Notes Organic Chemistry & Alkanes

History:
Vital Force Theory: organic molecules can only be created by living organisms.
In 1828, Professor Wöhler was finishing up his post-doctoral work as a student. While working
the laboratory he succeeded in synthesizing an organic compound, urea, previously observed
only in living tissue. Wöhler, pictured below, made this organic compound from a non-living
chemical substance, Ammonium Cyanate. He evaporated a solution of Ammonium Cyanate to
produce Urea. Organic Chemistry has undergone a substantial change since then. There are
well over a million synthetic organic compounds. Organic Chemistry is defined as the Chemistry
of Carbon and its compounds.

Carbon is a Lego like element.

I use the analogy Lego’s because these atoms tend to form bonds with themselves creating
different shapes. Like the two below, octane on the left and a steroid precursor on the right.

The shapes are created by the chemical property of carbon to form 4 bonds.

Hybridization:
The 4 bonds carbon forms is explained by Linus Pauling’s theory of hybridization. Carbon
atoms have an electron configuration of 1s2 2s2 2p2 This configuration corresponds to the
following energy level diagram.

2p

2s

1s

From the looks of this diagram, carbon might form 3 bonds as appears to be nowhere for a 4th
bond to form. Linus theorized that the two sublevels, s and p, in the second energy level formed
a hybrid sublevel.
This new energy level diagram is draw below

This shows four open orbitals, allowing for the formation of four bonds. Linus won a noble prize
for this theory. When carbon atoms are bonded using all single bonds the below shape forms
from the combination of one s orbital and three p orbitals. This hybridization is named sp3.
These shapes are verified by an analysis technique named X-Ray Crystallography. The
compound is frozen then photographed with X-Rays. The resulting pictures have show this
tetrahedral shape.

In this instance the carbon atom forms bonds with 4 different objects, resulting in a tetrahedral
shape, is shown above picture. This shape is formed by the repulsion of the electrons which
surround all atoms. So, if four objects are connected to a central object the farthest these
objects can be from each other forms a tetrahedral shape. The angle between these bonds is
109.5°. The blue balloon looking objects represent the orbitals where the four electrons in
carbons second energy level reside. This is the hybridization. Each of the four electrons have
equal energy and are all in the same orbitals, they have been moved to the same “Shell” instead
of having the 2s electrons located inside or underneath the 2p electrons.

This tetrahedral shape has also been verified by calculus. The addition of one sphere and three
dumbbell shapes produces this tetrahedral shape.
General Properties of Organic Molecules:
1. Flammable
2. High Vapor Pressure
3. Odorous
4. Covalently Bonded
5. Non-Polar – functional groups can change these from non-polar to polar or cause the
molecule to be bi-polar.
6. Low Solubility in Water – due to being non-polar as water is polar
7. Rate of Chemical Reaction is Normally Slow
8. Normally Found as Gasses and Liquids at Room Temp
9. Non-Conductive of Electrical Current

Alkanes:
The first classification for organic molecules is the most simple, the alkanet. The most simple
alkanet consists of only carbon and hydrogen atoms connected by single bonds.

Alkanes are common and for the most part chemically uncreative, the chemical reaction
combustion being the major exception.

Alkanes can be found in many common substances; natural gas, gasoline, plastics…

The chemical formula can be generalized as:

CnH2n+2
Where n represents the number of carbons and 2n+2 equals the number of hydrogen’s.
Nomenclature:
Nomenclature is the scientific term for naming compounds. The governing body is “The
International Union of Pure and Applied Chemistry”, or IUPAC for short. The following
statement is from their web site:

“The International Union of Pure and Applied Chemistry (IUPAC) serves to advance the
worldwide aspects of the chemical sciences and to contribute to the application of chemistry in
the service of Mankind. As a scientific, international, non-governmental and objective body,
IUPAC can address many global issues involving the chemical sciences.”

IUPAC was formed in 1919 by chemists from industry and academia. One of there main
functions is to objectively create rules for naming compounds in the most simplified manner
possible. This is equivalent to creating a new language, just like English grammar, there are
rules.

Even with the advent and acceptance of the IUPAC system some common names still persist,
when discussing a substance the IUPAC name should be used but the common name will be
accepted by most chemical organizations.
Alkane Nomenclature:
Naming of organic structures, unlike biological classification, follows a rigid set of rules. The
International Union of Pure and Applied Chemistry, abbreviated IUPAC, came up with a set of
rules that follows the same standards worldwide, and is accepted among all chemists. However,
common names of compounds, or names that have historical roots, are still used today for many
compounds.

The suffix for the alkane family is –ane.

prefix – root – suffix
prefix – where the substitutions are located
root – how many carbons are in the molecules longest chain
suffix – family – type of functional group (alkane, alkene, alcohol, ester, etc...)

