John E.

McMurry

[Link]

Chapter 1
Structure and Bonding

Richard Morrison • University of Georgia, Athens

Scientific Revolution
Scientific revolution leads to:
• Safer and more effective medicines
• Cures for genetic diseases
• Increased life span
• Improved quality of life

Scientific advances in medicine and biology require an

understanding of organic chemistry
Organic Chemistry
Organic and Biological Chemistry in Modern Medicine
• Coronary artery disease (CAD) is directly correlated with blood
cholesterol levels
• 75% of blood cholesterol (1000 mg each day) is biosynthesized
• Drugs known as Statins reduce the risk of CAD by lowering blood
cholesterol levels
• 3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate
conversion
• Crucial step in biosynthesis of cholesterol
• Atorvastatin (Lipitor) inactivates enzyme that catalyzes HMG-CoA to
vevalonate conversion
Organic Chemistry
Carbon
Organic chemistry
• All organic compounds contain the element carbon
• 4A element
• Shares four electrons
• Forms four strong covalent bonds
• Bonds to other carbons to create chains and rings
• Not all carbon compounds are derived from living
organisms
• Over 99% of 37 million known compounds contain
carbon
Common Elements in Carbon Compounds
1.1 Atomic Structure: The Nucleus
Structure of atom
• Nucleus
• Positively charged
• Made up of protons (positively charged) and neutrons (neutral)
• Small (10-14 to 10-15 m in diameter)
• Contains essentially all the mass of the atom
• Electron cloud
• Negatively charged electrons in cloud around nucleus
• Atomic diameter is about 2 Angstroms (Å)
• 1 Å = 10-10 m = 100 pm ; 1 pm = 10-12 m

• Atomic diameter in SI units is 2  10-10 m (200 picometers (pm))

Atomic Structure: The Nucleus
Atomic number (Z)
• Number of protons in the atom's nucleus
• All atoms of a given element have the same atomic
number
Mass number (A)
• Number of protons plus neutrons in the atom’s nucleus

Isotopes
• Atoms of the same element (same Z) that have different
Numbers of neutrons and therefore different mass
numbers (different A)
Atomic mass (atomic weight)
• Weighted average mass in atomic mass units (amu) of
an element’s naturally occurring isotopes
1.2 Atomic Structure: Orbitals
Quantum Mechanical Model
• Behavior of a specific electron in an atom described
by mathematical expression called a wave equation
• Wave equation is similar to mathematical expression
used to describe motion of waves in fluids
• Solution of wave equation is called a wave function

• Wave function is an orbital

• Orbital denoted by Greek letter psi, 
• Plot of  2 describes volume of space around
nucleus that the electron is most likely to occupy
• Electron cloud has no sharp boundary
Atomic Structure: Orbitals
Four different kinds of orbitals for electrons
• 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

• four cloverleaf-shaped and one dumbbell-doughnut

Atomic Structure: Orbitals
Orbitals are occupied by zero, one, or two electrons and are
grouped in electron shells of increasing size and energy
Electron Shell
• A group of an atom’s electrons with the same principal quantum number
• First shell contains one s orbital, denoted 1s, which holds only two
electrons
• Second shell contains four orbitals, one s orbital (2s) and three p orbitals
(2p), which hold a total of eight electrons
• Third shell contains nine orbitals, one s orbital (3s), three p orbitals (3p),
and five d orbitals (3d), which hold a total of 18 electrons
Atomic Structure: Orbitals
p Orbital
• In each shell, beginning with the second, there are three mutually
perpendicular p orbitals, px, py, and pz, of equal energy
• Lobes of p orbitals are separated by region of zero electron density, a
node
• Each lobe has a different algebraic sign, + and -, represented by
different colors
• Algebraic signs are not charges
1.3 Atomic Structure: Electron Configuration

