STRUCTURAL THEORY IN

ORGANIC CHEMISTRY

FUNCTIONAL GROUPS AND CHEMICAL BONDING

Carlos Mario Meléndez G. Qco. Ph.D

The behavior of organic compounds is now organized into patterns that are based
on recurrent groups of atoms—functional groups. The sites in molecules at which
chemical reactions occur are localized at the functional groups in the Molecule;
the rest of the molecule is the same after the reaction as before.

This turns out to be a huge simplification. Since the numbers of functional

groups are relatively small, it is possible to classify a very large number of
individual compounds by a relatively small number of functional groups

It is then possible to predict the chemical behavior of the molecule based on

the known chemistry of the functional groups that it contains.
Notice that not all functional groups contain only carbon atoms (e.g., the nitro group and the
carbodiimide groups), and some functional groups differ at atoms other than carbon (compare
the nitro and nitroso groups and the sulfoxide and sulfone groups).

Since functional groups are reference points for predicting and understanding the reactions of
individual organic molecules, it is very important to be able to recognize these functional groups
Notice that not all functional groups contain only carbon atoms (e.g., the nitro group and the
carbodiimide groups), and some functional groups differ at atoms other than carbon (compare
the nitro and nitroso groups and the sulfoxide and sulfone groups).

Since functional groups are reference points for predicting and understanding the reactions of
individual organic molecules, it is very important to be able to recognize these functional groups
A major reason that the behavior of organic compounds can be generalized
in terms of the functional groups they contain is because the bonds holding a
given functional group together are the same regardless of the compound
which contains that functional group
Bonds in functional groups can first be described by Lewis structures, which
are merely formalisms for denoting numbers of shared and unshared electron
pairs, formal charges, and types of bonds (numbers of shared pairs, single,
double, and triple).

The next level of insight into functional groups comes from the translation
of Lewis structures into more accurate bonding descriptions based on
modern bonding theories. Structural details including geometries also result
from the proper description of the bonding in the functional group.
 NOMENCLATURE
Name based on number of Carbons
• 1 • Methane
• 2 • Ethane
• 3 • Propane
• 4 • Butane
• 5 • Pentane
• 6 • Hexane
• 7 • Heptane
• 8 • Octane
• 9 • Nonane
• 10 • Decane
Alkanes
 Primary, Secondary, Tertiary

• A primary carbon has one other C directly bonded to it.

• A secondary carbon is directly bonded to two other C’s.
• A tertiary carbon is directly bonded to three other C’s.
• Multivalent atoms are 1º, 2º, or 3º by bonding to C’s.
• Univalent atom or group not really 1º, 2º, or 3º on its own - ID
depends on type of carbon it is bonded to.
Nomenclature of Alkyl Substituents

• There are four alkyl groups that contain

four carbons
Nomenclature of Alkyl Substituents

• The prefix sec- occurs only in sec-butyl

Nomenclature of Alkyl Substituents

• The prefix tert- can be used with butyl or

pentyl (also known as amyl) but not with
hexyl
 IUPAC Systematic Nomenclature -
Alkanes

• Determine longest continuous chain (i.e. parent

hydrocarbon)
• Cite the name of substituent before the name of the
parent hydrocarbon along with the number of the
carbon to which it is attached
 IUPAC Systematic Nomenclature -
Alkanes

• Number in the direction that gives the

lower number for the lowest-numbered
substituent. Substituents are listed in
alphabetical order – neglecting prefixes
such as di- tri- tert- etc.
 IUPAC Systematic Nomenclature -
Alkanes
• When both directions
yield the same lower
number for the lowest
numbered substituent,
select the direction
that yields the lower
number for the next
lowest numbered
substituent
 IUPAC Systematic Nomenclature -
Alkanes

• If same substituent numbers are obtained

in either direction, number in direction
giving lowest number to the first named
substituent
 IUPAC Systematic Nomenclature -
Alkanes

• If compound has two or more chains of the

same length, parent hydrocarbon is chain
with greatest number of substituents
 IUPAC Systematic Nomenclature -
Alkanes
• Names such as sec-butyl and tert-butyl are acceptable, but
systematic substituent names are preferable
• Numbering of the substituent begins with the carbon
attached to the parent hydrocarbon
• This number together with the substituent name is placed
inside parentheses
 Nomenclature of Cycloalkanes

