Alkanes and Cycloalkanes: Organic Chemistry BS Biology - 1 Semester, AY 2020 - 2021

Organic Chemistry BS Biology – 1st Semester, AY 2020 – 2021
Alkanes and Cycloalkanes
ALKANES are the simplest family of organic molecules. They are often described as SATURATED
HYDROCARBONS , since they contain only hydrogen and carbon (hydrocarbons) and they only have C–
C and C–H bonds, and thus have the maximum possible amount of hydrogens attached to carbons
(saturated). Alkanes are relatively unreactive and not often involved in chemical reactions, but they
still give us starting ideas for prior lessons in reactions and structures. We will start to discuss how
we name compounds following the INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY (IUPAC)
conventions and have initial insights on the three – dimensional nature of organic molecules. Also,
we would start to discuss how alkanes are produced, and what reactions they will have even with
their relative stability. Organic chemistry is a marathon, and every step that we take in our lessons
would still be vital to the succeeding ones, so retention is key for the subject.
Table of Contents
Alkane and Cycloalkane Nomenclature ........................................................................................................................................................... 2
Alkane Nomenclature ................................................................................................................................................................................................. 2
Cycloalkane Nomenclature.................................................................................................................................................................................. 13
Physical Properties of Alkanes and Cycloalkanes ................................................................................................................................. 16
Conformations of Alkanes and Cycloalkanes ........................................................................................................................................... 18
Newman Projections of Alkanes..................................................................................................................................................................... 18
Cis – Trans Isomerism in Cycloalkanes ..................................................................................................................................................... 22
Stability and Conformations of Cycloalkanes ................................................................................................................................... 24
Alkane and Cycloalkane Reactions ..................................................................................................................................................................... 31
Alkane and Cycloalkane Synthesis .................................................................................................................................................................... 35
Assessment Activity .........................................................................................................................................................................................................37
References................................................................................................................................................................................................................................ 38
Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 1

Alkane and Cycloalkane Nomenclature
Alkane Nomenclature
Alkanes have a general formula of C𝑛 H2𝑛+2 , in which 𝑛 is an integer. The simplest alkane would have
𝑛 = 1, so it will have one carbon and 2(1) + 2 = 4 hydrogens. The next alkane would have 𝑛 = 2
carbons and 2(2) + 2 = 6 hydrogens. A third alkane would have 𝑛 = 3 carbons and 2(3) + 2 = 8
hydrogens. These hydrocarbons are shown below, with their IUPAC names.
H
H H H
H H C
H H
H C C
C C H C
H H H H H
H H H
methane ethane propane
As we increase the number of carbons, the possibility of different structures increases. For example,
let us see the case for 𝑛 = 4 carbons [2(4) + 2 = 10 hydrogens]. One structure that we can do is that
all carbons are in a continuous chain. The other is when one of the carbons is on the sides. Both
structures, and their IUPAC names are shown below.
H
H H
H H H H C
H H
H C C C C H C C C
H H
H H H H H H H
butane 2-methylpropane
We describe butane as a STRAIGHT – CHAIN ALKANE or a normal alkane. They are described as alkanes
in which the carbons are all connected in a row. 2–methylpropane, on the other hand, is described
as a BRANCHED – CHAIN A LKANE. They are described as alkanes with side group attachments. Both

butane and 2–methylpropane have the same formula, C4 H10 , but they have different structures. We
describe them as ISOMERS , compounds that have the same numbers and kinds of atoms but differ in
the way the atoms are arranged in three – dimensional space. Specifically, butane and 2–
methylpropane are CONSTITUTIONAL ISOMERS , isomers in which the atoms are attached to each other
differently. Another type of isomerism would be discussed in the future.
The structures drawn before are based on the Lewis structures that we have already discussed.
However, drawing like this is sometime inconvenient, especially for bigger molecules. Take for
example, we draw aldosterone in Lewis structures. It would look something like this:
O H
O
O
H C H
H H H C
C H
O C C H
H H H C H C H
H C H C
H H
H C C C
C C C C H
H H
H H
C C C C
H
O C C H
H
H H
H H
As you can see, the structure looks complicated and confusing if we follow Lewis structures. For
organic molecules, we draw structures in what we call as the CARBON SKELETON formula. The carbon
skeletal formula for aldosterone is shown below:
O
O
OH
HO

Skeletal formulas usually follow the following rules:
1. We draw carbons in a zigzag pattern, in which the points are carbon atoms and lines are
bonds. All other atoms bonded to carbon, unless otherwise stated, are hydrogens.
2. We draw all bonds as far away as possible.
3. Drawing single bond carbons in any direction is equivalent.
4. Carbons always have four bonds, so account accordingly.
5. Optional: The carbons in the end of a structure are shown with the number of hydrogens
attached to it.
SAMPLE PROBLEM 1
Draw skeletal formulas for butane and 2–methylpropane.
Recall the structures of butane and 2–methylpropane from the beginning of the module (page 2).
For butane, there are four carbons in a row. So, butane in a skeletal form is a zigzag with four points.
Possible skeletal structures for butane are shown below:
CH3
H3C
2–methylpropane would have one branched carbon in three carbons in a row. Possible skeletal
structures for 2–methylpropane are shown below:
CH3
H3C
CH3

Another way to represent organic molecules is by showing their CONDENSED FORMULA . A condensed
formula is made up of the elemental symbols. The order of the atoms suggests the connectivity.
Condensed formulas can be read from either direction. So, an H3 C in the condensed formula is the
same as CH3 . Branched substituents and repeating units are inside parentheses after the carbon in
which it is attached.
SAMPLE PROBLEM 2
Write condensed formulas for butane and 2–methylpropane.
Since butane is a straight chain, we just write the elemental symbols as is. Following the rules, the
condensed formula for butane is CH3 CH2 CH2 CH3 . There are two CH2 units inside the condensed
formula, so a valid answer for the condensed formula for butane is CH3 (CH2 )2 CH3 , in which the
subscript of two outside the parentheses indicates the two CH2 units inside the formula.
For 2–methylpropane, there is a CH3 unit attached to the central CH unit. We then write the
condensed formula of 2–methylpropane as CH3 CH(CH3 )CH3.
SAMPLE PROBLEM 3
Show the skeletal formula and the condensed formula of the following organic compound.
H H H
H H
C C
H H H
H H H H
C C H
C C C C
H C C
H H H H
H H H C
H
H
H

