Alkanes

Alkanes are saturated hydrocarbons; they have only C-C and C-H single bonds (all carbons are SP3
hybridized) and these molecules contain the maximum possible number of hydrogens per carbon.

Alkanes have the general formula CnH2n+2 where n is an integer. For example, if a molecule has four
carbons it should have (2X4+2 = 10) hydrogen atoms and will have the formula C4H10.

Alkanes are also called aliphatic compounds (aliphatic means fatty compounds), this means they are
not soluble in water

For each of the chemical formulas C1H4, C2H6 & C3H8, only one chemical structure is possible:

While for formulas that have more than three carbons there will be more than one possible form. For
example, C4H10 can have two structures and C5H12 can have three structures:

Different structures in each formula are called Constitutional Isomers, in which they differe only on
the way how atoms are connected. These isomers are classified as either normal (or straight-chain)
alkane (denoted as n-alkane) or branched-chain alkane.

Constitutional isomers are not only found in alkanes, but also in other functional groups, as:

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 Strait-chain alkanes and alkyl group
Names of Strait-Chain Alkanes:

No. of C Name Formula No. of C Name Formula

1 Methane CH4 6 Hexane C6H14
2 Ethane C2H6 7 Heptane C7H16
3 Propane C3H8 8 Octane C8H18
4 Butane C4H10 9 Nonane C9H20
5 Pentane C5H12 10 Decane C10H22

Alkyl Groups:

If a hydrogen atom is removed from an alkane, the remaining structure is called an alkyl group. The
alkyl groups are named according to the parent alkane by replacing the ending -ane by -yl. The
following table provide some examples for alkyl groups generated for n-alkanes:

No. of Name Formula Alky gp Name Abbreviation

C
1 Methane CH4 -CH3 Methyl Me
2 Ethane C2H6 -CH2CH3 Ethyl Et
3 Propane C3H8 -CH2CH2CH3 Propyl Pr
4 Butane C4H10 -CH2CH2CH2CH3 Butyl Bu
5 Pentane C5H12 -CH2CH2CH2CH2CH3 Pentyl --

Alkyl groups can also be generated for branched alkanes, where sec-
(secondary) and tert- (tertiary) are prefixes used for C4 alkanes.

Primary carbon is bonded to one carbon and three hydrogens,

secondary carbon is bonded to two carbons and two hydrogens,
tertiary carbon is bonded to three carbons and one hydrogen,
quaternary carbon is bonded to four carbons.

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 Naming Alkanes
Each alkane can be named following IUPAC system, which has three parts:

Prefix Parent Suffix

The parent selects the main part of the molecule and tells how many carbon atoms are in that part.

The suffix identifies the functional group family the molecule belongs to.

The prefix gives the locations of the substituents on the parent

Naming steps:

Step 1: find the parent hydrocarbon

a) Find the longest continuous chain of carbon atoms

Examples:

b) If two different chains of equal length are present, choose the one with larger number of
branch points as the parent.

Examples:

Step 2: number the atoms in the parent chain:

Beginning at the end nearer the first branch point. If there is branching an equal distance away from
both ends of the parent chain, begin numbering at the end nearer the second branch point. Examples:

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Step 3: Identify and number the substituents

Assign a number to each substituent according to its point of attachment to the parent. If there are
two substituents on the same carbon give them both the same number.

Step 4: Writing the name:

- Use hyphens (-) to separate the different prefixes

- Use commas (,) to separate numbers
- If two or more substituents are present, cite them in alphabetical order
- If two or more identical substituents are present, use one of the multiplier suffixes (di, tri,
tetra and so forth), but don’t follow the alphabetical citation on them.

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Step 5: Naming a complex substituent.

We begin numbering at the point of attachment to the parent chain and name it by following the
previous rules. This substituent name is placed in parenthesis () when naming the complete structure.

Some of the simple branched chains have non-systematic or common names. For example, 2-
methylpropyl has a common name of isopropyl, so the full name can be:

6-isobutyll-2,3-dimethyldecane

The following structures are common names for simple branched chain alkyl groups:

Examples on full structures names:

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We can draw a chemical structure if the IUPAC is given by following the reverse strategy. Example:

Draw the chemical structure of 3-isopropyl-2-methylhexane.

