McMurry Chapter 1

STRUCTURE AND BONDING

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 ORGANIC CHEMISTRY

• Organic compounds are compounds containing carbon

• Carbon neither readily gives up nor readily accepts electrons

• Carbon shares electrons with other carbon atoms as well as with several different
kinds of atoms

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STRUCTURE OF THE ATOM AND ATOMIC ORBITALS

• atom consists of nucleus surrounded by electron cloud

electron cloud
nucleus

• electrons housed in orbitals that are grouped in shells of increasing size and energy

• an atomic orbital can hold two electrons at most

• a list of orbitals occupied by an atom’s electrons describes the atom’s
ground-state electron configuration SB-2

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 ELECTRON CONFIGURATIONS OF SOME
2ND ROW ELEMENTS

Atomic # 5 6 7 8 9 10

• use the following rules to assign electron configuration:

Aufbau Principle: the lowest energy orbitals are filled first

Pauli Exclusion Principle: a maximum of two spin paired electrons
may be placed in each orbital
Hund’s Rule: one electron is added to each degenerate (equal energy)
orbital before a second electron is added

The outermost shell is called the valence shell.

Electrons in the valence shell are the ones involved in bonding.
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LEWIS STRUCTURES OF ATOMS

• Lewis structures are concerned only with valence electrons

• nucleus represented by symbol of element of interest

• valence electrons represented by dots surrounding nucleus

B C N O F Ne

Atoms in the same group have the same number of valence electrons.
The number of valence electrons is the same as the group number.
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 ELECTRON CONFIGURATIONS OF SOME
2ND ROW ELEMENTS

Neon (a noble gas) has a full valence shell = 8 electrons (an octet).
For 2nd row elements, a valence shell octet = great stability. SB-5

THE OCTET RULE

Atoms form bonds to achieve a stable octet (noble gas configuration)

exceptions to the octet rule, e.g., P and S (may have “expanded octets”)

Atoms can donate, accept, or share electrons to achieve a noble gas

electronic configuration

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 VALENCY

Atoms in organic compounds form a fixed number of bonds.

Carbon can form one or more bonds to other carbon atoms.

Alkane Alkene Alkyne

Organic Nomenclature: McMurry 3.4, 4.1, 6.2, 10.1, 13.1

Extra help/practice available through SI workshop(s)

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Which of the following line bond structures is correct?

H H H H H H H H
H C C C H H C C C H H C C C H H C C C H
H H H H
A B C D

1. A and B
2. A and C
3. B and D
4. Only B
5. Only C

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 THE NATURE OF CHEMICAL BONDS.
A CLOSER LOOK AT ATOMIC STRUCTURE
Quantum Mechanics
• mathematical description of bonding that takes into account the wave nature of electrons
• wave equation is solved to yield a series of wave functions (Ψ ) for the atom
• wave functions may be positive, negative or zero
• Ψ describes a series of states with different energies for each electron
• Ψ 2 gives the probability of finding an electron in a particular location in space
• Heisenberg uncertainty principle: the position and momentum of an electron cannot
simultaneously be known
• plots of Ψ 2 in three dimensions generate electron “clouds” called orbitals
• four types of orbitals: s, p, d, f; only s and p orbitals are important in organic
chemistry
• atomic orbital: region in space where the probability of finding an electron
is large
• s orbital • p orbitals

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VALENCE BOND THEORY

Example: Bonding in H2

• two atomic orbitals overlap

• result is a σ-bond
• all purely single bonds are
σ-bonds

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 BONDING IN CARBON COMPOUNDS
ORBITAL HYBRIDIZATION
• recall: carbon has a valency of four

• cannot be adequately explained by ground-state electron configuration

electron orbital
promotion hybridization four hybrid
sp3 orbitals

• orbital hybridization is a mathematical combination of the 2s and 2p wave

functions to obtain wave functions for the new sp3 orbitals
• each sp3 orbital has ¼ s-character and ¾ p-character
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THE STRUCTURE OF METHANE

• the carbon of CH4 has four sp3 orbitals in a tetrahedral arrangement

• an sp3 orbital looks like a p-orbital with one lobe greatly extended
• each sp3 orbital overlaps with a 1s orbital of hydrogen

≡ ≡

• four identical C-H σ-bonds

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SHAPE OF ORGANIC COMPOUNDS. VSEPR THEORY

3D Shape

Virtually all molecules possess a 3-dimensional shape which is

often not accurately represented by drawings

Note that a dashed line indicates a

bond is behind the page

Note that a wedge indicates a bond is

coming forward

four bonds to carbon have tetrahedral arrangement

One explanation is Valence Shell Electron Pair Repulsion (VSEPR)