A glance on the Lewis structure of the compound shows that it has eight carbons in a row, with three
side group CH3 in some of the carbons. Taking a note as to where the side groups are attached is a
very important skill, as we rely on these attachments to correctly describe our compound.
Possible skeletal forms of the compound are as follows:
CH3
H3C
CH3
H3C CH3
The condensed formula of the compound is CH3 CH2 CH(CH3 )CH(CH3 )CH2 CH2 CH(CH3 )CH3 . We can
use another set of parentheses for repeat units, but it is better to just show it as is so that we will
not make some mistakes.
Straight-chain alkanes are named according to the number of carbon atoms they contain. We have
known methane (1 carbon), ethane (2 carbons), propane (3 carbons) and butane (4 carbons) from
examples before. Table 1 shows the names straight – chain alkanes.
Table 1 Straight Chain Alkane Nomenclature
No. of C Formula Name of No. of C Formula Name of

(𝒏) (𝐂𝒏 𝐇𝟐𝒏+𝟐 ) Compound (𝒏) (𝐂𝒏 𝐇𝟐𝒏+𝟐 ) Compound
1 CH4 methane 11 C11 H24 undecane
2 C2 H6 ethane 12 C12 H26 dodecane
3 C3 H8 propane 13 C13 H28 tridecane
4 C4 H10 butane 14 C14 H30 tetradecane
5 C5 H12 pentane 15 C15 H32 pentadecane
6 C6 H14 hexane 20 C20 H42 eicosane
7 C7 H16 heptane 30 C30 H62 triacontane
8 C8 H18 octane 40 C40 H82 tetracontane
9 C9 H20 nonane 50 C50 H102 pentacontane
10 C10 H22 decane 100 C100 H202 hectane

The first fifteen names in straight – chain nomenclature is the usually enough to memorize for
nomenclature, as we will see later that branched – chain nomenclature also use them commonly.
Removing one hydrogen from a straight – chain creates a partial structure called an ALKYL GROUP.
An alkyl group is a substituent attached to a main chain in a branched – chain alkane. Alkyl groups
are named by replacing the -ane ending of the parent alkane with an -yl ending. So, a −CH3 group
would be called a methyl group (from methane, CH4 ), and a −CH2 CH3 group would be called an
ethyl group (from ethane, C2 H6 ). This is how we name branched – chain alkanes, by identifying the
names of the alkyl groups attached to the main chain.
As a primer of naming organic compounds, we start with IUPAC rules. A chemical name typically has
four parts in the IUPAC system of nomenclature: prefix, parent, locant, and suffix. The prefix identifies
the various substituent groups in the molecule, the parent selects a main part of the molecule and
tells how many carbon atoms are in that part, the locants give the positions of the functional groups
and substituents, and the suffix identifies the primary functional group. We usually follow these steps
in naming:
1. FIND THE PARENT HYDROCARBON . Find the longest continuous chain of carbon atoms in the
molecule and use the name of that chain as the parent name. The longest chain may not
always be apparent from the manner of writing; you may have to “turn corners.” If two
different chains of equal length are present, choose the one with the larger number of branch
points as the parent.
2. NUMBER THE ATOMS IN THE LONGEST CHAIN . Beginning at the end nearer the first branch point,
number each carbon atom in the parent chain. 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.
3. IDENTIFY AND NUMBER THE SUBSTITUENTS . Assign a number, or locant, to each substituent to
locate its point of attachment to the parent chain. If there are two substituents on the same
carbon, give both the same number. There must be as many numbers in the name as there
are substituents.
4. WRITE THE NAME AS A SINGLE WORD . Use hyphens to separate the different prefixes and use
commas to separate numbers. If two or more different substituents are present, cite them in
alphabetical order. If two or more identical substituents are present on the parent chain, use

one of the multiplier prefixes di-, tri-, tetra-, and so forth, but don’t use these prefixes for
alphabetizing.
5. OCCASIONALLY IF NEEDED , NAME A BRANCHED SUBSTITUENT AS THOUGH IT WERE ITSELF A
COMPOUND . In some particularly complex cases, a fifth step is necessary. It occasionally
happens that a substituent on the main chain is itself branched. To name the compound fully,
the branched substituent must first be named.
There are two naming schemes for this, however, based on what IUPAC convention we follow: The
1979 convention and the 1993/2013 convention (they have the same rules for the naming).
1979 convention would follow that the longest chain should start on where the substituent is
attached, and refer additional substituents based on that numbering. 1993/2013 convention would
detect the longest chain (regardless of where the attachment is) and then identifying where is the
attachment is as a locator before the -yl prefix. This will be elaborated in the following sample
problems.
SAMPLE PROBLEM 4
Name the following compound.
If you look closely, this is the compound in SAMPLE PROBLEM 4. We first need to find the parent chain
of the compound. The longest possible chain for the compound is shown as the blue bold line.

Counting the number of points in the zigzag of the parent chain, we have eight carbons. This tells us
that the parent chain is an octane.
We will number the parent chain by identifying the start of the chain, based on substituents. If we
start at the left side, the first substituent is at C-3 (Carbon No. 3), while if we start at the right side,
the first substituent is at C-2 (Carbon No.2).
2 6 7 3
3 7 6 5 2 1
4 8
1 5 8 4
Following the rules, we will follow the one that will start on the right side.
Now we need to identify the alkyl groups attached to the parent chain. We show the substituents
as red, and the carbon counts of each substituent in red numbers.
1
7 3
6 5 2 1
8 4
1 1
All substituents have one carbon, which tells us that they are methyl groups. These groups are in
C-2, C-5, and C-7.
We can now name the compound. As a reminder, we have an octane parent chain, three methyl
substituents in positions 2, 5, and 7. The name of the compound then is 2,5,7–trimethyloctane.
2,5,7 are the locants. We add a tri- to the methyl since there are three methyl groups.

