical expert system * Query and substructure search (based on Simplified molecular-input line-entry system (SMARTS), a SMILES extension * Clique detection * QSAR ** Data mining ** Mole ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenBabel
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats. About Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, Linux, macOS, and Android. It is free and open-source software released under a GNU General Public License (GPL) 2.0. The project's stated goal is: "Open Babel is a community-driven scientific project assisting both users and developers as a cross-platform program and library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data." History Open Babel and JOELib were derived from the OELib cheminformatics library. In turn, OELib was based on ideas in the original chemistry program Babel and an unreleased object-oriented programming library called ''OBabel''. Major features * chemical expert system * interconversion of ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ethylene
Ethylene ( IUPAC name: ethene) is a hydrocarbon which has the formula or . It is a colourless, flammable gas with a faint "sweet and musky" odour when pure. It is the simplest alkene (a hydrocarbon with carbon-carbon double bonds). Ethylene is widely used in the chemical industry, and its worldwide production (over 150 million tonnes in 2016) exceeds that of any other organic compound. Much of this production goes toward polyethylene, a widely used plastic containing polymer chains of ethylene units in various chain lengths. Ethylene is also an important natural plant hormone and is used in agriculture to force the ripening of fruits. The hydrate of ethylene is ethanol. Structure and properties This hydrocarbon has four hydrogen atoms bound to a pair of carbon atoms that are connected by a double bond. All six atoms that comprise ethylene are coplanar. The H-C-H angle is 117.4°, close to the 120° for ideal sp² hybridized carbon. The molecule is also relatively weak: ro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ethanol
Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an alcohol with the chemical formula . Its formula can be also written as or (an ethyl group linked to a hydroxyl group). Ethanol is a volatile, flammable, colorless liquid with a characteristic wine-like odor and pungent taste. It is a psychoactive recreational drug, the active ingredient in alcoholic drinks. Ethanol is naturally produced by the fermentation process of sugars by yeasts or via petrochemical processes such as ethylene hydration. It has medical applications as an antiseptic and disinfectant. It is used as a chemical solvent and in the synthesis of organic compounds, and as a fuel source. Ethanol also can be dehydrated to make ethylene, an important chemical feedstock. As of 2006, world production of ethanol was , coming mostly from Brazil and the U.S. Etymology ''Ethanol'' is the systematic name defined by the International Uni ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Methane
Methane ( , ) is a chemical compound with the chemical formula (one carbon atom bonded to four hydrogen atoms). It is a group-14 hydride, the simplest alkane, and the main constituent of natural gas. The relative abundance of methane on Earth makes it an economically attractive fuel, although capturing and storing it poses technical challenges due to its gaseous state under normal conditions for temperature and pressure. Naturally occurring methane is found both below ground and under the seafloor and is formed by both geological and biological processes. The largest reservoir of methane is under the seafloor in the form of methane clathrates. When methane reaches the surface and the atmosphere, it is known as atmospheric methane. The Earth's atmospheric methane concentration has increased by about 150% since 1750, and it accounts for 20% of the total radiative forcing from all of the long-lived and globally mixed greenhouse gases. It has also been detected on other p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrogen Atoms
A hydrogen atom is an atom of the chemical element hydrogen. The electrically neutral atom contains a single positively charged proton and a single negatively charged electron bound to the nucleus by the Coulomb force. Atomic hydrogen constitutes about 75% of the baryonic mass of the universe. In everyday life on Earth, isolated hydrogen atoms (called "atomic hydrogen") are extremely rare. Instead, a hydrogen atom tends to combine with other atoms in compounds, or with another hydrogen atom to form ordinary (diatomic) hydrogen gas, H2. "Atomic hydrogen" and "hydrogen atom" in ordinary English use have overlapping, yet distinct, meanings. For example, a water molecule contains two hydrogen atoms, but does not contain atomic hydrogen (which would refer to isolated hydrogen atoms). Atomic spectroscopy shows that there is a discrete infinite set of states in which a hydrogen (or any) atom can exist, contrary to the predictions of classical physics. Attempts to develop a theoreti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simplified Molecular Input Line Entry System
The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. The original SMILES specification was initiated in the 1980s. It has since been modified and extended. In 2007, an open standard called OpenSMILES was developed in the open-source chemistry community. History The original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo (USEPA) and Albert Leo and Corwin Hansch ( Pomona College) for supporting the work, and Arthur Weininger (Pomona; Daylight CIS) and Jeremy Scofield (Cedar River Software, Renton, WA) for assistance in progra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alanine
Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side chain. Consequently, its IUPAC systematic name is 2-aminopropanoic acid, and it is classified as a nonpolar, aliphatic α-amino acid. Under biological conditions, it exists in its zwitterionic form with its amine group protonated (as −NH3+) and its carboxyl group deprotonated (as −CO2−). It is non-essential to humans as it can be synthesised metabolically and does not need to be present in the diet. It is encoded by all codons starting with GC (GCU, GCC, GCA, and GCG). The L-isomer of alanine (left-handed) is the one that is incorporated into proteins. L-alanine is second only to leucine in rate of occurrence, accounting for 7.8% of the primary structure in a sample of 1,150 proteins. The right-handed form, D-alanine, occurs ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Benzene
Benzene is an organic chemical compound with the molecular formula C6H6. The benzene molecule is composed of six carbon atoms joined in a planar ring with one hydrogen atom attached to each. Because it contains only carbon and hydrogen atoms, benzene is classed as a hydrocarbon. Benzene is a natural constituent of petroleum and is one of the elementary petrochemicals. Due to the cyclic continuous pi bonds between the carbon atoms, benzene is classed as an aromatic hydrocarbon. Benzene is a colorless and highly flammable liquid with a sweet smell, and is partially responsible for the aroma of gasoline. It is used primarily as a precursor to the manufacture of chemicals with more complex structure, such as ethylbenzene and cumene, of which billions of kilograms are produced annually. Although benzene is a major industrial chemical, it finds limited use in consumer items because of its toxicity. History Discovery The word "''benzene''" derives from "''gum benzoin''" (benzoin r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Markush Structure
A Markush structure is a representation of chemical structure used to indicate a group of related chemical compounds. They are commonly used in chemistry texts and in patent claims. Markush structures are depicted with multiple independently variable groups, such as R groups in which a side chain can have varying structure. This more general depiction of the molecule, versus detailing every atom in the molecule, is used to protect intellectual property. The company which applies for a patent makes a general claim for the usage of the molecule without revealing to their competitors the exact molecule for which they are declaring a useful application. History Markush structures are named after Eugene A. Markush, founder of the Pharma Chemical Corporation in New Jersey. He was involved in a legal case that set a precedent for generic chemical structure patent filing. The patent filing was US Application 611,637, filed January 9, 1923. Markush was awarded a patent from the US Pa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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