Density functional theoryDensity-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density.
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.
Van der Waals forceIn molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and therefore more susceptible to disturbance. The van der Waals force quickly vanishes at longer distances between interacting molecules. Named after Dutch physicist Johannes Diderik van der Waals, the van der Waals force plays a fundamental role in fields as diverse as supramolecular chemistry, structural biology, polymer science, nanotechnology, surface science, and condensed matter physics.
Chemical bondA chemical bond is a lasting attraction between atoms or ions that enables the formation of molecules, crystals, and other structures. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds, or through the sharing of electrons as in covalent bonds. The strength of chemical bonds varies considerably; there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force, and hydrogen bonding.
Covalent bondA covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs. The stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding. For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full valence shell, corresponding to a stable electronic configuration. In organic chemistry, covalent bonding is much more common than ionic bonding.
Valence bond theoryIn chemistry, valence bond (VB) theory is one of the two basic theories, along with molecular orbital (MO) theory, that were developed to use the methods of quantum mechanics to explain chemical bonding. It focuses on how the atomic orbitals of the dissociated atoms combine to give individual chemical bonds when a molecule is formed. In contrast, molecular orbital theory has orbitals that cover the whole molecule. In 1916, G. N. Lewis proposed that a chemical bond forms by the interaction of two shared bonding electrons, with the representation of molecules as Lewis structures.
Hydrogen bondIn chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond.
Nuclear structureUnderstanding the structure of the atomic nucleus is one of the central challenges in nuclear physics. Semi-empirical mass formula The liquid drop model is one of the first models of nuclear structure, proposed by Carl Friedrich von Weizsäcker in 1935. It describes the nucleus as a semiclassical fluid made up of neutrons and protons, with an internal repulsive electrostatic force proportional to the number of protons. The quantum mechanical nature of these particles appears via the Pauli exclusion principle, which states that no two nucleons of the same kind can be at the same state.
Electron densityElectron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either or . The density is determined, through definition, by the normalised -electron wavefunction which itself depends upon variables ( spatial and spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory.
Molecular solidA molecular solid is a solid consisting of discrete molecules. The cohesive forces that bind the molecules together are van der Waals forces, dipole-dipole interactions, quadrupole interactions, π-π interactions, hydrogen bonding, halogen bonding, London dispersion forces, and in some molecular solids, coulombic interactions. Van der Waals, dipole interactions, quadrupole interactions, π-π interactions, hydrogen bonding, and halogen bonding (2-127 kJ mol−1) are typically much weaker than the forces holding together other solids: metallic (metallic bonding, 400-500 kJ mol−1), ionic (Coulomb’s forces, 700-900 kJ mol−1), and network solids (covalent bonds, 150-900 kJ mol−1).
Implicit solvationImplicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
Acid–base reactionAn acid–base reaction is a chemical reaction that occurs between an acid and a base. It can be used to determine pH via titration. Several theoretical frameworks provide alternative conceptions of the reaction mechanisms and their application in solving related problems; these are called the acid–base theories, for example, Brønsted–Lowry acid–base theory. Their importance becomes apparent in analyzing acid–base reactions for gaseous or liquid species, or when acid or base character may be somewhat less apparent.
Valence (chemistry)In chemistry, the valence (US spelling) or valency (British spelling) of an atom is a measure of its combining capacity with other atoms when it forms chemical compounds or molecules. Different sources specify different definitions, but valence is generally understood to be the number of chemical bonds that each atom of a given element typically forms; for a specified compound the valence of an atom is the number of bonds formed by that atom. Double bonds are considered to be two bonds, and triple bonds to be three.
Non-covalent interactionIn chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The chemical energy released in the formation of non-covalent interactions is typically on the order of 1–5 kcal/mol (1000–5000 calories per 6.02 molecules). Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, and hydrophobic effects.
ElectronThe electron (_Electron or _beta-) is a subatomic particle with a negative one elementary electric charge. Electrons belong to the first generation of the lepton particle family, and are generally thought to be elementary particles because they have no known components or substructure. The electron's mass is approximately 1/1836 that of the proton. Quantum mechanical properties of the electron include an intrinsic angular momentum (spin) of a half-integer value, expressed in units of the reduced Planck constant, ħ.
Basis set (chemistry)In theoretical and computational chemistry, a basis set is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. The use of basis sets is equivalent to the use of an approximate resolution of the identity: the orbitals are expanded within the basis set as a linear combination of the basis functions , where the expansion coefficients are given by .
Acid–base homeostasisAcid–base homeostasis is the homeostatic regulation of the pH of the body's extracellular fluid (ECF). The proper balance between the acids and bases (i.e. the pH) in the ECF is crucial for the normal physiology of the body—and for cellular metabolism. The pH of the intracellular fluid and the extracellular fluid need to be maintained at a constant level. The three dimensional structures of many extracellular proteins, such as the plasma proteins and membrane proteins of the body's cells, are very sensitive to the extracellular pH.
HydrogenHydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-toxic, and highly combustible. Hydrogen is the most abundant chemical substance in the universe, constituting roughly 75% of all normal matter. Stars such as the Sun are mainly composed of hydrogen in the plasma state. Most of the hydrogen on Earth exists in molecular forms such as water and organic compounds.
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.
ColloidA colloid is a mixture in which one substance consisting of microscopically dispersed insoluble particles is suspended throughout another substance. Some definitions specify that the particles must be dispersed in a liquid, while others extend the definition to include substances like aerosols and gels. The term colloidal suspension refers unambiguously to the overall mixture (although a narrower sense of the word suspension is distinguished from colloids by larger particle size).
