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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!

Water, Wine, Milk or Beer? Perhaps none of the above.


Don't drink anything in this demo, or you'll end up sleeping, like this cute baby! (flickr user sat spade)

Hello everyone!

It’s time for another edition of Sidechain’s favorite chem demos.  The one I’ll be describing today holds a place near and dear to my heart.  When I was a young high schooler (a shorter polypeptide… get it?), my high school chem teacher showed this to our class.  She had a glass of what looked like water.  She poured it into a wine goblet, and the water turned to wine (cool, right!).  She then poured the ‘wine’ into another glass, where it became ‘milk’, which when poured into the final glass turned into ‘beer.’  When I first saw this, I really thought it was magic.  It turns out that the chemical principles are pretty simple!  All the student really needs to understand is acid-base chemistry, indicators, and precipitates.  Anyway, here’s what you’ll need:

  • Glass #1:  0.1 M Sodium Carbonate (NaHCO3).  What I did was make 100mL of a stock solution and add around 50mL to a clear water glass.
  • Glass/Goblet #2:  A few drops of phenophtalein in the bottom of a long-necked wine glass.  I usually use a plastic one and put some tape on the bottom to cover the indicator solution.
  • Glass #3:  5mL 1.0M BaCl in the bottom of a clear glass with some tape on the bottom.
  • Glass #4:  5mL 12M HCl and 5mL of bromothymol blue indicator, at the bottom of a pint glass/plastic clear solo cup

So if you can’t guess, the science behind this is pretty simple.

  • Sodium Carbonate is a basic solution that looks like water
  • Adding phenothalein will make the solution purple, and look like wine
  • Adding Barium ions will precipitate out a suspension of Ba(OH)2, which will look like an opaque white liquid (milk!)
  • In the last cup, the concentrated acid will (a) acidify the remaining base, eliminating the Ba(OH) (b) result in the evolution of CO2 gas and (c) make a beer-like color with the indicator

If you've done everything correct, it should look like this!

This demonstration is pretty easy to explain to a group of first-year chemists, and is a great application of the skills they have already learned!  Just remember not to drink any of these liquids, especially the “beer” (no matter how tempting it may be!)

How do Elephants Brush Their Teeth? Ask a chemist.

Look! My hand made a cameo!

Note: Do not use this to brush your teeth.

Outreach is becoming one of the most important aspects of undergraduate, graduate, and professional chemistry. Reaching out to kids at a young age and helping them get in to chemistry is a priority.  This is also one of the main focuses of the ACS’s International Year of Chemistry (IYC) 2011.

I remember in my first chemistry class when my teacher showed us the classic demo where she turned water to wine, then wine to milk, then the milk to beer. To me and my classmates, it seemed like magic.  It was pretty much the coolest thing since, well, the power rangers.  Or the Offspring.  Anyway, we now have a much different perspective.  These chemistry demonstrations utilize relatively simple chemistry to produce really fun and exciting results.  Does that mean that all the magic is gone?  I don’t think so.  A few weeks ago, I had the chance to do some of these demos to a crowded audience of elementary school kids.  Needless to say, I had a blast.  The kids did too.  Over the next couple weeks, I’m going to be profiling a couple of the demos I did, and how to do them for your friends, neighbors, or chemistry classes.  We all know that chemistry is fun:  other people just need some help remembering.

Today, I’m profiling one of my favorites:  The elephant’s toothpaste.  Here’s how it’s done:

What you need:

  1. One (1) Graduated cylinder, as large as you can find it.  Really, the bigger the better.  I used a 2.o L guy I found lying around in my lab,  but I imagine that doing this with a 4 L or 8 L would make some kid’s day.
  2. 150 mL of dish soap.  Really doesn’t matter what kind
  3. 150 mL 30% Hydrogen Peroxide.  This is dangerous – it’s an irritant and will hurt if you get it on you.  Wear gloves, a lab coat, and goggles.
  4. Food coloring (be very generous)
  5. ~5mL of saturated KI.  I do this by putting a lot of KI into a 50mL falcon tube and adding water.  Then I shake until I’ve dissolved all I can, and add 5mL

This is how it’s done:

  • Put the peroxide, soap, and food coloring (again, be generous)
  • Add some KI
  • Watch it happen

This demo is really fun.  Just don’t forget to lay down some newspaper so cleanup is a easier.  Also, a note about safety:  because of the peroxide, don’t be staring down the tube as you pour the KI in.  First, you’ll get burned by peroxide, then you’ll get majorly stained by KI.  Neither of these things will be enjoyable, I promise.  If you’re prepared correctly and introduced the demo in a fun and interesting way, this should go off great and be a highlight of your chemistry show!  Enjoy!


