Physical BioChemistry: BCHM 485

Spring 2021

Class meets ONLINE TuTh at 9:30 am
Professor: David Fushman
Office: Room 1121 Biomolecular Sciences Bldg (#296)
Office Hours: Tuesday, 4 - 5 pm



Quantum Chemistry & Spectroscopy by Thomas Engel
Thermodynamics, Statistical Thermodynamics, and Kinetics by Thomas Engel & Philip Reid
(The Thermodynamics textbook 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
05/11 Last lecture. Don't forget to submit your Graded HW #5!   Statistics of the current scores in this class are posted below. Answers/Solutions to graded HW #5 problems are here.  
05/06 Ch.17: 17.13-17.14 Graded HW #5 is here. It is due on Tuesday May 11.   Solutions to Exam #2 problems including some comments after exam grading are posted below together with the score statistics on the exam and also of the current total scores, after Exams 1-2 and HWs 1-4.  
05/04 Midterm Exam #2 Exam 2 problems are here. Equations sheet for the exam is here.  Solutions to Exam #2 problems can be found below.  
04/29 Prepare for the midterm exam #2 Equations sheet for the upcoming exam is here. Make sure you are familiar with these equations and which QM systems they correspond to.   Solutions to example problems from the previous years Exam #2 are here.  
04/27 Ch.17.1-17.6, 17.11. Ch.17: Ex.Pr 17.1; Qs: 17.3,10,14,15; Pr: 17.3,17.6. 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:  
The tentative equations sheet for the upcoming Exam #2 is here. Example problems from the previous years Exam #2 are here.  
04/22 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; Pr: 8.7 (what's wrong in this problem?), 8.14, 8.15. Solutions to HW#4 problems are available here  
04/20 Ch.8: 8.1-8.2, 8.9. See lecture notes Don't forget to submit your graded HW#4 which is due on April 22.  
04/15 Ch.12: 12.2-12.4; Ch.8: 8.1-8.2. Ch.8: Ex.Pr: 8.1; Q: 8.4. Don't forget to work on your graded HW#4 which is due on April 22.  
04/13 Ch.10: 10.1-10.3; and 6.2. Ch.10: Ex.Pr. 10.1-10.2; Pr: 10.2, 10.3(matrices), 10.6,10.7,10.10. Your graded Homework #4 (due on Tuesday April 22) is here.
For those who are curious about vector/matrix representations of the wavefunctions and operators -- here is an explanation with some examples. Also posted here is a detailed description of how to determine eigenfunctions of Sx operator and how to answer the question about measuring Sx in the example from the lecture.
Answers/solutions to graded Homework #3 problems are here. 
04/08 Ch.10.1 Ch.10: Qs: 10.1, 10.7, 10.12.  
04/06 Ch.9 to the end, Ch.10.1 Ch.9: Qs: 9.5,9.9; Pr: 9.9, 9.10, 9.12, 9.26. 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.  
04/01 Ch.9: 9.4-9.6 Ch.9: Ex.Pr: 9.3-9.6; Qs: 9.1,9.6,9.10,9.12,9.19; Pr: 9.4, 9.5, 9.7. Graded HW #3 is here. It is due on Thursday April 8.  
03/30 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?    
03/25 Ch.7: 7.5-to the end Ch.7: Ex.Pr 7.6; Qs: 7.7, 7.13; Pr: 7.35, 7.37. Prove the commutator relationship for the square and one of the projections of the angular momentum operator (see lecture notes). Answers/solutions to Exam 1 problems and the score statistics are posted below. 
03/23 Ch.7: 7.5-7.7 Ch.7: Qs: 7.1, 7.3, 7.12, 7.14; Pr: 7.7,7.20, 7.34. Do Exam 1 problem 4A.  
03/11 Midterm Exam #1 Exam 1 problems are here.    
03/09 Review sesssion in preparation for the midterm exam #1. Bring your questions Bring your questions.Solutions to graded homework #2 problems are here. Equations sheet for the upcoming Exam 1 is here Answers/solutions to Exam 1 problems from the previous year are here.  
03/04 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]. Example problems from the previous year Exam #1 are here.  
03/02 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 9, 2021) is here.  
02/25 Ch 7: 7.1,7.3, also 2.1 Ch.7: Qs: 7.1,7.6,7.8; Pr: 7.8,7.15,7.17. Calculate the penetration length for electron using the same model as we used in class for the Harry Potter and Platform 9 3/4 problem For those who are curious: here is a calculation of the probability to find quantum mech anical H.O. outside the allowed range for a classical H.O. To download it click here.  
02/23 Ch.5: 5.1-5.2, 5.6-5.8 Ch.5: Qs: 5.6; Pr: 5.7. Answers to graded Homework #1 problems are here. 
02/18 snowday Video recording of today's asynchronous lecture and the lecture notes have been posted on ELMS: BCHM485_L7_add_snowday.mp4 and BCHM485_L7_add_snowday_notes.pdf. Read: Ch.4: 4.3; Ch.5: 5.3 Ch.4: Pr: 4.17-19, 4.22, 4.23; Ch.5: Pr: 5.4, 5.5.  
02/16 Ch.4: 4.2-4 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.  
02/11 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. Your graded Homework #1 (due on Feb 18, 2021) is here.  
02/09 Ch.4: 4.1. Ch.4: Qs: 4.1,4.3-5,4.11; Pr: 4.4,4.6,4.13. Do the Schoedinger's cat problem from the last assignment.  
02/04 Ch.3: 3.4. Ch.4: Pr: 4.5. Question: Schroedinger's cat was found alive in 64% experiments and dead in 36%. Reconstruct the wavefunction of the cat. See also HW exercises on the last pages of the lecture notes  
02/02 Ch.3: 3.4-3.5 (3.6). Ch.3: Qs: 3.9-3.10; 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?  
01/28 Ch.2: 2.5,2.6,2.7; 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  
01/26 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 at ELMS. 
before 01/26 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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