MoleculeA molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.
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.
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.
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.
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.
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.
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.
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.
WaterWater is an inorganic compound with the chemical formula . It is a transparent, tasteless, odorless, and nearly colorless chemical substance, and it is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as a solvent). It is vital for all known forms of life, despite not providing food energy, or organic micronutrients. Its chemical formula, , indicates that each of its molecules contains one oxygen and two hydrogen atoms, connected by covalent bonds.
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.
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).
Quantum chemistryQuantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions to physical and chemical properties of molecules, materials, and solutions at the atomic level. These calculations include systematically applied approximations intended to make calculations computationally feasible while still capturing as much information about important contributions to the computed wave functions as well as to observable properties such as structures, spectra, and thermodynamic properties.
Hydrophobic effectThe hydrophobic effect is the observed tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules. The word hydrophobic literally means "water-fearing", and it describes the segregation of water and nonpolar substances, which maximizes hydrogen bonding between molecules of water and minimizes the area of contact between water and nonpolar molecules. In terms of thermodynamics, the hydrophobic effect is the free energy change of water surrounding a solute.
Iodine in biologyIodine is an essential trace element in biological systems. It has the distinction of being the heaviest element commonly needed by living organisms as well as the second-heaviest known to be used by any form of life (only tungsten, a component of a few bacterial enzymes, has a higher atomic number and atomic weight). It is a component of biochemical pathways in organisms from all biological kingdoms, suggesting its fundamental significance throughout the evolutionary history of life.
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.
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.
InterhalogenIn chemistry, an interhalogen compound is a molecule which contains two or more different halogen atoms (fluorine, chlorine, bromine, iodine, or astatine) and no atoms of elements from any other group. Most interhalogen compounds known are binary (composed of only two distinct elements). Their formulae are generally , where n = 1, 3, 5 or 7, and X is the less electronegative of the two halogens. The value of n in interhalogens is always odd, because of the odd valence of halogens.
Hydrogen fluorideHydrogen fluoride (fluorane) is an inorganic compound with chemical formula . It is a very poisonous, colorless gas or liquid that dissolves in water to yield an aqueous solution termed hydrofluoric acid. It is the principal industrial source of fluorine, often in the form of hydrofluoric acid, and is an important feedstock in the preparation of many important compounds including pharmaceuticals and polymers, e.g. polytetrafluoroethylene (PTFE). HF is also widely used in the petrochemical industry as a component of superacids.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Self-ionization of waterThe self-ionization of water (also autoionization of water, and autodissociation of water) is an ionization reaction in pure water or in an aqueous solution, in which a water molecule, H2O, deprotonates (loses the nucleus of one of its hydrogen atoms) to become a hydroxide ion, OH−. The hydrogen nucleus, H+, immediately protonates another water molecule to form a hydronium cation, H3O+. It is an example of autoprotolysis, and exemplifies the amphoteric nature of water.