Step 1: identify and draw the parent chain (only carbons)

The parent is hexane: C-C-C-C-C-C

Step 2: Identify the substituents and place them in the correct positions, then add hydrogens to
complete the structure

Substituents are: 3-isopropyl and 2-methyl

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 Stereochemistry of Alkanes

sp3-hybridized carbon has tetrahedral geometry results from σ bonds. Atoms can spin freely if they
are joined by σ bonds. Methane has the following 3D geometry:

Hydrogens are distributed equally around the carbon atom with equal angles and distances. So,
when carbon spin the geometrical shape of methane doesn’t change. Is it the case for ethane?

Both carbon atoms are joined by σ bond, which enable each atom to spin. Therefore, any rotation of
any of the carbons can change the geometry of the whole molecule. Examples:

This means that ethane can have many geometrical shapes depending on how each carbon rotates.
The different arrangements that result from rotation about sigma bond are called conformational
isomers, and each isomer is called conformer. Conformers are different from constitutional isomers;
different conformers have the same connections of atoms and cannot be isolated.

Conformational isomers are represented in two ways: Sawhorse representation and Newman
projection

We need to learn how to draw the conformational isomers in both ways.

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Example:

It seems that carbons can rotate freely about σ bonds, but it is not the case. The above two conformers
show different energy barriers, where the staggered conformer shows more relaxed geometrical
orientation when compared to the eclipsed conformer. The extra energy present in the eclipsed
conformation is called torsional strain (between electrons). A total of 12.0 KJ/mol torsional strain is
the barrier to rotation in the case of ethane, which caused by three H-H eclipsing interactions,
assigning 4.0 KJ/mol torsional strain to each single interaction. It is worth mentioning that there is an
infinite number of conformers between each two eclipsed rotations, being the staggered most stable
one and the eclipsed the least.

Propane
The staggered conformer is
lower in energy by 14 KJ/mol.

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Butane:

In C2-C3 bond in butane, not all staggered conformers have the same energy, neither the eclipsed
conformers. The energy maximum occurs when the two methyl groups eclipses each other, and the
energy minimum occurs when the two methyl groups are 180o apart, this conformer is called Anti.
The staggered conformation where the two methyl groups are 60 o apart, this is called Gauche. The
extra energy in both Gauche and Eclipsed conformers is because of the methyl groups are close to
each other resulting to what is called Steric strain (repulsive strain).

Therefore, the most stable alkane conformation is the one that has staggered substitutions:

Example:

Draw Newman projection for the most stable and least stable conformations sighting along C1-C2 of
1-chloropropane.

Practice:

1. Considered 2-methylpropane. Sighting along the C2-C1 bond, draw the most stable and least
stable conformations
2. Sight along the C2-C3 bond of 2,3-dimethylbutane and draw a Newman projection of the most
stable conformation.
3. Convert the following conformations from Newman projections to Sawhorse presentation:

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 Cycloalkanes

Alkanes can also exist in rings of carbon atoms and these compounds are called
cycloalkanes or alicyclic (aliphatic cyclic) compounds. The general formula of
cycloalkanes is CnH2n.
The following are some examples on cycloalkanes:

Cycloalkanes can also be part of structures that are consisted of other functional
groups. Examples:

Note that if there is one alicyclic ring in an alkane the whole molecule will have the
formula CnH2n. the above examples all are constitutional isomers of C11H22.

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Naming Cycloalkanes
Step-1: Find the parent.
If the number of carbons in the ring is equal or greater than the number in the largest
substituent, the compound is named as an alkylcycloalkane. If the number of carbons
in the largest substituent is greater than the number in the ring, the compound is
named as a cycloalkylalkane.

Step-2: number the substituents.

a. For alkyl and halo-substituted cycloalkanes, choose a point of attachment of
the first substituent as C1 and number the substituents on the ring so that the
second substituent has as low number as possible. If more than one possibility
for the second substituent then go for the third, fourth, and so on.
b. If two or more different alkyl groups that could receive the same numbers are
present, number them alphabetically.
c. Halogens are treated exactly like alkyl groups.
Examples:

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 Stereochemistry of Cycloalkanes
Cyclopropane:

Read Only

In cyclopropane, three types of strain can be noticed:

• Angle strain: this is due to compression of bond angles

• Torsional strain: strain due to eclipsing bonds on neighboring atoms
• Steric strain: strain due to repulsive interactions

