Chem 5

Review - Part 2

Afterword

December 16, 2002

 Energetics
General principle: Hess’ Law

Ionization energy: A(g) → A+(g) + e- (A and B not only atoms

but also molecules )
Electron affinity: B(g) + e- → B-(g)
Enthalpy of formation: Na(s) + ½ Cl2(g) → NaCl (S)

Bond energy: (average, only for gas phase)

Lattice energy: Na+ (g) + Cl-(g)→ NaCl(s) (Born-Haber Cycle)
Enthalpy of vaporization (Clausius-Clapeyron Eq.)
Enthalpy of freezing, fusion, condensation, sublimation, deposition ∆Hsub = ∆Hfus+∆Hvap

H2O
Enthalpy of solution NaCl(s) → Na+(aq) + Cl-(aq)
H2O H2O
Enthalpy of hydration Na+(g) → Na+ (aq); Cl-(g) → Cl-(aq)
Use Born-Haber cycle to calculate the lattice energy for NaNO2
Na+(g) + NO2 - (g) → NaNO2 (s) ∆H = ?
For the product:
∆Hf of NaNO2 : Na(s) + ½ N2(g) + O2 (g) → NaNO2 (s) -359 kJ/mol (1)
For the reactants:
Sublimation of Na : Na(s) → Na (g) 107 kJ/mol (2)
Ionization Energy of Na : Na(g) → Na+(g) + e- 496 kJ/mol (3)
∆Hf for NO2 : ½ N2 (g) + O2(g) → NO2 (g) +33 kJ/mol (4)
Electron affinity of NO2 : NO2 (g) + e- → NO2 - (g) -219 kJ/mol (5)
Na(s) + ½ N2(g) + O2(g) → Na+(g) + NO2 - (g) 417 kJ/mol (6)

(1) – (6) Na+(g) + NO2 - (g) → NaNO2 (s) -776 kJ/mol

The lattice energy of NaNO2
Calculate ∆Hf of NO2- (g), (4) + (5)
½ N2(g) + O2(g) + e- → NO2- (g) ∆Hf = -186 kJ/mol
Coordination number
Relating atomic radius and edge length
Closest Packing
Cubic
Closest
Cubic
Packed
Unit
Cells
ccp
Simple cubic Body-centered Face-centered
(sc) cubic (bcc) cubic (fcc)

Hexagonal
Closest
Bragg Diffraction Law Packed

nλ = 2d sinθ hcp
Hexagonal
unit cell
 Colligative Properties

• The lowering of the vapor pressure Raoult’s law PA= xAPAo

• The elevation of the boiling point ∆Tb = i Kb m

• The depression of the freezing point ∆Tf = - i Kf m

• The phenomenon of osmotic pressure π = nRT/V = MRT

 Afterword

“If you had only one sentence to

describe the most important scientific
knowledge we posses, what would
that sentence be? The answer is,
everything is made of atoms! ”

- Richard Feynman
In chemical texts, molecular interactions and chemical reactions
are described on a single-molecule basis. However, our knowledge
of molecular interactions and chemical dynamics has come almost
exclusively from experiments on ensembles of molecules, on the
order of Avogadro number of molecules – a number of enormity.

If a grain of sand has a volume of 1 mm3, an Avogadro number of

them creates a desert 60m deep over the entire area of the
United States.

“How many moles are one molecule?

It is 1 ‘guacamole’ = 1 / (Avogadro number)

- with apologies to Avogadro.”
W.E. Moerner
• Fluorescence detection is most sensitive.

• Fluorescence is induced by photo-excitation with a laser beam.

• A microscope is used to reduce excitation volumes.

• A single molecule is excited over and over again.

• A sensitive detector is used.

Cy5
Visualizing Single Molecules

Demo 1
Imaging single Cy5 molecules in a polymer film
- A dilute solution (10-11M) is used to assure that there is no more
than one molecule in a resolvable spot.

Demo 2
Imaging λ-phage DNA molecules stretched on a positively charged
glass surface
- A single DNA molecule is 16 µm long and has a diameter of 2 nm. It
is labeled with many fluorescent dye molecules.

Demo 3
Imaging λ-phage DNA molecules in solution undergoing Brownian
motion
- The diffusion of single globular DNA molecules is tracked by the
fluorescent labels.
In all three cases, a 633 nm laser is used.
Why study single molecules?

• The ultimate detection limit for chemical analysis

• Measure distributions of molecular properties instead of

only the ensemble averages

• Direct observations of dynamical processes in real time

Bacteriophage λ exonuclease is an enzyme that degrades one
of two strands in double-stranded DNA. It has a Mw~ 70,000 Da

Crystal structures only give static

pictures. We can make movies of
molecular motions and chemical
reactions of single molecules.

Kovall and Matthews, Science 277 (1997) 1824

Stretching tethered DNA by shear flow

Fluorescently labeled DNA

Objective lens
Single λ exonuclease activity

Force extension curves of DNA

dsDNA

ssDNA

Fluorescently labeled DNA

 Trajectory of the polymer bead as a function of time

The rate of the enzymatic reaction varies with time.

Our single-molecule experiments have shown that an enzyme is a
dynamical entity with fluctuations in structure and reactivity spanning a
broad range of time scales.
“Imagination is more important than knowledge.
Knowledge is limited. Imagination encircles the world."

- Albert Einstein