Is asking your PhD supervisor a basic question considered inappropriate? I've done my Master's degree in Computational Mathematics. Then, because of several reasons, I decided to pursue my Ph.D. in the field of Quantum Chemistry.

The problem is, obviously, my lack of knowledge in this area. I'm studying, but even in my second year there are still many things I don't understand or which I understand incorrectly.

Now I'm stuck on one, probably pretty basic, concept, where I'm not able to find the proper explanation either on the Internet or in my books and my friends seem to be also quite confused by it (they seem to have just some general idea, as they have, probably, never needed to use it).

Now I'm not sure if I should ask my Ph.D. supervisor about it. Is it considered appropriate to ask your advisor about (probably) basic concepts in Ph.D. program? I'm afraid he'll think that I'm not willing to study the topic myself and that I'm wasting his time.
If your colleagues in the department—presumably also PhD students—don't understand the concept, either, it doesn't strike me that the question is truly "basic." That said, if your advisor is aware of your background, then he should know that there will be some things that might not be "obvious" to you. 

Now, in this case, you have already "done your homework": you've searched for an answer on your own but couldn't find one. Mention this to your advisor when you ask the question. A good advisor will recognize that you have done what you're supposed to and provide some guidance to help you. He may not provide you all the answers but should at least be able to point you in the right direction.