Unit 2
How do we determine structure?
The central goal of this unit is to help you develop
ways of thinking that can be used to predict the
atomic and molecular structure of substances.
Chemistry XXI
M1. Analyzing Light-Matter Interactions
Using spectroscopy to derive
structural information.
M2. Looking for Patterns
Deducing atom connectivity
based on atomic structure .
M3. Predicting Geometry
Predicting the three dimensional
geometry of molecules.
M4. Inferring Charge Distribution
Analyzing the distribution of
electrons in molecules.
Unit 2
How do we determine
structure?
Module 3:
Chemistry XXI
Predicting
Geometry
Central goal:
To deduce the Lewis
structure of molecules and
predict their three
dimensional geometry
based on the analysis of
the number and type of
valence electron pairs
surrounding each atom.
The Challenge
Modeling
How do I predict it?
The properties of a substance are determined by
the structure of its molecules.
Chemistry XXI
Molecular structure
depends on:
Atomic Composition
Atom Connectivity
Molecular geometry
Aspirin
C 9 H 8 O4
How can we predict molecular geometry given
information about atomic composition and
atom connectivity ?
Electron Distribution
Chemistry XXI
We have seen that when two atoms of
nonmetallic elements combine, their valence
electrons are reorganized. The number of covalent
bonds that are formed are determined by the most
stable electron configurations (full valence shell).
We can use the
octet rule
(or full valence shell rule)
to make predictions
about how electrons will
distribute among the
different atoms in a
molecule.
O2
O
O
O
O
N2
N
N
N
N
Useful Tool:
Lewis Electron-dot
Structures
Lewis Structures
There are some simple rules that facilitate the
creation of Lewis structures. Let’s illustrate them
with the molecule of water H2O.
1. Choose the central atom; never H (it forms only
one bond). The central atom tends to be the one
with the lowest ionization potential.
Chemistry XXI
O is central in this case
2. Count valence electrons:
H = 1 and O = 6
Total = (2 x 1) + 6 = 8 valence electrons
This electrons will organize in 4 pairs
(spin pairing to minimize energy)
Lewis Structures
3. Use as many pairs as needed to form single
bonds between the central atom and the
surrounding atoms.
Chemistry XXI
Each bond line represents
a pair of electrons
4. Use the remaining pairs to
satisfy the full valence shell
rule in each atom as needed.
Start with terminal or
outside atoms, but not if H;
place any leftover electrons
on the central atom.
Lone e- pairs
Bond e- pairs
8 valence e-
Lewis Structures
Let’s consider another case: Carbon dioxide CO2.
1. What is the central atom?
2. How many valence e-? How many pairs?
4 + 2 x 6 = 16 valence e-  8 e- pairs
Chemistry XXI
3. What is the backbone?
4. How do we distribute the e- pairs left?
5. How do we satisfy the octet rule for all atoms?
Form double
bonds
Let’s Think
A variety of substances contribute to indoor air
pollution. Among the most common we find:
Chemistry XXI
Build the Lewis
structures of the
following
greenhouse gases:
CH4, CO ,NH3, CH2O
1.
2.
3.
4.
5.
STRATEGY
What is the central atom?
How many valence e-?
How many pairs?
What is the backbone?
How do we distribute the e- pairs left?
How do we satisfy the octet rule for all atoms?
Interesting Cases
For some molecules, the derivation of their actual
Lewis structure is not so straightforward.
Consider for example the ozone molecule, O3,
which plays a central role in our atmosphere.
Chemistry XXI
Experimental data indicates that both bonds in the O3
molecule have the same length, but the value is
intermediate between those of single and double bonds.
Bond Length (pm)
O O
O3
O O
148
127.8
121
How do we
explain it?
Let’s Think
Chemistry XXI
Build the Lewis
structure of O3.
This molecule
illustrates a structural
feature that we need
to take into account
when deciding how to
distribute electrons
among atoms in a
molecule.
What is it?
Molecular Hybrids
The structure is a hybrid of:
Resonance Structures
Chemistry XXI
3 e- pairs / 2 bonds
Intermediate
between single and
double
Resonance structures are drawn when a single
Lewis structure cannot represent the actual
electron distribution in a molecule.
Resonance
In molecules that exhibit resonance the electrons
are “delocalized” over the entire system.
This delocalization tends to stabilize the molecule
(reduces its potential energy).
Chemistry XXI
Benzene C6H6
Resonance
Hybrid
Let’s Think
Which of these
pollutants exhibits
resonance stabilization?
Chemistry XXI
How many resonance
structures do they have?
