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We’re not in Kansas anymore.

Nor are we in Boston anymore, either. It’s certainly been a while, but I’m back! And after:

-a very busy summer
-packing up all of my worldly possessions into a U Haul
-driving nearly 600 miles and 10+ hours (traffic and rain were terrible!) with only a cat as my co-pilot
-leaving an old home
-establishing a new one
-beginning grad school
-beginning research (already?! I know!)
-getting to know the new boss
-all the while wondering if this will be worth the effort,

I’m here. I’m officially a grad student, and they’re paying me¹ to be here. I’ve been collecting new ‘data’ to write about, and letting previous data stew for a while. I think I’ve reached a good point of stewing, steeping, and fermenting, and I should be able to distill out what Transition States is all about.

[1a] Well, not paying much, but they are paying. We’ll see how things go, because…

[1b] I haven’t been paid yet. We get paid at the end of each month we work. Although I’ve been here since the middle of August, of course orientation didn’t count as time worked. It’s been a very long month and a half, and although the weather’s been alright, I’ve dubbed this the ‘coldest September.’

What a GREat experience!

Hey everyone!

If you were following along, you’d know that I took the GRE last monday.  It was an… interesting experience.  This was my first computer test, so it was a little refreshing to not have a moderator or be in a room with a bunch of my stressed peers taking the same test at the same time.  Instead, I was sitting in a cubicle with noise-canceling headphones concentrating on my own exam.  I found it pretty fun, actually.  I was in the minority, however, as the tension in the waiting room was so thick you could probably cut it with a knife.  Finding out my score immediately after the exam was very refreshing as well, and made for a very fun afternoon (as I didn’t have to worry about how I did – I already knew!).

The test itself was in some ways challenging.  The prompts for the writing section I found to be topical and interesting to write on – I had no lack of examples to cite, though I may have used far too many from science, and I was able to choose positions I was passionate about.  A word of advice that was passed on to me:  read up on your utopian novels (1984, The Handmaid’s Tale, and Fahrenheit 451 to name a few) because they end up being great examples to use for these essays.  I think I might have used them on both.

I can’t really comment too much on the verbal section for several reasons.   The vocabulary was very challenging, and I had a hard time with the analogies.  However, if you’re taking the GRE any time after July, 2011 the verbal section will contain no analogies or antonyms.  This is nice, as those two questions are likely the most difficult on the test.  Also, I’m not entirely sure how important it is for chemistry graduate schools for the verbal section.  But, as I am neither a graduate student or on any admissions boards, I can only speculate.

Quantitative was a dream.  I enjoy math, and it was fun to be able to get lots of points on a test by using my knowledge of arithmetic and algebra.  Really fun stuff.  The only thing I wish I did differently was time myself while working through problems.  I ended up rushing at the very end.  But it was really fun.  The fact that if you do well, the problems get harder (another thing they’re getting rid of in the new GRE) made it very exciting to get to some really tough questions in the final minutes.  Well, I enjoyed it.

Overall, I had a pretty fun time with the GRE.  I didn’t take it too seriously, and got scores in the ranges I was expecting, if even a little higher.  If I were to do it all over again, I would do a little more vocab prep for the verbal and spend some more time in the books doing some practice problems, if just to get set with the test directions.  I hope this is helpful to any intrepid undergrads hoping to take the GRE.  If any of you (undergrad, grad, postgrad, ect.) have any advice or fun GRE memories, feel free to post below!  I’m returning in a few short days with a new installment of “What is Chemical Biology” – get pumped!

How has your week been? Mine has been GREat!

Hey everyone!

Sorry for the inexcusably long absence from the blog.  Summer time is research time for me, and I’ve (finally) gotten the chance to put in the long hours that I really don’t have the time for during the semester.  Maybe this is just my undergraduate naivete speaking, but to me there’s nothing like working full time in the lab.  It’s just nice to have no distractions.  The warm weather probably helps too.  Anyway, I apologize for my lack of posting.  Organic synthesis can, as many of you know, can be very distracting.

ooOOOoo... Rapamycin!

