Structure and

Bonding
Organic Chemistry
“Organic” – until mid 1800’s referred to compounds from
living sources (mineral sources were “inorganic”)
Wöhler in 1828 showed that urea, an organic compound,
could be made from a minerals
Today, organic compounds are those based on carbon
structures and organic chemistry studies their structures
and reactions
◦ Includes biological molecules, drugs, solvents, dyes
◦ Does not include metal salts and materials (inorganic)
◦ Does not include materials of large repeating molecules
without sequences (polymers)

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Atomic Structure

Structure of an atom
◦ Positively charged nucleus (very dense, protons and neutrons) and
smal (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
angstrom (Å) is 10-10 m = 100 pm]

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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

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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

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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 chemistry
s orbitals: spherical, nucleus at center
p orbitals: dumbbell-shaped, nucleus at middle

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Orbitals and Shells
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
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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Atomic Structure: Electron
Configurations
Ground-state electron configuration 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. 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).

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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

Note that a dashed line

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The Nature of the Chemical Bond
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 shown valence electrons of an atom as dots
◦ Hydrogen has one dot, representing its 1s electron
◦ Carbon has four dots (2s2 2p2)

Stable molecule results at completed shell, octet (eight dots) for

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Number of Covalent Bonds to an
Atom
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

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Valences of Carbon
Carbon has four valence electrons (2s2 2p2), forming four
bonds (CH4)

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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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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
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

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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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Hybridization: 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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Tetrahedral Structure of
Methane
sp3 orbitals on C overlap with 1s orbitals on 4 H atom to form
four identical C-H bonds
Each C–H bond has a strength of 438 kJ/mol and length of
110 pm
Bond angle: each H–C–H is 109.5°, the tetrahedral angle.

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Hybridization: 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 420 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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Hybridization: sp2 Orbitals and the
Structure of Ethylene
sp2 hybrid orbitals: 2s orbital combines with two 2p orbitals,
giving 3 orbitals (spp = sp2)
sp2 orbitals are in a plane with120° angles
Remaining p orbital is perpendicular to the plane

120
90

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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

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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 133 pm (C–C 154 pm)

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Hybridization: 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  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  bonds with hydrogens

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MCMURRY ORGANIC CHEMISTRY 6TH EDITION CHAPTER 1 (C) 2003 27