P.S:  The recipe above is optimized for a 2 L graduated cylinder.  If you want to use bigger or smaller, scale up or down respectively.

What is Chemical Biology? Perhaps it’s Peptidomimetics

Disclaimer: I am not an expert. In fact, this series of blog posts is as informative  to me as it is to you. Probabl

y even more so. My views and the views of people interviewed for this blog do not, in fact, reflect what exactly “chemical biology” is, but only a snapshot.  Please direct any comments or suggestions below!

This doesn't seem like Chemical Biology to me...

No, not THAT kind of mimicry! (Credit to Flickr user christopherasmith58102)

Peptidomimetics is something I think about all the time.  So, I decided it would be a pretty good starting point for this series, especially considering that right now it’s finals week and I barely have enough time to be running a synthesis, much less studying for finals.  But that’s beside the point, because I’m very excited to learn more about peptidomimetics (and who needs to study for finals when you can do research instead, am I right?)!

What is peptidomimetics?   From what I’ve seen, it’s pretty much exactly how it sounds.  The essential goal of the field is to take a peptide of interest, which usually means that it’s bioactive or important in some way physiologically, and synthesize and test organic mimics of it to fulfill a number of different goals.  So if we have bioactive peptides why not just use them as drugs?  Because peptides have some inherent problems to their usage that peptidomimetics seeks to solve:

  1. Protease Resistance/Serum Stability:  One of the main reasons that peptide drugs (mainly mimics of allosteric regulators) have been largely unsuccessful.  When a peptide is taken up by the body, either intravenously or orally, the body has a suite of enzymes (such as proteases and E3-Ubiquitin Ligases) which degrade small peptides and foreign ingested proteins.  While these processes are important in metabolism and immune function, we would rather our peptides not be degraded by the body.  One of the main goals of peptidomimetics is to avoid the body’s natural defense against peptides and to get at biological targets.
  2. Membrane permeability:  Most biological targets are located inside cells.  In order to get your favorite peptide into a cell, you need to cover it with lipophilic groups (or else somehow reduce the charge) to help it squeegee its way (technical term) into the cell.  Small molecules, being generally much smaller, rigid, and lipophilic, rarely have this problem.  Because peptides routinely break Lipinski’s Rule of Five for drug-likeness, special provisions must be taken in synthesis and design.
  3. Conformational Restriction:  Very often, peptides are considered “floppy.”  They require an optimal “active conformation” to bind to or inhibit other enzymes.  Very often, peptidomimetics seeks to modify peptides by constraining them into a more stable and active conformation, thus reducing the entropic cost of a peptide’s action.
A peptido-mimeticist's dream come true

Beta-Peptides and Peptoids have structures that make that protease resistant

So what kind of research do people in peptidomimetics do?  This kind of research is widely diverse but can be divided into a few categories.  Beta peptides are peptides which have the amine group bound to the beta carbon instead of the alpha.  This allows for (a) more membrane permeability and (b) greater protease resistance.  Already, beta-peptides are being researched as antimicrobials, and have been shown to readily form alpha-helices.  Peptides are another kind of amino acid mimic that are widely used.  Instead of having the R group on the alpha carbon, they have it on the amine group.  They’re also called N-substituted glycines.  Again, you see here greater protease resistance because proteases do not recognize these amino acid mimics.  In addition, the lack of amide protons and achirality of the alpha carbon gives rise to greater membrane permeability.  However, the pretty secondary structures you can get with beta-peptides are impossible to achieve with peptoids.  You can read more about beta peptides and peptoids and their antimicrobial potential in this great review from Chemical Biology and Drug Design.  For more reading, you can check out this cool review on incorporating beta-peptides and peptoids into the same chains from ChemBioChem.  Imagine how much trouble that would be without solid phase peptide synthesis.

Credit to the University of Maine MechE website

Gramicidin is a cyclic peptide that forms pores in bacterial cell membranes

Another branch of peptidomimetics involves regular, plain-old amino acids.  Very often, it is possible to restrict the conformation of a peptide to its active conformation by cyclizing it, especially if the active conformation of the peptide includes a loop or turn.    This accomplishes what I was talking about earlier:  paying the entropic barrier up front, and locking a peptide into a smaller series of conformational possibilities.  Cyclic peptides are also more protease-resistant due to a restricted conformation, and are more membrane permeable, because of (a) the smaller size and (b) the elimination of the N and C termini, making the molecule overall more nonpolar.  The European Journal of Organic Chemistry has another good review on peptidomimetics that you can check out at your leisure.

This sounds a whole lot like medicinal chemistry to me, so far.  So why put it into the large umbrella that is Chemical Biology?  I would argue that peptidomimetics belongs in Chemical Biology because (a) peptides are biological molecules, and bioactive molecules are the focus of Chemical Biology and (b) these peptidomimetic molecules can be modeled in vivo and in vitro and (c) the field incorporates aspects of organic chemistry, classic biochemistry, and some cell biology, and this duality of research (to me) characterizes Chemical Biology.

I hope this was as helpful to you as it was to me.  I think peptidomimetics is pretty cool, and wouldn’t mind going into it in grad school.  This review is really small in scope and I encourage you to read the reviews that I’ve linked to.  What would you like to see next Monday?  Right now I’m thinking about Native Chemical Ligation, but I could be persuaded otherwise.  Feel free to post in the comments below!

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!

What is Chemical Biology? No… seriously.

Disclaimer: I am not an expert. In fact, this series of blog posts is as informative  to me as it is to you. Probably even more so. My views and the views of people interviewed for this blog do not, in fact, reflect what exactly “chemical biology” is, but only a snapshot.  Please direct any comments or suggestions below!

NOT Chemical Biology

Maybe one day, research like this could be chemical biology

The next several months are pretty big for me.  Soon, I’ll be taking the GRE and deciding where to go for my PhD, but I honestly have no idea where I want to study.  Because of my current research and classes I’ve taken, I know that Chemical Biology is the field for me.  The only issue is, when asked recently by friends, family, and random strangers  what Chemical Biology really is, I’m kind of at a loss.

For me, Chemical Biology means probing biological systems with chemical agents.  Recently, I’ve had a chance to talk to a couple PhD candidates (including our very own  Christine Herman) in Chemical Biology, and they all had varied definitions.  Christine’s and my research could not be more different; she does research in bioassays, and I do a lot of work in peptidomimetics and drug discovery.  Her research is in the analytical department, and mine in the organic.  It surprised me to learn that she classified herself as a chemical biologist as well.  This led me to a couple conclusions:

Chemical Biology is less of a specific field but more of a classification encompassing a wide range of different kinds of research.  Things that would have once been considered organic chemistry (such as what I do), analytical chemistry (what Christine does), or even physical chemistry (see some later posts!) are now under the great big umbrella that is Chemical Biology.  So, what’s a young blogger to do?  Over the next several months, I’m going to examine different areas of research in Chemical Biology, one by one.  I’m planning on getting in touch with some of the leaders in field.  Hopefully, this will be fun for everyone, and help me decide where I want to do my PhD.

Next Monday tune in for a subject near and dear to my heart:  peptidomimetics!  Any suggestions on who to talk to?  Post below!

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.

Spring Break musings – chemistry in the old days

Hello all!

Sorry for the sparse updates over the past week and half or so.  It’s been spring break in college land, and for undergrads that means vacation.  I’m currently in the West Palm Beach airport in sunny FL, about to head back to the snow-and-windswept plains of the northeast (where I call my home).  While here, I had the pleasure of visiting with my girlfriend and grandparents and being treated to far too many gigantic meals.  Today at lunch I was eating with my grandmother and her friend, and learned that she was once a high-school chemistry teacher.  She told me all sorts of stories (including one of her in graduate school, when she mouth-pipetted snake venom!), and one of my favorites is below.  Feel free to share your favorites!

Once upon a time, in Illinois, my friend was taking her class (from Minn.) to a science fair.  They were working on irradiated chickens, and kept them and the irradiated eggs in the trunk of the car.  Of course, in order to keep the specimens alive, they needed to open the trunk every once and a while to give the poor guys some air.  In a small town in Illinois, the chickens got loose and my poor friend had to chase these irradiated (maybe radioactive?) chickens through the streets.

Why does this story speak to me?  Well, first, I find it absolutely hilarious – a scientist chasing her specimens through the streets of a small town just would not happen.  (Also, does anybody use chickens as a model system anymore)?  Second, we don’t even have what were called “Becquerel Chemicals” in high schools anymore, much less do radiation experiments on chickens.  It’s just a different day today.  Well anyway, in honor of Friday, spring break, and the good old times, feel free to share your favorite old time chemistry story in the space below – thanks!