Electrons pairs want to be as far away from one another as possible

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THE STRUCTURE OF ETHANE

• each carbon forms σ-bonds to three hydrogens by overlap of C sp3 orbitals

and H s orbitals

• C-C σ-bond formed by end-to-end overlap of two sp3 orbitals

• molecule is approximately tetrahedral around each carbon

• because a σ-bond has cylindrical symmetry along the bond axis, there is
relatively free rotation of groups joined by a single bond SB-14

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 THE STRUCTURE OF ETHENE
• ethene (C2H4) contains a carbon-carbon double bond and is in the class of
organic compounds called alkenes

• the geometry around each carbon is called trigonal planar (all atoms in
a single plane; bonds point toward corners of a regular triangle)
• explained by orbital hybridization:

electron orbital
promotion hybridization
three hybrid
sp2 orbitals

• hybridization of the 2s orbital and two 2p orbitals yields three sp2 hybrid
orbitals
• one 2p orbital remaining
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THE STRUCTURE OF ETHENE

• 2p orbital is perpendicular to plane of sp2 orbitals

• sp2 orbitals used to form single (σ

σ) bonds
• 2p orbital used to form π-bond

• combination of σ-bond and π-bond yields double bond typical of alkenes

• note difference in C-C bond length for ethane compared to ethene

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 THE STRUCTURE OF ETHYNE
• ethyne (C2H2) contains a carbon-carbon triple bond and is in the class of
organic compounds called alkynes

• the geometry around each carbon is linear with bond angles of 180°

• explained by orbital hybridization:

electron orbital
promotion hybridization

two hybrid
sp orbitals

• hybridization of the 2s orbital and one 2p orbital yields two sp hybrid

orbitals
• two 2p orbitals remaining SB-17

THE STRUCTURE OF ETHYNE

• 2p orbitals are perpendicular to each other and to plane of sp orbitals

• sp orbitals used to form single (σ

σ) bonds
• 2p orbitals used to form π-bonds

• combination of σ-bond and two π-bonds yields triple bond typical of alkynes
• note difference in C-C bond length for ethane compared to ethene compared
to ethyne

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What is the hybridization of the carbon
atom in the following molecule?

1. s
2. p
3. sp
4. sp2
5. sp3

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HYBRIDIZATION OF NITROGEN,
OXYGEN, PHOSPHORUS AND SULFUR
• Nitrogen

orbital
hybridization four hybrid
sp3 orbitals

• nitrogen is sp3-hybridized with 1 e-pair → trigonal pyramidal

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 HYBRIDIZATION OF NITROGEN,
OXYGEN, PHOSPHORUS AND SULFUR
• Oxygen

orbital
hybridization four hybrid
sp3 orbitals

• oxygen is sp3-hybridized with 2 e-pairs → bent

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HYBRIDIZATION OF NITROGEN,
OXYGEN, PHOSPHORUS AND SULFUR
• Phosphorus

• phosphorus is sp3-hybridized with no e-pairs → tetrahedral

• Sulfur

• sulfur is sp3-hybridized with 2 e-pairs → bent

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 Given the ground state electronic configuration of boron, predict its
hybridization state and geometry in its neutral compounds, e.g. BF3.
[Hint: BF3 readily accepts a pair of electrons to form a stable octet.]

1. sp3, tetrahedral
2. sp2, trigonal planar
3. sp3, trigonal pyramidal
4. sp2, trigonal pyramidal

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RELATIONSHIP BETWEEN
HYBRIDIZATION AND VSEPR THEORY

Hybridization Lone Pairs ~ Bond Angle Molecular Geometry

sp 0 180° linear

sp2 0 120° trigonal planar

sp2 1 120° bent

sp3 0 109.5° tetrahedral

sp3 1 109.5° trigonal pyramidal

sp3 2 109.5° bent

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BOND LENGTHS OF ETHANE, ETHENE AND ETHYNE

110 pm

sp3 (25% s-character) sp2 (33% s-character) sp (50% s-character)

• C-C bond length decreases with increase in number of bonds

• C-H bond length also decreases in the series

bond length decreases with an increase in s-character of bond

• 2s orbitals closer to the nucleus than 2p orbitals

• hybridized orbital with more % s character closer to the nucleus than orbital
with less s character

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A SECOND PICTURE OF BONDING.

