November 30, 2010

Now for the fun, happy, excited post! Over Thanksgiving break, I received a cryptic email from my PI, saying he needed contact info for a patent on the project I was working on. Any news of this had been previously unbeknown to me. So I emailed him my info, and then quickly emailed my grad student. “Hey, this sounds pretty legit. What’s the deal?”

On Thanksgiving day, I got a response back from him saying I’d be listed as second author on one paper, sixth author on another (at that point, do you even still bother counting? Anyway, it was a major collaboration amongst a few institutions, with about 10 names on the paper.) and that I’d also be listed on the patent for work relating to one of them. As far as I know, they’re drafted and pretty much ready for submission.

I’ve pretty much been grinning ear to ear ever since.

A rebuttal

November 29, 2010

The amount of response from y’all has been helpful, if not stressful. Regardless, it’s highly appreciated, and you’re all encouraged to keep posting rumors, fun facts, or reasons why I should drop chemistry all together and move to Fiji to become a massage therapist, or SCUBA instructor. Really, any information you can give me would be awesome.

Under normal circumstances, I’d wait a bit for responses to roll in, and take a bit more time to craft such a lengthy post, but considering that due dates for applications are fast approaching, I’d rather get as many questions/comments out there as soon as possible.

With regards to not selecting some of the obvious choices – Scripps, Harvard, MIT, Berkeley, Stanford. The latter three didn’t really have enough professors I was interested in.. pretty much the “two professors I’d like to work with, and then nothing else…” symptoms I had described in the previous post. MIT has Movassaghi and Danheiser, Berkeley has Sarpong and Vollhardt, and Stanford has Wender, Du Bois and Trost (but Trost’s on the older side of things…). Beyond the two obvious choices (for me, anyway) at each university, there’s not much else I’m super into.

Come to think of it, on second thought, although there’s only 2 I’d really like to work with, Wender also strikes me as synthesis oriented, but with an eye towards drug development as well… Stanford may be back on the list, lest my PI and other recommenders crucify me for switching anything up so late in the game.

Scripps and Harvard.. well.. I didn’t think I could get in. I have plenty of research experience, but my grades are (were) only so-so. Worst part of it, it’s really freshman grades and a little bit of soph grades that are lame. (most of which are not chemistry grades) However, at by the start of junior year, and taking on more advanced chem classes, things clicked, began firing on all cylinders, and since, I’ve generally been kicking ass, and taking names. However, at the end of the day, my overall GPA is still lower than I’d like, and (with no ‘supporting info’) I suspected that given the caliber of either institution, they’ll be looking for reasons to not accept people, and that would be mine…

(and for anywhere else, it’s a matter of addressing it on the personal statement or not, which is a tricky proposition in itself)

However, some news has come to me recently, that, while amazing, may be too little too late. Work I was involved with is getting published. I’m going to be on it. Despite the less than entusiastic and stressed nature of this post, there will be a celebratory post with all kinds of glee and exclamation points soon to come. In fact, I’m going to be on two publications. And a patent. Pretty sweet, right? Totally solidifies my application, and (ideally) shows an admissions committee that I’ve turned things around, and am down to work?

I learned that I was going to be on the publications over Thanksgiving break, some undisclosed time after they had been drafted. While I could not be happier with the fact that my name’s going on stuff, I can’t help but feel peeved that I wasn’t informed of their existence sooner… which would greatly have influenced my decision whether or not I’d be applying to places like Scripps. I can still apply to places like Scripps, but for Scripps itself, the deadline is Dec. 1st. In two days. Yeah… As for any other places that I’m scrambling to consider/re-consider, I have to take into account any lead time required for recommendation writers – all other deadlines I’m looking at are in January – so by adding any schools with hard deadlines of Dec 15th, I’ll need to clear it with other prof’s, and fast!

Then, there’s the “issue” of my PI. I came to him with my epic rough draft of the Master list, and he said “narrow it down to about 6 schools. 2 reach, 2 mid-range, and 2 safety.” So naturally, I whittled it down to 8 schools in total, that I thought packed most organic possibility per application. (Before learning of publications) Now, I would feel a bit more comfortable also applying to places with only two professors I’m interested, just to see what happens, especially the ones that claim “we try to not focus on one part of your application, but we do especially consider research experience.” However, I’m not the most comfortable asking my prof. for even more recs, because let’s face it, I’m a bit intimidated by him. I have the recurring fear that if my list were to expand to, say, 10, he’d go all “I thought I told you 6?” For all I know, the difference between 6, 8, and 800 is just a few more copy-paste sequences for him, but considering his recommendation will easily be the most important, I’d like to keep him as happy as possible while writing them.

