UNIT 6 – ORGANIC CHEMISTRY
CH1031
Mark Stacey
ORGANIC CHEMISTRY AND
BIOCHEMISTRY
In everyday language, the term “organic” can mean several different
things. In general it is used to imply something is pure, natural, or to do
with living things.
In chemistry, organic specifically refers to compounds of carbon. This
includes many of the chemicals that make up living things (life on Earth
is commonly referred to as carbon-based life) but it also includes non”living” compounds such as carbon dioxide or ethanol.
Biological chemicals (or biochemicals) are the term used to refer
specifically to the compounds that make up living things, regardless of
what elements comprise them.
Thus there are chemicals that are organic or biological exclusively and
those that are both.
ORGANIC CHEMISTRY AND
BIOCHEMISTRY
Carbon is one of the few elements that can readily form four covalent
bonds at once. This allows it to form the “backbone” of very complex
molecules. Carbon atoms can form chains, branches, sheets, loops,
rings, spirals and more.
However, the majority of organic compounds are not solely made of
carbon. Other elements (typically hydrogen) attach to the carbon
“skeleton”.
These other elements are often what defines the function and
properties of the compound. Compounds such as propane and ethanol
are not terribly different in terms of their carbon atoms, but the
presence of oxygen in ethanol creates the difference in properties.
ORGANIC CHEMISTRY AND
BIOCHEMISTRY
Organic molecules are often quite complex. They can contain tens or
hundreds or atoms in them. At this scale, multiple compounds are easily
possible from the same quantities of atoms (ie – multiple structures are
possible from one given chemical formula). Even chemicals with as few
as three carbon atoms can have more than one arrangement possible.
This is due to carbon’s ability to form up to four bonds – allowing
rings, loops, or chains to form from the same base elements.
For this reason, we most often name organics based on their structure
rather than just calling them by their constituent atoms. For example,
pentacarbon dodecahydride (C5H12) could refer to several different
compounds, each with different chemical properties.
HYDROCARBONS - ALKANES
The “simplest” organic compounds are hydrocarbons. They are named
such because they contain only hydrogen and carbon. As hydrogen
can only form one covalent bond, this means that the carbons
determine the real “skeleton” of the structure, while hydrogen atoms
simply attach to the “free” unused covalent “slots” of carbon atoms.
The most basic hydrocarbons are the alkanes. These are chains of
carbons linked together by single covalent bonds only. As such,
alkanes can be said to be saturated, as the molecules has as many
bonding “slots” filled by hydrogens as possible and none are tied-up
in double or triple bonds.
HYDROCARBONS - ALKANES
Alkanes can come in many
shapes and sizes
depending on how the
carbon atoms attach – be it
in straight lines, branched
lines, loops, etc.
The main chains are shown
in blue here, with branches
in red.
HYDROCARBONS - ALKANES
Straight-chain alkanes are named
based on the number of carbons
that make up the chain, with the
ending –ane to indicate that they
are an alkane.
All alkanes take the formula
CnH2n+2
9 carbons - nonane
10 carbons - decane
HYDROCARBONS - ALKANES
Drawing out organic compounds can
be tiring, repetitive and take up a
lot of space, as such, chemists have
invented various shorthand methods
to ease the process.
The simplest of these is condensed
form – where the hydrogen atoms
are grouped with the carbon atoms
they are attached to.
Note – both H3C- or CH3- are
considered acceptable, it is implied
that the bond is to the carbon atom.
Formula
Full Form
Condensed Form
HYDROCARBONS - ALKANES
Skeletal form is used for very
large molecules. This removes all
hydrogen and carbon atoms
leaving only the carbon-carbon
bonds as a skeleton.
HYDROCARBONS - ALKANES
Alkanes are oily chemicals. At room temperature the shortest alkanes
(between 1-4 carbons) are gasses. Longer-chain alkanes are liquid at
room temperature. Alkanes with over 20 carbon atoms are solid at STP.
Straight-chain alkanes are able to pack densely together, creating
many points for molecule-to-molecule attraction, giving them a higher
boiling point than a branched alkane of similar molar mass.
