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General Chemistry | 213
Chapter Fourteen
Organic Chemistry
Organic chemistry just now is enough to drive one mad. It gives me the impression of a
primeval forest full of the most remarkable things, a monstrous and boundless thicket,
with no way of escape, into which one may well dread to enter.— Friedrich Wöhler 1835
F
undamentally, organic chemistry is the study of carbon compounds. These
compounds are made out of carbon, hydrogen, and oxygen with the
occasional addition of nitrogen, chlorine, bromine, phosphorus and sulfur.
Even though organic compounds only use eight of the more than one hundred
elements found on the Periodic Table, the multitude of compounds made and the
manner in which they react are dizzying.
You may know someone who has taken organic chemistry and you have
probably heard stories about large stacks of notecards filled with thousands of
reactions and the hours it takes to memorize them all. The fear of organic
chemistry grips most budding science students and it is believed that organic
chemistry is something to be survived and not enjoyed.
Much of organic chemistry is learning the language of organic chemistry. When
an instructor says to use acetone or toluene in a reaction, a structure or formula
must come to mind. It could be quite deadly to mix the wrong set of chemicals
together. To this end, we will begin our study with organic nomenclature.
Nomenclature
Nomenclature is a system for naming compounds. In organic chemistry,
nomenclature starts with a root name that is based on the number of carbons in
the longest continuous chain in the compound. The root name is a prefix, it
begins the name, and other things are added to it to clarify precisely how the
molecule is put together. Let’s start with the root prefixes.
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Number of
Carbons
1
2
3
4
5
6
7
8
9
10
Root
Prefix
methethpropbutpenthexheptoctnondec-
The dash found at the end of each name indicates that something must come
after the prefix, specifically, a suffix, that will indicate something about the
bonding occurring in the compound.
Organic chemists organize compounds by their bonding structure. In its
simplest form, compounds containing just carbon and hydrogen are broken up
into three major bonding groups.
Bonding Group
All single bonds
One double bond
One triple bond
General Compound Name
Alkane
Alkene
Alkyne
Suffix
-ane
-ene
-yne
To name a compound you combine the prefix of the root name with the suffix
that indicates the type of bond found in the compound. Therefore, compounds
like methane, propene, and butyne are all possible. These and other compounds
are shown on the next page.
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Alkane
Name
Alkene
H
H
H
C
Methane
H
C
Alkyne
Ethene
C
H
H
Name
Name
H
H
C
C
Ethyne
H
H
H
H
H
H
C
C
H
H
H
Ethane
H
C
C
Propene
C
H
H
H
H
H
C
C
C
H
H
H
H
C
C
H
H
H
Propane
H
C
C
H
Propyne
H
H
H
C
C
H
H
H
C
C
H
C
H
H
H
H
H
H
H
Butene
C
H
C
H Butyne
Alkenes and Alkynes
A double or triple bond can be found anywhere within a compound. Based on
the simple rules presented thus far, it is impossible to distinguish the difference
between the following compounds,
H
H
C
H
C
H2C
H3C
CH3
C
CH3
H3C
C
H
C
H
H
H
C
H
H
C
CH3
H3C
C
CH2
H
All of these compounds have 4 carbons so generically, these are all some kind of
butene but the shape of these molecules and the placement of the double bond
changes, so they cannot all have the same name.
We can begin to distinguish between them by stating the placement of the
double bond.
H
H
C
H
C
H2C
1-butene
H3C
CH3
C
CH3
H
H3C
C
C
H
2-butene
H
H
H
C
H
C
CH3
2-butene
H3C
C
CH2
3-butene
H
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This helps, but there is no rule that says that you must start counting from the
left, but there is a rule that says that we need to keep our numbers as small as
possible. So, if we count from the right, rather than the left, we can see that,
counting from the right, 3-butene should have been named 1-butene which
makes the first and last compound on our list the same molecule.
So what about the middle two compounds both of which are named 2-butene? It
is clear that these molecules are not the same since the CH3 groups are in
different positions on the molecule. The first molecule has the CH3 groups on
the same side of the double bond and if you turn your head sideways you can
see that the general shape is “C” shaped. This form of the molecule is called
“cis” so the name of our molecule would now be cis-2-butene.
