Organic Chemistry

H B C N O F
Si P S Cl
Br
I

CHEMISTRY OF THE COVALENT

COMPOUNDS OF CARBON
Millions of things
contain organic
molecules….
UNIQUE PROPERTIES OF CARBON
Carbon is TETRAVALENT - which
means it bonds four times…. C

Carbon is one of the few elements that can form

Chains with itself…

C-C-C-C-C-C-C-C-C

Carbon can also form BRANCHED NETWORKS and RINGS

C C C C C C
C C
C C C
C C
C C
 Most organic molecules contain C-C and C-H bonds which are non-
polar…water, which has slight charge, is polar
Most organic
Because of this, most organic molecules do not dissolve in water – For
molecules have no example, oil and water do not mix!
charge…. Most organic molecules are gases or quickly evaporating liquids at
room temperature because they have no charge – they have weak
physical bonds (London Dispersion bonds)
Organic molecules will not have charge unless they contain a bond
with polarity
Those that do have slightly charged bonds – like C-O or O-H bonds
(as in alcohols) dissolve well in water!

Water - has slight Water - has slight

charge…is a liquid charge…is a liquid

NO ATTRACTION

Methane –
ATTRACTION!
has no
charge… Methanol –
is a gas Has slight charge
– is a liquid and
dissolves well in
water
 Hydrocarbons –
contain hydrogen
and carbon bonds

Aliphatic
hydrocarbons –
chains of
Functional
carbons and
groups – altered
hydrogens
hydrocarbons

Aromatic
hydrocarbons –
contain benzenec
Alkanes Alkenes – Alkynes
– all has some has some
single double triple
bonds bonds bonds

- Ether
- Ester
- Aldehyde
- Ketone
saturated unsaturated - Carboxylic acid
- alcohol
 Aliphatic Hydrocarbons

• Hydrocarbons are compounds composed

of carbon and hydrogen in chains
• Aliphatic – meaning chains of carbons –
either straight or branched chains
 Aliphatic Hydrocarbons
• Unsaturated: • Saturated: contains
contains carbon- all carbon-carbon
carbon double or single bonds.
triple bonds.
 Common Hydrocarbon Types
H
H H H H HH C H H
only
C H single
ALKANES H C C C C H
H C C C H
bonds
CnH2n+2 H H H H HH C H H
H
H H

H C H at least
ALKENES H H H one
H C C
CnH2n H
H C C C C H double
H C
H H H H bond
H

H H H H
at least
ALKYNES H C C C H H C C C C C H one
CnH2n-2 H H H H triple
bond
 Structural Formulas – show the structure
of the atoms
Unbranched
Branched Alkane
(“linear”) Alkane
Structural
Formulas

Condensed some
CH3CH2CH2CH2CH3 Structural bonds
Formulas shown

CH3CH(CH3)CH2CH(CH3)CH3
Molecular Formula –
C5H12 Tells me nothing about
Structure – just how many C7H16
of each element there are!
 Condensed Notation

H H
H C C C C H CH3CH2-CH=CH2
H H H H
CH3CH2CH=CH2
Alkene

H
H C C C H H-C C-CH3
H
HC CCH3 or
Alkyne
CH CCH3
 Condensed Notation
EVEN COMPLICATED BRANCHED STRUCTURES
CAN BE WRITTEN ON A SINGLE LINE

for this reason many

handbooks use
condensed notation

CH3CH(CH3)CH(CH2CH3)CH2CH3
Branched
Alkane
note use of parentheses -
these atoms are attached to the
Carbon atom that they follow
 Skeleton Notation
CH3
CH3CH2CH2CH2CH3 CH3 C CH3
CH3

H
CH3 C C CH3 CH3CH2CH CH2
H

H C C CH3 CH3 C C CH2CH3

 Cyclic Molecules
• For some molecules, the carbon chain
may close on itself to form a ring.
• These types of substances are called
cyclic molecules.
• These do not follow the general formulas
for alkanes, alkenes, and alkynes
(CnH2n+2, CnH2n, and CnH2n-2)
Examples of Cyclic Molecules
Caffeine

Testosterone
 How to name compounds…

Prefixes for organic are different than traditional naming…

Endings: -ane = single bonds – ene = double bonds – yne = triple bonds
Groups are named according to the number of carbon chains in the group….
The group has the ending –yl if it is a carbon group – the group has the
ending –o if it is a halogen

-CH3 methyl group -CH2CH3 ethyl group -Cl chloro group

 CH3 CH2 CH2 CH CH2 CH3
CH3

Longest chain….? Six carbons…. Hex….

