Is it possible to design molecules of desired qualities?
Your title and the question itself arise two different issues, and I'll try to address both.


Yes it is possible to design molecules of desired qualities, only it's not all that simple. It requires a great deal of calculations, practice, empirical laws, heuristics, experimentation, guesswork, and magic. Eventually this body of knowledge grew so wide that people started to count it a science in its own right. It became known as chemistry.
Yes we can take into account every property of every atom and compute the properties of any compound they constitute. The problem, though, quickly becomes prohibitively expensive in terms of computation time. The reverse problem (to come up with a molecule of desired properties via calculations alone) is even more costly.


So it goes.