H3C
CH3
C
C
H
H
cis-2-butene
The shape of the other molecule is “trans.” This makes sense since a transAtlantic flight is one that goes across the Atlantic. If we start on the first CH3
group we must go across the double bond (trans) to get to the other CH3. This
molecule is called,
H3C
H
C
H
C
CH3
trans-2-butene
You will notice that there is a dash between the various parts of this name. This
is because these are supposed to be one long name, so we connect the various
parts with dashes.
In similar fashion, we can name alkynes by adding the starting point of the triple
bond to the name.
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H
C
C
H
H
C
C
H
H
H
C
H
H H
1-butyne
H
C
C
2-butyne
C
H
H
Cis and trans do not apply to alkynes since their bonds are linear. Only double
bonds and rings can be cis and trans. We will discuss ring structures in a later
section.
Branching and Side Groups
A carbon chain need not be linear. It can have smaller carbon chains hanging off
of them. A carbon compound with side groups is said to be “branched.” These
side groups have the same root names as those presented earlier (meth-, eth-, etc)
but we distinguish between them and the main chain of the molecule by giving
the side groups a –yl ending. Therefore, a side group would have the following
name.
Number of Root
Carbons
Prefix
1
methyl
2
ethyl
3
propyl
4
butyl
Etc.
Suppose we had the following compound,
H
H
H
H
C
C
C
H
CH3 H
H
2-methylpropane
The longest chain of this compound has three carbons and it has all single bonds
so its root name is propane. But hanging off the second carbon is a methyl group
(circled in red) which must be added to the name. We must tell the reader which
side group is attached and where it is attached on the molecule so the name of
this compound is 2-methylpropane.
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If there are multiple carbon side groups on a compound we must tell the reader
where each of them are located and how many there are. In addition, if they are
not all the same, then the side groups are put alphabetically into the name of the
compound. When multiple copies of the same side group show up in a
compound we tell the reader how many are present by using a common prefix
used in non-metal/non-metal nomenclature,
Number of
Side Groups
2
3
4
5
6
Prefix
ditritetrapentahexa-
It may seem counterintuitive but we must state where every copy of a side group
is found and how many are found on a compound. For example, consider the
following,
H
CH3 H
CH3 H
H
C
H
1
C
2
C
CH3 H
3
C
H
4
C
5
H
H
The root name for this compound is pentane but it also has three methyl groups.
They are found on the number 2 and number 4 carbons, but since we must name
where EVERY methyl group is found AND the total number present, the name
of this compound is,
2,2,4-trimethylpentane
So we see that there is a methyl group on the number two carbon, another
methyl group on the number two carbon, and one methyl group on the number
four carbon. That makes three methyl groups so we say that this compound is a
trimethyl compound, in this case, 2,2,4-trimethylpentane.
If more than one kind of side group is present then they are placed into the name
alphabetically. Consider the following compound,
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CH3
H
H
C
CH3 H
1
H
C
2
C
CH2 H
3
CH3 H
C
4
H
C
H
5
H
C
6
H
H
This compound is six carbons long and has all single bonds, therefore its root
name would be hexane. On the number 2 carbon there are two methyl groups
and on the number 4 carbon there is a two carbon chain side group called an
ethyl group. Alphabetically, ethyl comes before methyl, so the name of this
compound would be,
4-ethyl-2,2-dimethylhexane
Halogen Side Groups
Carbon chains are not the only possible side group on a compound. Halogens
are often found as side groups of organic compounds also. To name a halogen as
a side group, the “-ine” ending of the halogen is removed and replaced with an
“o.”
Side Group
Halogen
Name
Name
F
Fluorine
fluoro
Cl
Chlorine
chloro
Br
Bromine
bromo
I
Iodine
iodo
As before, if we have multiple versions of the same halogen on a compound then
we number them and add di-, tri-, tetra-, etc., as appropriate. We also write them
alphabetically along with all of the other side groups. Adding chlorine and
bromine to our previous compound we would have,
CH3
Cl
H
C
1
CH3 H
C
2
C
CH2 H
3
C
4
C
H
5
C
6
H
H
CH3 Cl H
Br H
5-bromo-1,3-dichloro-4-ethyl-2,2-dimethylhexane
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Multiple Double Bonds and Side Groups
When a compound has more than one double bond we must indicate where each
double bond starts and state whether the double bond is cis, trans, or neither cis
nor trans. For example,
The first double bond is neither cis nor trans but the second double bond is cis.
