Re: If color depends on d orbitals where does color in chlorophyll come from?

The color of chlorophyll comes from the many double covalent bonds, specifically the p molecular orbitals, that form both the porphyrin ring and its tail. These double bonds can be shifted into many different configurations, so that any electrons added to the molecule can move freely around the ring, dispersing the negative charge across the whole molecule. The movement of double bonds like this is called resonance, and it allows the p orbitals involved to act as one massive electron cloud. Each p orbital alone gives off energy in the ultraviolet range, and as each subsequent orbital is added to the chain, it increases the wavelength of emitted energy when the electrons in the cloud are excited. Also important to the light emission from the resonant cloud is the electronegativity of atoms involved in the p orbitals, e.g. the presence of nitrogen atoms in the rings of chlorophyll hold the electrons in the cloud closer, giving its emitted light a shorter wavelength (green) than beta-carotene which has all carbon atoms (red-orange). So the color of chlorophyll is determined by the nature and number of resonant p molecular orbitals it has.

As suggested above, this resonance is an important part of many other molecules which are used as pigments to give things color. All of these molecules are called chromophores, and their color depends on the resonant frequency of the molecule: heme makes blood red, beta-carotene makes carrots orange, chlorophyll makes leaves green, and a variety of chromophores, including xanthophylls and carotenoids, give flowers their many colors. Even most food colorings and clothing dyes are resonant organic chromophores. In fact, much of the research done by the textile industry over the last century has been in designing novel dyes by altering the resonant bonds in preexisting dyes to get new colors. This has gone even farther in cell biology, where we use fluorescent dyes to label different components of the cell as part of studying their activities. Companies like Molecular Probes have gone so far as to design fluorophores (chromophores that fluoresce) with specific excitation and emission wavelengths, so that a cell with multiple labels will glow different colors depending on what color light (or in some cases, laser) you shine on it.