Advanced Molecular Dungeon Mapping

Now that we've covered the basics of molecular dungeon mapping, let's move on to some more advanced methods.

Aromatic and Hydrogen Bonds

A common feature in a lot of complex organic molecules are Aromatic and Hydrogen Bonds.

Aromatic Bonds
You'll see this Benzene structure a lot in the following pictures (with Hydrogen not shown). For complicated reasons, I can't tell you how this is different from a handful of carbon with alternating double and single bonds. You'll just need to trust me. Because it's so common in big organic molecules, I recommend treating this as a different route category than double or single bonds.

I recommend, if you're drawing it out, to use the bottom format,
to distinguish it from double bonds on the map.

I treat this "hexagon with three internal double bonds" as Dungeon Highway - well traversed area. Double wandering encounter checks.

~~~~~

Hydrogen Bonds

Hydrogen bonds, almost always between Hydrogen and either Oxygen or Nitrogen, are usually displayed as dashed or dotted lines. Because they're always connecting Hidden rooms with something else, I use these to represent Secret Passages.

Let's look at these two in Indigo Dye below:

"Two Ships Docking"
Indigo Dye

Common Rooms (Carbon): 16
Entrances (Oxygen): 2
Special Rooms (Nitrogen): 2
Hidden Rooms (Hydrogen): 2
High Traffic Areas (Aromatic Groups): 2
Movement Hazards (Double Bonds): 3

We have two entrances (O), two Hidden Rooms (H) connected to the entrances by Secret Tunnels (Dashed Line) and Not Common rooms (N). Two high traffic areas to the west and east (those hexagons on either end). There's an Inconvenient Movement Hazard (Double Line in the middle) bridging the two halves.

Not, perhaps, the most well-designed or imagined dungeon layout. Having Dungeon Highways on the ends is weird. But it's serviceable. Maybe we're looking at two locked ships, or the Lair of the Binary Wizard.

Elevation Changes

"Bugbear Ambush"
L-Alanine

The dashed line connections represent that the molecules are oriented in a direction away from the viewer (if they are solid black triangles, they'd represent going towards the viewer). We can treat these as stairs or elevation changes. So, if we pretend this entire dungeon is a flat plane, with us looking down on it from the sky, we have one Hidden Room on a lower elevation, and one Common Room on a higher elevation.

This molecule actually seems quite functional! I can see a cave complex here. Just needs some material to populate it and you're good to go.

Functional Groups

This guy right here.

What ho!
What about phosphate groups?! (Said exactly one person)
You'll find them in nucleotide-phosphates and DNA/RNA. Those are the things with a P surrounded by four O's.

I'd treat them as a single unit  PO4, so just a Pit (see previous post rules), 'cause four entrances around a pit is a bit redundant (or not, maybe, if we're talking about an open-air pit), and it's rare to find Phosphorus in an organic molecule without oxygen around it.

Metals and Ions

When it comes to organic molecules and metal ions, you tend to get two scenarios.
You get floaters like this guy here:

Sodium Acetate

Let's say that this represents a Unique Entrance. A portal opening, a guarded gatehouse, a big talking demon head on the side of a mountain - that sorta stuff.





2) Or big entrapped structures like here:

Let's say entrapped metals are Treasure Rooms if surrounded by Not Common rooms, or Massive Caverns if surrounded by Openings.

Cyanocobalamin

Proteins and Nucleic Acids

"Periodic Pits of the Acid Prince"
DNA

Common Rooms: 38
Entrances (O): 8
Special Rooms (N): 15
Hidden Rooms (H): 3
High Traffic Areas: 1 (in the Adenine)
Pits (P, surrounded by O's): 6
Movement Hazards: 11
Hidden Passages: 5

Whoo-ee! This dungeon is complicated. You've got Pits, tons of Special Rooms, and lots of Movement Hazards all around. Might be easier to split this up into four mini-dungeons, one for each nucleoside. Possibility exists that you could just chain these things forever (extending them along the squiggly lines) into a DNA-megadungeon.

"Riches in the Pools"
The active site of T7 DNA Polymerase.

Limitations

Heed my jargon, I'm going to talk about some problems and limitations with this mapping system.

Someone out there who took O-Chem in college is going to note some flaws in the room coding system. For one, Halogens rarely exist outside of single bonds to one atom in organic molecules, so you'll nearly always get F, Cl, and Br on the end of a branch, instead of the middle.

Similarly, metal ions will never be covalently bonded, so all passages to treasure rooms will be hidden passages. They'll nearly always be surrounded by Oxygen or Nitrogen, and while the later is fine, the former is rather silly for layout (do you really want your treasure rooms right next to a handful of entrances?).

My suggestion to fix these problems is: re-label elements to mean whatever you want them to be. Go nuts! Use the molecules as a template rather than gospel and work that imagination. Ask yourself: what kind of dungeon does this molecule remind me of?

The Gallery
or
(Drugs Make the Best Dungeons)

"Porous Cliffside"

"Back Broken Cathedral"
Cyclophosphamide

"Castle Funnel"
Selumetinib, a cancer drug.

"Triple Cathedral"
Dabrafenib, another cancer drug.

"World Snake"
Quizartinib, I'm digging that secret entrance in the middle.

"Rooster Colossus"
Meropenem. Antibiotics work great, too!

"Modest Library"
Ampicillin, another antibiotic.

"Fight Club"
Escitalopram, an antidepressant.

The Alexa dyes.

You basically have an infinite source of dungeon layouts with this method.

If someone makes a table (it won't be me) for random rooms for each atom type, you've got a procedural dungeon generator.

Hey, would this also work for city street generation?

Anyway, enjoy!