Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation 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. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
Ab initio quantum chemistry methodsAb initio quantum chemistry methods are computational chemistry methods based on quantum chemistry. The term ab initio was first used in quantum chemistry by Robert Parr and coworkers, including David Craig in a semiempirical study on the excited states of benzene. The background is described by Parr. Ab initio means "from first principles" or "from the beginning", implying that the only inputs into an ab initio calculation are physical constants.
Quantum chemistryQuantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions to physical and chemical properties of molecules, materials, and solutions at the atomic level. These calculations include systematically applied approximations intended to make calculations computationally feasible while still capturing as much information about important contributions to the computed wave functions as well as to observable properties such as structures, spectra, and thermodynamic properties.
Data typeIn computer science and computer programming, a data type (or simply type) is a collection or grouping of data values, usually specified by a set of possible values, a set of allowed operations on these values, and/or a representation of these values as machine types. A data type specification in a program constrains the possible values that an expression, such as a variable or a function call, might take. On literal data, it tells the compiler or interpreter how the programmer intends to use the data.
Semi-empirical quantum chemistry methodSemi-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.
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.
Primitive data typeIn computer science, primitive data types are a set of basic data types from which all other data types are constructed. Specifically it often refers to the limited set of data representations in use by a particular processor, which all compiled programs must use. Most processors support a similar set of primitive data types, although the specific representations vary. More generally, "primitive data types" may refer to the standard data types built into a programming language (built-in types).
Algebraic data typeIn computer programming, especially functional programming and type theory, an algebraic data type (ADT) is a kind of composite type, i.e., a type formed by combining other types. Two common classes of algebraic types are product types (i.e., tuples and records) and sum types (i.e., tagged or disjoint unions, coproduct types or variant types). The values of a product type typically contain several values, called fields. All values of that type have the same combination of field types.
Recursive data typeIn computer programming languages, a recursive data type (also known as a recursively-defined, inductively-defined or inductive data type) is a data type for values that may contain other values of the same type. Data of recursive types are usually viewed as directed graphs. An important application of recursion in computer science is in defining dynamic data structures such as Lists and Trees. Recursive data structures can dynamically grow to an arbitrarily large size in response to runtime requirements; in contrast, a static array's size requirements must be set at compile time.
Composite data typeIn computer science, a composite data type or compound data type is any data type which can be constructed in a program using the programming language's primitive data types and other composite types. It is sometimes called a structure or aggregate type, although the latter term may also refer to arrays, lists, etc. The act of constructing a composite type is known as composition. Composite data types are often contrasted with scalar variables. A struct is C's and C++'s notion of a composite type, a datatype that composes a fixed set of labeled fields or members.
Array (data type)In computer science, array is a data type that represents a collection of elements (values or variables), each selected by one or more indices (identifying keys) that can be computed at run time during program execution. Such a collection is usually called an array variable or array value. By analogy with the mathematical concepts vector and matrix, array types with one and two indices are often called vector type and matrix type, respectively. More generally, a multidimensional array type can be called a tensor type, by analogy with the physical concept, tensor.
Quantitative structure–activity relationshipQuantitative structure–activity relationship models (QSAR models) are regression or classification models used in the chemical and biological sciences and engineering. Like other regression models, QSAR regression models relate a set of "predictor" variables (X) to the potency of the response variable (Y), while classification QSAR models relate the predictor variables to a categorical value of the response variable.
Theoretical chemistryTheoretical 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. 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.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Molecular geometryMolecular 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 molecule, i.
Chemical structureA 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.
Artificial neural networkArtificial neural networks (ANNs, also shortened to neural networks (NNs) or neural nets) are a branch of machine learning models that are built using principles of neuronal organization discovered by connectionism in the biological neural networks constituting animal brains. An ANN is based on a collection of connected units or nodes called artificial neurons, which loosely model the neurons in a biological brain. Each connection, like the synapses in a biological brain, can transmit a signal to other neurons.
Boolean data typeIn computer science, the Boolean (sometimes shortened to Bool) is a data type that has one of two possible values (usually denoted true and false) which is intended to represent the two truth values of logic and Boolean algebra. It is named after George Boole, who first defined an algebraic system of logic in the mid 19th century. The Boolean data type is primarily associated with conditional statements, which allow different actions by changing control flow depending on whether a programmer-specified Boolean condition evaluates to true or false.
Generalized algebraic data typeIn functional programming, a generalized algebraic data type (GADT, also first-class phantom type, guarded recursive datatype, or equality-qualified type) is a generalization of parametric algebraic data types. In a GADT, the product constructors (called data constructors in Haskell) can provide an explicit instantiation of the ADT as the type instantiation of their return value. This allows defining functions with a more advanced type behaviour.
Abstract data typeIn computer science, an abstract data type (ADT) is a mathematical model for data types. An abstract data type is defined by its behavior (semantics) from the point of view of a user, of the data, specifically in terms of possible values, possible operations on data of this type, and the behavior of these operations. This mathematical model contrasts with data structures, which are concrete representations of data, and are the point of view of an implementer, not a user.
