Organic Chemistry

Kinetics
Lecture 1:
Review of General Chemistry: Electrons,
bonds and molecular properties

Instructor: Nhung N. Duong (Ph.D)

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 General Class Information

• Syllabus

• Textbook
Organic Chemistry by David R. Klein – 3rd edition

• Reading is strongly recommended

• Grading:
• Homework 10-15%
• In-class quizzes 15%
• Midterm 30-35%
• Final exam 40%
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 What is Organic Chemistry ?

• 1810: Jöns Jacob Berzelius defined organic compounds as very

complex and can only be obtained from living sources (vitalism)

• Vitalism: belief that a “magic” vital force in plants and animals is

necessary to synthesize organic compounds

• 1828: Friedrich Wöhler synthesized organic compound (urea) in the lab

Organic refers to compounds that contain carbon

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 “The Age of Organic Chemistry”

• A multitude of important substances vital to life contain carbon:

 Food: proteins, vitamins, lipid, carbohydrates
 Medicine: naturally occurring and synthetic drugs
 Materials: fabrics, plastics

• >95% of all known compounds composed of carbon

• >50% of chemists are organic

Structure Mechanism Synthesis

Determine the way in Understanding the Building complex
which atoms are put reactivity of molecules from
together in space to molecules: How and simple ones using
form complex Why chemical chemical reactions
molecules reactions happen
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 Chemistry can be Addictive…

Who likes coffee ??

Why does coffee help

you stay awake ?

• Coffee contains caffeine, a stimulant that can temporarily wards off

drowsiness and restore alertness in humans

• Principal of action: caffeine acts as an antagonist of adenosine

receptors in the brain

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https://lifehacker.com/what-caffeine-actually-does-to-your-brain-5585217
 Why Carbon?

• Carbon shares electron rather than gaining or losing

-> Carbon forms a variety of strong covalent bonds to itself and other atoms

• Organic compounds are structurally diverse

Why bond this way? 6

 Lewis Structure

• Each valence electron is symbolized by a dot

• Bonding pair of electrons is symbolized by a pair of dots or by a dash (−)

(methane)

or (ammonia)

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 In class exercise

1.

2.

3.

4. Tobacco kills more than six million people each year, translating to one
smoking-related death every five seconds. On average, smoking will cut 13 years
from your life expectancy and can directly cause cancer, heart diseases, stroke…
Tobacco smoke contains many chemicals that are harmful to both smokers and
nonsmokers. Draw the Lewis structure of the following dangerous compounds
found in tobacco smoke:

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 In class exercise

1.

(a) (b) (c)

(d) (e) (f)

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 In class exercise

2.

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 In class exercise

3.

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 In class exercise

4. Tobacco kills more than six million people each year, translating to one
smoking-related death every five seconds. On average, smoking will cut 13 years
from your life expectancy and can directly cause cancer, heart diseases, stroke…
Tobacco smoke contains many chemicals that are harmful to both smokers and
nonsmokers. Draw the Lewis structure of the following dangerous compounds
found in tobacco smoke:

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 Formal Charges

• Method to keep track of electrons

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 Formal Charges

Identify any formal charges in the structures below:

If you are having trouble paying attention during a long lecture, your levels of
acetylcholine (a neurotransmitter) may be to blame. Identify any formal charges
in acetylcholine.

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 Formal Charges

Identify any formal charges in the structures below:

-1 +1 -1 +1 -1
If you are having trouble paying attention during a long lecture, your levels of
acetylcholine (a neurotransmitter) may be to blame. Identify any formal charges
in acetylcholine.

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 Bond Formation

Bond: “glue” that holds atoms together

Lewis’s theory (Octet rule) : Atoms transfer or share electron to attain a
filled shell of electron

3 categories of bonds: (1) ionic, (2) covalent and (3) polar covalent
-> Depending on electronegativity (power to attract electron)

http://googlegalaxyscience.com/electronegativity-of-elements/

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 Ionic Bonding

• Attraction between ions of opposite charges (electrostatic attraction)

• Is formed with electrons transfer, not electron sharing
• Happens between atoms with widely different electronegativity (EN)

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 Covalent Bonding

• Very important in organic molecules!

• Bond is formed by electron sharing between atoms of similar EN

e.g. CCl4 is covalent

Each chlorine still has three unshared pairs of electrons (lone pair) 19
 Covalent Bonding: Polar vs. Nonpolar
∆EN < 0.5 ∆EN ~ 0.5-1.7 ∆EN > 1.7

 Electrostatic potential map shows charge distribution

Most negative Most positive

electrostatic potential electrostatic potential

Example: Identify polar

covalent bonds and show
their dipole moments (𝜇)?
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 Organic vs. Inorganic Compounds

Seager and Slabaugh, 2014, page 5

What happens when you heat salt vs. sugar?

inorganic organic
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 Principles of Atomic Structure

Dense, positively
• Proton: positive
charged nucleus
• Neutron: neutral contains most of
atom’s mass.
• Electron: negative
Negatively charged
electron cloud makes
up most of atom’s
Wade page 2, 2009 volume.

