The first week at the lab was really interesting and fun except for the fact that I almost broke a finger (which had nothing to do with the lab but I had to take a day off for it). Overall I was happy that I wasn't burdened with piles of articles but instead got to do a lot of hands-on work. The lab is pretty messy, my PI said that they don't do a very good job making things neat and orderly unless there's an inspection. There are only two other people besides my PI and me in the room, a grad student and an undergrad. They were pretty busy with their own projects (which were similar to what I'm doing) so I mainly worked with my PI directly and a post-doc who's working next door. Unlike some of the other labs, I didn't have to go through hours of training sessions. On the first day, basically as soon as I arrived, my PI started writing chemical structures on a blackboard and told me that this is the reaction that I'm doing. Then I followed the instructions to weigh out the solids and get the correct volume of liquids and put them in a round-bottom flask. Although I've used all the instruments before (analytical balance, weighing paper, syringes, pipettes) and the task wasn't particularly hard, I was still a little scared because I was handling all these glassware and chemicals on my first day. The reaction I set up was a reflux reaction in which the flask is placed in a hot wax bath with a condenser on top so any solvent that evaporates will go into the condenser instead of falling back into the reaction solution.The purpose of the reaction was to replace a proton with an isobutane, the first step in a three-step process that would result in an isostere of 1,3-cyclopentanedione, the chemical I'm currently working with.
On the second day, I worked with the post-doc the whole time. He demonstrated some of the more complicated (but actually really basic) processes like thin layer chromatography (determines the solvent condition suitable for the compound and checks if there are products made), column chromatography (a tedious process that may take over an hour, separates the product solution into fractions, the fractions are then tested using TLC to see which ones contain the desired product), and purification methods including using water to quench the reaction, using ethyl acetate to separate the organic and inorganic layers, and using sodium sulfate to eliminate any left-over water. These are the standard procedures for almost every reaction that I will do.
Next day morning I got a black fingernail and went to the lab in pain. My PI showed me the Liquid Chromatography-Mass Spectrocoply (LC-MS) machine and tested the solution I collected the day before. The LC-MS basically runs a mini-column and presents a graph on the computer that contains peaks. These peaks represent the compounds in the product solution; the machine gives the molecular weight of every compound and we are trying to find the peak with the molecular weight that corresponds to the product we want. If it is a big peak then that means the reaction is successful and we got the right product. There are other peaks on the graph that corresponds to the left-over reactants and some side-products. Unfortunately we could not find the right peak and even my PI couldn't figure out what happened. After lunch I went to the ER because the finger was starting to bother me a lot. Since I couldn't use my right hand, I stayed in the dorm the next day.
After the weekend, I still couldn't use the bruised finger but my PI said it's fine and he'll help me do anything that required my right hand index finger. I still got to set up the next reaction, this time in a cold bath made of dry ice and acetone. Meanwhile we did more LC-MS tests on the product of the previous reaction and found that our desired product exists but in a very small amount compared to the main peak that had a different molecular weight. So the week ended with an unknown product.
No comments:
Post a Comment