Proposal to Make BCHM 465 and BCHM 485 Required Courses for the Biochemistry Major

Introduction: The Department of Chemistry and Biochemistry is submitting a request to make BCHM 465 (biochemistry III) and the new BCHM 485 (physical biochemistry; proposed) required courses for biochemistry majors. The present status of 465 is that of an elective; 485 will replace CHEM 482 (physical chemistry II) as a required course. The science and math courses required for the major are outlined below.

Present Courses Supporting

Courses New Program (proposed)

CHEM 143 (5 cr) MATH 140 (4) CHEM 143 (5 cr) CHEM 153 (3) MATH 141 (4) CHEM 153 (3) CHEM 227 (4) BCSI 105 (4) CHEM 227 (4) CHEM 237 (4) PHYS 141 (4) CHEM 237 (4) CHEM 247 (4) PHYS 142 (4) CHEM 247 (4) BCHM 461 (3) BSCI 2xx (3-4) BCHM 461 (3) BCHM 462 (3) BSCI 4xx (3) BCHM 462 (3) BCHM 464 (3) BCHM 464 (3) CHEM 395 (1) BCHM 465 (3) CHEM 481 (3) CHEM 395 (1) CHEM 482 (3) CHEM 481 (3) CHEM 483 (2) BCHM 485 (3) CHEM 425 (4) CHEM 483 (2) Capstone CHEM 425 (4) Capstone Total 45 cr Total 26-27 cr Total 45-8 cr*

*BCHM 465 is an approved capstone. If BCHM 465 is used to satisfy this requirement the total credits would remain at 45 BCHM 465: Although, the addition of BCHM 465 to the major requirements adds three additional credits, there is, in practice, no net increase since the course can be used to satisfy the capstone requirement. Many biochemistry majors take three or more credits of CHEM 399 (undergraduate research, also a capstone) in addition to BCHM 465. Over the last two semesters, spring and fall 2003, the enrollment in BCHM 465 was 46 students. Timing: The BCHM 465 requirement will go into effect for students entering the biochemistry major in Jan. 2004 and after.

Rationale: Molecular biology (genomics, proteomics, bioinformatics, and systems biology) is likely to be one of the major areas of scientific and technological innovation in the coming century. In particular, the Maryland biotechnology corridor (Human Genome Sciences, Celera, TIGR, MedImmune, NIH, NCI, EPA, FDA, IGEN, EntreMed, Gene Logic, Oncor, hundreds of others) is vital to the continuing economic health of the State. Our biochemistry graduates are employed throughout this area and need a strong foundation in biological information processing.

Currently biochemistry majors are exposed to this material bit

by bit, over and over, in patchy and qualitative ways in lower-division biology courses. For example, biochemistry majors know what a DNA polymerase is, that ribosomes make proteins, but not how, and perhaps that DNA is continually damaged and repaired. It is essential the majors take a cohesive advanced course that covers this material (and more) from a rigorous bio/chemical perspective. BCHM 465 is that course, but to date it has not been a graduation requirement. It is estimated that about half of the biochemistry majors take 465, and up to half of the 465 enrollment comes from other majors, including chemistry.

A typical BCHM 465 syllabus is attached.

BCHM 485: The proposal to establish BCHM 485, physical biochemistry, has been submitted (VPAC log # 0313090). 485 will replace CHEM 482 (physical chemistry II) as a degree requirement for biochemistry majors starting in the Fall 2004 semester. It is hoped that the initial offering of 485 will take place in the spring 2004 semester. In the event a biochemistry major has already taken CHEM 482, it will be used as the major requirement in lieu of 485.

____________________ _____________________ Department PCC Chair Department Chair Chemistry & Biochemistry Chemistry and Biochemistry ___________________ Dean College of Life Sciences

Biochemistry 465 (Biochemistry III: Molecular Genetics) — Spring, 2002

TuTh, 9:30-10:45 a.m., Chemistry 0128

Assoc. Prof. Jason D. Kahn, Dept. of Chemistry and Biochemistry, UMCP

Office: Chemistry 2505 (in Biochemistry, Wing 5 of the Chemistry

complex)

Office hours: Weds. 2-3 p.m., Thurs. 1-2 p.m., Chemistry 2505; there is no

TA for the course

Contacting me: kahn@adnadn.umd.edu much preferred to 405-0058. Please do not

drop in to my office or lab, but I will be happy to set up

appointments outside of office hours if necessary. Class web site: http://www.biochem.umd.edu/biochem/kahn/bchm465; there will also be an e-mail reflector.

