Re: What chemical properties cause things to be perceived a certain color?

This is a hard question to answer as there are many layers to it. But 
assuming that what you are asking is "why is a green object green and
not yellow?", then the simple answer is that "the energy levels of the
molecules that compose it absorb photons at the complimentary wavelengths".

Okay, that is not really much of an answer as it doesn't get to the heart
of things. So, first of all, the way that all matter interacts is through
the exchange of photons. That is, atoms and molecules both absorb and 
emit photons. This is the way that one atoms "knows" that there are other
atoms out there, somewhere. (I should add that "bonds" are the internal
method for the atoms of a molecule to interact.)

Photons of light do not randomly strike an atom and are absorbed, though.
The method of absorption requires an electron to change its energy state
from one level to another. The size of the jump that the electron must
take is very carefully defined by the energies of the first and second
state. That is, to jump from the ground state to the next one for any atom
requires a specific amount of energy. And since light is energy, only
certain wavelengths of light will cause the electron to jump. Thus, you
can imagine that if white light hits an atom, then the colours 
corresponding to those wavelengths are removed. The colour of the reflected
light is changed slightly.

With atoms, energy is absorbed at very defined wavelengths. With molecules,
the situation is more complicated as there are many more energy levels and
other interactions - such as vibrations or rotations - make the energy
levels a little broader. The result is that instead of absorbing a single
line, a whole bunch of wavelengths get absorbed - say, the entire blue end
of the spectrum. In that case, the compound appears yellow as those are
the reflected or transmitted wavelengths - the ones not absorbed.

By the way, we perceive colour because of the structure of the molecules
in our eyes which have energy levels tuned to respond to certain 
wavelengths of light. Our brain interprets the signals from these molecules
and synthesizes the picture that is in our mind. Of course, this means that 
colour may be a very subjective and personal perception. But underlying it
is the notion that electrons in molecules jump from one energy level to
another in response to being struck by a photon of light. And only certain
jumps are allowed.

If you would like to read a book that explains the theory (called "quantum
electrodynamics"), I would strongly suggest the very excellent book, "QED" 
by Richard Feynman. It is a little advanced but worth the time.

Hope this helps.