Chapter 1

Bonding & Molecular Structure

Lewis Structures, Resonance Theory,
Molecular Orbitals, and Hybridization

What is Organic Chemistry?

1780: Organic compounds very complex and only obtained from living sources (vitalism)
Vitalism: Belief that a magic vital force, present in plants and animals, is necessary for
the synthesis of organic compounds
1789: Antoine Laurent Lavoisier observed that organic compounds are composed
primarily of carbon and hydrogen
1828: Friedrich Whler synthesized an organic compound (urea) from inorganic
compounds (lead cyanate and ammonium hydroxide).

Modern Organic Chemistry is the study of Carbon Compounds

>95% of All Known Compounds Composed of Carbon
Organic Chemistry Crucial to Our Way of Life: Dyes, Materials (Polymers), Petroleum,
Pesticides, Medications, a Molecular Understanding of the Humane Body, OUR BODIES.

Imatinib
Chronic myelogenous leukemia

The study and practice of organic chemistry can be subdivided into three areas:
STRUCTURE
Determining the way in
which atoms are put
together in space to
form complex molecules

MECHANISM
Understanding the
reactivity of molecules:
How and why chemical
reactions take place

SYNTHESIS
Building complex
molecules from simple
molecules using
chemical reactions

Why is an entire subject directed towards studying a single element of the periodic table?

Why Carbon?
Carbon forms a variety of strong covalent bonds to itself and other atoms (O, N, P, S, F, Cl,
Br, I).
This allows organic compounds to be structurally diverse. Carbon can bond to itself in
many different configurations, including chains, rings, and branched structures of varying
size and complexity.

DNA Bases

Hormones

Carbohydrates

Amino Acids

Why Does Carbon Bond in This Way?

Review of Atomic Structure

Nucleus is made up of protons and neutrons
Protons are positive charged
Neutrons are uncharged (electrically neutral)
Electrons are negatively charged and are in
motion
~99.9% of the mass of an atom comes from the
nucleus
Atomic Number (Z) = to the number of protons
in the nucleus
The atomic number also equals the number of
electrons surrounding the nucleus
Electrons surrounding the nucleus exist in shells
of increasing energy and at increasing distances
from the nucleus
Electron cloud is ~10,000 times
the diameter of its nucleus

Valence Electrons: exist in the valence shell, and

are the outermost electrons that are used in
making chemical bonds
5

I. Review of Lewis Bonding Theory

an atom is most stable if its outer shell is either
filled or contains eight electrons, and it has no
electrons of higher energy
Octet Rule: an atom will give up, accept, or share electrons in order
to achieve a filled outer shell or an outer shell that contains eight
electrons
G. N. Lewis

Atoms form bonds with other atoms to achieve a filled valence shell
(eight electrons), which gives them a stable Noble gas configuration
Particularly common among second-row elements of Groups 1A-7A
Group #

IA

IIA

IIIA

IVA

VA

VIA

VIIA

VIIIA

# Valence e-

He

Li

Be

Ne

Na

Mg

Al

Si

Cl

Ar

Full valence shell of electrons and are

thus quite stable/unreactive

The Correlation Between Chemical Bonds and Electronegativity

Electronegativity a measure of an atoms attraction for electrons that it shares in a
chemical bond with another atom
Increasing Electronegativity

H
2.1
Li
1.0

Be
1.5

B
2.0

C
2.5

N
3.0

O
3.5

F
4.0

Na
0.9

Mg
1.2

Al
1.5

Si
1.8

P
2.1

S
2.5

Cl
3.0

K
0.8

Br
2.8

Increasing
Electronegativity

I
2.5

Ionic Bond electron(s) are completely

transferred from one atom to another
Covalent Bond electrons are shared
between two atoms

Classification of Chemical Bonds

EN Between Bonded Atoms

Type of Bond

> 1.9

Ionic

0.5 to 1.9

Polar Covalent

< 0.5

Nonpolar Covalent
7

Ionic Bonding
Between atoms of widely different electronegativity (EN>2); usually a metal and a
nonmetal (results in the formation of ions, a cation(+) and an anion (-))