Bond types….? All single bonds…. -ane….

Attached groups…? -CH3 = methyl

Number from what The right….

side…?
The group is attached to
Why…? carbon 3, and not carbon 4

3-methyl hexane
• Nomenclature for other types of
hydrocarbons…

1, 1 dimethyl
cyclobutane
 • Longest chain…?
• Did you include the entire double
Cl bond…?
• Start numbering from what
end…?
CH3 CH2 CH CH-CH-CH2CHCH3
• Is the double bond or attached
groups more important…?
CH2CH3 • How many groups are
attached…?
• What are they?
5-chloro 7-methyl - 3 –
• Remember to report the groups
nonene alphabetically….!
Name this sucker….! 4-butyl 2-methyl 1, 5 heptene-yne
• Important things to remember…
• Double and triple bonds are most important when counting the longest
chain
• Always include both the double and triple bond in the longest chain – even
if it isn’t the most number of carbons!
• Start counting from the end closest to the double or triple bond –
whichever has the lowest number
• If there is a tie, and only then, do double bonds take priority over triple
bonds
• If there isn’t a double or triple bond, find the longest continuous chain of
carbons, and start counting from the end closest to an attached group –
• It doesn’t matter what the group is – all groups have the same importance
– CH3, -CH2-CH3, -Cl, etc.
• If there is a tie, start counting from the end that has the most groups on
the lowest number

Which end do you

number from?
 • Great websites for tutorials….

http://www.chem.ucalgary.ca/courses/351/orgnom/index.html
http://www.cem.msu.edu/~reusch/VirtualText/nomen1.htm
http://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistry
http://chemistry.boisestate.edu/people/richardbanks/organic/nomenclature
/organicnomenclature1.htm
http://www.chembio.uoguelph.ca/educmat/chm19104/nomenclature/quizes
.html
http://www.quia.com/jg/65803.html
http://eppe.tripod.com/orgtable.htm
http://www.cem.msu.edu/~reusch/VirtualText/Questions/Nomencl/nomencl
.htm
http://www.chemguide.co.uk/atoms/bonding/vdw.html
Boiling points of various
hydrocarbons…
Why do they increase…?
 • Boiling point as we halogenate, or add a halogen to a hydrocarbon,
goes…Up! Why????

• Methane = -1620C
• Fluoromethane = -78.20C
• Difluoromethane = -51.60C
• Trifluoromethane = -50C
• Tetrafluoromethane = -1280C
• Why would we want to halogenate a hydrocarbon…?
• Does it matter what halogen you add…?
 Halogenated hydrocarbons are used as refrigerants…

1.The compressor compresses cool Freon gas, causing it to become hot,

high-pressure Freon gas (red in the diagram above).
2.This hot gas runs through a set of coils so it can dissipate its heat, and it
condenses into a liquid.
3.The Freon liquid runs through an expansion valve, and in the process it
evaporates to become cold, low-pressure Freon gas (light blue in the
diagram above).
4.This cold gas runs through a set of coils that allow the gas to absorb heat
and cool down the air inside the building.
 Structural Isomers…
Molecules that have the same molecular formula,
meaning same numbers of carbons and hydrogens, but
different structures…

Isomers of octane…..there are 18 different arrangements!

2-methyl heptane

Octane Are these both

octane though?
 Structural Isomers…
The problem is that some chemists generically refer to both of the
following compounds as octane, since they both contain 8 carbons
and 18 hydrogens…

2-methyl heptane

Octane

The official naming system, the IUPAC naming system, does not
call both of these molecules octane though!

Look at these two molecules - both of these molecules are generically referred to as structural
isomers of hexane, because they both have 6 carbons and 14 hydrogens (C 6H14). They don’t have
the same IUPAC name at all – they are totally different molecules, with totally different properties!
 Geometric Isomers

Cis means same

side…

Trans means
opposite side…

• Molecules that have the same molecular formula, but differ in how
groups attached to the double bond are oriented
• Must have a double bond, and different groups on both the left and
right sides!
 Geometric Isomers

Both are the same

molecule!
1,2 dichloroethane

2 different molecules:
trans – 1,2 dichloroethene
cis – 1,2 dichloroethene

• This doesn’t happen with a single bond…

• The atoms are free to rotate around the single bond, to form both molecules….
• With a double bond, the atoms are locked into place by the p orbitals bonding in
the double bond!
 Which are isomers, and which are the same
Geometric Isomers molecule…?

