Tuesday, April 30, 2013

Reflections on Organic Chemistry...


            As one writing a reflection on taking two semester of organic chemistry, many things come to mind. Organic chemistry, as thought, was very challenging. But several valuable lessons were learned—many of which were not exclusive to chemistry. The first major lesson which was learned is that in science, patterns dominate. Though there exists (sometimes) confusing nomenclature, roundabout mechanisms, and a myriad of reactions, many of these are quite similar to each other. Learning to focus on the broad picture to see the little picture, through pattern recognition, was the major lesson taken from the course.
            Another very valuable lesson learned from organic was time management. The volume of information which is expected to be known in organic chemistry is sometimes overwhelming, and it took a great amount of planning on how to allocate study time in order to maximize study efficiency. Setting a plan of attack on how to study the material in order to learn it, and not just memorize it, was a very important lesson learned which can carry over into other fields of study as well.
            Though there are many other lessons which could be discussed, the last I would like to mention is that there is strength in numbers. No, these numbers don’t pertain to math (since math is sometimes oddly scarce in organic chemistry). Rather, forming study groups and making friendships and connections with others who are struggling to learn the same thing made organic a very enjoyable experience overall. Learning to reach out and talk with others in the class about the material proved invaluable time and time again. Friends build off of each other’s strengths. For example, I may have understood Monday’s lecture very well, but not Wednesday’s. Conversely, someone may not have understood Monday’s material but really knew Wednesday’s. I and that friend could share with each other what we knew best, so that both would benefit.
            The most difficult part of the course for me was time management. Much of the material was not incredibly difficult, but the volume seemed enormous at times. Making the time to devote to studying the material was challenging, but necessary. The most surprising thing about the course is what I previously mentioned: most of the material was not incredibly difficult. Much of the course was pattern and trend recognition. This was surprising, since most “horror stories” of organic are about how difficult the content is. But in my experience, it was the volume and not the content that made the course challenging.
            Because I am not the first, and definitely not the last, to take an organic chemistry course, I have compiled a list of what I consider to be the five essential steps which should be taken to complete organic chemistry successfully:
          1.     Do NOT Memorize Material- It is extremely tempting in organic to memorize the lingo and drawings of reaction mechanisms. But this is not a good idea, because without understanding why things react as they do, confusion will inevitably take over and leave you feeling very lost. Learn the patterns, but know why organic species behave the way they do.
          2.     Read the Chapter- It is crucial that you read the assigned texts in preparation for, and even after, class lecture. Preparatory reading will put you in the mindset to receive the new information, even if you don’t fully understand it. Reading after class will solidify what you just learned and fill in gaps that may have seemed confusing at first. Not reading is a plan for failure, not success.
          3.     Plan Ahead- As stated previously, the volume of material in organic can be overwhelming. Simply glossing over material before the exam will not work in organic. You must be prepared to carve out time slots in your schedule to really examine the material and learn it yourself. You cannot learn simply by attending class.
          4.     Answer Practice Problems- Looking at example problems is a good start to understanding the reactions which take place, but it won’t be enough. In your study time, you must be willing to work practice problems to be sure you really understand what is going on. I would highly recommend purchasing the solutions manual to the assigned textbook. Answers are not just given, they are explained to help you understand the material.
          5.     Connect with Peers- Organic is difficult, and your classmates will probably think so too. Do not be afraid to share what you don’t understand with others so that you can build off of each other’s strengths and fill in each other’s weaknesses. Organic can be done independently, but it will be exponentially more difficult than it has to be.
At the conclusion of two semesters of organic chemistry, you will be required to take a standardized ACS exam to test you over material from both semesters. This exam is a good litmus test for how well you have retained information from the course and how well you understand the concepts. In my experience, the test corresponded quite well to the course material. Though there were some portions which were not covered in class, the overwhelming majority were. Therefore, the exam is a “good” cumulative exam. In my experience, the most difficult part of the exam was over the content that was not covered. The most challenging question related to polymers, which we did not discuss to a great extent in class.
It is my hope that as you read this blog, you are encouraged to form good study habits and hit the ground running when you enroll in an organic chemistry course. Though the course is difficult, it is not impossible. Most of the difficulty comes from the volume and not the material. Pattern recognition and independent learning is the key. Do this and you will be on the road to success!

