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.
Dynamical systemIn mathematics, a dynamical system is a system in which a function describes the time dependence of a point in an ambient space, such as in a parametric curve. Examples include the mathematical models that describe the swinging of a clock pendulum, the flow of water in a pipe, the random motion of particles in the air, and the number of fish each springtime in a lake. The most general definition unifies several concepts in mathematics such as ordinary differential equations and ergodic theory by allowing different choices of the space and how time is measured.
Atomic orbitalIn atomic theory and quantum mechanics, an atomic orbital (ˈɔːrbɪtəl) is a function describing the location and wave-like behavior of an electron in an atom. This function can be used to calculate the probability of finding any electron of an atom in any specific region around the atom's nucleus. The term atomic orbital may also refer to the physical region or space where the electron can be calculated to be present, as predicted by the particular mathematical form of the orbital.
Molecular orbital theoryIn chemistry, molecular orbital theory (MO theory or MOT) is a method for describing the electronic structure of molecules using quantum mechanics. It was proposed early in the 20th century. In molecular orbital theory, electrons in a molecule are not assigned to individual chemical bonds between atoms, but are treated as moving under the influence of the atomic nuclei in the whole molecule. Quantum mechanics describes the spatial and energetic properties of electrons as molecular orbitals that surround two or more atoms in a molecule and contain valence electrons between atoms.
Molecular orbitalIn chemistry, a molecular orbital (ɒrbədl) is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region. The terms atomic orbital and molecular orbital were introduced by Robert S. Mulliken in 1932 to mean one-electron orbital wave functions. At an elementary level, they are used to describe the region of space in which a function has a significant amplitude.
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.
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.
Molecular mechanicsMolecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Gaussian orbitalIn computational chemistry and molecular physics, Gaussian orbitals (also known as Gaussian type orbitals, GTOs or Gaussians) are functions used as atomic orbitals in the LCAO method for the representation of electron orbitals in molecules and numerous properties that depend on these. The use of Gaussian orbitals in electronic structure theory (instead of the more physical Slater-type orbitals) was first proposed by Boys in 1950.
Dynamical systems theoryDynamical systems theory is an area of mathematics used to describe the behavior of complex dynamical systems, usually by employing differential equations or difference equations. When differential equations are employed, the theory is called continuous dynamical systems. From a physical point of view, continuous dynamical systems is a generalization of classical mechanics, a generalization where the equations of motion are postulated directly and are not constrained to be Euler–Lagrange equations of a least action principle.
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.
Basis set (chemistry)In theoretical and computational chemistry, a basis set is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. The use of basis sets is equivalent to the use of an approximate resolution of the identity: the orbitals are expanded within the basis set as a linear combination of the basis functions , where the expansion coefficients are given by .
Valence electronIn chemistry and physics, a valence electron is an electron in the outer shell associated with an atom, and that can participate in the formation of a chemical bond if the outer shell is not closed. In a single covalent bond, a shared pair forms with both atoms in the bond each contributing one valence electron. The presence of valence electrons can determine the element's chemical properties, such as its valence—whether it may bond with other elements and, if so, how readily and with how many.
Electron configurationIn atomic physics and quantum chemistry, the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. For example, the electron configuration of the neon atom is 1s2 2s2 2p6, meaning that the 1s, 2s and 2p subshells are occupied by 2, 2 and 6 electrons respectively. Electronic configurations describe each electron as moving independently in an orbital, in an average field created by all other orbitals.
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.
Plane waveIn physics, a plane wave is a special case of wave or field: a physical quantity whose value, at any moment, is constant through any plane that is perpendicular to a fixed direction in space. For any position in space and any time , the value of such a field can be written as where is a unit-length vector, and is a function that gives the field's value as dependent on only two real parameters: the time , and the scalar-valued displacement of the point along the direction . The displacement is constant over each plane perpendicular to .
Measure-preserving dynamical systemIn mathematics, a measure-preserving dynamical system is an object of study in the abstract formulation of dynamical systems, and ergodic theory in particular. Measure-preserving systems obey the Poincaré recurrence theorem, and are a special case of conservative systems. They provide the formal, mathematical basis for a broad range of physical systems, and, in particular, many systems from classical mechanics (in particular, most non-dissipative systems) as well as systems in thermodynamic equilibrium.
Dynamical billiardsA dynamical billiard is a dynamical system in which a particle alternates between free motion (typically as a straight line) and specular reflections from a boundary. When the particle hits the boundary it reflects from it without loss of speed (i.e. elastic collisions). Billiards are Hamiltonian idealizations of the game of billiards, but where the region contained by the boundary can have shapes other than rectangular and even be multidimensional.
Group schemeIn mathematics, a group scheme is a type of object from algebraic geometry equipped with a composition law. Group schemes arise naturally as symmetries of schemes, and they generalize algebraic groups, in the sense that all algebraic groups have group scheme structure, but group schemes are not necessarily connected, smooth, or defined over a field. This extra generality allows one to study richer infinitesimal structures, and this can help one to understand and answer questions of arithmetic significance.
Tight bindingIn solid-state physics, the tight-binding model (or TB model) is an approach to the calculation of electronic band structure using an approximate set of wave functions based upon superposition of wave functions for isolated atoms located at each atomic site. The method is closely related to the LCAO method (linear combination of atomic orbitals method) used in chemistry. Tight-binding models are applied to a wide variety of solids.