Alkanes are non-polar (the carbon-hydrogen bond is non-polar) and
extremely hydrophobic.
HYDROCARBONS – BRANCHED ALKANES
Branched alkanes are alkanes with at least one carbon bonded to
three other carbons, creating an offshoot from the main linear chain.
Branched hydrocarbons are still considered saturated, as they contain
no double or triple bonds.
Regardless of how a branched hydrocarbon is drawn, the “backbone”
is always the line of connected carbons that is the longest, and other
lines of carbons are branches from that.
HYDROCARBONS – BRANCHED ALKANES
The main backbone receives its name the same as any non-branched
alkane. The branch(es) are named using the same prefixes (meth-, eth-,
etc) buy receive the –yl ending.
As the branch could attach from several different positions, the branch
also receives a number, indicating which carbon it is attached to on the
main chain. This number is always chosen to be the lowest number
possible.
HYDROCARBONS – BRANCHED ALKANES
If there is more than one of the same chain, they are grouped and the
terms di- (2) or tri- (3) are used to indicate how many exist. The
numbers for both must be included.
HYDROCARBONS – BRANCHED ALKANES
If multiple chain lengths are present, they are named in alphabetical
order:
4-ethyl 3-methyl heptane
Note – remember to always use the lowest numbers possible. The above
compound should NOT be called 4-ethyl 5-methyl heptane, for example.
HYDROCARBONS – BRANCHED ALKANES
It is also important to check for the longest chain in the alkane. It is not
always the one drawn in a straight line.
This compound’s backbone is of 5 carbons, and as such is 3-methyl
pentane. It should NOT be labelled 2-ethyl butane.
HYDROCARBONS – BRANCHED ALKANES
Example 1 – name the following:
Step 1- find the longest chain.
HYDROCARBONS – BRANCHED ALKANES
Step 2 – with the longest chain now identified, label all the branches by
length.
The main chain has 6 carbons – therefore the base is hexane.
There are three 1-carbon branches – a trimethyl group.
The name of this compound will be ___-trimethyl hexane.
HYDROCARBONS – BRANCHED ALKANES
Step 3 – number the main chain in the direction that gives the lowest
numbers.
Numbering the main chain in the direction of the red arrow results in
3,5,5-trimethyl hexane.
Numbering the main chain in the direction of the green arrow results in
2,2,4-trimethyl hexane. As these numbers are lower, this is the correct
name.
HYDROCARBONS – ISOMERS
Organic compounds often contain many atoms and as such, it is
possible to form several very different structures with very different
chemical and physical properties from the same allotment of elements.
Two chemicals that share the same number of atoms (same chemical
formula) but have different structures are called isomers.
The more atoms involved, the greater the number of isomers. Even
compounds with 5-10 carbons can have many, many isomers.
HYDROCARBONS – ISOMERS
The formula C5H12 can refer to several structures:
In this case, we get the linear pentane, the single-branched 2-methyl
butane, and the two-branched 2,2-dimethyl propane.
Each of these has a very different boiling point. Pentane can pack
together the most densely of the three and has the highest boiling
point.
HYDROCARBONS – UNSATURATED
When a hydrocarbon contains a double bond, it is now an alkene. A
hydrocarbon with a triple bond is an alkyne.
Alkenes and alkynes are unsaturated as they lack hydrogen atoms on
the “slots” taken up by the double/triple bond.
Alkenes are named the same as alkanes, but receive the “-ene” ending
instead of “-ane”. Likewise, alkynes receive a “-yne” ending.
HYDROCARBONS – UNSATURATED
As the double or triple bond could
exist between various atoms in the
compound, they are numbered
much the same as branches.
If more than one double/triple
bond exists, the ending changes to
“-diene” / “-diyne” / “-triene” /
“-triyne”
HYDROCARBONS – UNSATURATED
The double and triple bonds are given priority to get the lowest
number possible regardless of the numbering of any branches.
As double and triple bonds connect two carbons, for clarity, they are
always numbered based on the lowest-numbered carbon they connect
to.
