Physical BioChemistry: BCHM 485

Spring 2020

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
E-mail: fushman@umd.edu

Syllabus

Textbooks

Required:
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.)
Recommended:
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.
 
Assignments:
Reading and problems are either from Quantum Chemistry & Spectroscopy [QCS] or from Thermodynamics, Statistical Thermodynamics, and Kinetics [TSK]
Date Reading Problems Q&A
05/15 Final Exam: Friday May 15, 8:00am(!!!).    
05/12 TSK: Ch.15: 15.2, 15.4, 15.5 Video recording of this lecture (Lecture #25) as well as a PDF version of the lecture notes are available via ELMS, under Files. The lecture notes are also temporarily available here. The video recording is also temporarily available at the following link: https://www.loom.com/share/2b8e3b735b6948d2afef209fa85b0c26 Ch.15: Pr: 15.3, 15.5, 15.12, 15.13. Prepare for your final exam (more info in the lecture video recording). Tentative equations help sheet for the final exam are here Answers/solutions to HW4 problems can be found here. The statistics of you current total scores (prior to the final exam) are posted below together with Exam #2 Statistics.
05/07 TSK: Ch.14: 14.3-14.7, 14.10 (you can skip 14.5.3). Video recording of this lecture (Lecture #24) as well as a PDF version of the lecture notes are available via ELMS, under Files. The lecture notes are also temporarily available here. The video recording is temporarily also available at the following link: https://www.loom.com/share/48acecf52e9f440ba25ba29034f8c707 Ch.14: Qs: 14.4, 14.9, 14:10; Ex.Pr: 14.1-4,14.6,14.10. Pr: 14.14,14.26. Don't forget to finish and upload your graded HW #4.  
05/05 TSK: Ch.13: to the end; Ch.15: 15.4 (skip 15.4.1). Video recording of today's lecture (Lecture #23) as well as PDFs of the lecture notes are available at ELMS, under Files. The lecture notes are also temporarily available here. The video recording is also temporarily available at the following link: https://www.loom.com/share/b5d9d5bc49254788b8e0d4ddfd9f3e5c Ch.13: Q: 13.6,9.11. Pr: 13.9,10,14, and 15.3. Your graded HW #4 is here. It's due by 10am on Tuesday May 12. Solutions to Exam #2 problems will be posted below along with the statistics of your current grades.  
04/30 Midterm Exam #2 Equations sheet for the exam is here.   
04/28 TSK: Ch.12 (refresh your memory on statistics and combinatorics), Ch.13: 13.1-5. The reading material can be found on ELMS website under Files: look for file names starting with TSK. Video recording of today's lecture (Lecture #22) as well as PDFs of the lecture notes and slides are available at ELMS, under Files. The lecture notes are also temporarily available here and copies of the slides shown in the lecture are here. The video recording is also temporarily available at the following link: https://www.loom.com/share/13f74b44cd6043dda6f5ef76576168b6 Ch.13: Ex.Pr: 13.5-6; Qs: 13.1-3,13.5; Pr: 13.1, 13.7, 13.12, 13.19, 13.20, 13.27. Using your calculator find out how big (or small) the values of N should be in order for the Stirling's formula to achieve 10% accuracy, 1% accuracy (see slides from today's lecture). Do the same for the logarithm formula: ln(N!) = N*lnN - N (you might need Matlab or other program for this).  
04/23 Ch.17: 17.3-17.5, 17.13-17.14. Video recording of today's lecture (Lecture #21) as well as PDFs of the lecture notes and slides are available at ELMS, under Files. The lecture notes are also temporarily available here and copies of the slides on the use of NMR in biochemistry are here. The video recordingis also temporarily available at the following link: https://www.loom.com/share/cc4cf3cf536848a28d87004efe6b9bf4 Ch.17: Ex.Pr 17.1; Qs: 17.3,10,14,15; Pr: 17.3,17.6.
Prepare for the second midterm exam that will be given on April 30.
An example of midterm exam #2 problems from last year is here.. My solutions to the exam problems can be downloaded from here. I strongly suggest you look at them only after you worked on solving the problems yourself.
 
