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 carbon–hydrogen 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 four—single, double, and triple bonds,

as well as various structures with delocalized electrons—make 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 carbon—even 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 carbon―it is organic.

Even the broader definition of "carbon-containing molecules" requires the exclusion of carbon-

containing 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. C-

C 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 C-

H 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 Wöhler produced the organic chemical urea (carbamide), a constituent of

urine, from the inorganic ammonium cyanate NH4CNO, in what is now called the Wöhler

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 elements—earth, water, air, and fire—by 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 Chevreul’s and Wohler’s experiments in medicine development

Chevruel’s experiment showed that organic substances can be produced without the vital force

that is presumed to be present in organisms. While Wohler’s 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 electro-

mechanical 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

1 s and 1 p orbital

2 sigma bonds present

2 unhybridized p orbital

surrounded by at least a a triple bond

linear (180°)

sp2 orbital

1 s and 2 p orbital

3 sigma bonds present

1 unhybridized p orbital

surrounded by at least a double bond

trigonal planar (120°)

sp3 orbital

1 s and 3 p orbitals

4 sigma bonds present

no unhybridized p orbital

surrounded by single bonds

tetrahedral (109.5°)

1. s – sp2

2. s – sp2

3. sp2 – sp2

4. p – p

5. sp2 – s

6. sp2 – s

Why can’t 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 can’t 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 don’t 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 Structural

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

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)

Alkyl Halide Chloroform (CHCl3)

Carbon tetrachloride (CCl4)

*in the molecular formulae, memorize only Chloroform’s

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 Suffix

Carboxylic Acid -oic acid

Ester alkoxycarbonyl- -oate

Amide amido- -amide

Aldehyde oxo-

formyl- -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