Syllabus

• Biophysical Chemistry (CH350)
• Physical Chemistry (CH351)

The official description of the course is provided in the Loras College Undergraduate Bulletin.  We will cover the properties and structure of gases, the laws of thermodynamics, the physical transformations of pure substances, the properties of mixtures, phase and chemical equilibrium, and electrochemistry.  These fundamental concepts will be discussed with examples of biochemical relevance.  The course has both a theoretical (class) and hands-on (lab) component.  We will discuss specific course goals and outcomes together.

Prerequisites: Chemistry 112, Math 150 or above, and Physics 110,111 or 223,224.

Where & When

• Lecture – Monday/Wednesday/Friday Science Hall 208 @ 1:30-2:20 pm
• Lab – Thursday Science Hall 225 @ 8:00-10:50pm

Staff

• Lecturer – Dr. Adam Moser (adam.moser@loras.edu), Science Hall 213
  • Office Hours: TBA

Materials

1. “Physical Chemistry: A Molecular Approach”  or “Molecular Thermodynamics” by McQuarrie & Simon
2. Lab goggles (if you don’t already own them)

Grading

To be discussed and decided by the class.  Your grade will be made up of quizzes, exams, homework, and laboratory.

There will be no make-up exams or make-up quizzes.

Laboratory

The laboratory section of this class will come in two types: labs we all do and a lab project you work on independently and report back to the class on.  Here are the lab topics.

1. Least-squares analysis of data – Use calculus and linear algebra to understand how data is fitted using least-squares analysis.  Use of Mathematica.
2. Determining parameter uncertainty in fit data – Determing uncertainty on parameters derived from least-squares analysis.  Development of how uncertain is generated.  Use of Mathematics.
3. Euler’s Chain Rule – Validate Euler’s chain rule for length, temperature, and tension of a rubber band.
4. Microstates & Macrostates: Population Distributions – Development of the relationship between microstates and macrostates as well as their relationship to entropy.  Use of Mathematica.
5. Boltzmann Distribution of Internal Bond Rotation – Derivation of how a Boltzmann distribution is formed from a potential energy surface.  Use of Mathematica and P.C. Spartan.
6. Constant Pressure Calorimetry – Determine enthalpy of reaction using calorimetry.  Development of heat capacity of solids through Dulong and Petit as well as Einstein’s heat capacity of crystalline solids.
7. Bomb Calorimetry – Determination of internal energy change from constant volume calorimetry for various combustions.
8. Gibb’s Function and Degree of Advancement – Theoretical development of the connection of degree of advancement and Gibbs and Helmholtz energies.  Use of Mathematica.
9. Gibb’s Transfer Energy and the Hydrophobic Effect – Calculation of transfer free energies between hydrophilic and hydrophobic solutions using visible spectroscopy.
10. Measuring Vapor Pressure of a Liquid as Function of Temperature – Determining liquid pressure-temperature coexistance and vaporization ethalpy for volitile organic molecules.
11. Thermodynamic Stability of a DNA Duplex – DNA Duplex thermal stability monitored with UV spectroscopy and analyzed for melting temperature and thermodynamic quantities.
12. Spectroscopic Determination of Protein-Ligand Binding Equilibrium – Binding constant for myoglobin and fluorine binding using visible spectroscopy.
13. Differental Scanning Calorimetry – Analysis of differential scanning calorimetry data with an emphasis on understanding how heat capacity is affecting in conformation changes.
14. Myoglobin Stability by Visible Spectroscopy – Chemical stability of myoglobin monitored by visible spectroscopy.  Determination of Gibbs energy of protein folding.
15. Role of Catalysts in Chemical Reaction Kinetics – Role of catalyst on hydrogen peroxide degradation.  Data analysis emphasis on determining rate constants.

Schedule

This semester we will work through the topics below, which correspond to the quantum introduction and chapter 16-29 in the textbook.

Additional reading will be provided that connects of theoretical development to biochemical examples.

Academic Conduct

Please refer to the  Loras College Academic Honesty Policy.  Cheating not only disrespects the college, your instructor, and you fellow students, but yourself as well.  I expect you to work together often, but cheating is any “[b]ehavior in which a deliberately fraudulent misrepresentation is employed in an attempt to gain underserved intellectual credit, either for oneself or for another person.  Students are required to actively protect their work against misuse by others (lending tests, projects, term papers).”

Make-up Policy

You must notify me  at minimum 1 day any the absence if you want to make up the work.  Exams will not be given any other time except for unforeseen emergency.

Learning Disabilities

In accordance with federal law, if you have a diagnosed disability or believe you have a disability that might require reasonable accommodations, please discuss your needs with me at soon as possible.  Documentation of your disability must be on file with the Lynch Office of Disability Services (LODS), 120 Academic Resource Center (563-588-7134) for you to receive accommodations.

Things can change …

The instructor reserves the right to change any portion of this course syllabus as needed.