• Cycloalkanes generally are shown as skeletal

structures
 Nomenclature of Cycloalkanes

• Ring is the parent hydrocarbon unless the alkyl

substituent has more carbons; in that case the
substituent becomes the parent hydrocarbon
• If only one substituent, no need to give it a
number
 Nomenclature of Cycloalkanes

• If the ring has 2 substituents, list in

alphabetical order and give number 1 to
first named group
 Nomenclature of Cycloalkanes

• If there is more than one substituent, list in

alphabetical order; one substituent is given the
position number 1; number either clockwise or
counterclockwise - lowest numbers
 Nomenclature of Alkyl Halides

• Common name - Name the alkyl group first,

followed by the name of the halogen
expressed as an -ide name
 Nomenclature of Alkyl Halides

• IUPAC name - The halogen is treated as a

substituent
 Nomenclature of Ethers
• Common name -
Name(s) of alkyl
group(s) listed first
followed by the
word “ether”
 Nomenclature of Ethers

• IUPAC name - The smaller alkyl group is

converted to an “alkoxy” name and used as
a substituent
 Nomenclature of Alcohols

• Common name -
Name of the Alkyl
group followed by
the word “alcohol”
 Nomenclature of Alcohols

• IUPAC name - The OH group is a site of reactivity (a

functional group)
• Functional group is denoted by the suffix, “ol”

CH3OH CH3CH2OH

methanol ethanol
 IUPAC Nomenclature of Alcohols

• Parent Hydrocarbon is the longest

continuous chain that contains the OH
• Number the chain in direction that gives
functional group the lowest number
• If both a substituent and a functional group
are present, the functional group gets the
lower number
 IUPAC Nomenclature of Alcohols

• If the functional group gets the same

number when counted from both directions,
use direction which gives the
substituent the lower number
• If there is more than one substituent, cite
substituents in alphabetical order
 IUPAC Nomenclature of Alcohols

• System is summarized as [Substituent]

[Parent Hydrocarbon] [Functional Group]
 Nomenclature of Amines

• Common name - Name of the Alkyl group(s) (in

alphabetical order) followed by the syllable
“amine”
• The whole name is a single word

methylamine methylpropylamine
 Nomenclature of Amines

• IUPAC name - The NH2 group is a site of

reactivity (a functional group)
• Functional group is denoted by the suffix,
“amine”
• Final “e” of longest alkane group replaced by
suffix “amine” (don’t run vowels together)
CH3CH2CH2CH2NH2
1-butanamine
butan-1-amine
 IUPAC Nomenclature of Amines

• Find the longest chain bonded to the

nitrogen
• Final “e” is replaced with “amine”
• Number the carbon to which nitrogen is
bonded
• Number any substituents on the alkyl chain
• Use italicized N- for each additional
substituent(s) on the nitrogen
 The next level of insight into functional groups comes from the translation
of Lewis structures into more accurate bonding descriptions based on
modern bonding theories.

The development of quantum mechanics and the particle–wave duality of the

electron and the uncertainty principle led to mathematical descriptions of the
behavior of electrons in the electric field of the nucleus. The solution of those
equations resulted in a new conceptual framework for understanding chemical
bonding.
ORBITALS

The theory suggests that the behavior of each electron in an atom can be
described by a wave function (ψ), which is a function of the space coordinates of
the electron and thus has spatial characteristics.

These one electron wave functions are called atomic orbitals (AOs). Atomic
orbitals describe electron densities in the atom at various distances and
directions from the nucleus.

The probability of finding an electron (ψ2) is highest inside the contour surface.
Thus instead of thinking of where an electron is, it is more correct to think
about where the electron is likely to be. Orbitals are thus regions of space where an
electron is more likely to be found. These regions of space, which have a significant
electron population (orbitals), have shape, size (distance from the nucleus),
and energy.