Yikes. That’s a lot of writing. Anyway, comments and concerns toward this, or anything else are appreciated.

In response to some previous comments:

Everybody: Don’t do total synthesis! It’s a trap!

Fair enough. It aint what it used to be. However, are these cries of warning also intended toward the combination of drug design/medicinal chemistry/molecular pharmacology type work in tandem with heavy duty synthesis and methods, or is that combo wide enough to better support different options in the future? (most likely, continue in academia, or go to pharma.) If that’s still not enough, then what? Is there a last bastion for those of us that want to “make stuff,” or will we forever run into the dilemma of choosing a field we like, but with less job security, or choosing a field we’d rather not do, but take content in being able to find a job later on?

Also, from everybody:

Pick a good PI who you can get along with

Duly noted! Long before I questioned the internet for opinions on grad school, I knew this was going to be a major influence. Hell, even now, with regard to getting recommendations, I’m seeing where it plays a key role. However, I should say that I’m kind of an odd ‘un, in that I still like the idea of spending more time in lab. So what some might consider a lot, I just consider “intense.” And I’m fine with intense, just so long as it does not become “insane.” Presumably with a reasonable professor, that distinction will remain clear…

Via a response to Chemjobber’s Post:

Regarding your personal statement, don’t mention specific profs since the assistant profs are often on admissions committees.

Huh… I’d always heard it doesn’t hurt to name-drop specific faculty if you can readily tie in their work to your overall plans for grad school. Supposedly, it shows why you’d be a good fit there, vs anywhere else. 3rd party opinions?

Paraphrasing: So-Cal ain’t that great, as rent and car insurance are expensive

The rent’s no better in Boston. As for the car situation, I’m very OK with biking everywhere, and Zipcar-ing when necessary (biking is my designated non-chemistry hobby. Also, please note the relative abundance of velodromes in southern California…) But I suppose I’d find out if that system really worked if/when I got there.


Paraphrasing: What about Penn, Princeton, or Columbia?

Looked into all 3. Columbia I’m only really interested in Snyder and Danishefsky (and Danishefsky’s gettin’ old), and at Penn I’m only really interested in Joullie. Actually, in light of recent events, I’d consider adding Princeton to the list for MacMillan, Sorensen, and Doyle. MacMillan and Sorensen for synthesis. No intent to work for Doyle, but just because she’s adorable. Abigail Doyle: Totally Cute.

If I were to add any new applications to the list, they would probably be 2 out of the following 3: Stanford, Berkeley, Princeton.

Have I forgotten anything?

The Master List

November 28, 2010

The list extends life. The list expands consciousness. The list is vital to grad school.
Ok, so, the list and “the spice” actually have little to do with each other…

Anyway, for those that are curious, here’s the full breakdown of places I’m applying, as well as professors I’m interested in working with. First and foremost, I’m all about total synthesis (and associated reaction development). However, if I can also find a lab that incorporates biologically active products¹(optimization/library type work), that would be icing on the cake. Living somewhere that doesn’t suck is not required, but highly recommended. The going theme generally tends to be 2 professors I’m really interested in, and 1-2 professors in doing related work. Commentary follows.

