Saturday, March 30, 2019

Bruice Organic Chemistry Notes #2

Now, I am going to continue my study in chapter 1. In this chapter, I will discuss some important points from Bruice book:
1. The structure of an atom
2. How the electrons in an atom are distributed
3. Covalent bond
4. How the structure of a compound is represented
5. Atomic orbitals
6. An introduction to molecular orbital theory
7. How single bonds are formed in organic compound
8. How a double bond is formed: the bonds in ethene
9. How a triple bond is formed: the bonds in ethyne
10. The bonds in the methyl cation, the methyl radical, and the methyl anion
11. The bonds in ammonia and in the ammonium ion
12. The bonds in water
13. The bond in a hydrogen halide
14. Hybridization and molecular geometry
15. Summary hybridization, bond lengths, bond strengths, and bond angles
16. Dipole moments of molecules

If we want to visualize an atom, let see like this, an atom comprises of a tiny dense of nucleus which is surrounded by electrons. The nucleus is composed of the neutron and proton. Neutron is neutral, proton is positively charged, while electron is negatively charged. In an uncharged atom, the number of protons equal to the number of electrons. 

The weigh of an atom is mostly from the nucleus, because protons and neutrons mass are about 1800 time more massive than electrons. While the volume of an atom is mostly occupied by the electron clouds.

In the atom structural study, we need to know 3 terms at least which are the atomic number, the mass number, and the atomic mass. The atomic number is based on the number of protons in its nucleus, the number of protons can become the representative of the atomic number because the number of protons is very unique and exactly different for each atom in the periodic table. While the number of electrons may vary due to electronic bonding. 

The mass number is the sum of protons and neutrons since we have known from previous explanation that neutrons and protons are extremely more massive than electrons, so that's why the total mass of the atom can ignore the mass of electrons and only consider the mass of neutrons and protons. The mass number of an atom can be more than one because the mass of neutrons sometimes varies. For example, the Carbon atom has two mass number: 98.89% of the Carbon atom available on earth, the mass number is 12 which consist of 6 protons and 6 neutrons, while the rest (1.11%) of the carbon atom has the mass number of 13 which consists of 6 protons and 7 neutrons. Besides that, Carbon atoms may also be found as C-14 which consists of 6 protons and 8 neutrons. We call this Carbon atom with different mass number as isotopes so we can say Carbon atom has 3 isotopes: C-12, C-13, and C-14.

While the atomic mass is the average of those isotopes of an atom. For Carbon atom, after the average calculation, we can have 12.011 amu. 

The electrons in an atom are distributed based on quantum mechanics. The most useful quantum mechanics version is proposed by Schrodinger in 1926. According to Schrodinger, the electrons in an atom are occupying a set of concentric shells that surrounds the nucleus. The rules are like this:
a. The first shell is the closest shell from the nucleus.
b. Each shells contain subshells that is called by atomic orbital. There is only 1 atomic orbital in the first shell which is s atomic orbital, while the second and higher shells also contain s atomic orbital with other degenerate atomic orbitals such as p, d, and f. Degenerate orbitals are the atomic orbitals that have the same energy. 
c. In each atomic orbitals, only 2 electrons can occupy it in maximum. 

[Picture Source: Bruice Organic Chemistry Book]

In a ground state, the electrons are available in the lowest energy which is the one closer to the nucleus. If there is energy applied to  an atom in a ground state, one or more electrons can jump to a higher-energy orbital and the condition is called as the excited-state. 

In addition, there are 3 principles about how the electrons occupy the atomic orbitals: aufbau principle, Pauli exclusion principle, and Hund's rule. Aufbau principle told that "an electron always goes into the available orbital with the lowest energy". The Pauli exclusion principle states that "no more than two electrons can occupy each atomic orbitals, and the two electrons must be of opposite spin". While, the Hund's rule states that, "when there are two or more atomic orbitals with the same energy, an electron will occupy an empty orbital before it will pair up with another electron". 

One more thing for this topic which is important is the term of valence and core electrons. Valence electrons are the electrons in an atom's outermost shell, while the electrons in the inner shells which is below the outermost shell are called as core electrons. 

The theory of the covalent bonds is proposed by G. N. Lewis. He said, "an atom is most stable if its outer shell is either filled or contains eight electrons, and it has no electrons of higher energy." This theory is further called as the octet rule.

[Picture Source: Bruice Organic Chemistry Book]

There are 2 kinds of covalent bonds: nonpolar and polar covalent bonds. Nonpolar covalent bonds are the bonds that the electronegativity difference between the bonded atom is less than 0.5.  Thus, the electron is shared equally. While the polar covalent bonds are the bond that the electronegativity difference is between 0.5 and 1.9. If the difference is more than 1.9 the bond is not called as covalent bond anymore, but the ionic bond. 

About polar covalent bond, since there is difference in electronegativity, the electron is not equally shared. Therefore, some electrons will concentrate on one atom. Based on the convention by the chemists, the direction of the bond polarity is visualized with an arrow. The head of the arrow is the negative end, while the perpendicular line near the tail of the arrow is the positive end.

[Picture Source: Bruice Organic Chemistry Book]

In the covalent bonds, there is also another way to visualize the distribution of the electrons, that is called as electrostatic potential maps. The colors indicate where is the negative and positive end. The red color signifies the most negative electrostatic potential. while blue is the area with the most positive electrostatic potential. 

[Picture Source: Bruice Organic Chemistry Book]
For the next points, I will discuss in the next posting.

Thank you for visiting. This is just my notes which all materials are taken from the book. I apologize if I did something wrong. Enjoy studying!

Wednesday, March 13, 2019


Terombang-ambing di atas danau biru yang pekat
Kelabunya langit dan bertitik-titik cahaya
kunang-kunang di sekelilingnya
Lentera kuning jingga

Perlukah ke tengahnya?

Ingin keluar,
air begitu dalam
bersama dengan ganggang hijau biru

Titik hitam dari jauh
Apakah dalam?
Apakah ada?

Seonggok batang pepohonan


Bersama dengan sebaris semut
Nyanyian jangkrik
Sesekali aungan serigala

Menatap gulita malam
Ribuan bintang mencongkak
Di atas rerumput
Semilir angin gugur

Kupanggil siang
Malam begitu lama

Dedaunan terus berayun

Rasanya di atas barisan bambu
genangan air bergelombang
ikatan kulit kayu
kesunyian kegelapan

Bukan nyanyian

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.

Sapporo, 12:53 am.