What is it? The spectrum tool allows you to explore the physics underlying absorbance and fluorescence spectra.
How does it work? The spectrum tool uses a model called the quantum harmonic oscillator to calculate the probability of an electron absorbing or emmitting a photon of a given energy.
Absorbing a photon causes an electron in a molecule to change energy, and is accompanied by a change in the way a molecule is vibrating (see the wikipedia page). This is called a transition. The wavelength of light absorbed or emitted by a molecule is determined by the energy difference between the available electronic and vibrational energy states.
The diagram in the bottom right is an abstract diagram of the energies involved in the absorption and emission. The two curves correspond to two electronic energy levels, and the lines within them correspond to vibrational states - the higher the energy, the wider the vibration.
The propensity to change between states depends on how well these energy states ‘align’, and is quantified using Franck-Condon factors. These factors determine the size each of the peaks.
The spectrum window shows absorption and fluorescence, and has vertical lines that show the wavelength of light corresponding to the the most common transitions between between energy levels.
These lines are discrete (because of the quantum nature of molecules) but the contribution to the spectrum from each transition is broadened by a number of processes. We model one, and one can change the size of it using the ‘broadening’ slider.