Ground-state electron configuration

• Most stable, lowest-energy electron configuration of an atom
Three rules:
1. Aufbau principle
• Lowest-energy orbitals fill first: 1s  2s  2p  3s  3p  4s 
3d
2. Pauli Exclusion Principle
• Electron spin can have only two orientations, up  and down 
• Only two electrons can occupy an orbital, and they must be of
opposite spin to have unique wave equations
Atomic Structure: Electron Configuration
3. Hund's rule
• If two or more empty orbitals of equal energy are available,
electrons occupy each orbital with parallel spins until all
orbitals have one electron
1.4 Development of Chemical Bonding
Theory
• 1858 - August Kekulé and Archibald Couper independently proposed
that carbon is tetravalent (always forms four bonds)
• Emil Erlenmeyer proposed a carbon-carbon triple bond for acetylene
• Alexander Crum Brown proposed a carbon-carbon double bond
• 1865 - Kekulé suggested that carbon chains can double back to form
rings of atoms
• 1874 - Jacobus van’t Hoff and Joseph Le Bel proposed four atoms to
which carbon is bonded sit at the corner of a regular tetrahedron
Development of Chemical Bonding Theory
Atoms bond because the compound that results is more stable
and lower in energy than the separate atoms
• Energy is released from the chemical system when a bond
forms
• Energy is consumed by the system when a bond breaks
Valence shell
• Outer most electron shell of an atom
• Eight electrons in valence shell (an electron octet) impart
special stability to noble-gas elements in 8A
• Ne (2 + 8); Ar (2 + 8 + 8); Kr (2 + 8 + 18 + 8)
• Chemistry of main group elements governed by their tendency
to take on electron configuration of the nearest noble gas
Development of Chemical Bonding Theory
Ionic compounds
• Some elements achieve an octet configuration by gaining or losing
electrons
• Ions form when an electron is gained or lost from a neutral atom
• Ions are charged because they have different numbers of protons and
electrons
• Ions are held together by an electrostatic attraction, like in Na + Cl-,
forming an ionic bond

Covalent compounds
• Covalent Bond
• Bond formed by sharing electrons between atoms
• Molecule
• Neutral collection of atoms held together by covalent bonds
• Carbon achieves an octet configuration by sharing electrons
Development of Chemical Bonding Theory
Lewis structures (electron-dot structures)
• Dot representations of covalent bonds in molecules
• Valence shell electrons of an atom are represented as dots

Kekulé structures (line-bond structures)

• Two-electron covalent bond is represented by a line
Development of Chemical Bonding Theory

Number of covalent bonds depends on how many additional

valence electrons needed to reach noble-gas configuration
• H (1s) needs one more electron to attain (1s2) and forms one bond
• N (2s22p3) needs three more electrons to attain (2s22p6) and forms
three bonds

Lone-pair electrons
• Valence-shell electron pairs not used for bonding
1.5 The Nature of Chemical Bonds: Valence
Bond Theory
Valence bond theory
• Bonding theory that describes a
covalent bond as resulting from the
overlap of two atomic orbitals
• Electrons are paired in overlapping
orbitals and are attracted to nuclei of
both atoms, thus bonding the two
atoms together
• H–H bond results from the overlap of
two singly occupied hydrogen 1s
orbitals
• H-H bond is cylindrically symmetrical
• Bonds formed by head-on overlap of
two atomic orbitals along a line drawn
between the nuclei are sigma ()
bonds
The Nature of Chemical Bonds: Valence
Bond Theory
Bond strength
• H2 molecule has 436 kJ/mol less energy than the starting 2
H• atoms, the product is more stable than the reactant
and the H-H bond has a strength of 436 kJ/mol
• Conversely, the bond dissociation energy of H2 is 436 kJ/mol
because it requires 436 kJ/mol of energy to break the H 2
bond
The Nature of Chemical Bonds: Valence
Bond Theory
There is an optimum distance between nuclei that leads to
maximum stability called the bond length

Bond length
• The distance between nuclei
at the minimum energy point
• Because a covalent bond is
dynamic, like a spring, the
characteristic bond length is
the equilibrium distance
between the nuclei of two
atoms that are bonded to
each other
1.6 sp3 Hybrid Orbitals and the Structure
of Methane
Carbon has four valence electrons (2s22p2) that form four
bonds
Methane CH4
• All four carbon-hydrogen bonds in methane are identical and are
spatially oriented toward the corners of a regular tetrahedron

