Chemistry 1102

Charlie Bond
MCS Rm 4.16/4.27
Charles.Bond@uwa.edu.au

What is Organic Chemistry?

Organic Reactions I II
Alkanes
Conformational Analysis I II
Stereochemistry I II III
Alkyl Halides I II
Alcohols and Ether I II
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Representing Organic Molecules

Palytoxin from the anenome Palythoa toxica

Isolated 0.15 mg/kg

of Anenome
Palytoxin
Lethal to humans
at 4 g

How do we draw an organic molecule in the best way?

Representing Organic Molecules

In general, organic compounds consist of two components:

When drawing molecules, think about laying out the hydrocarbon

backbone in an extended manner, and then decorate with functional
groups

Representing Organic Molecules

Take linoleic acid:
Molecular formula

C18H32O2

Structural Formula
CH3CH2CH2CH2CH2CH=CHCH2CH=CHCH2CH2CH2CH2CH2CH2CH2CO2H

Is this realistic? This kind of represenation is found in older books as it

was easier to print, but can we represent linoleic acid better?
4

Representing Organic Molecules

The experimentally-determined 3D structure of linoleic acid looks like this:

So a better representation is something like this.

Representing Organic Molecules

Finally, do we really need to see all of those C's and H's?

Representing Organic Molecules

Summary: Guidelines for drawing molecules
1. Draw chains of atoms as zig-zags
Arrange the molecule with the longest chain running horizontally
Use angles of ~120
2. Miss out Hydrogen atoms if attached to carbon unless absolutely
necessary*
Leave out C-H bonds too
3. Miss out the capital C for Carbon atoms atoms unless necessary*
*sometimes a particular C or H may be important in a functional
group or may be part of a reaction mechanism.
O
These are not rules, but guidelines to help
O
you communicate chemistry better

It's not always easy, though:

H
O

NOTE: Shorthand
Sometimes drawings of structures are simplified by using
shorthand for bulky groups. Don't ignore them if you see them.
For example AcOH, is ethanoic acid, not Actinium Hydroxide

Start simple:

Draw butanol

Draw butanoic acid

Draw phenol

Chemical Bonds

Three basic types of bonds:

Ionic

Covalent

Electrostatic attraction between ions

Sharing of electrons

Metallic

Metal atoms bonded to several other

atoms

Figure 7.1

Electronegativity
One way to classify bonds is through the
Pauling method of electronegativity
Electronegativity: The ability of an atom to attract electrons to itself when
part of a compound (or bound). Linus Pauling 1954 Noble
Prize, Chemical Bonding

Electronegativity has no scale, Fluorine is the highest at 4.0 and rest of the
elements are relative to this number
Definiton: How tightly an atom holds electrons it shares with another atom

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http://lpi.oregonstate.edu/lpbio/lpbio2.html

Electronegativity

Increases up the group, because of the decreasing distances of the

outer shell electrons from the nucleus
Increases to the right because of the increasing positive charge of the nucleus
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Elements which have low electronegativites are considered electropositve

Electronegativity
Additional classification

Examples
KCl (Potassium Chloride) 0.8 vs 3.0; difference is 2.2, thus Ionic
C-N single bond 2.5 vs 3.0; difference 0.5 thus Polar Covalent
H-Cl single bond 2.1 vs 3.0; difference 0.9, thus Polar Covalent
Can you think of an example of a Nonpolar Covalent bond?

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Electronegativity
Ionic Bond: Electron transfer and each of the atoms have formed a
distinctive ion and those ions are attracted to one another
Non-Polar covalent bond: An electron pair is sharing a region of space
between the two nuclei. This electron pair
has narrow limits between each nuclei
Polar covalent bond:

An electron pair is sharing a region of space

between the two nuclei, however unequally. It is
attracted more to one nucleus than the other

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Covalent Bonding and Lewis Dot Structures

Example: H2O

HOH

2 x Mutual Sharing of Electrons

In this case two single bonds

Lewis Dot Representation

O
H

Note: Shape of Molecule and

two lone pair of electrons

Example: CH4 - Methane

H
H C H
H

Note: No lone pairs of electrons

2-D representation
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Covalent Bonding and Lewis Dot Structures

Important Rules for More difficult examples: NF3
Step 1. Decide on the sequence of Atoms. Example NF3, place the atom with
the lower group number in centre. (usually lower elecronegativity)
F
F

Step 2. Determine the total number of valence electrons available. Example

NF3 = [1 x N (5e-)] + [3 x F (7e-)] = 5 + 21 = 26 valence electrons

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Covalent Bonding and Lewis Dot Structures

Important Rules for More difficult examples: NF3
Step 3. Draw a single bond from each surrounding atom to the centre atom
F
F

Subtract 2 e-s for each single bond from the total number of valence
electrons available, to find the number of electrons remaining
[26e- - (3 x 2e-) = 20 electrons]
Step 4. Distribute the remaining electrons in pairs so that each atom obtains
eight electrons (Place lone pairs on the surrounding more
electronegative atoms first)
F
F

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Covalent Bonding and Lewis Dot Structures

** Carry on only for when the central Atom has not enough electrons!
If Needed: Step 5. Central atom has not got 8 electrons!!!! We alter one
of the more electronegative lone pairs to a bonding pair to give each
atom an octet. In the case of Carbonate.
-2

O
O

to
O

-2

O
O

What is the Lewis dot structure for ethene C2H4?