SO3
CH2O
Electron Repulsion
Once the Lewis structure of a molecule is derived,
its geometry can be predicted applying a
simple principle:
Chemistry XXI
Regions of high electron density around any
single atom will be located as far as possible due
to electron repulsions.
Valence Shell Electron Pair Repulsion (VSEPR)
Theory
Minimizing repulsions allows us to find
the most stable shape (lower energy).
Let’s Think
Consider the following Lewis structures for
these molecules in our atmosphere:
Cl
Chemistry XXI
How many regions of
high electron density
do you identify
around each central
atom?
How will these
regions be located in
space due to electron
repulsions?
F
F
Cl
Molecular Geometry
# eregions
2
Example
e- pair
geometry
Molecular
geometry
Linear
(180o)
Linear
3
Trigonal
Planar
(~120o)
Chemistry XXI
118o
Trigonal planar
3
Trigonal
Planar
(< 120o)
Bent or Angular
Molecular Geometry
# eregions
Example
4
Cl
F
F
e- pair
geometry
Molecular
geometry
Tetrahedral
(109o)
Cl
4
Tetrahedral
Tetrahedral
(< 109o)
N
H
H
Chemistry XXI
lone pair of electrons
in tetrahedral position
H
4
107.8o
Trigonal Pyramid
Tetrahedral
(< 109o)
O
H
H
104.5o
Bent or Angular
Let’s Think
Apply VSEPR theory to derive the molecular
geometry of the following atmospheric molecules:
SO2, SO3, CH4, N2O
Estimate the bond angles in these molecules.
STEP 1
Chemistry XXI
Follow
the
sequence
STEP 2
STEP 3
Larger Molecules
The same ideas can be applied to deduce the
molecular geometry of larger molecules. The task
is simplified by recognizing the following patterns
for some of the most common central atoms:
C
Tetrahedral
Chemistry XXI
4 bond pairs, 0 lone pairs
Trigonal
planar
C
Linear
3 bond pairs, 1 lone pair
N
Trigonal
Pyramid
N
Trigonal
planar
2 bond pairs, 2 lone pairs
O
Bent
Larger Molecules
Consider the molecule of ethanol C2H6O:
109o
Bent
The molecule has three
main “centers”:
Chemistry XXI
Tetrahedral
The overall
geometry is
determined by the
geometry around
each of these
centers.
~105o
Let’s Think
Consider the molecule of acetone C3H6O:
How many centers
are in this molecule?
Chemistry XXI
What is the geometry
around each of these
centers?
What bond angle
characterizes each
center?
Chemistry XXI
Let′s apply!
Assess what you know
Functionality
Chemistry XXI
A central idea in chemistry is that the chemical
properties of many molecules are determined by
the presence of “distinctive arrangements of
atoms” that tend to behave as a single chemical
entity during a reaction.
This distinctive
arrangements of atoms are
called “functional groups”
and their properties are
determined by their atomic
composition, connectivity
and geometry.
R
Hydroxyl group
Let′s apply!
Functional Groups
Determine the geometry around the atomic centers
of the following “functional groups”:
Chemical
Class
Functional
group
Structural formula
Alcohol
hydroxyl
R
Ketone
R2
carbonyl
Chemistry XXI
R1
Carboxylic
acid
carboxyl
Amine
Primary
amine
R
Aromatic
phenyl
R
R
Molecular
geometry
Let′s apply!
Predict
Phenylalanine is an essential aminoacid needed by
our body to biochemically synthesize a wide
variety of proteins
1
Chemistry XXI
H
What functional
groups are
present in this
molecule?
C
H
H
C
C
C
C
H
C
H
H 2 H
O
3
C
C
C
O
H
N
H
4
H
5
Estimate the value of the marked bond angles and
make an sketch of the geometry of this molecule.
H
Chemistry XXI
Summarize in once sentence the
basic principle that determines
molecular geometry.
Predicting Geometry
Summary
The octet rule can be used to deduce the distribution
of valence electrons among the different atoms in a
molecule.
Chemistry XXI
Lone e- pairs
The distribution of
electrons is
represented through
the Lewis structure
of the molecule.
Bond e- pairs
8 valence e-
Predicting Geometry
Summary
Chemistry XXI
Once the Lewis structure of a molecule is
derived, its geometry can be predicted applying
a simple principle: Regions of high electron
density around any single atom will be located
as far as possible due to electron repulsions
(VSEPR Theory).
We can deduce the entire
molecular geometry of a complex
molecule by analyzing the
electron pair distribution around
each of its atoms.
Chemistry XXI
For next class,
Investigate how molecular composition and
geometry affect the distribution of electrons
within a molecule.
What is the difference between a polar and a
non-polar molecule?