1.1 What are Organic Compounds?

Organic chemistry is the chemistry of the compounds of carbon. They are in our food, medicines,
computers and in our bodies.

Though, we concentrate on the chemistry of carbon, there are other few elements that can partner with
it. These are hydrogen, oxygen, nitrogen, sulfur, phosphorus and halogens (fluorine, chlorine, bromine
or iodine).

Carbon is not even the most abundant element in the Earth's crust, which is mostly composed of oxygen
(49.5%) and silicon (25.7%). So why carbon? There are several reasons for this:

a.) historical reasons

In the early years of chemistry, scientist thought that all organic compounds are produced
from living things while inorganic compounds are those found in rocks (non-living things). The early
scientist believes that you need this "vital force", which only living thing has, to create or derive
organic compounds. This theory was disproved by Friedrich Wohler. He heated an aqueous solution
of ammonium chloride and silver cyanate (see Figure 1.1.1.), which both are inorganic compounds,
and produced urea. This experiment provided sufficient evidence to disprove the "doctrine of vital
force." A few year later, August Kekule provided a new definition to organic compounds which is
widely accepted in this modern times. He defined organic compounds to be compounds that contains
carbon.

Figure 1.1.1. Reaction between ammonium chloride and silver cyanate.

b.) large number of carbon atoms containing compounds you can create
Chemist synthesize a large number of these compounds as compared to inorganic
compounds. This is because of the uniqueness of the carbon's structure and bonding capabilities.
Carbon has four valence electrons which can equate to four different bond points. Carbon can link
together to form large number of carbon chains.

c.) interest in biochemical studies

This portion here is where you guys are most interested in - our biochemicals. Carbohydrates,
lipids, proteins (e.g. enzymes), nucleic acids (DNA and RNA), hormones, vitamins and any other
important chemical in our bodies are organic compounds.

d.) difference of the properties of inorganic compounds and organic compounds

A comparison of properties of Organic and Inorganic compounds
Inorganic Compounds Organic Compounds
Type of Bond Mostly ionic bonds Mostly covalent bonds
Physical state Mostly solid Many are gases, liquids or solids
Melting point Mostly very high Mostly very low (less than 360°C)
Solubility in water Mostly soluble in water Mostly insoluble in water
Electrical conductivity Aqueous solutions are mostly Aqueous solutions are not good
good conductor of electricity conductor or electricity
Flammability Very few burns Almost all burns and decompose
Rate of reaction Often very fast Usually very slow

Organic compounds can be sourced out in two ways, which is thru isolation from nature or synthesis
from the laboratory. These two tracks are mostly how our medicines are discovered. Compounds
isolated from the nature by using chromatographic techniques and are tested in vitro and/ or in vivo for
bioactivity. Afterward, if compound was found to be bioactive, chemist can choose to synthesize the
compound for more massive testing. This is part of drug discovery. Drug discovery can take years to
develop.
1.2 How to Write Structural Formulas?
A structural formula are how we represent our molecule and help us identify the location of each
chemical bonds between the atoms in a molecule. Structural formulas can be represented as expanded
structures, condensed structures and skeletal or line structures. Below are different structural
representation of ethanol or ethyl alcohol, the alcohol found in alcoholic beverages such as wine and
beer.

The VSPER Model

Based on Lewis structures, we can see that a carbon atom can have four bonds and these bonds can be
single bonds, double bonds or a triple bond. Connecting this to the VSEPR theory, carbon atoms in
covalent compounds can have approximately 109.5o, 120o and 180o for a tetrahedral, trigonal planar
and linear geometries, respectively.