When cis and trans are used, they always start the name. When multiple double
bonds are present, you must use di-, tri, and tetra- to indicate the number. In this
case, since this compound has two double bonds, it is a diene, specifically, 1,3pentadiene. But, one of the bonds is cis and this must be added to the name.
You do not need to indicate which of the bonds is cis (do not write 3-cis). Any
knowledgeable reader will understand that the cis only applies to the double
bond starting on carbon number three. Therefore the full name of this
compound is,
cis-1,3-pentadiene
Ring Structures
Alkanes are not limited to linear chains of carbon compounds, they can also be
rings. When an alkane is in a ring, the prefix “cyclo” is added to the name. For
example, consider the names of the following structures,
cyclopropane
cyclobutane
cyclopentane
cyclohexane
It might seem odd to write some of these structures this way, particularly
cyclobutane which is obviously a square but has been drawn here like a
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diamond. The reason for this is that, when the hydrogen’s are added to the
compound, we attach them using vertical straight lines;
cyclopropane
cyclobutane
cyclopentane
cyclohexane
This has the added advantage of helping to indicate the shape of the molecule.
cyclopropane
cyclobutane
cyclopentane
Above the ring
cyclohexane
Below the Ring
The same information can be conveyed by using dashed and solid triangular
bonds. Dashed triangular bonds are always pointing away from you and solid
triangular bonds are always pointing towards you. So, in similar fashion, we
could write,
cyclopropane
cyclobutane
Sometimes using triangular bonds is
the most convenient way to indicate
the shape of a molecule. For example,
in cholesterol, some of the bonds are
above the ring, others are below the
ring, and others are not on a ring but
are still pointing away from you. It is
inconvenient to attempt to draw this
large molecule in such a way that will
make these bonds easily shown. Using
triangular bonds accomplishes this
task.
cyclopentane
cyclohexane
H
H
H
H
H
H
H
Cholestrerol
H
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Cis and Trans in Rings
If drawn improperly, it is impossible to know the spatial relationship between
side groups attached to rings.
It is best to draw the bonds straight up and down or use wedges and dashed
lines to indicate up and down on a ring. The reason this is important is that
rings, like alkenes, can be cis and trans. For example, consider the following
molecules,
When both chlorines are on the bottom (or top) of the ring, they are cis to each
other and when one is on top and the other is on the bottom then they are trans
to each other. The bonds in the ring behave like a double bond. They keep the
atoms rigidly held into position which allows the molecule to be either cis or
trans.
Even so, when more groups are added to a ring or across a double bond it can
get difficult to determine whether a molecule is cis or trans. For example,
H
H
Br
H
I
Cl
I
Cl
Br
bromoiodo-2-chlorocyclopropane
Br
C
Cl
H
C
I
C
I
C
Cl
bromoiodo-2-chloroethene
Br
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We can rightfully ask, which of the compounds has the name listed below it?
The answer is that both molecules have this name but in organic chemistry that is
impossible. Two molecules with different structures cannot have the same name
so there must be a way to tell the difference between them. Unfortunately, cis
and trans does not help us because it doesn’t tell us which atoms we are choosing
to be cis and trans. We must use another kind of nomenclature to describe the
differences between these molecules. We will use E, Z nomenclature.
E, Z Nomenclature
You use E and Z when cis and trans fails to properly identify similar groups.
The method relies on the Cahn-Ingold-Prelog ranking system to determine
whether a compound is cis-like (Z) or trans-like (E).
Cahn-Ingold-Prelog Ranking System
To rank the groups using EZ nomenclature the Cahn-Ingold-Prelog ranking
system is used. This system ranks the attachments one atom at a time until a
difference is found. The group that is larger FIRST, wins! For example, consider
the two side groups;
Main Chain
H
F
H
C
C
C
H
H
H
1
2
3
Higher Rank
H
Main Chain
H
H
H
C
C
C
H
H
H
I
1
2
3
Lower Rank
Starting at the main chain you go to carbon number one of the side chain. Doing
so you will find that both side groups have a CH2 attached to a carbon. Thus far,
both sides groups are equal. Moving on to carbon number two the side group on
the left has a hydrogen, a carbon and a fluorine attached to it while the one on
the right has two hydrogens and a carbon. Since fluorine is larger than a
hydrogen, the left side chain is ranked higher than the one on the right even
though the one on the right is bigger since it has iodine on it. BUT, since you got
to the fluorine (on carbon #2) before you got to the iodine (which was on carbon
#3), the left side group wins. So rank has nothing to do with overall size; it has to
do with the size of the group that you come to first.
