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 12º 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?

Almost, Morpheus. I like your imagination though.

What about creating nano-machines? 

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

[2]Berna, J., Zerbetto, F. et al.; Nat. Mater., 2005, 4, 704-710
[3] MIT Review
[4] Zhai, L., Cohen, R. et al.; Nano Lett., 2006, 6, 1213-1217

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.

[1] http://www.oup.com/us/companion.websites/9780195326925/pdfs/8_GriepBlog_18Oct09.pdf

[2] http://en.wikipedia.org/wiki/Darmstadtium

[3] Pellerin, B. et al. Tetrahedron Lett. (1987) 28 5811-5814

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

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

Investing Your Humanity

"There's something about investing your humanity, your eccentricity, your exuberance in the things you do. Why do people watch tightrope walkers? Not to see them get to the other side. Its because they might fall. Not everything you do is going to be successful, but that's part of the allure. It's also what makes the work valuable: that you're really present and invested in what you're doing."- Louis Rossetto, Wired Editor and cofounder.

Last month, Wired Magazine celebrated its first twenty years with a special edition of the magazine. Rossetto closed the article with the above quote and it really struck a chord with me, not because I want to start a magazine but because I understand his passion. Originally I started this blog as a part of a fellowship requirement. But since completing that project, this has taken on a life of its own. I never knew that a somewhat mature ecosystem of different chemistry blogs existed, not just as a part of the major publishers but coming from research groups, PhD students and interested hobbyists alike.
I got onto Twitter for the same reason. and in addition to using it to keep up with the latest literature, @CrimsonAlkemist has become a vehicle to interact with other professionals on a social level- presenting cool quirky things and sometimes lamenting about #phdlife. The cool thing about all this is that in addition to creating a non-traditional networking system, I have been able to create something on my own to be proud of. Biz Stone, cofounder of Twitter said once in an interview,

"By simply announcing himself as a genius on his business card, Wile E. Coyote epitomized the spirit of the Silicon Valley entrepreneur. When you're starting a company, you sometimes have nothing more than an idea. You have to begin somewhere so you declare yourself an entrepreneur just like Wile E. declared himself a genius. then you make a business card and give yourself the title 'Founder and CEO'."
Biz went on to create Genius Labs (which was later acquired by Google), and then Twitter.

I find that science isn't so different. We, as inquisitive minds, invest a little part of ourselves in each question we ask and are fulfilled by each question we answer. Experiments and observations, hypotheses and data. Even the failure of a reaction is an act of creation- albeit a minor one. To continue asking different questions until you find the right one is no short act of will. It's valuable. To me, that's what makes my work in the lab and on this blog alluring.

So to my readers I ask, how did you find your passion? How did you come to blogging about chemistry, about science? What about Twitter's ecosystem keeps you hunting down little tidbits of information to share with people you may or may not have met (yet)?

+Joseph Meany

Science and open policy

People complain about how science needs to be more open. I just realized I'm thankful for how open science is today, especially compared with the days of early science and alchemy where findings were encoded in such a form that only those specifically trained were able to unravel their meaning. Since science has progressed to a more standardized form, however, this leaves researchers of historical texts with a large job of decoding the past. With so much information available online, it is important that we are able to communicate thoroughly and openly- but most importantly- truthfully.


"This has always been a problem, however, because the texts that [the alchemists] have left us are very secretive. They're often very metaphorical they're often in a kind of code; and they're filled with all sorts of extravagant imagery- often very beautiful wood cuts but forbidding in the sense of...what does it all mean?"

This comes from Professor Larry Principe of Johns Hopkins University. He works as a science historian trying to decode many of the historical alchemy texts and the American Chemical Society recently put out a video overviewing some of his work. He explains that his main hurdles are decoding these metaphors and symbols, to repeat reactions done by "the ancients" using their methods and glassware to see what it is they actually made.

J.R. Partington, in his book, "A Short History of Chemisty" outlines that many texts from ~1200-1500 are "largely unintelligible" alluding to the secretive nature of this pseudoscience during the time, a contrasting discussion to his earlier elaboration on the treatises written by the Ancient Greeks, Arabs, and Egyptians. Shamefully, as well, "the later history of alchemy is often that of fraud."


While peer review is not perfect in its mission to vet what is "good science" and "bad science," I firmly support the system in place today opposing the search for the philosopher's stone of yesteryear. In the discussion of how to improve science communication we need to not forget- some control is better than none.

http://gizmodo.com/meet-the-man-who-decodes-the-ancient-secrets-of-alchemy-633187520

 http://fc02.deviantart.net/fs71/i/2013/111/7/c/alchemy_woodcut_duos_caputis_melior_quam_unus_est_by_dashinvaine-d62i1y6.jpg

Makes the body shudder.

So recently, I made the conscious decision that I was going to drink less soda while at work. Mostly, it was because I just wanted to cut down on sugar and caffeine, but I just absolutely loved the mouthfeel of carbonated drinks. So I switched to naturally flavored tonic waters, like lemon and lime. It's been a good transition so far and I'm actually cutting back on consumption of those too. Next time I go shopping, I'll find something else to put in the refrigerator at work. This has an added bonus, and I'll tell you why.

We all hear about how bad soda is for us. "It's full of sugar and makes you fat!" "You'll rot your teeth!" "Dahhbetus (in your best Wilfred Brimley impression)" and a slew of other info from places like Quittingsoda.com. The sugar intake was what made me originally want to slough off sodas, and to be honest I could never get over the taste of artificial sweeteners. The word "chloro-sugar" makes my spine shiver. But today I saw a tweet that led me to a paper released in Langmuir in April on how fluoride ions in drinking water led to a decrease of bacterial adhesion on the surface of teeth. The authors note, however, that the prevailing wisdom of the times suggested that the fluoride ions integrated into the tooth enamel itself, strengthening it against mineral erosion was incorrect. The authors write,
"The cariostatic impact of fluoride treatment is often traced back to a decreased demineralization of the teeth: in comparison to hydroxyapatitie (HAP), fluoroapatite (FAP) exhibits a higher resistance to acids, leading to a lower demineralization (demineralization of HAP and FAP starts at pH 5.5 and 4.6, respectively)."
This means that the FAP is a better protection against acid attack than is HAP. They also note later in the article that original estimates on how thick the FAP layer forms was off by about 100times, 10nm as opposed to 1000nm. This thickness change made scientists question exactly what was going on. The conclusion of the paper states,
"AFM with bacterial probes revealed that fluoride treatment of HAP substrates reduces the adhesion of [tested bacteria] by a factor of two."

Let's look back at the pH dependency of the demineralization in acid. 5.5 and 4.6. That's all well and good, but what is the pH of a regular soda? QuittingSoda has a handy little chart showing that the tested pH of sodas all hang below 4.1- with most being below 3! So with every sip of soda you're actaully washing away the tooth enamel. A shuddering thought to say the least. So I'll save my teeth the trouble, and get on that transition for their sake. After all, I like my smile as it is.

https://www.youtube.com/watch?v=DLDxWH0meJM (DiaBEATus Remix)
http://quittingsoda.com/post/the-acidity-ph-of-soda-pop
http://pubs.acs.org/doi/abs/10.1021/la4008558