• Practical Kinetics - reaction order
• Reactions mechanisms and rate laws
• Rate constants and equilibrium constants
• Microscopic Reversibility
• First order reactions
• Second order reactions
• Numerical approaches - Iterative procedures in Mathematica (in notebook form)
• Sequential and parallel reactions
• Energy of activations and Arrhenius equation
• Diffusion limited rates
• Rapid reactions and transient kinetics
  • Relaxation processes
  • Stopped-flow methods and rapid mixing devices
  • Quench-flow methods
  • Temperature jump methods
  • Computer data analysis

  Homework Problem Set I: Problems 36.4, 36.15, 36.18, 36.22, 36.32. (Use Mathematica along with both analytical expressions and numerical procedures for comparison in answering 36.18 and 36.22. Note that N and No in 36.15a are numbers of cells, not colonies.) Due Jan 16.

• Homework Problem Set II: Download from here. Due January 23, 2008.

• From Classical to Quantum Mechanics- Waves and Particles (Planck, Einstein, Bohr, de Broglie) - Chapter 12
  • Blackbody radiation and Plank's constant
  • Temperature dependence of heat capacities - Dulong and Petit
  • Einstein explains Planck's constant - quantization
  • The Photoelectric effect - Einstein and the photon (particle or wave?)
  • Electron and atomic diffraction - Davisson and Germer - Particle-wave duality
  • Hydrogen spectra - the Rydberg constant
  • de Broglie - momentum and wave length
  • Bohr and the initial quantum theory - electrons and standing wave

• Schrödinger's equation - Chapter 13
  • Waves and complex numbers
  • Quantum mechanical waves
  • Operators, observables, eigenfunctions
  • Orthogonality and completeness

• Homework Problem Set III: Download from here.

• The Quantum Mechanical Postulates - Chapter 14
  • Physical meaning of a wave function
  • Observables and operators
  • Expectation values
  • Time dependence

• Quantum mechanics of translation - Chapter 15
  • Free particle
  • One dimensional box
  • 2 and 3 dimensions
• Homework Problem Set IV: Download from here.

• Particles in the real world - Chapter 16
  • Well of finite depth - bonding electrons
  • Tunneling
  • Scanning Tunneling Microscope and Atomic Force Microscope
  • Non-Arrhenius kinetics
  • Quantum dots

• Heisenberg uncertainty principle - Chapter 17
  • Commutation
  • Stern-Gerlach experiment
  • Heisenberg uncertainty principle
• Quantum mechanics of vibration - Chapter 18
  • Classical harmonic oscillator
  • Schrödinger equation and solutions

• Quatum mechanics of rotation- Chapter 18
  • Classical rigid rotor
  • Schrödinger equation and solutions
  • Angular momentum
  • Spherical harmonics
• Homework Problem Set V: Download here (Due Feb. 11, 2008)
• Homework Problem Set VI: Download here (Due Feb. 13, 2008) (optional problem for extra credit)

• Vibrational and Rotational Spectroscopy - Chapter 19 (skip19.7 and 19.8)
  • Absorption and emission
  • Selection rules
• Hydrogen atom - Chapter 20
  • Atomic orbitals
  • Radial probability distribution functions
• Homework Problem Set VII: Download here (Due Feb. 22, 2008)

• Multi-electron atoms - Chapter 21 (skip 21.6, pp. 474-481)
  • Electron spin
  • Periodic table
  • Good quantum numbers, term symbols (singlet and triplet states)
  (We will not cover Chapter 22)

III. Quantum Mechanics of Chemical Bonds and Transitions

(Primary source, ER and class notes)

• Quantum mechanics of the chemical bond - (Read Chap 23)
  • The simplest molecule: H2+
  • Born-Oppenheimer approximation
  • Overlap, Resonance, and Coulombic integrals
  • Bonding and Anti-bonding
  • The H2 molecule
  • Valence bond and molecular orbital models
  • Molecular wave functions, atomic orbitals, molecular orbitals
  • Linear combination of atomic orbitals (LCAO)

• Chemical bonding in diatomics - (Read Chap 24, skip pp. 523-525, 24.6, 24.7, 24.8)
  • LCAO and basis sets
  • Molecular orbital energy diagrams
  • Orbital symmetry

• Molecular structure and energy levels - (Read Chap 25 - sections 25.1 and 25.2 only)
  • Lewis structure
  • Valence shell electron pair repulsion (VSEPR model)
  • Hybridization

• Electronic Spectroscopy - (Read Chap 26, skip 26.10, 26.11)
  • Molecular term symbols
  • Vibrational fine structure
  • Absorption and fluorescence

EXAM II - Take home exam - distributed on Friday, Feb 29, and due at 9:00 AM, March 3, 2008.

