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In quantum mechanics, an atomic orbital is a function describing the location and wave-like behavior of an electron in an atom. This function describes the electron's charge distribution around the atom's nucleus, and can be used to calculate the probability of finding an electron in a specific region around the nucleus.
In chemistry, a chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, commas and plus (+) and minus (−) signs. These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a chemical name since it does not contain any words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulae can fully specify the structure of only the simplest of molecules and chemical substances, and are generally more limited in power than chemical names and structural formulae.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organisations.
In science, a formula is a concise way of expressing information symbolically, as in a mathematical formula or a chemical formula. The informal use of the term formula in science refers to the general construct of a relationship between given quantities.
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.
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.
Valence shell electron pair repulsion (VSEPR) theory is a model used in chemistry to predict the geometry of individual molecules from the number of electron pairs surrounding their central atoms. It is also named the Gillespie-Nyholm theory after its two main developers, Ronald Gillespie and Ronald Nyholm.
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 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.
Chemical table 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.
OBJ is a geometry definition file format first developed by Wavefront Technologies for its Advanced Visualizer animation package. The file format is open and has been adopted by other 3D graphics application vendors.
A potential energy surface (PES) or energy landscape describes the energy of a system, especially a collection of atoms, in terms of certain parameters, normally the positions of the atoms. The surface might define the energy as a function of one or more coordinates; if there is only one coordinate, the surface is called a potential energy curve or energy profile. An example is the Morse/Long-range potential.
The number density is an intensive quantity used to describe the degree of concentration of countable objects in physical space: three-dimensional volumetric number density, two-dimensional areal number density, or one-dimensional linear number density. Population density is an example of areal number density. The term number concentration is sometimes used in chemistry for the same quantity, particularly when comparing with other concentrations.
The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which has kept data on biological macromolecules in the newer PDBx/mmCIF file format since 2014.
The X-ray standing wave (XSW) technique can be used to study the structure of surfaces and interfaces with high spatial resolution and chemical selectivity. Pioneered by B.W. Batterman in the 1960s, the availability of synchrotron light has stimulated the application of this interferometric technique to a wide range of problems in surface science.
In chemistry, the Z-matrix is a way to represent a system built of atoms. A Z-matrix is also known as an internal coordinate representation. It provides a description of each atom in a molecule in terms of its atomic number, bond length, bond angle, and dihedral angle, the so-called internal coordinates, although it is not always the case that a Z-matrix will give information regarding bonding since the matrix itself is based on a series of vectors describing atomic orientations in space. However, it is convenient to write a Z-matrix in terms of bond lengths, angles, and dihedrals since this will preserve the actual bonding characteristics. The name arises because the Z-matrix assigns the second atom along the Z axis from the first atom, which is at the origin.
PLY is a computer file format known as the Polygon File Format or the Stanford Triangle Format. It was principally designed to store three-dimensional data from 3D scanners. The data storage format supports a relatively simple description of a single object as a list of nominally flat polygons. A variety of properties can be stored, including color and transparency, surface normals, texture coordinates and data confidence values. The format permits one to have different properties for the front and back of a polygon.
Surface second harmonic generation is a method for probing interfaces in atomic and molecular systems. In second harmonic generation (SHG), the light frequency is doubled, essentially converting two photons of the original beam of energy E into a single photon of energy 2E as it interacts with noncentrosymmetric media. Surface second harmonic generation is a special case of SHG where the second beam is generated because of a break of symmetry caused by an interface. Since centrosymmetric symmetry in centrosymmetric media is only disrupted in the first atomic or molecular layer of a system, properties of the second harmonic signal then provide information about the surface atomic or molecular layers only. Surface SHG is possible even for materials which do not exhibit SHG in the bulk. Although in many situations the dominant second harmonic signal arises from the broken symmetry at the surface, the signal in fact always has contributions from both the surface and bulk. Thus, the most sensitive experiments typically involve modification of a surface and study of the subsequent modification of the harmonic generation properties.
This glossary of chemistry terms is a list of terms and definitions relevant to chemistry, including chemical laws, diagrams and formulae, laboratory tools, glassware, and equipment. Chemistry is a physical science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions; it features an extensive vocabulary and a significant amount of jargon.
In chemistry, isovalent or second order hybridization is an extension of orbital hybridization, the mixing of atomic orbitals into hybrid orbitals which can form chemical bonds, to include fractional numbers of atomic orbitals of each type. It allows for a quantitative depiction of bond formation when the molecular geometry deviates from ideal bond angles.
Molecular symmetry in physics and chemistry describes the symmetry present in molecules and the classification of molecules according to their symmetry. Molecular symmetry is a fundamental concept in the application of Quantum Mechanics in physics and chemistry, for example it can be used to predict or explain many of a molecule's properties, such as its dipole moment and its allowed spectroscopic transitions, without doing the exact rigorous calculations. To do this it is necessary to classify the states of the molecule using the irreducible representations from the character table of the symmetry group of the molecule. Among all the molecular symmetries, diatomic molecules show some distinct features and they are relatively easier to analyze.
References
- ↑ "The XYZ file specification". OpenBabel.
- ↑ "XYZ man page (part of XMol)" . Retrieved 22 September 2015.