Core Course Overview AY 2011

The chemistry department offers 11 core courses, 10 of which are taught in any one year. These are:

• CHEM 2110 Chemical Symmetry: Applications in Spectroscopy and Bonding • CHEM 2120 Descriptive Inorganic Chemistry • CHEM 2210 Electroanalytical Chemistry • CHEM 2220 Chemical Separations • CHEM 2230 Analytical Spectroscopy • CHEM 2310 Advanced Organic Chemistry 1 • CHEM 2320 Advanced Organic Chemistry 2 • CHEM 2430 Quantum Mechanics & Kinetics • CHEM 2440 Thermodynamics & Statistical Mechanics • CHEM 2810 Biological Chemistry 1 • CHEM 2820 Biological Chemistry 2 Two of the italicized courses are taught each year.

For AY 2011 (beginning August 2010), we are offering in the Fall term (2011) the following courses (Instructor) • CHEM 2120 Descriptive Inorganic Chemistry (Meyer) • CHEM 2230 Analytical Spectroscopy (Saxena) • CHEM 2310 Advanced Organic Chemistry 1 (Nelson) • CHEM 2430 Quantum Mechanics & Kinetics (Coalson) • CHEM 2810 Biological Chemistry 1 (Weber)

In the spring (term 2014), we are offering these courses (Instructor) • 2110 – Chemical Symmetry: Applications in Spectroscopy and Bonding (H. Liu) • 2220 – Chemical Separatioins (Robinson) • 2320 – Advanced Organic Chemistry 2 (X. Liu) • 2440 – Thermodynamics and Statistical Mechanics (Jordan) • 2820 – Biological Chemistry 2 (Horne)

On the following pages, please find syllabuses for the courses that will be taught next year. In some cases, an older syllabus is provided. Chem 2110 Spring 2010

Group Theory and Physical Inorganic Chemistry Topics and Readings

Topic Cotton I. Group Theory and Molecular Symmetry A. Introduction 1 B. Symmetry operations and symmetry elements 1. Definitions 3.1, 3.2 2. Types of symmetry operations 3.3-3.10 C. Symmetry point groups 1. Criteria for abstract groups 2.1, 2.2 2. Symmetry point groups 3.11, 3.12 3. Assignment of point groups 3.14, 3.15 4. Subgroups and classes 2.3, 2.4, 3.13 D. Matrix representations of symmetry operations and symmetry point groups 1. Matrices Appendix 1 2. Matrix representations of symmetry operations 4.1 3. Representations of groups 4.2 4. Irreducible representations 4.3 5. Reducing reducible representations 4.3 6. The character table 4.4, 4.5 7. The direct product 5 II. Molecular vibrations A. Introduction 10.1 1. Molecular energy levels and spectra 10.1 2. Vibrational spectroscopic methods B. Molecular vibrations 1. Harmonic oscillator 2. Anharmonic oscillator 3. Normal modes C. Projection Operators 6 D. Construction of symmetry coordinates 1. Internal coordinates 2- 2. A worked example: [PtCl4] 10.7 3. Correlations with decreasing symmetry E. Selection rules 1. Direct product 5 2. Infrared selection rules 10.6, 10.8 3. Raman selection rules

Chem 2110 Spring 2010

Topic Cotton III. Chemical Bonding A. Introduction 1. Models of electronic structure a. Lewis structures b. Atomic orbital model c. Hybrid orbital (Valence bond) model d. Valence-shell electron-pair repulsion (VSEPR) model 2. Photoelectron spectroscopy a. Technique b. PES of atoms c. Molecular PES B. Basic concepts of bonding and orbital interaction 1. Molecular orbital theory 7.1, 7.2 a. Definitions b. Orbital overlap c. Orbital interaction energy d. Energetics of 2-center, 2-orbital interactions e. Molecular orbital coefficients 2. The construction of MOʼs a. Molecular orbitals of H2 b. Potential energy surfaces c. PES of H2 d. Diatomic molecules e. Molecular orbital coefficients C. Case studies 8.1-8.4 1. ABn-type molecules a. General procedures b. A worked example: NH3 c. Walsh correlation diagrams 2. Polyenes and conjugated systems 7.3-7.5, 7.7 IV. Metal complexes 8.6-8.8 A. Coordination complexes B. Rearrangements C. Organometallic complexes D. M-M bonded complexes E. M-L multiple bonding V. Optional Topics (Crystals, Materials, etc.)

Chemistry 2110 Spring 2010

Chemical Symmetry: Applications in Spectroscopy & Bonding

Instructor: Geoff Hutchison Important Dates: Office: Eberly 316 th Phone: 412-648-0492 January 5 – First class th E-mail: [email protected] February 4 – Exam 1 th Web: courseweb.pitt.edu March 6-14 – No class, Spring Break March 23rd – No class, ACS Meeting Meetings: Tu., Th. 11-12:15 March 25th – Exam 2 Due th Eberly 228 April 29 – Final Due

Textbook: F.A. Cotton, Chemical Reserve Reading List Applications of Group Theory; Group Theory 3rd ed., Wiley, 1990. • F. A. Cotton, Chemical Applications of rd Optional Materials: Group Theory; 3 ed., Wiley, 1990. • A. Vincent, Molecular Symmetry and Group Theory; 2nd ed., Wiley, 2001. Molecular Models (Foundation • J. S. Ogden, Introduction to Molecular Set for General and Organic Symmetry, Oxford UP, 2001. Chemistry, Jones and Bartlett Publishers; available in book store). General Inorganic Chemistry • D. F. Shriver, P. W. Atkins, C. H. Course Outline: Langford, Inorganic Chemistry, 2nd ed.; I. Molecular Symmetry Freeman, 1994. & Group Theory • S. H. Strauss, Guide to Solutions for II. Molecular Vibrations Inorganic Chemistry, 2nd ed.; Freeman, III. Chemical Bonds & MO Theory 1994. IV. Metals & Additional Topics • F. A. Cotton and G. Wilkinson, Advanced Inorganic Chemistry, 6th ed.; Wiley, 1999. Grading • J. E. Huheey, E. A. Keiter, R. L. Keiter, • Exam 1 25% Inorganic Chemistry, 4th ed.; Harper • Exam 2 (Take-Home) 30% Collins, 1993. • Final (Take-Home) 30% • B. Douglas, D. McDaniel, J. Alexander, • Homework & Quizzes 15% Concepts and Models of Inorganic Chemistry, 3rd ed.; Wiley, 1994. Homework Experimental Methods • R. S. Drago, Physical Methods for Homework assignments will be Chemists, 2nd ed.; Saunders, 1992 graded for completeness only. • E. A. V. Ebsworth, D. W. H. Rankin, S. Working in groups is encouraged but Cradock, Structural Methods in Inorganic each individual must hand in a Chemistry, 2nd ed.; CRC Press, 1991 separate set of answers. Chemistry 2120 Prof. N.L. Rosi Fall 2009

Descriptive Inorganic Chemistry

Chemistry 2120 Fall 2009

Instructor: Nathaniel Rosi Office: 1018 E-mail: [email protected]

Class: Course Outline:

T,Th 5:30-6:45 pm I. Introduction and Review of Basic Eberly 228 Concepts, Elementary Group Theory II. Coordination Chemistry Textbooks/Readings: III. Main Group and Organometallic Chemistry

IV. Special Topics Crabtree

The Organometallic Chemistry of the Transition Metals, 4th ed. Grading: John Wiley & Sons, 2005. Problem Sets Other Required Readings will be distributed (100 pts total) throughout the semester. 3 Exams I encourage you to supplement your studies by (I, 100pts; II, 100pts; III/Final, 200 pts) reading sections of an undergraduate inorganic textbook (I have placed several on reserve in the science library) which may be relevant to the Office Hours topics discussed in class. This is particularly important during the first two sections of the Schedule an Appointment on Monday, course. Tuesday, or Wednesday afternoons. For more details, see next page under ‘Office Hours’.