sp3 hybrid orbitals

• A hybrid orbital derived from the combination of an s atomic orbital with
three p atomic orbitals
• Linus Pauling (1931) showed mathematically how s orbitals and p
orbitals on an atom can combine, hybridize, to form four equivalent
atomic orbitals with tetrahedral orientation called sp3 hybrids
sp3 Hybrid Orbitals and the Structure of
Methane
Two lobes of a p orbital have different algebraic signs (+ and -)
in corresponding wave functions
• When a p orbital hybridizes with an s orbital
• Positive p lobe adds to s orbital generating larger lobe of sp3 hybrid
• Negative p lobe subtracts from s orbital generating smaller lobe of
sp3 hybrid
• Resulting asymmetrical sp3 hybrid is strongly oriented in one
direction
• Larger lobe of sp3 hybrid can overlap more effectively with an orbital
from another atom forming much stronger bonds than s or p orbitals
sp3 Hybrid Orbitals and the Structure of
Methane
When each of the four identical sp3 hybrid orbitals of carbon
overlaps with the 1s orbital of a hydrogen atom, four
identical C-H bonds are formed and methane results
• Each C-H bond in methane has a strength of 436 kJ/mol and a length of
109 pm
• The four C-H bonds of methane have a specific geometry
• The angle formed between two adjacent bonds describes a
characteristic bond angle
1.7 sp3 Hybrid Orbitals and the Structure
of Ethane
Orbital hybridization accounts for the bonding together of carbon
atoms into chains and rings

Ethane C2H6
• Tetrahedral
• Bond angles are near 109.5º
• Carbon-carbon single bond
• Formed by  overlap of sp3
hybrids from each carbon
• The remaining sp3 hybrids of
each carbon overlap with 1s
orbitals of three hydrogen
atoms to form six carbon-
hydrogen bonds
1.8 sp2 Hybrid Orbitals and the Structure
of Ethylene
Ethylene C2H4
• Carbon-carbon double bond
• Four shared electrons
• Planar (flat)
• Bond angles 120º

sp2 hybrid orbitals

• A hybrid orbital derived by
combination of an s atomic
orbital with two 2p atomic
orbitals
• One p orbital remains non-
hybridized
sp2 Hybrid Orbitals and the Structure of
Ethylene
Bonding in Ethylene
•  bond in ethylene formed by head-on overlap of two sp2 hybrid
orbitals
• Two non-hybridized 2p orbitals overlap sideways forming a 
bond
• Carbon-carbon double bond is shorter and stronger than carbon-
carbon single bond
1.9 sp Hybrid Orbitals and the Structure
of Acetylene
Acetylene C2H2
• Linear
• Carbon-carbon triple bond
• Six shared electrons
• Bond angles are 180º

sp hybrid orbital
• A hybrid orbital derived from
the combination of one s and
one p atomic orbital
• The two sp hybrids are
separated by an angle of 180º
• Two 2p orbitals remain non-
hybridized
sp Hybrid Orbitals and the Structure of
Acetylene
1.10 Hybridization of Nitrogen, Oxygen,
Phosphorus, and Sulfur
Elements other than carbon form covalent bonds using hybrid
orbitals
Nitrogen
• Methylamine CH3NH2
• Organic derivative of ammonia and the substance responsible for the
odor of rotting fish
• Bond angles are close to the 109.5º tetrahedral angle found in
methane
• Nitrogen hybridizes to form four sp3 orbitals
• One of the four sp3 orbitals is occupied by two nonbonding

electrons
Hybridization of Nitrogen, Oxygen,
Phosphorus, and Sulfur
Oxygen
• Methanol CH3OH
• Methyl alcohol
• Bonds are close to the109.5º tetrahedral angle
• Two of the four sp3 hybrid orbitals on oxygen are occupied by
nonbonding electron lone pairs
Hybridization of Nitrogen, Oxygen,
Phosphorus, and Sulfur
Phosphorus
• Most commonly encountered in biological molecules in
organophosphates
• compounds that contain a phosphorus atom bonded to four oxygens
with one of the oxygens also bonded to carbon
• Methyl phosphate CH3OPO32-
• sp3 hybrid orbitals on phosphorus
Hybridization of Nitrogen, Oxygen,
Phosphorus, and Sulfur
Sulfur
• Commonly encountered in biological molecules
• Thiols
• Have a sulfur atom bonded to one hydrogen and one

carbon
• Sulfides
• Have a sulfur atom bonded to

two carbons
• Methanethiol CH3SH
• Produced by some bacteria
• Simplest example of a thiol
• sp3 hybridization
• Dimethyl Sulfide (CH3)2S
• Simplest example of a sulfide
• sp3 hybridization
1.11 The Nature of Chemical Bonds:
Molecular Orbital Theory
Molecular Orbital Theory (MO)
• A description of covalent bond formation as resulting from a
mathematical combination of atomic orbitals (wave functions) to
form molecular orbitals
• Additive combination of two 1s orbitals
• Leads to formation of a low energy  bonding MO
Egg shaped
•

