Chapter 1

Remembering General Chemistry:

Electronic Structure
and Bonding
Organic compounds

 The Vital Force Theory

 by Berzelius, 1807
 Organic compounds from living organism (plant or animal)
only
 An organic compound still contains some of the life force of
the organism that makes them (vitamin C, saponin, etc.)
 compounds from living organisms ~ ‘organic’
 compounds from minerals ~ ‘inorganic’

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Organic compounds
 Death of the Vital Force Theory
 synthesis of urea (‘organic’) from ‘inorganic’ (F. Wöhler,
1828)

 Lab synthesis of acetic acid (H. Kolbe, 1844),

formic acid & methane from CO (M. Berthelot, 1860)
 Fermentation from yeast extracts, free of living cells:
E. Büchner, 1897 (Nobel Prize in 1907)

 Current definition of organic compounds

= “compounds that are based on carbon” 3
Natural vs. Synthetic
Are natural substances (those made in Nature) are
superior to synthetic ones?
 synthesized penicillin or estradiol
 exactly the same in all respects as the compound in nature
 Synthesized analogs of morphine
 (compounds with structures similar to but not identical to that of
morphine) that have pain-killing effects like morphine but, unlike
morphine, are not habit forming
 many times, synthetic much better
 when well-made [separation and purification]

A field of poppies in Afghanistan

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Chemistry of carbon comp’d

 Organic chemistry = chemistry of carbon comp’d

 why carbon?
 forms stable covalent bond to other carbon
 sharing electrons
 Li+, F− vs. C4+ or C4-
 forms chain  variety ~ 16M (known) org comp’ds
 forms bonds to heteroatoms [N, O, X, P, S, etc.]
 exceptions: CO, CO2, Na2CO3, etc. ~ inorganic

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What Makes Carbon So Special?

• Atoms to the left of carbon give up electrons.

• Atoms to the right of carbon accept electrons.
• Carbon shares electrons.
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Components of org chem
 organic compounds
 structure  molecule  bonding  atoms
 properties
 physical
 chemical
 Chapter 1, 2, 3, 4, 5, and 8
 organic (chemical) reactions
 mechanism
 thermodynamics
 kinetics
 Chapter 6, 7, 8, 9, and 10

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In org chem 1…
Chapter
1. electronic structure and bonding
2. acid-base
3. nomenclature [naming], physical properties
conformation, alkanes and cycloalkanes
4. isomers [configuration, stereochemistry]
5. alkenes
6. reactions of alkenes [addition reactions]
7. reactions of alkynes
8. electron delocalization [resonance structure]
9, 10. substitution and elimination reactions

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 1.1 The Structure of an Atom
• An atom consists of electrons, positively
charged protons, and neutral neutrons.
• Electrons form chemical bonds.

• Atomic number: numbers of protons in its nucleus

• Mass number: the sum of the protons and neutrons
of an atom
• Isotopes have the same atomic number but
different mass numbers.

• The atomic weight: the average weighted mass of its atoms

• Molecular weight: the sum of the atomic weights of all the atoms
in the molecule 9
 Carbon

98.89% of naturally occurring carbon atoms contain six neutrons:

a mass number of 12

1.11% have seven neutrons: a mass number of 13

An atomic mass unit (amu) is defined as exactly 1/12 of the mass of 12C.

The atomic mass of 12C is 12.0000 amu; the atomic mass of 13C is 13.0034
amu. Therefore, the atomic weight of carbon is 12.011 amu.
(0.9889 x 12.0000) + (0.0111 x 13.0034) = 12.011
A trace amount of 14C (six protons and eight neutrons) and this isotope of carbon is
radioactive (decaying with a half-life of 5730 years).
As long as a plant or animal is alive, it takes in as much 14C as it excretes or exhales.
When it dies, it no longer takes in 14C, so the 14C in the organism slowly decreases.
Then, the age of a substance derived from a living organism can be determined by its 14C

content. 10
 1.2 The Distribution of Electrons in an Atom
• Quantum mechanics uses the mathematical equation of wave
motions to characterize the motion of an electron around a
nucleus.
• Wave functions or orbitals tell us the energy of the electron and
the volume of space around the nucleus where an electron is
most likely to be found.
• The closer the atomic orbital is to the nucleus, the lower its energy.
• Degenerate orbitals have the same energy.