Course Description:

This course concerns the structure and function of nucleic acids and the mechanisms of nucleic acid transactions: a biochemical approach to molecular genetics. We will generally cover both prokaryotic and eukaryotic systems, emphasizing common logic and mechanisms. Topics are as follows:

• Chemistry and structure of DNA and RNA, from nucleotides to chromosomes,

and some methods for studying, sequencing and manipulating nucleic acids.

Simple bioinformatics.

• Interactions between nucleic acids and proteins.

• Selected aspects of the biochemistry and regulation of DNA replication,

transcription, recombination, and repair, and how these processes interact

with each other.

• Translation, RNA splicing, and general RNA catalysis.

Texts (note that the course is primarily lecture-based):

Required: Weaver, R. F. (2002). Molecular Biology. 2nd ed., WCB/McGraw-Hill, Boston. Excellent source for historical and modern experiments. Also see

http://www.mhhe.com/biosci/cellmicro/weaver2/.

Occasional required reading from the primary or review literature may be provided.

Recommended: Any of the standard Biochemistry texts you have used for BCHM 461, 462, or 463.

Other recommended sources, available on reserve in the White Memorial Chemistry Library:

Bates, A. D. and Maxwell, A. (1993). DNA Topology. Oxford: IRL Press at Oxford University Press. Excellent short monograph on this difficult topic.

Bloomfield, V.A., Tinoco, I., Jr. and Crothers, D.M. (2000). Nucleic Acids: Structure, Properties and Functions. University Science Books, Sausalito

CA. Nucleic acid structure, biophysical chemistry.

Kornberg, A. and Baker, T. A. (1992). DNA Replication. 2nd ed. New York: W.H. Freeman and Co. Great source for historical background, good breadth.

Ptashne, M. (1992). A Genetic Switch: Phage λ and Higher Organisms. 2nd ed. Cambridge, MA: Cell Press and Blackwell Scientific. Heuristics of gene regulation.

Schleif, R. (1993). Genetics and Molecular Biology. 2nd ed. Baltimore: The Johns Hopkins University Press. Eclectic, emphasizing experiments leading to conclusions.

Travers, A. (1993). DNA-Protein Interactions. London: Chapman & Hall. Focuses on DNA structure.

Wolffe, A. (1999). Chromatin: Structure and Function. 3rd ed. San Diego: Academic Press, Inc. Covers from structure to biology.

Requirements, Grading and Academic Honesty Policies:

There will be two 75-minute midterm exams (100 pts each), group class

projects in lieu of a third exam (75 pts), and a two hour final (150 pts).

Exams will be about 50% short-answer questions, testing your comprehension of

lecture material, and about 50% essay or computational questions, testing

your ability to apply and extend this basic knowledge. The final will

explicitly cover only the latter part of the course but will inevitably draw

on older material. There will be a review session before each exam (typically

Tuesday evening before a Thursday exam, or to be determined). Past years’

exams will be on the web site and the answers will be on reserve in the White

Memorial Chemistry Library.

The class projects, to be conducted by small groups, are intended to give you and others an understanding of the sources of our knowledge of molecular machines. Each group of 4-5 students will study a type of DNA/RNA transaction (e.g. replication, transcription, repair, RNA splicing, recombination, translation). The panoply of components involved in the process will be schematized in web page form, with links to pages on the experiments in which they were first identified, their essential functions identified, and their structures if available. Last year’s class did similar projects, with generally excellent results. This year, some groups will refresh previous web pages with more current information, while other groups will do similar work on new topics. The goal is that at the end of this class we will all be proud to make the work generally accessible as a teaching resource useful to the world at large. More information will be provided on the projects.

Your final letter grade will be based on your performance relative to the

class as a whole and to my expectations (i.e. it’s curved, but I draw the

lines between grade levels depending on how I felt the class as a whole

performed). Midterm letter grades will not be assigned. Final grades, with

plus/minus, will be given out only through the MARS system. The exams are

quite difficult, but in the past I have had few complaints about final

grades. I encourage questions and discussion in class, but class

participation does not affect grading.

