REVIEWER

Introduction to Organic Chemistry

Organic chemistry is the study of the structure, properties, composition, reactions, and
preparation of carbon-containing compounds, which include not only hydrocarbons but also
compounds with any number of other elements, including hydrogen (most compounds contain
at least one carbonhydrogen bond), nitrogen, oxygen, halogens, phosphorus, silicon, and
sulfur. This branch of chemistry was originally limited to compounds produced by living
organisms but has been broadened to include human-made substances such as plastics. The
range of application of organic compounds is enormous and also includes, but is not limited to,
pharmaceuticals, petrochemicals, food, explosives, paints, and cosmetics.
The very foundations of biochemistry, biotechnology, and medicine are built on organic
compounds and their role in life processes.
The bonding patterns open to carbon, with its valence of foursingle, double, and triple bonds,
as well as various structures with delocalized electronsmake the array of organic compounds
structurally diverse and their range of applications enormous.

The exemptions (C-bonded compounds that are inorganic)

Carbides
Carbonates
Simple oxides of Carbon
Cyanides

Why the term organic chemistry is partly erroneous?

Organic is supposed to mean any relation to living organisms so technically, organic chemistry
should focus on compounds found or manufactured only by living organisms. As we all know,
organic compounds can undergo chemical manipulation can be synthesized without any
derivation from a living organism. In fact, organic chemistry covers up several compounds that
are NOT related from organic substances, making the name erroneous.

Modern classification
Even though vitalism has been discredited, scientific nomenclature retains the distinction
between organic and inorganic compounds. The modern meaning of organic compound is any
compound that contains a significant amount of carboneven though many of the organic
compounds known today have no connection to any substance found in living organisms.
There is no single "official" definition of an organic compound. Some textbooks define an
organic compound as one that contains one or more C-H bonds. Others include C-C bonds in
the definition. Others state that if a molecule contains carbonit is organic.
Even the broader definition of "carbon-containing molecules" requires the exclusion of carboncontaining alloys (including steel), a relatively small number of carbon-containing compounds
such as metal carbonates and carbonyls, simple oxides of carbon and cyanides, as well as the
allotropes of carbon and simple carbon halides and sulfides, which are usually considered
inorganic.
The "C-H" definition excludes compounds that are historically and practically considered
organic. Neither urea nor oxalic acid is organic by this definition, yet they were two key
compounds in the vitalism debate. The IUPAC Blue Book on organic nomenclature specifically
mentions urea and oxalic acid. Other compounds lacking C-H bonds that are also traditionally
considered organic include benzenehexol, mesoxalic acid, and carbon tetrachloride. Mellitic
acid, which contains no C-H bonds, is considered a possible organic substance in Martian soil. CC bonds are found in most organic compounds, except some small molecules like methane and
methanol, which have only one carbon atom in their structure.
The "C-H bond-only" rule also leads to somewhat arbitrary divisions in sets of carbon-fluorine
compounds, as, for example, Teflon is considered by this rule "inorganic" but Tefzel organic.
Likewise, many Halons are considered inorganic, whereas the rest are considered organic. For
these and other reasons, most sources believe C-H compounds are only a subset of "organic"
compounds.
In summary, most carbon-containing compounds are organic, and almost all organic
compounds contain at least a C-H bond or a C-C bond. A compound does not need to contain CH bonds to be considered organic (e.g., urea), but many organic compounds do.

Carbon

C
nonmetallic
atomic number: 6
electronic configuration: 1s22s22p2
valence electrons: 4
tetravalent capable of four covalent bonds
has the unique ability to bond together, forming long chains and rings

History
In 1770, Torbern Bergman was the first to express the difference between inorganic and
organic substances, and the term organic chemistry soon came to mean the chemistry of
compounds from living organisms.
Before the nineteenth century, chemists generally believed that compounds obtained from
living organisms were endowed with a vital force that distinguished them from inorganic
compounds. According to the concept of vitalism (vital force theory), organic matter was
endowed with a "vital force". During the first half of the nineteenth century, some of the first
systematic studies of organic compounds were reported. Around 1816, Michel Chevreul started
a study of soaps made from various fats and alkalis. He separated the different acids that, in
combination with the alkali, produced the soap. Since these were all individual compounds, he
demonstrated that it was possible to make a chemical change in various fats (which
traditionally come from organic sources), producing new compounds without "vital force". In
1828, Friedrich Whler produced the organic chemical urea (carbamide), a constituent of
urine, from the inorganic ammonium cyanate NH4CNO, in what is now called the Whler
synthesis. He showed that organic compounds can be produced from inorganic compounds.

