John E.

McMurry

www.cengage.com/chemistry/mcmurry

Chapter 1
Structure and Bonding

Paul D. Adams • University of Arkansas

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 to the
right
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.
Origins of Organic Chemistry
Because of “vital force”, it was thought that organic
compounds could not be synthesized in laboratory like
inorganic compounds.

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

prepare soap from animal fat and an alkali and glycerol is
a product

1828, Woehler showed that it was possible to convert

inorganic salt ammonium cyanate into organic substance
“urea”
Origins of Organic Chemistry
 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.
Why This Chapter?
 Review ideas from general chemistry: atoms, bonds,
molecular geometry
1.1 Atomic Structure
 Structure of an atom
 Positively charged nucleus (very dense, protons and neutrons) and small (10 -15
m)

 Negatively charged electrons are in a cloud (10 -10 m) around nucleus

 Diameter is about 2  10-10 m (200 picometers (pm)) [the unit ångström (Å) is
10-10 m = 100 pm]
Atomic Number
and Atomic Mass
 The atomic number (Z) is the number of protons in the
atom's nucleus
 The mass number (A) is the number of protons plus
neutrons
 All the atoms of a given element have the same atomic
number
 Isotopes are atoms of the same element that have different
numbers of neutrons and therefore different mass numbers
 The atomic mass (atomic weight) of an element is the
weighted average mass in atomic mass units (amu) of an
element’s naturally occurring isotopes
The atom, proton, neutron
and electron - Video
1) Introduction to the atom: The atom, proton,
neutron and electron
http://www.khanacademy.org/science/
chemistry/v/introduction-to-the-atom
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, ψ

 A plot of ψ describes where electron most likely to be

 Electron cloud has no specific boundary so we show
most probable area.
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
Orbitals and Shells
(Continued)
 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
Orbitals and Shells
(Continued)
 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
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
Orbitals: An introduction
to orbitals - Video
1) Orbitals: An introduction to orbitals
http://learning.hccs.edu/faculty/paul.clemens/
chem2423/Organic%20Chemistry%20Lecture
%20Videos/chapter-1/orbitals-an-introduction-to-
orbitals

2) More on orbitals and electron configuration

http://www.khanacademy.org/science/chemistry/
v/more-on-orbitals-and-electron-configuration
1.3 Atomic Structure: Electron
Configurations
 Ground-state electron configuration (lowest energy
arrangement) of an atom lists orbitals occupied by its electrons.
Rules:
 1. Lowest-energy orbitals fill first: 1s  2s  2p  3s  3p 
4s  3d (Aufbau (“build-up”) principle)
 2. Electrons act as if they were spinning around an axis. Electron
spin can have only two orientations, up  and down . Only two
electrons can occupy an orbital, and they must be of opposite
spin (Pauli exclusion principle) to have unique wave equations
 3. If two or more empty orbitals of equal energy are available,
electrons occupy each with spins parallel until all orbitals have
one electron (Hund's rule).
Using the periodic table to determine
electron Configurations - Video
1) Electron Configurations: Introduction to
using the periodic table to determine electron
configurations
http://www.khanacademy.org/science/chemistry/
v/electron-configurations

2) Electron Configurations 2: Figuring out

configurations for the d-block elements
http://www.khanacademy.org/science/
chemistry/v/electron-configurations-2
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
Development of Chemical
Bonding Theory
 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)
 Development of Chemical
Bonding Theory
 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)
 Kekulé 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)
Development of Chemical
Bonding Theory
 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).
Development of Chemical
Bonding Theory
 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)
Development of Chemical
Bonding Theory
Non-Bonding Electrons
 Valence electrons not used in bonding are called nonbonding
electrons, or lone-pair electrons
 Nitrogen atom in ammonia (NH )
3
 Shares six valence electrons in three covalent bonds
and remaining two valence electrons are nonbonding
lone pair
 Bonding - Videos
1) Valence Electrons: Looking at valence
electrons to figure out reactivity
http://www.khanacademy.org/science/
chemistry/v/valence-electrons

2) Ionic, Covalent, and Metallic Bonds

http://www.khanacademy.org/science/
chemistry/v/ionic--covalent--and-metallic-
bonds
 Lewis Structure - Video
1) Lewis Dot Structures of Ionic and Covalent
Compounds
http://www.youtube.com/watch?
v=QKoA3fZ29B0&feature=player_embedded
1.5 Describing 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 () bond
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)
Bond Energy
 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
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)
The Structure of Methane
1.7 sp3 Orbitals and the
Structure of Ethane
 Two C’s bond to each other by  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 421 kJ/mol
 C–C bond is 154 pm long and strength is 377 kJ/mol
 All bond angles of ethane are tetrahedral
sp3 Hybridized Orbitals
and Sigma Bonds - Video
1) sp3 Hybridized Orbitals and Sigma Bonds
http://www.khanacademy.org/science/organic-
chemistry/v/sp3-hybridized-orbitals-and-sigma-
bonds
1.8 sp2 Orbitals and the
Structure of Ethylene
 Some Representations
of Ethylene are given
 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
Bonds From sp2 Hybrid
Orbitals
 Two sp2-hybridized orbitals overlap to form a  bond
 p orbitals overlap side-to-side to formation a pi () bond
 sp2–sp2  bond and 2p–2p  bond result in sharing four electrons and
formation of C-C double bond
 Electrons in the  bond are centered between nuclei
 Electrons in the  bond occupy regions are on either side of a line
between nuclei
Pi bonds and sp2
Hybridized Orbitals - Video
1) Pi bonds and sp2 Hybridized Orbitals
http://www.khanacademy.org/science/organic-
chemistry/v/pi-bonds-and-sp2-hybridized-
orbitals
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
Orbitals of Acetylene
 Two sp hybrid orbitals from each C form sp–sp  bond
 pz orbitals from each C form a pz–pz  bond by sideways
overlap and py orbitals overlap similarly
Bonding in Acetylene
 Sharing of six electrons forms C C

 Two sp orbitals form  bonds with hydrogens

Comparison of C–C and C–H Bonds in
Methane, Ethane, Ethylene, and
Acetylene
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.
1.11 Describing Chemical Bonds:
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
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
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.
Drawing Structures
(Continued)
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).
 Drawing Structures - Video
1) Representing Structures of Organic Molecules
http://www.khanacademy.org/science/organic-
chemistry/v/representing-structures-of-
organic-molecules
Summary
 Organic chemistry – chemistry of carbon compounds
 Atom: charged nucleus containing positively charged protons and
netrually charged neutrons 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
Summary (Continued)
 Sigma () 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
 Let’s Work a Problem

Draw an electron-dot structure for acetonitrile, C2H3N, which

contains a carbon-nitrogen triple bond. How many electrons
does the nitrogen atom have in its outer shell ? How many
are bonding, and how many are non-bonding?
Answer
To address this question, we must realize that the nitrogen
will contain 8 electrons in its outer shell. Six will be used in
the C-N triple bond (shaded box), and two are non-bonding