This guy thinks about synthesis all the time too! (Credit to Sidechain and Flickr user Glockoma)

In the midst of my synthesis-induced bliss, I came to a realization.  I want to get into graduate school, and in order to get into graduate school, it is important to take the Graduate Record Exam, or GRE.  Luckily, I had signed up for the test several months ago, for July 18th.  I figured that it was probably time to go ahead and start studying.  This realization came on Monday.

If you’re sitting at home doing the math, this would mean that I have a week to study for the GRE.  It turns out that a week is more than enough time, if you budget it correctly.  I had already purchased some good GRE review books, and got to work right away.  In my experience (which should not be mistaken for an expert’s), as long as you know how the text works

, you’ll be okay.  GRE questions, much like the SAT ones, come in very specific formats that, once you can recognize the pattern, are pretty easy to figure out.

So how am I studying if I only have a week?  Pretty carefully, actually.  Here’s how I’ve been doing it:  (Disclaimer:  DON’T wait until the last week to study for the GRE.  It’s not a good idea.)

  1. Figure out the format.  I’ve found the GRE workbook series to be very helpful, as they go over test-taking strategies for each question type on the exam, and give an hour’s worth of practice for each, so you can focus on one type of question at a time.  Another good source I’ve been using is the website Syvum to be very helpful in test prep questions.  They have some pretty tough ones there, and (so far) has been good in prepping for the verbal portion.
  2. Practice, Practice, Practice.  (This is where I’m at).  Use a book, use your friends, use the internet.  I’ve been looking at practice problems while reactions have been running, and at night before bed, which I hope is enough.  I’ll let you all know how it goes, I guess.
  3. Practice Tests.  Time yourself!  Because you only get to do one question at a time, it is important that you time each and every question.  Use all the time allotted, as well.  Be sure of the answer.

I hope this is helpful for all those procrastinators out there.  I’ll check back next Monday and give you all a play-by-play of how the test went!

The rumors of my death have been greatly something something…

Why hello there,

It’s been quite a while since I’ve posted, and my apologies to all readers. I’ve been every flavor of busy, and unfortunately I’ve had less time that I’d prefer to write. In the meantime, my co-blogger has had some space to stretch his legs, and I’m very proud of his work.

Regular updates will resume shortly, with tales of large scale chemistry for large scale people, GRE gripes, nitpicking, and calls for overhaul, along with the chilling realization that in two months, I’ll be in a new city, and officially a grad student.

Oh boy!

Fun With Quantum Mechanics: Scanning Tunneling Microscopes

Note:  Check out my new avatar!  Also, Chiral and I are in the process of updating the “about this blog” and blogrolls.

Credit to the Sykes Lab of Tufts University

A research-grade low pressure/temperature STM (top) and a portable laptop-capable STM (bottom)

I know what you’re thinking:  aren’t Scanning Tunneling Microscopes (STMs) hundreds of thousands or millions of dollars?  Who has that lying around, much less in grant money?     Well… almost nobody.

STMs do indeed cost a lot of money, but can tell you a whole lot of stuff about a surface.  They’re so expensive that a simple google search doesn’t yield any results for websites which sell STMs.  Going further, I found that DME-SPM sells a whole range of STMs.  However, the prices aren’t listed (kind of like an expensive restaurant, where you only get the price once the bill comes).  Not really too affordable.

However, if you have the cash, an STM can be a fun thing to have.  After all, who doesn’t want to see things on the atomic level?  One can move hydrogen atoms around under a Pd crystal or Xenon atoms on a metal surface.  This is done using an atomically sharp tip (and the electrons attached).  Using this method, Paul Weiss managed to spell out the PSU Logo on a Pd Crystal.  (He was also part of the team that wrote out the IBM Logo in Xenon atoms).

One of the coolest things about STMs is that you can get a gigantic apparatus which has space for liquid Helium and a super vacuum and can resolve images on a atomic level OR you can get a STM that can fit on your desk, plug into a laptop, and work at STP! Well, I had the chance recently to work with one of these STMs for a Quantum Mechanics lab.

Can you see individual monolayers? Etch points? Sections of C10 SAMs?

My very own STM image of SAMs on a Au surface!

