Chemistry and Chemical Biology

Faculty of the Department of Chemistry and Chemical Biology

Andrew G. Myers, Amory Houghton Professor of Chemistry and Chemical Biology (Chair)
Joanna Aizenberg, Gordon McKay Professor of Materials Science (on leave fall term)
Allen Dennis Aloise, Lecturer on Chemistry and Chemical Biology (spring term only)
James G. Anderson, Philip S. Weld Professor of Atmospheric Chemistry (on leave 2009-10)
Alán Aspuru-Guzik, Assistant Professor of Chemistry and Chemical Biology
Theodore A. Betley, Assistant Professor of Chemistry and Chemical Biology
Adam E. Cohen, Assistant Professor of Chemistry and Chemical Biology and of Physics
Timothy A. French, Preceptor in Chemistry and Chemical Biology
Cynthia M. Friend, Theodore William Richards Professor of Chemistry and Professor of Materials Science
Roy G. Gordon, Thomas Dudley Cabot Professor of Chemistry
Eric J. Heller, Abbott and James Lawrence Professor of Chemistry and Professor of Physics (on leave fall term)
Eric N. Jacobsen, Sheldon Emery Professor of Chemistry
Daniel E. Kahne, Professor of Chemistry and Chemical Biology (FAS), Professor of Biological Chemistry and Molecular Pharmacology (Medical School) (Co-Director of Undergraduate Studies)
Charles M. Lieber, Mark Hyman, Jr. Professor of Chemistry
David R. Liu, Harvard College Professor, Professor of Chemistry and Chemical Biology
Gavin MacBeath, Associate Professor of Chemistry and Chemical Biology
Sirinya Matchacheep, Preceptor in Chemistry and Chemical Biology
Logan S. McCarty, Lecturer on Chemistry and Chemical Biology
Erin K. O’Shea, Professor of Molecular and Cellular Biology and of Chemistry and Chemical Biology (on leave 2009-10)
Sang-Joon Pahk, Preceptor in Chemistry and Chemical Biology
Hongkun Park, Professor of Chemistry and Chemical Biology
Tobias Ritter, Assistant Professor of Chemistry and Chemical Biology
Cesar Rodriguez-Rosario, Lecturer on Chemistry and Chemical Biology
Alan Saghatelian, Assistant Professor of Chemistry and Chemical Biology
Semion Saykin, Lecturer on Chemistry and Chemical Biology
Stuart L. Schreiber, Morris Loeb Professor of Chemistry
Matthew D. Shair, Professor PF Chemistry and Chemical Biology (Co-Director of Graduate Studies)
Eugene I. Shakhnovich, Professor of Chemistry and Chemical Biology
Ryan M. Spoering, Lecturer on Chemistry and Chemical Biology
Marie Colleen Spong, Preceptor in Chemistry and Chemical Biology
Gregory C. Tucci, Senior Lecturer on Chemistry and Chemical Biology (Co-Director of Undergraduate Studies)
Gregory L. Verdine, Erving Professor of Chemistry
George M. Whitesides, Woodford L. and Ann A. Flowers University Professor
Xiaoliang Sunney Xie, Mallinckrodt Professor of Chemistry and Chemical Biology
Xiaowei Zhuang, Professor of Chemistry and Chemical Biology and of Physics (on leave 2009-10)

Other Faculty Offering Instruction in the Department of Chemistry and Chemical Biology

Tamara J. Brenner, Lecturer on Molecular and Cellular Biology
David A. Evans, Abbott and James Lawrence Professor of Chemistry, Emeritus
Suzanne Walker, Professor of Microbiology and Molecular Genetics (Medical School)
Vicki L. Sato, Professor of the Practice of Molecular and Cellular Biology

Incoming students should take advantage of Harvard’s Chemistry and Life Sciences Placement Test, as well as the science advising available in the Science Center the week before classes begin. Members of the Life and Physical Sciences departments will be available during this period to advise students. The Harvard Chemistry and Life Sciences Placement Test results recommend the appropriate starting level course for students interested in chemistry: Life and Physical Sciences A, Life Sciences 1a and/or Physical Sciences 1, or Chemistry 17/20.

Life Sciences 1a and Physical Sciences 1 together satisfy the one year general chemistry requirement for medical school.

