Ψ*Ψ's (unorthodox) GRE survival guide

Fair enough, disclaimer first: I don't have anything to do with ETS or its testing centers. But standardized tests are my one saving grace amidst the many things I fuck up on a daily basis. (Left or right? I don't know! Triangle geometry? All good!) Since I only took the (insert expletive of choice) computer-based general test--my chemistry subject isn't scheduled until November--my advice is limited. It's GRE season, though, so I'll give my $0.02 if it'll put some other poor undergrad's mind to rest.
Quantitative. I'm gonna assume (for the sake of my sanity?) that there are only a few biologists in the audience. For the rest of us--who had to suffer through entirely too much calculus--this should be the easy section.[1] That doesn't mean it's not a pain in the ass. Since you can't use a calculator (unless they changed the rules), it will help you a lot to re-learn how to do basic arithmetic on paper. Yeah, yeah, and go over high school math as well, because that's pretty much the hardest stuff on there. But the most useful advice I can give you is: finish the section. (If they haven't changed it) the scoring is based mostly on how you do on the first bunch of questions. It's entirely possible to guess on about the last 8 questions and not miss any points. If you run low on time, just pick random answers and hope you're lucky.

Verbal. This is brutal. If the SAT verbal was cake for you...don't expect the same here. It's the vocabulary that will kill you, because--if you're a chemist--you've spent three or four years learning very long and obscure words.[2] Unfortunately, they're not the ones you're tested on. Number2 has some (arguably) useful free vocabulary quizzes. I'd give them a try if I were you--ETS is supposed to send you free software to prepare for the monster, and usually they do, but in many cases it arrives well after the test date.[3] But the best advice I can give you is METAL. The scary-looking Scandinavian men in the picture above are here to guide you.[4] They use big words (if you can pick them out of the screaming). I'll credit Dimmu Borgir and Cradle of Filth (among others, of course) for a good chunk of my verbal score.
Writing. This one's hard to prepare for. Your lab reports may be nice for technical writing, but that isn't really what they want from you. Last I checked, they were looking for well-structured essayish stuff. I'd definitely be lying if I said I wrote essays to practice questions to prepare for this. Pfffft. I'm too lazy for that. A good way to learn how to write decent essays is to read them. Chuck Palahniuk (wrote Fight Club, remember?) has a book of essayish writings out. No promises here--I write a lot in the first place (and usually it's more structurally, um, cohesive than what you read on CBC) so I don't know exactly how much it helped. It's hella entertaining, though. Fun stories.

That's everything I did, anyway. It's not like the exam actually matters THAT much. But if you were looking for an excuse to listen to black metal...well...I have many excuses for that.[5]

[1] I haven't had to deal with the curly S of death for a year or so now. I think I've mostly recovered from it.
[2] Can't tell you how many engineers I saw stare at chemical names and shake their heads this summer during their presentations. "I'm not gonna try to pronounce that."
[3] I'm not sure whether this is accident or eeeeevil. I stand by my statement because it happened to me and several friends.
[4] Postdoc: "They're angry because they're really cold."

[5] And my labmates hear them. Often.

How Cassie and Wenzel Got Owned (or not)

Chances are good that unless you do a lot of surface chemistry, or read Langmuir extensively, that you don't know who Wenzel and Cassie are, nor are familiar with their work. I wasn't myself, so it was quite a surprise to me that someone would publish a paper in Langmuir entitled "How Wenzel and Cassie Were Wrong." To the novice surface chemist, the title certainly begs the question: who the hell are Wenzel and Cassie? What are they wrong about? And who on earth would be so hell-bent on proving them wrong as to publish a paper describing how wrong they are? Such provocation is quite unusual for Langmuir, which is probably the premier journal of surface chemistry. It's led the paper to be one of the most highly-accessed articles in the journal this year, and has led someone to publish a rebuttal this week in Langmuir's ASAP asking, "Were They Really So Wrong?"