Chemistry 2120 Prof. N.L. Rosi Fall 2009

Description Modern inorganic chemistry is an incredibly broad field. Chemists belonging to the ‘sub-fields’ of bioinorganic chemistry, organometallic chemistry, supramolecular coordination chemistry, solid-state chemistry, synthetic nanoscience, and polymer chemistry (among others) often have received formal training in inorganic chemistry. This diversity, naturally, is very exciting. In constructing a course on “Descriptive Inorganic Chemistry”, however, one must pick and choose only a few topics. Because students generally have different backgrounds and depths of experience in inorganic chemistry, we will begin by reviewing a selection of fundamental core topics. We will then proceed to focus mainly on coordination chemistry and organometallic chemistry. Throughout the semester, relevant papers and topics from the current literature will be used to illustrate the concepts addressed in the course. The last few class periods will be devoted to special topics.

Participation Feel free to participate in class and ask questions. If you have a question, chances are other students have the same question. I’ll do my best to answer them! In cases where a question requires a lengthy explanation, it is better to ask after class or schedule an appointment with me to discuss the topic 1-on-1.

Homework There will be a number of homework assignments which will be collected and graded. Homework counts for 20% of your grade. Homework is provided for practice and study purposes. As long as you demonstrate exceptional effort (see below) on the homework assignments, you can expect to earn most of the points. I will collect homework at very specific times (typically before lecture). I will not accept late homework.

Exceptional effort is defined as follows: 1) Clear, thorough, and thoughtful answers to all the questions 2) Neat and clean presentation of answers (you should give me the final draft of your homework, not a working draft) 3) Acknowledge your co-workers (if you worked in groups)

Exams Exam I will cover introductory and fundamental concepts material and will be worth 20% of your grade. Exam II will cover coordination chemistry and will be worth 20% of your grade. Exam III/Final will cover main group, organometallic chemistry, special topics, and selected topics from Exam I and II and will be worth 40% of your grade.

Although each of the exams cover specific blocks of material, you can expect to see concepts on the second exam which were covered on the first exam and likewise concepts on the third exam which were covered on the previous two exams.

Office Hours I do not keep formal office hours. If you would like to schedule a meeting with me to discuss the coursework, please e-mail me with a few possible meeting times. I am typically available to meet on Tuesdays and Thursdays.

Disability If you have a disability for which you are or may be requesting an accommodation, please contact both me and the office of Disability Resources and Services (Contact info below) as soon as possible so that we can make any necessary arrangements. The Disability Resources and Services office is located in William Pitt Union, Room 216. Their phone number is (412) 648-7890. They will be able to verify the disability and determine reasonable accommodations for this course. Chemistry 2120 Prof. N.L. Rosi Fall 2009

Summary of Lectures and Readings (in italics)

1. September 1 7. September 22 Distributed Reading a. Begin Coordination Chemistry a. Course Information b. Common Ligands/e- counting b. Basic Quantum c. Nomenclature c. Periodic Table d. Structure d. Shielding e. Isomerism e. Electron Configurations f. Periodic Trends 8. September 29—EXAM I g. Rules and Exceptions 9. October 1 2. September 3 Distributed Reading/Undergraduate Relevant Chapters from Undergraduate Inorganic Text Inorganic Text a. Bonding Theories a. Bonding b. Valence Bond Theory b. Lewis Dot Structures c. Crystal Field Theory c. VSEPR d. MO Theory d. Distribute Problem Set #1 e. Distribute Problem Set #3

3. September 8 10. October 6 My notes extract information from Distributed Reading various texts, primarily the distributed a. Crystal Field Theory (in depth) chapters from Miessler and Tarr a. Intro to group theory 11. October 8 b. Symmetry elements Distributed Reading c. Symmetry operations a. Preparative methods b. Trans effect 4. September 10 c. Mechanisms See Sept. 8 for reading d. COLLECT PROBLEM SET #3 a. Matrices e. Distribute Problem Set #4 b. Groups c. Character tables 12. October 13—NO CLASS d. COLLECT PROBLEM SET #1 e. Distribute Problem Set #2 13. October 15 Distributed Reading; Crabtree Chapter 5. September 15 13 See September 8 a. Isolobal Analogy a. Character Tables (ctd) b. Applications b. Bonding Theories c. Modern Coordination Chemistry c. Valence Bond Approach i. Bioinorganic d. MO Theory ii. Supramolecular iii. Solid-State 6. September 17 See September 8 a. MO Theory b. Walsh diagrams c. COLLECT PROBLEM SET #2

Chemistry 2120 Prof. N.L. Rosi Fall 2009

14. October 20 21. November 12 My notes extract information from Crabtree Chapter 4 & 6 various texts. All essential information a. Substitution Reactions will be included in my lecture and lecture b. Oxidative Addition notes. c. Reductive Elimination a. Main group chemistry d. COLLECT PROBLEM SET #5 b. COLLECT PROBLEM SET #4 e. Distribute Problem Set #6

22. November 17 15. October 22—EXAM II Crabtree Chapters 7&8 a. Migratory Insertion b. Nucleophillic and Electrophilic 16. October 27 Addition Crabtree Chapter 2 a. Start organometallic 23. November 19 b. Ligand types Crabtree Chapter 9 c. Electron counting a. Intro to Catalysis d. Basics of catalysis b. Hydrogenation e. Important background 24. November 24 17. October 29 Crabtree Chapters 9&12 Crabtree Chapter 3 & 4 a. Hydroformylation a. Lewis Base Ligands b. Carbonylation b. Carbonyls c. Polymerization c. Phosphines d. Coupling Reactions d. Hydrides e. COLLECT PROBLEM SET #6 e. Distribute Problem Set #5 25. Thanksgiving—No Class

18. November 3—NO CLASS 26. December 1 Crabtree Chapters 9&12 19. November 5 a. Coupling Reactions Crabtree Chapters 3&11 b. Metathesis a. Alkyls b. Aryls 27. December 3 c. Carbenes Crabtree Chapters 9&12 d. Alkylidenes a. More Catalysis e. Carbynes b. Special Topics

20. November 10 28. December 8 Crabtree Chapter 5 a. Special Topics/Review a. Alkenes b. Alkynes 29. December 10—EXAM III/FINAL c. Arenes d. Cp Ligands

SYLLABUS CHEM 2120 Fall 2010 INSTRUCTOR: TARA MEYER OFFICE: 1008 CSC IMPORTANT DATES

EMAIL: [email protected] Aug 30th First Day of Classes

October 6th (Exam 1-tentative) MEETINGS: October 11th: Fall Break (Class will meet on the Monday & Wednesday 8-9:15 am 12th instead) Eberly Hall 228 November 24-28th Thanksgiving Break December 13-18th Final exam TEXTBOOK: Required: Inorganic Chemistry 4/E Authors: PROJECT Miessler and Tarr ISBN 97801 361 28663 Publisher: Prentice Hall There will be an ongoing project with (An E-textbook subscription is available from assignments given throughout the semester CourseSmart: 978-0-321-67707-5). focused on identifying the frontiers and growth

areas of Inorganic Chemistry. Using the Optional: Solutions Manual 4/E Authors: Chemical Literature and the Internet, class Miessler and Tarr ISBN 97801-361-28670 Publisher: Prentice Hall members will define the frontiers, identify the leaders and the rising stars in the field, examine the problems driving the research, and judge COURSE OUTLINE: which areas will see the greatest growth in the next decade. Some assignments will be I. Bonding and Periodicity individual and some will be done in groups. II. Main Group Chemistry III. Coordination Chemistry IV. Organometallic Chemistry/Catalysis REVIEW V. Materials and Solid State Chemistry VI. Bioinorganic Chemistry Our textbook is an advanced undergraduate book which some of you may have used as a Note: Symmetry, Group Theory and text previously. We will review some of the Spectroscopy will not be emphasized since more basic material at the beginning of class those are the topics of focus in 2110 (offered in but we will proceed quite rapidly and move the Spring). through to the later chapters that were likely never discussed (or covered only briefly) in your GRADING: undergrad classes. Thus, a great deal of the responsibility for mastering the basics will be Mid-term exam 100 yours. I will, of course, be available to help you Final exam 150 if you need extra explanation and guidance. Homework 25 Frontiers Project and Presentation 100 Chemistry 2210: Electroanalytical Chemistry

Fall Semester, 2009.