Root words are named for its number of carbons:

# of carbons root
1 meth-
2 eth-
3 prop-
4 but-
5 pent-
6 hex-
7 hept-
8 oct-
9 non-
10 dec-
Example:
an alkane with 3 carbons is named propane
prop – for the 3 carbons
ane – for the family alkane (meaning all single bonds)

Formula Types:
A variety of methods are used to describe a chemical compounds composition. Sometimes you
will find a the chemical formula sufficient. Other times you need to see the structure drawn out,
this is referred to as the structural formula. This is a larger drawing which will show the atoms
are connected. Another is the condensed structural formula, this shows the connections in
around about manner. Lastly, a more lazy form is the line structure. This simplified drawing
assumes you know that carbon atoms make 4 bonds and that if you do not see a bond drawn
assume a hydrogen is occupying the undesignated bond. Also all ends and turns in the line
signify carbon atoms.
Examples:
Chemical Formula:
C4H10 Condensed Structural Formula:
CH3CH2CH2CH3
Structural Formula:
H H H H Line Structure:
H C C C C H
H H H H

Rules:
1. Find the longest chain of carbons, and use this number as the base/root/parent name
2. Number the chain with the end nearest the first subsistent carbon #1.
3. Give the location of the alkyl subsistent by the number of the main-chain carbon that it is
attached to.
4. Put the Constituents in alphabetical order (i.e. ethyl before methyl)
5. Substitution Syntax:
a. between numbers and words add a dash
b. between numbers add commas

Examples:

4-ethyl-octane 5-ethyl-octane
Correct Incorrect

4-ethyl-2-methylheptane 4-ethyl-6-methylheptane 2-methyl-4-ethylheptane

Correct Incorrect Incorrect
Side Chain Specific Rules:
4-propyloctane 4-isoproplyoctane
CH2CH2CH3 CH3CHCH3
CH3CH2CH2CH2CHCH2CH2CH3 CH3CH2CH2CH2CHCH2CH2CH3

5-butylnonane 5-secbutylnonane
CH2CH2CH2CH3 CH3 CHCH2CH3
CH3CH2CH2CH2CHCH2CH2CH2CH3 CH3CH2CH2CH2CHCH2CH2CH2CH3
5-isobutylnonane 5-tertbutylnonane
CH3
CH CH3 CH3
CH2 CH3 C CH3
CH3CH2CH2CH2CHCH2CH2CH2CH3 CH3CH2CH2CH2CHCH2CH2CH2CH3

Isomers:
Isomerization - same molecular formula, but different structure. Also creates different properties
for the molecule. The number of possible isomers increases rapidly as the length of the chain
increases. These molecules are isomers of the same chemical formula.

Examples:
Each of the following molecules has a chemical formula of C4H10 but they are different molecules
having different properties.
butane 2-methyl propane (isobutane)
More Examples:

hexane 2-methyl pentane 3-methyl pentane

2,2-dimethyl butane
2,3-dimethyl butane not
3,3-dimethyl butane
Chemical Equivalence – non-isomers:
When one first begins learning how to name organic compounds they typically have a difficult
time recognizing when two molecules are actually the same molecule. Depending on how the
structural formula is drawn, the same molecule may look different to the novice. Let’s look at
the following two structural formulas:
H H F H
F C C H H C C H
H H H H
These two molecules look different but they are actually the same. Single bonds are unique in
that the atoms on each side of the bond can rotate or spin around the bond. So, the difference
between the two above molecules is simply that the carbon-carbon bond is rotated to a different
position. At all times the fluorine and two hydrogens will be spinning about the carbon.

Let’s look a this molecule a little more, by the way, its name is fluoroethane. And the reason we
do not have to say 1-fluoroethane is because no matter which carbon we put the fluorine on,
that carbon will be carbon #1. The following structural drawings will all actually be of this same
molecule:
H H F H H H
F C C H H C C H H C C H
H H H H F H

H H H F H H
H C C F H C C H H C C H
H H H H H F

Yes, they look different, try using a molecular modeling kit and proving to yourself that yes
indeed, these are all the same. You will learn that you do not have to pull any of the atoms off
to have your model look like each structure above. You simply twist the carbon-carbon bond or
flip the molecule around.

Now lets talk about a new molecule, 1,2-difluoroethane. I just added another fluorine to our
fluoroethane molecule.
H H
F C C F
H H
These two fluorine atoms are said to be chemically equivalent. This means that both fluorines
will react, chemically, in exactly the same manner. To recognize you look at the carbon that the
fluorine is bonded to. Both fluorines have the exact same description, the fluorines are bonded
to a carbon that is singly bonded to another carbon and also bonded to two other hydrogens.
Since both fluorines fit this description they are chemically equivalent.

If we look at the hydrogens on this molecule we can demonstrate that they too are all chemically
equivalent. Each hydrogen fits this description, a hydrogen bonded to a carbon, the carbon is
singly bonded to another hydrogen, a fluorine and another hydrogen.

Looking back to the fluoroethane we can see that not all of the hydrogens are chemically
equivalent. On carbon #1, there is one fluorine and two hydrogens, on carbon #2 there are only
three hydrogens.

