Physical BioChemistry: BCHM 485

Spring 2017

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 Molecular Thermodynamics textbook by McQuarrie & Simon 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]
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Date Reading Problems Q&A
05/15 Final Exam: Monday, 8:00am(!!!).    
05/11 Review session. Bring your questions! Don't forget to do the online course evaluation!!!

Tentative equations help sheet for the final exam is here.  
The statistics of you current total scores (prior to the final exam) are posted below under Exam #2 Statistics. 
05/09 TSK Ch.15: Ch15: Pr. 15.5,7,12. Solutions to HW4 can be found here.  
05/04 TSK: Ch.14 and Ch.15: 15.4, 15.6. Ch.14: Ex. Pr: 14.4. Using your calculator find out how big the values of N should be in order for the Stirling formula to achieve 10% accuracy, 1% accuracy. Solutions to Exam #2 problems are posted below along with the statistics of your current grades.  
05/02 TSK: Ch.13 till the end; and Ch. 14. Ch.13: Qs: 13.6,13.9-11; Pr: 13.9,13.10,13.14. Your graded Homework #4 (due Tue May 9, 2017) is here.  
04/27 Midterm exam #2    
04/25 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 (https://myelms.umd.edu/) under Files. In McQuarrie: Ch.3.1-3.2, and MathChapters B, E TSK: Ch.13: Qs: 13.1-13.3,13.5; Pr: 13.1,13.7,13.12,13.19; Example Probl.13.5, 13.6. In McQuarrie: Pr.3.8. Slides from today's lecture lllustrating the use of NMR spectroscopy in Biochemistry and Structural Biophysics can be found on the course canvas website (https://myelms.umd.edu/) under Files.  
04/20 Ch.17: 17.3-17.6. Here is the link to educational videos illustrating various aspects of Nuclear Magnetic Resonance: http://www.magritek.com/support-videos. You want to watch videos 01, 02, and 04.

Prepare for the second midterm exam that will be given on April 27. A review session for the exam will take place on Mon, April 24, at 6pm in Rm 2118 Biomolecular Sciences Bldg. Tentative equations sheet for Exam #2 is here. Make yourself familiar with these equations.
An example of midterm exam #2 problems from last year is here.. My answers/solutions to these problems are here. I suggest you look at them after you worked on solving the problems yourself.
04/18 Ch.17: 17.1-17.2, 17.11. Ch.17: Ex.Pr 17.1; Pr: 17.3,17.4,17.6,17.7. Solutions to HW#3 problems are here.  
04/13 Ch.8: 8.6-8.8.    
04/11 Ch.8: 8.3-8.6. Ch.8: Ex.Pr: 8.2-8.6; Qs: 8.1,8.2,8.7,8.9,9.10,8.12,8.13; Pr: 8.7, 8.14, 8.15.  
04/06 Ch.8: 8.1,8.2,8.9 Ch.10: Pr: 10.3,10.6. Ch.8: Do Example problem 8.1. Q: 8.4. Your graded Homework #3 (due April 13 ) is here.  For those who are curious about vector/matrix representations of the wavefunctions and operators -- here is an explanation with some examples.
04/04 Ch.10: 10.1-10.3, Ch. 6.2 Ch.10 Ex.Problems: 10.1-10.2; Qs: 10.1,10.5,10.7,10.12,10.16; Pr: 10.2, 10.10.  
03/30 Ch.9: 9.4-9.6; Ch.10: 10.1 Ch.9: Example Problems: 9.1-9.6; Pr: 9.2,9.3-9.7. Assess a possibilty of an atom held together by the gravitational force. Consider a hypothetical atom formed by e and n, or n and n. Calculate the Bohr's radius (a0) and the energy of the ground state and compare them with the corresponding values for the hydrogen atom.  
03/28 Ch.9: 9.1-9.3 Ch.9: Qs: 9.2, 9.4,9.7-9.10, 9.16. Show that exp(-r/a) is a solution to the Shroedinger Eq. for H-atom; determine a and E.  Solutions to Exam #1 problems and scores statistics are posted below.
03/14 Midterm Exam #1 Don't forget to bring a pen/pencil and a calculator!  
03/09 Ch 7: 7.7 and Ch.9: 9.1-9.2. Prepare for Midterm Exam #1. The review session will be held on Monday March 13th at 5:30pm in Rm 2118 Biomolecular Sciences Bldg -- please come and bring your questions. Solutions to 2016 Exam #1 problems are here .  
03/07 Ch.7: 7.5-7.8 Ch.7: Qs: 7.2-7.4,7.12-7.14; Pr: 7.2,7.4,7.7,7.20,7.21. Answers/soluitions to graded Homework #2 problems are here . Equations sheet for the upcoming midterm exam #1 is here . Example problems from the previous year midterm exam #1 are here
03/02 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5; Q: 7.11,7.14; Pr: 7.10,7.21,7.35(b). What are the energies and wavefunctions for a particle in the potential that is infinitely high for x<0 and a harmonic potential for x>=0? A calculation of the probability to find QM HO in the classically forbidden areas can be found here.  
02/28 Ch 7: 7.1, 7.3 Ch.7: Ex.Pr.: 7.2,7.3. Qs: 7.1,7.5,7.6,7.8. Pr: 7.8,7.14,7.16,7.19. Your graded Homework #2 (due Mar 7, 2017) is here. Answers/soluitions to Homework #1 problems are here .  
02/23 Ch.5: 5.3; Ch 7: 7.1 Ch.5: Pr: 5.4,5.5; Ch.7: Ex.Pr.: 7.1.Harry Potter and the Platform 9 3/4: calculate the penetration length as we did in class, but this time for (1) a proton and (2) an electron. Reminder: Vo = m*g*H, where H = 2 meters. Assume the same velocity as for Harry, i.e. v = 4 m/s.  
02/21 Ch.6:6.1,6.3,6.4, (6.5,6.6) 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. Evaluate the commutator [A,BC]. Using Heisenberg's equation, estimate the minimum uncertainty in the velocity of a particle (piece of chalk) with mass of 1 g if its position is known with 1 micrometer precision. Will you be able to notice such an uncertainty? Perform the same calculation for the hydrogen atom.  
02/17 Ch.4: 4.3; Ch.5: 5.1-5.2, 5.6-5.8 Ch.4: Pr: 4.12,4.16-18; Ch.5: Qs: 5.6; Pr: 5.7.  
02/14 Ch.4: 4.4 (4.3) Ch.4: Ex.Pr.4.2-4.4; Compute the quantum number n and the wavelength for an oxygen molecule in the room at room temperature (assume a 1D box of length 10 m). Some trigonometric equations and and identities are here.  
02/09 Ch.4: 4.2 Ch.4: Ex.Pr.4.1; Qs: 4.1-2,4.6,4.9-11,4.14-15,4.18-20; Pr: 4.9,4.10,4.29. Your graded Homework #1 (due Feb 16, 2017) is here.  
02/07 Ch.4: 4.1 Ch.4: Qs: 4.3-5,4.11; Pr: 4.4-4.6,4.13.  
02/02 Ch.3: 3.1-3.5 (3.6) Ch.3: Qs: 3.9-3.10; Pr: 3.12,3.14,3.16 (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?  
01/31 Ch.2: 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:3.2-3.9; 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. 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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