|MadSci Network: Botany|
There are two different aspects of the answer: differences between molecules and differences between what is around the molecules.
The photosynthetic pigments (chlorophylls, carotenoids, xanthophylls) are all essentially chains of carbon molecules in different shapes and sizes with other atoms off to the side. (We have to get into a little organic chemistry, which you may not have had, but it is not too complicated.) The bonds between the carbon atoms are formed by sharing electrons. If two adjacent carbons share two electrons between them, it is called a "single bond". If two carbons share 4 electrons between them, it is called a "double bond". When single bonds and double bonds alternate along a carbon chain, this is called "conjugated double bonds". In effect, the electrons are shared along the chain and not just between adjacent carbon atoms.
Now to get back to photosynthesis. In the photochemical reaction, energy from a photon is absorbed by the pigment, elevating an electron to a higher energy state. These energy states are not just random energy levels, but specific steps of energy, you might say. A photon with enough energy to raise an electron to the next step must be absorbed. (It is okay to have too much energy, although the excess is usually just wasted as heat or some other irradiation.) The electrons in conjugated bonds require less energy to be elevated to the next level, and the more conjugated bonds in the system, the lower the energy required. To absorb in the visible range, at least 7 double bonds in conjugation are needed. Carotene has 7 double bonds, for a maximum absorption around 450 nm (blue light). Chlorophylls absorbs in the lower energy red part of the spectrum, and also in the higher energy blue part of the spectrum. The different arrangements of the bonds give the different chlorophylls (a, b, c, d) their slightly different absorption patterns.
The second part of the answer is that the pigments in the chloroplast are not just floating around. They are located in a membrane system called the "thylakoids". The absorption spectra you see in the references I'll give later are done with free chlorophylls in a solvent, which is not how the pigments behave in living organisms. In the membranes, pigments are connected to different proteins in what are called "chlorophyll-protein complexes" and there are several different chlorophyll protein complexes. So not all of the chlorophylls are in the same environment in the chloroplast. This means that the exact absorption of each chlorophyll molecule is determined by its surroundings as well as its structure.
So the short answer to your question is: the number of conjugated double bonds and environment around the pigment molecule are the main determinants of absorption.
For further information, find a plant biochemistry textbook (I use Goodwin and Mercer)(but this is at least an upper undergraduate topic).
For a nice review of photosynthesis try:
To see some good animated graphics on photosynthesic energy absorption go
http://www.uoguelph.ca/botany/courses/BOT2100/greenwood2001w/photorespiration_c4_cam.htm (this is really good stuff! Try lecture 18 also)
To search for the latest research on photosynthesis (and also to contact the people doing the research) go to the American Society of Plant Physiologists search site
Try the links in the MadSci Library for more information on Botany.