The following molecules have two colored atoms, these colored atoms are listed as either
chemically equivalent or non-equivalent.
Cl H
non-
F C C F
equivalent
H H
F H H H
H C C C C F equivalent
H H H H
Br Br non-
equivalent

The easiest way to recognize chemical equivalence, is to look for symmetry. If the two atoms
you are comparing have symmetry between themselves on the molecule, they are probably
chemically equivalent.
Cyclic Alkanes:
Alkanes can form compounds with themselves. By this I mean they commonly form rings.
Shown below is cyclohexane. It is a hexane molecule that has come around back onto itself.
The below you will find the chemical formula, structural formula and the line diagram.
H H
H H
C
H C C H
H C C H
H C
H HH
C6H12
Sources of Alkanes:
Crude oil is the main supplier. Crude oil is gently heated in a tower, this heating produces
vapors, the lighter compounds to rise higher in the tower, while the heavier compounds rise
very little. Collection equipment is stationed at various levels ready to remove hydrocarbons of
various masses. Alkanes tend to be light and very non-polar, thus they travel to the top of the
tower. Natural gas is the name given to the lightest of the alkanes, this gas is a combination of
methane, ethane and propane. Natural gas pockets are found above large deposits of crude oil.
See picture of refinement tower below.

Alkanes can also be made these synthetically in a lab, like Professor Wöhler, in 1828 made
urea. But his process is time consuming and expensive. Verify this yourself by pricing synthetic
motor oil verse regular motor oil. Synthetic can easily be 15 times more expensive.
 Modifications of Straight Chained Alkanes: Cracking
Hydrocarbons are indeed flammable, but as it turns out this is not enough to make a fuel a
“good” fuel. An important characteristic for fuels made up of different chemicals, like the mixture
named gasoline, is that all the fuels ignite at the same time. If some fuel ignites before it is
designed to ignite undesirable result occur. This phenomenon in your conventional internal
combustion engine is called “Engine Knock.” The effects of engine knocking vary, some
symptoms include; unpleasant sounds, poor fuel economy, poor engine performance or even
engine damage.

The timing of ignition is very important. Many processes are occurring in concert with each
other to deliver smooth power to the cars wheels. Pistons are rising then being forced down by
the explosion of these hydrocarbon vapors mixed with oxygen gas from the atmosphere. The
idea is to detonate this mixture, with a spark plug in gasoline engines, when the piston has
reached the top of the chamber, as the fuel explodes the piston is forced down, this downward
motion is mechanically converted to rotating motion and transferred to the wheels.

The knock occurs when some of the fuel enters the cylinder and ignites before the spark plug
has fired. This causes the piston to apply force to the parts in the motor at that are not designed
to accept this force, at this time. The reason for the premature ignition is due to the varied
flammability of the different hydrocarbons found in gasoline. Some hydrocarbons fire simply
because they find themselves in a hot cylinder, and ignite before the spark plug sparks.

You have no doubt seen the different ‘flavors’ of gasoline available at any gas station. Normally
“octane numbers” 87, 89 and 92 are available. The higher the number the less chance of
knocking. The alkane heptanes is considered the worst and is assigned an octane number of 0.
2,2,4-trimethylpentane, common name isooctane, earns an octane number of 100.

2,2,4-trimethylpentane

So, the more isooctane the higher the octane number and the less likely you will have a knock
occur. The more branching the better the fuel. Catalytic cracking, breaks apart straight chained
alkanes, then catalytic reforming “reforms” the bonds, as branched hydrocarbons. The above
isooctane could have been octane cracked and reformed as isooctane. The branching gives the
molecule increase stability. Is allows it to withstand higher temperatures as it waits to be ignited
by the firing spark plug. Aromatics, compound containing benzene rings, are also desirable
hydrocarbons due to their high stability.
Reactions of Alkane:
Combustion:
C3H8(g) + O2(g) → CO2(g) + H2O(g) + heat
complete – occurs in high oxygen environments

C3H8(g) + O2(g) → CO2(g) + CO(g) + H2O(g) + less heat

incomplete – occurs in low oxygen environments

Halogenation:
C3H8(g) + Br2(l) →
uv
C3H7Br (g) + HBr(g)

Dehydrogenation:
C3H8(g) →
Pt C3H6(g) + H2(g)

Organic Functional Groups:

Organic molecules can be very complex, not only for their ability to branch off but also for
specialized groupings of atom each of which give molecules special properties. Most any of
these groupings, named organic functional groups, can attach themselves to any organic
molecule in most any location. One molecule may have more than one of these groups giving
the molecule different properties. In our studies of “Organic Chemistry” the reactivity of these
functional groups will a main focus.
Another Classification for Carbons:
• primary carbon is bonded to one other carbon:
o both of these carbons
H H
H C C H
H H
• secondary carbon is bonded to two other carbons:
o the center red carbon only
H H H
H C C C H
H H H
• tertiary carbon is bonded to three other carbons:
o the center red carbon only
H
H C H
H H
H C C C H
H H H

• quaternary carbon is bonded to four other carbons

o the center red carbon only
H
H C H
H H
H C C C H
H H
H C H
H