Vitalism
The word organic is historical, dating to the 1st century. For many centuries, Western
alchemists believed in vitalism. This is the theory that certain compounds could be synthesized
only from their classical elementsearth, water, air, and fireby the action of a "life-force"
(vis vitalis) that only organisms possessed. Vitalism taught that these "organic" compounds

were fundamentally different from the "inorganic" compounds that could be obtained from the
elements by chemical manipulation.

The significance of Chevreuls and Wohlers experiments in medicine development

Chevruels experiment showed that organic substances can be produced without the vital force
that is presumed to be present in organisms. While Wohlers experiment showed that organic
compounds can be produced from inorganic compounds. With their discoveries, it is found that
organic substances do not have the vital force therefore it can be synthesized in laboratories or
outside living organisms. From literally organic substances in the form of herbs and other
plants, scientists were able to synthesize medicine which are synthesized on laboratories and
not directly manufactured by living organisms, and can be derived from inorganic substances.
Main point: the disproving of vital force theory and discovery organic-from-inorganic synthesis
paved way to medicine development

Properties
Physical properties of organic compounds typically of interest include both quantitative and
qualitative features. Quantitative information includes melting point, boiling point, and index of
refraction. Qualitative properties include odor, consistency, solubility, and color.

Melting and boiling properties

Organic compounds typically melt and many boil. In contrast, while inorganic materials
generally can be melted, many do not boil, tending instead to degrade. In earlier times, the
melting point (m.p.) and boiling point (b.p.) provided crucial information on the purity and
identity of organic compounds. The melting and boiling points correlate with the polarity of
the molecules and their molecular weight. Some organic compounds, especially symmetrical
ones, sublime, that is they evaporate without melting. A well-known example of a sublimable
organic compound is para-dichlorobenzene, the odiferous constituent of modern mothballs.
Organic compounds are usually not very stable at temperatures above 300 C, although some
exceptions exist.

Solubility
Neutral organic compounds tend to be hydrophobic; that is, they are less soluble in water
than in organic solvents. Exceptions include organic compounds that contain ionizable (which
can be converted in ions) groups as well as low molecular weight alcohols, amines, and
carboxylic acids where hydrogen bonding occurs. Organic compounds tend to dissolve in
organic solvents. Solvents can be either pure substances like ether or ethyl alcohol, or mixtures,
such as the paraffinic solvents such as the various petroleum ethers and white spirits, or the
range of pure or mixed aromatic solvents obtained from petroleum or tar fractions by physical
separation or by chemical conversion. Solubility in the different solvents depends upon the
solvent type and on the functional groups if present.
Solid state properties
Various specialized properties of molecular crystals and organic polymers with conjugated
systems are of interest depending on applications, e.g. thermo-mechanical and electromechanical such as piezoelectricity, electrical conductivity (see conductive polymers and
organic semiconductors), and electro-optical (e.g. non-linear optics) properties. For historical
reasons, such properties are mainly the subjects of the areas of polymer science and materials
science.

Inorganic vs. Organic substances

Organic

Inorganic

many boil

many DO NOT boil

low melting point

high melting point

insoluble/hydrophobic

soluble/hydrophilic

poor conductor of electricity

good conductor of electricity

flammable

non-flammable

Hybridization
It occurs when an atom bonds using electrons from both the s and p orbitals (s orbitals are
lower in energy than p orbitals), creating an imbalance in the energy levels of the electrons
and to equalize these energy levels, the s and p orbitals involved are combined to create hybrid
orbitals.
In other words, hybridization is the mixing of a set of unequal orbitals to obtain a new set of
equal orbitals with properties somewhere between the original unequal orbitals.

Why is hybridization necessary?

Electrons in the s orbital are nearer to the positively-charged nucleus, making these electrons
stable due to the opposite attraction of charges. The electrons in the p orbital are farther from
the nucleus because they are repelled by the electrons of the s orbital that surrounds the
nucleus. Due to the electron repulsion, the electrons are pushed to a higher orbital in which the
movement of the electrons increases the kinetic energy. Also, the potential energy of electrons
increases as they transfer from a lower orbital to a higher orbital.
The equalizing of the orbitals in the outermost shell (orbitals of the bonding pairs or the
valency shell) is required for stability of electrons which in turn is needed for the molecule to
be able to combine with other molecules.