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Using this system we can resolve our problem with the nomenclature of the
molecules shown above,
H
I
H
Br
Cl
Br
Cl
I
E
H
C
H
C
Cl
Z
trans-like
I
C
Br
E
bromoiodo-2-chlorocyclpropane
C
Cl
trans-like
cis-like
Br
I
Z
cis-like
bromoiodo-2-chloroethene
If we draw an imaginary line down the middle of the bond connecting the two
carbons of interest we can rank the constituents attached to each carbon atom.
Chlorine is bigger than hydrogen and iodine is bigger than bromine. By circling
the large of the two constituents we can see that the first molecule in each group
looks “trans-like” and the second molecule looks “cis-like.” We label these E and
Z respectively and add the designation to the name.
H
I
Cl
Br
H
Br
Cl
I
H
E-bromoiodo-2-chlorocyclpropane
Z-bromoiodo-2-chlorocyclpropane
I
C
E-bromoiodo-2-chloroethene
C
Cl
Br
H
Br
C
Cl
Z-bromoiodo-2-chloroethene
C
I
You will notice that the E and Z designation resolves the problem of identifying
the spatial orientation of the atoms on these molecules. Unfortunately, our
problem is not completely resolved. The cyclopropane molecules shown above
are not uniquely identified by using the E, Z designation. There are two possible
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configurations for both E and Z bromoiodo-2-cyclopropane. These are shown
below.
H
I
I
Cl
Br
Br Cl
H
Br
Br H
Cl
I
I
H
E-bromoiodo-2-chlorocyclpropane
Z-bromoiodo-2-chlorocyclpropane
Cl
Based on the information presented thus far, both pairs of molecules would
share the same name but are actually different molecules. You will notice that
the left hand molecule and the right hand molecule in each pair are related to
each other by being non-superimposable mirror images of one another. To
provide each molecule with a unique name we must find a way of indicating to
the reader which molecule is which. We do this by using a new naming
convention called an R, S configuration.
Optical Activity
Many molecules are related to each other by being mirror images of one another.
When molecules are related in this way they are said to show “handedness”, that
is, they are related to each other like your right hand is related to your left. To
discover which molecule is left handed and which one is right handed we use the
Cahn-Ingold-Prelog method of ranking side groups to decide. Molecules that
show handedness all share one thing in common, they all have at least one
carbon with four different things attached to them.
These molecules are mirror images of each other, but they are not the
same. You cannot convert one into the other without breaking a bond.
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Molecules that are non-superimposable mirror images of one another are known
as enantiomers. The carbon to which the four groups are attached is known as
the “chiral” carbon and molecules that have handedness are said to be chiral or
have chirality.
Chiral molecules have another unique property; they cause light to rotate as it
passes through their solution. As a consequence, another way of saying that a
molecule is chiral is to say that the molecule shows optical activity.
The only way to tell how much light rotates as it travels through a solution is by
direct observation. A polarimeter is used for this purpose. A light source sends
light through a polarizing filter which causes the light to travel only one
direction. As this light passes through a 1 decimeter long tube of solution, the
light begins to twist. At the other end there is another polarizing filter that is
moved until the maximum amount of light is observed as it passes through the
solution. The difference in the angle between the first filter and the second filter
is the specific rotation of the organic compound. Many things effect the amount
of rotation. The concentration of the solution, temperature, length of the tube,
and even the wavelength of the light all play a role in determining the amount of
observed rotation. As a consequence, an equation is used to normalize all of
these factors and determine the specific rotation of the molecule,
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Where T is the temperature (usually, 20°C) and λ is usually the 589 nm line of the
sodium spectrum which is also known as the “D” line. The sign of the rotation is
always given as either positive (+) or negative (-). So, if the observed angle of a
0.2 g/mL solution in a 1 decimeter tube is +1.3° at 20°C, then the specific rotation
would be,
+1.3°
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Unfortunately, the actual rotation of a molecule, or even the direction of rotation
cannot be easily predicted based solely on the molecules structure, so a
convention called R,S configurations are used to determine whether a molecule is
right or left handed. This convention does not predict optical rotation and there
is no direct connection between an R, S configuration and the actual rotation of a
molecule. An R, S configuration only helps us to draw optically active
compounds and not predict how they rotate light.
