Physical BioChemistry: BCHM 485

Spring 2022

Class meets TuTh at 9:30 am in CHEM1402
Professor: David Fushman
Office Hours: Thursday, 5 - 6:30 pm (via zoom)



Quantum Chemistry & Spectroscopy by Thomas Engel
Thermodynamics, Statistical Thermodynamics, and Kinetics by Thomas Engel & Philip Reid
(The Thermodynamics textbook that you might still 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
05/13 Final Exam: Friday May 13, 8:00am(!!!). The exam will take place in the same room as all the lectures.    
05/10 Last lecture + review session for the final exam Bring your questions.   Statistics of the current scores in this class are posted below under Statistics. Answers/Solutions to graded HW #4 problems are here.  
05/05 TSK Ch.14.1-2,10, 15.2,4,5 TSK Ch.15: Prs: 15.5, 15.13. Don't forget to submit your Graded HW #4 by 11:59 pm on Monday May 9.   Tentative equations sheets for the final exam are here.  
05/03 TSK Ch.14: 14.3-7 (skip 14.5.3) and 14.9 TSK Ch.14: Qs: 14.4,9,10. Prs: 14.1,4.14,26,27. Also follow the example problems in that chapter. Graded HW #4 is here. It is due by 11:59 pm on Monday May 9.   Solutions to Exam #2 problems are posted below.  
04/28 Midterm Exam #2 After the exam: Reading: TSK Ch.13 to the end; Ch. 15.4 (Entropy). Qs: 13.6,9,11. Prs: 13.8,10,14.   
04/26 Prepare for the midterm exam #2 Tentative equations sheet for the upcoming exam is here. Make sure you are familiar with these equations and which QM systems they correspond to. Review session for the upcoming Exam #2 will be held via zoom on Wednesday, April 27, at 5pm.    
04/21 TSK: Ch.13: 13.1-13.5, [Ch.12 -- refresher on probabilities] TSK: Ch.13: Qs: 13.1-5; Pr: 13.1,7,12,19,20,27. Review session for the upcoming Exam #2 will be held via zoom on Wednesday, April 27, at 5pm. Tentative equations sheet for the upcoming exam #2 is here.   Example problems from the previous year Exam #2 are here. Solutions to these problems are here.  
04/19 Ch.17.3-17.6, 17.11. Ch.17: Qs: 17.3, 17.14. Pr: 17.3,17.6. If you haven't done this yet, watch the educational YouTube videos from the prevous lecture homework assignment. Slides from today's lecture can be found on ELMS.   Solutions to graded HW #3 problems are here. 
04/14 Ch.8.8 and 17.1-17.2. Ch.17: Ex.Pr 17.1. Ch.8: Prs: 8.33,40,41. Below are links to educational YouTube videos illustrating basic aspects of Nuclear Magnetic Resonance which I will discuss in the next lecture. You want to watch videos 01 and 02.
video 1:
video 2:  
04/12 Ch.8: 8.3-8.6 [8.7]. Ch.8: Ex.Pr: 8.2-8.6; Qs: 8.1,8.2,8.7,8.10,8.12,8.17,20; Pr: 8.7 (what's wrong in this problem?), 8.14, 8.15.  
04/07 Ch.8: 8.1-8.2, 8.9. Q: 8.4 Don't forget to submit your graded HW#3 which is due on April 11.  
04/05 Ch.10: 10.1-10.3; and 6.2. Ch.12: 12.1-12.5 Ch.10: Ex.Pr. 10.6,10.7,10.10. Determine the angle between the vector of electron spin and the z-axis. Your graded Homework #3 (due by 11:59 pm on Monday April 11) is here.
Posted here is a detailed description of how to determine eigenfunctions of the Sx operator and how to answer the question about measuring Sx in the state described by the eigenfunction of the Sz operator. For those who are curious about vector/matrix representations of the wavefunctions and operators -- here is an explanation with some examples.
Answers/solutions to Exam #1 problems and the current distribution of the scores are posted below under Solutions and Statistics.
03/31 Ch.10.1 + 10.2-10.3 Ch.10: Qs: 10.7. Prs: 10.10, 10.13, 10.14, 9.9-9.11. Here is a copy of Exam #1 sheets. Solve these problems again, now without exam time pressure, and please read the problems and the questions carefully before solving them.  