Instructor: Prof. Adrian C. Michael [email protected] (preferred mode of contact) Rm 901, Chevron Science Center (the chemistry building) Office hours: by appointment

Textbook: Electrochemical Methods: Fundamentals and Applications, second edition By Allen J. Bard and Larry R. Faulkner Published by John Wiley and Sons (The solutions manual is optional but recommended)

Software: During this course, students will develop their own code to simulate electrochemical experiments. Students may select any programming language and graphics package for this work. The instructor recommends Excel and will provide instruction on the use Excel’s Visual Basic macro language.

Objectives: The main objective of this course is to understand electroanalytical experiments involving the flow of current under potential control. This requires an appreciation of thermodynamics, kinetics (heterogeneous and homogenous), and mass transport as they apply to electrochemical systems.

A secondary objective is to know the major figures in the field of electroanalysis and to know their respective contributions to the field. To meet this objective, readings from the original literature will be used to complement the text book.

A secondary objective is to foster independent thought and creativity. Students will develop a proposal that either develops or applies electroanalytical systems and/or techniques. Students will submit their proposal in written form to the instructor and will present (defend) their proposal to the class. Details will be provided in class.

Course Outline:

Please note: this class schedule is only approximate and is provided mainly to give an overview of the course topics and the order of the reading assignments.

Week 1 Overview of Echem Chapter 1 M, Aug 31 Basics of electrodes, cells, pot’l, and current. Estimates of W, Sept 2 i‐t and i‐V Week 2 Enjoy the week off!! M, Sept 7 No Class (Labor Day) W, Sept 9 No Class (Dr Michael travelling) Week 3 Thermodynamics Chapter 2 M, Sept 14 Cell potentials W Sept 16 Interfacial potential difference Week 4 Electrochemical Kintetics Chapter 3 M, Sept 21 Butler‐Volmer model W, Sept 23 Estimated i‐V w/kinetics Week 5 More Kinetics M, Sept 28 No Class (Dr Michael travelling) W, Sept 30 Marcus Theory (a brief look) Week 6 Mass Transport Chapter 4 M, Oct 5 Fick’s Laws – planar systems W, Oct 7 Fick’s Laws – other geometries A first look at simulations Appendix B Week 7 Potential Step Experiments Chapter 5 M, Oct 12 Semi‐infinite planar diffusion T, Oct 13 Microelectrodes W, Oct 14 Heterogeneous kinetics Sat, Oct 17 FIRST EXAM Week 8 Potential Sweeps Chapter 6 M, Oct 19 The i‐t‐V response W, Oct 21 Kinetics & Microelectrodes Week 9 Instrumentation Chapter 15 M, Oct 26 Op amps/analog circuits W, Oct 28 Application of computers Week 10 Hydrodynamic Methods Chapter 9 M, Nov 2 RDE and RRDE W, Nov 4 Electrochemical detectors (LC, CE, etc.) Parts of Chap 11 Week 11 Coupled Homogenous Reactions Chapter 12 M, Nov 9 Kinetic schemes W, Nov 11 Pulse and sweep results Week 12 The Double Layer Chapter 13 M, Nov 16 Models of the electrode‐solution interface W, Nov 18 Adsorbates Sat, Nov 21 SECOND EXAM Week 13 Modified Electrodes Chapter 14 M, Nov 23 Polymers, films, enzymes, etc. W, Nov 25 No Class (Thanksgiving Break) Week 14 Scanning Probe Techniques Chapter 16 M, Nov 30 Scanning electrochemical microscopy (SCEM), AFM, STM, W, Dec 2 etc. Week 15 Electrochemiluminescence (ECL) Chapter 18 M, Dec 7 Systems Proposals due today W, Dec 9 Applications Week 16 Time, date, and location TBA Final Exam Week

Class Activities:

Examinations: There will be three exams during the course, on the dates listed above. Details regarding the exam expectations will be given in class well prior to each exam. Please note that the two midterms are scheduled for Saturdays. This benefits students by removing the time constraint of the class period. However, the exams will not be open ended – again, we’ll discuss this closer to the time. The exams will take place on the scheduled dates – the covered material will depend on our progress through the material. The final exam will be partially comprehensive but the main focus will be material covered in the last third of the course. All exams will be in‐class (no take homes) and students are expected to work independently and in a manner consistent with the University’s academic code of conduct.

Homework: Students are urged to work the majority of the problems in the text book, using the Solutions Manual as an aid (but not a crutch!). However, these problems will not be collected and graded. Please consider this independent homework as necessary preparation for the exams. Some problems will be discussed in class, as appropriate and/or useful. Students wishing to hear a discussion of any particular problem should feel free to say so.

Projects: Throughout the semester, students will develop simulations of potential pulse and sweep experiments that include the effects of diffusion geometry (simple cases), heterogeneous kinetics, and coupled chemical reactions. These simulation projects must be completed in order to pass the course. However, since there can be no ‘partially correct’ simulation results (the simulations are either right or wrong, no one cares about the latter!), these simulation projects will not be graded. The idea is that the simulations will be a learning tool to promote your understanding: of course, examination questions based on the simulations are possible. For the advanced simulation projects later in the semester, small groups of students will be asked to tackle specific problems and report back to the class on their results – details will be discussed as the date approaches.

Biographies: Each student will research the life, times, and accomplishments of a prominent electroanalytical chemist and give a brief (5‐10 min) synopsis of the individual’s contributions to the field. Students should discuss their choice with Prof. Michael after preliminary research. Students may complete this assignment at any point during the semester (actually, the earlier the better). Several electrochemists have received Nobel Prizes and other internationally recognized awards (ACS Awards, etc.) or are (were) members of the National Academy in US or other prominent bodies in Europe and Asia – these should be high on your list of choices!

Proposal: Each student will develop a proposal idea that is based on, utilizes, or advances electroanalytical systems, principles, or techniques. The proposal will be in the form of a 10‐page (double spaced) paper, with appropriate citations. Each student will give an in‐class presentation of their proposal to the group: the audience (including Prof. Michael!) will ask “difficult” questions and the student presenter will vigorously defend his or her idea(s). The proposals will include a) a properly researched literature review to support a clearly stated hypothesis or main objective and b) a brief outline of a research plan. Each student will discuss his or her proposal idea with Prof. Michael before the end of October, after conducting preliminary literature research. Presentations will take place during November. Students may rewrite or otherwise adjust their written proposal based on feedback to the presentation. Proposals in their final form are due Dec 7th.

Determination of Semester Grades: Semester grades will be determined on the basis of your three exam scores, your grade on the proposal, and class participation (including but not limited to your biography and proposal presentations, response to questions, and questions posed, etc.). The three exams and the proposal will contribute roughly equally to the final semester grade. Class participation will be 10‐15% of the overall evaluation. Reminder: although the simulation projects will not be formally assigned a grade, your semester grade will be “F” if they are not completed properly and in a timely fashion. CHEM 2220 (37454 AT) CHEMICAL SEPARATIONS SPRING 2010

INSTRUCTOR: Dr. Renã A. S. Robinson Assistant Professor of Chemistry Office: Room 111, Eberly Hall E-mail: [email protected] (subject: CHEM 2220)

LECTURES: Mon & Wed 6:00-7:15 pm – Eberly Hall 307 OFFICE HOURS: appointment only

REQUIRED TEXT: There is no single textbook for this course. We will use a compilation of chapter excerpts from several textbooks and supplemental text materials. I have obtained copyright permission to provide you access to these excerpts. The fee for this permission will be no more than $50 and should be paid to Michele Monaco in the business office. A final grade will not be issued without payment of this fee.

SUPPLEMENTAL TEXT: The text books listed below are on reserve in the Chemistry Library. Visit Courseweb at http://courseweb.pitt.edu for the chapter excerpts, supplemental articles, reviews, lecture notes, problem sets, and grades.

