Transcript Lecture 3 - Chemistry at Winthrop University

Interion and Intermolecular
Forces
•Ion-Ion interactions are the strongest interactions
•Example of an ion-ion interaction?
•Let’s look at the various interactions given in the table
Ion-Dipole Interactions
•Best example: Hydrated Ions
•The polar character of the water molecule allows it to
interact with cations or anions
z = ion charge
z  µ = Electric
•We can describe the interaction energy: E p  - 2 dipole moment
r
r = distance
Dipole-Dipole interactions
• Let’s look at the interactions between
polar molecules
The Dipole-Dipole interactions force some order in the
solution
Dipole-Dipole interactions
Dipole-Dipole interaction energy:
Ep  -
12
µ1: Dipole moment of
molecule 1
r3
µ2: Dipole moment of
Molecule 2
The fact that the distance is cubed means that
the energy falls of much more rapidly than ionion interactions as the interacting species are
separated
Which molecule has the higher boiling point:
p-dichlorobenzene and o-dichlorobenzene
Dipole moment for the molecules?
Which molecule has the higher boiling point:
cis-dichloroethene or trans-dichloroethene?
Hydrogen Bonding
• A special type of dipole-dipole
interaction
• Hydrogen bonding only occurs between:
N-H
O-H
and
Lone pair e- on N, O, F
F-H
Hydrogen Bonding
• Hydrogen bonds are one of the most
important interactions in biological
systems
Hydrogen Bonds:
•Hold proteins together
•Allow DNA base pairs
to match up
•Allow structural
polymers to interact
Hydrogen bonds are the
strongest type of non-ionic
intermolecular force
Dipole - Induced Dipole
• The presence of a molecule with a
strong dipole moment can induce or
create a dipole in a non-polar molecule
– This depends on the strength of the dipole
and the polarizability of the nonpolar
molecule
Ep  -
1 2
r6
1: Dipole moment of
molecule 1
2: Polarizability of
molecule 2
London Forces
• London Forces are attractive forces
between non-polar molecules
(all molecules have them, but they are much weaker than other types)
• These are 1 of the two weakest
intermolecular forces
• How do these interactions arise?
London Forces
• The electron clouds are constantly
shifting and sometimes the molecule
gets a small dipole moment
– Neighboring nonpolar molecules will have
their electron clouds distorted and will form
a dipole of opposite orientation
• Then the process starts over (Dipole
disappears and reforms) (1x10-16 sec
to form and disappear)
London Forces
Ep  r6 !!!!
1 2
1: Polarizability of
molecule 1
r6
2: Polarizability of
molecule 2
Very short range effects!!
•What determines Polarizability?
•Large atomic radii
•Low Zeff
•High Polarizability = Large London Interactions
Let’s look at London Forces and Polarizability with
respect to physical properties
As we go down a group, the atomic radius increases and
the melting and Boiling points increase (takes More energy)
London Forces and Molecular Shape
• Because the London Force energy drops off
VERY sharply as a function of distance,
molecular shape is a major contributor to
London Force energy
Which has the higher boiling point?
Thinking about Biology Chemically
•All living organisms
use energy
•Energy comes from
chemical reactions
•The energy stored
in chemical bonds is
harnessed by
proteins to catalyze
other reactions
Functional Groups of Biologically Active
Molecules
•All the
chemistry of life
is performed
using these
chemical
entities
•We’ll go over
these in MUCH
greater detail in
the next lecture
ATP: The Energy Currency of the Cell
Formation of Biomolecules
•How did the vast array of biologically active
molecules come to be?
•Initially, it is thought that only NH3, H2S, CO, CO2,
CH4, N2, H2 and H2O were present on the early Earth
•However, the planet was volcanically active (heat
and pressure) and there was significant electrical
activity in the atmosphere
The Miller-Urey Experiment
•Formaldehyde and
hydrogen cyanide are
usually formed, BUT, after
prolonged reaction, so are
AMINO ACIDS
•The experiment can be
taken a step further and be
performed with simple
amino acids as starting
material.
•Protein like molecules
are formed
Biological Polymers and Directionality
Biological Polymers have
a specific direction to them
based upon their
sequence
•Proteins: Amino terminus
to Carboxy terminus
•Nucleic Acids: From 5’ to
3’
•Carbohydrates: From
nonreducing terminus to
reducing terminus
Types of Cells
•The different biologically active molecules and polymers
arrange themselvs to form cells
•The formation of a lipid bilayer is instrumental in this!
•We can distinguish between types of cells based upon the
presence of organelles, especially the nucleus
•Prokaryotic do not have a nucleus or other organelles
but Eukaryotic cells do
•Organelles are specialized compartments that allow unique
reactions to occur within them
Types of Cells
Types of Cells
Section 1.9: Biochemical Energetics
•All cells need energy to catalyze the reactions of life
•ATP (Adenosine triphosphate) is the energy currency of the
cell
•The gamma phosphate is hydrolyzed off
•This is an example of a high-energy bond
Thermodynamics
Let’s review some topics we covered in CHEM105:
•Spontaneous Reaction: A reaction that occurs without
outside intervention
•May be very fast or slow
•Free Energy: G, is a measure of the capacity of a system
to do thermodynamic work
•Only G can be measured
•Enthalpy: H, is a measure of the heat stored in a
chemical bond
•Entropy: S, is a measure of the disorder of a system
G = H - TS
Think About It…
If all systems in the universe tend towards disorder,
how can cells exist in the first place?
Biochemical Thermodynamics
1. The Free Energy of a system decreases in a
spontaneous reaction
G < 0
This is also called an Exergonic reaction
2. A system at equilibrium has no Free Energy Change at All
G=0
3. In a nonspontaneous reaction, energy must be input into
the system
G>0
This is also called an Endergonic reaction
Acids, bases and pH
•We talked about strong acids and bases last lecture in our
discussion of Electrolytes
•A strong acid completely dissociates in solution
HA --> H+ + ApH = -log [H+] or pH = -log [H3O+]
For a strong acid, the pH will equal the -log[H+]
Remember: Some acids are polyprotic (H2SO4, H3PO4)
Acids, Bases and pH
• For strong bases, we need to remember
that ph and pOH are related:
pH + pOH = 14
• Take the negative log of the [OH-] and
subtract it from 14 to determine the pH
Acids, Bases and pH
• Weak acids (and bases) pose a new
problem: The fact that they do not
completely dissociate in solution
– They exist in an equilibrium between the
acid and conjugate base
HA (aq) + H2O (l) --> H3O+ (aq) + A- (aq)
[H  ][A ]
KA 
= Acid dissociation constant (lower values means weaker acid)
[HA]
pK A  - logK A (The smaller the number,
the stronger the acid)
Common Biochemical Acids
Henderson-Hasselbach Equation
Enzymes have very specific pH ranges in which
they will function
Henderson-Hasselbach Equation
[H  ][A ]
KA 
[HA]
[A ] 
logK A  log[H ] + log 

[HA] 

-log[H ]  - logK A
+
pH = pK A

[A ] 
+ log 

[HA] 
[A ] 
+ log 
 We can use this equation to predict the pH of a weak acid
[HA] 
Titration Curves
• When we mix an acid and a base together in
small increments and then measure the pH,
we can make a Titration Curve
HA (aq) + OH- (aq)  H2O (l) + A- (aq)
The equivalence or endpoint (EP) is
the point in the titration at which all
of the acid molecules have reacted
with base
Halfway to the EP: [HA]=[A-]
•The pH at this point is the pKa.
Why?
At the EP: [A-] = Initial [HA]