SAMPLE PROBLEM 5
The first three steps are represented by the following images, like the steps we did in SAMPLE
PROBLEM 4:
2 2
1
1 1
4 3 4 3
5 1 5
7 7
6 6
2
8 1 8 9
9
Note: The numbering is the same whether we started on the top portion, or the bottom portion, so
any numbering order would be correct.
So, we have one methyl group in C-5, and two ethyl groups in C-4 and C-6. Alphabetically, ethyl
would be before methyl, so that will be the order in the naming. The name of the compound is
4,6–diethyl–5–methylnonane.

SAMPLE PROBLEM 6
The longest chain of the molecule is shown below, with the following numbering:
6
5
8 3
7 4
2
1
9
The substituent in C-2 is a simple methyl group. The substituent in C-5 is a little more complicated.
We will need to refer to Step 5 of the naming scheme. First, we need to identify the “longest chain”
of the substituent. Remember that there are two conventions for this.
If we follow 1979 conventions, then we need to identify the longest chain starting from the
attachment of the substituent. This is shown in the following figure.

2
1
6
5
8 3
7 4
2
1
9
The substituent group would then have a propyl “parent chain”, and two methyls are attached to
C-1 and C-2 of the substituent. Following the rules, we consider dimethylpropyl as alphabetically
after methyl. The name of the compound is 2–methyl–5–(1,2–dimethylpropyl)nonane. Notice that
the more complicated substituent is inside the parentheses.
If we follow 1993/2013 convention, we need to find the longest chain independent of where the
attachment of the substituent is. This is shown by the following figure.
1
3
2
6 5
4
8 3
7 4
2
1
9
We can see that the butyl “parent chain” of the substituent is attached to its C-2. This will be the
locator of the -yl suffix. Following this scheme, the name of the compound is
2–methyl–5–(3–methylbutan–2–yl)nonane.
Note that both names are considered correct. However, a good thing to do is to practice using the
new conventions, since some compounds are impossible to name using old conventions.

Cycloalkane Nomenclature
Not all alkanes are open chains, however. CYCLOALKANES are hydrocarbons that form rings rather
than the chains we have previously discussed. Because of the ring formation, there will be two less
hydrogens as compared to the chains, so cycloalkanes have a general formula of C𝑛 H2𝑛 . They are
named based on the number of carbons in the ring, similar to the ones used in chain alkanes, but
adding a cyclo- prefix (Note that the minimum number of carbon required to form a ring is three, so
the simplest cycloalkane is cyclopropane). Table 2 shows the common cycloalkanes that we will
encounter. Notice that we usually draw cycloalkanes as polygons.
Table 2 Cycloalkanes and their Structures
No. of C (𝒏) Formula (𝐂𝒏 𝐇𝟐𝒏 ) Name of Compound Structure
3 C3 H6 cyclopropane
4 C4 H8 cyclobutane
5 C5 H10 cyclopentane
6 C6 H12 cyclohexane
7 C7 H14 cycloheptane
8 C8 H16 cyclooctane

Substituted cycloalkanes are named by rules like open-chain alkanes. Most of the compounds follow
these two rules:
1. FIND THE PARENT . Count the number of carbon atoms in the ring and the number in the largest
substituent. If the number of carbon atoms in the ring is equal to or greater than the number
in the substituent, the compound is named as an alkyl-substituted cycloalkane. If the number
of carbon atoms in the largest substituent is greater than the number in the ring, the
compound is named as a cycloalkyl-substituted alkane.
2. NUMBER THE SUBSTITUENTS AND WRITE THE NAME . For an alkyl- substituted cycloalkane, choose
a point of attachment as carbon 1 and number the substituents on the ring so that the second
substituent has as low a number as possible. If ambiguity still exists, number so that the third
or fourth substituent has as low a number as possible, until a point of difference is found.
SAMPLE PROBLEM 7
We compare the ring to the longest chain attached to it to see how we will name the compound.
Showing the counting, we have:
1
2 3
4
1
4
3 2 5
Since the chain is longer, we treat the ring as a substituent. The compound is then called as
2–cyclobutylpentane.

SAMPLE PROBLEM 8
We compare the ring to the longest chain attached to it to see how we will name the compound.
We have four members in the ring, and the longest chain is two carbons (Never ever count a member
of a ring as a member of the attached chain). Therefore, we treat the ring as the parent. We then
have two numbering schemes that have the same numbers here:
2 1
3 4
1 2
4 3
How do we choose then? If this is the case where we have the same number of substituents and
same locants, priority favors the ones who are first alphabetically. So, we assign the lower number
to the ethyl group (alphabetically before the methyl group), hence the one on the right side is what
we choose. Following previous rules, the name of the compound is 1–ethyl–2–methylcyclobutane.
Special cases of compounds with attached rings (polycyclic compounds and spiro compounds) are
also possible. We will discuss them later in the subject’s timeline.