03/29 Ch.9: 9.4-9.6 Ch.9: Ex.Pr: 9.3-9.6; Qs: 9.1,9.6,9.12,9.13,9.19; Pr: 9.4, 9.12 (9.5), 9.7. Calculate the average potential energy of 2p (and 2s) electron and assess if the relationshiop = 2*En which we obtained in class for the 1s electron still holds.  
03/17 Ch.9: 9.1-9.3 Ch.9: Qs: 9.4,9.7,9.8,9.16. Pr: 9.2. Ex.Pr: 9.1,9.2. Show by direct substitution and calculation that exp(-r/a) is a solution to Shroedinger's Eq. for H-atom when l=0; determine the values of a and E. What is the degeneracy of the state(s) of H atom with the principal Q.N. n?    
03/15 Midterm Exam #1    
03/10 Review sesssion in preparation for the midterm exam #1 will be on Friday at 5:30pm. Bring your questions Bring your questions. Equations sheet for the upcoming Exam 1 is here Answers/solutions to Exam 1 problems from the previous year will be posted here.  
03/08 Ch.7: 7.5-to the end Ch.7: Ex.Pr 7.6; Qs: 7.7, 7.13; Pr: 7.35, 7.37. Example problems and equations sheet from the previous year Exam #1 are here. Review session for the upcoming midterm exam 1 is tentatively set for Friday at 5:30 pm. Answers to graded HW #2 problems are here.  
03/03 Ch 7: 7.1- 7.4 Do the graded HW #2 and the homework problems from the previous assignments. For those who are curious: here I show how to calculate the probability to find quantum mechanical H.O. outside the allowed range for a classical H.O.  
03/01 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5. Qs: 7.11,7.19. Pr: 7.10,7.17, 7.35(b). Your graded Homework #2 (due on Mar 7, 2022) is here.  
02/24 Ch 7: 7.1,7.3 Ch.7: Qs: 7.1,7.6,7.8; Pr: 7.8,7.15,7.17.  
04/22 Ch.6: 6.1,6.3,6.4 Ch.6: Example Prs: 6.3, 6.4. Qs: 6.5,5.7-8. 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].  
02/17 Ch.4: 4.3; Ch.5: 5.3 Ch.4: Pr: 4.17-19, 4.21, 4.22, 4.23; Ch.5: Pr: 5.4, 5.5. Harry Potter and the Basilisk problem. Answers to graded Homework #1 problems are here. 
02/15 Ch.5: 5.1-5.2, 5.6-5.8 Ch.5: Qs: 5.6; Pr: 5.7. Harry Potter and the Platform 9 3/4 problem: Calculate the penetration length for Harry Potter using the model discussed in class to find out if the penetration through the wall phenomenon documented in this story is related to Q.M. or is just magic. Repeat the same calculation but now for a proton, and for an electron.  
02/10 Ch.4: 4.2-to the end Ch.4: Ex.Pr.4.1-4.3; Pr: 4.12,4.16. Some useful trigonometric identities and other formulae can be found here and on ELMS.  
02/08/b> Ch.4: 4.2. Ch.4: Qs: 4.2,4.9-10,4.14-15,4.18-20; Pr: 4.9,4.10,4.28,4.29. + The Schroedinger's cat problem from the previous homework assignment. Your graded Homework #1 (due on Monday Feb 14, 2022) is here.  
02/03 Ch.4: 4.1. Ch.4: Qs: 4.1,4.3-5,4.11; Pr: 4.4-4.6,4.13. Question: Schroedinger's cat was found alive in 80 out of 100 experiments and dead in 20. Reconstruct the wavefunction of the cat.  
02/01 Ch.3: 3.4-3.5 (3.6). Ch.3: Qs: 3.8,3.10; Pr: 3.12,3.16. Question: How can you tell from the outcome of your experiments if the QM system is in a pure state or in a superposition state?  
01/27 Ch.2: 2.5,2.6,2.7; Ch.3: 3.1-3.3 (+3.4). Ch.2: Ex.Pr. 2.3,2.4; Pr: 2.12, 2.14; Ch.3: Qs:3.2-3.7,3.9; 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, perform the following calculations: (1) estimate λmax for your body radiation, and (2) assuming that the maximum of Sun's radiation is in the yellow range, i.e. λmax ~ 580 nm, 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 below and also on ELMS. 
before 01/25 Prepare yourself for the course. The relevant information can be found here.  Pepare 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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