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

•We can describe the interaction energy:

€

E p ∝ -zμ

r2

z = ion charge

µ = Electric dipole moment

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:

€

E p = -μ1μ2

r3

µ1: Dipole moment of molecule 1

µ2: Dipole moment of Molecule 2

The fact that the distance is cubed means that the energy falls of much more rapidly than ion-ion 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

€

E p = -μ1α 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

€

E p = -α 1α 2

r6

1: Polarizability of molecule 1

2: Polarizability of molecule 2

r6 !!!! 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 - TS

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+ + A-

pH = -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)

€

KA =[H+][A−]

[HA] = Acid dissociation constant (lower values means weaker acid)

pKA = - logKA (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

€

KA =[H+][A−]

[HA]

logKA = log[H+] + log[A−]

[HA]

⎛

⎝ ⎜

⎞

⎠ ⎟

-log[H+] = - logKA + log[A−]

[HA]

⎛

⎝ ⎜

⎞

⎠ ⎟

pH = pKA + log[A−]

[HA]

⎛

⎝ ⎜

⎞

⎠ ⎟ We can use this equation to predict the pH of a weak acid

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]