So, who the hell are Wenzel and Cassie? They were two physicists back in the thirties and forties who worked on the physical nature of surface wettability, and published two major papers on the subject (the original Wenzel paper is not online). Sounds pretty boring to the non-surface chemist, but in reality, the wettability of surfaces combines many of chemistry's and physics' most pressing fundamental problems: what happens when two phases interact, how can we measure the energy of the interaction, and how do microscopic interactions affect macroscale properties. A major way in which the wettability of surfaces are quantified is with the "contact angle" θ. The contact angle is the angle that forms between a droplet and a surface that the droplet is on.



A droplet "wets" the surface if θ is zero, and forms a hemispherical shape at the interface if it does not wet the surface. Contact angles can be as high as 180° (ie. the droplet does not interact with the surface at all). The properties of the liquid and surface affect the contact angle: a hydrophilic surface (like clean glass) will be wetted by water, while a hydrophobic surface (like Teflon) will not. Furthermore, the topography of the surface (smooth, rough or patterned surfaces) also affects the contact angle. You measure the contact angle with an instrument called a goiniometer, which isn't much more than a lens that renders objects on a stage opaque. The free energies of the interaction between solid/liquid (γ_SL) solid/vapor (γ_SV), and vapor/liquid (γ_VL) relate to the contact angle θ by Young's equation: cos θ = (γ_SV - γ_SL) / γ_VL.

To be VERY brief, Wenzel and Cassie's contributions were to explain the relationship between energy and contact angles on rough and biphasic surfaces, by adding a few basic modifiers to Young's equation. The McCarthy group's paper with the provocative title is a response to the greatly-increased number of citations to these two fundamental papers, particularly with the increasing interest in "superhydrophobic" surfaces. McCarthy claims the major flaw in their thinking was assuming that the contact area was the determining factor in the energy and contact angles, as opposed to the line of contact. They underwent a series of experiments with various patterned and rough surfaces to show that the area of contact is completely independent of the contact angle measurement, showing that the calculated contact angles using the Cassie and Wenzel modified equations do not coincide at all with the measured contact angles. In effect, Cassie and Wenzel's assertions don't pan out, McCarthy says. Furthermore, claims McCarthy, previous experimental findings in the literature which contradict the Wenzel and Cassie models have been largely ignored.

Next time, I'll look a little deeper into McCarthy's findings, whether the provocation was worthwhile, and the latest rebuttal in Langmuir.

Kiddies Teaching The Kiddies

When I was an undergrad, I was a TA for the sophomore organic chemistry labs for a few years. Of all the things I look fondly back on as an undergrad (a pretty short list), being an undergrad TA is near the top. As an undergrad, I was still in love with the subject and how much it made sense to me, and I loved helping other people learn it. Educationally, the way organic chemistry just clicked for me was a first: never had any subject made so much sense on the first attempt. I lived and breathed it after taking it as a freshman (I was an overacheiving prick in high school, too). I know there are lots of undergrads who, like me, have a particular fondness for sophomore o-chem. These people, among the crowds of premeds and wannabe biologists, are in the minority, but it's these people I'm addressing this to; the kind of undergrads who would regularly read (AND WRITE IN HINT HINT) this blog.

If you ever have the opportunity to teach as an undergraduate, DO IT. It's fun and not really that hard. I could extol the virtues of helping other people and educating the community and it takes a village to raise a child and all that bullshit, but such altruism is so... med school application. There are better reasons for you to do it. Here are but a few.

• Pre-meds. If you like chemistry, you probably don't like them. We all know the type- they're the ones who make up for their lack of intelligence with an ambition rivaling Caesar's. The ones who don't talk about anything other than tests, grades, med school, and how awesome they (think they) are- I especially feel for those who had to live in the dorms with these sycophantic, arrogant twits. If you ever pined to play Marcus Brutus for these types, step right up. You won't be able to get them all, but god willing, you'll be able to give a B, or maybe a C, to a few of them. If you do end up teaching a bunch of them, you might want to chip in and get one of Kyle's med bracelets. Also, teaching premeds will make you never want to go to a hospital ever again, even if you are dying of cancer. So there's that.


