Organic Chemistry: Overview

2nd part
Prof. Ronald Jefferson A. Narceda

 Electronegativity
Electronegativity is the ability of an atom to attract
electrons
It increases from left to right and from bottom to
top in the periodic table (noble gases excluded)
Fluorine is the most electronegative atom and can stabilize
excess electron density the best

Chapter 1

 Formal charge
A formal charge is a positive or negative charge on
an individual atom
The sum of formal charges on individual atoms is
the total charge of the molecule or ion
The formal charge is calculated by subtracting the
assigned electrons on the atom in the molecule
from the electrons in the neutral atom
Electrons in bonds are evenly split between the
two atoms; one to each atom
Lone pair electrons belong to the atom itself

 Examples
Ammonium ion (NH4)+

Nitrate ion (NO3)-

 An atom will always have the same formal

charge depending on how many bonds and
lone pairs it has regardless of which particular
molecule it is in

For example a singly bonded oxygen with 3

lone pairs will always have a negative charge
and an oxygen with three bonds and one lone
pair will always have a positive charge

 Resonance
Often a single Lewis structure does not accurately
represent the true structure of a molecule
The real carbonate ion is not represented by any of
the structures 1,2 or 3

Experimentally carbonate is known not to have two

carbon-oxygen single bonds and one double bond;
all bonds are equal in length and the charge is
spread equally over all three oxygens

 The real carbonate ion can be represented by a

drawing in which partial double bonds to the
oxygens are shown and partial negative charge
exists on each oxygen
The real structure is a resonance hybrid or mixture
of all three Lewis structures
Double headed arrows are used to show that the
three Lewis structures are resonance contributors
to the true structure
The use of equilibrium arrows is incorrect since the three
structures do not equilibrate; the true structure is a
hybrid (average) of all three Lewis structures

 One resonance contributor is converted to another by the use

of curved arrows which show the movement of electrons
The use of these arrows serves as a bookkeeping device to assure all
structures differ only in position of electrons

A calculated electrostatic potential map of carbonate clearly

shows the electron density is spread equally among the three
oxygens
Areas which are red are more negatively charged; areas of blue have
relatively less electron density

Chapter 1

 Ethane (C2H6)
The carbon-carbon bond is made from overlap of
two sp3 orbitals to form a s bond
The molecule is approximately tetrahedral around
each carbon

 The representations of ethane show the tetrahedral

arrangement around each carbon
a. calculated electron density surface b. ball-and-stick model c.
typical 3-dimensional drawing

Generally there is relatively free rotation about s bonds

Very little energy (13-26 kcal/mol) is required to rotate around the
carbon-carbon bond of ethane

 Overlap of sp2 orbitals in ethylene results in

formation of a s framework
One sp2 orbital on each carbon overlaps to form a carboncarbon s bond; the remaining sp2 orbitals form bonds to
hydrogen

The leftover p orbitals on each carbon overlap to

form a bonding p bond between the two carbons
A p bond results from overlap of p orbitals above
and below the plane of the s bond
It has a nodal plane passing through the two bonded nuclei and between the
two lobes of the p molecular orbital

 In ethyne the sp orbitals on the two carbons

overlap to form a s bond
The remaining sp orbitals overlap with hydrogen 1s
orbitals

The p orbitals on each carbon overlap to form two

p bonds
The triple bond consists of one s and two p bonds

Chapter 1

 Bond Lengths of Ethyne, Ethene and Ethane

The carbon-carbon bond length is shorter as more bonds hold the carbons together
With more electron density between the carbons, there is more glue to
hold the nuclei of the carbons together
The carbon-hydrogen bond lengths also get shorter with more s character of the
bond
2s orbitals are held more closely to the nucleus than 2p orbitals
A hybridized orbital with more percent s character is held more closely to the
nucleus than an orbital with less s character
The sp orbital of ethyne has 50% s character and its C-H bond is shorter
The sp3 orbital of ethane has only 25% s character and its C-H bond is longer

Chapter 1

13

 Methane
The valence shell of methane contains four pairs or
sets of electrons
To be as far apart from each other as possible they
adopt a tetrahedral arrangement (bond angle
109.5o)
The molecule methane is therefore tetrahedral

Chapter 1

14

 Ammonia
When the bonding and nonbonding electrons are
considered there are 4 sets of electrons
The molecule is essentially tetrahedral but the
actual shape of the bonded atoms is considered to
be trigonal planar
The bond angles are about 107o and not 109.5o
because the non-bonding electrons in effect are
larger and compress the nitrogen-hydrogen bond