Same molecule.. Isomers!

Isomers! Same molecule..

To have geometric isomers:

1. You must have a double bond in the molecule

2. You must have two different groups on the left hand side of the bond, and two different groups on the
right hand side of the double bond. The left side groups do not have to be the same as the right side
groups!
 Stereoisomers

• Molecules that have the same

molecular formula, have the
D-alanine L-alanine same sequence of bonded
atoms, but differ in their 3-d
orientation!
• Stereoisomers can be non-
superimposable mirror
images!
• We call the carbons that they
are attached to chiral, or
asymmetric!
• This means they are non-
symmetrical!
• Our hands are chiral!
 - In nature, only one stereoisomer of biological molecules is usually present (example – amino acids)
- In medicine, different stereoiomers of a compound may have substantially different biological
effects.
- For example, for certain cancer drugs, such as cisplatin and leucovorin, only one of the two
stereoisomers are effective in combating cancer – the other stereoisomer is either ineffective or
poisonous!
- Robutissin contains D-methorphan – a powerful cough suppressant – the stereoisomer of this
molecule, L-methorphan, is an illegal opiate that has totally different effects in the body!
- How do they separate stereoisomers, if their only difference is the fact that they are mirror
images? Chemically, they look nearly identical!

The two stereoisomers of the

amino acid alanine…proteins
contain only L-alanine!

D-methorphan L-methorphan
Benzene….
• Any compound
containing benzene is
called an aromatic or
arene compound…
• Any compound
containing straight or
branched chains of
carbons is called
aliphatic…
Notice the resonance in the
benzene ring…
 Common benzene compounds

toluene
toluene phenol anisole aniline xylene

cresol styrene benzoic acid salicylic acid

 Benzene rings with two
attached groups use a
special naming system…
They use the ortho, meta,
and para system…
Ortho (o) means one
p-bromo phenol apart…
Meta (m) means two
apart…
Para (p) means three
apart…
This only applies to
benzene rings with TWO
groups…

o-chloro toluene
1,4 dibromo aniline

Names…?

m-ethyl anisole

2-chloro 3-ethyl
toluene
 Benzene can also be called phenyl when you
want to treat it as an attached
group….either name is acceptable!

3-ethyl-2-phenyl pentane 2-chloro-2-phenyl heptane

 1,3,5 tri-nitro
toluene…
TNT!

Dichloro-Diphenyl-
Trichloroethane

DDT…
http://www.chem.ucalgary.ca/courses/351/orgnom/functional/func.html

Functional Group Name Ending

• Alcohol -ol

• Aldehyde -al

• Ketone - one

• Ether - oxy (small)

normal chain (large)
• Carboxylic Acid - oic acid

• Ester -yl -oate

 Aldehyde… 1-butanal

alcohol… 2-butanol

aldehyde… 1-pentanal

ketone… 1-phenyl 1-butanone

Carboxylic acid… 1-propanoic acid

 Carboxylic acid… 1-butanoic acid

ketone… 3-hexanone

ester… Ethyl butanoate

ether… 2-ethoxy propane

ketone… 5-chloro 3-hexanone

Methanal
Ethanoic acid
Formaldehyde
Acetic acid
(nickname!)
(nickname!)

Methanoic acid
Formic Acid
(nickname!)
 Example Structures of complex organic
molecules…

nicotine cholesterol

N
H
CH3
Meth N HO
amphetamine
O CH3
CH3
N CH3O NH2
N

O N N
CH3O
CH3 OCH3

caffeine mescaline
Think nomenclature is hard…?
ZITHROMAX (azithromycin tablets
and azithromycin for oral suspension)
contain the active ingredient
azithromycin, an azalide, a subclass of
macrolide antibiotics, for oral
administration. Azithromycin has the
chemical name (2R,3S,4R,5R,8R,
10R,11R,12S,13S,14R)-13-[(2,6-dideoxy-
3-C-methyl-3-O-methyl-α-L-ribo-
hexopyranosyl) oxy]-2-ethyl-3,4,10-
trihydroxy-3,5,6,8,10,12,14-heptamethyl-
11-[[3,4,6-trideoxy-3- (dimethylamino)-
β-D-xylo-hexopyranosyl]oxy]-1-oxa-6-
azacyclopentadecan-15-one.
Azithromycin is derived from
erythromycin; however, it differs
chemically from erythromycin in that a
methyl-substituted nitrogen atom is
incorporated into the lactone ring. Its
molecular formula is C38H72N2O12,
and its molecular weight is 749.00.
H H

C=C