Atoms held together by electrostatic attraction, not electron sharing

e.g. LiF is ionic (EN: Li = 1.0 and F = 4.0)
H = +123.6 kcal/mol
(ionization potential)

H = -78.3 kcal/mol
(electron affinity)

Using Lewis Dot Structures: showing valence electrons

Covalent Bonding (Electron Sharing)

Very important in organic molecules!
Between atoms of similar electronegativity; usually non-metallic
e.g. CH4 (methane) is nonpolar covalent (EN <0.5) [EN: C = 2.5 and H = 2.1] .Why?
Large thermodynamic penalty for ionization of carbon to C+4

H = +1480.7 kcal/mol
(ionization potential)

Instead, each hydrogen atom shares its one valence electron with carbon so that
carbon has a filled octet, and hydrogen has a [He] configuration.

Covalent Bonding (Electron Sharing)

e.g. CCl4 is polar covalent (EN 0.5 to 1.9) [EN: Cl = 3.5 and C = 2.5] .Why?
each chlorine atom shares one valence electron with carbon so that every atom has a
filled octet
Polar Covalent Bond: unequal sharing of bonding electrons
more electronegative atom gains a greater fraction of the shared electrons and acquires
a partial negative charge (-)
The less electronegative atom has a smaller fraction of the shared electrons and
acquires a partial positive charge (+)

each chlorine atom still has three lone pairs of electrons

Lone Pair: unshared pair of electrons; non-bonding pair of electrons

10

How can you tell how many bonds and how many lone pairs an atom will have?

Count the Valence Electrons!

Neutral atom

# valence es

# bonds

# lone pairs

H
C
N
O
F
Second row elements want to be surrounded by eight valence electrons (an octet)
e.g. Carbon wants four more electrons (4 bonds)

e.g. Nitrogen wants three more electrons (3 bonds, one lone pair)

11

Multiple Covalent Bonding

Two atoms can share more than one pair of electrons to gain a filled valence shell
(very common in organic molecules)
e.g. Ethylene (C2H4)

e.g. Acetylene (C2H2)

e.g. Hydrogen cyanide (HCN)

Each line represents one shared electron pairs

12

Formal Charges and How to Calculate Them

Not all atoms are neutral in a Lewis or Kekule structure
Formal charges help chemists to keep track of the placement of electrons in molecules
Does not indicate that all of the charge is actually localized on one atom

Formal Charge = (group #) (# non-bonding es) 1/2(# shared es)

Which atom has the formal charge?

Carbon

Hydrogen

Carbon

Oxygen

Carbon

Oxygen

Oxygen

Oxygen

Group#
# non-Bonding es
(# shared es)
Formal Charge

Always indicate formal charge on problem sets and exams!

13

Summary of Bonding and Formal Charges

Each line represents one shared electron pairs

Be able to recognize common bonding patterns

The formal charges and the octet rule must coexist
10 electrons in
valence shell of
Nitrogen

CORRECT

NOT CORRECT

14

Line-Angle Formulas: Short-Hand for Chemists

(Drawing Complex Molecules Quickly)

Electron-dot formula

Dash formula

Lewis Structure

Kekule drawing

Testosterone
(not so easy!)

Condensed formula

Line-Angle formula

much easier!
15

Line-Angle Formulas: Short-Hand for Chemists

(Drawing Complex Molecules Quickly)

CH3CH2CH2OH
Electron-dot formula

Dash formula

Lewis Structure

Kekule drawing

Condensed formula

Line-Angle formula

Brevetoxin A (!!)
16

Rules for Drawing Line-Angle Formulas

Bonds are represented by lines (one line = two shared electrons)
Each bend in a line or terminus of a line represents a carbon atom
(unless another group is shown explicitly)
Do not draw carbon (C) atoms, except optionally at termini (for aesthetics)
Do not draw hydrogen (H) atoms, unless showing stereochemistry
(more detailed explanation next slide)
Assume enough C-H bonds to give each carbon atom four bonds (an octet)
(unless a charge is indicated)
Draw heteroatoms (N, O, S, P, F, Cl, Br, I)
Explicitly write hydrogen atoms bonded to heteroatoms
e.g. isopropanol:

e.g. cyclohexanone

17

Organic Molecules Are Not Flat, They Are Three-Dimensional!