Table below summarizes the number of covalent bonds each atom found in organic compounds can have.
Table 1.2.1 Summary of number of covalent bonds and valence electrons for atoms commonly found in organic chemistry.
Atoms Valence electron Number of covalent Number of unshared
bonds formed pair of electrons
carbon 4 4 0
nitrogen 5 3 1
oxygen 6 2 2
hydrogen 1 1 0
halogens 7 1 3

With this knowledge, we can now try how to draw structural formulas. Let us try to draw the expanded
structure of ethyl amine (CH3NH2). Expanded structures are structures where all the bonds are visible. It
is based on Lewis structures. We follow the steps represented below:

Always to remember to check the electrons surrounding each atom. Make sure they follow the octet
rule.

Next, we now draw condensed structures. Condensed structure is a system to write structures in a line
text. It shows all the atoms in the structural formula without the bonds. Let us look some examples
below.
Look at the expanded structures of propane and 2-methylpropane. Their main difference is the extra
methyl (-CH3) attached to carbon-2 of 2-methylpropane. This extra methyl (-CH3) is called a substituent.
Note that the methyl substituent in 2-methylpropane is enclosed in a parenthesis.

In line structures, carbon atoms are represented as a "corner" between two bonds. You will not see
hydrogen atoms in line structures except if they are attached to oxygen or nitrogen. See examples
below:

1.3 What are Functional Groups?

Functional groups are structural features in organic compounds other than carbon-carbon single bonds
and carbon-hydrogen single bonds. Multiple bonds between carbon atoms and bonds of carbon atoms
with other atoms such as oxygen, nitrogen, sulfur and halogens are components of functional groups.
These functional groups help us to predict the physical and chemical characteristics of a certain group of
organic molecules. As we go along the course, we will see that organic compounds fall into the same
functional group will undergo the same set of reactions because this functional group is the site where
the reaction happens.

We can divide the functional groups into:

a. ) hydrocarbons. These contain carbon to carbon multiple bonds and carbon to hydrogen bond.
Examples of these are alkenes (double bonds), alkynes (triple bonds) and aromatic hydrocarbons.

b.) oxygen-containing. There are two types of oxygen containing functional groups: oxygen single
bonded to carbon atoms and carbonyl (C=O) containing compounds. There are two kinds of functional
groups that contains oxygen single bonded to carbon, these are alcohols and ethers.
Alcohols are compounds with hydroxyl (-OH) group bonded to a tetrahedral carbon. A general formula is
presented with the R groups representing carbon groups. It has three classifications - primary (1o),
secondary (2o) and tertiary (3o) alcohols, which depends on the number of carbon atoms attached to
the carbon bearing the hydroxyl (-OH) group.

Ether functional group contains an oxygen bonded to two carbon atoms. These carbon atoms can be a
part of a long chain hydrocarbon (called epoxides or oxirane) (2) or two different carbon groups.

For carbonyl (C=O) containing functional groups, we start off with aldehydes and ketones. Aldehydes are
functional groups that contains a carbonyl bonded to at least one hydrogen. In condensed structural
formula, the aldehyde group is written as CH=O or -CHO. For ketones, its carbonyl group is bonded to
two carbon groups.

Carboxylic acids and its derivatives (anhydride, esters and amides) are examples of functional groups
that contains carbonyl groups. Carboxylic acids have carboxyl group (-COOH) in its structural formula.
Variations of carboxylic acids (carboxylic acid derivatives) varies on the attachment that replaces the
hydrogen in the -COOH of the carboxylic acid. Like for esters, the H group in the -COOH of the carboxylic
acid was replaced by another carbon group.
Another carboxylic acid derivative is amide. Amide contains an amino group (-NH2) replacing the
hydroxyl group (-OH) in the carboxylic acid. It can also be further classified as primary (1o), secondary
(2o) and tertiary (3o), depending on the number of carbons attached to the nitrogen group.

b.
)

nitrogen-containing. Another nitrogen containing functional group is amines. Amines are hydrocarbon
chains that contains amino (-NH2) group. They can also be further classified as primary (1o), secondary
(2o) and tertiary (3o), depending on the number of carbons attached to the nitrogen group

d.) sulfur-containing. Thiols and sulfides have similar structures to alcohols and ethers, respectively.
Their difference is the replacement of the oxygen atom to sulfur atom.