1.) ―An Introduction to Separation Science‖ Karger, Snyder, and Horvath , 1973 John Wiley & Sons

2.) ―Unified Separation Science‖ Giddings, 1991 John Wiley & Sons

3.) ―Principles and Practice of Modern Chromatographic Methods‖ Robards, Haddad, & Jackson Academic Press 1994

4.) ―The Essence of Chromatography‖ Poole Elsevier Science 2002

COURSE OBJECTIVES:

In this course we will address the fundamental aspects associated with the theory of various separation techniques, an overview of the instrumentation and specifics governing instrumental components, and applications of the various methods in different fields and industries. A broad thermodynamic and kinetic framework compassing all chemical separations is used to classify techniques. Concepts such as band broadening and separation efficiency are generalized. The most powerful and widely used separations techniques are chromatographic, thus solution chemistry will be discussed to provide a chemical framework for chromatography. Other separation methods are also widely used such as electrophoretic separations both in the condensed phase and gas-phase (i.e. ion mobility spectrometry), solid-phase extraction, and centrifugation. Finally, mass spectrometry detection will be introduced as it is often coupled to chromatographic and electrophoretic separations. CLASS LECTURE SCHEDULE – Spring 2010

Date Topic Reading Assignments

Week 1 Wed, Jan 6 Course Introduction & History

Week 2 Mon , Jan 11 Diffusion, Mass & Flow Transport KSH Chap 3, Giddings Chap 3, 4 Wed, Jan 13 ―‖

Week 3 Mon, Jan 18 NO CLASS – MLK HOLIDAY Wed, Jan 20 Thermodynamics & Equilibrium KSH Chap 2, Giddings Chap 2

Week 4 Mon, Jan 25 ―‖ Wed, Jan 27 Chromatography Theory & Background KSH Chap 5, Giddings Chaps 10-12

Week 5 Mon, Feb 1 ―‖ Wed, Feb 3 ―‖

Week 6 Mon, Feb 8 ―‖ Wed, Feb 10 Exam 1

Week 7 Mon , Feb 15 Gas Chromatography RHJ Chap 3, Poole Chaps 2,3 Wed, Feb 17 ―‖

Week 8 Mon, Feb 22 ―‖ Wed, Feb 24 Liquid Chromatography RHJ Chaps 5, 6

Week 9 Mon, Mar 1 LC Wed, Mar 3 Problem Sets – PITTCON

Week 10 Mon, Mar 8 NO CLASS – SPRING BREAK Wed, Mar 10 NO CLASS – SPRING BREAK

Week 11 Mon, Mar 15 LC Wed, Mar 17 Problem Sets – PITTCON LECTURE

Week 12 Mon, Mar 22 LC Wed, Mar 24 LC-Instrumentation

Week 13 Mon , Mar 29 Centrifugation/SPE Banff, Simpson Chap 5 Wed Mar 31 Exam 2

Week 14 Mon, Apr 5 Electrophoresis Theory & Background Wed, Apr 7 Gel Electrophoresis

Week 15 Mon, Apr 12 Capillary Electrophoresis/MEKC Wed, Apr 14 Ion Mobility Spectrometry

Week 16 Mon, Apr 19 IMS/Mass Spectrometry Wed, Apr 21 Mass Spectrometry de Hoffmann & Stroobant Chaps 1-3

Week 17 Mon, Apr 26 Paper Due Mass Spectrometry Wed, Apr 28 Exam 3

** Every effort will be made to keep to the lecture schedule but note that the schedule is tentative. However, exam dates will be given as shown in the schedule.

GRADING:

Three Exams: 60% Written report: 15% Oral presentation: 15% Problem sets: 10%

Final letter grades will typically be assigned as follows, however I reserve the right to adjust the scales for letter grades depending on the overall performance of the class:

A > 90%, B 80-89.9%, C 70-79.9%.

There will be no make-up exams for missed exams unless arranged in advance for appropriate reasons.

ASSIGNMENTS:

Reading assignments are expected to have been read prior to class.

In-class Participation: As this is a graduate course, in-class participation is expected, encouraged, and is mandatory.

Problem Sets:

Problem sets will be assigned in lecture periodically throughout the course. Students will be placed into small groups (of 3 or 4) and will work together to complete the problem sets. Different groups will be assigned for each problem set. One member of the group (decided by you) will be responsible for submitting the assignment, however all group members should sign their names on the assignment. It is your responsibility to master the skills necessary to successfully complete each of the problems. A single grade will be provided to all group members. You will be asked to complete peer evaluations in which case I will only consider individual grading for extreme cases where there is an unequal distribution of work. There will be opportunities during the semester for students to work on problem sets during the assigned lecture times.

Written assignment:

Papers must be turned in on or before the beginning of class on the assigned date - NO EXCEPTIONS will be made to this policy. Students will submit a paper that does one of the following: 1) describe a novel separation method, 2) suggest a significant improvement to a current separation method, or 3) summarize and critique a very recent (within last 5 years) development in one of the separation methods discussed in the course. Regardless of the option chosen, the paper should address at least two of the fundamental principles of separation such as selectivity, peak capacity, detection limits, multidimensional separations, resolution, band broadening, sensitivity, analysis time, etc. The paper should be written in the form of a grant proposal (e.g., NIH format) and include the following sections: Title, Abstract, Background and Significance, Specific Aims, Introduction, Experimental Design, Preliminary Results (can come from the literature), Major Findings (or Expected Findings if Options 1 and 2 are chosen), and Conclusions/Future Outlook. The total number of pages should be no more than 8 pages, 1 ½ spacing, 11 point Arial font, ½‖ margins, not including figures, tables, and references. Plagiarism will not be tolerated in any fashion on this assignment. Cite your sources and others’ work appropriately. I strongly encourage you to discuss your plans for this assignment with me as early as possible.

Oral presentation:

Each student will give an individual presentation that covers a recent application (within 10 years) of one of the separation methods discussed in the course. The presentation can cover more than one peer-reviewed journal article, especially if the applications or techniques are similar or if a series of papers come from the same research group. The articles should come from highly respected journals within the field and have a considerable impact factor. The presentation should provide a clear summary of the article and students are expected to critique the experiments, results, and/or significance of the work presented. Areas for critique can be based on the fundamentals covered in this course. The article selection(s) and an outline of the presentation should be approved with Dr. Robinson at least one week prior to the scheduled presentation date. The article chosen for this assignment must be different than the written assignment.

ACADEMIC INTEGRITY:

Students in this course will be expected to comply with the University of Pittsburgh's Policy on Academic Integrity. Any student suspected of violating this obligation for any reason during the semester will be required to participate in the procedural process, initiated at the instructor level, as outlined in the University Guidelines on Academic Integrity. This may include, but is not limited to, the confiscation of the examination of any individual suspected of violating University Policy. Furthermore, no student may bring any unauthorized materials to an exam, including dictionaries and programmable calculators.

Cheating/plagiarism will not be tolerated. Students suspected of violating the University of Pittsburgh Policy on Academic Integrity, noted below from the February 1974, Senate Committee on Tenure and Academic Freedom reported to the Senate Council, will be required to participate in the outlined procedural process as initiated by the instructor. A minimum sanction of a zero score for the quiz or exam will be imposed.

The integrity of the academic process requires fair and impartial evaluation on the part of faculty, and honest academic conduct on the part of students. To this end, students are expected to conduct themselves at a high level of responsibility in the fulfillment of the course of their study. It is the corresponding responsibility of faculty to make clear to students those standards by which students will be evaluated, and the resources permissible for use by students during the course of their study and evaluation. The educational process is perceived as a joint faculty-student enterprise which will perforce involve professional judgment by faculty and may involve –without penalty—reasoned exception by students to the data or views offered by faculty.

Disabilities:

If you have a disability for which you are or may be requesting an accommodation, you are encouraged to contact both your instructor and the Disability Resources and Services 216 William Pitt Union, (412) 648-7890/(412) 383-7355 (TTY), as early as possible in the term. DRS will verify your disability and determine reasonable accommodations for this course. Chemistry 2230: Spectroscopy Spring 2004 – 3 Credits Course Information and Syllabus

Instructor: Sunil K. Saxena, 801 Chevron Science Center Phone: (412) 624-8680 Email: [email protected]

Course Hours and Location: Tue Thu 11:00 am - 12:15 pm, Eberly 228

Recommended texts: “Symmetry and Spectroscopy”, Daniel C. Harris and M. D. Bertolucci This book will be useful for discussing electronic and vibrational spectroscopies. “Spin Dynamics: Basics of Nuclear Magnetic Resonance”, Malcolm Levitt Class lectures on magnetic resonance will follow the approach used in this book.