If you absolutely must miss a midterm exam, you must call me in advance or

within 24 hours after the exam, and you must also present a valid University

excuse, in order to be eligible for the assignment of a grade based on the

remaining course work. If you miss the final, do not turn in a project, or

miss both hour exams, you will receive a failing grade.

The University has an active Student Honor Council, which administers an

Honor Code. The Honor Council sets high standards for academic integrity, and

I support its efforts. Please note in this regard the University Honor

Pledge. The Student Honor Council proposed and the University Senate approved

this Pledge: “I pledge on my honor that I have not given or received any

unauthorized assistance on this assignment/examination.” The Pledge statement

should be handwritten and signed on the front page of all examinations and

the group project. Students who fail to write and sign the Pledge will be

asked to confer with me. (Adapted from

http://www.inform.umd.edu/CampusInfo/Departments/JPO/AI/honorpledge/.)

Furthermore, I otherwise expect and enforce adherence to the University’s Code of Academic Integrity, found at http://www.inform.umd.edu/CampusInfo/Departments/JPO/code_acinteg.html. Specifically, “plagiarism” will be interpreted in its broadest sense: ideas from others must be referenced; words from others must be in quotation marks and referenced (from Phil DeShong). Paraphrasing without referencing will be considered plagiarism. Extensive paraphrasing from a single source is unacceptable, referenced or not. You are hereby specifically directed to read my personal statement on plagiarism as a condition of taking this course, at http://www.biochem.umd.edu/biochem/kahn/plagiarism.html. Please do not test me on this. Plagiarism is surprisingly easy to detect and I will pull the trigger without hesitation.

Lecture Schedule (approximate):

READING ASSIGNMENTS ARE FOR REFERENCE, NOT REQUIRED UNLESS EXPLICITLY STATED.

ALL ASSIGNMENTS REFER TO WEAVER, MOLECULAR BIOLOGY.

I. Nucleic Acid Structure and Chemistry, Protein-Nucleic Acid Interaction (12 lectures)

1. Introduction; nucleic acid building blocks Chapters 1, 2, 3 Central dogma, nucleotide structure, primary structure, chemical stability, nomenclature

1/29/02

2. Structures of double helices Chapter 2 A, B, and Z form helices, base pairing and hydrogen bonding

1/31/02

3. DNA and RNA hybridization and thermodynamics Chapters 2, 5 Base-pair stability rules, melting, hypochromism, hybridization, gene chips

2/5/02

4. RNA structure and triple helices Chapters 2, 19 Tertiary structure and tRNA, prediction of RNA folding, antisense and modified DNA

2/7/02

5. DNA bending, twisting, and supercoiling; topoisomerases Chapters 6, 7, 20 Persistence length, linking number, superhelix structure, topo reaction mechanisms

2/12/02

6. Enzymatic manipulation of nucleic acids Chapters 4, 5 Restriction enzymes, nucleases, radiolabeling, basic genetic engineering, polymerases, PCR

2/14/02

7. Sequencing and synthesis of DNA and RNA Chapters 5, 24 Maxam-Gilbert and Sanger sequencing, genomics, bioinformatics

2/19/02

8. Catch-up day on nucleic acid sequence and structure 2/21/02

9. Methods for studying protein-nucleic acid complexes Chapters 5, 9 Binding curves, mobility shifts, footprinting, in vitro and in vivo crosslinking, structural methods

2/26/02

10. Protein structural motifs for nucleic acid binding Chapters 9, 12 Helix-turn-helix, zinc fingers, bZIP proteins, TBP, hnRNP, etc.