*Orbitals it is the region of space where there is a high probability of finding an electron in
an atom

Hybrid Orbital Formation

1. When forming hybrid orbitals, the number of hybrid orbitals formed equals the number
of orbitals mathematically combined or mixed. For example, if an s orbital is combined
with a p orbital, the result is two sp hybrid orbitals.
2. Hybrid orbitals have orientations around the central atom that correspond to the
electron-domain geometry predicted by the VSEPR Theory.
3. The hybrid orbitals have shapes that maximize orbital overlap with other atoms
orbitals. This increases bond strength.
4. Hybrid orbital overlap between atoms creates sigma bonds. On the other hand,
unhybridized p orbitals are responsible for the pi bonds.

*sigma bond
strongest type of covalent bond
formed by head-on overlapping between atomic orbitals
allows free rotation
*pi bond
covalent chemical bonds where two lobes of one involved atomic orbital overlap
sideways two lobes of the other involved atomic orbital
restricts rotation

Orbitals

Characteristics

s orbital

spherical shape

p orbital

loop-shaped

sp orbital

sp2 orbital

sp orbital

1 s and 1 p orbital
2 sigma bonds present
2 unhybridized p orbital
surrounded by at least a a triple bond
linear (180)
1 s and 2 p orbital
3 sigma bonds present
1 unhybridized p orbital
surrounded by at least a double bond
trigonal planar (120)
1 s and 3 p orbitals
4 sigma bonds present
no unhybridized p orbital
surrounded by single bonds
tetrahedral (109.5)

1.
2.
3.
4.
5.
6.

s sp2
s sp2
sp2 sp2
pp
sp2 s
sp2 s

Why cant CH2 exist? Why VB theory fails to explain Methane?

Carbon has 2 unpaired electrons in its valency shell (p) or outermost shell so it needs 2 H atoms
to covalently bond with. But such bond will give C only with 6 electrons, dissatisfying the octet
rule. It needs 4 covalent bonds to satisfy the octet rule and become stable in bonding with
other atoms. On the other hand, it cant form two double bonds with 2 hydrogen atoms
because H has one electron and it needs one covalent bond to be stable. Considering the
situation of carbon and hydrogen, carbon bonds with 4 H atoms so that both can be stable and
successfully form the bond.
Can ionic bonds exhibit hybridization?
NO. Atoms can broadly bond to form either covalent or ionic compounds. The concept of
hybridization was introduced to explain covalent bonding. So, if atoms are combining to form
ionic compounds like NaCl, they use ions to combine, i.e they are losing or gaining electron(s),
so the concept of hybridisation is not required here. When atoms bond covalently, some of the
atomic orbitals undergo intermixing of energies to yield a set of hybridized orbitals which are
equivalent in energy. These new, hybrid orbitals are used to overlap with hybrid or
unhybridized orbitals of other atoms, forming a covalent bond. Of course, hybridization is not a
real, happening thing. It is just a good, consistent theory to account for lots of things being
observed in covalent molecules like shapes, bond lengths, bond angles, etc. You dont need to
use the theory of hybridization in case if ionic compounds because concepts like crystal and
lattice enthalpies explain many observations.

First 10 straight chain alkanes

Alkanes

Condensed
Formula

Methane

CH4

Ethane

CH3CH3

Propane

CH3CH2CH3

Butane

CH3(CH2)2CH3

Pentane

CH3(CH2)3CH3

Hexane

CH3(CH2)4CH3

Heptane

CH3(CH2)5CH3

Octane

CH3(CH2)6CH3

Nonane

CH3(CH2)7CH3

Decane

CH3(CH2)8CH3

Structural

Simplest compound of every functional group

Functional
Group

Simplest
Compound

Formula

Alkane

Methane

(CH4)

Alcohol

Methanol

(CH4O)

Thiol

Methanethiol

(CH4S)

Amine

Methylamine

(CH5N)

Aldehyde

Methanal

(CH2O)

Carboxylic Acid

Methanoic acid

(CH2O2)

Ester

Methyl Methanoate

(C2H4O2)

Ether

Dimethyl ether

(C2H6O)

Ketone

2-propanone

(C3H6O)

Alkene

Ethylene

(C2H4)

Alkyne

Ethyne

(C2H2)

