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Theoretical Chemistry
Theoretical chemistry is the branch of chemistry which develops theoretical generalizations that are part of the theoretical arsenal of modern chemistry: for example, the concepts of chemical bonding, chemical reaction, valence, the surface of potential energy, molecular orbitals, orbital interactions, and molecule activation. Overview Theoretical chemistry unites principles and concepts common to all branches of chemistry. Within the framework of theoretical chemistry, there is a systematization of chemical laws, principles and rules, their refinement and detailing, the construction of a hierarchy. The central place in theoretical chemistry is occupied by the doctrine of the interconnection of the structure and properties of molecular systems. It uses mathematical and physical methods to explain the structures and dynamics of chemical systems and to correlate, understand, and predict their thermodynamic and kinetic properties. In the most general sense, it is explanation of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jacobus Van 't Hoff By Perscheid 1904
A Jacobus is an English gold coin of the reign of James I, worth 25 shillings. The name of the coin comes from the Latin inscription surrounding the King's head on the obverse of the coin, IACOBUS D G MAG BRIT FRA ET HI REX ("James, by the grace of God, of Britain, France and Ireland King"). Isaac Newton refers to the coin in a letter to John Locke: '' The Jacobus piece coin'd for 20 shillings is the : part of a pound Troy, and a Carolus 20s piece is of the same weight. But a broad Jacobus (as I find by weighing some of them) is the 38th part of a pound Troy.'' dated September 19, 1698, to , concerning the weight and fineness of various coins. [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Spectroscopy
Spectroscopy is the field of study that measures and interprets the electromagnetic spectra that result from the interaction between electromagnetic radiation and matter as a function of the wavelength or frequency of the radiation. Matter waves and acoustic waves can also be considered forms of radiative energy, and recently gravitational waves have been associated with a spectral signature in the context of the Laser Interferometer Gravitational-Wave Observatory (LIGO) In simpler terms, spectroscopy is the precise study of color as generalized from visible light to all bands of the electromagnetic spectrum. Historically, spectroscopy originated as the study of the wavelength dependence of the absorption by gas phase matter of visible light dispersed by a prism. Spectroscopy, primarily in the electromagnetic spectrum, is a fundamental exploratory tool in the fields of astronomy, chemistry, materials science, and physics, allowing the composition, physical structure and e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein-protein Docking
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein–nucleic acid complexes. The ultimate goal of docking is the prediction of the three-dimensional structure of the macromolecular complex of interest as it would occur in a living organism. Docking itself only produces plausible candidate structures. These candidates must be ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. The term "docking" originated in the late 1970s, with a more restricted meaning; then, "docking" meant refining a model of a complex structure by optimizing the separation between the interactors but keeping their relative orientations fixed. Later, the relative orientations of the interacting partners in the modelling was allowed to vary, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Docking (molecular)
In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore, docking is useful for predicting both the strength and type of signal produced. Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target bind ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Force Field (chemistry)
In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates. ''All-atom'' force fields provide parameters for every type of atom in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PM3 (chemistry)
PM3, or Parametric Method 3, is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Differential Diatomic Overlap integral approximation. The PM3 method uses the same formalism and equations as the AM1 method. The only differences are: 1) PM3 uses two Gaussian functions for the core repulsion function, instead of the variable number used by AM1 (which uses between one and four Gaussians per element); 2) the numerical values of the parameters are different. The other differences lie in the philosophy and methodology used during the parameterization: whereas AM1 takes some of the parameter values from spectroscopical measurements, PM3 treats them as optimizable values. The method was developed by J. J. P. Stewart and first published in 1989. It is implemented in the MOPAC program (of which the older versions are public domain), along with the related RM1, AM1, MNDO and MINDO methods, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Semi-empirical Quantum Chemistry Method
Semi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive. The use of empirical parameters appears to allow some inclusion of electron correlation effects into the methods. Within the framework of Hartree–Fock calculations, some pieces of information (such as two-electron integrals) are sometimes approximated or completely omitted. In order to correct for this loss, semi-empirical methods are parametrized, that is their results are fitted by a set of parameters, normally in such a way as to produce results that best agree with experimental data, but sometimes to agree with ''ab initio'' results. Type of simplifications used Semi-empirical methods follow what are often called empirical methods where the two-electron p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Density Functional Theory
Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density. DFT is among the most popular and versatile methods available in condensed-matter physics, computational physics, and computational chemistry. DFT has been very popular for calculations in solid-state physics since the 1970s. However, DFT was not considered accurate enough for calculations in quantum chemistry until the 1990s, when the approximations used in the theory were greatly refined to better model the exchange and correlation interactions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Post-Hartree–Fock
In computational chemistry, post-Hartree–Fock methods are the set of methods developed to improve on the Hartree–Fock (HF), or self-consistent field (SCF) method. They add electron correlation which is a more accurate way of including the repulsions between electrons than in the Hartree–Fock method where repulsions are only averaged. Details In general, the SCF procedure makes several assumptions about the nature of the multi-body Schrödinger equation and its set of solutions: * For molecules, the Born–Oppenheimer approximation is inherently assumed. The true wavefunction should also be a function of the coordinates of each of the nuclei. * Typically, relativistic effects are completely neglected. The momentum operator is assumed to be completely nonrelativistic. * The basis set is composed of a finite number of orthogonal functions. The true wavefunction is a linear combination of functions from a complete (infinite) basis set. * The energy eigenfunctions are assum ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Science
Computational science, also known as scientific computing or scientific computation (SC), is a field in mathematics that uses advanced computing capabilities to understand and solve complex problems. It is an area of science that spans many disciplines, but at its core, it involves the development of models and simulations to understand natural systems. * Algorithms ( numerical and non-numerical): mathematical models, computational models, and computer simulations developed to solve science (e.g., biological, physical, and social), engineering, and humanities problems * Computer hardware that develops and optimizes the advanced system hardware, firmware, networking, and data management components needed to solve computationally demanding problems * The computing infrastructure that supports both the science and engineering problem solving and the developmental computer and information science In practical use, it is typically the application of computer simulation and other fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