• Do you panic unnecessarily when anything bad happens in lab? Being a TA will help you calm down, because the labs are typically much safer than research labs and the stupid shit that students do 90% of the time, things that you might have done while taking lab, are laughable. Eventually you'll learn to be aloof about things that go wrong and able to calmly and quickly fix any problem that might come up. Here's an example. When I was a senior, I had two years of teaching behind me, and a few of my students decided to boil some ether in beakers on a hot plate. The ether ignited. Had this happened when I was a freshman, I would have screamed and ran in circles, but instead, I just ran and got a big beaker and smothered the flamin' beakers. Many of my students were surprised at how I didn't freak out when ZOMG THE HOOD WAS ON FIRE WTFBBQ!!!11oneone. It takes some time to develop the psychological callous that keeps you from freaking out, and it might take longer for some than others, but it's a trait you'll want if you go into research.


• Teaching forces you to learn everything. Feigning brilliance to your students is important to keep your image up, but you can't feign knowledge of the material. You have to know your shit, or you will be screwed. This is ultra-handy if you plan on taking the chem GRE or MCAT, as it keeps the material for the class you're teaching fresh in your head.


• Ego. Teaching as an undergradute is an amazing ego booster. I mean, teaching as a grad student is cool too, cause your students will automatically think you're Einstein until you manage to convince them otherwise. But undergrads teaching undergrads has an even bigger effect, since you're essentially their age. In that vein, teaching as an undergraduate is a more informal introduction to teaching, and if you end up going to grad school, you'll already know what to expect in terms of workload and responsibility. Some students will not appreciate their classes being taught by undergrads, but in general, the selection process for undergrad students to teach is much more rigorous than grad student admission, and undergrad TAs are usually quite successful when implemented accordingly.


• Fucking with your students. This is especially fun to do with pre-meds. As we all know, a million things can go wrong when performing an experiment, and most of them can be easily corrected or are completely inconsequential. In this grey area you can learn to have a little fun with your students. Solution turned yellow? Sorry, you fail. No precipitate? Start over (but I only have a half hour left!). You're on fire? Who isn't nowadays! Fucking around with your students also helps with their stress too, usually, because if, in this situation where EVERYTHING ISN'T WORKING AAGHHH, you can manage to joke about it, then that can really calm down the students' worries too. (if your student is on fire, consider putting him/her out before joking. First things first.)

But why are you listening to me? Just go out and do it! It looks awesome on a resume, too.

I Can See Clar-ly Now, Part 2: Hexacene's Revenge

Not too long after my lil' unsolicited advice post on Clar's aromatic sextets comes this Org. Lett. paper in ASAP today about the synthesis of hexacene. (While Ψ*Ψ has much more experience with linear acenes, I think she's out of town, so I'm scooping her on this one. Sorry hon.)

Hexacene is a green polycyclic aromatic hydrocarbon (PAH) with six fused, six-membered rings. In PAH's, the number and position of aromatic sextets (that is, benzene-like 6π electron systems) determines the reactivity of the PAH. As is the case with all linear acenes, such as naphthalene, anthracene, and pentacene, hexacene has only one aromatic sextet dispersed about the whole molecule. In other words, it's VERY reactive. It reacts with molecular oxygen readily, and will also rapidly dimerize to form a butterfly-looking molecule. It will even react with bananas.*


(Ψ*Ψ may want to school me on what the dimer actually looks like.)

You might be wondering how one even goes about these long, linear acenes. Well, hexacene is so reactive that the amount of information in the literature on it is scarce, and previous syntheses of it are inconsistent at best. Functionalized hexacenes of marginal stability have been synthesized and characterized, however. Nonetheless, these long linear acenes are of particular interest because of their interesting electronic properties and potential applications in organic field-effect transistors (oFETs).

The Shah and Neckers groups at BGSU have found a nicer alternative to previous syntheses of hexacene, and even found a cute way to keep it around long enough to characterize it. Using a reaction known as the Strating−Zwanenberg photodecarbonylation as the final hexacene-making step, they were able to make hexacene in a paltry six steps. Hexacene only stuck around for a couple minutes in solution before deciding to dimerize or react with oxygen. It was long enough, however, to get a nice UV/Vis and mass spec on it. It's green! Whee!



