Category
Computational chemistry
Related concepts (59)
Hybrid functional
Hybrid functionals are a class of approximations to the exchange–correlation energy functional in density functional theory (DFT) that incorporate a portion of exact exchange from Hartree–Fock theory with the rest of the exchange–correlation energy from other sources (ab initio or empirical). The exact exchange energy functional is expressed in terms of the Kohn–Sham orbitals rather than the density, so is termed an implicit density functional. One of the most commonly used versions is B3LYP, which stands for "Becke, 3-parameter, Lee–Yang–Parr".
Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Energy minimization
In the field of computational chemistry, energy minimization (also called energy optimization, geometry minimization, or geometry optimization) is the process of finding an arrangement in space of a collection of atoms where, according to some computational model of chemical bonding, the net inter-atomic force on each atom is acceptably close to zero and the position on the potential energy surface (PES) is a stationary point (described later).
Reaction coordinate
In chemistry, a reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway. It is usually a geometric parameter that changes during the conversion of one or more molecular entities. In molecular dynamics simulations, a reaction coordinate is called collective variable. These coordinates can sometimes represent a real coordinate system (such as bond length, bond angle...), although, for more complex reactions especially, this can be difficult (and non geometric parameters are used, e.
Fock matrix
In the Hartree–Fock method of quantum mechanics, the Fock matrix is a matrix approximating the single-electron energy operator of a given quantum system in a given set of basis vectors. It is most often formed in computational chemistry when attempting to solve the Roothaan equations for an atomic or molecular system. The Fock matrix is actually an approximation to the true Hamiltonian operator of the quantum system. It includes the effects of electron-electron repulsion only in an average way.
Energy profile (chemistry)
In theoretical chemistry, an energy profile is a theoretical representation of a chemical reaction or process as a single energetic pathway as the reactants are transformed into products. This pathway runs along the reaction coordinate, which is a parametric curve that follows the pathway of the reaction and indicates its progress; thus, energy profiles are also called reaction coordinate diagrams.
Parallel tempering
Parallel tempering, in physics and statistics, is a computer simulation method typically used to find the lowest energy state of a system of many interacting particles. It addresses the problem that at high temperatures, one may have a stable state different from low temperature, whereas simulations at low temperatures may become "stuck" in a metastable state. It does this by using the fact that the high temperature simulation may visit states typical of both stable and metastable low temperature states.
Protein design
Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function. Proteins can be designed from scratch (de novo design) or by making calculated variants of a known protein structure and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Dihydrogen cation
The dihydrogen cation or hydrogen molecular ion is a cation (positive ion) with formula H2+. It consists of two hydrogen nuclei (protons) sharing a single electron. It is the simplest molecular ion. The ion can be formed from the ionization of a neutral hydrogen molecule (H2) by electron impact. It is commonly formed in molecular clouds in space by the action of cosmic rays. The dihydrogen cation is of great historical, theoretical, and experimental interest.
Spin contamination
In computational chemistry, spin contamination is the artificial mixing of different electronic spin-states. This can occur when an approximate orbital-based wave function is represented in an unrestricted form – that is, when the spatial parts of α and β spin-orbitals are permitted to differ. Approximate wave functions with a high degree of spin contamination are undesirable. In particular, they are not eigenfunctions of the total spin-squared operator, Ŝ2, but can formally be expanded in terms of pure spin states of higher multiplicities (the contaminants).