Thursday, August 29, 2013

Nanomechanics

"By irradiating the surface through appropriate filters, the controlled mechanical  motion of the bistable [2] rotaxane molecules were harnessed to push droplets of iodomethane uphill on a substrate positioned at a 12ยบ incline." [1]
This line comes from a 2012 Chem. Soc. Rev. article titled "High Hopes: Can Molecular Electronics Realize its Potential?" In short, the authors of the original article[2] were able to utilize light energy to push a fluid against its normal direction of flow. By changing the physical location of one molecule with respect to another in a thin film, the scientists were able to control how a liquid acted in real-time on this thin film.

If that doesn't blow your mind, think about it this way. The potential energy in light was transferred to a molecule, which was able to undergo a mechanical change. So potential energy was converted into kinetic energy. This change, affected by the movement of the molecule, then caused a change of potential energy of the liquid on its surface which was eased by converting this new energy into movement- more kinetic energy. Shine light, move liquid. 
Heck, shine light-move anything is a staggering possibility. Controlled surface wetting has implications for cool new polymer films. Maybe even one that will collect water from rain (or the atmosphere![3,4]).  The Cohen paper [4] also discusses controlled drug release but why limit it to medicine?
http://images.tweaktown.com/imagebank/News_duracell_matrix.jpg
Almost, Morpheus. I like your imagination though.
What about creating nano-machines? 
http://www.graygoo.net/blog/wp-content/uploads/2011/05/smoky_the_nanobot.jpg
Oh. Well thanks anyway graygoo.net
 Still, it's an interesting thought.

[1]Coskin, A., Stoddart, F. et al.; Chem. Soc. Rev., 2012, 41, 4827-4859

Wednesday, August 21, 2013

Bond...Covalent Bond

Ahhh, Hollywood. You can be so impressively close to reality when it comes to creating interesting situations. Last night, I was really interested when a "chemical structure" was actually displayed in Moonraker featuring Roger Moore as James Bond. The old publishing style of structure caught my attention initially, and I wanted to have a closer look at the structure, which looked slightly odd to me at first glance. The fused tricyclohexane rings caught my attention first since I had never seen something like that before- even hormones which have fused polycyclic systems aren't attached in a linear fashion. Then there's the question of the DS on the structure. What could that be? And then other problems started to show themselves.
Image courtesy of Prof. Mark Griep [1]

 Pictured above is the antiquated typeset for the chemical structure of the Moonraker "hypertoxin." Below, I've redrawn the structure in the modern ChemDraw format. No stereochemical centers were specified around the chiral centers so I just left that alone without making any presumptions. Several problem areas should be readily evident. (ChemDraw had red boxes in some areas, telling me I'm wrong!)

1- There are WAY too many bonds around phosphorus. I know that it can hybridize- but that atomic arrangement just doesn't make a lot of sense. What exactly is (C2H3O) ? My best guess, if that extra (2) is supposed to be outside the parentheses is that they are acetyl groups. However I'll discuss below for a way for the phosphorus atom to make a bit more chemical sense.
2- What is -CHCO2 ? There is a serious deficiency of atoms somewhere in that side chain.
3- The original structure shows a -OCCH3. In my updated structure I changed it to another acetyl group.
4- Are there actually any chemicals with a linearly fused tricyclohexane? A quick SciFinder search says yes, in fact there are a plethora of chemicals with this functional group. However, most of them are based around interconnected ring systems like adamantane derivatives.
5- That DS structure. What what what?

With regard to that last problem, I searched around Google for a little bit and came up with an interesting answer on someone who's written on this topic before. Dr. Mark Griep, a professor of biochemistry at University of Nebraska- Lincoln manages a blog called ReAction- Chemistry in the Movies. In 2009 he wrote 
"Within the script, I found the dialog for the scene in which the “molecular structure” was revealed but there was no accompanying description or drawing of it. I assumed this meant the screenwriter left that issue to the set designer..."[1]
 And from a quick correspondence with Dr. Griep, he never did get an answer after being in touch with several of the people involved with the pre-production process of Moonraker. 
"The DS probably stands for Derivative something-or-other. The portion of the molecule near the bottom resembles one of the WWI nerve toxin like DIFP, diisopropylfluorophosphonate, and is what makes this a toxin."

