Organic Chemistry
H
B
C
N
O
F
Si
P
S
Cl
Br
CHEMISTRY OF THE COVALENT
COMPOUNDS OF CARBON
COMBINED WITH A FEW OTHER
COMMON ELEMENTS:
H B N O Si P S F Cl Br I
I
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 have no
charge….
Most organic molecules contain C-C and C-H bonds which are
non-polar…water, which has slight charge, is polar
Because of this, most organic molecules do not dissolve in
water – For example, oil and water do not mix!
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
charge…is a liquid
Water - has slight
charge…is a liquid
NO ATTRACTION
ATTRACTION!
Methane –
has no
charge…
is a gas
Methanol –
Has slight charge
– is a liquid and
dissolves well in
water
Hydrocarbons –
contain hydrogen
and carbon bonds
Aliphatic
hydrocarbons –
chains of
carbons and
hydrogens
Functional
groups – altered
hydrocarbons
Aromatic
hydrocarbons –
contain benzenec
Alkanes
– all
single
bonds
saturated
Alkenes –
has some
double
bonds
unsaturated
Alkynes
has some
triple
bonds
-Ether
-Ester
-Aldehyde
-Ketone
-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:
contains carboncarbon double or
triple bonds.
H
H
C
H
H
C
• Saturated: contains
all carbon-carbon
single bonds.
H
H
C
H
H
H
C
C
H
H
H
Common Hydrocarbon Types
H
ALKANES
CnH2n+2
ALKENES
CnH2n
H H H H
H
C
H C
C C C
H H H H
H
H
H
HH C H H
H
H C
H
H H
H C C C C H
H H H H
H
H
ALKYNES
CnH2n-2
C H
HH C H H
C H
H
H C C
H
H C
C
H C C C H
H
only
single
bonds
H
H H
H C C C C C H
H
H H
at least
one
double
bond
at least
one
triple
bond
Structural Formulas – show the
structure of the atoms
Unbranched
(“linear”) Alkane
Structural
Formulas
CH3 CH2 CH2 CH2 CH3
CH3CH2CH2CH2CH3
Condensed
Structural
Formulas
Branched Alkane
CH3 CH CH2 CH CH3
CH3
CH3
CH3CHCH2CHCH3
CH3
CH3
some
bonds
shown
CH3CH(CH3)CH2CH(CH3)CH3
C5H12
Molecular Formula –
Tells me nothing about
Structure – just how many
of each element there are!
C7H16
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
Alkyne
or
CH CCH3
Condensed Notation
EVEN COMPLICATED BRANCHED STRUCTURES
CAN BE WRITTEN ON A SINGLE LINE
CH3
CH3 CH CH CH2 CH3
CH2 CH3
Branched
Alkane
for this reason many
handbooks use
condensed notation
CH3CH(CH3)CH(CH2CH3)CH2CH3
note use of parentheses these atoms are attached to the
Carbon atom that they follow
Skeleton Notation
CH3
CH3
CH3CH2CH2CH2CH3
C CH3
CH3
H
CH3
C
CH3CH2CH CH2
C CH3
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
H
H
C
H
CH2
H
C
CH2 CH2
C
H
H
Cyclopropane
H
H
H
C3H6
H
C
C
C
C
H
CH2 CH2
H
H
CH2 CH2
H
Cyclobutane
H
H
Testosterone
C
H
C4H8
CH2
H
C
C
CH2
H
CH2
H
C
H
C
H H
CH2 CH2
H
Cyclopentane
C5H10
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
C
Six carbons….
Longest chain….?
Bond types….?
All single bonds….
Attached groups…?
-CH3 = methyl
Number from what
side…?
Why…?
Hex….
-ane….
The right….
The group is attached to
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
bond…?
•Start numbering from what end…?
•Is the double bond or attached groups
more important…?
•How many groups are attached…?
5-chloro 7-methyl - 3 –
nonene
•What are they?
•Remember to report the groups
alphabetically….!
CH2
C
CH2 CH
CH3
Name this sucker….!
C
C CH3
CH2CH2CH2CH3
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?