Monday, April 15, 2013

Can Organic Synthesis Products Alleviate Seasonal Allergies?

              Around this time every year, millions of allergy sufferers around the country are impacted by the effects of seasonal allergies. Stuffy noses, sneezing, and watery eyes are all symptoms of the common allergy nuisance. Thankfully, long ago scientists developed antihistamines which can be taken by allergy sufferers to alleviate their symptoms. One of the most common taken antihistamines is Zyrtec, commonly cetirizine. 


The recognized IUPAC name of cetirizine is (+-)-[2-[4-[(4-chlorophenyl)phenylmethyl]-1-piperazinyl]ethoxy] acetic acid.1 The molecular formula is somewhat large at C12H25ClO2N3. A figure of the molecule is below:

             As can be seen above, there are several functional groups in the molecule. They have been 

color coded as described for easy recognition: two phenyl groups (red), a cyclic diammine 

group (yellow), an ether (green), carboxylic acid (blue) and halogen (purple). 


              A synthesis was prepared for cetirizine which may be found at the website http://chemistrybydesign.oia.arizona.edu/app.php and selecting “Zyrtec.”3 The given synthesis has five main steps that can be viewed by clicking the above link; briefly described, the steps are:4, 5



Step 1: This step converted a carbonyl group of a ketone to a 2° alcohol. This is mainly completed using the reagent NaBH4. In Organic Chemistry class lectures, the reduction of ketones to alcohols by NaBH4 was discussed in the textbook in Chapter 20, page 728.
Step 2: Step 2 uses thionyl chloride, SOCl2, to convert a 2° alcohol to a chloride substituent. This process was also discussed in the textbook in Chapter 9, page 335.
Step 3: Here, a nucleophilic substitution reaction occurs where Cl- is a leaving group and is replaced with the given reagent. Nucleophilic substitution reactions were discussed in Chapter 7.
Step 4: This is another substitution reaction, but here OH- is the leaving group.
Step 5: This step converts an amide to a carboxylic acid. This conversion has not been greatly discussed as of yet in the author of this post’s current organic chemistry class.

Several of the reagents needed to perform this synthesis are readily commercially available. These include NaBH4, SOCl2, toluene, NaOH, sodium methoxide. Some of the more specific reagents used in the substitution reactions may need to be custom prepared.

The following mechanism shows by curved arrow notation the conversion of the carbonyl functional group from Step 1 to a 2° alcohol:The borohydride anion attacks the carbonyl carbon and leaves a new hydrogen bond on that carbon, while electrons are pushed onto the elctronegative oxygen atom. The negatively charged oxygen then abstracts a hydrogen from water to form the alcohol.



So if you find that your eyes are watering after reading this, and you have a tickle in your throat, you may just need to take a personal evaluation of the effectiveness of the synthesized compound you just learned about.

References:
1) RxList. Zyrtec. <http://www.rxlist.com/zyrtec-drug.htm>. (Accessed April 13, 2013).
2) Wikipedia. Cetirizine. <http://en.wikipedia.org/wiki/File:Cetirizine_structure.svg> (Accessed April 13, 2013).
3) Arizona.edu. Chemistry By Design. <http://chemistrybydesign.oia.arizona.edu/app.php> (Accessed April 13, 2013).
4) Reiter, J.; Trinka, P.; Bartha, F.; Pongo, L.; Volk, B.; Simig, G. New Manufacturing Procedure of Cetirizine. Journal of the American Chemical Society. 2012, 16, 1279-1282.
5) Smith, J. Organic Chemistry, 3rd ed.; McGraw-Hill: New York, 2011.