Interatomic potentialInteratomic potentials are mathematical functions to calculate the potential energy of a system of atoms with given positions in space. Interatomic potentials are widely used as the physical basis of molecular mechanics and molecular dynamics simulations in computational chemistry, computational physics and computational materials science to explain and predict materials properties.
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.
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.
Hartree–Fock methodIn computational physics and chemistry, the Hartree–Fock (HF) method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system in a stationary state. The Hartree–Fock method often assumes that the exact N-body wave function of the system can be approximated by a single Slater determinant (in the case where the particles are fermions) or by a single permanent (in the case of bosons) of N spin-orbitals.
Slater determinantIn quantum mechanics, a Slater determinant is an expression that describes the wave function of a multi-fermionic system. It satisfies anti-symmetry requirements, and consequently the Pauli principle, by changing sign upon exchange of two electrons (or other fermions). Only a small subset of all possible fermionic wave functions can be written as a single Slater determinant, but those form an important and useful subset because of their simplicity.
Ewald summationEwald summation, named after Paul Peter Ewald, is a method for computing long-range interactions (e.g. electrostatic interactions) in periodic systems. It was first developed as the method for calculating the electrostatic energies of ionic crystals, and is now commonly used for calculating long-range interactions in computational chemistry. Ewald summation is a special case of the Poisson summation formula, replacing the summation of interaction energies in real space with an equivalent summation in Fourier space.
Molecular modelA molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected.
Coarse-grained modelingCoarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water.
Bonding molecular orbitalIn theoretical chemistry, the bonding orbital is used in molecular orbital (MO) theory to describe the attractive interactions between the atomic orbitals of two or more atoms in a molecule. In MO theory, electrons are portrayed to move in waves. When more than one of these waves come close together, the in-phase combination of these waves produces an interaction that leads to a species that is greatly stabilized. The result of the waves’ constructive interference causes the density of the electrons to be found within the binding region, creating a stable bond between the two species.
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.
