Summary post

 

I had a super awesome summer working in the lab. Research can be boring and tedious sometimes, but whenever I got some new findings for my research project, I could feel the thrilling pulse running through my blood vessels. The experience of conducting individual research in the lab is also invaluable because it gives me the freedom to explore the mystery behind the reaction and have a peek at my newly synthesized molecules. Throughout the summer, my lab techniques got improved a lot, and I also sense that I have become more manageable and productive when I am working in the lab. More importantly, my way of thinking has been reshaped more into a scientist, for example, planning out my tasks so that I can be organized and productive; reflecting on my mistake; reading through literature to find out a problem, etc. I am very grateful that I am able to work with a knowledgeable and supportive advisor and learn the nature of doing scientific research. I really enjoyed my time in the lab, and I can’t wait to continue my research project next semester. Thank you all for reading my blog post!

Week 7: August 12th – August 16th

Last week of summer research! Last week, the reaction was not going in the way as I expected. Therefore, it took longer time to finalize the optimization reaction, and finally, the reaction temperature was nailed down and I spent two days to monitor the reaction very closely in order to find out the time when the production of our desired product is the highest. Other than that, I worked up the reaction with benzoquinone, did a column on that and obtained NMR spectra for the single spot. So far, I am not sure whether it is a single pure molecule, or it contains isomers. More spectra are needed in order to decipher its identity, but I am staying very optimistic about that. For the optimization reaction, I am glad that it is almost done, but meanwhile, I also had some interesting findings that there are still some intermediate molecules which may be able to be converted into the final product. In order to do that, some extra chemicals may be needed to facilitate the reaction. I read some literature on a similar reaction, and hopefully, I can get some exciting result next semester.

Week 6: August 5th – August 10th

I did 5 reactions trying to reproduce the reaction results under the optimal reaction condition last week. The reaction was run under the exact same condition, with different temperature and reaction time; however, it is still impossible to produce a high percentage yield of the desired product. I was getting very frustrated about the result because an experimental result should be reproducible. I have even checked all the NMR of the starting material to make sure that things haven’t gone wrong. However, I still kept getting an unwanted result. It was also the nature of research that sometimes you will just feel lost in a wild forest, unable to find you treasurable experiment result. I went through all the spectrum that the previous student did and found out that he made a calculation mistake. Therefore, he produced a false experimental result. I felt relieved when I finally found out the essential problem with the result. I need to pause my project process with all the other molecules to redo the optimization reaction to find out the best reaction condition. It was pretty much running the reaction and check how the reaction goes hourly with GC-MS.

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Week 5: July 29th – August 2nd

I can’t believe how time flies, and it is already the fifth week of the summer research. I have been having a ton of fun in the lab so far. I forgot to mention in last week’s blog post that I started running a new reaction with 1,4-benzoquinone. Prior this summer, another student worked in the lab with methyl-p-benzoquinone, and he found out an optimized reaction condition for the cyclization reaction. I applied the same condition for my reaction with 1,4-benzoquinone to see how the reaction will go. To my disappointment, the reaction rarely proceeded. When I ran any organic reaction, I will monitor its reaction process with GC-MS, abbreviation for gas chromatography and mass spectrometry. This piece of instruments consists of two parts: the gas chromatography and mass spectrometry. Only one microliter of the reaction mixture is needed for the analysis. As soon as it is being injected into the machine, the high temperature will vaporize the reaction mixture. Based on the difference of the molecule’s affinity with the column inside the machine, the molecules will go through the column using a varied amount of time. Therefore, the job of the gas chromatography is to separate the molecules. The mass spectrometry measures the mass-to-charge ratio of the molecules after it goes out of the gas chromatography. It can give information about the molecular mass of the molecule and some fragmentations of the molecule, which can be used as a way of having a general idea of what molecules are possibly present in the mixture. It seems that I went on a little bit too much on GC-MS. The main point here is that I used GCMS to elucidate the reaction result and found out that under the “optimized reaction condition” the yield of the product is very low. I was skeptical about the reaction condition and tried to reproduce the reaction with methyl-benzoquinone. The result will be included in next week’s blog post

Week 4: July 22nd – July 26th

I was working on 2-tert-Butyl-1,4-benzoquinone and 2-phenol-1,4-benzoquinone for the previous week and managed to isolate some single spots using column chromatography, and then I did NMR spectrum on these isolated molecules. NMR is the abbreviation for nuclear magnetic resonance, and it is a way of obtaining information about the molecule’s structural information. The NMR spectrum showed that both molecules undergo the cyclization reaction. For 2-tert-Butyl-1,4-benzoquinone product, the spectrum shows that it is pretty pure with traces of solvent; however, 2-phenol-1,4-benzoquinone cyclization product is a mixture of isomers. Isomers are compounds with the same chemical formula but different structures. Because of the close similarity of the two isomers, it is difficult to separate them well. I have tried several solvent systems for the purpose of separate, but none of them work. I may keep trying to look for a method to separate the compound. Hopefully, it will work the next time. It is the nature of scientific research that you will face a lot of surprises and failures. Maybe the isomers won’t be able to be isolated; maybe a solvent system will do the job. I will stay optimistic and keep all the trials. Starting from last week, I also started working on the reaction mixture from 2-chloro-1,4-benzoquinone as starting material. It was a crude product from the reaction, meaning it hadn’t been worked up yet. I extracted the reaction mixture with multiple solvents to get rid of the solvent which we used for the reaction. Other than that, it was all of the same experimental procedure of column chromatography, TLC and NMR. It turns out that 2-chloro-1,4-benzoquinone also undergoes the cyclization reaction. It was pretty amazing because halogens usually make things a little bit strange, but the result was exciting. However, after being identified using NMR, the product is a mixture of similar isomers.