Physical Properties of Alkanes and Cycloalkanes

Alkanes are sometimes referred to as paraffins, a word derived from the Latin parum affinis, meaning
“little affinity.” This term aptly describes their behavior, for alkanes show little chemical affinity for
other substances and are chemically inert to most laboratory reagents. They are also relatively inert
biologically and are not often involved in the chemistry of living organisms. Alkanes do, however,
react with oxygen, halogens, and a few other substances under appropriate conditions.
Alkanes show regular increases in both boiling point and melting point as molecular weight increases.
The reason that longer chain molecules have higher boiling points is that longer chain molecules
become wrapped around and enmeshed in each other much like the strands of spaghetti. More
energy is needed to separate them than short chain molecules which have only weak forces of
attraction for each other. This trend is shown in Figure 1.
Figure 1 Melting and Boiling Points of Saturated Hydrocarbons as a Function of the Number of their Carbons

Another effect seen in alkanes is that increased branching lowers an alkane’s boiling point. Thus,
pentane has no branches and boils at 36.1 °C, isopentane (2-methylbutane) has one branch and boils
at 27.85 °C, and neopentane (2,2-dimethylpropane) has two branches and boils at 9.5 °C. Similarly,
octane boils at 125.7 °C, whereas isooctane (2,2,4-trimethylpentane) boils at 99.3 °C. Branched-chain
alkanes are lower-boiling because they are more nearly spherical than straight-chain alkanes, have
smaller surface areas, and consequently have smaller dispersion forces.
Alkanes are non-polar solvents. Since only C and H atoms are present, alkanes are nonpolar. Alkanes
are immiscible in water but freely miscible in other non-polar solvents. Alkanes consisting of weak
dipole-dipole bonds cannot break the strong hydrogen bond between water molecules, thus it is not
miscible in water.
Because alkanes contain only carbon and hydrogen, combustion produces compounds that contain
only carbon, hydrogen, and/or oxygen. Like other hydrocarbons, combustion under most
circumstances produces mainly carbon dioxide and water. However, alkanes require more heat to
combust and do not release as much heat when they combust as other classes of hydrocarbons.
Therefore, combustion of alkanes produces higher concentrations of organic compounds containing
oxygen, such as aldehydes and ketones, when combusting at the same temperature as other
hydrocarbons.
Generally, the melting point, the boiling point and the density of cycloalkanes increase as the number
of carbons increases. This trend occurs because of the greater number of bonds that are in higher
membered rings, thus making the bonds harder to break. The physical properties of cycloalkanes are
like those of alkanes, but they have higher boiling points, melting points and higher densities due to
the greater number of London forces that they contain. Cycloalkanes are also non-polar and do not
have intermolecular hydrogen bonding; they are usually hydrophobic (meaning they do not dissolve
in water) and are less dense than water.

Conformations of Alkanes and Cycloalkanes
Newman Projections of Alkanes

We will see on many occasions that the exact three-dimensional structure of a molecule is often
crucial to determining its properties and biological behavior. The different arrangements of atoms
that result from bond rotation are called CONFORMATIONS , and molecules that have different
arrangements are called conformational isomers, or CONFORMERS. Unlike constitutional isomers,
however, different conformers often cannot be isolated because they interconvert too rapidly.
We represent conformers using Newman projection. The NEWMAN PROJECTION views the carbon–
carbon bond directly end-on and represents the two carbon atoms by a circle. Bonds attached to the
front carbon are represented by lines to the center of the circle, and bonds attached to the rear
carbon are represented by lines to the edge of the circle. For example, let us see the Newman
projection of ethane. Three – dimensional models and the Newman projection of ethane is shown in
Figure 2.
H H
H H
H H
Figure 2 3D Projections of Ethane in Staggered Conformation. The Center projection, in which one Carbon is
behind the other, is represented by the Newman projection on the right.
Sigma (σ) bonds are cylindrically symmetrical. In other words, the intersection of a plane cutting
through a carbon–carbon single-bond orbital looks like a circle. Because of this cylindrical symmetry,
rotation is possible around carbon–carbon bonds in open-chain molecules. In ethane, for instance,
rotation around the C–C bond occurs somewhat freely, constantly changing the spatial relationships
between the hydrogens on one carbon and those on the other. Experiments show that there is a
small (12 kJ/mol) barrier to rotation and that some conformations are more stable than others. The
lowest-energy, most stable conformation is the one in which all six C–H bonds are as far away from
one another as possible, is shown in Figure 2. We call this as the STAGGERED CONFORMATION.

The most energetic, least stable form is the one in which all the C–H bonds are as close as possible,
is shown in Figure 3. We call this as the ECLIPSED CONFORMATION.
HH
H
H
HH
Figure 3 3D Projections of Ethane in Eclipsed Conformation. The Center projection, in which one Carbon is
behind the other, is represented by the Newman projection on the right.
At any given instant, about 99% of ethane molecules have an approximately staggered conformation
and only about 1% are near the eclipsed conformation. The extra 12 kJ/mol of energy present in the
eclipsed conformation of ethane is called TORSIONAL STRAIN. Its cause has been the subject of
controversy, but the major factor is an interaction between C–H bonding orbitals on one carbon with
antibonding orbitals on the adjacent carbon, which stabilizes the staggered conformation relative to
the eclipsed one. The barrier to rotation that results can be represented on a graph of potential
energy versus degree of rotation, in which the angle between C–H bonds on the front and back
carbons as viewed end-on (the dihedral angle) goes full circle from 0 to 360°. Energy minima occur
at staggered conformations, and energy maxima occur at eclipsed conformations. This potential
diagram is shown in Figure 4.
HH
H A A A A
A Eclipsed H
HH
E
H H B B
B
B Staggered H H
0 60 120 180 240 300 360
H H Degrees of Rotation q
Figure 4 Potential Energy Graph as a Function of Bond Rotation Degrees in Ethane.