Course Goals: To provide you the necessary tools to judiciously integrate the use of various spectroscopic methods in your research.

Course Objectives: Systematically survey spectroscopic methods associated with each part of the electromagnetic spectrum, and gain familiarity with current literature on applications of these techniques to problems in chemistry, physics and biophysics.

Office Hours: Please feel free to contact me about any issue relating to the class. It is best if you seek an appointment. Emailing me with suggestions of times suitable for you would be the best approach. This will also be a good way to get a quick response to a short question. You can always drop by my office or lab (718 CSC) if you like. If this arrangement is inconvenient we can schedule formal office hours.

Course Grading: In class examinations, term-project and project-presentation. Grades Distribution: Mid-Term 1: 20 % Mid-Term 2: 20 % Final Exam: 30 % Term Project: 20 % Presentation: 10% Exams: There will be two in-class exams during the semester. The first exam will be on Tuesday February 17th and the second on Thursday March 18th. Each will be about 75 minutes long. Final exam is tentatively scheduled for April 22nd. Coverage for each exam will be outlined in class at least a week before the exam. You will be allowed to bring in a 8.511 inch sheet of paper with fundamental constants, parameters, and any key equations or material that you will feel will help in the exam. No make-up exams will be given unless arranged in advance for a serious illness or extreme emergency. Make-up must be taken within a week of the scheduled exams. Assignments: To aid the study of class material you will be given regular assignments (roughly one every two weeks). You will find that a thorough understanding of each problem set will help you in the examinations. You are encouraged to work collaboratively to solve the problem sets. Assignments will not be graded. Term Project: You will be asked to choose a research paper and write a term paper on this research. You paper should identify key technical issues and critically assess the use of a spectroscopic technique within this area. The hope is that this project will allow you to integrate this coursework with your research interests and will serve as a useful resource over the years to come. I expect that you will make several one- on-one appointments with me to help you define and execute your projects. By Tuesday February 3rd, you will need to prepare a short description (maximum 1 page) of your paper. Your write-up should clearly highlight the problem as well as THE key reference that you plan to use for your term paper. There should be no more than 3 references overall. This report will not be graded but I will offer suggestions for the final term paper. No duplication of term papers will be allowed. I expect that you will make several one-on-one appointments with me to help you define and execute your project. By Thursday April 8th, you will submit a final written report that describes the background, methodology, and results of your chosen research article in your own words. Present the material in a logical way. You should start with the motivations and important questions that the authors address, and the techniques they use. Clearly outline the technical issues that were addressed to make scientific progress. Then present their new discovery and end with your assessment of the work and future research directions. This summary should not exceed 5 pages or include more than 15 references. This report will be graded. Your report should clearly go beyond class and book material and rely on recent research articles. You should seek at least one meeting with me in order to best define your research area. Please bring a brief abstract (half a page) and some journal articles with you for that meeting. Plagiarism: Your reports will be based on published material but should be demonstrably your own. Each report should encapsulate your understanding of the research material in your own words. You should carefully acknowledge any phrase or idea that is somebody else’s. Simply rephrasing someone else’s argument is still considered plagiarism. Plagiarism in any form is completely unacceptable in professional science. It is therefore important to give credit where it is due. Ask me if you are unsure of what is and isn’t appropriate. Presentation: You will educate the rest of the class about your paper by giving a short 15-minute oral presentation. Your talk should be targeted to a Pitt graduate student who has not taken this spectroscopy class, i.e. do not assume that your audience is familiar with the subject material.

Syllabus

Introduction to Spectroscopy: Review of Quantum mechanics, Quantization, electromagnetic radiation, interaction of radiation with matter. General Principles of Spectroscopy.

Vibrational Transitions: Vibrational/Rotational levels, transitions, selection rules, IR and Raman Spectroscopy, Instrumentation, Applications.

Electronic Transitions: Molecular Orbitals, Absorptions and UV/Vis Spectroscopy, Fluorescence, Green Fluorescent Proteins, applications to single molecule biophysics and polymer physics. Instrumentation

Transitions between Zeeman Levels: Spins, Zeeman levels, Magnetization and its evolution, detecting magnetic resonance signals, Spectrometer. Relaxation, multiple Pulses, 2D NMR/ESR, Applications: diffusion, Imaging, and dynamics. Course Schedule

Note: The schedule of lectures is tentative, although every effort will be made to stay on schedule. However, the dates of the exams are definite.

January 6 (T) 8 (Th) Lecture 1 Lecture 2 - Syllabus - Radiation - Introduction to Spectroscopy

13 (T) 15 (Th) Lecture 3 Lecture 4 - Review of Quantum Mechanics - Quantization of Energy levels

20 (T) 22 (Th) Lecture 5 Lecture 6 - Selection Rules, Einstein Coefficients, populations - Interaction of Radiation with matter

27 (T) 29 (Th) Lecture 7 Lecture 8 - Diatomics-Electronic and Vibrational levels - anharmonic oscillators

February 3 (T) 5 (Th) Lecture 9 Lecture 10 - Rotational-vibrational spectra of Gaseous - IR spectroscopy of Polyatomics molecules Application: Photoactive Yellow Protein (Research Summary Due)

10 (T) 12 (Th) Lecture 11 Lecture 12 - Raman Spectroscopy, CARS Imaging -Electronic Transitions, Molecular Orbits

17 (T) 19 (Th) Lecture 13 Midterm Exam 1 (OUT OF TOWN) - UV/Vis: Selection Rules

February 24 (T) 26 (Th) Lecture 14 Lecture 15 - Fate of the Excited State - single molecule biophysics, optical tweezers, and thermal motions of DNA

March 2 (T) 4 (Th) Lecture 16 Lecture 17 - Spins, magnetization, T - Flourescence Resonance Energy Transfer 1

16 (T) 18 (Th) Lecture 18 Lecture 19 - Spins in a magnetic field, precession Midterm Exam 2

23 (T) 25 (Th) Lecture 20 Lecture 21 - RF pulses, MR Spectrometer - Details: Chemical Shifts and couplings

30 (T) April 1 (Th)

Lecture 22

- J-coupling continued - multiple pulses, T1, dynamics, correlations and 2D NMR

6 (T) 8 (Th) Lecture 23 Lecture 24 - COSY and J-couplings Imaging (one- - 2D Spectroscopy dimensional) (Write-Up due)

13 (T) 15 (T) Lecture 25 Lecture 26 - Special Topics - Special Topic

20 (Th) 22 (T)

Lecture 27 - Special Topics Final Examination (tentative)

Chemistry 2310 Advanced Organic Chemistry MW 12:00-1:15 PM

Instructor Paul Floreancig CHVRN 1203 (412)624-8727 [email protected]

Course Overview In addition to being a vibrant field on its own, physical organic chemistry is the cornerstone for many other diverse disciplines of study such as synthesis, medicinal chemistry, molecular design, and bioorganic chemistry. A solid foundation in physical organic principles will be essential for organic chemists to explore applications in nanotechnology. Physical organic chemistry encompasses numerous areas of study, and cannot be covered completely in one semester. This course approaches the subject largely from a qualitative perspective, with the ultimate objective being the ability to apply first principles to relevant issues like enhancing reactivity, manipulating equilibria, improving binding interactions, and suppressing undesired reactions. The course will cover thermodynamic analyses of molecules and reactive intermediates, kinetics, and reaction mechanisms. If time permits we will cover molecular recognition. While the material will focus on principles, literature examples that highlight applications of topics to synthesis and other disciplines.

Prerequisites A strong background in undergraduate level organic chemistry and a good work ethic are required.

Grading Grades will be based on two midterm exams, one final exam, and one special project. Tentative dates for the midterms are October 6 and November 15. Problem sets will be handed out weekly but will not be graded. We will discuss the problem sets in recitation. Feel free to work in groups. Most of your future work will be done at least somewhat collectively, so get used to working together as soon as possible.

Recitation We will have one recitation each week. The time will be set through class consensus. No new material will be introduced at the recitation, but we will look at course topics in greater detail.