R, S Configurations
The molecule, 2-butanol, has two versions, a right handed and a left handed
version. These two are optical isomers of each other and are related by being
mirror images of one another.
To distinguish between them we will use the Cahn-Ingold-Prelog ranking system
to rank the four groups attached to the central carbon atom. In this case, the
oxygen, with a mass of 16, has the highest rank (1). The next highest is the –C2H5
group (2) and then the –CH3 (3). Finally, hydrogen has the lowest rank (4) of the
four groups attached to the central carbon.
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The system works best if the group of lowest rank is pointing away. In this case,
hydrogen is the lowest ranking group and it is pointing away as indicated by the
dashed line. Starting at the OH group (and ignoring the attachment of lowest
rank, the hydrogen (4)) we move clockwise until we get to the C 2H5 group and
then continue clockwise to the CH3. This clockwise rotation indicates that this
molecule is right handed and is labeled R which stands for recto, the Latin word
meaning “right.” The optical isomer is S-2-butanol. The “S” stands for sinister,
the Latin word for “left.”
If the attachment of lowest priority is not pointing away then the actual rotation
will be the opposite of how it appears. For example, if we draw 2-butanol so that
the hydrogen is pointing towards us, by following the ranking of the
attachments, the molecule appears to S. But, we are looking at the molecule
wrong. The eye in the picture below is looking at the molecule from the right
direction, where the hydrogen is away. From that perspective, the red arrow is
moving clockwise or R. So although the molecule looks S to us, it is actually R,
so this molecule is R-2-butanol.
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We can now resolve the problem that we had earlier with the cyclopropane
molecule.
Earlier, we called these molecules E-bromoiodo-2-chlorocyclopropane but found
that we could draw two versions of this molecule with the same name. One of
these molecules is shown above but drawn twice to show the rotation around the
two different chiral atoms in the molecule. On the left, the carbon with the blue
dot has four different groups of atoms attached to it. In order of their rank, this
chiral carbon is attached to,
1: Chlorine
2: A carbon with iodine and bromine
3: A carbon with two hydrogens
4: A hydrogen atom
The hydrogen has the lowest rank. It is on the top of the molecule and by
convention, this means that it is pointing towards us. Therefore, the rotation that
we see is opposite to the actual rotation so, although the rotation appears to be S,
it is actually R. This carbon atom is R.
In order of rank, the chiral carbon on the right molecule is attached to,
1: Iodine
2: Bromine
3: A carbon with hydrogen and chlorine
4: A carbon with two hydrogens
In this case the carbon with two hydrogens has the lowest rank and because of
the orientation of the molecule, it is pointing away from us. Therefore, the
rotation that we see is correct. The rotation is clockwise. This carbon atom is R.
Therefore, this molecule is R, R-bromoiodo-2-chlorocyclopropane. The mirror
image of this molecule would be S, S-bromoiodo-2-chlorocyclopropane. By
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using R, S nomenclature rather than E, Z, the problem of their nomenclature has
been resolved.
Labeling Carbon Atoms
Sometimes it is useful to discuss molecular structures by referring to a carbon
atom by the number of other carbons attached to it. A carbon atom can have as
many as four other carbon atoms attached to it or as few as none. Each of these
conditions is given a special name, they are,
These designations sometimes show up in the names of compounds. For
example, 2-butanol is sometimes known as sec-butanol since the OH group is on
a secondary carbon. Also, it is very common to refer to 2-chloro-2methylpropane as t-butyl chloride, since the chlorine is on the tertiary carbon
and there are four carbons in the structure.
A molecule usually has several different kinds of carbons in its structure. For
example, the molecule below has five 1° carbons, one 2° carbon, one 3° carbon
and one 4° carbon.
