John E.
McMurry
Chapter 1
Structure and Bonding
Paul D. Adams • University of Arkansas
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: small diameter (2 10-10 m = 200 pm)
Nucleus very dense
protons (positively charged)
neutrons (neutral)
small (10-15 m)
Electrons
negatively charged
located in space remindful of a cloud (10-10 m) around nucleus
[ångström (Å) is 10-10 m = 100 pm]
Atomic Number
and Atomic Mass
The atomic number (Z): number of protons in nucleus
The mass number (A): number of protons plus neutrons
All atoms of same element have the same Z value
Isotopes: atoms of the same element with different
numbers of neutrons and thus different A
The atomic mass (atomic weight) of an element is
weighted average mass in atomic mass units (amu) of
an element’s naturally occurring isotopes.
Carbon:
(98.9 12.000)
(1.113.000) 12.011
100
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
1.3 Atomic Structure: Electron
Configurations
Ground-state electron configuration (i.e.,
lowest energy arrangement) of 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)
1.3 Atomic Structure: Electron
Configurations
Ground-state electron configuration (i.e.,
lowest energy arrangement) of atom
lists orbitals occupied by its electrons.
Rules:
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
1.3 Atomic Structure:
Electron Configurations
Ground-state electron configuration (i.e.,
lowest energy arrangement) of atom
lists orbitals occupied by its electrons.
Rules:
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).
To the chalkboard (p-orbital filling as example)
1.4 Development of
Chemical Bonding Theory
Atoms form bonds because the resulting compound is
more stable than the separate atoms
Ionic bonds in salts form by 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) due to 4 e- in valence shell
Kekulé structures (line-bond structures) have a line drawn between two atoms
indicating a 2 e- 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.
valence e- valence e-
Development of Chemical
Bonding Theory
Atoms with four or more valence electrons form as
many bonds as electrons needed 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).
valence e-
Development of Chemical
Bonding Theory
Nitrogen has five valence electrons (2s2 2p3) but forms
only three bonds (NH3).
valence e-
Development of Chemical
Bonding Theory
Oxygen has six valence electrons (2s2 2p4) but forms
two bonds (H2O)
valence e-
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 (NH3)
Shares six valence electrons in three covalent bonds
and remaining two valence electrons are nonbonding
lone pair
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
1.5 Describing Chemical Bonds:
Valence Bond 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
cylindrically symmetrical
Bond Energy
Reaction 2 H· H2 releases 436 kJ/mol
i.e., product has 436 kJ/mol less energy than two atoms:
H–H has bond strength of 436 kJ/mol
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
Describing 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
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: an s orbital and three p orbitals
combine: form four equivalent, unsymmetrical,
tetrahedral orbitals (s + ppp = sp3)
Linus Pauling (1931): his picture near men’s bathroom across from elevators
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 439 kJ/mol and
length of 109 pm
Bond angle: each H–C–H is 109.5°: the tetrahedral
angle.
1.7 sp3 Orbital-based Structure
of Hexane
1.8 sp2 Orbitals and the
Structure of Ethylene
Some Representations of Ethylene are given
To explain planar geometry and trigonal shape about C’s in
ethylene
1.8 sp2 Orbitals and the
Structure of Ethylene
sp2 hybrid orbitals: 2s orbital combines with two 2p
orbitals, giving 3 orbitals (s + pp = 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
Bonds From sp2 Hybrid
Orbitals
Electrons in the bond are centered between nuclei
Electrons in the bond occupy regions are on either
side of a line between nuclei
Structure of Ethylene
H atoms form 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)
1.9 sp Orbitals and the
Structure of Acetylene
Sharing of six electrons forms C C
Two sp orbitals form bonds with hydrogens
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
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.
1.10 Hybridization of Sulfur
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
(Avoided in this Class)
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 Skeletal Structures
(Commonly Used)
General Rules:
1) Carbon atoms aren’t usually shown
Drawing Skeletal Structures
(Commonly Used)
General Rules:
2) Instead a carbon atom is assumed to be at each
intersection of two lines (bonds) and at the end of
each line.
Drawing Skeletal Structures
(Commonly Used)
General Rules:
3) Hydrogen atoms bonded to carbon aren’t shown.
Drawing Skeletal Structures
(Commonly Used)
General Rules:
4) Atoms other than carbon and hydrogen ARE shown
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