Functional Groups
The number of known organic compounds is quite large. In fact, there are many times more organic
compounds known than all the other (inorganic) compounds discovered so far, about 7 million organic
compounds in total. Fortunately, organic chemicals consist of a relatively few similar parts, combined in
different ways, that allow us to predict how a compound we have never seen before may react, by
comparing how other molecules containing the same types of parts are known to react.

These parts of organic molecules are called functional groups and are made up of specific bonding
patterns with the atoms most commonly found in organic molecules (C, H, O, N, S, and P). The
identification of functional groups and the ability to predict reactivity based on functional group
properties is one of the cornerstones of organic chemistry. Functional groups are structural units within
organic compounds that are defined by specific bonding arrangements between specific atoms. Below
is a brief introduction to the major organic functional groups.
Hydrocarbons are organic compounds that are entirely made up of only two kinds of atoms – carbon
and hydrogen. Typically, hydrocarbons are colourless gases that have very weak odours. Hydrocarbons
can feature simple or relatively complex structures and can be generally classified into four
subcategories, namely alkanes, alkenes, alkynes

The simplest organic compounds are hydrocarbons, compounds composed of carbon and hydrogen
atoms only. Some hydrocarbons have only single bonds and appear as a chain (which can be straight-
chain or can have branches) of carbon atoms also bonded to hydrogen atoms. These hydrocarbons are
called alkanes (saturated hydrocarbons). Each alkane has a characteristic, systematic name depending
on the number of carbon atoms in the molecule. These names consist of a stem that indicates the
number of carbon atoms in the chain plus the ending -ane. The stem meth- means one carbon atom, so
methane is an alkane with one carbon atom. Similarly, the stem eth- means two carbon atoms; ethane is
an alkane with two carbon atoms. Continuing, the stem prop- means three carbon atoms, so propane is
an alkane with three carbon atoms. This gives them a general formula: CnH2n+2. Figure 5.2 gives the
formulas and the molecular models of the three simplest alkanes.

Figure 5.2 The three smallest alkanes, methane, ethane, and propane.

The first 10 members of this series are given in Table 5.2

5.2 The First 10 Straight-Chain Alkanes.

Some hydrocarbons have one or more carbon-carbon double bonds (denoted C=C). These hydrocarbons
are called alkenes.( CnH2n )Note that the names of alkenes have the same stem as the alkane with the
same number of carbon atoms in its chain but have the ending -ene. Thus, ethene is an alkene with two
carbon atoms per molecule, and propene is a compound with three carbon atoms and one double bond.

Figure 5.3 Formulas and Molecular Models of the Two Simplest Alkenes, ethene, and propene.

Alkynes are hydrocarbons with a carbon-carbon triple bond (denoted C≡C) as part of their carbon
skeleton. The names for alkynes have the same stems as for alkanes but with the ending -yne.

(CnH2n-2)

Figure 5.4 Formulas and Molecular Models of the Two Simplest Alkynes, ethyne ( acetylene) and
propyne.

The carbon–carbon double and triple bonds are examples of functional groups in organic chemistry. A
functional group is a specific structural arrangement of atoms or bonds that imparts a characteristic
chemical reactivity to a molecule. A carbon-carbon double bond is considered a functional group
because carbon-carbon double bonds chemically react in specific ways that differ from reactions of
alkanes. A carbon-carbon triple bond also undergoes certain specific chemical reactions.

Alcohols (R-OH) R =refers to the alkyl group (one less of H from the alkane) CH 4 (methane)

CH3 (methyl)

If an OH group (also called a hydroxyl group) is substituted for a hydrogen atom in a hydrocarbon
molecule, the compound is an alcohol. Alcohols are named using the parent hydrocarbon name but with
the final -e dropped and the suffix -ol attached. The two simplest alcohols are methanol (methyl alcohol)
and ethanol.* (ethyl alcohol)
Figure 5.5 The Two Simplest Organic Alcohol Compounds. Alcohols have an OH functional group in the
molecule.