The most common elements present in organic compounds are first-row elements
(C, H, N, O); therefore 1s, 2s, and 2p AOs are most commonly encountered.
Molecular Orbital Theory

In molecules, the problem of understanding the interactions of electrons with

the nuclei is more complicated because there are more nuclei and more electrons
that interact. Imagine, however, the situation that occurs when two nuclei
approach one another. If the two atoms come close enough together, an AO of
one atom which contains a single electron will occupy to some extent the same
region of space as an AO of the second atom which contains a single electron.

When those AOs overlap, an electron from one atom shares a region of space
with the electron from the other atom. When such an event occurs, each electron is
no longer influenced by just one nucleus but by two. This requires a new
mathematical description of the behavior of electrons influenced by two nuclei
This requires a new mathematical description of the behavior of electrons
influenced by two nuclei. gain the solution to those equations defines a new
region of space where there is a high probability of finding both electrons.
Furthermore, only two electrons can occupy any particular region of space. This
new region of space is called a molecular orbital (MO), the electrons in the MO
are of lower energy than when they were in their separate AOs, and the lowered
energy gives rise to a chemical bond between the atoms.

In other words, chemical bonds result from the overlap of singly occupied AOs
to give a doubly occupied MO (called a bonding MO) in which each electron
of the pair interacts with both nuclei.
In order to simplify things, we’ll consider the interaction of the orbitals containing
valence electrons to create molecular orbitals. The wave functions of hydrogen
atom A and hydrogen atom B can interact either constructively or destructively.

Constructively:
Ψ(σ) or Ψ+ = (1/√2 ) [φ(1sa) + φ(1sb) ]
Destructively:
Ψ(σ*) or Ψ- = (1/√2 ) [φ(1sa) - φ(1sb) ]
 The bonding orbital
results in increased
electron density
between the two nuclei,
and is of lower energy
than the two separate
atomic orbitals.
 The antibonding
orbital results in a node
between the two nuclei,
and is of greater energy
than the two separate
atomic orbitals.
 The result is an
energy level diagram
with the bonding orbital
occupied by a pair of
electrons. The filling of
the lower molecular
orbital indicates that
the molecule is stable
compared to the two
individual atoms.
 Molecular Orbital Theory
The bonding orbital is
+ - sometimes given the
notation σg, where the
g stands for gerade, or
+ symmetric with respect
to a center of inversion.

The signs on the molecular orbitals indicate the sign of

the wave function, not ionic charge.
 Molecular Orbital Theory
The anti-bonding orbital
+ - is sometimes given the
notation σu, where the
u stands for ungerade,
+ or asymmetric with
respect to a center of
inversion.
The signs on the molecular orbitals indicate the sign of
the wave function, not ionic charge.
 Rules for Combining Atomic Orbitals
1. The number of molecular orbitals = the
number of atomic orbitals combined.
2. The strength of the bond depends upon the
degree of orbital overlap.
BONDING SCHEMES
Bond formation between atoms occurs primarily to enable each atom to achieve
an inert gas electron configuration in the valence level (a valence octet for all
elements except hydrogen which requires only two electrons to achieve the
electronic configuration of helium).

An atom can achieve an inert-gas electronic configuration by giving up

electrons, accepting electrons, or sharing electrons with another atom.

An ionic bond is formed when one atom gives up one or more electrons to reach an
octet electronic configuration (as a positively charged ion) and a second atom
accepts one or more electrons to reach an octet electronic configuration.

The cesium atom has been converted to a positively charged cesium ion with the
octet electronic configuration of xenon, and the chlorine has been converted to a
negatively charged chloride ion with the octet electronic configuration of argon.
 Most bonds in organic molecules, however, are covalent bonds in which
electrons are shared between two atoms. Sharing electrons is a way to
enable each atom of the bonded pair to reach an octet electronic
configuration without having to give up or gain an electron.

Covalent bonds are formed by the

overlap of singly occupied AOs to
form new MOs that contain a pair
of electrons. Each atom in
essence gains an electron by
sharing.

The reaction of a chlorine atom with a fluorine atom occurs by the overlap of
a singly occupied 3p orbital of chlorine with a singly occupied 2p orbital of
fluorine to give a bond between the two atoms that contains two electrons.
In addition to electron sharing to reach octet electronic configurations,
other considerations such as the number of bonds to an atom, the number
of electron pairs that are shared between two bonded atoms, and repulsion
energies that are present between electron pairs require some modification of the
picture.