On making pretty structures

I had an exchange with @fluorogrol today talking about poorly thought out chemical structures.  It began when the pseudonymous blogger tweeted out the (less than optimal) structure of this alkaloid:

Wrong, indeed. Representing complex stereochemistry can be quite tricky.  But bonds extending halfway across the molecule is generally not the way to go.  Chemical structures must satisfy two requirements: 1) they must be unambiguous, and 2) they must accurately represent the 3-dimensional shape of the the actual molecule.  I responded with my take:

…which was straightened out and rotated a bit, giving us this final, unambiguous structure:

No exaggerated bonds, no stereocenters consisting of a cluster of wedges.  Plus, now you can quickly get an idea for the actual shape of the molecule.  Now, admittedly, I have no idea where the original structure appeared, but I’m going to assume it’s from a publication.  Which means a group of scientists, and presumably at least one organic chemist, collectively decided that structure was the best way to represent akuammine (the wikipedia page structure is equally bad).

And to think, this tragedy could have been easily avoided.  Here’s a quick checklist on how to draw an accurate, sexy structure of your molecule.

1) Does the molecule have any cyclic or bicyclic motifs common in organic chemistry?

To list a few...

…to list a few

If yes, start there.  These structures are so ubiquitous in organic chemistry that they give readers a quick and easy 3-D reference point.  Not sure if there’s one of these in your molecule? Proceed to step 2.

2) Load you molecule up in the three-dimensional molecule viewer of your choice.  The professional edition of ChemDraw comes with Chem3D, which will do the trick.  As will whatever you may use for energy calculations.  Don’t have access to any 3D chemistry software?  MolView has you covered with its in-browser tool, which can even perform simple energy minimization calculations.

Rotate the structure around a bit.  Look for any of the aforementioned motifs.


Still can’t find one?  Then…

3) Find and angle from which all atoms are more or less visible.  Of course, your ChemDraw structure doesn’t need to perfectly match all bond angles and distances, but try to replicate them as faithfully as possible.  A good angle is one from which stereochemistry is unambiguous and doesn’t require dashes and wedges everywhere to makes sense of the structure.  Also, don’t forget the ever underutilized “structure perspective” tool in ChemDraw; make judicious use of it.

Maybe I’ll start featuring a “bad structure of the week” here.


My Baby Blue


When I started writing this, I planned on it being a single post covering some background about organic chemistry methods discussed in Breaking Bad.  But more importantly, how accurate those methods are.  However, I soon realized covering everything I wanted to would turn this post into an essay.  So I decided the best course of action would be to break it into parts.  Part one will cover the structure and properties of the drug, while parts two and three will discuss its synthesis in regards to the show.

Part One

Welcome back, faithful viewers.  As promised, this time around I will tackle (with no spoilers!) some of the chemistry from the series Breaking Bad.  For those of you living under a rock for the last five years, Breaking Bad chronicles protagonist Walter White’s descent from beloved high school chemistry teacher to methamphetamine-producing drug kingpin “Heisenberg.”  You also may be quite tired of your friends’ raving reviews about the show, and probably wish they’d shut up about it already.  But I digress.

Let’s briefly discuss the structure and properties of meth.  This is methamphetamine:

meth full formula

Or more succinctly (in what chemists call “skeletal formula”):

meth skeletal

You’ll notice the wavy line representing a carbon-carbon bond.  A wavy line exists because there are two possible enantiomers of methamphetamine.  The dash (left) represents a bond going into the screen, while the wedge (right) represents a bond sticking out at you. Remember, organic molecules are three-dimensional, not flat.


We differentiate these two enantiomers with the Latin prefixes dextro and levo, or simply d and l for short.  The structure on the left is levo-methamphetamine.  It’s rather innocuous and there’s a good chance you’ve unknowingly used it before; it goes by the brand name Vick’s VapoInhaler.  The one on the right is dextro-methamphetamine, and that’s the one favored by recreational methamphetamine users.  A seemingly minor difference in structure turns a highly addictive and very destructive drug into a nasal decongestant.

Methamphetamine is a psychostimulant, belonging to the broader class of psychoactive drugs.  It acts on the central nervous system by increasing the amount of dopamine in the body, causing a variety of physical and psychological effects; hyperactivity, alertness, headaches, increased libido and self-confidence, heart palpitations, psychosis, stroke, and paranoia are just a few of the many effects induced by methamphetamine usage.

Recreationally, the drug is introduced to the body virtually any way you could imagine, and in at least one way you probably can’t.  Meth tablets were given to pilots during WWII to help them stay awake on long bombing runs, and it’s currently prescribed to treat attention deficit hyperactivity disorder (ADHD) and as a last-ditch treatment for severe obesity.

Look out for my next post, where I’ll be talking about Walt and Jesse’s first cook in that run-down Winnebago.