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 temperingParallel 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.
Dihydrogen cationThe 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 contaminationIn 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).
Helium atomA helium atom is an atom of the chemical element helium. Helium is composed of two electrons bound by the electromagnetic force to a nucleus containing two protons along with either one or two neutrons, depending on the isotope, held together by the strong force. Unlike for hydrogen, a closed-form solution to the Schrödinger equation for the helium atom has not been found. However, various approximations, such as the Hartree–Fock method, can be used to estimate the ground state energy and wavefunction of the atom.
Electronic structureIn physics, electronic structure is the state of motion of electrons in an electrostatic field created by stationary nuclei. The term encompasses both the wave functions of the electrons and the energies associated with them. Electronic structure is obtained by solving quantum mechanical equations for the aforementioned clamped-nuclei problem. Electronic structure problems arise from the Born–Oppenheimer approximation. Along with nuclear dynamics, the electronic structure problem is one of the two steps in studying the quantum mechanical motion of a molecular system.
John Lennard-JonesSir John Edward Lennard-Jones (27 October 1894 – 1 November 1954) was a British mathematician and professor of theoretical physics at the University of Bristol, and then of theoretical science at the University of Cambridge. He was an important pioneer in the development of modern computational chemistry and theoretical chemistry. Lennard-Jones was born on 27 October 1894 at Leigh, Lancashire, the eldest son of Mary Ellen and Hugh Jones, an insurance agent.
Lennard-Jones potentialIn computational chemistry, the Lennard-Jones potential (also termed the LJ potential or 12-6 potential; named for John Lennard-Jones) is an intermolecular pair potential. Out of all the intermolecular potentials, the Lennard-Jones potential is probably the one that has been the most extensively studied. It is considered an archetype model for simple yet realistic intermolecular interactions. The Lennard-Jones potential models soft repulsive and attractive (van der Waals) interactions.
Quantum Monte CarloQuantum Monte Carlo encompasses a large family of computational methods whose common aim is the study of complex quantum systems. One of the major goals of these approaches is to provide a reliable solution (or an accurate approximation) of the quantum many-body problem. The diverse flavors of quantum Monte Carlo approaches all share the common use of the Monte Carlo method to handle the multi-dimensional integrals that arise in the different formulations of the many-body problem.
PyMOLPyMOL is an open source but proprietary molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrodinger, LLC.
