STRUCTURE AND BONDING

Based on McMurry’s Organic Chemistry, 6th edition, Chapter 1

©2003 Ronald Kluger | Department of Chemistry | University of Toronto

Organic
OrganicChemistry
Chemistry Atomic Number and Atomic Mass

• “Organic” – until mid1800’s referred to • The atomic number (Z) is the

compounds from living sources number of protons in the atom's
(mineral sources were “inorganic”)
nucleus
• Wöhler in 1828 showed that urea, an
organic compound, could be made
• The mass number (A) is the
from a minerals number of protons plus neutrons
• Today, organic compounds are those • All the atoms of a given element
based on carbon structures and have the same atomic number
organic chemistry studies their • Isotopes are atoms of the same
structures and reactions element that have different
- Includes biological molecules, numbers of neutrons and
drugs, solvents, dyes therefore different mass numbers
- Does not include metal salts • The atomic mass (atomic weight)
and materials (inorganic)
of an element is the weighted
- Does not include materials of average mass in atomic mass
large repeating molecules
units (amu) of an element’s
without sequences (polymers)
naturally occurring isotopes
1.1
1.1Atomic
AtomicStructure
Structure
1.2 Atomic Structure: Orbitals
• Structure of an atom
Positively charged nucleus (very
- • Quantum mechanics: describes
dense, protons and neutrons) electron energies and locations
and smal (10-15 m) by a wave equation
- Negatively charged electrons are - Wave function solution of
in a cloud (10-10 m) around wave equation
nucleus
- Each Wave function is an
• Diameter is about 2  10-10 m (200
orbital,
picometers (pm)) [the unit
• A plot of 2 describes where
angstrom (Å) is 10-10 m = 100 pm]
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

1 | McMurry Organic Chemistry 6th edition Chapter 1 (c) 2003

 • s and p orbitals most important in • Lobes of a p orbital are
organic chemistry separated by region of zero
• s orbitals: spherical, nucleus at electron density, a node
center
• p orbitals: dumbbell-shaped, 1.3 Atomic Structure: Electron
• nucleus at middle 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)
Orbitals and Shells
2. Electron spin can have
• Orbitals are grouped in shells of
only two orientations, up  and
increasing size and energy
down . Only two electrons can
• Different shells contain different occupy an orbital, and they must
numbers and kinds of orbitals be of opposite spin (Pauli
• Each orbital can be occupied by exclusion principle) to have
two electrons unique wave equations
• First shell contains one s orbital,
denoted 1s, holds only two 3. If two or more empty
electrons orbitals of equal energy are
• Second shell contains one s available, electrons occupy
orbital (2s) and three p orbitals each with spins parallel until all
(2p), eight electrons orbitals have one electron
• Third shell contains an s orbital (Hund's rule).
(3s), three p orbitals (3p), and five
1.4 Development of Chemical
d orbitals (3d), 18 electrons
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
p-Orbitals
Note that a dashed line
• In each shell there are three indicates a bond is
perpendicular p orbitals, px, py, behind the page
and pz, of equal energy
Note that a wedge indicates
a bond is coming forward
2 | McMurry Organic Chemistry 6th edition Chapter 1 (c) 2003
 1.5 The Nature of the Chemical Bond Valences of Oxygen

• Atoms form bonds because the • Oxygen has six valence electrons
compound that results is more (2s2 2p4) but forms two bonds
stable than the separate atoms (H2O)
• 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
Valences of Nitrogen
completed shell, octet (eight
dots) for main-group atoms (two • Nitrogen has five valence
for hydrogen) electrons (2s2 2p3) but forms only
three bonds (NH3)
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 Non-bonding electrons
they need electrons to fill the s
and p levels of their valence • Valence electrons not used in
shells to reach a stable octet bonding are called nonbonding
electrons, or lone-pair electrons
sssValences of Carbon - Nitrogen atom in ammonia
(NH3)
• Carbon has four valence − Shares six valence
electrons (2s2 2p2), forming four electrons in three
bonds (CH4) covalent bonds and
remaining two
valence electrons are
nonbonding lone pair