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Functional Groups
Hydrocarbons are not particularly reactive compounds. Since carbon and
hydrogen have very similar electronegativities (2.5 and 2.1 respectively) the
bonds between them are almost entirely covalent. This renders these molecules
essentially inert. If a highly electronegative atom like oxygen, nitrogen, or a
halogen is bonded to a hydrocarbon, these atoms polarize the molecule and this
gives the molecule a site where reactions can take place. With the addition of an
electronegative atom, hydrocarbons become reactive and can do interesting
chemistry. The kinds of chemistry that can be done depend on the nature of
these additional electronegative atoms. These atoms convert an otherwise inert
hydrocarbon into a functioning molecule capable of all kinds of chemistry. They
are, therefore, called functional groups.
Name
Functional Group
Alkyl Halide
Alcohol
Amine
Ether
Aldehyde
Aromatic (Arene)
Name
Acid Halide
Acid
Amide
Ester
Ketone
Functional Group
Alkyl Halides
As stated previously, hydrocarbons, that is, alkanes, are essentially inert. To
make them reactive an electronegative atom must be added to the compound.
While it is possible to add oxygen to a hydrocarbon, doing so is not really an
organic reaction, it is a combustion. Burning a hydrocarbon is not very useful
procedure toward organic synthesis.
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Hydrocarbons are so unreactive that very few reactions are known to occur with
them. The most important of these reactions is called Free Radical Halogenation,
a reaction that converts a hydrocarbon into an alkyl halide.
௎.௏. ௟௜௚௛௧
CH4 + Cl2 ሱ⎯⎯⎯⎯⎯ሮ CH3Cl + HCl
The product of Free Radical Halogenation is an alkyl halide (CH3Cl) and the
hydrohalide (HCl). Free Radical Halogenation is not restricted to chlorine;
bromine is often used and is usually preferred. The reactivity of the halogens
follows their reactivity on the Periodic Table. On a relative scale the reactivity’s
are,
Fluorine (108) > Chlorine (1) > Bromine (7×10−11) > iodine (2×10−22)
Fluorine is the most reactive, but because it is so reactive the products are
difficult to control so it is rarely used. Chlorine reactions rates are relatively fast
but not so fast that they cannot be controlled so chlorination is very common.
The bromine reaction is slow and takes high levels of UV light to cause the
reaction to go, but the reaction usually gives just one, or a few very selective
products to it is commonly used. The reaction with iodine is so slow as to be
essentially non-existent so it is not used for Free Radical Halogenation.
It is important to note that Free Radical Halogenation does not occur just
anywhere on a molecule. The halogens prefer to replace the hydrogen’s found
on the most substituted carbons. That’s just a fancy way of saying that
halogenation will occur preferentially on a tertiary carbon if one is present, or in
the absence of a tertiary carbon, halogenation will occur on a secondary carbon.
Actually, this reaction can be quite selective. Consider the following table,
Reactivity of Halogens on Various Carbons
1°
2°
3°
Chlorine
1
3.5
5
Bromine
1
97
∞ (infinite)
This table shows us that a tertiary carbon is five times more reactive than a
primary carbon while being chlorinated, and infinitely more reactive when
brominated. If a tertiary molecule is brominated, the bromine will end up on the
tertiary carbon and nowhere else. Overall, we can see that a halogen will end up
on the most substituted carbon during Free Radical Halogenation.
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The Free Radical Halogenation of an alkane is the first reaction learned by most
students in organic chemistry. The reason, of course, is because it takes a
relatively inert alkane hydrocarbon and makes it reactive by adding a halogen.
The halogen is electronegative which means that it pulls electrons toward itself
which gives the halogen a partial negative charge and makes the carbon to which
it is attached, slightly positively charged. These charges provide a site for further
reactions to occur. Thus, the relatively inert hydrocarbon is now ready to be
turned into other more interesting compounds, like alcohols.
Alcohols
Alcohols are organic compounds with –OH groups. Very often they are made
from alkyl halides. The reaction is simple enough,
Alcohols are named by adding “ol” to the root name of the longest chain. Any
molecule with an “ol” on the end is an alcohol. Cholesterol, propylene glycol
(anti-freeze), estradiol (a hormone), and nonoxynol-9 (spermicide) are all
alcohols.
When necessary, we must name where the alcohol is found along the chain.