This is 2-butene, not 3-butene.
HYDROCARBONS – UNSATURATED
The double/triple bond MUST be included in the backbone main chain
even if a longer chain is possible using other carbons.
Even though the green arrow makes a shorter chain it is correct as it
includes the double bond. This compound is 2-ethyl-1-hexene.
HYDROCARBONS – UNSATURATED
In general, alkenes and alkynes have similar properties to their alkane
counterparts.
The double/triple bond will typically interfere with traditional linearmolecule packing, and so alkanes and alkynes will have a different
boiling point than the equivalent alkane.
For straight-chain hydrocarbons, alkenes have the lowest boiling points,
alkanes fall in the middle, and alkynes have the highest.
It becomes more complicated with branched hydrocarbons, and there is
not always a direct trend in boiling points.
HYDROCARBONS – UNSATURATED
Alkenes and alkynes are generally more reactive than alkanes. Many
compounds will react with the double/triple bond, reducing it to a
single bond (or sometimes only reducing a triple bond to a double
bond) and adding new atoms to the compound:
Alkene and alkynes can be made into alkanes by adding hydrogen in
a hydrogenation reaction:
HYDROCARBONS – UNSATURATED
Alkenes “lose” two hydrogen atoms compared to the equivalent alkane,
and as such their general formula follows CnH2n.
Alkynes “lose” a further two hydrogen atoms to form the triple bond,
and as such have a general formula of CnH2n-2.
HYDROCARBONS – CYCLIC
When a carbon chain becomes long enough, it becomes possible for it
to bond with itself and form a loop/ring.
Rings made of 3 or 4 carbons are highly reactive (ie unstable) as there
is tremendous stress on the bond given their angles.
Note that the angle between the two carboncarbon bonds is 60°. A “normal” tetrahedral
atom would have its bonds at 115° apart. This
stress of having its bonds so close together
explains why this compound is unstable.
HYDROCARBONS – CYCLIC
Larger carbon rings are more stable as the bond angles is more in line
with what a “normal” carbon atom would have.
Keep in mind that rings larger than 4 carbons are not flat – they form
zig-zag ups and downs:
The picture on the right is
more accurate to the true
shape of this compound.
It does not exist as a flat
hexagon.
HYDROCARBONS – CYCLIC
Rings that contain only single carbon-carbon bonds are cycloalkanes.
They are named the same as alkanes, but with “cyclo-” added.
The ring is always the main chain when naming branched cycloalkanes:
Branches are named to give the lowest numbers, meaning you can start
anywhere on the ring. This compound is 1,1-dimethyl-3-propyl
cyclopentane
HYDROCARBONS – CYCLIC
Cyclic alkenes and alkynes are also possible. They are generally much
more unstable as the bond geometries of a double or triple bond can
drastically interfere with the bond angles needed to form a ring. This is
more noticeable on smaller rings than larger ones.
For example, cyclopropene is extremely reactive. Cyclopropyne does
not even form as the bonds angles needed for a triangle (60) are too
far off from the typical angle of a triple bond (180).
HYDROCARBONS – CYCLIC
Cycloalkenes and cycloalkynes are named like their alkane
equivalents.
The double/triple bond MUST start at the “one” position and then
proceed through the bond. That is, the double/triple bond connects
carbon 1 and carbon 2. Outside of that, number the ring in the
direction that produces the lowest numbers for the branches, if any.
HYDROCARBONS – CYCLIC
As the double/triple bond must be at the 1 position, it’s number can be
omitted unless there are multiple double/triple bonds.
Remember that the double/triple bond takes priority!
This is not 1,1,4-trimethyl-2cyclohexane, even though
those numbers are lower.
HYDROCARBONS – AROMATIC
A special effect happens if a cyclic compound has alternating single
and double bonds. In these cases (typically seen in a 6-carbon ring),
the bonds do not remain as single or double bonds and instead all
hybridize into something in between. This is an aromatic compound. The
name comes from the fact that many of these chemicals produce strong
scents.
In this case, the 3 double bonds are “spread” among all 6 carbons, creating a
“ring” of shared bonding in the molecule.