Amide

Ethanamide

(C2H5NO)

Chloroform

(CHCl3)

Carbon tetrachloride

(CCl4)

Alkyl Halide

*in the molecular formulae, memorize only Chloroforms

Forms of formula

Molecular formula

Extended structural formula

Condensed structural formula

Line-angle formula

Functional Groups
These are specific groups of atoms or bonds within molecules (covalently bonded with C
atoms) that are responsible for the characteristic chemical reactions of those molecules. The
same functional group will undergo the same or similar chemical reaction(s) regardless of the
size of the molecule it is a part of. However, its relative reactivity can be modified by nearby
functional groups.
The functional group gives the molecule its properties, regardless of what molecule contains
it; they are centers of chemical reactivity. The functional groups within a molecule need to be
identified when naming. It can be used to predict the chemical behavior or reactivity of a
biomolecule.
The unique functional groups present on a biomolecule determine reactivity, solubility, and
other physical properties that lead to its biological role in living organisms. Understanding how
common functional groups affect chemical reactivity improves our ability to understand the
chemical behavior and cellular roles of all biomolecules.
1. Hydrocarbons
Alkanes
simplest organic molecules because it consists only of C-H single bonds
have single bonds therefore saturated
used as the basis for naming the majority of organic compounds (their
nomenclature)
general formula: CnHn+2

Alkenes

unsaturated compounds that contain at least one carbon-to-carbon

double bond
general formula: CnH2n

Alkynes
unsaturated hydrocarbons that contain at least one triple bond between
two C atoms
general formula: CnH2n-2
Aromatic Hydrocarbons
has benzene rings (consists of alternating double and single bonds)
cyclic (forms rings)

*Benzene

simplest aromatic hydrocarbon with a general formula of C6H6

very stable molecules
unreactive due to its stability
alternating single and double bonds

*Cycloalkanes types of alkanes that have one or more rings connected by single bonds of C
atoms in the chemical structure of their molecules. General formula: CnH2n

2. Oxygen-containing
Alchohol
Carboxylic acid
Ether
Ester
Ketone
Aldehyde

3. Nitrogen-containing
Amines
Amides
4. Sulfur-containing
Thiols
5. Halogen-containing
Alkyl halides or haloalkanes
*general formulae of hydrocarbons apply to compounds with only one of their specified bond
and no other functional groups present

Functional
Group

Prefix

Carboxylic Acid

Suffix
-oic acid

Ester

alkoxycarbonyl-

-oate

Amide

amido-

-amide

Aldehyde

oxoformyl-

-al

Ketone

oxo-

-one

Alcohol

hydroxy-

-ol

Thiol

mercapto-

-thiol

Amine

amino-

-amine

Alkene

alkenyl-

-ene

Alkyne

alkynyl-

-yne

Alkane

alkyl-

-ane

Ether

alkoxy-

ether

Alkyl Halide

halo-

Nitro

nitro-

*structural formulae are general formulae without the R but SF of hydrocarbons is shown instead

*R = alkyl group; X = halogen

Isomerism
Isomerism is the phenomenon whereby certain compounds, with the same molecular formula,
exist in different forms owing to their different organizations of atoms or their spatial
arrangement.
1. Structural Isomerism - molecules have the same molecular formula but different
structural formula
a. Chain isomerism different C skeletons
b. Position isomerism different position of functional groups
c. Functional group isomerism different functional groups
2. Stereoisomerism molecules have the same molecular formula and bond order but
different spatial arrangements
a. Geometric isomerism
also cis-trans isomerism
involves double bonds that do not allow free rotation
b. Optical isomerism

involves an atom, usually carbon, bonded to four different atoms or

groups of atoms

exist in pairs, in which one isomer is the mirror image of the other
*see examples

Conformations
Conformations are an atomic spatial arrangements that results from rotation of carbon atoms
about single bonds within an organic molecule
Conformational isomers - isomers where the atoms and connectivity remains the same, but
can be interconverted to one another by rotation around a single bond
Newman projection - visualizes chemical conformations of a carbon-carbon chemical bond
from front to back, with the front carbon represented by a dot and the back carbon as a circle

Staggered and Eclipsed Conformations of Ethane

Why staggered conformation is more stable?

In eclipsed conformation, the electrons of both sides are parallel and the parallelism of the
electrons creates an electrostatic repulsion. Therefore, it has a lesser stability because of the
higher energy created by the repulsion of the electrons.
Boat and Chair Conformations of Cyclohexane

Why chair conformation is more stable?

