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!

Bruice, P. Y. 2017. Organic Chemistry Eighth Edition. England: Pearson Education Limited.


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