Cyclobutane:
Cyclobutene has less angle strain than cyclopropane but has higher torsional strain due to its larger
number of hydrogens in the ring. Therefore, the total strain is almost equal in both rings. For
cyclobutene to overcome some of the torsional strain it twists slightly itself, so hydrogens are not
fully eclipsed.
Read Only

Cyclopentane:
Planar cyclopentane has no angle strain (angle ~ 109o), but it has a large amount of torsional strain,
so it twists to give puckered, nonplanar conformation. Four carbons are in approximately the same
plane, with the fifth carbon atom bent out of the plane.
Read Only

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Cyclohexane
Chair conformation

Like cyclopentane, planar cyclohexane has no angle strain, but it has a large amount of torsional
strain, so it twists to give puckered, nonplanar, chair conformation.

Read Only

From the Newman projection, it can be noticed that cyclohexane has no torsional strain; all
neighbouring C-H bonds are staggered.

Tips for drawing chair conformation of cyclohexane:

Axial and equatorial bonds in Cyclohexane:

Positions of substitutions on cyclohexanes are of two kinds: axial and

equatorial positions. There are six axial hydrogens (Hax) and six
equatorial hydrogens (Heq):

Conformational mobility of cyclohexane

The chair conformer of cyclohexane is conformationally mobile at room temperature. Chair

conformations readily interconvert, resulting in the exchange of chair conformations, this is usually
referred to as a ring-flip:

Because of the ring-flip, the middle four carbons will be kept in place while folding the two ends in
opposite directions. In addition, the axial substituents become equatorial, and vice versa.

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Examples on ring-flipped cyclohexanes

Axial and equatorial methylcyclohexane

1. Axial and equatorial bromocyclohexane

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Conformations of monosubstituted cyclohexanes

The energy difference between axial and equatorial conformers is due to steric strain caused by so-
called 1,3-diaxial interactions:

Therefore, for monosubstituted cyclohexane the equatorial position is less energetic than axial. The
energy difference depends on the size of the substituent, e.g. tert-butyl > isopropyl > ethyl > methyl.

Look carefully at the following examples and find out the effect of the size on the energy difference:

Conformations of the disubstituted cyclohexanes

For 1,2-dimethylcyclohexane, there are four chair conformations:

The 1,3-diaxial interactions determine the most stable conformation. Generally, when the
substituents are in equatorial positions this is less energetic than in axial positions. As can be seen

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also, when the two methyl in different positions (axial-equatorial) the energy is similar in both
conformations because of the similar 1,3-diaxial interactions in both conformations.

What is the situation if the substituents are different?

As example is 1-tert-butyl-2-methylcyclohexane:

The tert-butyl has more size than the methyl, so when in the tert-butyl goes to the equatorial position
this is more favourable and less energetic than the other conformation.

Another example: 1-fluoro-2-methylcyclohexane

Cis and Trans isomerism in cycloalkanes:

Due to the cyclic structures of cycloalkanes, they have two sides: a “top” side and a “down” side
leading to the possibility of isomerism in the substituted cycloalkanes generating a relashionship
between two substituents. When both substituents are in the same side (top or down) then they have
“cis” relationship, but if they are in different sides (one top and one down) then they have “trans”
relationship. Examples:

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Cis and Trans isomerism in chair conformations of cyclohexanes:

In case of cis isomerism, both substituents should be in one direction. In case of trans isomerism, both
substituents should be in opposite directions. Examples:

The red labelled atoms are in equatorial positions and the blue labelled ones are in axial positions. So,
cis or trans isomerism depends mainly on the direction of the atoms “up” or “down”.

In cyclohexanes, the stability of the cis and trans isomers depends on the 1,3-diaxial interactions and
their ability for ring-flipping. This means the substituted cyclohexanes will “flip” to have the least
strained conformation. Examples:

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Homework

1. Draw the most stable conformation of the following molecules.

a. trans-1-chloro-3-methylcyclohexane
b. cis-1-ethyl-2-methylcyclohexane
c. cis-1-bromo-4-ethylcyclohexane
d. cis-1-tert-butyl-4-ethylcyclohexane

2. Name the following compounds, showing for each compound the most stable chair
conformation.

3. Decalin consists of two cyclohexane rings joined to share two carbon atoms. It can exist in both
cis and trans isomers, draw the chair conformation of both isomers and identify which one is less
strained.