Text Modern Physical Organic Chemistry by Eric Anslyn and Dennis Dougherty. A solutions manual can also be purchased and is recommended. While we will not be using it directly for the class, The Art of Writing Reasonable Organic Reaction Mechanisms by Robert Grossman is a good resource for the topic.

Order of Topics • Molecular geometries - Classical models - Deviations from the ideal - Molecular orbital theory - Structures of reactive intermediates • Thermodynamics - Entropy explained (sort of) - Bond dissociation energies - Heats of formation and additivity tables - Conjugation and aromaticity - Sources of strain • Conformational analysis - Saturated acyclic and cyclic systems - Unsaturated systems - Molecular mechanics • Stability trends in reactive intermediates - Cation stability - Acidity and anion stability • Stereochemistry - Terminology and examples - Transient chirality - Analytical methods • Transition state theory - Rates and rate constants - Practical consequences • Mathematical kinetics - Analysis of numerous scenarios - Steady state approximation • Experimental kinetics - Isotope effects - Linear free energy relationships • Catalysis - Origins - Various models • Reaction mechanisms - Nucleophilic displacement reactions - Enolate reactions - Elimination reactions - Additions to carbonyl groups - Additions to alkenes and alkynes - Radical reactions - Migrations - Pericyclic reactions • Molecular associations Syllabus: Advanced Organic Chemistry II Chem 2320, Spring 2010 Course Number 12612 MW 12:00-1:15, Eberly 228

Instructor: Professor Kay M. Brummond, Ph.D. E-mail: [email protected] Office Location: 807 Chevron Science Center Office Hours: By Appointment

Course Schedule:

Jan 6, 11, 13 *Chapter #1, The Basics ¶ Pages 1-79 The basics of retrosynthetic analysis and synthetic strategies. Synthesis of six membered rings and the Diels-Alder reaction January 20 quiz #1 Jan 25, 27, Feb 1 *Chapter #2, Polar Reactions Under Basic Conditions And §Pages 3-54, Planning Organic Synthesis and Selectivity $Study Named reactions from the Grossman Chapter #2 in “Strategic Applications of Named Reactions in Organic Synthesis” Feb 3 quiz #2 Feb 8, 10, 15 *Chapter #3, Polar Reactions Under Acidic Conditions $Study Named reactions from the Grossman Chapter #3 in “Strategic Applications of Named Reactions in Organic Synthesis” Feb 17 quiz #3 Feb 22, 24, March 1, Synthesis of five membered rings and the Pauson-Khand reaction §Pages 71-87, Planning Organic Synthesis and Selectivity March 3 Midterm Exam March 8, 10 Spring Break March 15, 17, 22, 24, 29 *Chapter #4, Pericyclic Reactions $Study Named reactions from the Grossman Chapter #4 in “Strategic Applications of Named Reactions in Organic Synthesis” Additional Reading, Chapter #6, Thermal Pericycic Reactions in Ian Feming’s “Molecular Orbitals and Organic Chemical Reactions”

March 31 quiz #4 April 5, 7 *Chapter #5, Free Radical Reactions $Study Named reactions from the Grossman Chapter #5 in “Strategic Applications of Named Reactions in Organic Synthesis” April 12 quiz #5 April 14, 19 *Chapter #6, Transition Metal Catalyzed and Mediated Reactions $Study Named reactions from the Grossman Chapter #6 in “Strategic Applications of Named Reactions in Organic Synthesis” April 21 quiz #6 April 28 Final Exam (9:00-noon) Chevron 135 Exams and Grading: There will be one midterm exam and one final exam and each is worth 150 points. The final exam will be comprehensive. Six quizzes will be assigned periodically, and will count 300 points toward your final grade.

Textbooks: *The chapters in the syllabus are referring to this textbook. “The Art of Writing Reasonable Organic Reaction Mechanisms, second edition” by Robert B. Grossman. § Page numbers refer to the textbook “Organic Synthesis Strategy and Control” by Paul Wyatt and Stuart Warren. ¶ Page numbers refer to the textbook “The Logic of Chemical Synthesis” by E.J. Corey and Xue-Min Cheng $“Strategic Applications of Named Reactions in Organic Synthesis” by Lazlo Kurti and Barbara Czako.

Academic Integrity: Students in this course will be expected to comply with University of Pittsburgh's Policy on Academic Integrity.

Disabilities: If you have a disability that requires special testing accommodations or other classroom modifications, you need to notify both the instructor and the Disability Resources and Services no later than the 2nd week of the term. The Office is located in 216 William Pitt Union. Chemistry 2430 Fall Term, 2002

Quantum Chemistry

Any fundamental description of a chemical phenomenon requires the use of quantum mechanics, since chemistry is the science of molecules, and molecules are very small. In this course, we will discuss the principles of quantum mechanics, describe the various ways that such principles manifest themselves in chemical phenomena, and show how one can take advantage of such principles in modern science and technology.

An approximate syllabus for the course is given overleaf. The required text is Principles of Quantum Mechanics, by Donald D. Fitts, Cambridge U. P., 1999. Also recommended is The Physical Basis of Chemistry, by Warren S. Warren, Academic Press, 2000 and a number of books on reserve in the library (Eberly Hall). Both texts are available in paperback editions.

Lectures will be given on Mondays, Wednesdays, and Fridays from 8-9:00 AM in Room 130 Chevron Science Center beginning August 26.

Problem sets will be handed out weekly, to be turned in and graded. Answers will be placed on reserve or on CourseWeb.

Two one-hour exams will be given, the first in late September/early October. A term paper, presentation, and/or final exam also will be required. Grading guidelines will be provided.

The instructor is Professor David Pratt (605 CHVRN, (412) 624-8660, email: [email protected]). His office hours are Mondays, Wednesdays, and Fridays from 11-12:30 PM. USE THEM!

CRN 03075 Chemistry 2430 Fall Term, 2002

Approximate Syllabus

Week Topic(s)

August 26 Waves and wavefunctions September 2 Schroedinger wave mechanics September 9 Postulates/principles of QM September 16 Harmonic oscillator September 23 Angular momentum September 30 Review and exam October 7 The hydrogen atom October 14 Spin October 21 Systems of identical particles October 28 Approximation methods November 4 Molecular structure November 11 Review and Exam November 18 Applications November 25 Applications December 2 Applications December 9 Applications December 16 Review and Final Exam

Several applications that come to mind include Hückel theory, magnetic resonance, IR and Raman spectroscopy in biological systems, high resolution electronic spectroscopy, analytical instrumentation, sensors, potential energy surfaces and reaction dynamics, orbital symmetry control, surface science and materials, teleportation, Bose-Einstein condensation, and a variety of time-dependent phenomena. Students are encouraged to contribute to this list, by suggesting topics in applied quantum mechanics that they would like to see discussed. Chemistry 2430 Fall Term, 2002

Course Grades

Your final grade in this course will depend on your ability to assimilate the material, and to demonstrate knowledge of the principles and applications of quantum mechanics to chemical problems.

This knowledge will be revealed by your active participation in class activities, including (but not limited to) lectures, study groups, office hours, email exchanges, and student presentations. Twenty percent (20%) of your final grade will be based on this participation.

Your acquired knowledge also will be tested by problem sets, hour examinations, and class presentations. Problem sets will be assigned weekly, turned in, and graded. A total of 20% of your grade will be based on your problem sets.

Two hour exams, each also worth 20% of your final grade, will be given during the course of the term.

Finally, each student will be asked to make a 30-minute oral presentation to the class, during the last four weeks of the term. This activity also will contribute to 20% of your final grade. Students who do not wish to give such presentations may write a 10-page term paper, in lieu of a final exam.

The topic to be addressed in your presentation/term paper is a specific application of quantum mechanics to a current problem in chemistry. This could be a problem with which you are already familiar, a problem that you might pursue as a Ph.D. student, or just a topic about which you would like to know more.