Tetra-Substituted Carbon Is Tetrahedral (more on this later)

lines: in the plane of the paper

dashes: going back into the paper (away from you)
wedges: coming out of the paper (toward you)

18

Quantum and Wave Mechanics

Moving Particles Exhibit the Properties of a Wave

Each wave function () corresponds to a different energy state for an electron

Each energy state is a sublevel where one or two electrons can reside
The energy associated with the state of an electron can be calculated from the wave
function

The relative probability of finding an electron in a given region of space can be

calculated from the wave function
The phase sign of a wave equation indicates whether the solution is positive or
negative when calculated for a given point in space relative to the nucleus
19

Constructive interference occurs when wave functions with the same phase sign
interact. There is a reinforcing effect and the amplitude of the wave function increases.

Destructive interference occurs when wave functions with opposite phase signs interact.
There is a subtractive effect and the amplitude of the wave function goes to zero or
changes sign.

20

Molecular Orbital Theory

Electrons Are Waves!
They Exist as 3-D Standing Waves (Orbitals)

Orbital: a region of space where the probability of finding an electron is high.

Atomic Orbitals: unhybridized orbitals on an atom (s, p, d, f)
Linear Combination of Atomic Orbitals: individual wave functions (orbitals)
combine to form hybrid atomic orbitals (sp3, sp2, and sp) and molecular orbitals
(, *, , *)
Hybrid Atomic Orbital: combination of atomic orbitals from the same atom
Molecular Orbital: combination of atomic orbitals from different atoms
Conservation of Orbitals: when you add orbitals together, you always end up
with the same number of orbitals that you started with.
21

Atomic Orbitals
The s- and p-orbitals are the most important in organic compounds.
Orbital pictures are actually electron probability clouds
The volumes shown contain the electron 90-95% of the time

s-orbitals: spherical, electrons held close the nucleus, one sign

p-orbitals: two lobes with opposite signs, electrons further from nucleus
There are three degenerate (orbitals of equal energy) 2p orbitals that are higher
in energy than the 2s orbital
Remember, the sign of the orbital does not indicate charge.
It represents the sign of the wavefunction and lets us think qualitatively about
whether orbital interactions are constructive (bonding) or destructive (anti-bonding)
22

Electron Configuration
Rule 1. The Aufbau Principle. Orbitals fill in order of increasing energy, from lowest to
highest. Orbitals fill in the order 1s, 2s, 2p, 3s, 3p, and so on.
Rule 2. The Pauli Exclusion Principle. Only two electrons can occupy an orbital and their
The quantum mechanical
spins must be paired.
property of spin gives an
electron a tiny magnetic
field

When their tiny magnetic

fields are aligned N-S, the
electron spins are paired

Rule 3. Hunds Rule. When orbitals of equal energy (degenerate orbitals) are available we
add one electron to each orbital before a second electron is added to any one of
them; and the spins of the single electrons in the degenerate orbitals should be
aligned. Partially filling orbitals as much as possible minimizes electrostatic
repulsion between electrons.

Energy Level Diagram

23

Molecular Orbital (MO)

Represents the region of space where one or two electrons are being shared by two
different atoms (covalent bond) and are likely to be found

24

The number of molecular orbitals that are created is

equal to the number of atomic orbitals that combine
A bonding molecular orbital results when two orbitals of the same phase overlap

An antibonding molecular orbital results when two orbitals of opposite phase overlap

25

Sigma-Bonding ()
Sigma-bonding orbitals are cylindrically symmetrical molecular orbitals.
Electron density is centered along the axis of the bond.
Single bonds are sigma-bonds.
e.g. H2 is the simplest sigma-bond

Bonding: (+/+ or -/-) electron

density centered between nuclei
Anti-bonding: (+/-) generally has a
node between nuclei
Node: area of zero electron density

In stable bonding situations,

usually only the bonding
orbitals (, ) are occupied

26

Sigma bonds arent necessarily between two s-orbitals

s+p

p+p

These are all examples of single bonds

27

Pi-Bonding ()
Pi-bonding orbitals are not cylindrically symmetrical
Electron density is located above and below the axis of the bond
Double and triple bonds are pi-bonds
Double bond = +
e.g. Ethylene

To simplify drawing of orbitals

28

3-Dimensional View
-bond
(-orbitals overlap)
H

H
C

C
H

Planar structure
Carbon with (3 + 1) bonds

29

Orbital Overlap
Orbitals must have the correct symmetry to overlap
Orthogonal orbitals do not overlap
Good Overlap

Orthogonal: No Overlap

30

If all bonding occurred between simple sand p-orbitals, then all bond angles would
be approximately 90

We know that isnt true!

