Chemistry Notes For Class (1)
Introduction to Organic Chemistry (1)
By Yuan Han
Introduction to Organic Chemistry
Organic Chemistry is defined as a sub-discipline of chemistry, together with other subdisciplines such as inorganic chemistry, analytical chemistry, and physical chemistry. It
primarily deals with carbon-based compounds, hydrocarbons, and their derivatives; but have
many overlaps with inorganic chemistry. Organic compounds are elementally simple but
structurally complex. This means that they consist of a few elements, again relative to
inorganic chemistry, but these few elements combine in a dizzying array of shapes and sizes
to give the general class of organic compounds.
Presumed Knowledge
In this notes, readers are assumed to have knowledge of the following:
1. A-level H2 Chem topics:
a. Atomic structure
b. Periodicity
c. Chemical bonding (including VSEPR and Hybridisation theory)
2. Basic nomenclature for organic compounds.
Functional Groups
In chemistry, we are studying the various types of reactions that occur when 2 or more
reactants come into contact with each other. In organic chemistry, the types of reactions that
occur between organic compounds are usually due to the different functional groups that are
present in the organic compound.
Each functional group will impart to the molecule its own characteristic reactions. All organic
molecules containing a certain functional group can hypothetically undergo all the reactions
that are described by the functional group. Therefore, functional groups determine the
chemistry of the organic compound.
Functional groups range widely in their size and scale. Simple functional groups such as the
hydroxyl group, the alkene, the carboxylic acid group are typically present on many
molecules. However, there are many more functional groups that are a combination of the
simple functional groups. Moreover, if a certain structure in the compound gives a very
distinctive reaction, the structure is commonly defined as a structural backbone and a new
class of organic compounds can be defined as compounds having this backbone.
Some common functional groups:
Functional Group
−C = C −
−OH
−COOH
−COOC −
−CHO
− CO −
Name
Alkene
Hydroxyl/alcohol
Carboxylic acid
Ester
Aldehyde
Ketone
Question 1:
Give 3 other examples of simple functional groups and draw their chemical structures.
Note that the above table only lists a few of the simplest functional groups and is not
exhaustive by a long run.
Note that alkanes are typically not defined as a functional group.
An example of a compound with a structural backbone is 2-phenyl chromen-4-one
This is the structural backbone of a class of compounds called flavones and other functional
groups can be placed at the different positions (3,8,7,6,5,2’,3’,4’,5’,6’…). This backbone
gives characteristic biological activities that are present in all compounds within this class.
Functional groups are important in the naming of the compound. Most organic compounds
are named are named as the parental chain and the substituents on the parental chain. The
parental chain is commonly defined as the structural backbone or the longest alkane chain
containing the functional group with the highest priority. Priority in naming is generally
given to the functional group that imparts the most distinctive chemistry to the molecule.
For example:
This molecule has 3 functional groups:
1. Benzene ring
2. Aldehyde
3. Carboxylic acid
Therefore, using the IUPAC nomenclature, the molecule can have 3 names:
1. 1-carboxyl 4-formyl benzene
2. 4-carboxyl benzaldehyde
3. 4-formyl benzoic acid
Thus, in order to establish a unique name for the molecule, we look at the priority given to
each functional group. We can find that carboxylic acid is given the highest priority followed
by aldehyde, followed by the benzene ring.
Thus, the name should be 4-formyl benzoic acid.
Structural and Constitutional Isomerism
Isomerism is defined as the occurrence of difference molecules with the same molecular
formula. There are many different types of isomerism that occur between organic compounds.
One of the most common types of isomerism is structural isomerism or constitutional
isomerism. In alkanes, structural isomerism exists in the form of branching. A simple
example is butane and 2-methylpropane:
Both have the molecular formula C4H10. Since 2-methylpropane is an isomer of butane, it is
often called isobutane; this name is accepted by IUPAC. To differentiate butane from
isobutane, the straight-chain butane is also sometimes called n-butane.
As we increase the number of carbons, the number of isomers also increases. Pentane, C5H12,
has three isomers:
Isomers of the same compound have different physical properties. For example, the melting
points of isobutane and n-butane are 261 K and 273 K respectively. This is because the
isobutane molecule, being more branched, has a smaller surface area than the n-butane
molecule. This means that there is less area available for induced dipole-dipole attractions
amongst isobutane molecules.
Reactions
Reactions between all chemical compounds are similar. They all involve the movement of
electrons. Thus, the central theme of chemistry is how electrons move. Therefore, it is clear
that all that functional groups do is influence the way that electrons move during a chemical
reaction.
However, exactly how do electrons move during a reaction? To answer this question, we
must look into an unlikely, but familiar topic: acids and bases.