2/28/02

11. Recognition of nucleic acids Chapters 9, 12 Major groove vs. minor groove, hydrogen bonding, direct vs. indirect readout, deformability

3/5/02

—> EXAM I <— Covers through lecture 10 3/7/02

12. Chromosome structure Chapter 13 Nucleosomes, chromatin, higher-order structure, telomeres, effects on transcription

3/12/02

II. DNA Transactions (10 lectures)

13. DNA replication: fundamental mechanisms Chapters 3, 20, 21 Polymerization reaction mechanisms, fidelity, structure

3/14/02

14. Genome replication Chapters 20, 21 Origin recognition and polymerase holoenzyme in E. coli; the cell cycle

3/19/02

15. Transcription: fundamental mechanisms Chapters 6, 8, 10, 11 RNA polymerases, transcription cycle, transcription bubble, supercoiling

3/21/02

Spring Break March 25-29

16. Regulation of transcription in prokaryotes Chapters 7, 8 Repression and activation paradigms: lac operon, araC, ntrC; searching mechanisms

4/2/02

17. Transcription in eukaryotes Chapters 10, 11, 12, 13 Holoenzyme vs. initiation complex assembly, activators, chromatin, recruitment

4/4/02

18. Catch-up day —> PROJECT OUTLINES DUE <—

4/9/02

19. Homologous recombination Chapter 22 Holliday junctions, recABCD

4/11/02

20. Site-specific recombination Chapter 23 λ phage integration/excision, HIV integrase

4/16/02

—> EXAM II <— Covers through Lecture 19 4/18/02

21. DNA repair Chapter 20 BER, NER, mismatch repair, cancer

4/23/02

22. “Interprocess communication” Review of regulatory and biochemical connections among replication, transcription, repair

4/25/02

III. RNA Transactions (5 lectures)

23. Translation: fundamental chemistry, fidelity Chapters 18, 19 tRNA synthetases, peptidyl transferase chemistry, proofreading

4/30/02

24. Translation: mechanism and regulation Chapters 18, 19 Ribosome structure, elongation cycle, mRNA degradation

5/2/02

25. Catalytic RNA Chapter 14 Self-splicing RNA, ribozymes, origin of life

5/7/02

26. RNA splicing Chapters 14, 16 mRNA splicing mechanisms —> PROJECTS DUE <—

5/9/02

27. Review 5/14/02

FINAL EXAM: Covers Lectures 20-27 Tuesday, 5/21/02, 1:30-3:30 p.m., Chem. 0128

A proposal for a new course, Physical Biochemistry (BCHM 485), to replace CHEM 482 as a requirement for the Biochemistry major

BCHM 485, Physical Chemistry for Biochemists Rationale

Biochemistry 485? Why change physical chemistry for biochemists? There are several excellent reasons. First, even our best biochemistry students do not understand the applicability of physical chemistry to their interests in biology and biochemistry. A course tailored more to the application of physical chemistry to biological systems will be much more interesting, useful, and attractive to them. Second, there is far too much physical chemistry to be taught in a year, and inevitably some topics are emphasized more than others. The physical chemistry most useful for biomolecular science, versus a traditional physical chemistry course, concentrates more on statistical mechanics, on modeling and simulation, on the liquid phase, and on polymer dynamics. Finally, biochemistry is becoming a more and more physical science. The recent revolutions in single-molecule methods, in the structural determination of macromolecular complexes like the ribosome, in quantitative simulation methods, and in the understanding of genetic and metabolic networks are all based on physical chemistry techniques and principles. A working knowledge of biophysical chemistry is essential to tomorrow’s biochemist. We are attempting to send our graduates out with rigorous yet practical training in the ideas that will help them bring biology into the 21st century. History and Scheduling

The biochemistry and physical chemistry divisions met in December to discuss these issues, and agreed in outline to the plans below. A committee (Kahn, Fushman, Muñoz, Walker, Weeks) was formed to hash out the details of articulation between 481 and 482 and reasonable syllabi. The goal is to have BCHM 485 in place for the spring, 2004 semester. Drs. Fushman and Muñoz will teach the course initially, with Dr. Fushman as the first instructor. Other faculty who might be suitable include Beckett, English, Hu, Kahn, Lorimer, Thirumalai and future hires in the areas of physical and biochemistry. We anticipate enrollment of about 30-40 students per year. The course is a core requirement for biochemistry majors and will offered both fall and spring semesters. The number of CHEM 482 sections (physical chemistry II for chemistry and chemical engineering majors) will be reduced from 3 to 2 per year. Details of the Proposal 1. Biochemistry majors will continue to take CHEM 481 as before. 481 is slatted to become more

molecules-oriented and less formalism-oriented. As part of this process, it is suggested covering more statistical mechanics in CHEM 481 and reducing some coverage of classical thermodynamics. Rob Walker’s previous and revised 481 syllabi are appended below. In addition, more examples and problems drawn from biochemistry will be used in 481.

