Chem 5

Review - Part 2 Afterword

December 16, 2002

Energetics
General principle: Hess’ Law Ionization energy: Electron affinity: A(g) → A+(g) + eB(g) + e- → B-(g)
(A and B not only atoms but also molecules )

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

Enthalpy of solution NaCl(s) → Na+(aq) + Cl-(aq) Enthalpy of hydration Na+(g)
H2O

H2O

Na+

(aq); Cl-(g)

H2O

→ Cl-(aq)

Use Born-Haber cycle to calculate the lattice energy for NaNO2
Na+(g) + NO2 - (g) → NaNO2 (s) For the product: ∆Hf of NaNO2 : Na(s) + ½ N2(g) + O2 (g) → NaNO2 (s) For the reactants: Sublimation of Na : ∆Hf for NO2 : Na(s) → Na (g) Na(g) → Na+(g) + e107 kJ/mol 496 kJ/mol +33 kJ/mol -219 kJ/mol 417 kJ/mol -776 kJ/mol (2) (3) (4) (5) (6) Ionization Energy of Na : -359 kJ/mol (1) ∆H = ?

½ N2 (g) + O2(g) → NO2 (g)

Electron affinity of NO2 : NO2 (g) + e- → NO2 - (g) Na(s) + ½ N2(g) + O2(g) → Na+(g) + NO2 - (g)

(1) – (6) Na+(g) + NO2 - (g) → NaNO2 (s) Calculate ∆Hf of NO2- (g), (4) + (5) ½ N2(g) + O2(g) + e- → NO2- (g)

The lattice energy of NaNO2 ∆Hf = -186 kJ/mol

Coordination number Relating atomic radius and edge length

Cubic Unit Cells Simple cubic (sc)

Closest Packing Cubic Closest Packed ccp Body-centered Face-centered cubic (bcc) cubic (fcc) Hexagonal Closest Packed Hexagonal unit cell hcp

Bragg Diffraction Law

nλ = 2d sinθ

Colligative Properties

• The lowering of the vapor pressure • The elevation of the boiling point • The depression of the freezing point • The phenomenon of osmotic pressure

Raoult’s law PA= xAPAo ∆Tb = i Kb m ∆Tf = - i Kf m 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

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