Module 1

MODULE 2: BONDING AND STRUCTURE OF ORGANIC COMPOUNDS

Electrons don’t behave like particles;

Review: The Electron they’re better described as waves.
(YT_Crash Course)
Nuclei
1865 - Solid particles
- a young chemist, and activist, John
Newlands published a paper on Electrons
the periodicity of elements - are wave-particle dualities
- he compared their repetition, the
first two rows of it, to a musical Erwin Schrodinger's mathematical model
scale treated electrons as standing waves,
1865 leading to the concept of electron orbitals
- Mendeleev published the first and shells.
periodic table
Orbitals, representing the harmonics of
John Dalton electrons, determine the electron
- determined that elements only configuration of atoms, influencing their
exist in discrete packets of matter reactivity, ionization energy, and electron
affinity, all of which contribute to the
Neil Bohr beauty and stability of the periodic table.
- “Quanta” root of the term
“Quantum mechanics”

1913 Orbitals
- Neil Bohr came up with a simple (YT_Crash Course)
model for describing these energy
levels for a single electron in Misconception of Atom Structure
hydrogen merely assuming circular - Atoms are commonly visualized as
orbits balls connected by sticks, but this
representation is incorrect.
Bohr Model - Nuclei can be ball-like, but larger

( )
−18
2
Z unstable ones may appear oblong.
- E=−2.178 x 1 0 J 2 Electrons surround the nucleus in
n
a spherical cloud.
- Molecules and bonds are not
simple balls on sticks; they involve
overlapping electron clouds and
quantum mechanical 3-
dimensional wave functions.

Water's Unique Structure

- Water's Lewis structure is linear,
but the molecule is bent. The
arrangement of electrons in sp3
 hybridized orbitals forces a
tetrahedral structure, making water
asymmetrical.
- Water's Lewis structure is linear,
but the molecule is bent. The
arrangement of electrons in sp3
hybridized orbitals forces a
tetrahedral structure, making water
asymmetrical.

Orbital Hybridization:
- Orbitals, such as s, p, and d
orbitals, can hybridize to form
different molecular shapes.
- Hybridization, like sp3
hybridization in water, results in
unique molecular structures like
tetrahedra.

Double and Triple Bonds:

- Sigma and pi bonds play roles in
double and triple bonds. For
example, sp2 orbitals form a
trigonal plane, leading to sigma
and pi bonds in double bonds.
- The interaction of unhybridized p
orbitals contributes to pi bonds in
double bonds.
Nucleus
- contains positively charged
D and F Orbitals' Role:
protons and uncharged neutrons
- d and f orbitals can hybridize with
- contains most of the mass of the
sp orbitals, creating diverse and
atom
complex 3-dimensional molecular
shapes.
Electron cloud
- The shapes of molecules,
- is composed of negatively
determined by orbital
charged electrons
configurations, influence their
- comprises most of the volume of
behavior and properties.
the atom

Cation
BONDING AND STRUCTURE OF
- is positively charged and has fewer
ORGANIC COMPOUNDS
electrons than protons
(Lecture Slides)
Anion
- is negatively charged and has
more electrons than protons
Only electrons are involved

Theory of Quantum Mechanics

Quantum Mechanics
- electrons have properties of both a
particles and wave

Schrödinger wave equation (Ψ-psi)

- gives the total energy of an
electron at a given point in space
(x,y,z)

Ψ2 = probability of finding an electron at a

given point in space

Orbital = space where an electron spends

~95% of its time

Atomic orbitals (AOs)

- electrons are arranged in “shells”
at various distances from the
nucleus
- shells are arranged in increasing
energy
- within each shell, electrons are
paired into orbitals with each
orbital holding two electrons
- paired electrons within an orbital
have opposite spins

S -spherical
P orbital - can hold 6 because it has 3
shapes which holds 2 electrons each
(dumbbell)

Atomic Orbitals
Electron Configuration Hund’s rule:
- If two or more electrons
Rule I. degenerate orbitals are available,
Aufbau principle: one electron is placed in each
- Orbitals are filled so that those of orbitals with their spins parallel
lowest energy are filled first, until all are half-full
according to the order

1s → 2s→ 2p→ 3s→ 3p→ 4s→ (Practice Problem | PPT, p. 9 | p1_1)

3d

The Periodic Table of Elements

- Rows represent the period
- Columns represent groups.
- Elements in the same group have
similar properties
- Chemical Abstract services labeled
the groups in Roman numerals
with A/B, with A for main groups &
B for transition metals

- International Union of Pure and

Applied Chemistry changed the
Rule 2 labeling in numbers from 1-18
Pauli exclusion principle (new IUPAC)
- A maximum of two electrons may
be placed in each orbital but only
when the spins of the electrons are
paired.

RECALL: Lewis Structure

Valence Electrons
- electrons in the outermost shell;
Paired with opposite spin to stabilize the electrons involved in bonding
electron
Rule 3 Octet Rule
 - Atoms will give up, accept, or
share electrons in order to achieve
a noble gas configuration

Example:

(Practice Problem | PPT_p.19 | p1_3)

Exceptions to Octet Rule
Molecular Shape
- Lewis structure tells us which
Less than an octet atoms are connected to each
other, but it implies nothing about
the geometry - affected by bond
length and bond angle.
- To determine the geometry:
1. Draw a valid lewis structure
2. Count groups around a
More than an octet given atom

Bond Length
- distance between the nuclei of two
(Practice Problem | PPT_ p.15 | p1_2) atoms joined by a covalent bond.
- Decreases across a row in
the periodic table as the
Formal Charge size of the atom decreases.
- The charge assigned to individual - Increases down a column
atoms in a lewis structure of the periodic table as the
size of an atom increases.

- the best Lewis structure…

- is the one with the fewest
charges
- puts a negative charge on
the most electronegative
atom
Bond Angle Examples:

- determines the shape around

bonded to two other atoms
- two group = linear (180°)
- Three group = trigonal
planar (120°)
- four groups = tetrahedral
(109.5°)

(Practice Problem | PPT_p.27 | p1_3)

Recall: Types of Bonds

- Bonding is the joining of two atoms

in a stable arrangement
VSEPR Theory
- Joining two or more elements
forms compounds
- Valence-shell Electron-pair
- Through bonding, atoms attain a
Repulsion (VSEPR) Theory - the
complete outer shell of valence
most stable arrangement keeps
electrons
the groups as far away as possible
from other to minimize repulsion.
- There are two different kinds of
bonding:
- Ionic Bonds result from
the transfer of electrons
from one element to
another
- is based on the fact that electron - Covalent Bonds result
pairs repel each other, so we need from the sharing of
to consider the lone pairs. electrons between two
nuclei.
-
(Practice Problem | PPT_p.29 | p1_3)

Covalent Bonding
- covalent bonds are much more
common in organic chemistry than
ionic bonds
- A covalent bond consists of the
simultaneous attraction of two
nuclei for one or more pairs of
electrons
Types of Covalent Bonds
- a sigma (σ) bond results when the
bonding orbitals point along the
axis connecting the two bonding
nuclei:
- either standard atomic
orbitals or hybrid
- s-to-s, p-to-p, hybrid-to-
hybrid, s-to-hybrid, etc.

- a pi (π) bond results when the

bonding orbitals are parallel to
each other and perpendicular to
the axis connecting the two
bonding nuclei:
- between unhybridized
parallel p orbitals

- the interaction between parallel

orbitals is not as strong as
between orbitals that point at each
other; therefore σ bonds are
stronger than π bonds.

- σ bonds are stronger than π

bonds