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XYZ File Format
The XYZ file format is a chemical file format. There is no formal standard and several variations exist, but a typical XYZ format specifies the molecule geometry by giving the number of atoms with Cartesian coordinates that will be read on the first line, a comment on the second, and the lines of atomic coordinates in the following lines. The file format is used in computational chemistry programs for importing and exporting geometries. The units are generally in ångströms. Some variations include using atomic numbers instead of atomic symbols, or skipping the comment line. Files using the XYZ format conventionally have the extension. Format The formatting of the .xyz file format is as follows: comment line ... Connectivity information in the XYZ file format is implied rather than explicit. According to the main page for XYZ (part of XMol), Note that the XYZ format doesn't contain connectivity information. This intentional omission allows for greater flexibili ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical File Format
A chemical file format is a type of data file which is used specifically for 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 ) * ''f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule Geometry
Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of a molecule, i.e. they can be understood as approximately local and hence transferable properties. Determination The molecular geometry can be determined by various spectroscopic methods and diffraction methods. IR, microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction can give molecul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Atoms
Atoms are the basic particles of the chemical elements. An atom consists of a nucleus of protons and generally neutrons, surrounded by an electromagnetically bound swarm of electrons. The chemical elements are distinguished from each other by the number of protons that are in their atoms. For example, any atom that contains 11 protons is sodium, and any atom that contains 29 protons is copper. Atoms with the same number of protons but a different number of neutrons are called isotopes of the same element. Atoms are extremely small, typically around 100 picometers across. A human hair is about a million carbon atoms wide. Atoms are smaller than the shortest wavelength of visible light, which means humans cannot see atoms with conventional microscopes. They are so small that accurately predicting their behavior using classical physics is not possible due to quantum effects. More than 99.94% of an atom's mass is in the nucleus. Protons have a positive electric charge a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cartesian Coordinates
In geometry, a Cartesian coordinate system (, ) in a plane is a coordinate system that specifies each point uniquely by a pair of real numbers called ''coordinates'', which are the signed distances to the point from two fixed perpendicular oriented lines, called '' coordinate lines'', ''coordinate axes'' or just ''axes'' (plural of ''axis'') of the system. The point where the axes meet is called the '' origin'' and has as coordinates. The axes directions represent an orthogonal basis. The combination of origin and basis forms a coordinate frame called the Cartesian frame. Similarly, the position of any point in three-dimensional space can be specified by three ''Cartesian coordinates'', which are the signed distances from the point to three mutually perpendicular planes. More generally, Cartesian coordinates specify the point in an -dimensional Euclidean space for any dimension . These coordinates are the signed distances from the point to mutually perpendicular fixed h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems. It uses methods of theoretical chemistry incorporated into computer programs to calculate the structures and properties of molecules, groups of molecules, and solids. The importance of this subject stems from the fact that, with the exception of some relatively recent findings related to the hydrogen molecular ion (dihydrogen cation), achieving an accurate quantum mechanical depiction of chemical systems analytically, or in a closed form, is not feasible. The complexity inherent in the many-body problem exacerbates the challenge of providing detailed descriptions of quantum mechanical systems. While computational results normally complement information obtained by chemical experiments, it can occasionally predict unobserved chemical phenomena. Overview Computational chemistry differs from theoretical chemistry, which involves a mathematical description of chem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ångström
The angstrom (; ) is a unit of length equal to m; that is, one ten- billionth of a metre, a hundred-millionth of a centimetre, 0.1 nanometre, or 100 picometres. The unit is named after the Swedish physicist Anders Jonas Ångström (1814–1874). It was originally spelled with Swedish letters, as Ångström and later as ångström (). The latter spelling is still listed in some dictionaries, but is now rare in English texts. Some popular US dictionaries list only the spelling ''angstrom''. The unit's symbol is Å, which is a letter of the Swedish alphabet, regardless of how the unit is spelled. However, "A" or "A.U." may be used in less formal contexts or typographically limited media. The angstrom is often used in the natural sciences and technology to express sizes of atoms, molecules, microscopic biological structures, and lengths of chemical bonds, arrangement of atoms in crystals, wavelengths of electromagnetic radiation, and dimensions of integrated circuit p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Connectivity Information
Connectivity may refer to: Computing and technology * Connectivity (media), the ability of the social media to accumulate economic capital from the users connections and activities * Internet connectivity, the means by which individual terminals, computers, mobile devices, and local area networks connect to the global Internet * Pixel connectivity, the way in which pixels in 2-dimensional images relate to their neighbors. Mathematics *Connectivity (graph theory), a property of a graph. * The property of being a connected space in topology. * Homotopical connectivity, a property related to the dimensions of holes in a topological space, and to its homotopy groups. * Homological connectivity, a property related to the homology groups of a topological space. Biology Neurobiology *Homotopic connectivity - connectivity between mirror areas of the human brain hemispheres. * Brain connectivity *Functional connectivity *Dynamic functional connectivity Ecology * Landscape connectivity, t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pyridine
Pyridine is a basic (chemistry), basic heterocyclic compound, heterocyclic organic compound with the chemical formula . It is structurally related to benzene, with one methine group replaced by a nitrogen atom . It is a highly flammable, weakly alkaline, water-miscible liquid with a distinctive, unpleasant fish-like smell. Pyridine is colorless, but older or impure samples can appear yellow, due to the formation of extended, unsaturated Polymer, polymeric chains, which show significant electrical conductivity. The pyridine ring occurs in many important compounds, including agrochemicals, pharmaceuticals, and vitamins. Historically, pyridine was produced from coal tar. As of 2016, it is synthesized on the scale of about 20,000 tons per year worldwide. Properties Physical properties Pyridine is diamagnetism, diamagnetic. Its critical point (thermodynamics), critical parameters are: pressure 5.63 MPa, temperature 619 K and volume 248 cm3/mol. In the temperatur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jmol
Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the mol file format. JSmol is an implementation in JavaScript of the functionality of Jmol. It can hence be embedded in web pages to display interactive 3D models of molecules and other structures without the need for any software apart from the web browser (''it does not use Java''). Both Jmol and JSmol render an interactive 3D representation of a molecule or other structure that may be used as a teaching tool, or for research, in several fields, e.g. chemistry, biochemistry, materials science, crystallography, symmetry or nanotechnology. Software Jmol is written in the programming language Java, so it can run on different operating systems: Windows, macOS, Linux, and Unix, as long as they have Java installed. It is free and open-source so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and Visualization (computer graphics), visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan (software), RenderMan, Tachyon (software), Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python (programming language), Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. History VMD has been developed under the aegis of principal investigator Klaus Schulten in th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