SAMPLE PROBLEM 9
Draw Newman Projections of Eclipsed and Staggered conformations for butane, looking at the C1–C2
bond.
If we project butane in the C1–C2 bond, we need to identify what is attached to C1 and C2.
H H CH3
H C1 C2 CH2
H H
We can see that C1 has three hydrogens attached, while C2 has two hydrogens and an ethyl group
(−CH2 CH3 ) as its attachments. The staggered conformation for the C1–C2 projection of butane would
then be the following:
H H
H CH2CH3
H H
The eclipsed conformation for the C1–C2 projection of butane would then be the following:
HH
CH2CH3
H
HH

The conformational situation becomes more complex for larger alkanes because not all staggered
conformations have the same energy and not all eclipsed conformations have the same energy. For
more complicated structures, we have additional conformations. The ANTI CONFORMATION is a
staggered conformation in which the lowest – energy arrangement in which all groups, that are not
hydrogen, are as far away as possible. The GAUCHE CONFORMATION is a staggered conformation that
have groups near each other, causing steric strain. STERIC STRAIN is the repulsive interaction that
occurs when atoms are forced closer together than their atomic radii allow. It is the result of trying
to force two atoms to occupy the same space. For example, let us look at the C2–C3 projection of
butane. We have the following projections shown in Figure 5.
H
H3CCH3 H3C CH3 H3C
H CH3
H H H H
HH H H HH
0° 60° 120°
Eclipsed – A Gauche – B Eclipsed – C
H H H
H3C H3C H3C
H
H H H H3C H
H CH3 HCH H H
3
180° 240° 300°

Anti – D Eclipsed – E Gauche – F
Figure 5 Newman Projections of C2 – C3 bond of Butane, showing the Bond Rotation Angles as we rotate the
C3 (behind) while we keep the position of C2 (front) constant.

From the projections, we could see the possible interactions of the methyl group to the hydrogens
or to the other methyl group. The Anti conformation has the lowest energy because the methyl
groups are far away from each other. The Gauche conformations have additional energies since the
methyl groups are relatively close to each other. The Eclipsed conformation C would have the highest
energy since the methyl groups are closest to each other in that projection. The energetics of the
bond rotations of butane is shown in Figure 6.
Figure 6 Potential Energy as a Function of Bond Rotation Degrees in the C 2–C3 projection of Butane. Letters in
the graph represent the structures shown in Figure 5.
Cis – Trans Isomerism in Cycloalkanes

In contrast with the relatively free rotation around single bonds in open-chain alkanes, there is much
less freedom in cycloalkanes. Cyclopropane, for example, must be a rigid, planar molecule because
three points (the carbon atoms) define a plane. No bond rotation can take place around a
cyclopropane carbon–carbon bond without breaking open the ring. Larger cycloalkanes have
increasing rotational freedom, and very large rings (25 carbons and up) are so floppy that they are
nearly indistinguishable from open-chain alkanes. The common ring sizes (Three to seven carbons),
however, are severely restricted in their molecular motions.

Because of their cyclic structures, cycloalkanes have two faces when viewed edge-on, a “top” face
and a “bottom” face. As a result, isomerism is possible in substituted cycloalkanes. For example, there
are two different 1,2-dimethylcyclopropane isomers, one with the two methyl groups on the same
face of the ring and one with the methyl groups on opposite faces. Both isomers are stable
compounds, and neither can be converted into the other without breaking and reforming chemical
bonds.
H3C H H3C CH3
H CH3 H H
Note that a bold bond indicates that the bond is projected in front of the plane (in other words, the
bond is forward or nearer our view). A dashed bond, in contrast, indicates that the bond is projected
behind the plane (in other words, the bond is farther in our view). The two compounds have the
same order of connections but have a different spatial orientation in 3D space. Such compounds,
with atoms connected in the same order but differing in three-dimensional orientation, are called
stereochemical isomers, or STEREOISOMERS . More generally, the term STEREOCHEMISTRY is used to
refer to the three-dimensional aspects of chemical structure and reactivity.
The 1,2-dimethylcyclopropanes are members of a subclass of stereoisomers called CIS–TRANS

ISOMERS . The prefixes cis- (Latin “on the same side”) and trans- (Latin “across”) are used to distinguish
between them. Cis–trans isomerism is a common occurrence in substituted cycloalkanes and in many
cyclic biological molecules.
Commonly, we project the ring in a flat surface. In these views, the ring is roughly in the plane of the
page, a wedged bond protrudes out of the page, and a dashed bond recedes into the page. Two
substituents are cis if they are both out of or both into the page, and they are trans if one is out of
and one is into the page.

SAMPLE PROBLEM 10
H CH3
H3C
H
Same rules of naming still applies to the compound. However, we need to account for the positions
of the atoms in 3D space, as it is indicated in the compound.
Following our naming schemes from before, the compound is 1–ethyl–3–methylcyclopentane. Based
on the figure, the methyl group and the ethyl group are both in front of our ring. Since they are in
the same side, we assign the cis- configuration for the molecule. The complete name of the molecule
then is cis–1–ethyl–3–methylcyclopentane.
A more general discussion of cis – trans isomerism would be discussed in a future topic.
Stability and Conformations of Cycloalkanes

Chemists in the late 1800s knew that cyclic molecules existed, but the limitations on ring size were
unclear. Although numerous compounds containing five-membered and six-membered rings were
known, smaller and larger ring sizes had not been prepared, despite many efforts.
A theoretical interpretation of this observation was proposed in 1885 by Adolf von Baeyer, who
suggested that small and large rings might be unstable due to ANGLE STRAIN—the strain induced in
a molecule when bond angles are forced to deviate from the ideal 109° tetrahedral value. Baeyer
based his suggestion on the simple geometric notion that a three-membered ring (cyclopropane)
should be an equilateral triangle with bond angles of 60° rather than 109°, a four-membered ring
(cyclobutane) should be a square with bond angles of 90°, a five-membered ring should be a regular
pentagon with bond angles of 108°, and so on. Continuing this argument, large rings should be
strained by having bond angles that are much greater than 109°.
Baeyer’s theory is only partially correct, based on experimental evidences. Cyclopropane and
cyclobutane are indeed strained, just as predicted, but cyclopentane is more strained than predicted,

and cyclohexane is strain-free. Cycloalkanes of intermediate size have only modest strain, and rings
of 14 carbons or more are strain-free.
The reason that the theory is wrong is because of the assumption that the rings are flat or planar.
Most cycloalkanes are not flat; they adopt puckered three-dimensional conformations that allow
bond angles to be nearly tetrahedral. As a result, angle strain occurs only in three- and four-
membered rings, which have little flexibility. For most ring sizes, particularly the medium-ring (seven
to eleven carbons) cycloalkanes, torsional strain caused by H ←→ H eclipsing interactions at adjacent
carbons and steric strain caused by the repulsion between nonbonded atoms that approach too
closely are the most important factors. Thus, three kinds of strain contribute to the overall energy of
a cycloalkane.
• Angle strain—the strain due to expansion or compression of bond angles