MOLECULAR ORBITAL (MO) THEORY
• LCAO: mathematic operation by which wave functions are added or subtracted

• number of MOs that result must always equal the number of AOs used
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 A SECOND PICTURE OF BONDING.
MOLECULAR ORBITAL (MO) THEORY
• σ-bonds can also be formed by end-to-end overlap of p-orbitals

• σ-bonds can also be formed by end-to-end overlap of one s-orbital and one
p-orbital
Is there another way by which p-orbitals may overlap?
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A SECOND PICTURE OF BONDING.

MOLECULAR ORBITAL (MO) THEORY
• “sideways” overlap of p-orbitals is also possible

• result is a π-bond SB-28

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 RELATIVE ENERGIES OF σ- AND π-ORBITALS

• σ-bonding orbital is lower in energy than π-bonding orbital

• lower energy = greater stability

• σ-bonds are more difficult to break than π-bonds

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LEWIS STRUCTURES OF ATOMS

• Lewis structures are concerned only with valence electrons

• nucleus represented by symbol of element of interest

• valence electrons represented by dots surrounding nucleus

B C N O F Ne

Atoms in the same group have the same number of valence electrons.
The number of valence electrons is the same as the group number.
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 DRAWING CHEMICAL STRUCTURES.
LEWIS STRUCTURES OF MOLECULES
representation of a molecule showing electron pairs as a pair
of dots or as a dash
only valence electrons are indicated

number of valence electrons is determined by position in

periodic table (valence number = group number)
1 8
2 3 4 5 6 7

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LEWIS STRUCTURES OF MOLECULES

drawing Lewis structures…

Example: C2H4

determine total number of valence electrons required to satisfy octet rule

for carbon and to provide each hydrogen with two electrons
2 x 8 + 4 x 2 = 24
determine total number of electrons available from valence shell of each
atom
2 x 4 + 4 x 1 = 12
the difference represents the number of electrons that must be shared (12)
the number of shared electrons / 2 = number of bonds required (6)
Recall valency: C → 4 bonds; H → 1 bond

Answer: H H

C C

H H

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 LEWIS STRUCTURES OF MOLECULES

drawing Lewis structures…

Try: CH3F

determine total number of valence electrons required to satisfy octet rule

for carbon and fluorine, and to provide each hydrogen with two electrons
2 x 8 + 3 x 2 = 22
determine total number of electrons available from valence shell of each
atom
1 x 4 + 3 x 1 + 1 x 7 = 14
the difference represents the number of electrons that must be shared (8)
the number of shared electrons / 2 = number of bonds required (4)
Recall valency: C → 4 bonds; H → 1 bond; F → 1 bond

Answer: Note: 14 electrons available; 8 used; 6 remaining

H
.... Extra electrons are nonbonding electrons;
H C
..F distribute to satisfy octet rule
H

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LEWIS STRUCTURES OF MOLECULES

drawing Lewis structures…

Try: CO32-

determine total number of valence electrons required to satisfy octet rule

for carbon and oxygen
1 x 8 + 3 x 8 = 32
determine total number of electrons available from valence shell of each
atom +/- any existing charge
1 x 4 + 3 x 6 + 2 = 24
the difference represents the number of electrons that must be shared (8)
the number of shared electrons / 2 = number of bonds required (4)
Recall valency: C → 4 bonds; O → 2 bonds if neutral

2- Note: 24 electrons available; 8 used; 16 remaining

Answer:
..O..
Extra electrons are nonbonding;distribute to
.... C .... satisfy octet rule
..O ..O

There are some exceptions that require “experience”

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 LEWIS STRUCTURES OF MOLECULES

drawing Lewis structures…

Try: SO42-

determine total number of valence electrons required to satisfy octet rule

for sulfur and oxygen
1 x 8 + 4 x 8 = 40
determine total number of electrons available from valence shell of each
atom +/- any existing charge
1 x 6 + 4 x 6 + 2 = 32
the difference represents the number of electrons that must be shared (8)
the number of shared electrons / 2 = number of bonds required (4)

2- Note: 32 electrons available; 8 used; 24 remaining

Answer: 2-

X
O

O S O
Extra electrons are nonbonding;distribute to
satisfy octet rule
O

2-
O

O S O

O
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REPRESENTATION OF STRUCTURAL FORMULAS

Lewis structures

• used to emphasize connectivity

• relatively free rotation around single bonds

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 REPRESENTATION OF STRUCTURAL FORMULAS

Condensed structures

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REPRESENTATION OF STRUCTURAL FORMULAS

Bond-line structures

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How many hydrogen atoms are present in the
naturally-occurring terpene α-terpinene shown
below?

1. 14
2. 15
3. 16
4. 17
5. 18
SB-39

REPRESENTATION OF STRUCTURAL FORMULAS

3-D Structures

• used to emphasize tetrahedral arrangement at carbon

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