• Subtractive combination of two 1s orbitals

• Leads to formation of a high energy * antibonding MO
• Elongated dumbbell shaped with a node between the nuclei

MO diagram
for molecular
hydrogen
The Nature of Chemical Bonds: Molecular
Orbital Theory
• Additive combination of two 2p orbitals
• Leads to formation of a low energy  bonding MO
• The  bonding MO is formed by combining p orbital lobes with the same
algebraic sign
• No node between nuclei
• Subtractive combination of two 2p orbitals
• Leads to formation of a high energy * antibonding MO
• The * antibonding MO is formed by combining p orbital lobes with different
algebraic signs
• Node between nuclei
• Only the bonding  MO is occupied in ethylene

MO diagram
of C-C  bond
in ethylene
1.12 Drawing Chemical Structures
Condensed Structures
• A shorthand way of writing structures in which carbon-
hydrogen and carbon-carbon bonds are understood rather
than explicitly shown
• 2-Methylbutane
Drawing Chemical Structures
Skeletal Structure (Line-Bond Structure)
• A shorthand way of writing structures in which carbon atoms
are assumed to be at each intersection of two lines (bonds)
and at the end of each line
Three rules:
1. Carbon atoms not usually
shown, they are assumed
2. Hydrogen atoms bonded
to carbon are assumed
3. Atoms other than carbon
and hydrogen are shown

Note: Sometimes the writing order of

atoms is inverted to make bonding
connections clearer
Drawing Chemical Structures
Thanks for your attention!
Worked Example 1.1
Predicting the Number of Bonds to Atoms in a
Molecule
How many hydrogen atoms does phosphorus bond to
in phosphine, PH??
Worked Example 1.1
Predicting the Number of Bonds to Atoms in a
Molecule
Strategy
• Identify the periodic group of phosphorus, and tell
from that how many electrons (bonds) are needed
to make an octet.
Worked Example 1.1
Predicting the Number of Bonds to Atoms in a
Molecule
Solution
• Phosphorus, like nitrogen, is in group 5A of the
periodic table and has five valence electrons. It
thus needs to share three more electrons to make
an octet and therefore bonds to three hydrogen
atoms, giving PH3.
Worked Example 1.2
Predicting the Structures of Simple Molecules
from Their Formulas
Commonly used in biology as a tissue preservative,
formaldehyde, CH2O, contains a carbon-oxygen
double bond. Draw the line-bond structure of
formaldehyde, and indicate the hybridization of the
carbon atom.
Worked Example 1.2
Predicting the Structures of Simple Molecules
from Their Formulas
Strategy
• We know that hydrogen forms one covalent bond,
carbon forms four, and oxygen forms two. Trial and
error, combined with intuition, is needed to fit the
atoms together.
Worked Example 1.2
Predicting the Structures of Simple Molecules
from Their Formulas
Solution
• There is only one way that two hydrogens, one carbon, and
one oxygen can combine

• Like the carbon atoms in ethylene, the carbon atom in

formaldehyde is sp2-hybridized
Worked Example 1.3
Interpreting Line-Bond Structures
Carvone, a substance responsible for the odor of spearmint,
had the following structure. Tell how many hydrogens are
bonded to each carbon, and give the molecular formula of
carvone.
Worked Example 1.3
Interpreting Line-Bond Structures
Strategy
• The end of a line represents a carbon atom with 3
hydrogens, CH3
• A two-way intersection is a carbon atom with 2
hydrogens, CH2
• A three-way intersection is a carbon atom with 1
hydrogen, CH
• A four-way intersection is a carbon atom with no
attached hydrogens
Worked Example 1.3
Interpreting Line-Bond Structures
Solution