Monday, March 4, 2019

Bruice Organic Chemistry Notes #1



Organic Chemistry Book written by Paula Yurkanis Bruice is a must-read book for a chemist recommended by my sensei. My first time reading the book, I was so impressed how easy to read the book it is since English is my second language, not my mother language. Bruice was able to make the reader understand just in one-time reading. 

The eighth edition of Bruice Organic Chemistry book contains 28 chapters:
1. Remembering the general chemistry: electronic structure and bonding
2. Acids and bases: central to understanding organic chemistry
3. An introduction to organic compounds: nomenclature, physical properties, and structure
4. Isomers: the arrangement of atoms in space
5. Alkenes: structure, nomenclature, and an introduction to reactivity. Thermodynamics and kinetics
6. The reactions of alkenes. The stereochemistry of addition reactions
7. The reactions of alkynes. An introduction to multistep synthesis
8. Delocalized electrons: their effect on stability, pKa, and the products of a reaction. Aromaticity and electronic effects: an introduction to the reaction benzene
9. Substitution and elimination reactions of alkyl halides.
10. Reactions of alcohols, ethers, epoxides, amines, and sulfur-containing compounds
11. Organometallic compounds
12. Radicals
13. Mass spectrometry; infrared spectroscopy; UV/Vis spectroscopy
14. NMR spectroscopy
15. Reactions of carboxylic acids and carboxylic acid derivatives
16. Reactions of aldehydes and ketone. More reactions of carboxylic acid derivatives.
17. Reaction at the alfa-carbon
18. Reactions of benzene and substituted benzenes
19. More about amines. Reactions of heterocyclic compounds
20. The organic chemistry of carbohydrates
21. Amino acids, peptides, and proteins
22. Catalysis in organic reactions and in enzymatic reactions
23. The organic chemistry of the coenzymes, compounds derived from vitamin
24. The organic chemistry of the metabolic pathways
25. The organic chemistry of lipids
26. The chemistry of the nucleic acids
27. Synthetic polymers
28. Pericyclic reactions

Wow, so many chapters, right? I hope, I can master all 28 chapters. Right now, I am super not knowledgeable enough about this all chapters. I only received the basic of organic chemistry in my first year of my undergraduate study. Until here, when I started to study in Hokkaido University, in the Laboratory of Chemistry and Biology, in Transdisciplinary Life Science Course, knowing and understanding about organic chemistry is very important. That's why it is a must for me to learn this in more detail.

Most of the Japanese students in my laboratory have already received this all 28 chapters in 2 years when they were in the undergraduate study. So, I have to run after them, if I want to succeed in doing my research.   

Anyway, this post is purposed to make me reminded what I have learned and which part is important from this book. I will be happy too if this post will also help you. 

Now, let's talk about the first chapter, yet in this post, I am not going to talk about all the content in chapter 1, I might talk about the contents in separate posts. 

CHAPTER 1: Remembering General Chemistry: Electronic Structure and Bonding. Bruice started chapter 1 by introducing the meaning of organic chemistry and why we must learn about it. I don"t know before, that in 1807, by Berzelius, the compound was divided into 2 types: organic and inorganic. Organic compound is coming from living organism which was believed to have a vital force, while inorganic compound is coming from minerals which lack of vital force. Hence, since that time, it was believed that chemist could not create organic compound which has immeasurable vital force which is very beneficial for life, so if they want to get the vital force, they only can get it from living organisms such as plants and animals and they think it was impossible to get the vital force in the laboratory. 

And you know what? The theory was not applicable anymore after 1828, Friedrich Wohler was able to produce urea (an organic compound) by heating ammonium cyanate which is an inorganic compound. Hence, by that time, chemist was able to create organic compound in the laboratory and the belief of organic compound is only can be obtained from living organism was not applicable anymore since Wohler has already shown how urea can be created from inorganic compounds. 

This big finding opened a very wide knowledge for the future of organic chemistry. Therefore, the definition of organic compounds now is enhanced. Organic compounds are defined as the compounds that are based on carbon.

Why carbon? Because about all the organic compounds that make life possible such as protein, enzymes, vitamins, carbohydrates, DNA, and RNA are all containing carbon. 

Since the definition of organic compound now is the compounds containing carbon, the compound now is not limited only from the nature. The synthetic compound such as plastics, teflon, rubbers, and even some medicines are all containing carbon so those are the part of the organic compound. 

By the way, you may have questions about why carbon? When there are numerous of atom in the periodic table. Bruice explained that because the character and position of carbon which is in the middle in the periodic table, so it neither readily gives up nor readily accepts electrons. Carbon shares electron instead which as the consequent will make a stable compound with other atoms. 

One more thing I want to talk before I close the post, I am interested in talking about natural versus organic compound which was also discussed in this book. There is a common belief that compound from the nature is always better than the synthethic one. However, as I learned for 5 years in pharmacy school and now is continuing study in chemical and biology laboratory, I learned how synthesizing and modifying the structure of a compound will able to improve the activity of the compound. Hence, please do not underestimate synthetic compound. We are, the pharmacist and chemist always struggle to develop better drugs for all the people needed. 

As an example, Penicillin, a popular antibiotic obtained from nature is known to have allergic response for some people. Then, chemist was able to synthesize the analog of Penicillin (having similar structure with Penicillin, but was modified) and improve the activity by not producing allergic response.

So, now, I hope your belief can be changed that nature is not always better than synthetic one.

That's all for today, I have already felt super sleepy.

Reference:
Bruice, P. Y. 2017. Organic Chemistry Eighth Edition. England: Pearson Education Limited.
Sapporo, 12:53 am.

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