Molecular modellingMolecular 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.
Density functional theoryDensity-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.
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.
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.
Quantum potentialThe quantum potential or quantum potentiality is a central concept of the de Broglie–Bohm formulation of quantum mechanics, introduced by David Bohm in 1952. Initially presented under the name quantum-mechanical potential, subsequently quantum potential, it was later elaborated upon by Bohm and Basil Hiley in its interpretation as an information potential which acts on a quantum particle. It is also referred to as quantum potential energy, Bohm potential, quantum Bohm potential or Bohm quantum potential.
De Broglie–Bohm theoryThe de Broglie–Bohm theory, also known as the pilot wave theory, Bohmian mechanics, Bohm's interpretation, and the causal interpretation, is an interpretation of quantum mechanics. In addition to the wavefunction, it also postulates an actual configuration of particles exists even when unobserved. The evolution over time of the configuration of all particles is defined by a guiding equation. The evolution of the wave function over time is given by the Schrödinger equation.
Molecular cloudA molecular cloud, sometimes called a stellar nursery (if star formation is occurring within), is a type of interstellar cloud, the density and size of which permit absorption nebulae, the formation of molecules (most commonly molecular hydrogen, H2), and the formation of H II regions. This is in contrast to other areas of the interstellar medium that contain predominantly ionized gas. Molecular hydrogen is difficult to detect by infrared and radio observations, so the molecule most often used to determine the presence of H2 is carbon monoxide (CO).
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
MoleculeA molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.
Slater-type orbitalSlater-type orbitals (STOs) are functions used as atomic orbitals in the linear combination of atomic orbitals molecular orbital method. They are named after the physicist John C. Slater, who introduced them in 1930. They possess exponential decay at long range and Kato's cusp condition at short range (when combined as hydrogen-like atom functions, i.e. the analytical solutions of the stationary Schrödinger equation for one electron atoms). Unlike the hydrogen-like ("hydrogenic") Schrödinger orbitals, STOs have no radial nodes (neither do Gaussian-type orbitals).
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 .
Lagrangian (field theory)Lagrangian field theory is a formalism in classical field theory. It is the field-theoretic analogue of Lagrangian mechanics. Lagrangian mechanics is used to analyze the motion of a system of discrete particles each with a finite number of degrees of freedom. Lagrangian field theory applies to continua and fields, which have an infinite number of degrees of freedom.
Orion molecular cloud complexThe Orion molecular cloud complex (or, simply, the Orion complex) is a star-forming region with stellar ages ranging up to 12 Myr. Two giant molecular clouds are a part of it, Orion A and Orion B. The stars currently forming within the complex are located within these clouds. A number of other somewhat older stars no longer associated with the molecular gas are also part of the complex, most notably the Orion's Belt (Orion OB1b), as well as the dispersed population north of it (Orion OB1a).
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.
Diatomic moleculeDiatomic molecules () are molecules composed of only two atoms, of the same or different chemical elements. If a diatomic molecule consists of two atoms of the same element, such as hydrogen () or oxygen (), then it is said to be homonuclear. Otherwise, if a diatomic molecule consists of two different atoms, such as carbon monoxide () or nitric oxide (), the molecule is said to be heteronuclear. The bond in a homonuclear diatomic molecule is non-polar.
Geometric phaseIn classical and quantum mechanics, geometric phase is a phase difference acquired over the course of a cycle, when a system is subjected to cyclic adiabatic processes, which results from the geometrical properties of the parameter space of the Hamiltonian. The phenomenon was independently discovered by S. Pancharatnam (1956), in classical optics and by H. C. Longuet-Higgins (1958) in molecular physics; it was generalized by Michael Berry in (1984). It is also known as the Pancharatnam–Berry phase, Pancharatnam phase, or Berry phase.
Molecular biologyMolecular biology məˈlɛkjʊlər is the study of chemical and physical structure of biological macromolecules. It is a branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena—uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology.
Electron densityElectron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either or . The density is determined, through definition, by the normalised -electron wavefunction which itself depends upon variables ( spatial and spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory.
Phase-space formulationThe phase-space formulation of quantum mechanics places the position and momentum variables on equal footing in phase space. In contrast, the Schrödinger picture uses the position or momentum representations (see also position and momentum space). The two key features of the phase-space formulation are that the quantum state is described by a quasiprobability distribution (instead of a wave function, state vector, or density matrix) and operator multiplication is replaced by a star product.
Molecular physicsMolecular physics is the study of the physical properties of molecules and molecular dynamics. The field overlaps significantly with physical chemistry, chemical physics, and quantum chemistry. It is often considered as a sub-field of atomic, molecular, and optical physics. Research groups studying molecular physics are typically designated as one of these other fields. Molecular physics addresses phenomena due to both molecular structure and individual atomic processes within molecules.
