Alexandra's Blog: Organic Chemistry at UCD YSP

Alexandra's Blog: Organic Chemistry at UCD YSP

7/14/16

Hey guys! I'm Alexandra H. Li, a rising senior, and I'm spending 6 weeks at UC Davis at the Young Scholars Program, website here & facebook page here. The program accepts 40 students who each get their individual lab projects and professors, but we also have a lecture series (and exam) and field trips every Saturday. Even though the program mainly focuses on the agricultural and natural sciences, I received an organic chemistry project based on my application.

My main goal is to synthesize and purify 2,3,4,5,6-pentafluorobenzene diazonium tetrafluoroborate so it can be tested whether it can be a p-type dopant. Although it sounds pretty complicated, it's not a very complex reaction.

This was the general reaction I did in late June - since then, I've changed the solvent and used the tetrafluoroboric acid in an ether complex, but it's generally the same. Looking at the cation of the product, the large amount of fluorine make it very electrophilic, so it may be able to withdraw an electron from an electron rich organic polymer (basically a long chain of molecules, like graphene). There would be one "hole" in a sea of electrons called a defect, and this hole moves along the polymer, conducting an electric current. A dopant is an agent that allows another substance to conduct an electric current, and a p-type dopant is one that creates a hole in an electron rich substance. One thing about my product, the diazonium salt, is that its electrophilic nature makes it highly reactive to air and water, so Schlenk techniques must be used:

The apparatus in the middle is a Schlenk line, which allows all reactions to be carried out under either vacuum or Argon, so the sample won't react with air or water. (It's a lot harder than you think to not let your reaction touch air or water at all).

edit: My compound is significant because it's expected to be a more efficient, soluble, and stable p-dopant than any other p-type dopant diazonium salt. One salt (shorted to F4TCNQ b/c those orgo compounds just have such long names) is well known to be a standard dopant, but since it is insoluble in organic solvents, it limits its doping capacity. Our only worry is that pentafluorobenzene diazonium tetrafluoroborate may decompose before its doping capabilities could be tested, and then it wouldn't really be a useful dopant.

That's a general overview of my project! I'll try to talk more about different lab equipment and techniques or other aspects of YSP later. Until next time!

-Alexandra

7/17/16

Hey everyone,

I've just finished 4 weeks at YSP and it's hard to believe that it's 2/3 over! I'll go over my typical days here.

Weekdays (Lecture Days)

6:45 am - Wake up

7:00 am - Go for a run / shower

8:00 am - Head to Dining Commons for breakfast

8:20 am - Bike to lecture hall (sadly everyone goes early so they can get a good seat)

9-11:30 am - Lecture

Noon - Lunch

1-5:30 pm - Lab

5:45 pm - Dinner

6:00 pm-midnight/1 am: Study for the exam, prepare for lab, complete assignments, head downtown, etc.)

^Time after dinner is supposedly "free time," or "time to yourself," but after reading + understanding the articles in preparation for the next morning's lecture and whatever lab work assigned, in addition to trying to study for the exam, the free time I had was definitely less than 6 hours a day. The program expects us to be prepared for lectures and spend our energies into lab, so no one really takes all the time after dinner as free time, although theoretically we could.

Weekdays (Full lab days)

7:30 - Wake up

7:50 am - Breakfast

9am-5pm - Lab (with lunch in between)

~5:30pm - dinner

6:00 pm-midnight/1 am: Exercise, prepare for lab, complete assignments, head downtown, etc.

This is really rough in terms of time because we really don't have a set schedule. Individual lab professors/mentors tell YSPers when to come in, so I know a few people who have lab from 8 am-4pm or even 2pm-10 pm. Even meals aren't at a set time; we could get "free" meals at the Dining Commons included with our tuition, or go out to eat ourselves whenever and pay. I also used to try to run every day in the morning when we had lecture, but I ended up being pretty tired and switched to only a few times a week, sometimes at night. I also had a lot less free time in the beginning of YSP when we were just starting lab and I had to do a lot of readings and safety fundamentals in order to familiarize myself with the lab and the specific project. We were also expected to read (scholarly) articles regarding the researchers work that would be explained at lecture the next day.

The program gives us a lot of freedom - how you spend you spend your time other than lab is really up to you. However, with the warning of "the hardest exam you'll ever take in your life" looming in my mind (and the fact that the program gives 5 college credits only if you pass), I tried my best to balance studying, getting to know people, exercise, and sleep. Things have been a little more relaxed since the exam passed, but now we're starting to get on the grind for the final paper and symposium presentations.