Acids and Bases
Acids and bases are familiar to everyone. However, the central theme of acids and bases are
the definitions, i.e. what is defined as an acid or a base and what are the reactions described
by these definitions.
Firstly, please note that there is no such thing as the H + ion. This species is a proton and is
much too reactive to exist as a stable species. In water, the H + ion exists predominantly as the
hydronium ion, H3 O+ . However, for simplicity, this ion is still represented as H + in chemical
equations and mechanisms. Also, note that only H + in water forms H3 O+ , H + in another
solvent like pure ethanol does not form H3 O+ .
Conventionally, there are 3 definitions of acids and bases. The most basic acid-base
definition is the Arrhenius definition.
An Arrhenius acid is defined as a compound that produces 𝐻 + ions when dissolved in water.
Similarly, an Arrhenius base is defined as a compound that produces 𝑂𝐻 − ions when
dissolved in water.
A more well-known acid-base definition, which is the standard definition for A-levels, is the
Br∅nsted-Lowry definition.
In a reaction, a Br∅nsted-Lowry acid is a proton (𝐻 + ) donor while a Br∅nsted-Lowry base is
a proton acceptor.
This definition allows a neutralisation reaction to occur outside an aqueous medium, which is
impossible based on the Arrhenius definition. For example, the reaction between hydrogen
chloride and ammonia to form ammonium chloride,
HCl + NH3 → NH4 Cl
is now an acid-base reaction with HCl as the acid and NH3 as the base. Under the Arrhenius
definition, there was no acid-base reaction as H+ and OH − are not involved.
Also, the Br∅nsted-Lowry definition introduced the concept of conjugate acids and bases.
Every acid has one conjugate base, and every base has one conjugate acid. The conjugate
base of an acid is just the deprotonated form of the acid. For example, the conjugate base of
HCl is Cl− . The conjugate acid of a base is the protonated base. For example, the conjugate
acid of NH3 is NH4+ .
With that, the concept of neutralization is also effectively removed. An acid and a base
reacted not to form salt and water but the conjugate base of the original acid and the
conjugate acid of the original base.
The third definition is by far the loosest definition. The special thing is that it encompasses
virtually all reactions and the acids and bases are defined based on the role they play in the
reaction.
In a reaction, a Lewis base is an electron pair donor. Similarly, a Lewis acid is an electron
pair acceptor.
Therefore, we can see that a chemical species that acts as a Lewis acid in one reaction may
act as a Lewis base in another.
All 3 definitions of acids and bases are present in organic chemistry. For example, a
carboxylic acid dissociated when dissolved in water, showing that it is clearly an Arrhenius
acid. Amine groups are commonly Br∅nsted-Lowry bases. But by far, the most useful
concept in organic chemistry is the Lewis acid-base definition because it details… yes,
you’ve guessed it…electron movement during a reaction.
It is clear that a Lewis acid donates a pair of electrons to a Lewis base. From the definition of
Lewis acids and bases, a similar definition in organic chemistry is born: the electrophile and
nucleophile.
A nucleophile is a Lewis base. The term nucleophilic comes from ‘nucleus-loving’; it is clear
that nucleophiles ‘like/are attracted to’ the positive charge in the nucleus. It has a high
electron density, and thus tends to donate electrons. Also, nucleophiles cannot be positively
charged or contain a partial positive charge. Generally, nucleophiles have lone pairs and/or
electrons in a π bond. Notable nucleophiles are N atoms, O atoms and C=C double-bonds.
Conversely, an electrophile is a Lewis acid. The term electrophile comes from ‘electronloving’; it is thus clear that electrophiles are ‘attracted to’ the negative charge of electrons.
Electrophiles are generally electron deficient and thus tend to accept electrons from a
nucleophile. Electrophiles tend to positively charged and may also lack a complete octet.
Notable electrophiles are the C atom in C=O, and H+ions.
Most reactions in organic chemistry occur due to the movement of electrons from a
nucleophile to an electrophile.
Reaction Mechanisms
This term has been introduced in reaction kinetics, where the order of the reaction with
respect to one reactant is equal to the number of molecules of that reactant that must be
present at the rate-determining step of the reaction. Here, reaction mechanism is the way
scientists determine the rate-determining step.
Reaction mechanisms are a way of showing how the reaction occurs step-by-step. It details
the electron movement of all the reactants in the reaction. Different classes of reactions have
different mechanisms. Here, I will provide an example of a reaction mechanism, the addition
of HBr to ethene.
We know the overall equation for the reaction:
We can see that the HBr molecule adds across the double-bond of ethene to give
bromoethane. In this case, the HBr dissociates into hydrogen and bromine, which then adds
to the double-bonded carbon atoms.
