Ab initio Molecular orbital Calculations which use all the molecular orbitals in a calculation, not just the valence electron orbitals. Absolute configuration The way, in 3-dimensional space, in which 4 different substituents are arranged off a chiral carbon. This can only be determined by X-ray Crystallography. However other compounds which can be related to one with known configuration, by syntheses where there are no changes at a chiral centre, bcan also be assigned an absolute configuration
active site The portion of a protein where a ligand binds
alpha carbon The carbon in an amino acid which has the functional groups attached. The term is usually used when talking about protein sequence or structure as a protein is composed of a sequence of amino acids.
alpha helix A helical portion of a protein structure
amino acid The basic building block of proteins. A molecule with an amine and a carboxylic acid substituent on a single carbon.
asymmetric carbon A carbon with four different substituents.
beta sheet A portion of a protein structure which forms a sheet like structure due to how it hydrogen bonds to and adjacent protein strand
Cahn-Ingold-Prelog priority rules These are a series of rules which prioritises atoms according to atomic weight, higher atomic weight have higher priority, so that the four substituents off a chiral carbon can be ordered. The substituent of lowest priority is arranged away from the viewer and the ordering of the 3 highest ranking substituents examined. If they are arranged clockwise then the chirality of the chiral carbon is assigned an R (rectus) configuration. If anticlockwise, a S (sinster) configuration.
Cartesian coordinates The usual X Y Z coordinate system; with the axes at 90 degrees to each other.
Chiral An atom, usually a carbon atom, which has four different substituents off it.
Conformer A particlar 3-dimensional arrangement of atoms in one molecule
Configuration The manner in which 4 different substituents are arranged off a chiral carbon
Configurational Isomers Molecules with the same chemical formula, the same connectivity and which are not identical after rotation around single bonds
Conformation One particular 3-dimensional arrangement of a molecule
Conformational isomersA series of related 3-dimensional arrangements of a molecule
Connolley's surface The surface formed over a molecule when a ball of water is run over the van der Waal's surface. This is often used to identify cavities on proteins which have the possibilty of being a binding site.
CPK model This is a model of a molecule which gives an idea of the volume of a molecule as it has a surface at the van der Waal's radius of each atom of the molecule.
Constitutional isomers Molecules with the same molecular formula but a different atom connectivity.
Crystallographic coordinates Coordinates in which the positions of atoms are described with respect to (in proportion to) the sides of the unit cell. These sides are not necessarily at right angles to each other.
Diastereomers Molecules with the same chemical formula, the same functional groups of the same carbon,
Diastereotopic Two identical functional groups with exactly the same chemical connectivity but which are in different chemical environments due to (an adjacent) chiral centre).
Electrostatic potential A measurement of areas which are electronegative and areas which are electropositive around a molecule.
Enantiomer One of a pair of chiral molecules. Each enantiomer is the mirror image of the other.
Enantiotopic Two identical functional groups with exactly the same chemical connectivity and the same chemical environment. These can be exchanged via a rotation or reflection axis.
Epimerisation The change of chirality at one and only one chiral centre in a molecule with more than one chiral centre.
Epimers Two molecules with more than one chiral centre that differ in configuration at one and only one chiral centre.
Fischer projections A specific method of converting 3-dimensional data into 2 dimensions withoutlosing information on chirality
Homotopic Two identical functional groups with exactly the same chemical connectivity and in identical chemical environments.
Hydrogen bond An interaction between an electropositive hydrogen (bonded to an electronegative atom) and an electronegative atom it is not bonded to.
Hydrophilic "Water loving". Those functional groups or molecules which prefer to be in an aqueous environment or in proteins, those amino acids which prefer to be in an aqueous environment.
Hydrophobic "Water hating". Those functional groups or molecules which prefer to be in an environment where there is no water; an oily environment.
Internal coordinates A method of describing the geometry of a molecule by using distances, angles and torsion angles.
Isomers Molecules with the same molecular formula but different atom connectivities
Ligand A small molecule that binds to another larger molecule.
Lipophilic "Oil loving" Those functional groups or molecules which prefer to be in an environment where there is no water; an oily environment.
Molecular dynamics
Molecular mechanics
Optical resolution The separation of enantiomers from a mixture of both enantiomers.
Optical rotationThe amount a polarised light beem is rotated while passing through a chiral molecule.
Peptide bond An amide bond making up the backbone of a peptide or protein.
Polar coordinates A coordinate system based on a sphere.
Prochiral A molecule which is not chiral but which has a particular shape whereby it has, in effect 4 different functional groups arranged close to tetrahedrally in space. Such a molecule is frequently a ring system; e.g valium, a benzodiazepine.
Protein A very large polypetide
Racemerisation The chemical process of converting one enantiomer into the other.
Ramachandran map A schematic diagram showing favourable torsion angles for a protein backbone.
Re- (rectus) face A method of describing which face of a non-chiral molecule or portion of a molecule you are viewing. Groups are prioritised according to the Kahn-Ingold-Prelog rules and if these are arranged clockwise then an Re face of the molecule is being examined.
Resolution A method of describing how precise a physically determined 3-dimensional structure is.
Rotamers Conformations of a molecule differing only by rotation around single bonds.
Si- (sinster) face A method of describing which face of a non-chiral molecule or portion of a molecule you are viewing. Groups are prioritised according to the Kahn-Ingold-Prelog rules and if these are arranged anti-clockwise then an Si face of the molecule is being examined.
Space group A way of describing how unit cells pack and how to generate an array of molecules from the original unit cell.
Stereochemistry The study of how the shape of a molecule affects its chemistry.
Stereoisomers Isomers have the same atom connectivity.
Torsion angle The angle between four atoms which may or maynot be sequentially connected.
Unit cell The minimum repeat unit within a crystal.
van der Waals forces
van der Waals radius The most favourable distance between two atoms, the equilibrium separation of the two atoms is characteristic for a particular pair of atoms. Half this distance is the van der Waals radius of the atom.
For more information, contact Margaret Wong.