The Interaction of Light with Biological Molecules Glossary

conjugated double bonds

Double bonds on alternating pairs of carbon molecules in a linear or cyclic organic molecule. An example is as follows -C=C-C=C-C=C- The electrons in conjugated double bonds form a resonance structure that is smeared over the double bond system. These electrons are responsible for light absorption.


Light emitted by an excited singlet molecule as part of the de-excitation process. Because a small amount of the energy in the original exciting photon is lost by molecular vibration before the emission of the fluorescence, the wavelength of fluorescence is greater (i.e. less energy) than the wavelength of the exciting photon.

free radical

A molecule with an unpaired electron. These are extremely reactive species and are capable of damaging a wide variety of cellular molecules.


A measure of the number of times per second (units of sec-1) that the electric field in a photon vibrates.


The removal of one or more electrons from a molecule. For a metal like iron, the oxidation appears as a simple change in valence (e.g. Fe2+ is reduced, Fe3+ is oxidized). For an organic molecule, the removal of electrons is usually accompanied by the removal of hydrogen atoms and often the addition of oxygen or double bonds.


Light emitted by an excited triplet molecule as part of the de-excitation process. Because a significant amount of the energy in the original exciting photon is lost in the conversion from the excited singlet to the excited triplet state, the wavelength of phosphorescence is greater (i.e. less energy) than the wavelength of the exciting photon and greater than the wavelength of any fluorescence from the excited singlet state in that molecule.


The basic unit of light. Although light has some properties consistent with a wave, light from the sun is in individual packages. Each photon is a particle of electromagnetic radiation traveling with the speed of light (3 X 108 m sec-1). The energy in each photon is dependent on the frequency with which the electromagnetic field vibrates.


Molecules which have efficient conversions to the triplet state after absorption of a photon. These triplet state molecules either reduce other molecules to generate free radicals, or they excite O2, normally a triplet, to the excited singlet state; singlet oxygen is very reactive and can cause significant cellular damage.


The opposite of oxidation. When a molecule acquires one or two electrons it becomes more reduced.

singlet states

An orbital to which an electron may move after being excited by a photon. Singlet state orbitals require that the excited electron have a spin opposite to that of the spin on the electron remaining in the ground state.

triplet state

A normally forbidden excited electron orbital that is reserved for an electron with the same spin as the electron remaining in the ground state. Upon excitation to an excited singlet state, there is some possibility that the electron will reverse spin. When this happens, the electron then drops down to the triplet state, which is at a lower energy level than the excited singlet state. Once in the triplet state, the electron must remain there until its spin is again reversed. Molecular oxygen is unusual in that it is normally in a triplet state.


The distance between equivalent positions in the electromagnetic wave formed by a photon as it moves through space. For visible photons, the wavelengths are in the range of 400 to 700 nm.