Except for methanol( methyl alcohol) all alcohols can be classified as primary, secondary, or tertiary. In
primary alcohol, the carbon bonded to the OH group is also bonded to only one other carbon. In
secondary alcohol (isopropyl alcohol ) and tertiary alcohol, (tert-butyl alcohol) the carbon is bonded to
two or three other carbons, respectively. When the hydroxyl group is directly attached to an aromatic
ring, the resulting group is called phenol.

Figure 5.6 Classification of alcohols.

The sulfur analog of an alcohol is called a thiol (the prefix thio, derived from the Greek, refers to sulfur).

Figure 5.7 Structures of Thiols

Ethers (R-O-R) (C2H5OC2H5)

In an ether functional group, a central oxygen is bonded to two carbons. Below are the line and Lewis
structures of diethyl ether, a common laboratory solvent and also one of the first medical anaesthesia
agents.

Figure 5.8 Diethyl ether structure

Aldehydes (R-C=O)

Ketones (R-C=O)

There are a number of functional groups that contain a carbon-oxygen double bond, which is commonly
referred to as a carbonyl. Ketones and aldehydes are two closely related carbonyl-based functional
groups that react in very similar ways. In a ketone, the carbon atom of a carbonyl is bonded to two other
carbons. In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen, and on the other side
to a carbon. The exception to this definition is formaldehyde, in which the carbonyl carbon has bonds to
two hydrogens.

Figure 5.9 Structure of an Aldehyde and Ketone.

Carboxylic Acids (R-COOH)

Another important family of organic compounds has a carboxyl group, in which a carbon atom is double-
bonded to an oxygen atom and to an OH group. Compounds with a carboxyl functional group are called
carboxylic acids and their names end in -oic acid. The carboxyl group is sometimes written in molecules
as COOH.

Figure 5.10 The two smallest carboxylic acids are formic acid (found in the stingers of ants) and acetic
acid (found in vinegar).

Esters (R-COO-R') ( R can be the same or different)

In esters, the carbonyl carbon is bonded to an oxygen which is itself bonded to another carbon. Another
way of thinking of an ester is that it is a carbonyl bonded to an alcohol. Esters are known for their
distinctive odors and are commonly used for food aroma and fragrances.

Figure 5.11 Examples of Esters

Amides (R-CONH2). In amides, the carbonyl carbon is bonded to nitrogen. The nitrogen in an amide can
be bonded either to hydrogens, to carbons, or to both. Another way of thinking of an amide is that it is a
carbonyl bonded to an amine.

Figure 5.12 Amide structures

Amines (RNH2)
Amines are characterized by nitrogen atoms with single bonds to hydrogen and carbon. Just as there are
primary (RNH2), secondary, and tertiary alcohols, there are primary , secondary(R2NH), and tertiary (R3N)
amines. Ammonia is a special case with no carbon atoms. One of the most important properties of
amines is that they are basic, and are readily protonated to form ammonium cations.

Figure 5.13 Structures of Amines

Aromatics

The aromatic group is exemplified by benzene (which used to be a commonly used solvent in the
organic lab, but which was shown to be carcinogenic), and naphthalene, a compound with a distinctive
'mothball' smell. Aromatic groups are planar (flat) ring structures and are widespread in nature. It is
characterized by a ring of six carbon atoms, bonded by alternating single and double bonds. The six
carbon atoms form a perfectly regular hexagon. All of the carbon-carbon bonds have exactly the same
lengths - somewhere between single and double bonds.

Figure 5.14 Benzene structure and napthalene

The table here summarizes the structures discussed and examples.

Table 5.3 Common functional groups with formulas and names.