Chapter 1

15

 Water
There are four sets of electrons including 2 bonding
pairs and 2 non-bonding pairs
Again the geometry is essentially tetrahedral but
the actual shape of the atoms is considered to be
an angular arrangement
The bond angle is about 105o because the two
larger nonbonding pairs compress the electrons
in the oxygen-hydrogen bonds

Chapter 1

16

 Boron Trifluoride
Three sets of bonding electrons are farthest apart in a
trigonal planar arrangement (bond angle 120o)
The three fluorides lie at the corners of an equilateral
triangle

Beryllium Hydride
Two sets of bonding electrons are farthest apart in a
linear arrangement (bond angles 180o)

Chapter 1

17

 Carbon Dioxide
There are only two sets of electrons around the
central carbon and so the molecule is linear (bond
angle 180o)
Electrons in multiple bonds are considered as one set of
electrons in total

A summary of the results also includes the

geometry of other simple molecules

 Hydrocarbons: Representative Alkanes, Alkenes

Alkynes, and Aromatic Compounds
Hydrocarbons contain only carbon and hydrogen atoms
Subgroups of Hydrocarbons:

Alkanes contain only carbon-carbon single bonds

Alkenes contain one or more carbon-carbon double bonds
Alkynes contain one or more carbon-carbon triple bonds
Aromatic hydrocarbons contain benzene-like stable structures
(discussed later)

Saturated hydrocarbons: contain only carbon-carbon single

bonds e.g. alkanes
Unsaturated hydrocarbons: contain double or triple
carbon-carbon bonds e.g. alkene, alkynes, aromatics
Contain fewer than maximum number of hydrogens per carbon
Capable of reacting with H2 to become saturated

 Representative Hydrocarbons
Alkanes
Principle sources of alkanes are natural gas and
petroleum
Smaller alkanes (C1 to C4) are gases at room temperature

Methane is
A component of the atmosphere of many planets
Major component of natural gas
Produced by primitive organisms called methanogens
found in mud, sewage and cows stomachs

20

 Alkenes
Ethene (ethylene) is a major industrial feedstock
Used in the production of ethanol, ethylene oxide and the
polymer polyethylene

Propene (propylene) is also very important in

industry
Molecular formula C3H6
Used to make the polymer polypropylene and is the
starting material for acetone

Many alkenes occur naturally

Chapter 2

 Alkynes
Ethyne (acetylene) is used in welding torches because it
burns at high temperature

Many alkynes are of biological interest

Capillin is an antifungal agent found naturally
Dactylyne is a marine natural product
Ethinyl estradiol is a synthetic estrogen used in oral
contraceptives

 Benzene: A Representative Hydrocarbon

Benzene is the prototypical aromatic compound
The Kekul structure (named after August Kekul who formulated it)
is a six-membered ring with alternating double and single bonds

Benzene does not actually have discreet single and double

carbon-carbon bonds
All carbon-carbon bonds are exactly equal in length (1.38 )
This is between the length of a carbon-carbon single bond and a
carbon-carbon double bond

Resonance theory explains this by suggesting there are two

resonance hybrids that contribute equally to the real structure
The real structure is often depicted as a hexagon with a circle in the
middle

Chapter 2

 Molecular orbital theory explains the equal bond

lengths of benzene by suggesting there in a
continuous overlap of p orbitals over the entire
ring
All carbons in benzene are sp2 hybridized
Each carbon also has a p orbital

Each p orbital does not just overlap with one adjacent p

but overlaps with p orbitals on either side to give a
continuous bonding molecular orbital that encompasses
all 6 carbons
All 6 p electrons are therefore delocalized over the
entire ring and this results in the equivalence of all of
the carbon-carbon bonds

 Polar Covalent Bonds

Polar covalent bonds occur when a covalent bond
is formed between two atoms of differing
electronegativities
The more electronegative atom draws electron density
closer to itself
The more electronegative atom develops a partial
negative charge (d-) and the less electronegative atom
develops a partial positive charge (d+)
A bond which is polarized is a dipole and has a dipole
moment
The direction of the dipole can be indicated by a dipole
arrow
The arrow head is the negative end of a dipole, the crossed
end is the positive end

 Example: the molecule HCl

The more electronegative chlorine draws electron
density away from the hydrogen
Chlorine develops a partial negative charge

The dipole moment of a molecule can be

measured experimentally
It is the product of the magnitude of the charges (in
electrostatic units: esu) and the distance between the
charges (in cm)
The actual unit of measurement is a Debye (D) which
is equivalent to 1 x 10-18 esu cm

