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.
NitrogenNitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at seventh in total abundance in the Milky Way and the Solar System. At standard temperature and pressure, two atoms of the element bond to form N2, a colorless and odorless diatomic gas. N2 forms about 78% of Earth's atmosphere, making it the most abundant uncombined element in air.
Molecular orbitalIn chemistry, a molecular orbital (ɒrbədl) is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region. The terms atomic orbital and molecular orbital were introduced by Robert S. Mulliken in 1932 to mean one-electron orbital wave functions. At an elementary level, they are used to describe the region of space in which a function has a significant amplitude.
Potassium fluoridePotassium fluoride is the chemical compound with the formula KF. After hydrogen fluoride, KF is the primary source of the fluoride ion for applications in manufacturing and in chemistry. It is an alkali halide salt and occurs naturally as the rare mineral carobbiite. Solutions of KF will etch glass due to the formation of soluble fluorosilicates, although HF is more effective. Potassium fluoride is prepared by reacting potassium carbonate with hydrofluoric acid. Evaporation of the solution forms crystals of potassium bifluoride.
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.
Intermolecular forceAn intermolecular force (IMF) (or secondary force) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules.
SolvationSolvation describes the interaction of a solvent with dissolved molecules. Both ionized and uncharged molecules interact strongly with a solvent, and the strength and nature of this interaction influence many properties of the solute, including solubility, reactivity, and color, as well as influencing the properties of the solvent such as its viscosity and density. If the attractive forces between the solvent and solute particles are greater than the attractive forces holding the solute particles together, the solvent particles pull the solute particles apart and surround them.
IodineIodine is a chemical element with the symbol I and atomic number 53. The heaviest of the stable halogens, it exists as a semi-lustrous, non-metallic solid at standard conditions that melts to form a deep violet liquid at , and boils to a violet gas at . The element was discovered by the French chemist Bernard Courtois in 1811 and was named two years later by Joseph Louis Gay-Lussac, after the Ancient Greek Ιώδης 'violet-coloured'. Iodine occurs in many oxidation states, including iodide (I−), iodate (IO3-), and the various periodate anions.
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.
Protein–protein interactionProtein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.