2. The physical chemistry track will bifurcate in the second semester. Chemistry majors will take CHEM 482 as before. Biochemistry majors will take BCHM 485 or may opt to take CHEM 482 as before. Credit will not be given for both CHEM 482 and BCHM 485. BCHM 485 will have the same prerequisites as CHEM 482 and will not be a prerequisite for any other course. Many students will have had BCHM 461 and 462 first and these will be useful but not necessary.

3. Biochemistry 485 will be a rigorous, mathematically demanding physical chemistry course emphasizing the principles and applications most relevant to biochemistry. It will focus on three

main areas: (1) statistical mechanics with applications to biochemistry, (2) kinetics from Maxwell-Boltzmann to physical-organic and enzymes, and (3) quantum mechanics with applications to spectroscopy and structure determination. See the attached proposed syllabus by Fushman, Kahn, and Muñoz, which has benefited substantially from commentary by the physical chemistry division. A CHEM 482 syllabus from spring 2003 is included for comparison. The BCHM 485 syllabus is feasible, although ambitious, for a one-semester course. It is similar to courses taught at Madison (offered as a one-semester physical chemistry replacement), UNC (optional course in addition to 2 semesters of physical chemistry), Harvard (one-semester physical chemistry replacement), and Berkeley (two-semester physical chemistry for biologists).

ATTACHED: Syllabi for BCHM 485 (proposed), CHEM 481, fall 2003, CHEM 482, spring 2003.

PHYSICAL BIOCHEMISTRY (PHYSICAL CHEMISTRY FOR BIOCHEMISTS)

BCHM 485

One-semester course, two 75 min or three 50 min lectures per week

Pre-requisite: CHEM 481 Credit will not be granted for both CHEM 482 and BCHM 485

PROPOSED SYLLABUS

Week General area Specific topics, description Reading

1 Statistical thermo-

dynamics

Review the concept of partition functions. Applications to binding equilibria, single- and multicomponent systems, phase transitions. Crystallization.

B: 166-201

2 Statistical thermo-

dynamics

Statistical mechanics of biomolecules as polymer chains: helix-coil transition, protein folding, lattice models, wormlike chain.

EC: 649-686

3 Statistical thermo-

dynamics

Review of solutions (non-ionic and ionic) and polyelectrolytes. Applications in biochemistry: dialysis, equilibrium sedimentation, liquid chromatography.

EC: 271-358

4 Statistical thermo-

dynamics

Transport phenomena, channels, diffusion equation, Brownian motion. Applications in biochemistry: sedimentation and electrophoresis.

EC:700-739

5 Kinetics Kinetic theory of gases. Maxwell-Boltzmann. General kinetics. Differential and integrated rate laws.

B: 651-696

6 Kinetics Transition state theory. Statistical mechanical treatment. Physical organic chemistry: mechanisms of chemical reactions.

B: 702-725

7 Kinetics Liquid phase kinetics. Diffusion limited processes. Kinetics methods in biochemistry: relaxation methods. Enzyme kinetics.

EC: 212-258

8 Quantum Postulates of quantum mechanics. Observables and operators (+operator algebra), the uncertainty principle, wave functions and eigenvalues, Schrödinger equation.

B:273-287

9 Quantum Postulates of quantum mechanics. Quantization of energy, particle-in-a-box, harmonic oscillator, rigid rotor, separation of variables. Quantization of angular momentum.

B: 288-306,316-347

10 Quantum Postulates of quantum mechanics. Hydrogen atom. Electron spin, Pauli principle. Atomic states. Spectroscopy. Selection rules.

B: 352-365,371-382.

11 Quantum Molecules, rotation and vibration, Born-Oppenheimer approximation. Electronic spectra. Optical spectroscopy. Applications to biomolecules: absorption, circular dichroism, vibrational spectroscopy.

B: 403-405, 481-516. EC: 593-604

12 Quantum Fluorescence. Techniques, applications to biomolecules

EC: 582-589

13 Quantum Magnetic resonance spectroscopy (ESR, NMR). Applications to biomolecules.

B:560-582; EC: 605-636

14 Diffraction Scattering. X-ray, electron, neutron diffraction, crystal structures, space symmetry groups. Methods for biomolecular structure determination.