 Molecular Dipole
In diatomic molecules a dipole exists if the two
atoms are of different electronegativity
In more complicated molecules the molecular
dipole is the sum of the bond dipoles
Some molecules with very polar bonds will have no
net molecular dipole because the bond dipoles
cancel out
The center of positive charge and negative charge
coincide in these molecules

Chapter 2

 Examples
In carbon tetrachloride the bond dipoles cancel and the
overall molecular dipole is 0 Debye

In chloromethane the C-H bonds have only small dipoles

but the C-Cl bond has a large dipole and the molecule is
quite polar

An unshared pair of electrons on atoms such as oxygen

and nitrogen contribute a great deal to a dipole
Water and ammonia have very large net dipoles

 Some cis-trans isomers differ markedly in their

dipole moment
In trans 1,2-dichloroethene the two carbon-chlorine
dipoles cancel out and the molecular dipole is 0
Debye
In the cis isomer the carbon-chlorine dipoles
reinforce and there is a large molecular dipole

 Functional Groups
Functional group families are characterized by the
presence of a certain arrangement of atoms called a
functional group
A functional group is the site of most chemical
reactivity of a molecule
The functional group is responsible for many of the
physical properties of a molecule

Alkanes do not have a functional groups

Carbon-carbon single bonds and carbon-hydrogen bonds
are generally very unreactive

 Alkyl Groups and the Symbol R

Alkyl groups are obtained by removing a hydrogen from an
alkane
Often more than one alkyl group can be obtained from an
alkane by removal of different kinds of hydrogens

R is the symbol to represent a generic alkyl groups

The general formula for an alkane can be abbreviated R-H

 A benzene ring with a hydrogen removed is called a

phenyl and can be represented in various ways

Toluene (methylbenzene) with its methyl hydrogen

removed is called a benzyl group

 Alkyl Halides
In alkyl halides, halogen (F, Cl, Br, I) replaces the
hydrogen of an alkane
They are classified based on the carbon the halogen
is attached to
If the carbon is attached to one other carbon that carbon
is primary (1o) and the alkyl halide is also 1o
If the carbon is attached to two other carbons, that
carbon is secondary (2o) and the alkyl halide is 2o
If the carbon is attached to three other carbons, the
carbon is tertiary (3o) and the alkyl halide is 3o

 Alcohols
In alcohols the hydrogen of the alkane is replaced
by the hydroxyl (-OH) group
An alcohol can be viewed as either a hydroxyl derivative
of an alkane or an alkyl derivative of water

Alcohols are also classified according to the carbon

the hydroxyl is directly attached to

 Ethers
Ethers have the general formula R-O-R or R-O-R where R is
different from R
These can be considered organic derivatives of water in which both
hydrogens are replaced by organic groups
The bond angle at oxygen is close to the tetrahedral angle

Amines
Amines are organic derivatives of ammonia
They are classified according to how many alkyl groups replace the
hydrogens of ammonia
This is a different classification scheme than that used in alcohols

 Aldehydes and Ketones

Both contain the carbonyl group

Aldehydes have at least one carbon attached to the carbonyl group

Ketones have two organic groups attached to the carbonyl group

The carbonyl carbon is sp2 hybridized

It is trigonal planar and has bond angle about 120o

 Carboxylic Acids, Esters and Amides

All these groups contain a carbonyl group bonded
to an oxygen or nitrogen
Carboxylic Acids
Contain the carboxyl (carbonyl + hydroxyl) group

Esters
A carbonyl group is bonded to an alkoxyl (OR) group

 Amide
A carbonyl group is bonded to a nitrogen derived from
ammonia or an amine

Nitriles
An alkyl group is attached to a carbon triply bonded
to a nitrogen
This functional group is called a cyano group

Summary of Important Families of Organic

Compounds

 Summary (cont.)

INFRARED ABSORPTION
SPECTROSCOPY
Important tool to analyze various organic compounds

The Electromagnetic Spectrum

Energy Levels in Molecules

Modes of Vibration
the infrared "selection rule" states that for a
particular vibrational mode to be observed
(active) in the infrared spectrum, the mode
must involve a change in the dipole moment
of the molecule. Only bonds that have a
dipole moment are capable of absorbing
infrared radiation.

Stretching
- occurs at higher frequencies than bending
-asymmetric stretching vibrations occur at
higher
frequencies than symmetric vibrations

Bending
includes scissoring, wagging, rocking, and
twisting

Vibrations of CO2

Typical apparatus

Example of IR spectra

Example of FT-IR Spectra

Next Topic. . .

Macromolecules

Carbohydrates
Lipids
Proteins
Nucleic Acids