Puzzle Number 7: Molecular Tagging

Taking a break from the word puzzles, I thought I would offer a more science oriented puzzle. I am not sure if my puzzle scenario is entirely clear, however, so if you have any questions please don't hesitate to send an email or leave a comment.

The Puzzle: You are working for a nanotechnology company on a project that involves suspending small molecules in a solution and subsequent detection as a method of labeling (kind of like a chemical bar-code). Your company has developed two possible compounds to use, and wants you to determine whether one compound is better (although it is possible there is no difference). Compound A is a relatively simple molecule and can be activated to form non-polar bonds with up to three other A molecules. Compound B is slightly more complicated, and has two different types of binding sites that can be activated to form polar bonds with the complementary binding sites on up to two other B molecules. Bonds need to be activated to form, so molecules will not spontaneously bond in solution. Your company can detect the presence and polarity of a bond when analysing the compound in a solution.

Two A molecules bound together.

Two B molecules bound with unequal polar bonds.

Due to the higher complexity of molecule B, it costs the same amount of money to synthesize three B molecules as four A molecules. Your project leader therefore wants you to decide between two different molecular alphabets: either four A molecules with varying intermolecular bonds or three B molecules with varying intermolecular bonds. Each element of an alphabet must be constructed so that all molecules are bound to a single network, but not all bonds need to be activated on a given molecule, thus allowing distinct and distinguishable bond networks to be constructed.

Your task, therefore, is to determine whether networks of four A molecules or three B molecules are more effective at encoding information.

Note: Yes, I made the diagrams in Paint. Yes, they are ugly. Hopefully, though, they get the point across clearly.

Note: Solutions to the puzzle can be found here.