Physical BioChemistry: BCHM 485

Spring 2018

Course meets in Chem 2201, TuTh 9:30 am
Professor: David Fushman
Office: Room 1121 Biomolecular Sciences Bldg (#296)
Office Hours: Tuesday, 12:30 - 2:30 pm



Quantum Chemistry & Spectroscopy by Thomas Engel
Thermodynamics, Statistical Thermodynamics, and Kinetics by Thomas Engel & Philip Reid
(The Molecular Thermodynamics textbook by McQuarrie & Simon that you might have from the CHEM481 course could be sufficient.)
Physical Chemistry by Peter Atkins and Julio de Paula, Vol.2 Quantum Chemistry, Spectroscopy, and Statistical Thermodynamics;
Physical Chemistry with Applications to the Life Sciences by David Eisenberg and Donald Crothers;
Principles of Physical Biochemistry by van Holde, Johnson & Ho;
Molecular Driving Forces by Dill & Bromberg;
Biophysical Chemistry by Cantor & Schimmel.
Reading and problems are either from Quantum Chemistry & Spectroscopy [QCS] or from Thermodynamics, Statistical Thermodynamics, and Kinetics [TSK]
Date Reading Problems Q&A
05/14 Final Exam: Monday, 8:00am(!!!).    
05/08 Read handout material on polymer chain statistics. The handout materials are here . The associated homework problems are here. Do homework problems 1-3. Solutions to the graded HW4 can be found here. Tentative equations sheet for the final exam is here. Statistics of the distribution of the current total scores (before the final exam) s posted below (together with the Exam #2 Statistics).
05/03 TSK: Ch.14: 14.1-14.8 (you can skip 14.5.3,14.5.4,14.6,14.7.1) and Ch.15: 15.4-15.6. Ch.14: Ex.Pr: 14.1-4,14.6,14.10. Pr: 14.1,14.14,14.26, 15.3, 15.5. Solutions to Exam #2 problems are posted below along with the statistics of your current grades.  
05/01 TSK: Ch.12 (refresh your memory on statistics and combinatorics), Ch.13 till the end Ch.13: Ex.Pr: 13.1-6; Qs: 13.1-3,13.5-6,13.9-11; Pr: 13.1, 13.7, 13.12, 13.14, 13.19. Using your calculator find out how big the values of N should be in order for the Stirling's formula to achieve 10% accuracy, 1% accuracy. Your graded Homework #4 (due Tue May 8, 2018) is here. Slides from today's lecture are here  
04/26 Midterm Exam #2 Don't forget to bring a pen/pencil and a calculator!   
04/24 TSK: Ch.12 (refresh your knowledge of probabilities); Ch.13: 13.1-13.5. The reading material can be found on the course canvas website ( under Files. In McQuarrie: Ch.3.1-3.2, and MathChapters B, E Prepare for the second midterm exam that will be given on April 26. Make yourself familiar with the the equations sheet.
My answers/solutions to the problems from the last year midterm exam #2 are here.. I suggest you look at them only after you worked on solving the problems yourself.

Here is the link to educational videos illustrating various aspects of Nuclear Magnetic Resonance that we discussed in class: You want to watch videos 01, 02, and 04.

