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.
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
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.
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.
Arieh WarshelArieh Warshel (אריה ורשל; born November 20, 1940) is an Israeli-American biochemist and biophysicist. He is a pioneer in computational studies on functional properties of biological molecules, Distinguished Professor of Chemistry and Biochemistry, and holds the Dana and David Dornsife Chair in Chemistry at the University of Southern California. He received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Martin Karplus for "the development of multiscale models for complex chemical systems".
Water modelIn computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
Molecular geometryMolecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i.
Equipartition theoremIn classical statistical mechanics, the equipartition theorem relates the temperature of a system to its average energies. The equipartition theorem is also known as the law of equipartition, equipartition of energy, or simply equipartition. The original idea of equipartition was that, in thermal equilibrium, energy is shared equally among all of its various forms; for example, the average kinetic energy per degree of freedom in translational motion of a molecule should equal that in rotational motion.
Properties of waterWater () is a polar inorganic compound that is at room temperature a tasteless and odorless liquid, which is nearly colorless apart from an inherent hint of blue. It is by far the most studied chemical compound and is described as the "universal solvent" and the "solvent of life". It is the most abundant substance on the surface of Earth and the only common substance to exist as a solid, liquid, and gas on Earth's surface. It is also the third most abundant molecule in the universe (behind molecular hydrogen and carbon monoxide).
