Friday, October 06, 2006

it's like one plus one equals nothing at all

Tomorrow, a group of SJM's "favorite SF ladies" (his words, flame him at your leisure) congregate for dinner. Sunday, I head out with KL to Sonoma. Sunday's excursion is technically work-related, but also a way to make work more tolerable. I am forced to be at a work-related meeting Monday and Tuesday in the North Bay. This usually makes my head explode, because it feels like working 48 hours straight when you have to spend entire days with coworkers. However, KL and I hatched a plan to go up a day early, hit a few vineyards, soak in a little of Sonoma, before the mind-numbing onslaught of ropes courses and trust exercises straight out of plots from The Office.

That is something I have learned, though. I am a fairly simple-minded person, and as such, if you give me a decent chaser, I can handle even some of the most distasteful shots (in the case of the horrendous Jagermeister, I don't even need a chaser, just an unhealthy amount of jeering beforehand and cheering after the face). I always like to state the obvious, but it really is true that a spoonful of sugar makes the medicine go down.

Anyway, masking the nasty with the pleasant is what probably caught my attention in a research highlight covered in Nature's latest issue. You see, there are things about myself that I know are fairly vile. And, most of the time, I do my best to shield my friends from that ugly underbelly. In some ways, it is unfortunate, because maybe no one really knows me as a result. But on the other hand, they are not subjected to some of the inner rage and irrational ramblings that fuel my mind at such times. You know, I am just trying to be polite.

For example, when I was in graduate school, I had a particularly miserable project. Since I was one of the last ones to land in an untenured professor's lab, I was really scraping the barrel in terms of projects. Not to mention, I had no real sense for what I had gotten myself into until it was too late. The very first step of the synthesis I was working on involved formation of an isonitrile. There are two things to note about this:
  • Isonitriles are some of the nastiest smelling compounds ever to be made in this world.
  • Because this was the first step in my synthesis, I had to make large quantities of isonitriles.

The particular isonitrile I was working on was volatile, which basically means it evaporates into the air to assault everyone's sense of smell all the more rapidly than your average putrid isonitrile. When I set about making the material, it was an absurd production. Every week, after our lab meeting, everyone would leave for the night, and I would stay behind. I did all of my work in a glovebox, which always made me feel like I was doing some sort of really precarious research that could end with me getting exposed to some sort of substance that transformed me into a superhero.

Alas, if the research did end that way, then my superpower was repulsion. Even with the glovebox keeping all the chemicals contained and unexposed to the atmosphere, just the split second of contamination that occurred when I transferred materials from the glovebox to a sealed flask was enough to let loose an odor so insufferable that anyone who had not heeded my previous warnings scattered out of the lab like cockroaches when the light has been turned on.

Being an organic chemist means swagger and bravado, so you have to hitch up your pants and shrug off the smells that come with the work. I tried to put on an indifferent air, tried to focus on the fact that this was the first step on a fascinating journey. But really, the journey wasn't all that fascinating to me, it turned out. And the smell of that g*d-forsaken isonitrile did not seem worth the reward of getting to the next step.

Of course, some other cowboy chemist persevered where I never could. Subir Gorai no doubt spent an unfortunate amount of his graduate years synthesizing isonitriles, and then manipulating them, to see if there was a way to mask the odor. The result is a practically important discovery. The idea is actually simple. Anyone who took basic organic chemistry lab might have thought of it, if they had connected the dots. In most organic chemistry labs, at some point, you synthesize an ester. It is easy, because it is usually a 1 or 2 step reaction, and is a rapid reaction. And it is a good place to learn lab techniques, because inevitably, you separate the ester from its starting material by distilling off the ester. Of course, if you have done this in real life, you know that this usually means that, in the process of distilling your ester, the entire chemistry department smells like some variation of bananas, mint, or cinnamon, depending on what ester your professor has you synthesize. This reminds that a few times when I was a teaching assistant, I really wanted to hurt the organic chemistry professors; they let the students decide which esters they wanted to make, and let me tell you, an amalgam of banana, mint, and cinnamon oil wafting through corridors is way too much for the nose to take.

Anyway, Gorai's work relies on the relatively pleasant aroma of the ester acting as a neutralizer of sorts. By tacking on an ester to the molecule, isonitriles can be formed without clearing the lab with their terrorizing smell. Then, once they have been transformed to the more stable, less putrid next step in your synthesis, you can get rid of the ester. So basically, the ester is your chaser, for the horrible shot of isonitrile.

This idea is the same as the idea of a protecting group. You can silence an unruly part of your molecule, freeing it later, when it's more convenient for you. Thinking this over this afternoon, I really question why I ever quit chemistry. It's certainly more interesting than the conversations that occupied my afternoon, which involved:
  • dispensing stock options to people
  • explaining something about budgets which I don't even fully understand myself
  • talking three people out of having utter meltdowns about mostly political bullsh*t at work

I miss the days when some dude in a white coat sidled up next to me in lab and started scribbling excitedly on my hood with a Sharpie. There are no mad scientists around this joint. Except perhaps for me. Maybe I will find one while searching for my next Grey Goose and Tonic tonight. But I doubt it.

No comments: