Wading in Vs. Jumping in the Deepend

As I have been toiling away in the lab day in and day out and learning so much that I didn’t even know I didn’t know, it is hard to find the time to reflect on what I have been learning outside of the numerous papers and reviews I read and outside of my data. This summer I have had the pleasure of working on two very, very different projects. My main project is the organic synthesis of small molecules that contain key functional groups from the adhesive proteins of marine mussels in order to understand their function on the native proteins. This project entails what most people think of when they think of a chemist. Hunching over a fume hood working with expensive equipment and toxic chemicals and most of the time mixing together liquids and solids and waiting for things to happen. My second project is studying the shape of small iron binding molecules called siderophores to better understand the structural basis of how they bind iron. This project mostly involves staring at a computer, running simulations and models, and trying to figure out how to get your model out of a fourth order saddle point in the energy surface it just seems to love to find.

It really shows that research even on very related topics can be very different in methods, but that’s not the main difference that has made this such a rewarding experience for me. The difference that I would like to talk about is simply the way I was given the projects.

For the organic synthesis project I have been working with my amazing mentor, Greg Maier. The first few weeks I was instructed and trained in how to carry out the procedures in the lab and now we work daily side-by-side to try and synthesis the molecules, sharing ideas and thoughts on how to best carry out the synthesis.

The computational project spawned from a set of conversations with my outstanding P,I Dr. Alison Butler, which lead me into jumping into a very challenging pool of research with only having played in the kiddy pool before (jumping from having read like 2 papers on siderophores and taking a class that involved making very basic calculations on very small molecules to working on computational siderophore chemistry). An additional effect of how this project got started is that I am the only one in my lab working on this project and as a result have had to design the experiments and try to answer the surprisingly complicated question of how can this be proven either way. Finally having the challenge of trying to distill what parts of the extensive literature in the fields of siderophores and computational chemistry are important, relevant, and that I actually have time to read.

This is not to say that I didn’t have a lot of help. From almost daily discussions with Dr. Butler to talking to experts in computational chemistry and molecular modeling around campus I have received amazing help from around campus and the helpfulness of the faculty, staff, postdocs, and grad students and their willingness to take time out of their hectic days to help with my research problems continues to amaze me.

It is hard to say from which project I have learned the most.  The synthesis project has greatly expanded my understanding of organic synthesis and how to work in the lab in general in addition to helping me better understand how to work as part of a team on a complex research problem. From the computational project I learned how to approach leading my own project, how to adsorb a lot of information very fast and I became much better at networking and getting help from experts who I have never met before.

Finally from both projects I learned the central tenet of research and learning in general, failure. Both projects have had times when nothing was working even things you had done before and when you go home at the end of the day you question why you are even bothering to study that topic, why you should even get out of bed the next day to go to the lab because nothing is going to work. But alas I stated the central tenet incorrectly or more of incompletely it really is ‘persistence through failure to learn’ getting back on the horse and learning from your failures because failures sometimes lead to the most interesting conclusions. If you are an experienced researcher or just now considering whether to try research, the biggest thing you have know is YOU WILL FAIL, and that is good as long as you keep on trying.

Day to day of summer research

Many of you may be wondering what the day to day life is like for a student doing research over the summer. While I can’t give you a picture into what every interns days are like I can give you a picture into what my research experience has been like and what my day to day is like during the week.

My mornings start off at an early 5:30 most days and are started with a workout, light breakfast and shower. I walk to work and try to be in my office by 8:00am (I know I’m crazy getting to work that early). My mornings start with reading scientific papers (so many papers!!! so much information!!!) and carrying out some computational chemistry and molecular modeling on either my laptop or via remote access to the Knot Computer Cluster of the Center for Scientific Computing on campus. At 9:30 or so I set up a longer computation then head into the wet lab with my mentor to purify the products of the reactions that we left running overnight. For the purifications we pretty much use the same techniques that you learn in ochem lab classes such as: extractions, filtration, rotovaps, and (shudder in fear!!!) flash columns. The purifications normally take a couple of hours. Then we take the samples upstairs to the mass spectrometry lab to analyze the products and answer the big question, did we make what we tried to? The answer to that question varies everyday. Today we had 3 reactions run well and 1 that ran…decently. After finding out if the reactions worked we set up new reactions to run overnight, they may be continuations of the synthesis or scale ups of the reactions we ran the previous night. We normally try to set up 4 reactions and are in the wet lab until 3:50 to 5. After finishing in the wet lab I go back to my office and check on the computations I left running and analyze the results if I have any. I head back home at around 5:30 but my day of research is normally far from over.

After grabbing dinner and going for a quick run, I’m back to reading papers on anything from how to remove a trityl protecting group from histidine to what is the best basis set to for carrying out calculations on an iron-ligand system and doing computations on my laptop. Then I take a break, watch some TV then crash for the night for it all to begin again the next day.  Naturally this schedule varies with my internship’s scheduled meetings and events, but you get the picture.

One thing that will surprise you if you start doing research is how hard it is to not do research. Once you have been exposed to the questions that dig into your brain about your project it is difficult to not think about them. Whether you’re showering, hanging out with friends, or binge watching Friends, your thoughts drift to wondering about the questions that your research has presented you with and wondering what if I try this? What will happen?  It’s a fun adventurous time to spend your summer doing research and one that you should try.