Potential energy surfaceA potential energy surface (PES) describes the energy of a system, especially a collection of atoms, in terms of certain parameters, normally the positions of the atoms. The surface might define the energy as a function of one or more coordinates; if there is only one coordinate, the surface is called a potential energy curve or . An example is the Morse/Long-range potential. It is helpful to use the analogy of a landscape: for a system with two degrees of freedom (e.g.
Molecular symmetryIn chemistry, molecular symmetry describes the symmetry present in molecules and the classification of these molecules according to their symmetry. Molecular symmetry is a fundamental concept in chemistry, as it can be used to predict or explain many of a molecule's chemical properties, such as whether or not it has a dipole moment, as well as its allowed spectroscopic transitions. To do this it is necessary to use group theory. This involves classifying the states of the molecule using the irreducible representations from the character table of the symmetry group of the molecule.
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.
Random coilIn polymer chemistry, a random coil is a conformation of polymers where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules. The conformation's name is derived from the idea that, in the absence of specific, stabilizing interactions, a polymer backbone will "sample" all possible conformations randomly.
SurfaceA surface, as the term is most generally used, is the outermost or uppermost layer of a physical object or space. It is the portion or region of the object that can first be perceived by an observer using the senses of sight and touch, and is the portion with which other materials first interact. The surface of an object is more than "a mere geometric solid", but is "filled with, spread over by, or suffused with perceivable qualities such as color and warmth".
Protein secondary structureProtein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Physical chemistryPhysical chemistry is the study of macroscopic and microscopic phenomena in chemical systems in terms of the principles, practices, and concepts of physics such as motion, energy, force, time, thermodynamics, quantum chemistry, statistical mechanics, analytical dynamics and chemical equilibria. Physical chemistry, in contrast to chemical physics, is predominantly (but not always) a supra-molecular science, as the majority of the principles on which it was founded relate to the bulk rather than the molecular or atomic structure alone (for example, chemical equilibrium and colloids).
ExcimerAn excimer (originally short for excited dimer) is a short-lived dimeric or heterodimeric molecule formed from two species, at least one of which has a valence shell completely filled with electrons (for example, noble gases). In this case, formation of molecules is possible only if such atom is in an electronic excited state. Heteronuclear molecules and molecules that have more than two species are also called exciplex molecules (originally short for excited complex).
A valueA-values are numerical values used in the determination of the most stable orientation of atoms in a molecule (conformational analysis), as well as a general representation of steric bulk. A-values are derived from energy measurements of the different cyclohexane conformations of a monosubstituted cyclohexane chemical. Substituents on a cyclohexane ring prefer to reside in the equatorial position to the axial.