Some common alcohols and their names are given below,
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A couple of these alcohols are worthy of discussion. One of the names for
propanol is n-propanol. The “n” stands for “normal” propanol and this is
always understood as meaning propanol with the OH on the end carbon. We
would also write n-butanol and n-pentanol if these alcohols had their OH on
their end carbons.
The other alcohol that should be discussed is 2-propanol which is more
commonly known as isopropyl alcohol or rubbing alcohol. The term “isopropyl”
is common in organic chemistry so it is important that it be understood.
You will notice that the term “isopropyl” as well as “t-butyl” have the familiar
“yl” ending that indicates that it is a carbon side group, in this case, it is a side
group to an alcohol OH group. All “iso” groups can be written as
(CH3)2CH(CH2)n- where n can be any number between 0 and 3. The term “iso”
means “the same” so isobutyl means that this compound has the same number of
carbons as butane, but a different structure.
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(CH3)2CH-
(CH3)2CHCH2-
(CH3)2CH(CH2)2-
Alcohols that are smaller than about 6 carbons are soluble in water. If the alcohol
is any larger than about six carbons, the alcohol becomes insoluble. Even though
an alcohol has an –OH group, it is not a base. Alcohols behave like acids, that is,
they give off an H+ ion. This is because the carbon-oxygen bond tends to be very
strong. The resulting structure behaves like water, where the oxygen gives off an
H+ ion.
Most of the reactions done with alcohols can be explained by remembering that
alcohols behave as acids.
Aldehydes and Ketones
Aldehydes and ketones are two of a large class of compounds called carbonyls.
Carbonyl compounds include aldehydes, ketones, acids, amides, acid halides
and esters. What all carbonyls share in common is the functional group, C=O.
What makes aldehydes and ketones different from other carbonyls is that these
compounds only have a C=O and no other electron withdrawing groups.
The only difference between an aldehyde and a ketone is where the C=O is
found. If the C=O is found on a primary carbon, then the molecule is an
aldehyde, and if it is found on a secondary compound then the molecule is a
ketone. In terms of nomenclature, an aldehyde always ends in –al, and a ketone
ends with an –one. Common ketones are acetone (used in fingernail polish
remover) and testosterone (a male sex hormone). Most aldehydes are known by
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their common names. Formaldehyde is use in embalming and benzaldehyde is
the active ingredient in almond extract. Glucose is an aldehyde even though it is
not named like an aldehyde and fructose is a ketone even though there is no
indication of the presence of a ketone in its name.
Aldehydes and ketones are usually made by oxidizing an alcohol though many
other methods could be used.
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Carboxylic Acids
Carboxylic acids have the functional group, COOH. They are named by adding
-oic acid to the root name of the molecule. Some carboxylic acids are shown
below along with their common names.
Carboxylic acids are generally soluble in water but when the carbon chain
exceeds about six carbons (hexanoic acid/caproic acid) the compounds become
insoluble. Very large acids like stearic acid are insoluble and they will float on
the surface of water. Nearly all oils are very large acid molecules and when they
get about twelve carbons long they are called “fatty” acids. Both lauric acid and
stearic acid are fatty acids.
All carboxylic acids are weak acids. They only partially dissociate in water.
Vinegar (acetic acid) is the most common carboxylic acid, and it smells the best.
Butanoic acid smells like rancid butter and hexanoic acid is the source of order
among goats. The Latin name for goat is “caprinus” from which caproic acid
derives its name.
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Esters
Many esters smell very good. The smell of a banana, wintergreen, a crisp green
apple, and pineapple are all due to the presence of esters. As a consequence,
esters were once used in perfumes. Unfortunately, the chemical link that makes
an ester is also easily broken and so you could leave home smelling like cherries
(geranyal butyrate) but return home smelling like rancid butter (butyric acid).
As a consequence, esters are no longer used in perfumes.
Since esters are easily broken, pharmaceutical companies use the property to
their advantage. Acids often cause indigestion while esters do not. Products like
Ester-C effectively change the acidic property of vitamin c (ascorbic acid) but
make the vitamin fully available since the ester bond will be broken and the
vitamin made available in the gut. Aspirin is also an ester whose active
ingredient is salicylic acid but whose ester is more easily tolerated.