Each student will be required to select his/her topic by Friday, October 18 in consultation with Dr. Pratt. One-page outlines (with references) of your presentation or paper, also to be approved by Dr. Pratt, will be due on Monday, November 4, and scheduled for presentation at that time. Copies of these outlines will be distributed to the class one week in advance of your presentation, to give your classmates time to read the background material prior to coming to class. Their participation in the 20-minute discussion that will follow your presentation will be an essential component of their final grade. Chemistry 2430 Fall Term, 2002

Books on Reserve. In addition to the required and recommended texts, the following books have been placed on reserve in the Chemistry Library (200 Eberly Hall) for your use in this course.

P. W. Atkins, Physical Chemistry (6th edition), Freeman, 1998.

P. W. Atkins, Quanta (2e), Oxford, 1991.

P. W. Atkins and R. S. Friedman, Molecular Quantum Mechanics, Oxford, 1997.

F. A. Cotton, Chemical Applications of Group Theory, Wiley, 1990.

C. A. Coulson (revised by R. McWeeny), The Shape and Structure of Molecules, Oxford, 1982.

P. A. Cox, The Electronic Structure and Chemistry of Solids, Oxford, 1987.

D. D. Fitts, Principles of Quantum Mechanics, Cambridge University Press, 1999.

R. K. Harris, NMR Spectroscopy, Longman, 1986.

G. Herzberg, Atomic Spectra and Atomic Structure, Dover, 1944.

G. Herzberg, Electronic Spectra and Electronic Structure of Polyatomic Molecules (Vol 3), Van Nostrand, 1966.

G. Herzberg, Infrared and Raman Spectra of Polyatomic Molecules (Vol 2), Van Nostrand, 1945.

J. M. Hollas, Modern Spectroscopy, (2nd edition), Wiley, 1996.

M. Karplus and R. N. Porter, Atoms and Molecules, Benjamin, 1970.

C. Kittel, Introduction to Solid State Physics, Wiley, 1996.

I. N. Levine, Quantum Chemistry, (5th edition), Prentice Hall, 2000.

R. G. Mortimer, Mathematics for Physical Chemistry, Macmillan, 1981.

L. Pauling, The Nature of the Chemical Bond, Cornell, 1960.

L. Pauling and E. B. Wilson, Introduction to Quantum Mechanics, McGraw-Hill, 1985.

C. H. Townes and A. L. Schawlow, Microwave Spectrosopy, McGraw-Hill, 1955.

W. S. Warren, Physical Basis of Chemistry, Academic Press, 2000.

J. E. Wertz and J. R. Bolton, ESR. Elementary Theory and Practical Applications, McGraw-Hill, 1986. Chemistry 2430 – Quantum Chemistry

Instructors: Professors K. D. Jordan and R. D. Coalson

Rm: 330 and 321 Eberly Hall

Text: Molecular Quantum Mechanics bt Atkins and Friedman

Lectures: Mon. and Wed. 5:30 PM – 6:45

Office hours: by appointment

Grading: two 1 hr. exams (25% each); homeworks (10%), final exam (40%). All exams are open book, i.e., you can use your text and notes, but no other sources. Makeup exams are permitted only in the case of medical emergencies.

Week 1 (Aug. 31, Sept. 2): Chpt. 1, Foundations of quantum mechanics

Week 2 (Sept. 9): Chpt. 2, Linear motion, and the harmonic osc.

Week 3 (Sept. 14,16): Chpt. 3, Rotational motion,; H atom

Week 4 (Sept. 21,23): Chpt. 4, Angular momentum

Week 5 (Sept. 28,30): Chpt. 6, Techniques of approximation

Week 6 (Oct. 5, 7): Chpt. 7, Atomic Structure; Exam 1 (Mon.)

Week 7 (Oct. 13,14): Chpt. 8 Molecular Structure Week 8 (Oct. 19, 21): Born-Oppenheimer Approximation; H_2+ Molecule Ion

Week 9 (Oct. 26,28): Molecular Orbital Theory of Diatomics

Week 10 (Nov. 2, 4): Hückel Theory of Pi-Bonding; Band Structure Theory

Week 11 (Nov. 9,11): Dynamics of a 2-level System; Decay of a Doorway State

Week 12 (Nov. 16, 18): Hartree-Fock Theory

Week 13 (Nov. 23): Exam 2

Week 14 (Nov 30, Dec. 2): Rotation-Vibration Spectroscopy

Week 15 (Dec. 7,9) Electronic Spectroscopy

Week 16 (Dec. 16): Final Exam

Chemistry 2440, Thermodynamics and Statistical Mechanics

Instructors: Ken Jordan ([email protected]), Rob Coalson ([email protected])

Offices: 330 EH (KJ), and 321 EH (RC)

Course web page: www.pitt.edu/~jordan/education/chem2440

Lectures: M, W. F, 11:00 AM – 10:50 AM, 228 EH

Office Hours: anytime we are free

Required texts:

D.A. McQuarrie, Statistical Mechanics

D. Chandler, Introduction to Statistical Mechanics

Grading: two one-hour exams (25% each), final exam (40%), homeworks (10%)

Tentative syllabus:

Week 1: Review of thermodynamics fundamentals (Chandler, Ch. 1)

Week 2: Conditions for Equilibrium and Stability (Chandler, Ch. 2)

Weeks 3-5: Stat. Mechanics Foundations (ensembles) (Chandler, Ch. 3; McQ., Chs. 1-3)

Hourly Exam: Feb. 10

Weeks 6-8: Applications of Eq. Stat. Mech. to Non-interacting Systems, I (Chandler, Ch. 4; McQ., Chs. 4-6;8,11) (i) Harmonic solids (ii) Ideal Gases

Week 9: Applications of Eq. Stat. Mech. to Non-interacting Systems, I (Chandler, Ch. 4; McQ., Chs. 9,10) (i) Chemical Equilibrium (ii) Quantum Statistics

Week 10-11: Classical Stat Mech: Theory and Numerical Simulation Techniques (Molecular Dynamics, Monte Carlo) (Chandler, Ch. 6,7; McQ., Ch. 7)

Hourly Exam: March 19

Week 12-14: Application of Equil. Stat. Mech. to Interacting Systems (Chandler, Ch. 5,7; McQ., Chs. 12-14) (i) Phase Transitions (ii) Imperfect gases and liquids

Week 15: Non-equil. Stat. Mech. (Chandler, Ch. 8; McQ., Chs. 20-22)

Final Exam: April 26???

Syllabus Chem 2810 Biological Chemistry 1

Fall 2010 This course is intended to provide a foundation for a research program that studies biological molecules, systems, or similar, complex systems.

Prerequisite Bachelor’s degree in chemistry. A course in biochemistry will be helpful, but it is not a prerequisite.

Overview Biological systems are made of chemicals, so shouldn’t the study of chemistry be sufficient to study biological systems? Yes and no. First, the ‘yes’. The core undergraduate curriculum applies well to biological systems. Weak acid/weak base chemistry and related chemical equilibria help to explain respiration; electrochemistry is a key component to energy use; proteins, DNA, lipids are all organic compounds; inorganic coordination compounds are very important in oxygen carriers and many enzymes – and of course the skeleton! Principles of physical chemistry apply broadly, and form the basis for posing many of the key questions about life such as how do self-organization, protein folding, selective transport work for example. And the ‘no’. The ‘no’ arises from the level of complexity displayed in biological systems, and from the remarkable techniques that have been created specifically to study aspects of biomolecules, biological structures, organelles, cells, and organisms. This course is based on chemistry, broadly speaking, but it will emphasize the study of biological systems. A focus will be on motion – molecular and ionic motion by diffusion and ‘pumps’ - as well as motion of parts of macromolecules with respect to other parts. We will look at some important techniques and tools for understanding these things as well.

Grading There will be two exams, a paper, and a presentation.

Tentative schedule

2810 BIOLOGICAL CHEMISTRY 1 MW 5:30-6:45 PM EBERLY 228

Nelson, Philip 2008. Biological Physics. Energy, Information, Life. New York: W.H. Freeman and Company. Other readings will be assigned.