04/21 Ch.8: 8.8, [8.7], and 17.1-17.2, 17.11. Video recordings of today's lecture (Lecture #20, parts 1 and 2) as well as PDFs of the lecture notes are available at ELMS, under Files. The lecture notes are also temporarily available here for part 1 and for part 2. The video recordings are also temporarily available at the following links: https://www.loom.com/share/1a7af440f7d54fdca4a2d64f2583fc9a https://www.loom.com/share/28ef336f2bd744d5ae8cea7279ac2ba2 Ch.17: Ex.Pr 17.1; Qs: 17.14. Here is the link to educational videos illustrating basic aspects of Nuclear Magnetic Resonance discussed in today's lecture: http://www.magritek.com/support-videos. You want to watch videos 01 and 02. They are also available on YouTube:
video 1: http://www.youtube.com/watch?v=7aRKAXD4dAg
video 2: https://www.youtube.com/watch?v=jUKdVBpCLHM&t=336s  
 
04/16 Ch.8: 8.3-8.6 [8.7]. A video recording of today's lecture (Lecture #19) as well as a PDF of the lecture notes are available at ELMS, under F iles. The lecture notes are also temporarily available here. The video recording is also temporarily available at the following link: https://www.loom.com/share/dd33a528d300438a8f0047a690b7cfd6 Ch.8: Ex.Pr: 8.2-8.6; Qs: 8.1,8.2,8.7,8.10,8.12,8.17,8.20; Pr: 8.7 (what's wrong in this problem?), 8.14, 8.15. Solutions to graded homework #3 problems are here. 
04/14 Ch.8: 8.1-8.2, 8.9. A video recording of today's lecture (Lecture #18) as well as a PDF of the lecture notes are available at ELMS, under Files. The lecture notes are also temporarily available here. The video recording is also temporarily available at the following link: https://www.loom.com/share/15fee8e987d345a9aceb115daf704544 Ch.8: Ex.Pr: 8.1; Q: 8.4.  
04/09 Ch.10: 10.1-10.3; Ch. 12: 12.1-12.4. A video recording of today's lecture (Lecture #17) as well as a PDF of the lecture notes are available at ELMS, under Files. The lecture notes are also temporarily available here. The video recording is also temporarily available at the following link: https://www.loom.com/share/b6be78eca8b44b1ea9bc0e54372c106a Ch.10: Ex.Pr. 10.1-10.2; Pr: 10.2, 10.3, 10.6,10.7. Your graded Homework #3 (due on Thursday April 16 ) is here.
For those who are curious about vector/matrix representations of the wavefunctio ns and operators -- here is an explanation with some examples.
 
04/07 Ch.10: 10.1-10.3 & Ch.6: 6.2. A video recording of today's lecture (Lecture #16) as well as a PDF of the lecture notes are available via ELMS, under Files. The lecture notes are on Canvas and temporarily here. The video recording is also temporarily available at the following link: https://www.loom.com/share/db05f5ef2727478280c85db691e2e9f1 Ch.10: Ex. Pr. 10.1-10.2, Qs: 10.1,10.7,10.12, 10.15. Pr: 10.2, 10.10.
 
04/02 Ch.9: 9.4-9.6 Lecture 15: video recordings of parts 1 and 2 of this lecture can be found on Canvas and temporarily are also available at https://www.loom.com/share/e1d10230c3ee438b897dc9a92a0d2cbe https://www.loom.com/share/4554bcbbb1594f66894ec36d2e414231
Lecture notes are on Canvas and temporarily here.
Ch.9: Example Problems: 9.3-9.6; Qs: 9.6,9.12,9.13,9.19; Pr: 9.4, 9.5, 9.7. In addition, do the following problems:

Calculate the average potential energy of electron in the 2s and 2p orbitals and assess if the relationshiop = 2*En which we obtained in class for the 1s orbial still holds.