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Covalent Bonding and Lewis Dot Structures

What about molecular oxygen?

O2

O O
Has 12 valence electrons, however when
these are arranged with a single bond
each oxygen only has 7 electrons

O O
Thus, the single lone electron is paired
to form another bond

Oxygen Bar

O O
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Covalent Bonding and Lewis Dot Structures

What about the Cyanide ion CN-

C N
Has 9 valence electrons in total plus one for the charge
(10) Subtract two for the bond, 8 electrons left

NaCN
Used in gold
Extraction,
Suicide tablets
WWII

C N

Carbon has not enough electrons

C N

Carbon has not enough electrons

C N

Correct both have eight electrons, but the

charge is in brackets. Where is the formal
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charge?

Polyatomic Ions and Formal Charge

C N

The cyanide ion is a polyatomic ion and the overall charge

Is 1. However for the reactivity and structural aspects
It is important to determine which of the atoms bears the charge

The charge on the atom in a polyatomic ion is the formal charge

Formal charge = Number of valence electrons (

For Nitrogen = 5 (2 + 6/2)

For Carbon = 4 (2 + 6/2)

-1

One half of
All unshared
+
)
all shared
electrons
electrons

C N

Formal charges are written as

+ + or

and are written next to the atom

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Formal Charge
Q. Determine the formal charge on the blue atoms in the
following species:
H

H3C

CH3

O
N

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Organic Reactions

Understanding structure is just a part of organic chemistry.

Understanding reactions and predicting reactivity is very
important.
1. Why dont molecules generally react with one another?
2. Why do molecules sometimes react with each other?
3. In chemical reactions, electrons move from full orbitals to
empty orbitals.
4. How do we represent the movement of electrons in
reactions (mechanisms)?
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Molecular Collisions
As well as vibrating, molecules move with respect to another.
Collisions with each other, with solvent molecules and the walls
of the container are very frequent.

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Most collisions do not result in chemical change (a reaction)

Reaction Mechanisms
To write mechanisms for organic chemistry, we show the flow of electrons
from electron-rich species to electron-poor species with curly arrows.
Placement of the curly arrow is important!
It originates at the electron pair and terminates
at the electron-poor atom

a curly arrow represents the

movement of two electrons

Example:
bond making
Write reaction mechanism between hydroxide ion and proton:

O H

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Reaction Mechanisms
Example: bond breaking
chlorine
had gained
one
Cl gains
an electron
electron and becames
and becomes
negatively
charged

Cl

curly arrow is directed from

single bond to electronegative
atom

Cl

negatively charged

carbone
lostone
one
C loses
electron and becomes
electroncharged
and
positively

becomes positively
charged

Lone pairs: nonbonding electrons can also be used in bond-making process.

Write the reaction between water and a proton:

H
O
H

H
H O H
an oxonium
cation

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Reaction Mechanisms
CARBON
-

has valency of four

carbon can also bond to just three other atoms by donating a pair of
electrons to one of the atoms originally bonded (breaking the bond)
-

tetravalent carbon

curly arrow is directed from

single bond to electronegative
atom

C
CARBOANION

CARBOCATION
carbone lost one
electron and becomes
positively charged

H
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NITROGEN
-

has valency of three

has three bonding electrons and a lone pair

however it can also bond to four atoms by donating its lone pair, in
which case it will than carry a positive charge.
-

Write reaction between ammonia and proton:

H N H
H
trivalent nitrogen

H
H N H
H

What shape is ammonia?

What shape is an
ammonium ion?

an ammonium
cation

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OXYGEN
-

has two bonding electrons and two lone pairs

it can bond to two other atoms and it is usually divalent

it can also bond to one atom in a negatively charged form, or to three

atoms in positively charged form.
-

O
divalent oxygen

an oxide anion

H
O

H
O
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an oxonium cation

BOND POLARITY
because different atomic nuclei have a particular ability to attract electrons
bonds between unlike atoms may not be shared equally. This leads to
charge imbalance, with one of the atoms taking more than its share of
electrons.
-

an atom that is more electronegative than carbon will polarize the bond,
this is indicated by putting partial charge + and - above the atoms. It
can also be represented by putting an arrowhead on the bond in the
direction of electron excess.
+
H3C
Br
Br
H3C
-

bromine is more
electronegative than carbon
polarity in C-O and C-N bonds

+
C O

+
C N

+
C O

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