Slides from today's lecture lllustrating the use of NMR spectroscopy in Biochemistry and Structural Biophysics can be found on the course canvas website ( under Files.  
04/19 Ch.17: 17.3-17.6, 17.11. Ch.17: Ex.Pr 17.1; Qs: 17.3,10,15; Pr: 17.3,17.6. Prepare for the second midterm exam that will be given on April 26. A review session for the exam will take place on Tue, April 24, at 5(?)pm in Rm 2118 Biomolecular Sciences Bldg. Tentative equations sheet for Exam #2 can be found in the sample from the previous year exam. Make yourself familiar with these equations. An example of midterm exam #2 problems from last year is here.. Solutions to HW#3 problems are here.  
04/17 Ch.8: 8.8, [8.7], and 17.1-17.2 Ch.17: Q: 17.14; Pr.17.3 + do the homework problems from the previous lecture.    
04/12 Ch.8: 8.3-8.6. Ch.8: Ex.Pr: 8.2-8.6; Qs: 8.1,8.2,8.7,8.10,8.12,8.17; Pr: 8.7 (what's wrong in this problem?), 8.14, 8.15.  
04/10 Ch.8: 8.1-8.2, 8.9. Ch.8: Ex.Pr: 8.1; Q: 8.4.  
04/05 Ch. 12: 12.2-12.3 Ch.10: Pr: 10.6. Your graded Homework #3 (due April 12 ) is here.  For those who are curious about vector/matrix representations of the wavefunctions and operators -- here is an explanation with some examples.
04/03 Ch.10: 10.1-10.3, Ch. 6.2 Ch.10 Ex.Problems: 10.1-10.2; Qs: 10.5,10.6; Pr: 10.2, 10.10, [10.3].  
03/29 Ch.9 to the end; Ch.10: 10.1 Ch.9: Qs: 9.6,9,12,13,19; Pr: 9.5-9.7,9.12. Ch.10: Qs: 10.1,10.7,10.12.  
03/27 Ch.9: 9.2-9.6 Ch.9: Example Problems: 9.1-9.6; Do all the problems and Qs from the previous homework assignment (prior to spring break). In addition, do the following problems: (1) Calculate the minimum energy required for ionization of the hydrogen atom from its ground state. Estimate the temperature of a gas of molecules at which the average kinetic energy trabsferred through collisions would be sufficient to cause ionization of the hydrogen atom. (2) Calculate the average potential energy of electron in the 2p orbital and assess if the relationshiop = 2*En which we obtained in class for the 1s orbial still holds.  
03/15 Ch.9: 9.1-9.3 (9.4) Ch.9: Qs: 9.2,9.4,9.7,9.10,9.16. Pr: 9.2,9.4,9.24. Ex.Pr: 9.1,9.2. Show that exp(-r/a) is a solution to the Shroedinger Eq. for H-atom when l=0; determine a and E. Solutions to Exam #1 problems as well as the score statistics are posted below.  
03/13 Midterm Exam #1 Don't forget to bring a pen/pencil and a calculator!  
03/08 Preparation for the midterm exam #1 Solutions to example problems from previous years Exam #1 are here. Solutions to graded homework #2 problems are here.  
03/06 Ch 7: 7.5-7.8. Ch.7: Qs: 7.4,7.13. Pr: 7.2,7.4,7.34. Prepare for Midterm Exam #1 (on March 13).
03/01 Ch.7: 7.5-7.7 Ch.7: Qs: 7.2,7.3,7.12,7.14; Pr: 7.6,7.7,7.20. Equations sheet for the upcoming midterm exam #1 is here . Example problems from the previous years midterm exam #1 are here
02/27 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5. Qs: 7.11,7.19. Pr: 7.10,7.21,7.15,7.35(b). Your graded Homework #2 (due Mar 6, 2018) is here.  
02/22 Ch.5: 5.3; Ch 7: 7.1,7.3 Ch.5: Pr: 5.4,5.5; Ch.7: Ex.Pr.: 7.1, 7.2; Qs:7.1,7.6,7.8; Pr: 7.8,7.14,7.16,7.18 Answers to graded Homework #1 problems are here.  
02/20 Ch.6:6.1,6.3,6.4, Ch.6: Example Prs: 6.3, 6.4, Qs: 6.5-8,6.14; Pr: 6.3,6.6,6.7 ,6.9,6.11,6.23. Prove the genearal relationships for the commutators which I gave you in class. Specifically, evaluate the commutator [A,BC].  
02/15 Ch.4: 4.3; Ch.5: 5.1-5.2, 5.6-5.8 Ch.4: Pr: 4.17-18; Ch.5: Qs: 5.6; Pr: 5.7. Harry Potter and Platform 9 3/4: was it a quantum effect or just magic? Estimate the penetration depth assuming a 2m high gravitational barrier and a particle (Harry Potter) of mass 50 kg running at 2 m/sec toward the barrier.  
02/13 Ch. 2.1; Ch.4: 4.2, 4.4 Ch.4: Ex.Pr.4.1-4.3; Pr: 4.12,4.16. Estimate your wavelength when you move with 10 m/s velocity. Compute the wavelength for an oxygen molecule at room temperature.  
02/08 Ch.4: 4.2 Ch.4: Qs: 4.1-2,4.6,4.9-11,4.14-15,4.18-20; Pr: 4.9,4.10,4.29. Think of the Happy Potter and the Basilisk problem. Your graded Homework #1 (due Feb 15, 2018) is here. Some useful trigonometric equations and and identities are here.  
02/06 Ch.4: 4.1 Ch.4: Qs: 4.3-5,4.11; Pr: 4.4-4.6,4.13.  
02/01 Ch.3: 3.1-3.5 (3.6) Ch.3: Qs: 3.9-3.10; Pr: 3.12,3.16 (3.5,3.6). Q#1: Schroedinger's cat was found alive in 64% experiments and dead in 36%. Reconstruct the wavefunction of the cat. Q#2: How could you tell from the outcomes of your experiments if the QM system is in a pure state or in a superposition state?  
01/30 Ch.2: 2.3,2.6,2.7; Ch.3: 3.1-3.3. Ch.2: Ex.Pr. 2.3,2.4; Pr: 2.12, 2.14; Ch.3: Qs:3.2-3.9; Pr: 3.1,3.2,3.8,3.9  
01/25 QCS: Ch.1 & Ch.2: 2.2-2.3 Ch.1: Do Example problem: 1.3 from Ch.1: determine the radius of the lowest-energy orbit of electron in Bohr;s planetary model of the hydrogen atom. Using Wien's displacement law, λmax*T=1.44/5 cm*K, do the following calculations: (1) estimate λmax for your body radiation, and (2) assuming that λmax ~ 550 nm for the Sun's radiation, estimate the temperature of the Sun's surface. It's not too late to prepare yourself for the course. The relevant information can be found here.   
Exam # 1: Exam # 2: Final Exam:
Statistics Statistics Statistics
Solutions Solutions Solutions

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