• Torsional strain—the strain due to eclipsing of bonds between neighboring atoms
• Steric strain—the strain due to repulsive interactions when atoms approach each other too
closely
Cyclopropane is the most strained of all rings, primarily because of the angle strain caused by its 60°
C–C–C bond angles. In addition, cyclopropane has considerable torsional strain because the C–H
bonds on neighboring carbon atoms are eclipsed. Cyclobutane has less angle strain than
cyclopropane but has more torsional strain because of its larger number of ring hydrogens. Although
planar cyclopentane has practically no angle strain, it has a large torsional strain. Cyclopentane
therefore twists to adopt a puckered, nonplanar conformation that strikes a balance between
increased angle strain and decreased torsional strain. Four of the cyclopentane carbon atoms are in
approximately the same plane, with the fifth carbon atom bent out of the plane. We term this
conformation as an envelop conformation, since it looks like an open envelop. The 3D structures of
the three compounds are shown in Figure 7.

Figure 7 3D Structures of Cyclopropane, Cyclobutane, and Cyclopentane. Notice that cyclopropane has planar
carbons, while cyclobutane has a slight fold, and cyclopentane has one carbon not in plane to the other four
carbons.
The most common ring system in nature is the cyclohexane. Many compounds, including steroids
and many pharmaceutical agents, have cyclohexane rings.
Cyclohexane adopts a strain-free, three-dimensional shape that is called a CHAIR CONFORMATION

because of its similarity to a lounge chair, with a back, seat, and footrest. Chair cyclohexane has
neither angle strain nor torsional strain—all C–C–C bond angles are near the 109° tetrahedral value,
and all neighboring C–H bonds are staggered. Figure 8 shows various cyclohexane chair projections.
Figure 8 The Chair Conformation of Cyclohexane. Each subsequent structure is the 3D structure as we flip the
molecule towards the view of the eye.
In drawing the chair conformation of cyclohexane, it is helpful to know that it is similar to the white
region in the messenger icon, as shown in Figure 9. When viewing cyclohexane, it is helpful to
remember that the lower bond is in front and the upper bond is in back. If this convention is not
defined, it can appear that the reverse is true.

Figure 9 Representations of the Chair Conformation of Cyclohexane as Compared to the Facebook Messenger
Logo (right). The middle top figure is how it is drawn usually, while the middle bottom figure shows that the
lower side of the drawing is in front, like how it is shown in the ball and stick model on the left.
YOUR INSTRUCTOR’S TWO CENTS: CHAIR CONFORMATION DRAWING
My preference of drawing is as follows:
First, I draw offset parallel lines that are slanted downward to the right as a basis.
Second, I draw two parallel lines that are attached to the opposite points of the lines I drew first that
would form an angle that is slightly higher than 90°.
Finally, I attach the ends of each line to each other, like this:
And voilà, you have made a cyclohexane drawing!
You can have your own style in drawing a chair conformation. This is how I do it usually, and I hope
it helps you in finding your own.

In addition to the chair conformation of cyclohexane, there is an alternative conformation of

cyclohexane that bears a slight resemblance to a boat. The BOAT CONFORMATION of cyclohexane has
no angle strain but has many eclipsing interactions that make it less stable than chair cyclohexane. A
“twist” on this alternative can be found in TWIST–BOAT CONFORMATION, which is also nearly free of
angle strain. It does, however, have both steric strain and torsional strain and is about 23 kJ/mol (5.5
kcal/mol) higher in energy than the chair conformation. As a result, molecules adopt the twist-boat
geometry only under special circumstances. Finally, the most energetic form of cyclohexane is the
HALF–CHAIR CONFORMATION . This confirmation is the transition state between the chair
conformation and the twist-boat conformation. We represent these conformations as shown in
Figure 10.
Figure 10 Less Stable Configurations of Cyclohexane: Left – Boat Conformation, Middle – Twist–Boat
Conformation, Right – Half–Chair Conformation.
The chair conformation of cyclohexane is that it leads to two kinds of positions for substituents: The
six AXIAL positions are perpendicular to the ring, parallel to the ring axis, and the six EQUATORIAL
positions are in the rough plane of the ring, around the ring equator. We represent the differences
of these positions in Figure 11.
A A
E
E A E
E A E
E
A A
Figure 11 Axial (A) and Equatorial (E) Positions in Cyclohexane

Note that we have not used the words cis and trans in this discussion of cyclohexane conformation.
Two hydrogens on the same face of the ring are always cis, regardless of whether they are axial or
equatorial and regardless of whether they are adjacent. Similarly, two hydrogens on opposite faces
of the ring are always trans.
Because chair cyclohexane has two kinds of positions, axial and equatorial, we might expect to find
two isomeric forms of a monosubstituted cyclohexane. In fact, we do not. There is only one
methylcyclohexane, and so on, because cyclohexane rings are conformationally mobile at room
temperature. Different chair conformations readily interconvert, exchanging axial and equatorial
positions. This interconversion, usually called a RING -FLIP.
Hx Hx Hy Hy
H Hx
C6 y C4 C1 C5
Hy C5 Hy Ring-flip Hx C6 Hx
Hx Hy
Hx Hy
Hy C2 Hy Hx C3 Hx
C1 C3 C2 H C4
Hy x
Hx Hx Hy Hy
A chair cyclohexane can be ring-flipped by keeping the middle four carbon atoms in place while
folding the two end carbons in opposite directions. In so doing, an axial substituent in one chair form
becomes an equatorial substituent in the ring-flipped chair form and vice versa. To help you visualize
the ring flip, we can use Figure 12 as a reference.
Figure 12 Relative Positions of Substituents after a Ring-flip in Cyclohexane. Obtained from Sloop, J., Anagho,
L., Coppock, P., Giles, G., Park, S., Pennington, R., Pursell, D., Rudd, G., Mai, Y., & Tsoi, M.Y. (2013). Conformational
Analysis, Modeling, Stereochemistry and Optical Activity of Cyclohexane Derivatives. Journal of Laboratory
Chemical Education. 1. 39-44. 10.5923/j.jlce.20130103.01.

