CH348 (BYS348)
Biophysical Chemistry - Course Syllabus
Chemistry and Biological Sciences 348
Text: Physical Chemistry by Thomas Engel and Philip Reid, 2nd Ed. (abbreviated ER below)
Course Information: Syllabus. See also information for CH347: Supplement-1 (pdf).
You must attend class and take good notes on this material to do well in this class.
I. Kinetics of Biological Interactions and Reactions
(Primary source, ER Chapter 36, and class notes)
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 14.
Homework Problem Set II: Download from here. Due January 21
EXAM I - Friday - January 23
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II. Principles of Quantum Mechanics
(Primary source, ER and class notes)
A. From Classical to Quantum Mechanics-
Waves and Particles (Planck, Einstein, Bohr, de Broglie) - Chapter 12
B. Schrödinger's equation - Chapter 13
Homework Problem Set III: Download from here. Due Monday, Feb 2
C. The Quantum Mechanical Postulates - Chapter 14
D. Quantum mechanics of translation - Chapter 15
Homework Problem Set IV: Download from here. Due Monday, Feb 9
E. Particles in the real world - Chapter 16
F. Heisenberg uncertainty principle - Chapter 17
G. Quantum mechanics of vibration - Chapter 18
H. Quatum mechanics of rotation- Chapter 18
Homework Problem Set V: Download here Due February 16
I. Vibrational and Rotational Spectroscopy - Chapter 19 (skip19.7 and 19.8)
J. Hydrogen atom - Chapter 20
Homework Problem Set VI: Download here Due February 23
K. Multi-electron atoms - Chapter 21 (skip 21.6, pp. 474-481)
(We will not cover Chapter 22)
III. Quantum Mechanics of Chemical Bonds and Transitions
(Primary source, ER and class notes)
A. Quantum mechanics of the chemical bond - (Read Chap 23)
B. Chemical bonding in diatomics - (Read Chap 24, skip pp. 523-525, 24.6, 24.7, 24.8)
C. Molecular structure and energy levels - (Read Chap 25 - sections 25.1 and 25.2 only)
D. Electronic Spectroscopy - (Read Chap 26, skip 26.10, 26.11)
EXAM II - March 2
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IV. Basics of Statistical Thermodynamics
(Primary source, ER and class notes)
A. Probability - Chapter 30
B. Boltzman Distribution - Chapter 31
Homework Problem Set VII: Download here (Due March 9)
C. Ensemble and Molecular Partition Functions - Chapter 32
Homework Problem Set VIII: Problems 31.3, 31.8, 31.12, and 33.1 in Engel and Reid. (Due March 13)
D. Calculation of thermodynamic quantities- Chapter 33
E. Kinetic theory of gases, diffusion, and random walks
EXAM III - March 23
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V. Principles of Spectroscopy
(Primary source, ER and class notes; see also the Spectroscopy Now website.)
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.)
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. )
Homework IX: download here. (Due April 8)
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. )
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.
A. Magnetization, pulses, and FT NMR - Chapter 29
B. Data acquisition considerations
C. Practicalities
D. Nuclear Interactions
E. Multidimensional NMR Methods
G. Amide hydrogen exchange
EXAM IV: April 17
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FINAL EXAM: April 29
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Biophysical Chemistry - Course Syllabus
Chemistry and Biological Sciences 348
Text: Physical Chemistry by Thomas Engel and Philip Reid, 2nd Ed. (abbreviated ER below)
Course Information: Syllabus. See also information for CH347: Supplement-1 (pdf).
You must attend class and take good notes on this material to do well in this class.
I. Kinetics of Biological Interactions and Reactions
(Primary source, ER Chapter 36, and class notes)
- 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 14.
Homework Problem Set II: Download from here. Due January 21
EXAM I - Friday - January 23
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II. Principles of Quantum Mechanics
(Primary source, ER and class notes)
A. 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
B. 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. Due Monday, Feb 2
C. The Quantum Mechanical Postulates - Chapter 14
- Physical meaning of a wave function
- Observables and operators
- Expectation values
- Time dependence
D. Quantum mechanics of translation - Chapter 15
- Free particle
- One dimensional box
- 2 and 3 dimensions
Homework Problem Set IV: Download from here. Due Monday, Feb 9
E. 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
F. Heisenberg uncertainty principle - Chapter 17
- Commutation
- Stern-Gerlach experiment
- Heisenberg uncertainty principle
G. Quantum mechanics of vibration - Chapter 18
- Classical harmonic oscillator
- Schrödinger equation and solutions
H. Quatum mechanics of rotation- Chapter 18
- Classical rigid rotor
- Schrödinger equation and solutions
- Angular momentum
- Spherical harmonics
Homework Problem Set V: Download here Due February 16
I. Vibrational and Rotational Spectroscopy - Chapter 19 (skip19.7 and 19.8)
- Absorption and emission
- Selection rules
J. Hydrogen atom - Chapter 20
- Atomic orbitals
- Radial probability distribution functions
Homework Problem Set VI: Download here Due February 23
K. 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)
A. 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)
B. 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
C. 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
D. Electronic Spectroscopy - (Read Chap 26, skip 26.10, 26.11)
- Molecular term symbols
- Vibrational fine structure
- Absorption and fluorescence
EXAM II - March 2
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IV. Basics of Statistical Thermodynamics
(Primary source, ER and class notes)
A. Probability - Chapter 30
- Basics
- Stirling's approximation
- Probability distributions
B. Boltzman Distribution - Chapter 31
- Derivation
- Physical meaning
Homework Problem Set VII: Download here (Due March 9)
C. 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 VIII: Problems 31.3, 31.8, 31.12, and 33.1 in Engel and Reid. (Due March 13)
D. Calculation of thermodynamic quantities- Chapter 33
- Energy
- Heat capacity
- Enthalpy
- Entropy
- Residual entropy
- Helmholtz and Gibbs free energies
E. 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 - March 23
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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 IX: download here. (Due April 8)
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.
A. 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
B. Data acquisition considerations
- Linewidth - Lorentzian lineshape and T2 times
- Sample concentration, salt, precipitate, etc.
C. Practicalities
- Chemical shift - chemical shift references
- Spectrometer basics - probes, tuning, shimming, variable temperature
D. Nuclear Interactions
- J-coupling
- Karplus relationship
- T1 and T2 relaxation, saturation
- NMR linewidth and chemical exchange
- Nuclear Overhauser Effect
E. Multidimensional NMR Methods
- 2D NOESY, TOCSY, COSY
- HSQC
- HNCO, HNCA, CBCACONNH, CBCANH, HSQC-TOCSY
G. Amide hydrogen exchange
EXAM IV: April 17
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FINAL EXAM: April 29
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