3-D representations of the 2px, 2py,

and 2pz atomic orbitals and their
orientation in space relative to one
another

Most bond angles in organic molecules are ~ 109, ~120, and ~180

How do we account for this?

Valence Shell Electron Pair Repulsion (VSEPR)

Electrons repel each other!
Lone pairs and bonds want to be a far apart as possible

31

Simply
Di-substituted
linear (180)

Tri-substituted
trigonal planar (120)

Tetra-substituted
tetrahedral (109)

e.g. acetylene

e.g. ethylene

e.g. methane

But, how do we think about this in terms of orbitals?

In 1930, Linus Pauling introduced a theory that combines VSEPR with
quantum mechanics (orbitals)

HYBRIDIZATION
32

Hybridization (Linear Combination of Atomic Orbitals)

Atomic orbitals on the same atom combine to form

hybride atomic orbitals.

Why?
Hybrid orbitals are more directional, so they have more effective bonding interactions
Second row elements hybridize using their s- and p-orbitals (sp, sp2, sp3)

Remember Conservation of Orbitals!

When you add orbitals together, you always end up
with the same number of orbitals that you started with.

33

sp3 Hybridization (Tetrahedral)

Ground State

Promotion of elections

Excited State

sp3-Hybridized State

Hybridization

34

sp2 Hybridization (Trigonal planar)

Ground State

Promotion of elections

Excited State

sp2-Hybridized State

Hybridization

35

sp2 Hybridization (Trigonal planar)

Three sp2-orbitals

3 sp2-orbitals
1 p-orbital

C
Enhanced electron
density in bonding
regions

For simplicity, can leave

out small back lobes.

36

Model of Bonding Molecular Orbitals of Ethylene (H2C=CH2)

Sigma-bonds () and lone pairs involve hybrid orbitals
Pi-bonds () involve unhybridized p-orbitals
Electrons of the bond have greater energy than electrons of the bond

37

sp Hybridization (Linear)

Ground State

Promotion of elections

Excited State

sp2-Hybridized State

Hybridization

38

sp Hybridization (Linear)

Two sp-orbitals

Enhanced electron
density in bonding
regions

2 sp-orbitals
2 p-orbital

For simplicity, can leave

out small back lobes.
39

Model of Bonding Molecular Orbitals of Ethyne (HCCH)

40

Drawing Hybridized Orbitals

sp3 Hybridized Orbital

sp2 Hybridized Orbital

sp Hybridized Orbital

41

Drawing Bonding Molecular Orbitals of Propene (CH3-CH=CH2)

For simplicity, draw lines connecting p-orbitals to represent -bonds

42

Drawing Bonding Molecular Orbitals of Ethyne (HCCH)

For simplicity, draw lines connecting p-orbitals to represent -bonds

43

Assigning Hybridization to Atoms in a Molecule

You need to be able to do this!
Count the hybrid atomic orbitals
# of hybrid orbitals =
# Hybrid orbitals

Hybridization

Geometry

~ bond angles

sp3

Tetrahedral

109

sp2

Trigonal planar

120

sp

Linear

180

44

Assigning Hybridization to Atoms in a Molecule

You need to be able to do this!

45

Bond Lengths of Ethyne, Ethylene, and Ethane

sp orbital 50% s character, 50% p character
sp2 orbital 33% s character, 66% p character
sp3 orbital 25% s character, 75% p character

The greater the s orbital character in one or both atoms, the shorter is the bond. This is
because s orbitals are spherical and have more electron density closer to the nucleus than
do p orbitals
The greater the p orbital character in one or both atoms, the longer is the bond. This is
because p orbitals are lobe-shaped with electron density extending away from the
46
nucleus

Rotation of Ethane versus Ethylene

Sigma-bonds are cylindrically symmetrical: rotation does not disrupt bonding
Sigma-bonds rotate freely

Ethane

(much more on the energetics

of this rotation later!)