Handwritten notes on solving Schroedinger equation for H atom are temporarily here 
03/31 Ch.9: 9.1-9.4. Lecture 14: video recording of this lecture is on Canvas and temporarily also available at https://www.loom.com/share/e951262061c7428682d47cb5befe9d17. Lecture notes are on Canvas and temporarily here. Ch.9: Qs: 9.1,9.4,9.7,9.8,9.10,9.16. Pr: 9.2,9.6. Ex.Pr: 9.1,9.2,9.3. Show by direct calculation that exp(-r/a) is a solution to the Shroedinger Eq. for H-atom when l=0; determine the values of a and E. What is the degeneracy of the energy level of hydrogen atom with the principal quantum number n Solutions to Exam 1 problems and class scores statistics are posted below. 
03/12 Ch.7: 7.5-7.8; Ch.9: 9.1-9.2 Qs: 7.2,7.3,7.112,7.14, Prs: 7.6,7.34. 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.   The video materials related to lectures 2-4 will be removed from ELMS after March 30th in order to make space for the new lecture materials. If you want to have access to these videos, please download them before that date.
03/10 Midterm Exam #1 Don't forget to bring a pen/pencil and a calculator!  
03/05 Preparation for the midterm exam #1. After the exam: Ch.7: 7.5,7.7 Example problems (with solutions) from the previous year Exam #1 are here. A review session for the upcoming midterm exam will be held on Friday March 6 from 4-5 pm in Rm 2118 in Biomolecular Sciences Bldg (2nd floor of the same building where my office is located). Bring your questions. After the exam: Ch.7: Qs: 7.12, 7.14; Pr: 7.7,7.20. Solutions to graded homework #2 problems are here.  
03/03 Ch.6: 6.1,6.3,6.4 Ch.6: Example Prs: 6.3, 6.4, 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].  
02/27 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5. Qs: 7.11,7.19. Pr: 7.10,7.21, 7.35(b). Your graded Homework #2 (due on Mar 5, 2020) is here. Example problems from the previous year Exam #1 are here.  
02/25 Ch 7: 7.1,7.3, also 7.2 Ch.7: Ex.Pr.: 7.3; Qs: 7.1,7.6,7.8; Pr: 7 .8,7.15,7.17. Answers to graded Homework #1 problems are here. 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.  
02/20 Ch.4: 4.3; Ch.5: 5.3 Ch.4: Pr: 4.17-19, 4.22, 4.23; Pr. Ch.5: Pr: 5.4, 5.5. Calculate the penetration length for a hydrogen atom and for electron using the same model as we used in class for the Harry Potter and Platform 9 3/4 problem.  
02/18 Ch.5: 5.1-5.2, 5.6-5.8 Ch.5: Qs: 5.6; Pr: 5.7. Happy Potter and the Basilisk problem.  
02/13 Ch.4: 4.2,4.4; also Ch. 2.1 Ch.4: Ex.Pr.4.1-4.3; Pr: 4.12,4.16. Think of the Happy Potter and the Basilisk problem.  
02/11 Ch.4: 4.2 Ch.4: Qs: 4.1-2,4.9-10,4.14-15,4.18-20; Pr: 4.9,4.10,4.28,4.29.Do the Schroedinger's cat problem from the last assignment. Your graded Homework #1 (due on Feb 18, 2020) is here. Some useful trigonometric equations and and identities are here.  
02/06 Ch.4: 4.1. A video recording of a last year ecture containing some of the mateal covered today is available on ELMS (BCHM485_L_4.mp4) along with a PDF version of that lecture notes. Ch.4: Qs: 4.3-5,4.11; Pr: 4.4-4.6,4.13. Question: Schroedinger's cat was found alive in 64% experiments and dead in 36%. Reconstruct the wavefunction of the cat.  
02/04 Ch.3: 3.1-3.5 (3.6) A video recording of this and the previous lecture is available on ELMS (BCHM485_L2_3.mp4). A PDF version of the lecture notes from that video is also available on ELMS as well as here. 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?  
01/30 Ch.2: 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  
01/28 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 01/28 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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