• Atomic number (Z): Number of protons • Atomic weight: The average

in the nucleus
• Mass number: Sum of the protons and
neutrons of an atom
• Isotopes: Atoms that have the same
atomic number but different mass
numbers.
weighted mass of all possible
atoms of an element.
• Molecular weight: The sum of
the atomic weights of all the
atoms in a molecule.
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 Electronic Structure of the Atom
Electron: both particle-like and wave-like properties

Quantum mechanics - uses math equations (wave functions Ψ 2 ) to describe

the motion of an electron around a nucleus (developed by Schrödinger)

Orbital: a spatial distribution of electron density – places where electrons

are most likely to be found (90-95% probability).
z z z z
y y y y
s p
orbital orbital
x x x x

Orbitals have specific shape, energy and volume.

Analogy: usual cloud vs. electron cloud (orbital). Thoughts?

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 Electron Configuration

Orbitals are described by:

• Specifies shell, n (1,2,3…)
• Orbital shape or subshell: s, p, d, f
• Directional properties (x,y,z)

3 principles:
• Aufbau principle - electrons occupy orbitals with the lowest energy first.
• Pauli exclusion principle - only two electrons can occupy one atomic orbital and
the two electrons have opposite spin.
• Hund’s rule - electrons will occupy empty, degenerate orbitals with before pairing
up another electron

Valence electrons: e in the outermost shell -> determine properties of atoms

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 In class exercise

5. Write electronic configurations of these following elements

6.

7.

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 In class exercise

1. Write electronic configurations of these following elements

2. 1s22s22p3 1s22s22p2

1s22s22p1 1s22s22p5
3.

1s22s22p63s23p2
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 Atomic Orbitals

Electron: wave-like property

~ standing wave
Quantum mechanics: uses math
(wave functions Ψ) to describe the
motion of an electron around a nucleus

1s orbital

Wave function Ψ with positive sign

Sign of Ψ is NOT
electrical charge

Wave function Ψ with negative sign 27

 Atomic Orbitals
2p orbital

Wave function Ψ Probability function Ψ 2

z z z (energy density)
z z
y y y y
y

x x x
x x

2s 2s 2px 2py 2pz

Atomic orbitals can combine/overlap :

• Molecular orbital theory use math to explore atomic orbitals overlap
• Math method : Linear combination of atomic orbitals (LCAO)
• Number of orbitals formed = number of orbitals original
• Orbitals of different atoms interact → molecular orbitals (MO)
• Orbitals of same atom interact → hybrid atomic orbitals 28
 Formation of H2

When 2 H atoms come together, the electrostatic forces change:

• Attraction between electrons and nuclei
• Repulsions between the 2 nuclei
• Repulsion between the 2 electrons

Attractive forces
Max net attraction increase
Most stable state 29
 Formation of H2

Constructive interaction:
2 waves combine and
reinforce each other

𝜎 bonding MO

Destructive interaction:
2 waves combine and
oppose each other

𝜎 ∗ antibonding MO
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 Formation of H2

LUMO: lowest unoccupied

molecular orbital

HOMO: highest occupied

molecular orbital

In stable compounds, bonding orbitals are filled and antibonding orbitals are empty

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 Methane and sp3 Hybridization
Carbon atom

4 degenerate
sp3 orbitals

sp3 hybridized C orbital

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 Ethane
sp3 - sp3 orbitals overlap

sp3 - s orbitals overlap

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 Double Bonds and sp2 Hybridization

3 degenerated
sp2 orbitals

sp2 hybridized C orbital ethylene

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 Double Bonds and sp2 Hybridization
𝝅 bond: overlap of two p orbitals perpendicular to the line connecting nuclei

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 Triple Bonds and sp Hybridization

acetylene

sp hybridized C orbital
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 In-class Exercise
1*.

2*.

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 Skills to Master

1. Drawing constitutional isomers of molecules

2. Drawing Lewis dot structures of an atom and a molecule
3. Calculating formal charges
4. Location partial charges
5. Identifying electron configurations
6. Identifying hybridization states
7. Predicting geometry
8. Identify molecular dipole moment
9. Predicting physical properties

This drug is not soluble in water or blood but dissolve well in soybean oil

Use lecithins (similar to soap) to make propofol and soybean oil soluble in water

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Skills to Master

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Skills to Master

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Skills to Master

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 Skills to Master

Practice: Do all of the problems indicated at Try Problems sections of all 10 skills
above(1.1 to 1.10)

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