SAMPLE PROBLEM 11
Draw two different chair conformations of trans–1,4–dimethylcyclohexane that shows a ring-flip.
Trans- requires that the two methyl groups be on opposite sides of the compound, regardless if they
are axial or not. What we need to do is to draw one correct chair conformation, and then so a ring-
flip for the other.
Since it is 1,4–, we need to have two carbons between the ones with the methyl groups. We can
choose the following carbons:
1
Drawing the axial and equatorial positions for each carbon, we have:
ax
eq
eq
ax
For them to be opposite sides, one should be on top and the other on the bottom. We could either
have two axial positions, or two equatorial positions (as that gives us opposite sides). Using the axial
positions for one structure and applying a ring-flip on that structure, we have:
CH3 H
H H3C
H CH3
Ring - flip
CH3 H

Alkane and Cycloalkane Reactions

As mentioned before, we have only few reactions involving alkanes and cycloalkanes because of
their relative stability. Before everything else, we need to discuss first how reactions are described
in organic chemistry.
For example, let us look at the reaction of methane, the simplest hydrocarbon, with oxygen to form
carbon dioxide and water vapor as products, through a reaction which we call as a combustion
reaction.
CH4 (𝑔) + 2 O2 (𝑔) → CO2 (𝑔) + 2H2 O(𝑔)
In general, a COMBUSTION REACTION is a reaction that involves a combustible material (methane in

this case, and generally fuels are the combustible material) and an oxidizer (which we will define for
now as a substance to initiate the combustion of the material, in this case we have oxygen as the
oxidizer).
It is helpful in organic chemistry to know what specific bonds are formed, and what specific bonds
are broken, as it helps us understand the reaction more. If we represent our reaction in which we see
its bonds, we will have the following:
H H
H O
H O O
C + O C O +
H O O
H H H
O
As we can see, for the reaction we need to break the C–H bonds of methane and the O=O bonds of
oxygen, and we need to create the C=O bonds of carbon dioxide and the O–H bonds of water.
Overall, we need to break 4 C–H bonds, and 2 O=O bonds, and form 2 C=O bonds and 4 O–H bonds.
For organic chemistry reactions, knowing what specific bonds are broken and formed is an important
skill. This will help us understand how and why these bonds are formed.
As we see here, alkanes can do combustion reactions when oxygen is available. Complete
combustion (given sufficient oxygen) of any hydrocarbon produces carbon dioxide and water. The

hydrocarbons become harder to ignite as the molecules get bigger. This is because the bigger
molecules do not vaporize so easily – the reaction is much better if the oxygen and the hydrocarbon
are well mixed as gases. If the liquid is not very volatile, only those molecules on the surface can
react with the oxygen. Bigger molecules have greater Van der Waals attractions which makes it more
difficult for them to break away from their neighbors and turn to a gas.
Provided the combustion is complete, all the hydrocarbons will burn with a blue flame. However,
combustion tends to be less complete as the number of carbon atoms in the molecules rises. That
means that the bigger the hydrocarbon, the more likely you are to get a yellow, smoky flame.
Incomplete combustion (where there is not enough oxygen present) can lead to the formation of
carbon or carbon monoxide.
HALOGENATION is the replacement of one or more hydrogen atoms in an organic compound by a

halogen (fluorine, chlorine, bromine, or iodine). Unlike the complex transformations of combustion,
the halogenation of an alkane appears to be a simple substitution reaction in which a C–H bond is
broken, and a new C–X bond is formed. This requires the presence of heat (Δ) or light (ℎ𝜈) for it to
proceed.
Δ or hν
RH + X2 RX + HX
One complication is that all the hydrogen atoms of an alkane may undergo substitution, resulting in
a mixture of products. The relative amounts of the various products depend on the proportion of the
two reactants used. In the case of methane, a large excess of the hydrocarbon favors formation of
monosubstituted alkyl halides, whereas an excess of chlorine favors formation of polysubstituted
alkyl halides.
Larger alkanes would have a lot of possibilities of products, since again any C–H bond could be
broken by the reaction. (Note that there is a priority in which C–H bonds are broken, this concept
would be discussed in a future topic).

SAMPLE PROBLEM 12
Draw the possible products when the compound 3–ethyl–2–methylpentane reacts with one
equivalent of chlorine in the presence of light.
The compound that we have could be drawn as the following:
We need to identify the locations where a C–H bond occurs, and in which are unique ones. Showing
the hydrogens, we have:
H H H
H
C C H
H
C
H
H
H C H
C C H
H C C
H H H
H H H
Hydrogens attached in the same carbon are the equivalent hydrogens. So, in first glance, we have
eight unique regions. We color coded them for now:
H H H
H
C C H
H
C
H
H
H C H
C C H
H C C
H H H
H H H
We need to account for symmetrical regions of the compound, too. Symmetrical carbons are color
coded in the following structure:

H H H
H
C C H
H
C
H H
H C H
C C H
H C C
H H H
H H H
So, we only have five unique C–H bonds:
H H H
H
C C H
H
C
H H
H C H
C C H
H C C
H H H
H H H
In the original structure, the regions that we have are:
e
b
d c
e a
So, the possible answers would be the following:
Cl
Cl
Cl
Cl
Cl
We will name them in a future topic.