EC: 798-841

Exams and assignments: 3 hour exams (lowest dropped, 40%) final exam (30%) graded homework assignments every 2 weeks (30%) This syllabus is designed to cover topics that are particularly relevant to problems and applications of physical methods to modern biochemistry. Therefore the course is focused on the physical properties of the liquid state, polyelectrolytes, kinetic theory, and statistical mechanics of polymer chains. There is significant emphasis on various experimental techniques: sedimentation, chromatography, electrophoresis, relaxation kinetics, a broad range of spectroscopies applied to biomolecules, and on methods for structure determination. These techniques are used in the everyday work of the biochemistry lab, and a student graduating with a degree in biochemistry must be familiar with their physical background. Mathematical level required: biophysical chemistry is a quantitative discipline. Many of the problems and techniques discussed throughout the course require familiarity with the following mathematical methods: basic vector analysis, derivation and integration techniques, methods to solve differential equations, determinant and matrix calculus. Additional elements of linear algebra will be introduced in the quantum part of the course as required. Textbooks: B : David Ball, Physical Chemistry. Brooks/Cole –Thomson Learning. (Same textbook as CHEM 481) EC : David Eisenberg, Donald Crothers, Physical Chemistry with Applications to the Life Sciences. Benjamin/Cummings Publishing Co. (available in softcover for $69.).

Physical Chemistry I Chemistry 481

FALL 2003 SYLLABUS

General info instructor: Dr. Rob Walker

office: 2224D Chemistry email: rw158@umail.umd.edu phone: 301-405-8667 office hours: Th. 2 p.m. – 3:30 p.m. or by appointment

Lecture: MWF 8:00 am – 8:50 am

1402 Chemistry

Instructional Materials Physical Chemistry by D. Ball (1st edition) Additional reading in Engines, Energy and Entropy (J. Fenn) Class Format Attendance is important and expected. The lectures will supplement the text, define goals, and hopefully stimulate thought and questions. Please try to keep ahead of the lectures in your reading of the assigned text. If a session is missed, it is the student’s sole responsibility to make up any work missed.

Expectations of Students Material Covered in Lecture and Assigned Reading: Students are responsible for all material covered in lecture and in the assigned reading materials that includes supplemental handouts. All attempts will be made by your instructor to adhere to the outline as indicated below. However, the presentation may vary somewhat from that of the textbook.

Academic Honor Principle: Students are expected to observe the University’s Code of Student Conduct. Cheating on examinations and/or problem sets is not acceptable and will be met with zero tolerance!

Problem Sets: There will be no quizzes in Chemistry 481. Instead, problem sets will be handed out weekly or bi-weekly. Often these will consist of assigned problems from the text and several supplemental questions. You are expected to work the problems and hand in the results in discussion. The TA will grade your answers and solution sets will be provided. You are encouraged to discuss these problems with each other. However, it is important for you to learn to work these problems independently, since they mimic typical exam questions and (we hope) the kinds of problem solving skills used by practicing scientists. You may drop your lowest score provided that it comes on a problem set that was handed in. (You will not be able to drop a 0 if you fail to hand in a problem set.)

Exams: You will take three 1-hour exams during the semester in addition to the Final Exam. The hour exams will cover primarily material discussed since the last exam but may include earlier material as well. As you probably have realized by now, chemistry is a subject that builds upon what is already known. Accordingly questions on exams (and problem sets) will frequently require that you use knowledge learned earlier in the semester. The exams themselves will focus on applying

problem solving skills developed in class to new, chemically significant situations. The best way to prepare for exams is to be completely familiar with the problem sets and to relax.