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The ground-state electronic configuration describes the orbitals
occupied by the atom’s electrons with the lowest energy

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 The following principles determine which orbitals
electrons occupy:

• Aufbau principle: an electron goes into the atomic orbital with the lowest
energy

• Pauli exclusion principle: only two electrons can occupy one atomic
orbital and the two electrons have opposite spin

• Hund’s rule: electrons will occupy empty degenerated orbitals before

pairing up in the same orbital

Electrons in inner shells (those below the outermost shell) are called core
electrons and they do not participate in chemical bonding.
Electrons in the outermost shell are called valence electrons and they determine
an element’s chemical properties.
So, the chemical behavior of an element depends on its electronic configuration.

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 1.3 Ionic and Covalent Bonds
Lewis’s theory: 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 → octet rule

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 Ionic Bonds : Formed by the Transfer of Electrons

Attractive forces between opposite charges are called electrostatic

attractions
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A hydrogen atom achieves an empty shell by losing an electron
or a filled outer shell by gaining an electron.

Covalent Bonds : Formed by Sharing Electrons

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How Many Bonds Does an Atom Form?

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The Greater the Difference in Electronegativity,
the More Polar the Bond

Nonpolar covalent bond: electonegativity difference < 0.5

Polar covalent bond: electonegativity difference 0.5 – 1.9

Electronegativity difference > 1.9: electrons are not shared;

atoms are held together by
the attraction of opposite charges

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• Equal sharing of electrons: nonpolar covalent bond (e.g., H2)
• Sharing of electrons between atoms of different electronegativities:
polar covalent bond (e.g., HF)

less shells

more protons

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Polar covalent bonds

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 A Polar Bond Has a Dipole Moment
• A polar bond has a negative end and a positive end
dipole moment (D) = m = e x d
(e) : magnitude of the charge on the atom

(d) : distance between the two charges

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 Dipole Moment
Dipole moment = size of the charge x the distance between the charges

The greater the difference in electronegativity,

the greater the dipole moment and the more polar the bond.
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Electrostatic Potential Maps

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 1.4 How the Stucture of a Compound is
Represented: Lewis Structure

Formal Charge = the # of valence electrons –

(the # of lone-pair electrons + the # of bonds)

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Nitrogen has five valence electrons

Carbon has four valence electrons

Hydrogen has one valence electron and halogen has seven

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 Important Bond Numbers
Neutral

Cationic

Anionic

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 How to Draw a Lewis Structure
NO3–
Determine the total number of valence electrons (5 + 6 + 6 + 6 = 23).
Because they are negatively charged, add another electron = 24.

Avoid O—O bonds.

Check for formal charges.

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 Non-Octet Species
• In the 3rd and 4th rows, expansion beyond the octet to 10
and 12 electrons is possible.

Sulfuric Acid Periodic Acid Phosphoric Acid

• Reactive species without an octet such as radicals,

carbocations, carbenes, and electropositive atoms (boron,
beryllium).

Nitric Oxide
Radical Carbocation Carbene Borane
Radical,
Mammalian
Signaling Agent
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Kekulé Structures

Condensed Structures

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Kekulé Structures and Condensed Structures

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Kekulé Structures and Condensed Structures

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 Skeletal Structures

Skeletal structures show the carbon-carbon bonds as lines,

but do not show the carbons
or the hydrogens that are bonded to the carbons.

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1.5 Atomic Orbitals
An atomic orbital is the region of space around the nucleus
where an electron is most apt to be found.
Heisenberg uncertainty principle: both the precise location and
the exact momentum of an atomic particle cannot be
simultaneously determined. We can never say precisely where
an electron is - we can only describe its probable location.

The orbital letters are related to angular momentum

quantum number (l =0-3). The s, p, d, and f stand for names
given to groups for lines noted in the spectra of alkali
metals.

s - sharp for l =0
p - principal for l =1
d - diffuse for l =2
f - fundamental for l =3. 33
The s Orbitals

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A node is a consequence of the wavelike properties of an electron.

