Week Three
As of the second week, several batches of my starting material were synthesized. In a previous entry I mentioned that introducing new functionalities to the reactive sites (called meso positions) is difficult because they are all equal. The goal of my research is to determine if is possible to introduce a functionality known as a protection group to only one site, and then to remove it when desired. The third week is when I started to attempt the protection group reaction.
The purpose of the protection group is to temporarily occupy one of the reactive sites, not allowing anything else to be introduced to that specific site, but allowing other functionalities to be introduced to other sites. The protection group should also have the ability to be easily removed by changing the conditions of the reaction like introducing a new catalyst or changing the acidity.
Here’s an analogy for the non-scientific audience: think of the protecting group as a bouncer and the reactive sites as doors. The bouncer is standing at door A in which he doesn’t allow anybody to pass and party with the rock stars behind that door, but he doesn’t care about the equivalent door B nearby that people are interested in passing through (reacting with) to hang out (bind with) with those rock stars.
Later on, the bouncer’s boss (the researcher changing the catalyst or condition) tells him to go home for the day and stop protecting the door (removing the protection group), which now allows for people to pass through the door (new reactions with that site, different than previous reactions with the other sites).
Developing a system that allows for the introduction and removal of a protection group whenever desired gives the researcher the ability to manipulate porphyrin synthesis in time and space. This will take quite sometime and from now on out, I will most likely be repeating the same reactions over and over, slightly changing conditions.
The protection group addition is a time consuming reaction as well. The reaction itself will run for at least 4 hours, and that doesn’t include set up and the time it takes me to perform tests that monitor the reaction such as thin layer chromatography (TLC) and mass spectrometry (MS). Once the reaction is done, I have to isolate all of the products using column chromatography, which can take several hours depending on the conditions of the column.
Because this reaction that I am focusing on is so time consuming Dr. Balaz has requested that one of his grad students, Urice, to help me by making batches of starting material. The batches he will be making will be various types of porphyrins, so we may be able to show that this reaction is applicable to multiple types, not just limited to the porphyrin I have been working with. For the non-scientific audience: different types of porphyrins mean there are various functionalities already attached to two of the reactive sites on the porphyrins. Those functionalities can have different effects on the compound as a whole and can alter the reactivity of the remaining sites. That is why it is important to test this reaction on multiple types of porphyrins.
Every so often there is down time. There are always things to do during down time, such as cleaning glassware, reading literature, and preparing schemes and data sets for presentations. At the end of the ten weeks, I am required to give a formal presentation on the work I have done, similar to my senior comp presentation that I will be giving next spring.
I have good news about my presentation skills that I somehow forgot to report on. During my second week, Dr. Balaz asked me to give a formal presentation to him an his students on the research I have been doing at Nazareth. Overall, it was good. To give you more detail, I’ll write another entry.