Cl
CH3
CH3CCH2CH2CCH3
CH3
• 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!
CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH3
Octane
Are these both
octane though?
2-methyl heptane
CH3
CH3 CH2 CH2 CH2 CH2 CH2 CH3
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…
CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH3
Octane
2-methyl heptane
CH3
CH3 CH2 CH2 CH2 CH2 CH2 CH3
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 (C6H14). They don’t have the same IUPAC
name at all – they are totally different molecules, with totally different
properties!
CH3
CH3-CH2 - CH2-CH2-CH2-CH3
CH3-CH2 - CH-CH2-CH3
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!
Geometric Isomers
CH3
H
C
C
C
Same
molecule..
H
H
CH3
H
C
CH2CH3
C
C
C
CH3
H
CH2CH3
C
H
Which are isomers, and
which are the same
molecule…?
CH3
C
H
H
CH3
Isomers!
CH3
C
C
H
H
CH3
H
C
C
H
CH3
Isomers!
H
CH3
H
H
H
CH3
C
C
Same
molecule..
CH3
CH3
H
C
H
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 same
sequence of bonded atoms, but
differ in their 3-d orientation!
•Stereoisomers can be nonsuperimposable mirror images!
•We call the carbons that they are
attached to chiral, or asymmetric!
•This means they are nonsymmetrical!
•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…
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
cresol
phenol
styrene
anisole
aniline
benzoic acid
xylene
salicylic acid
p-bromo phenol
CH3
Cl
o-chloro toluene
Benzene rings with two
attached groups use a
special naming system…
They use the ortho, meta,
and para system…
Ortho (o) means one
apart…
Meta (m) means two
apart…
Para (p) means three
apart…
This only applies to
benzene rings with TWO
groups…
NH2
1,4 dibromo aniline
Br
Br
Names…?
CH2CH3
Cl
CH3
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
CH3
1,3,5 tri-nitro
toluene…
TNT!
NO2
NO2
NO2
Dichloro-DiphenylTrichloroethane
DDT…
http://www.chem.ucalgary.ca/courses/351/orgnom/functional/func.html
OH
R
Functional Group Name
Ending
•Alcohol
-ol
•Aldehyde
-al
•Ketone
- one
•Ether
- oxy (small)
normal chain (large)
•Carboxylic Acid
- oic acid
•Ester
-yl -oate
O
R
C
H
O
R
C
R
R
O
R
O
R
C
OH
O
R
C
OR
O
Aldehyde…
CH3CH2CH2
C
H
OH
CH3CHCH2CH3
1-butanal
alcohol…
2-butanol
O
H
C CH2CH2CH2CH3
aldehyde…
1-pentanal
ketone…
1-phenyl 1-butanone
Carboxylic acid…
1-propanoic acid
O
C CH2CHCH3
O
CH3CH2
C
OH
O
CH3CH2CH2
C
OH
Carboxylic acid…
1-butanoic acid
ketone…
3-hexanone
O
CH3CH2 C CH2CH2CH3
O
CH3CH2CH2
C
O
CH2CH3
ester…
Ethyl butanoate
CH2CH3
O
ether…
2-ethoxy propane
CH3CHCH3
O
Cl
CH3CH2 C CH2CHCH3
ketone…
5-chloro 3-hexanone
O
O
H
C
CH3C
H
OH
Methanal
Ethanoic acid
Formaldehyde
(nickname!)
Acetic acid
(nickname!)
O
H
C
OH
Methanoic acid
Formic Acid
(nickname!)
Example Structures of complex
organic molecules…
nicotine
cholesterol
N
H
Meth
amphetamine
N
O
CH3
N
HO
CH3
N
N
O
CH3
N
CH3
caffeine
NH2
CH3O
CH3O
OCH3
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-dideoxy3-C-methyl-3-O-methyl-α-L-ribohexopyranosyl) oxy]-2-ethyl-3,4,10trihydroxy-3,5,6,8,10,12,14-heptamethyl11-[[3,4,6-trideoxy-3- (dimethylamino)β-D-xylo-hexopyranosyl]oxy]-1-oxa-6azacyclopentadecan-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.