There are two types of waves: traveling waves and standing waves.

Traveling waves move through space; light is an example of a traveling

wave.

A standing wave is confined to a limited space. A vibrating string of a

guitar is an example of a standing wave—the string moves up and down.

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The p Orbitals

The lobes of a p atomic orbital have opposite phases.

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 1.6 Molecular Orbitals

• Molecular orbitals belong to the whole molecule.

• s bond: formed by overlapping of two s orbitals.

• Bond strength/bond dissociation energy: energy required to break a

bond or energy released to form a bond.

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The change in energy that occurs as two 1s atomic orbitals
approach each other.
The internuclear distance at minimum energy is the length of the
H-H covalent bond.
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Waves Can Reinforce Each Other
Waves Can Cancel Each Other

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 Atomic Orbitals Combine
to Form Molecular Orbitals

In-phase overlap : bonding MO

out-of-phase overlap : antibonding MO
The strongest covalent bonds are formed by electrons that occupy the
molecular orbitals with the lowest energy.
Orbitals are Conserved : # of Molecular Orbitals = # of Atomic Orbitals Combined 40
H2+ would not be as stable as H2 because it has only one
electron in the bonding orbital.

He2 does not exist: because each He atom would bring

two electrons, He2 would have four electrons: two filling
the lower energy bonding molecular orbital and the
remaining two filling the higher energy antibonding
molecular orbital.

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Sigma bond (s) is formed by end-on overlap of two
p orbitals:

A s bond is stronger than a p bond

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Side-to-Side Overlap of In-Phase p Orbitals Forms a π Bond

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44
 1.7 HOW SINGLE BONDS ARE FORMED IN
ORGANIC COMPOUNDS
Bonding in Methane

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Hybridization of One s and Three p Orbitals

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The orbitals used in bond formation determine the bond angles

• Tetrahedral bond angle: 109.5°

• Electron pairs spread themselves into space as far from

each other as possible

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The Bonds in Ethane

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Hybrid Orbitals of Ethane

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1.8 Bonding in Ethene: A Double Bond

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The Bonding in Ethene
 Diamond, Graphite, Graphene

Diamond is hardest of all substances: carbon bonded to others via

sp3 orbitals.
Graphite is a slippery and soft solid: carbon atoms are sp2 hydridized.
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1.9 Bonding in Ethyne: A Triple Bond

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The Bonding in Ethyne
 1.10 THE BONDS IN THE METHYL CATION,
THE METHYL RADICAL, AND THE METHYL ANION

Bonding in the Methyl Cation

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Bonding in the Methyl Radical

Bonding in the Methyl Anion

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1.11 THE BONDS IN AMMONIA AND
IN THE AMMONIUM ION

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The Ammonium Ion (+NH4)

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1.12 THE BONDS IN WATER

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1.13 THE BOND IN A HYDROGEN HALIDE

A halogen has 1 unpaired valence electron and forms 1 bond.

A halogen uses hybrid orbitals.

• The 3 lone pairs are energetically identical.
• Lone pairs position themselves to minimize electron repulsion.

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Overlap of an s Orbital
with an sp3 Orbital

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The Length and Strength of a
Hydrogen Halide Bond

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1.14 HYBRIDIZATION AND MOLECULAR GEOMETRY

The orbitals used in bond formation

determine the bond angle.

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 1.15 SUMMARY
If it forms no p bonds, it is sp3 hybridized;
if it forms one p bond, it is sp2 hybridized;
if it forms two p bonds, it is sp hybridized.

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• The shorter the bond, the stronger it is

• The greater the electron density in the region of orbital overlap, the
stronger is the bond
• The more s character, the shorter and stronger is the bond
• The more s character, the larger is the bond angle

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 • The shorter the bond, the stronger it is

• The greater the electron density in the region of orbital overlap, the
stronger is the bond

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• The more s character, the larger is the bond angle

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• The more s character, the shorter and stronger is the bond

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 1.16 THE DIPOLE MOMENTS OF MOLECULES
The vector sum of the magnitude and the direction of the individual
bond dipole determines the overall dipole moment of a molecule

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