A consistent synthesis of hexacene alone was probably enough to get this paper in Org. Lett., but then they went a step further. Incorporating the dione into a solid matrix of poly(methyl methacrylate) and irradiation formed hexacene. The polymer matrix kept the hexacene from dimerizing or reacting with oxygen for about 12 hours, until oxygen started to creep in.

So there you have it! Isn't aromatic chemistry FUN? Just remember one of Clar's findings if you deal with them: the prettier the PAH, the less likely it'll be around for long.

*Yes, this shit IS bananas. B-A-N-A-N-A-S.

I Can See Clar-ly Now

It's Monday, I don't feel like doing a lit review, nor have I found any good chem-related poop jokes, so it must be time for another unsolicited advice column.
One of the stranger tenets of aromatic chemistry, when first diving into it, is that not all molecules we'd call aromatic by definition are very stable. We learn as sophomores that benzene is remarkably stable, by nearly 30 kcal/mol, due to its 6π-electron, cyclic, conjugated system, and, if you were like me as a sophomore, you were entranced by the idea that a simple formulation such as that would impart such stability into a molecule. My fascination with organic chemistry started with benzene, and suffice it to say, that fascination hasn't gone away. Just check out the background.

But after benzene, things get kind of weird with aromatic molecule with more than one ring (polycyclic aromatic hydrocarbons, or PAH's). Naphthalene isn't as stable as benzene, as it'll react with conc. sulfuric acid at room temperature. Anthracene can react as a diene in Diels-Alder reactions. But they all conform to Hückel's 4n+2 rule, so what gives? In the middle 20th century, Eric Clar developed a theory of PAHs laid out in two now-classic books: The Aromatic Sextet and Polycyclic hydrocarbons. In them, he gives an explanation for the increased reactivity of those systems, which I'll briefly introduce here. In any case, The Aromatic Sextet, from 1972, is a quick read, complete with some ass-old NMRs for your amusement. His thesis is, put simply: Hückel's 4n+2 rule doesn't necessarily apply to PAH's, and a far more important factor in the stability of PAH's is the setup of their aromatic sextets.

Benzene contains what Clar defines as an aromatic sextet: that is, the six π electrons in benzene constitute a sextet. These sextets can be written as circles. Note, however, that only sextets can be written as circles: in naphthalene, there is only one sextet, and four other electrons, so writing two circles in for the electrons is wrong. It's something we teach sophomores to do, even though a lot of teachers and grad students get it wrong too:



Of course, since the two rings have equal electron density due to resonance, that sextet isn't on the one ring alone. Clar denotes that there is only one sextet in the molecule, although it is dispersed about the ring, with arrows.



An example of reactive non-sextets is phenanthrene. Phenanthrene has two sextets, shown here on the outside rings, that are in resonance with the middle ring, which contains a double bond. Even though there is resonance, the middle ring's double bond acts like a real double bond, and the outer rings have benzene-like stability.



With linear acenes, there is only one available sextet, and the longer the system, the more reactive the rings. Anthracene is reactive, tetracene is even more reactive, and the violet pentacene is so reactive that it'll dimerize and must be stored under nitrogen and in the dark.



In general, the more sextets that can be utilized to represent the pi-system of a PAH, the more "stable" it is. Molecules that can be represented with only sextets, called "fully-benzenoid" by Clar, are extremely stable. Triphenylene, isolated from coal tar, is very unreactive. peri-hexabenzocoronene (HBC), which I've blagged about before, is so stable that you can't use a mel-temp to find the melting point, because the glass will melt before the compound does.



This lil' introduction only scratches the surface of the large, rather diverse, and exceptionally pretty-colored field of arene chemistry. Next week, I'll share my award-winning* recipe for chicken parmesan.

*My mom likes it

THE TOP PIC: According to legend, Kekulé's discovery of benzene's ring structure was sparked by a day-dream of a snake biting its own tail. In ancient cultures, a snake or dragon biting its own tail is known as Ouroboros, representing the cyclic nature of the universe, among other things.

I've got a fever, and the only prescription is more BINAP

Apologies from Ψ*Ψ and I regarding the lack of posts as of late: we have been quite busy and, despite living in different states, we have come down with similar illnesses at the same time. Nevertheless, I believe it's time for another of my unnecessary advice posts. This week: how to distinguish between R- and S-BINAP.