The reactions of the cycloalkanes are generally just the same as the alkanes, except for the very small
ones – particularly cyclopropane. In the presence of UV light, cyclopropane will undergo substitution
reactions with chlorine or bromine just like a non-cyclic alkane. However, it also could react in the
dark. In the absence of UV light, cyclopropane can undergo addition reactions in which the ring is
broken. For example, with bromine, cyclopropane gives 1,3-dibromopropane.
+ Br2 Br Br
This can still happen in the presence of light - but you will get substitution reactions as well. The ring
is broken because cyclopropane suffers badly from ring strain. The bond angles in the ring are 60°
rather than the normal value of about 109.5° when the carbon makes four single bonds. The overlap
between the atomic orbitals in forming the carbon-carbon bonds is less good than it is normally, and
there is considerable repulsion between the bonding pairs. The system becomes more stable if the
ring is broken.
Alkane and Cycloalkane Synthesis

SYNTHESIS REACTIONS in organic chemistry is defined as reactions that would yield the target product.
It may or may have side products. For synthesis reactions, we will just have a glance on them, and
we will talk about them in their respective reaction sections.
ALKENES / ALKYNES – CATALYTIC HYDROGENATION
2 2
R H2 R
1 1
R Ni R
2
1 2 H2 R
R R 1
Ni R
ALKYL HALIDES – COUPLING WITH ORGANOCUPRATES (GILMAN REAGENTS )
R
1
I + (R2)2CuLi R
1
R
2
+ R2Cu + LiI

ALDEHYDES / KETONES – R EDUCTION (DEOXYGENATION )
O
KOH
+ N2H4
Δ R CH3 + N2 + H2O
R H
O
KOH 1 2
1 2
+ N2H4
Δ R R + N2 + H2O
R R
ORGANOMETALLICS – REACTION WITH WATER
R M + H2O R H + M OH

Assessment Activity
Answer the following:
1. Name the following molecules:

2. Draw the following molecules:

a. 3–ethyl–3,4–dimethyloctane
b. 2,3,4,5–tetramethylnonane
c. 1–cyclobutyl–1–cyclopropylhexane
d. 1,3,5–tripropylcyclohexane
e. 4 –(2–methylpentan–3–yl)decane
f. 1 – methyl – 3 –(3–methylpentan–2–yl)cyclohexane
g. 1–cyclobutyl–3–cyclopropylcyclopentane
3. Draw the possible Newman projections of 2,3–dimethylbutane from the C2 – C3 perspective,
keeping C2 in its place while rotating C3. Sketch an energy diagram as a function of the
degrees of rotation.
4. Draw two different chair conformations of trans–1,3–dimethylcyclohexane that shows a ring-
flip.
5. How many unique products would we have when 4 – ethyl – 1,2 – dimethylcyclopentane
reacts with one equivalent of chlorine in the presence of light? Draw each of the following
products.
References
• Organic Chemistry, 7th Ed. by Bruice, PY
• Organic Chemistry, 9th Ed. by McMurry, J
• Organic Chemistry, 10th Ed. by Solomons, TWG and Fryhle, CB
• Organic Structures created using ACD/ChemSketch Freeware – obtained from
https://www.acdlabs.com/resources/freeware/chemsketch/download.php

Alkanes and Cycloalkanes: Organic Chemistry BS Biology - 1 Semester, AY 2020 - 2021

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Organic Chemistry BS Biology – 1st Semester, AY 2020 – 2021

Alkanes and Cycloalkanes

Alkane Nomenclature ................................................................................................................................................................................................. 2

Physical Properties of Alkanes and Cycloalkanes ................................................................................................................................. 16

Conformations of Alkanes and Cycloalkanes ........................................................................................................................................... 18

Newman Projections of Alkanes..................................................................................................................................................................... 18

Cis – Trans Isomerism in Cycloalkanes ..................................................................................................................................................... 22

Stability and Conformations of Cycloalkanes ................................................................................................................................... 24

Alkane and Cycloalkane Reactions ..................................................................................................................................................................... 31

Alkane and Cycloalkane Synthesis .................................................................................................................................................................... 35

Assessment Activity .........................................................................................................................................................................................................37

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 1

Alkane and Cycloalkane Nomenclature

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 2

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 3

Skeletal formulas usually follow the following rules:

Draw skeletal formulas for butane and 2–methylpropane.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 4

Write condensed formulas for butane and 2–methylpropane.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 5

Possible skeletal forms of the compound are as follows:

Table 1 Straight Chain Alkane Nomenclature

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

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 6

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 7

Name the following compound.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 8

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 9

Name the following compound.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 10

Name the following compound.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 11

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 12

Table 2 Cycloalkanes and their Structures

No. of C (𝒏) Formula (𝐂𝒏 𝐇𝟐𝒏 ) Name of Compound Structure

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 13

Name the following compound.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 14

Name the following compound.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 15

Physical Properties of Alkanes and Cycloalkanes

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 16

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 17

Conformations of Alkanes and Cycloalkanes

Newman Projections of Alkanes

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 18

Figure 4 Potential Energy Graph as a Function of Bond Rotation Degrees in Ethane.

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 19

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 20

180° 240° 300°

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 21

Cis – Trans Isomerism in Cycloalkanes

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 22

H3C H H3C CH3

The 1,2-dimethylcyclopropanes are members of a subclass of stereoisomers called CIS–TRANS

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 23

Name the following compound.

Stability and Conformations of Cycloalkanes

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 24

• Angle strain—the strain due to expansion or compression of bond angles

Instr. Jose Mari Felicita Alkanes and Cycloalkanes | 25

Cyclohexane adopts a strain-free, three-dimensional shape that is called a CHAIR CONFORMATION