From these pieces of given information, we can get a rough idea of how the reaction proceeds.
Step 1a:
H—Br is clearly highly polarized, with the electrons on average being closer to the
electronegative Br atom than the H atom. The HBr atom undergoes heterolytic fission, where
both electrons in a bond go to one atom. (In contrast, homolytic fission occurs when the
electrons in a bond is shared equally between both atoms when the bond breaks.) Here it is
clear that both electrons will go to the electronegative Br atom, producing H + and Br − .
In reaction mechanisms, electron movement is denoted by drawing a curved arrow from the
origin of the pair of electrons to the destination of the pair of electrons. (Note that if only 1
electron is moving, a fishhook arrow is used.)
Thus, we draw a curved arrow from the single σ-bond to the Br atom.
Step 1b:
This step occurs simultaneously with step 1a.
The previous dissociation of HBr produces a H+ ion. This is a very good electrophile. As we
know, electrophiles attack nucleophiles during a reaction. So, it is clear that we have to
identify a nucleophilic site on the ethene molecule that the H+ ion reacts with. (Note that Br −
is also a nucleophile and some of the H + ions produced do react with it.) We begin our search
for the nucleophilic site by considering 1 of the defining characteristics of nucleophiles; that
nucleophiles tend to have high electron-density.
If we look at the ethene molecule, only the C=C double-bond has significantly higher
electron-density than anywhere else in the molecule. Thus, the C=C double-bond has to be
the nucleophile in this reaction.
The H+ ion reacts with the C=C double-bond in the following way:
C1
C2
The π-bond in the C=C double-bond breaks and the electrons move from the broken bond to
the unfilled 1s orbital of the H+ ion. As the result of the movement of electrons, there is a
positive charge on the C1 atom. This is known as a carbocation (literally carbon-cation).
However, in actual fact, the H+ ion is not formed during the reaction at all. As steps 1a and 1b
occur simultaneously, the dissociation of HBr occurs at the same time as the addition of “H+”
to the C=C double-bond. The H+ ion is only included to simplify explanation. The actual
mechanism is as shown below:
C1
C2
This is the first step of the reaction mechanism.
Question 2:
This reaction must be conducted in an inert solvent such as hexane or benzene and not in
water. Please determine the reason for this and explain what may happen if water is used as
a solvent.
A carbocation is an ion with a positively-charged carbon atom. How do we know that a
carbocation is formed? As the starting reactants (HBr and ethene) are both neutral and the
product of the step 1 includes a Br − ion, then by the conservation of charge, the other product
must be positively charged. Note that strictly speaking, the products of step 1 are known as
intermediates rather than products.
In the resulting carbocation, the C1 atom bears the positive charge. This is because one of the
electrons in the double bond “belongs” to it, and when the double bond is broken, it will have
one less electron than before.
Question 3:
Determine the number of valence electrons of the unipositively-charged carbon atom. Hence
determine the shape of the molecule with respect to the unipositively-charged carbon center
using VSEPR theory.
This step characterises the mechanism of HX addition to alkenes, and thus this reaction is
also called electrophilic addition (as the HBr reacts through the electrophilic H atom).
Step 2
However, it is clear that the reaction does not stop here. The two intermediates produced are
charged and high in energy. In order to become more stable, they will react with each other to
from the final product.
The bromide ion reacts with the carbocation to give the final addition product.
Question 4:
Determine if the bromide ion, 𝐵𝑟 − , is electrophilic or nucleophilic.
Question 5:
Identify the corresponding site in the carbocation where the bromide ion reacts and
determine if this site is electrophilic or nucleophilic. Explain the reason for your answer.
The reaction mechanism of step 2 is shown as below:
Question 6:
Name the compound according to IUPAC convention.
Again, note the direction of the arrow, from the lone pair (the origin of the electrons) to the
positive charge (the destination).
Conclusion and Summary
Note that the 2 steps must be combined if a reaction mechanism is requested.
Question 7:
Draw the entire reaction mechanism of the electrophilic addition of HBr to ethene.
The steps described above are the basis of all electrophilic addition reactions to alkenes. The
defining step of the reaction is step 1, the addition of an electrophilic group to the C=C
double-bond.
Question 8:
Without calculation, determine the sign of the enthalpy change for this reaction. Explain how
you arrived at the answer.
Question 9:
The electrophilic addition of water with alkenes is known as hydration. Draw a mechanism
for the hydration of but-2-ene. Hence, name the product formed in this reaction according to
IUPAC convention. This reaction typically requires a catalyst to proceed at an appreciable
rate. Deduce the nature of the catalyst and explain why.
Question 10:
Determine the rate-determining step in the reaction and explain your answer. Hence
determine the rate equation for the reaction.