BINAP is a chiral, bidentate phosphine ligand that's used a whole lot in asymmetric synthesis. One of its first and most well-known uses is in the Ru-BINAP catalyzed Noyori hydrogenation, which, with his other works, won Noyori a Nobel prize in 2001. It's an interesting molecule: it is chiral, yet it has no chiral center. It exhibits what is known as atropisomerism, where two stereoisomers are conformers of one molecule, separable only by hindered rotation about a bond. In BINAP's case, rotation about the bond between the two naphthalene units is strongly hindered by the phosphine units. If there were free rotation about that bond, the molecule would be achiral. You can racemize one enantiomer of BINAP by heating the hell out of it.

Whenever a prof showed BINAP in synthesis, they neglected to mention how the R- and S- designations are made, and I always had trouble distinguishing the two. Finally, one professor did manage to explain it simply to our class, and so, here is how you do it in case anyone else is in a similar position. This explanation works for BINAP and other atropisomers. Pretend as if you are walking on the naphthalenes of BINAP. Start at 12 o'clock and walk "up,". In this case, looking at the molecule from the side, "up" is coming toward you. In one enantiomer, you're always walking counterclockwise to go "up"- by convention, that is the S enantiomer. In the other one, you walk clockwise to go "up"- that is the R enantiomer.


You can do this with other atropisomers, like the cute helicenes. Same deal- just walk "up" the molecule. This might be easier to visualize.



Well, that's all for today's unnecessary advice post. I do enjoy writing these, and I hope someone gets something out of it. Maybe some real chemistry, with real pretty colors, next time!

I Hate O-Chem Terminology Sometimes

Since it was brought up in an earlier post that I mixed up the terms "stereoselective" and "stereospecific," I busted out my phys org notes to relearn the terms, so I don't get pwn3d by professors on it later. I'll post it here for everyone else's benefit too.

Stereoselectivity: A reaction is stereoselective when one stereoisomer is formed in preference to another.
Lindlar hydrogenation of alkynes is stereoselective. The cis alkene is generated preferential to the trans isomer.


Stereospecificity: A reaction is stereospecific when one stereoisomer of a reactant gives a stereoisomer of a product, while another stereoisomer of that reactant gives a stereoisomer of that product.
Bromination of alkenes is stereospecific. trans-2-butene gives a meso product, while cis-2-butene gives a chiral product plus its enantiomer. The meso product and the chiral product (and its enantiomer) are diastereomers.

Stereospecific reactions are necessarily stereoselective. However, not all stereoselective reactions are stereospecific. In the above example, Lindlar hydrogenation of alkynes is not stereospecific because, quite simply, there are no stereoisomers of alkynes. Bromination of alkenes are stereoselective as well as stereospecific. However, because a reaction is stereospecific does NOT mean it is 100% stereoselective.

I think a good rule of thumb is if you want to use the term "stereospecific," don't, unless you think REALLY hard about it beforehand. And if you do, you better be talking about two different reactions where the reactants are stereoisomers and the products are stereoisomers.

There are nearly countless numbers of terms that refer to some aspect of stereochemistry, whether referring to orientation or symmetry of a molecule (woo group theory), comparing one molecule to another molecule, distinguishing particular sites in a molecule, or distinguishing its reactivity. The current terminology is extremely precise in regards to these subjects; one need only pick up a copy of Eliel's 1,200 page bible of stereochemistry to see what I mean. Nevertheless, people understandably (owing to the massive number of terms and their occasional close proximity in meaning) mangle up a lot of the terms. Some people (especially professors) are very picky about the terminology, so be careful when asking them why a particular reaction is stereospecific if it, in fact, is not; not only will you have to endure a long explanation of the CORRECT terminology, but you might even forget you had a different question in the first place. The terminology is in place to be precise about meaning, even though you can usually get away with explaining yourself correctly using mangled terminology, assuming the person you're communicating with is either sympathetic to the mangled terminology or mangles the terminology in similar ways. Meaning is subjective like that, try as we scientists do to avoid it. It's a fun conundrum: we create terminology to avoid confusion, then confuse the terms. Organic chemistry is a lot like that.