Chemistry: Lost in Translation (sort of)

I’m Jason Hoshikawa, a 2nd year PhD student in the Kitagawa Lab at Kyoto University in Kyoto, Japan.My main area of focus is polymer synthesis and heterogenous catalysis using porous coordination polymers (PCPs).

The thing about working in the sciences (and maybe the arts too) is that we generally work in a multi-cultural environment. During my undergrad and Masters in the US, I was the native surrounded by foreign students. It was a wonderful experience. Many of the members of that group were from India, specifically from around the Hyderabad area. This turned out nicely for me because Indian food is my favorite food. When I entered my first research lab as an undergrad, I was assigned to work with a woman that makes the most amazing food. She quickly learned the key to motivating me to work hard in the lab. If I worked late enough, she would bring me dinner. I miss those dinners more than you can imagine.

Kyoto University's clocktower. - Image Courtesy of Wikipedia.

Kyoto University’s clock tower – Image Courtesy of Wikipedia.

But, now, I live in Japan where I am the foreign student surrounded by natives. Aside from learning about chemistry, I’ve learned a lot about myself. This is not the first time I’ve lived in Japan, but this time it’s very different from my previous experiences.

More than the simple difference in culture between the US and Japan, the other bit of context that may be important is that the Chemistry Department at my previous university is relatively small compared to our department at Kyoto University. The change in environment was quite significant. Going from a department where everyone basically knows everyone else to a department where there are simply too many people to know hardly anyone outside one’s own research group was rather shocking.

In my research group, all of the students are assigned various jobs. Most students are assigned to manage an instrument or two, and some students, like myself, are assigned to administrative roles. I have two administrative roles, actually. Firstly, I am the lab manager. I’m responsible for the general day-to-day operation of the lab (i.e., the room where experiments are performed). I purchase all the expendables (e.g., gloves, vials, pipette tips, glassware, weigh paper, etc). In a separate (but related) administrative role, I’m also responsible for buying all of the solvents (both regular and deuterated) and common reagents (acids, bases, metal salts, etc). Basically, I buy everything except specific reagents that only one or two people would use, and instrument-specific expendables.

An average day

In our lab, we work Monday through Saturday, and the layout of my day is basically the same, unless there is something special that requires me to leave early.

My alarm is set for 07:00. The actual time that I wake up varies seasonally. I don’t have blackout curtains in my room, and Japan doesn’t observe summer time (which I’m happy about), so right now, the sun rises at around 05:00. During the summer, I wake up often before my alarm, but during the winter, I can usually sleep until my alarm wakes me up.

I like to leave my apartment at 08:45 so that I can get to the bus stop early enough to get a seat on the 09:00 bus. The trip to campus takes about 10 mins. If you’d like to see the area around where I live on the bus ride to campus, watch the video below.

I take breakfast at the bakery on campus. They have a lovely breakfast set for Â¥270, and I usually add to that a donut (Â¥151). While I eat breakfast, I like to look at twitter, reddit or Instagram, while listening to a podcast. My work day starts between 09:30 and 10:00. Everyone usually gets in during this time, and we generally think of 10:00 as the start of our workday. The first work period is 10:00 to 12:30. During this time I like to look over new ASAPs in my RSS reader, and then try to write for an hour, or look up papers. Then at 12:30 we have an hour for lunch. My hearing is not so good, so I tend to eat lunch by myself in the office rather than going to the cafeteria with everyone else. I used to go, but it’s just so noisy that I can’t really hear anyone. So, I sit at my desk and watch the PBS Newshour (@pbsnewshour) on YouTube.

After lunch is the second work period that runs from about 13:30 to 19:30. During this block of time, I like to do heavy synthetic work. I try to start reactions, end reactions, and do work up during this period. If at all possible, I try to do all synthesis related work during that six hours.

Dinner from 19:30 to 20:00. After dinner, I try to focus mainly on characterization. After 20:00, the number of students starts to decrease, and it’s easier to make reservations on the instruments. I can use them in peace and quiet.

I generally go home on one of the two busses in the 22:00-hour. Once home, I decompress by taking a shower and reading until I fall asleep. With that ideal in mind, here is reality…

An average week

Saturday

I like to think of my week starting on a Saturday. The reason is because that it’s the last day of the research week. I go through and take inventory of the lab in order to figure out what I need to order. It’s not as involved as it may sound. It usually occupies the first work period. I have lists of everything so I can check through quickly, and for most things, I can stand in one spot and just look around the room while marking off my list. The solvents are easy too. I open the cabinet and count the bottles remaining.

I place the orders by writing them into the order notebooks for each of the suppliers. In Japan, representatives from manufactures and suppliers come around several times a day to collect the orders, and then they deliver them directly. Each lab manages its own finances, so as long as one isn’t buying and NMR spectrometer, there is almost no red tape.

Figure 1

Figure 1

On this particular day, I spent most of it cleaning as my workbench was a complete disaster (Figure 1). Also, I didn’t want to start any reactions because the reactions that wanted/needed to do I did not want to leave running unchecked on Sunday.

Sunday

Sunday is the one day a week off that we have. I treasure those days. Getting to sleep in late, and getting to do what I want all day is a luxury I try not to squander. However, there are still practical things that must be done. As if cleaning my workbench wasn’t enough, I clean my apartment and do laundry. I also cook lunch and dinner for the next seven day period. I try to do as much pleasure reading as I can because during the rest of the week, I read mainly research related materials. It’s a nice break.