3 | McMurry Organic Chemistry 6th edition Chapter 1 (c) 2003

 1.6 Valence Bond Theory 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

• 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 1.7 Hybridization: sp3 Orbitals and the
attracted to nuclei of both atoms Structure of Methane
- H–H bond results from the
overlap of two singly ◼ Carbon has 4 valence electrons
occupied hydrogen 1s (2s2 2p2)
orbitals ◼ In CH4, all C–H bonds are
- H-H bond is cylindrically identical (tetrahedral)
symmetrical, sigma ( ) ◼ sp3 hybrid orbitals: s orbital and
bond three p orbitals combine to form
Bond Energy four equivalent, unsymmetrical,
tetrahedral orbitals (sppp = sp3),
◼ Reaction 2 H· → H2 releases 436 Pauling (1931)
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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 Tetrahedral Structure of Methane • 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

1.9 Hybridization: sp2 Orbitals and the

• sp3 orbitals on C overlap with 1s
Structure of Ethylene
orbitals on 4 H atom to form four
identical C-H bonds • sp2 hybrid orbitals: 2s orbital
• Each C–H bond has a strength of combines with two 2p orbitals,
438 kJ/mol and length of 110 pm giving 3 orbitals (spp = sp2)
• Bond angle: each H–C–H is • sp2 orbitals are in a plane
109.5°, the tetrahedral angle. with120° angles
• Remaining p orbital is
perpendicular to the plane

90 120

1.8 Hybridization: sp3 Orbitals and the

Structure of Ethane

Bonds From sp2 Hybrid Orbitals

• Two sp2-hybridized orbitals

overlap to form a s bond
• p orbitals overlap side-to-side to
formation a pi () bond
• sp2–sp2 s bond and 2p–2p  bond
result in sharing four electrons
and formation of C-C double
bond
• Electrons in the s bond are
• Two C’s bond to each other by s centered between nuclei
overlap of a sp3 orbital from each • Electrons in the  bond occupy
regions are on either side of a line
between nuclei

5 | McMurry Organic Chemistry 6th edition Chapter 1 (c) 2003

 Structure of Ethylene - 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 s bond
• pz orbitals from each C form a
• H atoms form s bonds with four
pz–pz  bond by sideways overlap
sp2 orbitals
and py orbitals overlap similarly
• 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)
Bonding in Acetylene

1.10 Hybridization: sp Orbitals and the • Sharing of six electrons forms C ºC

Structure of Acetylene • Two sp orbitals form s bonds with
hydrogens

1.11 Hybridization of Nitrogen and

Oxygen

• C-C a triple bond sharing six

electrons
• Carbon 2s orbital hybridizes with
a single p orbital giving two sp
hybrids

6 | McMurry Organic Chemistry 6th edition Chapter 1 (c) 2003

 • Elements other than C can have found (specific energy and
hybridized orbitals general shape) in a molecule
• H–N–H bond angle in ammonia • Additive combination (bonding)
(NH3) 107.3° MO is lower in energy
• N’s orbitals (sppp) hybridize to • Subtractive combination
form four sp3 orbitals (antibonding) forms MO is higher
• One sp3 orbital is occupied by
two nonbonding electrons, and Molecular Orbitals in Ethylene
three sp3 orbitals have one
electron each, forming bonds to • The  bonding MO is from
H combining p orbital lobes with
the same algebraic sign
Hybridization of Oxygen in Water • The  antibonding MO is from
combining lobes with opposite
• The oxygen atom is sp3-hybridized signs
• Oxygen has six valence-shell • Only bonding MO is occupied
electrons but forms only two
covalent bonds, leaving two lone
pairs
• The H–O–H bond angle is 104.5°

1.12 Molecular Orbital Theory

• A molecular orbital (MO): where

electrons are most likely to be

7 | McMurry Organic Chemistry 6th edition Chapter 1 (c) 2003

 SUMMARY
• Organic chemistry – chemistry of carbon compounds
• Atom: positively charged nucleus 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
• Sigma (s) 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

NOTES:
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8 | McMurry Organic Chemistry 6th edition Chapter 1 (c) 2003