Physical BioChemistry: BCHM 485

Spring 2013

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
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
05/13 Final Exam: Monday, 8:00am(!!!).    
05/09 The second part of the class today will be a mini-review session to help you prepare for the final exam: please bring your questions!!! Don't forget to do the online course evaluation!!! Equations help sheet for the final exam can be found here
05/07 Read handout material on polymer chain statistics to the end . Do homework problems 4-8. Solutions to HW4 can be found here.
05/02 Ch.15: 15.1-15.6. Handout material on polymer chain statistics can be downloaded from here. Read pages 1-4. Handout notes on the random-walk model are here. Follow the derivations. Homework problems (+solutions) on polymer chain statistics are here. Do problems 1-3. An example of Homework #4 from the previous year is here. Statistics of the distribution of the scores on Exam #2 and of the current total scores are posted below.
04/30 Ch.14: 14.1,14.2; Ch.15: 15.1-15.6 (skip 15.3.6) Ch.15: Qs: 15.1-15.10; Pr: 15.2-15.4,15.12,15.28. Your graded Homework #4 (due Tue May 7, 2013) is here. Solutions to exam #2 problems are posted below.
04/25 TSK: Ch.14: 14.3-14.10 + Example Problems. Ch.14: Qs: 14.3-14.6, 14.10-14.13; Pr: 14.1, 14.10, 14.14, 14.18. Consider 1 mole of He gas at standard conditions. Calculate the molecular partition function of He.  
04/23 Midterm Exam #2 Don't forget to bring a pen/pencil and a calculator.After the exam: TSK: Read Ch.13 till the end; Ch.13: Qs: 13.4,13.8; Prs: 13.6,13.9,13.11,13.18,13.22.  
04/18 Prepare for the midterm exam #2 Answers and solutions to your graded Homework #3 problems are here.  
04/16 TSK: Ch.12; Ch.13: 13.1-13.5 Ch.13: Qs: 13.1-13.3,13.5; Pr: 13.1,13.5,13.12,13.16; E xample Probl.13.5, 13.6. Using a calculator, assess the accuracy of Stirling's approxi mation for N!: at what value of N the accuracy becomes better than 10%? 1%? Equations help sheet for the upcoming exam #2 can be found here. An example of midterm exam #2 problems (with solutions) from last year is here.
04/11 Ch.17: 17.3-17.6, 17.9, [17.14]. Ch.17: Pr: 17.3, 17.6, [for those who are curious how matrix/vector representation of quantum mechanics works: 17.7]. Determine the resonance frequencies for 1H, 13C, 15N at the magnetic field of the Earth (~50,000 nT). Compare your results with the resonance frequencies of the same nuclei when placed in the 600 MHz spectrometer (i.e. at the magnetic field corresponding to 1H frequency = 600 MHz). The magnetogyric ratios can be found in Table 17.1.  
04/08 Ch.17: 17.1-17.2, 17.11, [17.12-17.13]. Ch.17: Ex.Pr 17.1; Pr: 17.3. 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 1 and 2.
04/04 Ch.8: 8.8 plus previous assignments (8.3-8.7). Ch.8: Qs: 8.8 + 8.1, 8.7, 8.10, 8.12 ; Pr: 8.36 + 8.6, 8.11, 8.25, 8.28. Do your graded Homework #3! An example (with solutions) of HW3 from the previous year is posted here: HW3_2012 
04/02 Ch.8: 8.3-8.7. Ch.8: Ex.Pr: 8.2-8.6; Qs: 8.1,8.2,8.7,8.9,9.10,8.12,8.13; Pr: 8.6, 8.7, 8.14, 8.25, 8.28. Your graded Homework #3 (due April 11, 2012) is here.  
