Transcript M2_3

Unit 3
How do we predict properties?
The central goal of this unit is to help you develop
ways of thinking that can be used to
predict the physical properties of chemical
compounds based on their submicroscopic structure.
Chemistry XXI
M1. Analyzing Molecular Structure
Predicting properties based
on molecular structure .
M2. Considering Conformations
Predicting properties based
on spatial conformations.
M3. Characterizing Ionic Networks
Predicting properties based
on ion charge and size.
M4. Exploring Electronic Structure
Predicting properties based on
electron-configurations.
Unit 3
How do we predict properties?
Chemistry XXI
Module 2:
Considering
Conformations
Central goal:
To explain and predict the
physical properties of
macromolecular compounds
based on nature and
strength of the interactions
between different parts of a
molecule, or between
different molecules.
The Challenge
Modeling
How do I explain it?
Chemistry XXI
Large molecules (macromolecules) have properties
that depend on how their different geometric centers
orient with respect to each other in space. A small
change in this conformation may alter the properties or
vital function that the molecule has.
The specific conformations
that molecules adopt
depend on intra and
intermolecular interactions.
How can we explain and predict the conformation that
these macromolecules have?
Dynamic Structures
Chemistry XXI
Molecules are dynamic
structures that are in
constant movement even in
solid systems.
For molecules with more
than one geometric center,
this movement may allow
them to take different
conformations.
Click
The most stable conformations are determined by
the nature of the interactions within the molecule
and between the molecule and its surroundings.
Conformational
Analysis
Let’s consider the molecule
of ethane C2H6.
Chemistry XXI
How do you explain the
variations in Ep? Which
conformation is most stable?
Staggered
(stable)
More likely
Less likely,
but possible
Eclipsed
(unstable)
Steric Effects
Chemistry XXI
When atoms in a molecule get too close together
as parts of the molecule vibrate or rotate, electric
repulsions between electrons may hinder some
conformations and favor others
(Steric effects).
Steric effects lead to
conformations in
which repulsions are
minimized; this lowers
the potential energy of
the molecule
(more stable).
Let’s Think
Chemistry XXI
Which of these
conformations
of “butane”
(C4H10) is the
most stable?
Draw an schematic
representation of the most
stable conformation of
“isooctane” (C8H18).
Macromolecules
Chemistry XXI
Conformational analysis is of central importance
in explaining and predicting the properties and
function of molecules with hundreds of atoms,
such as synthetic and natural polymers.
For example, the main
macromolecules in our
body, nucleic acids and
proteins, are large
molecular chains that
adopt very specific
structures which
determine their function.
DNA
Myoglobin
Chemistry XXI
Polymers
Polymers,
natural or
synthetic,
are
composed
of repeating
structural
units
(monomers)
connected
by covalent
bonds.
Monomer
Polymer
Synthetic Polymers
Length, size (branching), and functionality affect
the conformations that polymer chains can adopt
and how they interact with themselves and other
chains in a given material.
PVC
H
C
N
O
Chemistry XXI
Nylon
Polyethylene
Cl
F
Teflon
Cellulose
Design
Chain length and branching in
polymer synthesis is used to control
properties such as rigidity,
elasticity, and thermo-plasticity.
Chemistry XXI
Let′s think!
In which ways
could the
properties of
these types of
polymeric
materials
differ?
Let’s Think
Chemistry XXI
Changing functionality will alter not only how the
polymer chains interact with themselves, but also
with other materials.
Consider three solid
surfaces made with the
following materials.
Which of them are likely to
be wetted by water (H2O will
stick to them), and which
ones are likely to be
dissolved by water (H2O will
be able to separate the
chains)? What would happen
if we use acetone or hexane?
Let’s Think
Mixing the polymer with other substances is also
a common way to alter and control its properties.
Chemistry XXI
Consider
Polyvinyl alcohol
(PVA)
Predict how the properties
could change when mixing
with a Boric Acid.