On Thursdays, I either get dinner with a lab mate or bike back to the Dining Commons for an early dinner then go back to the Chem building for our research group meeting (6-8:30pm). My individual lab room is just me and my graduate student, but my professor has a few post docs, masters, undergrads, one other high school student, and a man who's done with his PhD and postdoc but just works under him. All these people are in scattered labs on the same floor. During the group meetings, each person prepares a transparency of the reactions they did in the past week, and the results. Together, the professor and the senior members of the group try to brainstorm how to best proceed next, and other various suggestions as to how to improve the reaction/yield/etc. It can get a little dull sitting in the same room for that long, but it really is a valuable experience to hear what other research is going underneath my professor and try to learn the mechanisms behind it. (Even though I do not yet understand all of organic chemistry, although I have a textbook that I try to study from frequently.) Here's a picture of the transparency I prepared for the most recent group meeting:

On Saturdays we have field trips, and although we have to wake up early, it's really worth the experience. The bus rides are always at least 2.5 hours, but they seem to pass by pretty quickly with sleep and conversations and the occasional sing-along. We always learn something new at our field trips too - just this weekend we went on a research vessel at Lake Tahoe and a man there spoke about his career and the significance of his research.

Our Sundays are our free days, and I usually catch up on sleep the morning of, and try to get in a balance of work and spending time with people. Those are also the days we have the opportunity to go to the pool or watch a movie downtown, or spend a good amount of time at the ARC (activities and recreation center, UC Davis's amazing gym).

Overall, YSP is more than just research. Lab work takes up a majority of our time and is the main focus of the program, but we do get our freedoms and I'd highly recommend applying to a program as opposed to just doing research! I can see myself maintaining these friendships for a really long time, and it really has been one of my greatest experiences I've had.

Well I should probably get started on that final paper rough draft that's due in a few days, so I'll speak more about my experience next time!

-Alexandra

8/5/16, 8/6/16

Whoops guys, YSP is over and I kind of hit a post camp depression since it ended. I'll summarize what I've done and learned during the program though!

Since my last post, I got hit pretty hard with work as I had to finish my draft and eventually my final paper. I also had to prepare for a 10-12 minute presentation and 3-5 minute question session in front of the program, all while trying to get results for my project. Nonetheless, I still tried to balance all this work with spending some last times with the wonderful people there and exercising (did not really get that much sleep though).

Lab:

Like I said last time, I modified some materials in my procedure to synthesize the diazonium salt, which worked pretty well. After carrying out the reaction at -41 degrees Celsius (an acetonitrile and dry ice cooling bath), it was left to stir for an hour to return to room temperature (which is usually when I went to eat lunch). What remained was a white precipitate in a yellow solution. The next step was to decant (suck off the top) the solution off the product and "wash" it with anhydrous diethyl ether.

left flask: process of decanting - 2nd wash of diethyl ether; right flask: dry diethyl ether (yes, the flask had to be evacuated and filled with argon)

The final product in powder form - the whiter, the less decomposed.

Trying to keep the compound as pure as it could be was a big challenge. Working under Schlenk techniques was quite difficult, because if the tube slipped off the manifold and just a little bit of air got into the flask, the diazonium salt would immediately change color and decompose. After the product was decanted, washed, and put under high vacuum, NMR scans were taken of the product. This was also pretty difficult, because a small septum had to be put on an NMR tube, then evacuated with air and filled with argon. Then, the flask would be exposed to air to allow for a spatula to take out a small portion of the sample, to be mixed with anhydrous deuterated acetonitrile in a test tube, then extracted with a syringe and put into the NMR tube. The process had to be done quickly, and there were a lot of little details that could have contaminated the sample. Since the first day of lab, I learned the "3 times rule," in which you make sure your materials are under argon by evacuating it least three times. This involved putting the flasks that were used under vacuum then argon, then vacuum, then argon, etc. Also, all needles and syringes were filled with argon at least three times before use in extracting starting material.

I took a lot of NMR scans..

Also, I spent a lot of my time in the lab crushing dry ice, whether it before the vacuum trap first thing in the morning (it had to be filled with dry ice and acetonitrile prior to the vacuum being turned on), the rotovap, or the cooling baths.

Example of a pretty makeshift acetonitrile and dry ice cooling bath.

The main equipment I used and familiarized myself with was the NMR instrument, but I also learned to use the IR machine, TLC, and rotovap (and the basic chemistry/physics behind how they worked).

The software we used to take and process the NMR scan.