IV. Basics of Statistical Thermodynamics

(Primary source, ER and class notes)

• Probability - Chapter 30
  • Basics
  • Stirling's approximation
  • Probability distributions
• Boltzman Distribution - Chapter 31
  • Derivation
  • Physical meaning
• Homework Problem Set VIII: Download here (Due March 5, 2008)
• Ensemble and Molecular Partition Functions - Chapter 32
  • Canonical ensemble
  • Molecular energy levels
  • Translation, rotation, and vibration partition functions (Skip 32.5.1, 32.5.2, 32.5.3, 32.6)
  • Equipartition theorem
• Homework Problem Set IX: Problems 31.3, 31.8, 31.12, and 33.1 in Engel and Reid. (Due March 14, 2008)
• Calculation of thermodynamic quantities- Chapter 33
  • Energy
  • Heat capacity
  • Enthalpy
  • Entropy
  • Residual entropy
  • Helmholtz and Gibbs free energies

• Kinetic theory of gases, diffusion, and random walks
  • Velocity distributions (Sections 34.1 - 34.3)
  • Maxwell-Boltzman velocity distribution
  • Transport and diffusion (Sections 35.1-35.3)
  • Random Walks (Section 35.4)
  • Diffusion, flexibility, and noise

EXAM III -

V. Principles of Spectroscopy

(Primary source, ER and class notes; see also the Spectroscopy Now website.)

• Biochemical Uses of Spectroscopy
• Electromagnetic spectrum
• Absorption and Dispersion - handout here in pdf form
• Polarizabilities

VI. UV-Visible Spectroscopy

(Primary source, ER and class notes. This part of the course will be supplemented heavily with material beyond what is in the text. You must either attend class or obtain good notes from someone who does. See also "Ultraviolet Absorption Spectroscopy" Chapter 4, in Protein Stability and Folding (Bret Shirley, Ed.), Vol 40 in Methods in Molecular Biology, Humana Press, 1995.)

• Radiation induced transitions
• Beer Lambert Law
• Protein spectra
• Extinction coefficients - relative contributions of amino acids
• Nucleic acid spectra
• Isosbestic points
• First and Second Derivative spectroscopy
• Difference spectroscopy
• Light scattering and limits to the Beer Lambert Law
• Calibration of spectrophotometer absorbance and wavelength accuracy
• Dichroism and birefringence

VII. Fluorescence

(Primary source: ER and class notes and handouts. This part of the course will be supplemented heavily with material beyond what is in the text. You must either attend class or obtain good notes from someone who does. )

• Excited states, radiationless transitions, intersystem crossing
• Fluorescence vs. phosphorescence
• Intrinsic (tryptophan, tyrosine, etc.) and extrinsic (fluorescein, ethenoAMP, ANS, IAEDANS, etc.) fluorophores
• Sensitivity relative to absorbance spectroscopy
• Quenching
• Fluorescence lifetimes and quantum yields
• Measurement of fluorescence lifetimes
• Förster energy transfer and distance measurements
• Molecular beacons, quantum dots, etc.
• Single molecule methods - download pdf version of review article
• Optical tweezers (not a fluorescence method- but very useful with single molecules)
• Fluorescence depolarization and fluorescence anisotropy
• Molecular motion and rotational correlation times

Homework X: download here. Due April 7, 2008

VIII. Circular Dichroism

(Primary source: ER and class notes and handouts. This part of the course will be supplemented heavily with material beyond what is in the text. You must either attend class or obtain good notes from someone who does. )

• Polarized light
• Optical rotation and circular dichroism - see handout on CD and ellipticity
• Molecular ellipticity and decadic molar circular dichroism
• Protein secondary structure and circular dichroism
• Isodichroic points
• Prediction of secondary structure from CD data
• DNA structure and circular dichroism

IX. Nuclear Magnetic Resonance

(Primary source: ER and class notes and handouts. This part of the course will be supplemented heavily with material beyond what is in the text. You must either attend class or obtain good notes from someone who does.)

See the online text "The Basics of NMR" by Joseph Hornak

Please download these additional notes: BioNMR Basics (black background version and "printer friendly" version) notes (pdf). You will be responsible for the material covered here and in class.

• Magnetization, pulses, and FT NMR - Chapter 29
  • Fundamentals - magnetic moments, gyromagnetic ratios
  • 1H, 13C, 15N, 31P - spin 1/2 nuclei and natural abundance
  • Larmor precession
  • Pulsed NMR - 90° pulses, resonance, and spin populations (temperature)
  • Free induction decay - relaxation
  • Fourier transform
• Data acquisition considerations
  • Linewidth - Lorentzian lineshape and T2 times
  • Spectral Resolution, Sampling Rate, and Nyquist Frequency - notes.
  • Apodization, linewidth effects, resolution enhancement
• Practicalities
  • Chemical shift - chemical shift references
  • Spectrometer basics - probes, tuning, shimming, variable temperature
• Nuclear Interactions
  • J-coupling
  • Karplus relationship
  • T1 and T2 relaxation, saturation
  • NMR linewidth and chemical exchange
  • Nuclear Overhauser Effect
• Multidimensional NMR Methods
  • 2D NOESY, TOCSY, COSY
  • HSQC
  • HNCO, HNCA, CBCACONNH, CBCANH, HSQC-TOCSY
• Structure determination
• Amide hydrogen exchange

Homework:

EXAM IV: April 18, 2008

FINAL EXAM: April 30, 2008 (8:00 AM)