1.

Structure and Bonding

Based on McMurry’s Organic Chemistry, 7th edition

What is Organic Chemistry?
 Living things are made of organic chemicals
 Proteins that make up hair
 DNA, controls genetic make-up
 Foods, medicines
 Examine structures below

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Origins of Organic Chemistry
Foundations of organic chemistry from mid-1700’s.

Compounds obtained from plants, animals hard to

isolate, and purify.

Compounds also decomposed more easily.

Torben Bergman (1770) first to make distinction

between organic and inorganic chemistry.

It was thought that organic compounds must contain

some “vital force” because they were from living
sources.
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Because of “Vital force”, it was thought that organic
compounds could not be synthesized in laboratory
like inorganic compounds.

1816, Chervrut showed that not to be the case, he could

prepare soap from animal fat and an alkali

1828, Wholer showed that it was possible to convert

inorganic salt ammonium cyanate into organic
substance “urea”

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• Organic chemistry is study of carbon compounds.
• Why is it so special?
- 90% of more than 30 million chemical
compounds contain carbon.
- Examination of carbon in periodic chart answers
some of these questions.
- Carbon is group 4A element, it can share 4
valence electrons and form 4 covalent bonds.

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Why this chapter?
• Review ideas from general chemistry: atoms, bonds,
molecular geometry

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1.2 Atomic Structure: Orbitals
 Quantum mechanics: describes electron energies
and locations by a wave equation
 Wave function solution of wave equation
 Each wave function is an orbital, 

 A plot of 2 describes where electron most likely to

be

 Electron cloud has no specific boundary so we show

most probable area

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Shapes of Atomic Orbitals for
Electrons
 Four different kinds of orbitals for electrons based on
those derived for a hydrogen atom
 Denoted s, p, d, and f
 s and p orbitals most important in organic and
biological chemistry
 s orbitals: spherical, nucleus at center
 p orbitals: dumbbell-shaped, nucleus at middle
 d orbitals: elongated dumbbell-shaped, nucleus at
center

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Orbitals and Shells part 1
 Orbitals are grouped in shells of increasing size and
energy
 Different shells contain different numbers and kinds
of orbitals
 Each orbital can be occupied by two electrons

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Orbitals and Shells part 2
 First shell contains one s orbital, denoted 1s, holds
only two electrons
 Second shell contains one s orbital (2s) and three p
orbitals (2p), eight electrons
 Third shell contains an s orbital (3s), three p orbitals
(3p), and five d orbitals (3d), 18 electrons

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p-Orbitals
 In each shell there are three perpendicular p orbitals, px, py,
and pz, of equal energy

 Lobes of a p orbital are separated by region of zero

electron density, a node

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1.4 Development of Chemical Bonding
Theory
 Kekulé and Couper independently observed that carbon
always has four bonds

 van't Hoff and Le Bel proposed that the four bonds of

carbon have specific spatial directions
 Atoms surround carbon as corners of a tetrahedron

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 Atoms form bonds because the compound that results is
more stable than the separate atoms
 Ionic bonds in salts form as a result of electron transfers
 Organic compounds have covalent bonds from sharing
electrons (G. N. Lewis, 1916)
 Lewis structures (electron dot) show valence electrons
of an atom as dots
 Hydrogen has one dot, representing its 1s electron
 Carbon has four dots (2s2 2p2)
 Kekule structures (line-bond structures) have a line
drawn between two atoms indicating a 2 electron
covalent bond.
 Stable molecule results at completed shell, octet (eight
dots) for main-group atoms (two for hydrogen)

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 Atoms with one, two, or three valence electrons form one,
two, or three bonds.

 Atoms with four or more valence electrons form as many

bonds as they need electrons to fill the s and p levels of their
valence shells to reach a stable octet.

 Carbon has four valence electrons (2s2 2p2), forming four

bonds (CH4).

 Nitrogen has five valence electrons (2s2 2p3) but forms only
three bonds (NH3).

 Oxygen has six valence electrons (2s2 2p4) but forms two
bonds (H2O)

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Non-bonding electrons
 Valence electrons not used in bonding are called
nonbonding electrons, or lone-pair electrons
 Nitrogen atom in ammonia (NH3)
 Shares six valence electrons in three covalent

bonds and remaining two valence electrons are

nonbonding lone pair

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1.5 The Nature of Chemical Bonds:
Valence Bond Theory
 Covalent bond forms when two atoms approach
each other closely so that a singly occupied
orbital on one atom overlaps a singly occupied
orbital on the other atom
 Two models to describe covalent bonding.

Valence bond theory, Molecular orbital theory

Valence Bond Theory:

 Electrons are paired in the overlapping orbitals
and are attracted to nuclei of both atoms
 H–H bond results from the overlap of two
singly occupied hydrogen 1s orbitals
 H-H bond is cylindrically symmetrical, sigma
(s) bond

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Bond Energy
 Reaction 2 H·  H2 releases 436 kJ/mol
 Product has 436 kJ/mol less energy than two atoms:
H–H has bond strength of 436 kJ/mol. (1 kJ =
0.2390 kcal; 1 kcal = 4.184 kJ)

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Bond Length
 Distance between
nuclei that leads to
maximum stability
 If too close, they
repel because both
are positively
charged
 If too far apart,
bonding is weak

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1.6 sp3 Orbitals and the Structure of
Methane
 Carbon has 4 valence electrons (2s2 2p2)
 In CH4, all C–H bonds are identical (tetrahedral)
 sp3 hybrid orbitals: s orbital and three p orbitals
combine to form four equivalent, unsymmetrical,
tetrahedral orbitals (sppp = sp3), Pauling (1931)

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The Structure of Methane
 sp3 orbitals on C overlap with 1s orbitals on 4 H
atoms to form four identical C-H bonds
 Each C–H bond has a strength of 436 (438) kJ/mol
and length of 109 pm
 Bond angle: each H–C–H is 109.5°, the tetrahedral
angle.

