John E.

McMurry

http://www.cengage.com/chemistry/mcmurry

Chapter 1
Structure and Bonding

Javier E. Horta, M.D., Ph.D. University of Massachusetts Lowell

Organic Chemistry
Scientific advances in medicine and biology require an understanding of
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
mevalonate 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 ()
-10 m = 100 pm ; 1 pm = 10-12 m
1 = 10
Atomic diameter in SI units is 2 10-10 m (200 picometers (pm))

Atomic Structure: Orbitals

Important kinds of orbitals in Organic Chemistry

Atomic Structure: Orbitals

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

Atomic Structure: Electron Configuration

1.4 Development of Chemical Bonding

Theory

1858 - August Kekul 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 - Kekul suggested that carbon chains can double back to form
rings of atoms
1874 - Jacobus vant 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

Chemistry of main group elements governed by their tendency to
take on electron configuration of the nearest noble gas (i.e., 8 e-)

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

Molecular compounds
Achieve their octet by sharing electrons between atoms via
covalent bonds
Most organic compounds are molecular compounds

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

Kekul 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

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.

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

HH 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

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

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 the same strength and length
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 109.5
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 carbonhydrogen bonds

1.8 sp2 Hybrid Orbitals and the Structure

of Ethylene
Ethylene C2H4
Carbon-carbon double bond

Four shared electrons

Planar (flat)
Bond angles 120

sp2 hybrid orbitals

A hybrid orbital derived by
combination of an s atomic
orbital with two 2p atomic
orbitals
One p orbital remains nonhybridized

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 carboncarbon single bond

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
Solution
There is only one way that two hydrogens, one carbon, and
one oxygen can combine

Like the carbon atoms in ethylene, the carbon and oxygen

atoms in formaldehyde are sp2-hybridized

1.9 sp Hybrid Orbitals and the Structure

of Acetylene
Acetylene (HCCH)
Linear
Carbon-carbon triple bond

Six shared electrons

Bond angles are 180

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 180
Two 2p orbitals remain nonhybridized

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 109.5 tetrahedral angle found in
methane
Nitrogen hybridizes to form four sp3 orbitals
3
One of the four sp orbitals is occupied by two nonbonding
electrons

Hybridization of Nitrogen, Oxygen,

Phosphorus, and Sulfur
Oxygen
Methanol CH3OH

Methyl alcohol
Bonds are close to the109.5 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

1.12 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

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