DIFP, courtey of Wikipedia
I had a few ideas of my own, but none of them really made sense. As you can see, the D of DS is attached to the carbon atom in question. This would prevent the compound from being a deuterated thiol. And how would you selectively deuterate that thiol anyhow? Obviously the movie glosses over the chemical details but it does hint that the chemical is based off of a chemical that is naturally produced by a South American orchid. 
Maybe the S was supposed to be lowercase then? That would make the DS into a Ds, which is the chemical symbol for Darmstadtium, a real element. There's a catch to this though. Darmstadtium[2] is element 110 which makes it highly radioactive (it has a half-life of 11 seconds) and thus unsuitable for industrial production of an apocalyptic nerve gas. The element has another big glaring problem as an acceptable answer. It was discovered in 1994, 15 years after the release of the movie! Unless someone has a TARDIS laying around for use in Bond films, then I'm pretty sure that's just a happy coincidence. 

All this in mind, I've gone about "correcting" the molecule in a way that makes a bit more chemical sense. Interestingly enough, the P-S bond actually exists in chemistry too[3], and is called a phosphothionous acid. My own boss, when I showed him the molecule said "Oh yeah, that phosphorous looks like it wants to be hydrolized."
I won't go through point-by-point on what I changed, but it wasn't terribly drastic. I would say congratulations and good show to whomever "created" the Moonraker Toxin, it was an interesting journey to see that chemicals really can come in many shapes and forms. It would probably be more than someone's PhD work to create a total synthesis for this molecule, but if anyone ever does I really want to see that paper.
3D Energy minimized model of the molecule. Hydrogen eliminated for clarity.
We may never know what DS stands for, or what it does really. But now a curiosity turned puzzle has been put together. 
And if you're a movie/TV producer looking to put chemical structures in your product, I am completely available to proofread your structures.

Friday, August 9, 2013

Chemistry "glassware"...at home???

You'd better believe it. I picked these little puppies up from Thinkgeek not too long ago because really- who doesn't love creative ideas for shot glasses? A little creative lighting, some balance adjustment and boom! The picture you see above came to life.
Had to celebrate the purification of a new compound today, something finally worked in the lab!

+Joseph Meany

Tuesday, August 6, 2013

Awesome Nicknames

So I'm reading J. R. Partington's "A Short History of Chemistry" (Harper Torchbooks, 1965) partly because it's an old book that I saved from destruction by a local library and partly because no chemistry course I've ever taken really touches on the development of the science that is so central to my life. I know it's dated and there are probably a lot of other texts that are more modern or may be more comprehensive- but I got it for a bargain. Get off my back alright? Okay. Thanks.

I'm working my way through the section right now that's basically discussing the high-times of alchemical study (which interestingly enough coincide with the European Middle Ages) and I've found that many of those researchers had names attributed to them, some based on scholastic significance while others have no evident origin and others just gave it to them[1]. Paracelsus, known also by his real name Theophrastus Bombast von Hoenheim, fits this latter description.
Theophrastus Bombast von Hoenheim...and his brother, Bombad Boss Nass von Hoenheim

Robert Bacon, and many of the other Franciscan Monks earned the scholarly titles, for example Bacon's Doctor Mirablis or Thomas Aquinas' Doctor Angelicus. Albert the Great, Albertus Magnus, was given his nickname by his peers during his lifetime because he brought to public attention many of the philosophical works which had become esoteric at that time.
From that, my question is- why can't we have cool nicknames again? I know it would complicate authorship attribution (which was rife in the Middle Ages), but how awesome would it be to be known as something other than your direct name? I guess that's what Twitter handles are for- I'm looking at you @SeeArrOh! But really. Can't we get a bit of grandiosity generated here? I mean something to really shed light on the SHEER AWESOME of the work that we do? Maybe something just  little bit more varied than Philosophiae Doctor!

What name might you choose, or what name do you think others might ascribe to you? Myself? I would choose Molectronicus.
+Joseph Meany

[1] http://www.naturasophia.com/Paracelsus.html Accessed 6 Aug 2013