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1.7 sp3 Orbitals and the Structure
of Ethane
 Two C’s bond to each other by s overlap of an sp3
orbital from each
 Three sp3 orbitals on each C overlap with H 1s
orbitals to form six C–H bonds
 C–H bond strength in ethane 423 kJ/mol
 C–C bond is 154 pm long and strength is 376 kJ/mol
 All bond angles of ethane are tetrahedral

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1.8 sp2 Orbitals and the Structure
of Ethylene
 sp2 hybrid orbitals: 2s orbital combines with two 2p
orbitals, giving 3 orbitals (spp = sp2). This results in a
double bond.
 sp2 orbitals are in a plane with120° angles
 Remaining p orbital is perpendicular to the plane

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Bonds From sp2 Hybrid Orbitals
 Two sp2-hybridized orbitals overlap to form a s bond
 p orbitals overlap side-to-side to formation a pi ()
bond
 sp2–sp2 s bond and 2p–2p  bond result in sharing
four electrons and formation of C-C double bond
 Electrons in the s bond are centered between nuclei
 Electrons in the  bond occupy regions are on either
side of a line between nuclei

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Structure of Ethylene
 H atoms form s bonds with four sp2 orbitals
 H–C–H and H–C–C bond angles of about 120°
 C–C double bond in ethylene shorter and stronger
than single bond in ethane
 Ethylene C=C bond length 134 pm (C–C 154 pm)

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1.9 sp Orbitals and the Structure of
Acetylene
 C-C a triple bond sharing six electrons
 Carbon 2s orbital hybridizes with a single p orbital
giving two sp hybrids
 two p orbitals remain unchanged
 sp orbitals are linear, 180° apart on x-axis
 Two p orbitals are perpendicular on the y-axis and
the z-axis

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Orbitals of Acetylene
 Two sp hybrid orbitals from each C form sp–sp s
bond
 pz orbitals from each C form a pz–pz  bond by
sideways overlap and py orbitals overlap similarly

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Bonding in Acetylene
 Sharing of six electrons forms C C

 Two sp orbitals form s bonds with hydrogens

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1.10 Hybridization of Nitrogen and
Oxygen
 Elements other than C can have hybridized orbitals
 H–N–H bond angle in ammonia (NH3) 107.3°
 C-N-H bond angle is 110.3 °
 N’s orbitals (sppp) hybridize to form four sp3 orbitals
 One sp3 orbital is occupied by two nonbonding
electrons, and three sp3 orbitals have one electron
each, forming bonds to H and CH3.

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1.11 Molecular Orbital Theory
 A molecular orbital (MO): where electrons are most likely
to be found (specific energy and general shape) in a
molecule

 Additive combination (bonding) MO is lower in energy

 Subtractive combination (antibonding) MO is higher

energy

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Molecular Orbitals in Ethylene
 The  bonding MO is from combining p orbital lobes
with the same algebraic sign
 The  antibonding MO is from combining lobes with
opposite signs
 Only bonding MO is occupied

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1.12 Drawing Structures
 Drawing every bond in organic molecule can
become tedious.
 Several shorthand methods have been
developed to write structures.
 Condensed structures don’t have C-H or C-C
single bonds shown. They are understood.
e.g.

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3 General Rules:
1) Carbon atoms aren’t usually shown. Instead a carbon
atom is assumed to be at each intersection of two lines
(bonds) and at the end of each line.

2) Hydrogen atoms bonded to carbon aren’t shown.

3) Atoms other than carbon and hydrogen are shown (See

table 1.3).

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Summary
 Organic chemistry – chemistry of carbon compounds
 Atom: positively charged nucleus surrounded by negatively charged
electrons
 Electronic structure of an atom described by wave equation
 Electrons occupy orbitals around the nucleus.
 Different orbitals have different energy levels and different shapes
 s orbitals are spherical, p orbitals are dumbbell-shaped

 Covalent bonds - electron pair is shared between atoms

 Valence bond theory - electron sharing occurs by overlap of two
atomic orbitals
 Molecular orbital (MO) theory, - bonds result from combination of
atomic orbitals to give molecular orbitals, which belong to the entire
molecule

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Summary (cont’d)
 Sigma (s) bonds - Circular cross-section and are formed by head-on
interaction
 Pi () bonds – “dumbbell” shape from sideways interaction of p
orbitals
 Carbon uses hybrid orbitals to form bonds in organic molecules.
 In single bonds with tetrahedral geometry, carbon has four sp3
hybrid orbitals
 In double bonds with planar geometry, carbon uses three
equivalent sp2 hybrid orbitals and one unhybridized p orbital
 Carbon uses two equivalent sp hybrid orbitals to form a triple
bond with linear geometry, with two unhybridized p orbitals
 Atoms such as nitrogen and oxygen hybridize to form strong, oriented
bonds
 The nitrogen atom in ammonia and the oxygen atom in water are
sp3-hybridized

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