HYDROCARBONS – AROMATIC
The net effect of hybridization is
a new hybrid bond, somewhere
between a single and double
bond in length, reactivity and
strength.
This also has an effect on the
molecule’s geometry. While
cyclohexane forms a zig-zagged
shape, this compound is a flat
hexagon.
HYDROCARBONS – AROMATIC
The most common aromatic compound is 1,3,5-cyclohextriene, more commonly
known as benzene.
When naming branched compounds of benzene, the name “benzene” can
replace the much longer full name of 1,3,5-cyclohextriene.
1,3,5-cyclohextriene
(benzene)
1-Ethyl-1,3,5-cyclohextriene
(1-ethylbenzene)
HYDROCARBON DERIVATIVES
Hydrocarbons may come in various shapes and sizes, but ultimately they
are only made of carbon and hydrogen. When other elements are added
to the structure, they can drastically alter the properties of the compound.
Hydrocarbon derivatives contain collections of elements other than
carbon and hydrogen called functional groups. This name reflects the
fact that their presence will drastically change the properties, and
therefore function, of the chemical.
HYDROCARBON DERIVATIVES - ALCOHOLS
Alcohols add the function group –OH to the hydrocarbon chain. Oxygen
has a very different electronegativity than either carbon or hydrogen,
resulting in a polar bond.
This polar bond allows easier solubility in water than regular
hydrocarbons.
The polar bond also allows hydrogen-bonding to occur, making alcohols
have a higher intramolecular attraction, and thus higher boiling point.
Methane (CH4) is a gas while methanol (CH3-OH) is liquid at room
temperature.
HYDROCARBON DERIVATIVES - ALCOHOLS
Alcohols are named by replacing the “-ane” of alkanes with an “-ol”
ending. For compounds of 3 carbons or longer, the OH group should be
numbered as it could appear in multiple positions.
1-ethanol
(the 1 may be omitted
as it is in the 1-position
regardless of which
carbon it is attached to)
1-propanol
2-propanol
HYDROCARBON DERIVATIVES - ALCOHOLS
If a compound contains both a double/triple bond and an OH, the bond
is named first, then the OH. However, the OH is given priority in terms of
receiving the lowest number.
3-methyl-2-buten-2-ol
HYDROCARBON DERIVATIVES - ETHERS
Alcohols only contain an oxygen bonded to one carbon and one hydrogen. If
the oxygen is bonded to two separate carbon atoms, it becomes an ether.
Ethers are relatively fragile at the oxygen atom and readily decompose into
alcohols and other oxygen-based hydrocarbon derivatives.
HYDROCARBON DERIVATIVES - ETHERS
Ether linkages are common in biological settings. Complex carbohydrates
(polysaccharides) are formed by linking simple sugars (monosaccharides)
using an ether bond.
HYDROCARBON DERIVATIVES - ETHERS
The proper naming scheme for ethers is to name the longest chain as per
normal, and refer to the other chain(s) as a “-oxy” group.
HYDROCARBON DERIVATIVES –
ALDEHYDES AND KETONES
Aldehydes and ketones both add a double-bonded oxygen as a
functional group. As with alcohols, the presence of oxygen creates a polar
region in the molecule.
Aldehydes have the double-bonded oxygen attached to a terminal
carbon. These compounds receive the “-al” ending.
Ketones have the double-bonded oxygen attached to an internal carbon.
These compounds receive the “-anone” ending.
As ketones require an internal carbon to attach to, ketones of one or two
carbons in length do not exist – those are aldehydes.
HYDROCARBON DERIVATIVES –
ALDEHYDES AND KETONES
As with alcohols, priority goes to the aldehyde/ketone group to get the
lowest number.
HYDROCARBON DERIVATIVES –
CARBOXYLIC ACIDS
Carboxylic acids add both a double-bonded oxygen (like an aldehyde)
and a OH group (like an alcohol) to a terminal carbon. This is often written
as a –COOH group.
This structure allows easy solvation in water. The hydrogen from the –
COOH group readily will disassociate from the acid, leaving a –COO- ion.