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 Diastereomers
Diastereomers are stereoisomers that are not mirror images of each other. Chiral diastereomers
have opposite configuration at one or more chirality centers, but have the same configuration at
others. Example:

Both (A & B) and (C & D) pairs are mirror images and termed as enantiomers. While (A & C), (A & D),
(B & C), (B & D) are not mirror images and termed as diastereomers.

Meso compounds: tartaric acid

Both A and B are mirror images and considered as enantiomers, in which there is no plane of
symmetry that can cut the molecule into two halves. C & D are mirror images, but when any of them
vertically rotates it will give the other one, which means both are one molecule. The later pair (C &
D) are called meso compounds. In addition, when a symmetry plane that can cut the molecule into
two identical halves is present, so the compound is achiral. Therefore, tartaric acid exists in three
stereoisomeric forms; two enantiomers and one meso form.

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 Fischer Projection
A tetrahedral carbon is represented in a Fischer projection by two crossed lines. The horizontal lines
represent bonds coming out of the page and the vertical lines represent bonds into the page:

Examples:

Fischer projection can be moved around on the paper, only two kinds of motions are allowed:

1. A Fischer projection can be rotated on the page by 180o without affecting the configuration
of the chiral center, but not 90 o or 270 o.

2. A Fischer projection can have one group held steady while the other three rotate in either a
clockwise or a counter-clockwise direction without affecting the configuration.

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Assigning R,S configurations to Fischer projections

Steps:

1- Assign priorities to the four substituents in the usual way (according to atomic number)
2- The group of the lowest priority (4th) should be up in the Fischer projection. If it is not up,
then rotate the molecule by one of the allowed motions mentioned before to place the
group of the lowest priority up.
3- Determine R,S configuration in the usual way (by rotating 1→ 2 → 3 of the remaining three
groups).

Example:

Assign R or S configuration to the following Fischer projection of alanine:

Step 1. give priority numbers:

Step 2. Place the lowest priority group up:

Step 3. Assign R or S:

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Practice

1. Identify whether each of the following compounds is chiral or achiral compound:

2. How many chiral centres is found in the chemical structure of each of the following drugs?

3. Assign R or S configurations to the chirality centers in the following molecules:

4. Identify weather each of the following pairs are considered as enantiomers, diastereomers or
same compound (meso form:)

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 Alkenes and Alkynes

Naming of alkenes
Steps 1. Find the parent: find the longest carbon chain containing the double bond, and name the
compound accordingly using the suffex -ene. Example:

Step 2. Number the carbon atoms in the chain: begin at the end nearer the double bond. If the
double bond is equidistant from the two ends, begin at the end nearer the first branch point:

Step 3. Write the full name:

- Number the substituents according to their positions in the chain and list them
alphabetically.
- Indicate the position of the double bond by giving the number of the first alkene carbon and
placing that number immediately before the parent name.
- If more than one double bond is present, indicate the position of each, and use the suffixes
diene, triene and so on.

- In cycloalkenes, the double is between C1 and C2 and the first substituent has as low a
number as possible. It is not necessary to indicate the position of the double bond in the
name because it is always between C1 and C2:

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Cis-Trans and E,Z isomerism in Alkenes

When alkene is disubstituted (which means both alkene’s carbons are bonded to substituents other
than hydrogens), then the two substituents are either in the same side of the double bond or on
opposite sides. We call such compounds cis-trans stereoisomers: when both substituents are in the
same side they are called “cis” and in opposite sides they are called “trans”:

What if one or both carbons of the alkene double bond are disubstituted, in this case there is no cis-
trans stereoisomers:

If the two substituents on each carbon of the alkene’s double bond are not similar, then a more
general method is applied to describe the geometry of the double bond, which is called E,Z
designation:

Rule: Considering each of the double bond carbons separately, identify the two atoms directly
attached and rank them according to atomic number. If the directly attached atoms are similar look
at the second, third …. Away from the double bond until the first difference is found.

Naming of alkyne

Naming of alkyne follows the general rules discussed for alkanes and alkenes, but with using the
suffix -yne. If both double bond and triple bond are present in the molecule, then numbering start
from the end nearer to the multiple bond. If both are in equidistance from both ends, then double
bond takes lower numbering than triple bond. Examples:

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