Chem Adventure

One of the nice things about organic chemistry — perhaps the one nice thing? — is the systemic naming of compounds. Without a common nomenclature, it becomes harder to communicate the names of various compounds.

(10R,13R)-10,13-dimethyl-17-(6-methylheptan-2-yl)-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol

Yeah...ok, maybe not. This is super great for compounds covered in a typical two-semester course on organic chemistry (e.g., chlorobenzene, trinitrotoluene), but it generally flops when you get into the really interesting stuff. Like cholesterol shown above.

So things get special names — like cholesterol — because things just get too wild to get systematic about the name. Aspartylarginylvalinyltyrosinylisoleucinylhistidinylprolinylphenylalanine: I would prefer Angiotensin II. You?

The problem I faced is knowing the non-systemic name when a molecule is slightly modified. For example, what is the name of guanine when C-3 is changed from an amino to a carbonyl? Xanthine. You might get lucky and a site like Wikipedia will show or explain such simple changes, but often not. Maybe KEGG has a pathway showing a biological pathway modifying caffeine to guanine which goes through xanthine. Maybe.

So what is a fella to do? Enter the 1976 computer game Colossal Cave Adventure aka Adventure.

Adventure started a genre of computer games where the player navigates some form of interactive story. Adventure was a text-based game where the player navigated a map and moves one position at a time. This gave me the idea of navigating molecules by modifying the current "position" molecule to get to the next one. Thus, Chem Adventure was born.

The idea is to start with a molecule you know, say guanine, and look at the available modifications to jump to the next molecule.

• If you add a ribose you get guanosine.
• If you add a deoxyribose you get deoxyguanosine.
• If you deaminate C-2 you get hypoxanthine.
• If you substitute a carbonyl for amine at C-2 you get xanthine.

Nothing here is intended or to be concerned with known reactions or mechanisms. In fact, such limitations are strictly ignored with gusto and joy. And I really do not care about hydrogen around here except where hydrogen explicitly matters (e.g., NAD vs. NADH). The goal is simply to be able to navigate molecules.

What can you do?

• Look at the list of molecules and pick one and bum around
• Start with benzene
• Start with methane
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