Monday

I had run out of a ligand that I need to make several of the MOFs that I use. To start the process, I perform a Suzuki-Miyaura coupling reaction. I use the reaction to couple an arylbromide with an arylboronic acid.

Figure 2

Figure 2

Figure 2 shows the progression of the reaction. In the upper left is the start of the reaction. The brown color is from the palladium(II) acetate that I’m using as the catalyst. The upper right shows the reaction mixture right before I stop the reaction. The palladium has formed palladium black over the course of the reaction. During the catalytic cycle, palladium(0) is formed, and in this oxidation state, if two palladium(0) atoms bump into each other, they can begin to form palladium nano particles, which kills the catalyst. Basically, the reaction is over. The lower right shows the result after liquid-liquid extraction. Many people try to get rid of the palladium black, but I find it too much trouble to deal with, plus I always end up with a lower yield. I prefer to just let most of it get clumped onto the magnesium sulfate that I used to dry the organic extract, and if it still persists after filtration, it will be stopped by the column when I purify by chromatography. In the lower right is the nice white powder that I obtain after purification.

Incidentally, I love watching the condenser of the rotavap.

Tuesday

It’s lab clean up day! Every Tuesday morning, everyone gets together and cleans the lab. At my university, every lab is responsible for taking out the trash and the recycling. The cleaning staff are only responsible for common areas. The labs are our responsibility. This is an average load of refuse for a week (Figure 3):

Figure 3

Figure 3

The product from the previous reaction has a methyl group attach to a phenyl ring. This methyl group can be easily oxidized to a carboxylic acid. A synonymous reaction would be that of turning toluene into benzoic acid. The method I prefer is heating the starting material in a hydrothermal vessel in the presence of about 30% nitric acid (Figure 4).

Figure 4

Figure 4

This reaction makes me nervous because it heats nitric acid to 170 ℃. The product of this reaction, aside from the carboxylic acid, is a lot of nitric oxide gas. I made a video showing the opening of the vessel after the reaction.

Wednesday

After the ligand has been purified, it’s time to make the PCPs. The PCPs that I use are made of a mix of ligands. That means I combine more than one ligand to form the framework in the hopes of altering the pore surface functionality. I made two different PCPs on this day. One is a copper(II)-based PCP, and it’s synthesized in two steps.

In the first step, one set of ligands are combined with a copper(II) salt. This is then stirred for two days. The video below shows the mixing of reagents at the beginning of the reaction.

The other MOF is aluminium(III)-based. It’s a one step reaction that performed in a glass vial in the oven at 120 ℃. Unfortunately, that’s all I can say about those projects until they are published!

Thursday

I spent most of this day performing spectroscopy. Of all the spectroscopic techniques, NMR is my favorite. I fell in love with NMR the first day I had ever heard of it.

Figure 5

Figure 5

Our NMR lab (Firgure 5) has three spectrometers, all made by JEOL. In the foreground is the 400 MHz, behind that is the 600 MHz (my workhorse), and in the back on the right side is a 500 MHz. The sample that I was measuring that day was of a polymer that I had synthesized. I was doing a full set of characterization, so I set up a whole set of experiments: 1-D 1H and 13C, COSY, HSQC and I measured relaxation t1 with a double pulse experiment.

Figure 6

Figure 6

The sample (Figrue 6) was dissolved in benzene-d6, and I was was worried that since this sample would be running for 3 or 4 days that the solvent would slowly evaporate, so I sealed it rather than using a cap.

Friday

I realized that I forgot to add the group meeting schedule to my calendar. I’m presenting on Monday of the next week. There’s two things you should know about me. First, I have a terrible memory. If my Google calendar doesn’t remind me about important things like group meetings, I will surely forget them. Of course this isn’t a fail proof system because I have to remember to put these important reminders into the calendar first!

Normally, I do it right when I get the e-mail from the boss with the schedule for the next month. Somehow, I forgot.

The second thing is, I really hate making presentations. I often wish I could pay someone to do it for me. In some ways, I think this might make me a failure as a scientist (Editor’s note: Far from it!) While I love using my computer, I hate being chained to it. That’s how I feel when I have to sit and work on a presentation, or poster, or paper. I would much rather just work in the lab. However, I realize that it doesn’t work that way. My results, success or failure, are meaningless unless I report them.

However true that may be, making presentations is still probably my least favorite thing to do in science. And so, since I forgot, I spent most of the Friday and Saturday compiling data and making figures and putting together a presentation.

Maybe next week won’t be so crazy.

Yeah, that’s what I always tell myself.

Author biography:

wLT3vNAF_400x400Jason Hoshikawa is a 2nd year PhD student working in the Kitagawa Lab at Kyoto University under Assoc. Prof. Takashi Uemura. He was born in Dallas, Texas. After working in the television and radio industry as a high-power transmitter engineer, he started his undergrad education at the University of Hawaii at Manoa, but returned to Texas to finish his BS in Chemistry (2010) and MSc in Organic Chemistry (2012) at the University of North Texas under Prof. Mohammad A Omary. After being awarded a Japanese Government Scholarship for Research Students (2013) he entered the Graduate School of Engineering at Kyoto University to complete his PhD studies.

You can follow Jason on Twitter (@ChemistInJapan), on YouTube (https://www.youtube.com/user/ChemistInJapan), and Instagram (@ChemistInJapan).

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2 comments

  1. jershypershy · May 27, 2015

    This was a great read! Recently, a buddy of mine and I have been considering doing research of polymers at our school and this was extremely relevant! I would definitely love to know more about the specifics of your research!

  2. George Dionne · November 2, 2015

    Thank you for sharing. Hope to hear more from you.

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