My group made the road trip through time and space (well, really just space) to the Sykes lab of Tufts University, where we had the chance to explore the world of atoms.  This was especially fun considering my lab group consisted of myself, an undergrad interested in synthetic chemstry, and another undergrad currently researching inorganic chemistry but going to business school.  If you’ve keeping score, that equals exactly zero people who would be interested in Quantum Mechanics.  Even so, we all had a blast playing with an STM.  Predictably, we didn’t get to use the giant STM that the lab has (which uses liquid He to cool and contains a very, very strong vacuum).  Instead, we had the chance to use a portable STM that hooks right up to a laptop.  Using this setup, we analyzed surface-assembled monolayers (alkanethiols of C8 and C10 length) on a gold surface.  Pictures on the side.

If you were curious, you can get one of these desktop STMs for around $9000 (so told by a friend in the Sykes lab).  It’s on my graduation wish list for sure.  Check back soon for more posts – now that school is winding down, Chiral and I will be on GlobCasino more.  Also tune in next monday for a look at peptidomimetics!

Not at #ACSAnaheim, but still having fun in lab!

Tin foil, it just makes the world go 'round


Look at all that heating tape!

I hope you’re all having fun at the ACS conference.  Don’t forget to go to Disneyland, and know that we on the east coast are all thinking fondly of you.  This morning I’m “stuck” in lab doing some exciting assays and studying for a Biological Anthropology exam (which I’m taking for the social science credit, due to the fact that I can’t handle ‘regular’ social science classes).  The week before spring break, I got the chance to do a really fun Quantum lab – examining the fluorescence spectra of Iodine gas.  If you’ve ever done this lab, you know that you have to heat an evacuated chamber up to around 170C – much, much higher than is comfortable.  But you get some pretty cool pictures out of it!  These were taken with a DROID camera, so are not of the best quality.  I hope you can forgive me, blogosphere.

Hey, I’m Sidechain!

Hello, blogosphere!

Sidechain Bob here.  Just a couple of words about myself:  I’m a junior also in my second full year of undergraduate research, and my scientific interests lie mostly in chemical biology and drug discovery.  I also moonlight as a molecular biologist.  This explains the psuedonym:  most of my life is taken up by worrying about side chains.  And apparently I’m a big fan of the Simpsons.

On this blog you’ll find my musings on biochemistry, quantum chemistry (or whatever cool class I’m taking at the time), and the graduate school admissions process.  Chiral and I hope that this will be useful to any undergrads who come across C&EN’s website and have no idea (like me) of what to do about graduate education.  Anyway, we’re both looking forward to this blog and the wild ride its sure to become- can’t wait to get started!

Stay tuned for a look at summer REU programs…


For the past week or so, perhaps you’ve noticed the curious “Transition States” link just beneath the search bar, without any content. After getting things situated, we’re finally ready to open up shop. So, welcome to Transition States!

In general, our focus here will be about the transition from undergrad researcher to grad student, and all that goes along with it. Maybe one day from grad student to post doc and beyond, but let’s not get ahead of ourselves. We hope to document the process: between applications, campus visits, talking with grad students, post docs, and professors, it’s all new territory to us, to the point we’d like to write about it, and share it. It’s our hope to generate response, and advice for our own situations, and more importantly, we hope to develop a detailed account of the whole endeavor, with tips, tricks, and questions we wish we would have asked, to help future batches of up-and-comers.

Obviously, life as an undergrad researcher extends beyond grad school applications, and we’ll be covering those aspects, too, including life in lab, classes, ‘the literature,’ the future job market, ethics, trends, or just general musings. It’s all stuff we (still) find exciting enough to write about it, even after working all day around it; we want to present it in a way that even those who also work in chemistry will still find it interesting to read.

C&EN has been gracious enough to ask us to write for them, and we’re beyond excited to oblige.

Now, that the official ‘mission statement’ is out of the way, who’s the “we?”

Well, I go by Chiral Jones, and my co-blogger is Sidechain Bob (who will be making his introduction shortly). Best pseudonyms ever, right? Anyway, I’m a senior undergrad in my second full year of research, and I’ve been blogging for over a year at Chiral Jones. Primarily, I’m interested in total synthesis, but I also like to dabble in diversity-oriented work. Luckily, I get to do both right now, and I hope to continue this kind of work in grad school.

Check back soon for full “About” sections, and the introduction of Sidechain Bob!