Crosslinking
One common way to
alter the properties of a
polymeric materials is
by cross-linking.
IMF
Chemistry XXI
Covalent bonding
It is common to add
molecules that can act as
a binder between
polymer chains, which
tends to increase
strength and rigidity.
Vulcanized Rubber
Proteins
Proteins are natural polymers made by the combination
of smaller molecules called amino acids (monomers).
Amino Acid
Chemistry XXI
Amine
Carboxyl
Peptide
bond
Primary Structure
Every protein has a unique sequence of amino
acids or “primary structure.”
Backbone
Chemistry XXI
Side chain
Backbone and side chain polarities determine the
3D structure that proteins adopt.
Let’s Think
Analyze the “geometry” and “polarity” of the
backbone. Assign partial charges (d+ and d-) to
the different atoms. What types of IMFs can exist
within the backbone itself or with another chain?
Hydrogen Bonding
Chemistry XXI
The stronger interactions are hydrogen bonding in the
same or in different chains.
d-
d+
d+
d-
HYDROGEN BONDING
Although hydrogen bonds are
not “real” bonds and are weaker
than covalent bonds, there are
so many of them within a single
protein that they determine the
3-D structure of these
macromolecules.
Helices and Sheets
Chemistry XXI
H-bonding between regions in the backbone of the
protein chain leads to regions of ordered structures:
secondary structure.
Alpha helix
Beta sheet
Folding
Interactions between elements of the side chain
(residues) cause the protein to “fold” into its final
conformation.
Chemistry XXI
Side chain
Will all the residues
interact with each
other?
Which interactions
are stronger?
Let’s Think
Consider this
“folded” protein.
3
Chemistry XXI
What types of
intermolecular
forces are present
in this system
Arrange these interactions from strongest to weakest
Why do you think the protein is folded in this
particular way?
Similar with Similar
Although there are attractive interactions between
all types of residues (or particles), energy is
minimized when parts, or particles, with interactions
of similar strength are close together.
The residues of
similar types
tend to
“segregate”
from each other.
3
Chemistry XXI
Induced dipole <>
Induced dipole
Ion<>Dipole
Dipole<>Dipole
(H-bond)
Chemistry XXI
Let′s apply!
Assess what you know
Let′s apply!
Solvent Effects
Chemistry XXI
Proteins do not exist isolated in our body.
They are surrounded by water or by lipids in cell
membranes.
Discuss how you would expect this protein to
fold if you immerse it in a) water; b) lipid (oil).
Justify your reasoning.
Let’s Apply
Let’s explore the validity of your predictions:
Go to:
http://www.chem.arizona.edu/chemt/C21/sim
Chemistry XXI
Folding
Explore and explain the effect of changing the solvent and
the type of amino acids on protein folding.
The simulation allows you to change the nature of the
solvent and of each amino acid in the chain:
Charged Polar (Hydrophilic) Non-Polar (Hydrophobic)
Chemistry XXI
Identify one topic of your interest
in which the ideas discussed in
this module are relevant.
Considering Conformations
Summary
Chemistry XXI
Molecules are dynamic structures that are in
constant movement. This movement may allow them
to take different conformations.
The most stable conformations
are determined by the nature of
the interactions between
different parts of the molecule
(intramolecular interactions)
and between the molecule and
its surroundings.
Considering Conformations
Summary
Chemistry XXI
Conformational analysis is of central importance
in explaining and predicting the properties and
function of molecules with hundreds of atoms,
such as synthetic and natural polymers.
Polymers are composed of
repeating structural units
(monomers) connected by
covalent bonds. Composition,
structure, and functionality
affect the conformations that
they adopt.
Nylon
Myoglobin
Chemistry XXI
For next class,
Investigate what types of compounds are
formed when metals react with nonmetals .
In which ways fundamental ways are these
types of compounds different from molecular
compounds?