In boat conformation, the electrons are eclipsed or both sides are parallel. This parallelism
creates energy due to the repulsion of electrons, making boat conformation lesser stable.

*Torsional strain or the eclipsing strain; is the increase in potential energy of a molecule due
to repulsion between electrons in bonds that do not share an atom
Puckered conformations slight deviations from planar conformations

Cyclobutane

Cyclopentane
Ortho, Meta, and Para structures

Electron delocalization distribution of density of the electrons that are not directly associated
with a single atom and can freely move around the compound
Electron delocalization is present in benzene rings.

Benzene vs. Cycloalkenes

Both have double bonds.

Benzene has alternating single and double bonds (conjugated double bonds) which accounts
for its stability.
Cycloalkenes have random double bonds (non-conjugated double bonds).

Why benzene is more stable than cycloalkenes?

Benzene is more stable than simple alkenes. Benzene has alternating single and double bonds
which are proximal to each other and thus, the p orbitals or the pi bonds are adjacent and
parallel. This proximity of the single and double bonds causes the transfer of pi bonds to the
previously single bond and the double bond becomes a single one. Since the electrons are
moving from one atom to another atom or, in other words, moving freely around the
compound making it delocalized. If the electrons are delocalized, this means that the electron
density within the compound is similar, making it stable.
On the other hand, cycloalkenes DO NOT have alternating single and double bonds, making the
pi bonds distant from each other. The distance of the pi bonds disables the transfer of

electrons, making them localized or isolated. If the electron density is not similar within the
compound, also considering electron repulsion, the compound is not stable.

Reminders for nomenclature of organic compounds

First step is always to find the parent chain which is the longest carbon chain.
Substituents are arranged alphabetically in the nomenclature of organic compounds,
disregarding the prefixes.
Alkyl group - group of carbon and hydrogen atoms derived from an alkane molecule by
removing one hydrogen atom
Alkanes have single bonds
Alkenes have double bonds
The presence of pi bonds restricts rotation. The different spatial arrangements of two
comparable substituents create different properties. Cis-trans naming is used.
Alkynes have triple bonds
In cases of multiple functional groups present in a compound, the one with higher
priority gets the lower locant and credits for the last name of the compound.
Write down the locants as you count the carbon chain.
Always check the affixes.
Substituents with lower priority use their prefixes.
A hydroxyl is a chemical functional group containing an oxygen atom connected by a
covalent bond to a hydrogen atom. (OH)
Carboxylic acids are always in the terminal carbon. The locant is not needed anymore.
Ethers and thiols are derivatives of alcohol.
Ketones and aldehydes both have carbonyl group.
A carbonyl group is a functional group composed of a carbon atom double-bonded to
an oxygen atom: C=O.
Aldehydes are always in the terminal carbon. Therefore, locant is not needed to be
stated anymore.
Double-bonded O in aldehydes are only located if the aldehyde group in the compound
is the lesser subsituent.
Carboxylic acids have the carboxyl group. They are always terminal. No locant is needed.
The carboxyl group is an organic functional group consisting of a carbon atom double
bonded to an oxygen atom and single bonded to a hydroxyl group.

In case of multiple carboxyl groups are present in a compound, the C in the carboxyl
groups are not counted to the mother chain.
Esters have no locants.
Amines are derivatives of ammonia (NH3).
Locants are needed on disubstituted benzene, and not on monosubstituted.
Phenyl- - used when bezene is considered as the substituent.

For hydrocarbons:
1. function group through the bonds
2. number of similar bonds
3. number of C in the mother chain
4. substituents
5. number of similar substituents
6. location of the substituents
For other functional groups (general):
1. functional groups present
2. higher prioritized functional group
3. number of C present in the mother chain
4. location of the functional group
5. lesser prioritized functional group / substituent
6. number of similar substituents
7. location of the subsituents
Ethers
1. shorter and longer R
Ketones
1. location of the double-bonded O
Esters
1. single-bonded O
2. double-bonded O

3 ways to name a monosubstituted benzene

1. common name
2. name of substituent + benzene
3. phenyl- + functional group

3 ways to name a disubstituted benzene

1. location of the s + s + common name
2. ortho-meta-para, instead of numbers
3. equal substituents with their locations (alphabetical) + benzene