How does molecular structure affect physical properties?
Predicting (approximate) physical properties starting with molecules is complicated, below.  Nobody has ever produced a way to accurately predict how molecules will pack in a crystal structure.  Big Pharma is desperate to predict crystal polymorphs and their properties. Slightly vast amounts of grant funding pursued predicted super-explosive octanitrocubane.  When it was finally synthesized it crystallized in a less dense crystal structure than expected, deeply disappointing the DoD.

http://www.chemspider.com/ACDLabs.aspx 
http://pubs.acs.org/doi/abs/10.1021/ed064p575 
http://molsoft.com/mprop/ 

If you have a way to predict crystal structures given complex formula units, you're a big winner.