Thus, these chemicals act as weak acids through their donation of their H+
ions to the solution.
HYDROCARBON DERIVATIVES –
CARBOXYLIC ACIDS
Carboxylic acids are named by adding the ending “-oic acid”. As with other
functional groups, the COOH group is given priority in naming. As with
aldehydes, as the COOH must be on a terminal carbon, it is often not
numbered.
Name
Common Name
Methanoic acid
Ethanoic acid
Butanoic acid
Hexanoic acid
Structure
Source Name Origin
HYDROCARBON DERIVATIVES – ESTERS
Esters are similar to carboxylic acids in that they contain a double-bonded
oxygen and a single-bonded oxygen on a terminal carbon. However,
instead of that oxygen being bonded to a hydrogen, in esters it is bonded
to a second carbon-based chain.
The chain containing the carbon doublebonded to oxygen is considered the
main chain. The one connected via the
single-bonded oxygen is the secondary
chain.
HYDROCARBON DERIVATIVES – ESTERS
Esters can be formed from a carboxylic acid and an alcohol. This is an
Esterification Reaction. This is a common linking reaction in living things
where it is often called a dehydration synthesis.
HYDROCARBON DERIVATIVES – ESTERS
Esterification is a reversible reaction. Depending on the conditions (such as
acidity and temperature) the reaction will proceed in one direction or
another. The reverse of esterification is called a hydrolysis reaction.
HYDROCARBON DERIVATIVES – ESTERS
Esters are named based on their main chain and receive the ending of “–
oate”. The secondary chain is named with a “–yl” ending, similar to
sidechains in branched alkanes.
HYDROCARBON DERIVATIVES – AMINES
Amines work similarly to an alcohol. However, instead of oxygen, nitrogen
is used. Amines behave similar to alcohols, but with some differences in
comparable melting points as the nitrogen-hydrogen bond is less polar
than oxygen-hydrogen in alcohols and the fact that amines can form up to
two hydrogen bonds compared with the one in an alcohol.
Alcohol
Amine
HYDROCARBON DERIVATIVES – AMINES
As Nitrogen can form three bonds, this means that amines can have up to
three carbon-based chains. Amines with one, two, or three carbon chains
are called primary, secondary, and tertiary amines, respectively.
HYDROCARBON DERIVATIVES – AMINES
Primary amines are named similar to alcohols in that the amine group
takes priority in numbering. Amines receive the “-amine” ending. For
carbon chains of 3 or longer, the position of the amine must be included.
HYDROCARBON DERIVATIVES – AMINES
Secondary and tertiary amines are named with the longest chain as the
main chain, with the others treated as side chains. Their position isn’t
numbered, but referred to as in the “N-” position.
HYDROCARBON DERIVATIVES – AMIDES
Amides are similar to carboxylic acids and esters in that they have a
terminal carbon with a double-bonded oxygen. However, unlike a
carboxylic acid or ester, the other atom is not another oxygen, but instead
a nitrogen. Like comparing alcohols and amines, amides are similar in
reactivity and physical properties to carboxylic acids and esters.
In this case R’ and R’’ can be a hydrogen or
a carbon chain.
If both R’ and R’’ are hydrogen, it is a
primary amide.
If only one of R’ and R’’ are hydrogen, it is a
secondary amide.
If neither R’ and R’’ are hydrogen, it is a
tertiary amide.
HYDROCARBON DERIVATIVES – AMIDES
The amide bond is quite strong. The electrons between the oxygen, carbon,
and nitrogen can be shared (much like those in aromatics). This is often
called a peptide bond. Proteins are made using repeating peptide bonds
to link amino acids and are often called polypeptides to reflect this.
HYDROCARBON DERIVATIVES – AMIDES
Amides are named similarly to amines. The main chain gets the “-amide”
ending and any other chains are referred to being at the the “N-” position.
HYDROCARBON DERIVATIVES – AMIDES
Amides can be made from a carboxylic acid and a primary of secondary
amine.
Note that a tertiary amine cannot undergo this reaction as it would have
no hydrogen atom to lose.