Organic Chemistry

The structure of atoms, molecules, ions

and ionic compounds
The nature of chemical bonds in organic
chemistry

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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? 7

 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 Ψ2 ) 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).
y y y y
z z
z z
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

1. Write electronic configurations of these following elements

2.

3.

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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) 12
 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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 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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 Bond Length and Bond Strength

• Bond length: 0.74 Å

• Bond strength: 436 kJ/mol

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most stable state

 Multiple Bonding
• Two atoms can share more than one pair of electrons to gain a filled shell
(very common in organic molecules)

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 Formal Charges

• Method to keep track of electrons

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 Representing Molecules

1. Condense structural formulas

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 Representing Molecules

2. Line-angle formulas

Practice:

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 Representing Molecules

3. Using dashes and wedges: draw molecules in 3D

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Representing Motion of Electrons

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 In-class Problem
Use what we have learned so far to predict the movement of electron
and the product of this reaction
H3N + BH3 ?

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 In-class Problem
Use what we have learned so far to predict the movement of electron
and the product of this reaction
H3N + BH3 ?

Formal charge ?
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 Resonance
• Electron also moves within one molecule

• A single Lewis structure is not enough to explain reactivity of some molecules

• When 2 or more valence bond structures are possible, molecule shows

characteristics of both (resonance hybrids)

Example: ion [H2CNH2]+

Resonance forms of a resonance hybrid Resonance hybrid

• Positive charge is delocalized

• Spreading the (+) over 2 atoms makes ion more stable

-> resonance-stabilized cation 27
Resonance

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 Resonance

• Is this resonance?

Only electrons can be delocalized

• Draw the resonance forms of [CH3OCH2]+

Minor contributor Major contributor

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 Major and Minor Resonance Contributors

Resonance forms are not energetically similar

(more stable – major contributor, less stable – minor contributor)
Some rules to remember: (order of importance)
i. Maximized octet
ii. Negatively charge located on atoms with greatest electronegativity
iii. Minimized charge separation

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Major and Minor Resonance Contributors

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Major and Minor Resonance Contributors

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 Acids and Bases

Acids and bases are fundamental of organic chemistry

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 Bronsted Acids and Bases
Acids: donate proton (H+) Bases: accept proton (H+)

After acid donates proton → a base which can accept that proton back
→ called conjugated base
After base accepts proton → an acid which can return that proton
→ called conjugated acid

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 Acid Strength

Acid strength: ability to lose H+

Math expression by Ka (acid-dissociation constant)

𝑝𝐾𝑎 = − log10 𝐾𝑎

Strong acid: large 𝐾𝑎 -- small

𝑝𝐾𝑎
Strong acid Weak conjugate base

easily to lose H+ stable base that not easy to accept H+ back

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And vice versa…

 Base Strength

Base strength: math expression by Kb (base-dissociation constant)

Relationship between acidity of an acid and basicity of its conjugate base

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 In-class exercise
1.Calculate 𝐾𝑎 and 𝑝𝐾𝑎 of water.
2.For each following acid-base reaction, draw a mechanism and clearly label acid,
base, conjugate acid and conjugate base

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3.
 Structure Affects Acidity
• Electronegativity

Negative charge on more

electronegative element

-> stable

• Size

Negative charge is spread

over a large region

-> stable

• Resonance: phenol vs. cyclohexanol (previous slide) 38

 Lewis Acids and Bases

Lewis: looking acid-base reaction from perspective of bond formation/cleavage

• Lewis acid: accept e- pair, electrophile

• Lewis base: donate e- pair, nucleophile

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 Homework

• HW1 be posted on Blackboard. Due next week.

• Reading assignment for next class include in syllabus (Blackboard)

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