Pi-bonds require ovelap of the p-orbitals: rotation disrupts overlap

Pi-bonds do not rotate

Ethylene

-overlap

p-orbitals orthogonal:
no overlap

This rotation does not occur!

47

Representing Molecules
Lewis Structures: Represent atoms sharing electrons to form bonds

Line-Angle Structures: Simplify the drawing of complex molecular structures

Dashes and Wedges: Allow chemists to draw molecules in 3-D

BUT! These simplified structures do not accurately represent the

electronic nature or reactivity of organic molecules!

It helps to think about electrons in motion

BUT HOW DO WE REPERESENT ELECTRONS IN MOTION?
48

Curved Arrow Formalism (Arrow Pushing)

Chemists use arrows to represent the motion of electrons within and between molecules.

Double Arrow:
2 electrons moving

Fishhook Arrow:
1 electron moving

1. The tail of the arrow starts at the electrons that are moving (lone pair or bond)
2. The head of the arrow shows where the electrons end up (lone pair or bond)
Always show the flow of electrons from a site of higher electron density
to a site of lower electron density

NOT CORRECT!

49

Resonance: Electronic Motion Within a Molecule

In a Lewis structure, we draw a well-defined location for the electrons in a molecule.
The reactivity of a molecule is not always explained by one Lewis structure
In many molecules and ions (especially those containing bonds), more than one
equivalent Lewis structure can be drawn which represent the same molecule
e.g. carbonate ion (CO3-2)

Contributing Resonance Structures

Hydrid

Molecules can be thought of as hybrids or weighted averages of

two or more Lewis structures, each with a different placement of
electrons
These structures, called resonance structures are not real or
detectable, but they are a useful conceptual tool for
understanding the reactivity of molecules

50

Rules for Drawing Resonance Structures

1) Only electrons move! The positions of nuclei must be the same in all contributing
structures; that is, contributing structures differ only in the distribution of valence
electrons. (Resonance occurs in the pi-system: conjugated lone pairs and pi-bonds)

2) Every resonance structure must be a valid Lewis structure

3) Keep track of lone pairs and formal charges. All contributing structures must have the
same number of paired and unpaired electrons.
4) Use arrow-pushing formalism to interconvert and identify possible resonance
structures.
5) Always use double-headed arrow () in between resonances structures.
Resonance structures do not represent an equilibrium, do not use (
)
6) Resonance stabilization: the energy of the resonance hybrid is lower than the energy of
any contributing structure.
7) Lower energy resonance structures contribute more to the overall structure of the
molecule.
How do you predict when one resonance structure
contributes more to the hybrid than another?
51

Guidelines for Estimating the Relative Importance (Energies)

of Contributing Resonance Structures
1) Filled Valence Shell: Structures in which all atoms have filled valence shells (completed
octets for C, N, O, F) contribute more than those in which one or more valence shells are
unfilled. Because C is the least electronegative, structures in which C has 6 electrons, 3
bonds, and a positive charge are possible (not possible with N, O, F)

Greater Contribution:
both carbon and oxygen have
complete valence shells

Lesser Contribution:
carbon has only six electrons
in its valence shells

2) Maximum Number of Covalent Bonds: Structures with a greater number of covalent

bonds contribute more than those with fewer covalent bonds.

Greater Contribution:
8 covalent bonds

Lesser Contribution:
7 covalent bonds

52

Guidelines for Estimating the Relative Importance (Energies)

of Contributing Resonance Structures
3) Least Separation of Unlike Charges: Structures that involve separation of unlike charges
contribute less than those that do not involve charge separation because separation of
charges costs energy.

Greater Contribution:
no separation of
unlike charges

Lesser Contribution:
separation of unlike charges

4) Negative Charge on a More Electronegative atom: Structures that carry a negative

charge on a more electronegative atom contribute more. Conversely, structures that carry
a positive charge on a less electronegative atom contribute more.

Lesser Contribution

Greater Contribution

Should not be drawn:

violates all 4 guidelines

53

Draw the Contributing Resonance Structures

54