  • Yale – Herzon (thanks paul!), Phillips. Considering Miller, Ellman, Spiegel. I’m very interested in the chemistry here. Herzon and Phillips are my choice professors for straight up synthesis, but the other profs’ biological/methodology work is nothing to sneeze at, and also, if the planets align, some possibility of doing some heavy-duty synthesis as well. Of course, this would mean having to live in New Haven for a few years. Frankly, I’ve had my fill of New Haven after spending time waiting to change trains, so I don’t know how a few years would tread on me, but we’ll see
  • UCSB – Pettus, Zakarian. Considering Read de Alaniz and Lipshutz. I like Zakarian’s chemistry a little more, but I’d be happy as a clam on Pettus’ work, too. Read de Alaniz’s or Lipshutz are a different story. Read de Alaniz is a total mystery – brand new faculty, and only 1 publication thus far at UCSB. Claims to do carbon-nitrogon bond forming methodology, to be used for alkaloid synthesis. I’m not enthralled with fledgling faculty and the idea of just methodology, but methodology AND alkaloid total synthesis? I could be into that… Similar sentiments toward B-Lip. Bonus points for california weather, double bonus points for getting to hang out with Ψ*Ψ.
  • UCLA – Garg, Kwon, Jung. Considering Merlic. This one’s actually a curiosity: at the current moment, there’s nobody that scores insanely high on who I’d like to work with, but I’m generally intrigued by the “all around” aspect of the professors I’m interested in. Although recently, Garg’s work has been a little more methodology-y, I’m curious about future total synthetic prospects. With respect to Kwon, her syntheses aren’t exactly as hard-core as I’d like, and like Garg, recent looks slightly more methods focused, but the prospect for legit synthetic work is there, alongside diversity oriented work. Jung and Merlic round out the lot for some (in my opinion) “standard” total synthesis and methodology, respectively.
  • UC Irvine – Rychnovsky, Vanderwal, Overman. Considering Jarvo. So… if you’re beginning to see the thought process here: Rychnovsky and Vanderwal for synthesis, Jarvo for methods. Overman’s a possibility, but he’s on the older side of professors I’m looking at, and I don’t know how much longer he intends on staying in the game.
  • Colorado State – Wood, Ferreira. Considering Rovis. Wood and Ferreira are doing stuff synthetically interesting, but don’t really offer much of a look into the biology of anything. Rovis for methods. Bonus points: I got the opportunity to see Wood give a presentation, and I liked his research and how he appears as a mentor. Minus points: CSU scores lowest on my NMR scale of grad school interest. (access to 300/400/500, but regular walkup use seems pretty much relegated to the 300)
  • UT Austin – Martin, Magnus, Siegel. Considering Krische. Martin and Siegel for synthesis (especially interested in Siegel’s work. He seems to strike the exact balance I’m looking for), Krische for methods. Like Overman, Magnus is also one of the older prof’s I’m lookin to work for, but I like his work more.
  • UNC – Crimmins, Johnson, Nicewicz. Considering Alexanian. I like the list of synthetic guys here, but there’s not a lot of options for looking at biology of anything. Regardless, whereas most other schools have only 2 professors I’m really into, I’d like to work with any of the three here. Plus, backup plan of Alexanian if I should defect to methods…
  • U. Pitt. – Wipf, Curran, Koide. Originally, I had not really considered it until a professor I’m getting a rec from suggested I check it out. I’ve since taken quite a shine to U Pitt. Wipf and Koide are in the right vein of synthesis, and Curran looks like he does a fairly decent mix of synthesis and biologically relevant stuff (although, I’d like a bit more biological breadth than just tagging everything with fluorines) In the Northeast “bracket,” I think Yale edges out Pitt a little bit when it comes to chemistry, but when it comes to living somewhere that’s not New Haven, Pittsburgh wins, hands down.

Most likely, I’ll have two or three templates for my personal statements. Something along the lines of:

  1. blah blah blah I want to do organic synthesis. Specifically, I’m interested in the work of professors so-and-so, et al. Let me in.
  2. blah blah blah I want to do organic synthesis. Specifically, I’m interested in the work of professors so-and-so, et al. Additionally, I’m interested in biological studies and optimization of biological activity, alongside heavy synthetic work. I believe that professor whats-his-face offers the best opportunity towards this kind of research. Let me in. 
  3. I’ll bake you cookies. Please let me in.

Now then… if you happen to have any comments on this list, please let me know. If you think I’m on the right track, or think I’ve forgotten a professor at one of these universities, I’d be glad to hear it.

If you have any scathing comments toward certain professors, I’d certainly like to hear them too, so I can get as comprehensive a view as possible. However, at the least, be diplomatic if you’re going to leave a comment, or if you want to be extra hateful, just email it to me.

If you also think I should look into XYZ university that was not listed here… well, I’ve probably already looked at it/ruled it out. Most commonly, there would be 1 professor I’d like to work with, and a bunch of “back up” professors that I wasn’t too interested, or in rare cases, maybe 2 professors I’d like to work with, but zero “backup” options I’d really want to/consider doing. The master list is an attempt to optimize the amount of professors I’d truly like to work for, as well as the amount of “back up” options that I wouldn’t mind working for.

[1] Not that I’m exactly looking to do the assays on anything… I’m no biochemist. However, having the option of working with collaborators (in-house, or external) where I can make stuff, and they can test it would be the dopest. (dope-est? most dope? whatever, it’d be cool.) That’s the system I used on the previous project I was working on, and it was a pretty sweet deal.

it’s not me, it’s you.