1) Building blocks and biomolecular classes Amino acids peptides proteins Nucleic acids nucleosides nucleotides RNA DNA Fatty acids phospholipids Carbohydrates glycosaminoglycans

2) The cell Membrane, cytoskeleton, integral membrane proteins Mitochondria – energy metabolism Nucleus Endoplasmic reticulum – protein synthesis and processing Central dogma

3) Chemical Communication Diffusion Fluid flow

4) Free Energy and Boltzmann Osmotic pressure Electrostatics and the double layer Water

5) Chemical Forces and Self Assembly Membrane Polymers Helix – coil transition

6) Some important systems Synaptic release Glutathione

Begin - August 30, 2010 (M) End - December 18, 2010 (Sa) Last Undergraduate Day Class - December 10 (F) Reading Day – December 11 (Sa) Final Exam Period - December 13-18 (M-Sa) Grades Due - December 22 (W) Holidays: September 6 (M) - Labor Day November 24 - 28 (W-Su) - Thanksgiving recess for students

Important Dates:

Begin - August 30, 2010 (M) End - December 18, 2010 (Sa) Last Undergraduate Day Class - December 10 (F) Reading Day – December 11 (Sa) Final Exam Period - December 13-18 (M-Sa) Grades Due - December 22 (W) Holidays: September 6 (M) - Labor Day November 24 - 28 (W-Su) - Thanksgiving recess for students CHEM 2820 Biological Chemistry 2 Spring 2010 M W F 10:00-10:50 a.m., 228 Eberle

Instructor: Professor W. Seth Horne Office: 1405 Chevron Science Center Office Hours: by appointment E-mail: [email protected]

Course Description: This course covers current research in chemical biology. We will discuss how chemical principles are being applied to address complex problems in biological science.

Organization and Goals of the Course: We will begin the semester with a discussion of the structure of major classes of biomolecules (proteins, nucleic acids, oligosaccharides) as well as the non-covalent forces that influence their intermolecular and intramolecular interactions. The goal in the first portion of the course will be to gain an appreciation of biomolecules as chemical entities. In the second part of the semester, we will examine commonly encountered methods used for the preparation and characterization of biomacromolecules. The goal here will be to understand these methods well enough to critically interpret their use in modern chemical biology research. The third part of the course will consist of a survey of research topics in the recent literature that are relevant to chemical biology. Our discussions will center on journal articles and will rely heavily on our understanding of the principles and methods covered in the early part of the semester. The goal in the late part of the course will be to highlight frontier scientific challenges and questions being addressed through research at the chemistry/biology interface. Beyond the goals outlined above, we will also work to develop each student’s written and verbal communication skills, which are essential for a successful career in the sciences. This goal will be achieved through an assigned term paper and oral presentation related to the course material.

Required Course Materials: Essentials of Chemical Biology: Structure and Dynamics of Biological Macromolecules, by Miller and Tanner

A significant portion of the course material will come from recently published journal articles. References to relevant articles will be provided, and students will be expected to acquire and read these papers online or through the university library.

Chem 2820 W. Seth Horne

Supplemental Texts: (Placed on reserve in the Chemistry Library) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, by Fersht Fundamentals of Biochemistry, by Voet, Voet, and Pratt Introduction to Protein Structure, by Branden and Tooze

Exam Schedule: Exam 1 - Structure and Function in Biomacromolecules February 5 Exam 2 - Preparation and Characterization of Biomacromolecules March 5 (Exam dates are tentative. Actual dates will be announced in class.)

Term Paper: One of the main goals of the course is to provide students with the knowledge necessary to understand and critically interpret cutting edge research in chemical biology. Each student will be required to complete a written review of a research article in the recent literature. The article can be selected from any area related to chemical biology but must be approved by the instructor.

In the written review, students will be expected to summarize the key conclusions of the paper and explain how the authors’ reach the conclusions based on the experiments performed. Students should place the results in context based on other published research in the area. Does the paper represent a significant advance in the field or incremental progress that builds on older work? Are the conclusions of the paper fully justified by the data presented? Are there alternate interpretations of the data? Did the authors do appropriate control experiments? If not, what additional experiments would strengthen the conclusions? Propose the next direction you would take this research if you were in charge of the project.

Article selections should be provided for approval by Monday, March 1. The written review should be 4-5 pages in length (single spaced, 12 point font, excluding references). The due date for the assignment is Friday, April 2.

Student Presentation: Students will be divided into groups of two, and each pair will give an in-class presentation reviewing a research article from the recent literature. The basis for selection of papers and expectations for the content of the presentations will be the same as outlined above for the written reviews.

Group assignments and paper selections will take place in mid-March. Presentations will take place during the last two weeks of the semester. Talks should be 20 minutes in length with an additional 5 minutes for questions. A laptop and projector will be provided.

Grading: Each of the two midterm exams will count 25% toward the final grade. The group presentation and term paper will each count 20% toward the grade for the course. Chem 2820 W. Seth Horne

10% of the course grade will be based on attendance and participation in class discussions. There will be no final exam for the course.

Academic Integrity: Students in this course will be expected to comply with University of Pittsburgh's Policy on Academic Integrity (http://www.bc.pitt.edu/policies/). Any student suspected of violating this obligation for any reason during the semester will be required to participate in the procedural process, initiated at the instructor level, as outlined in the University Guidelines on Academic Integrity.

Disability Resources: If you have a disability for which you are or may be requesting an accommodation, you are encouraged to contact both your instructor and Disability Resources and Services, 140 William Pitt Union, 412-648-7890 or 412-383-7355 (TTY) as early as possible in the term. DRS will verify your disability and determine reasonable accommodations for this course.

Chem 2820 W. Seth Horne

CHEM 2820 Lecture Schedule (tentative)

I. Structure and function in biomacromolecules 1. (Jan. 6) Introduction 2. (Jan. 8) Non-covalent interactions I 3. (Jan. 11) Non-covalent interactions II 4. (Jan. 13) Protein structure I – amino acids and amide bonds 5. (Jan. 15) Protein structure II – secondary and tertiary structure 6. (Jan. 20) Protein structure III – folding thermodynamics 7. (Jan. 22) Carbohydrates 8. (Jan. 25) Nucleic acids I 9. (Jan. 27) Nucleic acids II 10. (Jan. 29) Chemical catalysis – transition state theory and basic principles 11. (Feb. 1) Enzyme catalysis I – fundamentals and kinetics 12. (Feb. 3) Enzyme catalysis II – case studies 13. (Feb. 5) Exam 1

II. Methods for the preparation and characterization of biomacromolecules 14. (Feb. 8) Chemical synthesis of DNA and the polymerase chain reaction (PCR) 15. (Feb. 10) Manipulation of nucleic acids in biological systems 16. (Feb. 12) Heterologous protein expression, isolation and purification 17. (Feb. 15) Chemical synthesis of peptides 18. (Feb. 17) Native chemical ligation and the total synthesis of proteins 19. (Feb. 19) X-ray crystallography 20. (Feb. 22) NMR spectroscopy 21. (Feb. 24) UV-VIS, CD and IR spectroscopy 22. (Feb. 26) Fluorescence spectroscopy, including FRET and FP 23. (Mar. 1) Mass spectrometry 24. (Mar. 3) Microscopy and chemical approaches for chromophore generation in vivo 25. (Mar. 5) Exam 2

III. Advanced topics from the recent literature 26. (Mar. 15) Protein-protein interactions and their inhibition 27. (Mar. 17) Post-translational modification of proteins 28. (Mar. 19) Epigenetics – histones, chromatin and modifying enzymes 29. (Mar. 22) Protein engineering – biosynthesis of chemically modified proteins 30. (Mar. 24) Genomics – DNA sequencing and microarrays 31. (Mar. 26) Proteomics – activity based protein profiling 32. (Mar. 29) Biomaterials in nature 33. (Mar. 31) Prebiotic chemistry 34. (Apr. 2) In vitro evolution 35. (Apr. 5) Bio-orthogonal ligation techniques 36. (Apr. 7) Synthetic biology – folding and function in non-biological oligiomers 37. (Apr. 9) Student literature presentations – topics TBA 38. (Apr. 12) Student literature presentations – topics TBA 39. (Apr. 14) Student literature presentations – topics TBA Chem 2820 W. Seth Horne

40. (Apr. 16) Student literature presentations – topics TBA 41. (Apr. 19) Student literature presentations – topics TBA 42. (Apr. 21) Student literature presentations – topics TBA 43. (Apr. 23) Student literature presentations – topics TBA