Esters are made by linking an acid with an alcohol. The link occurs through the
oxygen on the alcohol rather than the acid. The water that is produced is made
from an H+ coming from the alcohol and the OH- from the acid. This means that
the alcohol is acting like an acid (an important point that was made earlier) and
the acid is acting like a base. The general reaction is shown below,
Ester Nomenclature
The name of an ester begins with the alcohol and ends with the name of the acid.
They alcohol takes the root name of the alcohol and adds a –yl and the acid
removes the –ic acid ending and adds an –ate. In our example, the alcohol is
ethanol and the acid is ethanoic acid so the name of the ester is,
ethanol + yl ethanoic acid + ate
ethyl
ethanoate
In the example above, ethanol reacts with ethanoic acid. The resulting
compound is ethyl ethanoate. Some representative esters are shown below.
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Ester Name
Formula
Odor or occurrence
Allyl hexanoate
pineapple
Benzyl acetate
pear, strawberry, jasmine
Ethyl pentanoate
apple
Butyl butyrate
pineapple
Ethyl acetate
nail polish remover, model
airplane glue
Ethyl butyrate
banana, pineapple, strawberry
Ethyl hexanoate
pineapple, waxy-green banana
Methyl salicylate (oil of
wintergreen)
Modern root beer, wintergreen
Amyl acetate (pentyl
acetate)
apple, banana
Amines
Esters smell very nice. Amines on the other hand do not. Consider yourself
fortunate if the amine only smells as bad as ammonia. Most amines have a very
offensive smell and their names often suggest the foul nature of their odor.
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Names like putrescine and cadaverine suggest the odor of rotten and dying flesh
and the strong odor of fish is also associated with amines.
Amines are soluble in water since they can hydrogen bond with water. Like
most other organic compounds, only the smaller amines are soluble because as
the chain length grows, dispersion forces take over making the compounds
insoluble.
Amine Nomenclature
Amines are distinguished by the presence of an –NH2 on an alkane. There are
two ways in which this group is used in the name of a compound, either as a side
group called an “amino” group, or as the main functional group when it is called
an “amine.”
When an –NH2 is the main functional group “amine” is added as a suffix to the
root name of the compound. Unfortunately, there is great variation in the
nomenclature of amines and sometimes the carbon chain is expressed like a side
group and given a –yl ending, and depending on the situation, the –NH2 can be
described as a side group and it takes on the typical “o” of a side group (chloro,
oxo, amino).
CH3-CH2-CH2-NH2
propane + amine = propanamine
propylamine
aminopropane
All three of these names can be found as the name of this compound. Many
compounds that do not end in “amine” are amines but their name will indicate
the presence of the amine by ending in “in” or “ine.” There are many such
compounds that we use in daily life, most of them act as drugs.
Penicillin
Amoxicillin
Epinephrine
Ephedrine
Morphine
Dopamine
Serotonin
Acetaminophen
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Primary Amines
Amines can be divided into four groups, primary, secondary, tertiary, and
quaternary amines. These designations indicate the number of carbon chains
attached to the amine group. Propanamine is a primary amine since it has only
one carbon chain attached to it. Other primary amines are given below.
Secondary Amines
Secondary amines are compounds with two carbon chains attached to the amine
group. Very often, the longest carbon chain is chosen as the root name and the
shorter carbon chain is selected as a side group. Technically, it is possible to
have the shorter side group found anywhere on the compound, but since it is
attached to the nitrogen (as opposed to the longer main chain) then an “N” is
used to describe this position. For example, suppose that we have the following
compound;
CH3-NH-CH2-CH2-CH3
The longest chain has three carbons so the root name of this compound,
including the amine group, is propanamine. Since this compound also has a
methyl group attached to the nitrogen, the full name of this compound would be,
N-methylpropanamine.
It is also possible to name this compound by listing the carbon chains as side
groups. In this case, this compound would be called methylpropylamine or Nmethylpropylamine. In similar fashion, if both side chains are the same, then the
name of the following compound would be diethylamine,
CH3-CH2-NH-CH2-CH3
diethylamine
A number of secondary amines are given below,
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Tertiary Amines
Tertiary amines have had all of their hydrogen’s replaced with carbon chains.
Even without a nitrogen-hydrogen bond, these molecules can still bond through
their lone pair electrons so these compounds are usually soluble in water.