The process of shimming. The NMR instrument used in this photo was only 300 MHz, so shimming wasn't actually too arduous.

NMR spectroscopy uses the magnetic properties of elements, in order to analyze the contents of a sample. There are whole classes on certain aspects of NMR, but I just got a brief understanding through my graduate student and the textbook. By the end, I had a much better understanding of how to analyze an NMR spectra than the workings of how the spectra was obtained by the machine.

Example of a Fluorine scan of the product.

A slide from my final presentation about NMR analysis.

After NMR scans were taken of the white powder, analysis showed that it wasn't completely pure. Some impurities from the fluoroboric acid transferred into the final sample, as well as some starting material and solvent used. Also, the powder wasn't too stable.

Some of the samples were left under argon and sealed, yet it still decomposed visibly after a few days.

So, the next step was purification through recrystalization, done through vapor diffusion. The product is put into a solvent it's soluble in and is surrounded by an antisolvent, one that it is insoluble in. Over time, the vapors diffuse and the solvent that the product is in slowly changes in polarity and the sample slowly becomes insoluble in it, thus forming crystals.

Vapor diffusion! Realizes that I had to parafilm those two flasks in the back after I took this picture..

Crystal formation! Still don't know why it's not white, but it definitely wasn't decomposed.

After the compound crystallized and its contents were confirmed through NMR, IR, and x-ray crystal analysis, its decomposition chemistry and stability were studied. I discovered it decomposed thermally, when exposed to air or water, and tends to react on the Fluorine in the para- position of the aromatic.

Overall, I got a pretty good idea of what working in a lab all day was like through YSP. I'm grateful that I was able to do a lot of hands-on work in a chemistry lab, rather than some of the other students' projects which were just programming at a computer. There were some pretty fascinating subjects that didn't require a lab at all, and one group of three mainly worked in our dorms on exploring Tyrosine Sulfation. However, I cannot imagine pursuing a day-to-day job that is overwhelmingly computer work. On the other hand, standing up and carrying out reactions for the whole day was pretty tiring, and it could get dull, as there wasn't much communication in the lab once I knew what I was doing, and was repeating my reaction. My lab room also was just my grad student and me, and I was actually left alone quite a few times. In the end, I'm thankful to have gotten the opportunity to work under the guidance of my professor and the supervision of my graduate student. Working in a synthetic chemistry lab was just really cool and I could see the potential applications for the compound I was making. Though the lab group meetings basically had me at the lab from 9am to 8:30 pm once a week, I really admired and was in awe of the sort of work all the people were doing in organic chemistry, even the other high school student in my lab. I even learned some basics of organic chemistry through the textbook my professor gave me and even some hours of being tutored by my graduate student over the course of 6 weeks.

The chemistry building! aka my second home

The final vials of all the crystallized versions of the pentafluoro diazonium salt, under argon and parafilmed in the fridge.

Our mostly-clean lab from the back.

The middle corridor.

Desk space - I got the window seat! At the desk, I read journal articles, downloaded and used software such as Chem Draw and MestReNova, and worked on my paper.

The washing area - All flasks, etc. had to be washed with acetone to get off any organic residue, then tap water, then de-ionized water, then acetone again for fast drying. (I voluntarily chose to do this often because my graduate student was nice enough to be my mentor and answer all my questions)

The mechanism of my reaction, as written by my professor at a group meeting. Ar represents aromatic, not Argon.

Not lab:

The program had a goal to simulate what college life was like, and it did a pretty good job of that (except we did have building and room curfew). YSP is a special group of people, and I think the counselors really chose not only hardworking and accomplished, but genuine 16 or 17 year olds. I felt like I could have had quality conversations with pretty much anyone there. We ate every meal together at the dining commons, biked together downtown or to lab, and explored different places on the field trips together. Most of the people were from California, and I learned a lot about the culture there (the slang especially). By the end, we all knew a ton about each other and had countless inside jokes. It was definitely the people that I met, the friends and memories I made that'll stick with me the most from this program.

The beach next to Bodega Bay Marine Lab

San Francisco

Watching the sun rise after the all nighter of the last night

There's a lot of pictures on the facebook page too!!

I guess that's about it! I apologize for the huge post.

Message me if you want to know anything else about the program and my experience, I also have my final (supposedly journal quality) paper which is a lot more formal and detailed than this post, a link to my presentation, and google slides. I'm also required to do a presentation on my experience and my project at school, so if you go to MHS feel free to attend it sometime this fall!

-Alexandra