November 18, 2010

Alfa Aesar, we need to talk. You haven’t been giving me what I need, so I think it’s time I found somebody else.

My carbon tetrabromide stock fell low, and that’s when you fell into my life. Drawn to you by your fair prices, and impressed by your quick shipping, I would never have thought you to be such a source of aggravation later on.

Two steps after using the carbon tetrabromide, I ran into issues. Reactions not reacting how they should. At first, I thought it was me: impure products, glassware not dried thoroughly enough, bad luck. Back tracking through the reactions, I still couldn’t find the source of the problem, not even thinking about the CBr4, because “Oh, it’s new, it should be fine.” It was not.

The last thing I could have possibly checked in the reaction was your “fresh” CBr4. I… I should have told you before, but I got some from Aldrich instead. It was better. Turns out, your weird CBr4 gave me some kind of dimer. It went undiagnosed for a little bit, hence the cause of my frustration, but you might want to get that checked out. Yeah, so we’re like, over.

Corey-Fuchs-ing someone else
-Chiral Jones


November 18, 2010

Applying to graduate school is part odyssey, part Sisyphean task. Presumably, sometime around mid January I can stop stressing about where I’m applying and start to relax, and stress about where I’ll be accepted. In the meantime, aside from getting ones ducks in a row with regards to recs, statements, apps, application dollars… it’s also paramount to actually figure out where to send those ducks.

Classical methods involve balancing: where I’d like to go, who I’d like to work for once I’m there, who else is there if the top research pick doesn’t work out, and where I’d actually like to live, so on, and so forth. It’s a slow-going process, to say the least. Whether you’d consider it being “picky” or being “precise”, striking this perfect balance is nigh-impossible. Hell, even Scripps doesn’t even hold up to ALL the desirable attributes (never mind the odds against actually getting accepted): Realistically, out of the power-trio of Baran, Boger, and Nicolaou, I’m not that interested in Boger’s work, and preliminarily, I think I’d only like to actually work with Baran. Nicolaou’s great and all, but the straight up factory-like nature of his work is a little off-putting. Thus, we have a violation of the “3 or more” rule for the average grad student. What with my narrowest of criteria, I’d be willing to take two, but holding out for just one professor is obviously a dicey move.

If my graduate school experience is going to involve a grueling look at numerous different pathways, with the distinct possibility of finding out that each different route is only “ok,” then I can at least try to cut some needless toil out the application process. Might I present:

Combinatorial Approach to Grad Schools for the Organic Chemist: Pick a general field of study, and tally the number of professors at each university that have any interest in that. You don’t need to get embroiled in the nitty gritty of what each one does, and don’t worry if they’re not actually doing stuff you want to, it’s just a starting point. Now, plot these values against the “rank” of the NMR facilities offered at that institution. (highest field walkup spectrometer is first, and so on. in the event of a tie, which ever one has more higher-field units wins. Eg, School 1 with 600, 500, and 400MHz walkup NMRs beats School 2 with 500, 400, 300, but loses to School 3 with 600, 500, 500, 400.) Start looking at schools along diagonal, if need be, “diversify” from “lead” schools.

Presto. Grad school applications solved!

But for real though, once the heat of application season is over, I’m curious to see if analysis like this could have better predicted the “spread” of applications of myself and friends better than we could by the “traditional” means….

Requiem for a Meme

November 16, 2010

Long, long, long overdue, but I’m finally getting around to that old “Favorite Lab Things” list. For those of you just joining us, the “favorite things” meme was, I believe, started by Chemjobber, and plenty of other chemistry blogs hopped on board. Although I’m quite late to the party, I’m generally quite late to just about everything so don’t take it personally. Here’s my thoughts on my top 10 favorite things in (around) lab.