03/28 Ch.8: 8.1,8.2,8.9 Do Example problem 8.1. Q: 8.4.  
03/26 Ch.10: 10.2-3; Ch.12: 12.1-12.2, 12.4-12.8. Ch.12: Ex.Pr: 12.3; Q: 12.14,15,17,18,19.  
03/14 Ch.10: 10.1-10.3, [10.4-10.6 optional], Ch. 6.2 Ch.10 Ex.Problem: 10.2; Qs: 10.1,10.5,10.7,10.10,10.12,10.16; Pr: 10.2, 10.3 (matrices), 10.6,10.7. Solutions to midterm exam #1 problems and some score distribution statistics can be found below. Solutions to midterm exam #1 problems and some score distribution statistics can be found below.
03/12 Ch.9: 9.4-9.6 Ch.9: Example Problems: 9.3,9.4,9.6; Qs: 9.7,9.9,9.10,9.12,9.15,9.16,9.18,9.19; Pr: 9.4, 9.6-9.8, 9.12, 9.13; Determine Bohr's radius if the the only interaction in the H atom was gravitational. The same for a proton-neutron or neutron-neutron pair.  
03/07 Ch.9: 9.1-9.3 Ch.9: Example Problems: 9.1-9.2; Qs: 9.1-4, 9.8; Show that exp(-r/a) is a solution to the Shroedinger Eq. for H-atom; determine a and E. Compute the degeneracy of the energy level corresponding to the principal quantum number n.  
03/05 Midterm Exam #1. Don't forget to bring a pen/pencil and a calculator! An example of midterm exam problems (with solutions) from last year is here. Answers/solutions to HW#2 problems are here.  
02/28 Ch.7: 7.5-7.8 Ch.7: Qs: 7.2-7.4,7.12,7.14; Pr: 7.2,7.4,7.6,7.7 Equations help sheet for the upcoming exam can be found here. Answers/solultions to HW1 problems are here.
02/21 Ch 7: 7.2, 7.4 Ch.7: Ex.Pr.: 7.4,7.5; Q: 7.4,7.5,7.11,7.15,7.19; Pr: 7.10,7.21,7.25,7.35(b). Your graded Homework #2 (due Feb 28, 2013) is here. An example (with answers/solutions) of HW#2 from the previous year can be found here. Also you can find some useful Equations and table integrals here
02/19 Ch.7: 7.1, 7.3 Ch.7: Ex.Pr.: 7.3, 7.4; Qs: 7.1,7.10; Pr: 7.11,7.13,7.14,7.16,7.18. Normalize the wavefuncion corresponding to the ground state of H.O. Calculate the average x^2 in this state.  
02/14 Ch.6:6.1,6.3,6.4, (6.5,6.6) Ch.6: Example Prs: 6.3, 6.4, Qs: 6.5-6.8, 6.14,6.15,6.19; Pr: 6.7,6.9,6.11,6.16,6.23  
02/12 Ch.5: 5.1-5.3, 5.6-5.8 and Ch.2.1 Ch.5: Pr: 5.4, 5.7; estimate your wavelength  
02/07 Ch.4: 4.2-4.4 Ch.4: Qs: 4.15,4.20; Pr: 4.11,4.16,4.28,4.29. Your graded Homework #1 (due Feb 14, 2013) is here. Q&A2.   An example (with solutions) of HW#1 from the previous year is here.
02/04 Ch.4: 4.1-4.2 Ch.4: Ex.Pr. 4.1; Qs: 4.1,4.3-5,4.9,4.11,4.12,4.14; Pr: 4.4,4.9,4.10,4.12,4.27  
01/31 Ch.3: 3.1-3.5 Ch.3: Qs: 3.10-3.12; Pr: 3.5,3.6,3.12 Q&A1 
01/29 Ch.2: 2.3,2.4-2.7; Ch.3: 3.1-3.4. Ch.2: Ex.Pr: 2.3,2.4; Pr: 2.12; Ch.3: Qs:3.2,3.3,3.6-3.10; Pr: 3.2,3.8,3.9  
01/24 QCS: Ch.1 & Ch2:2.2-2.3 Example probl: 1.3. Questions in the end of Ch.1: 1.1-1.3,1.5. Using Wien's displacement law ( λmax*T=1.44/5 cm*K ), do the following: (1) estimate λmax for your body radiation, and (2) assuming that λmax = 600 nm for the Sun's radiation, estimate the temperature on the Sun's surface  
Exam # 1: Exam # 2: Final Exam:
Statistics Statistics Statistics
Solutions Solutions Solutions
     

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