Grading

Exam 1 (The laws of thermodynamics & free energy) 20% Exam 2 (chemical equilibrium & phase transitions) 20% Exam 3 (ionic solutions & electrochemistry) 10% Final Exam (Cumulative) 25% Problem Sets 25%

Tentative dates for Exams 1-3 are as follows: October 6 (Hour Exam 1); November 14 (Hour Exam 2); December 3 (Hour Exam 3). Different weightings of the hour exams approximately reflects the amount of material covered. The Final Exam is Scheduled for Monday, 15 December from 10:30 am – 12:30 pm and will be cumulative. Course Outline Week topics Reading Assignment 3 Sept Equations of state, math review 1.1-1.5 8 Sept Non-ideality (virial, vdW), intro to energy 1.6-1.8, 2.1-2.4 PS1 15 Sept First Law, Enthalpy, Thermochemistry 2.5-2.12 22 Sept Entropy – 2 definitions & Second Law 3.1-3.7 PS2 29 Sept Fund. Eqn., Gibbs Energy 4.1-4.7 PS3 6 Oct Chem potential, fugacities 4.8-4.9, 4.10 HE1 13 Oct Equilibrium: an introduction 5.1-5.6 20 Oct Equilibrium: phanse transitions 6.1-6.7 PS4 27 Oct Equilibrium: multiple components 7.1-7.5 3 Nov Excess functions, activities 7.5-7.9 PS5 10 Nov Ionic solutions (& Debye-Hückel) 8.2, 8.6-8.8 HE2 17 Nov Equilibrium: electrochemical (Nernst Eqn) 8.3-8.5 24 Nov Chem 481 challenge?, T’giving PS6 1 Dec Elements of statistical thermodynamics 17.1-17.5b HE3 8 Dec State functions from stat. thermo. 17.6-17.8, 18.8 PS7 15 Dec. Final Exam! (Monday, 15 December, 10:30 am – 12:30 pm)

PHYSICAL CHEMISTRY II CHEM 482, SECTION 0101, MWF 8

SPRING 2003 CHE-2108

PROFESSOR: Dr. J. H. Moore CHM-2216A tel: 405-1867; e-mail: jm89@umail.umd.edu office hours M 9, W3, and by appointment TEXT: Physical Chemistry by John S. Winn Week Topics Read 29 Jan the calculation of average properties molecular velocities the Maxwell-Boltzmann distribution mean free path pressure from gas molecule dynamics 899-915 3 Feb transport phenomena diffusion thermal conductivity viscosity 952-982 10 Feb Planck relation de Broglie relation postulates of quantum mechanics operators and operator algebra uncertainty principle wave functions and eigen values Schrödinger Equation 349-371 17 Feb particle-in-a-box harmonic oscillator separation of variables rigid rotor 388-415 24 Feb hydrogen atom angular momentum electron spin 415-440 EXAM 1 (28 Feb) 3 Mar helium atom orbital approximation antisymmetrization 451-459, 468-475, 479-488 term symbols 10 Mar H2+ molecular orbitals (MO's) H2

FEMO 498-516, 519-527 17 Mar molecular electronic configurations molecular term symbols 536-553 BREAK 31 Mar molecules rotation and vibration Born-Oppenheimer approximation 691-717 EXAM 2 (4 Apr) 7 Apr spectroscopy selection rules rotation-vibration spectra electronic spectra 665-682, 720-732 14 Apr reaction kinetics rate law reaction mechanisms 997-1016 21 Apr temperature dependence collision theory 1018-1022, 1039-1058 28 Apr transition state theory catalysis 1058-1063, 1081-1089 EXAM 3 (2 May) 5 May a brief introduction to statistical mechanics thermodynamic variables from statistical mechanics transition-state theory from statistical mechanics 819-826, 830-833, 852-859, 864-865, 1063-1067 __________________________________________________________________ PREPARATION: Physical chemistry is a fairly rigorous and mathematical topic. It is important to keep abreast

of the reading and lectures. With reading, homework problems and exam preparation, you may anticipate a minimum of six hours/week of work outside class. The reading assignment for each week should be read before coming to lecture Monday morning. Take notes as you read. Pay particular attention to the "Practice with Equations" at the end of each chapter. The professor for this course is notoriously lazy and can be expected to crib from this section when writing exams.

QUIZZES: A brief quiz on the reading assignment each Monday morning. Reading notes may be used

when taking the quiz. HOMEWORK: Homework will be assigned each Friday and will be due the following Friday. Late homework

will not be accepted. GRADING: Homework--20% Quizzes--20% Hour Exams--20% each, one exam grade will be dropped, no makeups Final--20% FINAL EXAM: 10:30 AM-12:30 PM, Friday, 16 May in CHE-2108.