  1. Clickable Sharpies: This one’s a no-brainer, but for labeling anything, these bad larrys are where it’s at. If you don’t have some, get some. Despite their utility, I think I’m the only one in my lab who swears by them. Apparently everyone else is still fumbling with caps…
  2. The 500 NMR: So nice. Unbelievably nice. Ridiculously nice. Even “crappy” results look good. Furthermore, otherwise “underconcentrated” samples come out with pretty decent resolution, and overconcentration is rarely an issue: I’ve been able to have enough material for a ~5-10 minute carbon, cued up a proton, and a carbon, and with no further parameter tweaking, I get nice looking spectra of each. I only hope to have the need to run a bunch of 2D spectra sometime soon, just to further abuse it’s power.
  3. Grooveshark: Imagine Pandora. Now, imagine Pandora, without the ads, without the limits on how many songs you can skip, and being able to play any song you want, when you want. Because that’s grooveshark. To be honest, the “radio” feature is way less in depth than Pandora’s (you’ll get pretty highly similar stuff, as opposed to the broader range/individual musical aspects that pandora uses to generate a radio station). However, the weak auto-radio aside, you can cue up a playlist to last all day, have the radio fill in the rest, and if you decide you don’t like a song, you never have to decide if it’s really worth it to skip it.
  4. Headphones: When at my desk, and listening to my beloved grooveshark, having headphones is key. That way I can listen to what ‘ere I please, without becoming an nuisance to the girl at the neighboring desk. Besides, she’s new, and I’d like her to think I’m as not weird as possible. My playlist of Lilly Allen, followed by Crystal Castles, followed by Wagner, followed by Manowar doesn’t really support that.
  5. The purple “Cobalt” brand gloves: Best gloves I’ve come across yet. They slide on and off of glove-liners with ease, and don’t get clammy. The exterior is nicely textured for extra grippyness. They don’t rip sometimes, immediately as you put them on. The deep bluish/purple looks totally cool. They’re no more resistant to solvent than normal gloves, but it seems that the quality control is just better over at Cobalt. Best part: they cost the same as the standard, light blue, cheapo quality nitrile gloves. Shame that we just ordered a whole bunch of the cheapie gloves – my own personal stash of cobalt gloves comes at the generosity of a friend whos lab stocks them…
  6. Glove liners: Also a no-brainer. Easily forgotten when they’re there, but quickly noticed when they’re not.
  7. Post It Notes: For the longest time, I didn’t really use post-it notes, up until about two weeks ago. I honestly don’t know what took me so long. They’re nifty and not surprisingly, pretty useful.
  8. Beer.
  9. The burrito place next door: it’s so good, and it’s open til 8. Keeps me fed and happy for hours. Also every 10th burrito is free.
  10. Antics: Chemistry is all well and good, but a lab with zero personality would suck pretty hard. Labmates who are helpful and intelligent are nice. Labmates who are helpful, intelligent, and willing to play dry ice baseball from time to time are nicer. If you find you rarely take part in antics to any extent, you’re probably one of those soul-less people that would make lab suck if it weren’t for such antics. Or, maybe you’re in industry, where I’m sure dry ice baseball is more heavily frowned upon…

honorable mention: Hood-mounted speakers. I haven’t put this into practice, but two labmates have put computer speakers inside their hoods. Seems like a good enough idea, and cheap speakers are easy enough to come by, and disposable enough (there’s probably a pair kicking around your department right now in one of those piles of discarded computer parts)Only definite downside: finding an appropriate music player that I wouldn’t mind leaving in lab/touching with gloved hands…

hello again.

November 12, 2010

Holy jeez, I’ve neglected blogging for a while. Summer was excellent, and aside from research, I spent as much time as possible outside and generally disconnected from the interwebs. You know, bein’ youthful and junk. Since then, this semester has been all kinds of busy, but despite the time crunch, I’ve actually been more inclined to blog lately.  I guess a greater understanding and appreciation for everything: physical organic class, as well as a reaction mechanism class have been the perfect yin and yang to each other. One has been churning through name reactions at a blistering pace, the other relaxed and in-depth: A one-two punch of organic fury. It could not be a better combo, with professors who I enjoy learning from.

Oh, and there’s biochem, too. Too bad biochem sucks, though.*

Otherwise, first semester of senior year is incredibly hectic, and at the current moment, I’m rather jealous of anyone not intending to go to grad school. However, the Chiral Jones North American Grad School Visitation Tour 2011 looks hopefully promising, and will totally make up for the epic undertaking that is applying to grad school. (OK, for the epic undertaking following my previous procrastination about grad school) The CJNAGSVT ’11 just might be coming to a school near you this spring, with applications currently going out to the east, west, south, and decidedly not in the midwest! (Maybe a little bit in the Midwest, but the prospect of spending 5+ years in a cornfield doesn’t strike me as incredibly appealing.) So mark you calendars.

More to come.

*Not the subject of biochem, but the specific class I’m taking. Bad prof, mediocre labs, etc. But that’s for another time. Anyway, in case I hurt the feelings of any biochemists, I’m sorry and want you to know I love you.



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