Certain courses in biochemistry and biophysics are listed under Molecular and Cellular Biology or Biophysics (see cross-listings at end of middle group course section.). The School of Engineering and Applied Sciences, the Department of Physics, and the Department of Earth and Planetary Sciences also list a number of courses of interest to chemists.

Primarily for Undergraduates

Because of the sequence of prerequisites for chemistry courses, the Department strongly recommends some work in mathematics as well as chemistry in the first year. Freshmen contemplating this program should consult a member of the Chemistry Department in planning their first year. Advice may be obtained in the Associate Director of Undergraduate Studies’ Office, Science Center 114.

Life and Physical Sciences

Life and Physical Sciences A. Foundational Chemistry and Biology
Catalog Number: 3956
Gregory C. Tucci and Tamara J. Brenner
Half course (fall term). M., W., F., at 9, and one hour of discussion section, a three-hour laboratory session, and one hour of review per week. EXAM GROUP: 2
This course introduces fundamental concepts in chemistry and biology. Topics in chemistry include stoichiometry, acids and bases, aqueous solutions, gases, thermochemistry, electrons in atoms, and chemical bonding. Topics in biology include the transfer of information from DNA to RNA to protein, genetic inheritance, mitosis and meiosis, and cell structure.
Note: Students should use their scores on the Chemistry and Biology Placement Tests to determine whether to enroll in Life and Physical Sciences A or Life Sciences 1a. This course assumes fluency with high school algebra. Students who have completed Life Sciences 1a, Physical Sciences 1, Chemistry 17 or Chemistry 20 may not take Life and Physical Sciences A for credit. This course, when taken for a letter grade, meets the General Education Requirement for Science of Living Systems or the Core area requirement for either Science A or Science B.

Life Sciences 1a. An Integrated Introduction to the Life Sciences: Chemistry, Molecular Biology, and Cell Biology
Catalog Number: 2137
Robert A. Lue and Daniel E. Kahne
Half course (fall term). Tu., Th., 1–2:30, and three hours of laboratory/discussion weekly. EXAM GROUP: 15, 16
What are the fundamental features of living systems? What are the molecules imparting them and how do their chemical properties explain their biological roles? The answers form a basis for understanding the molecules of life, the cell, diseases, and medicines. In contrast with traditional presentations of relevant scientific disciplines in separate courses, we take an integrated approach, presenting chemistry, molecular biology, biochemistry, and cell biology framed within central problems such as the biology of HIV and cancer.
Note: This course, in combination with Life Sciences 1b, constitutes an integrated introduction to the Life Sciences. This course, when taken for a letter grade, meets the General Education requirement in Science of Living Systems or the Core area requirement for Science A.

Physical Sciences 1. Chemical Bonding, Energy, and Reactivity: An Introduction to the Physical Sciences
Catalog Number: 2225
Hongkun Park and Adam E. Cohen
Half course (spring term). M., W., F., at 10. EXAM GROUP: 3
Physical Sciences 1 engages the principles of chemistry and physics within major conceptual themes that underpin critical contributions of the physical sciences to societal objectives. In particular, the concepts central to chemical bonding, kinetic theory of molecular motion, thermochemistry, kinetics, equilibria, entropy and free energy, acids and bases, electrochemistry, and nuclear chemistry will be taught in the context of (1) world energy sources, forecasts and constraints, (2) global climate change, and (3) modern materials and technology.
Note: This course is part of an integrated introduction to the physical science intended for students who plan to pursue a concentration in the physical or life sciences and/or satisfy pre-medical requirements in Chemistry. May not be counted toward a degree in addition to the former Chemistry 7. Students interested in Physical Sciences 1 should take the Chemistry Placement Exam. This course, when taken for a letter grade, meets the General Education requirement for Science of the Physical Universe or the Core area requirement for Science A.
Prerequisite: A few operations of calculus are developed and used. Fluency in pre-calculus secondary school mathematics is assumed. Students are expected to have AP or honors level high school chemistry, or have completed Life and Physical Sciences A (LPS A) with a satisfactory grade.

Physical Sciences 2. Mechanics, Elasticity, Fluids, and Diffusion
Catalog Number: 6053
Logan S. McCarty and Vinothan N. Manoharan
Half course (fall term). Tu., Th., 9:30-11, and a weekly section and lab to be arranged. EXAM GROUP: 11, 12
An introduction to classical mechanics, with special emphasis on the motion of organisms in fluids. Topics covered include: kinematics, Newton’s laws of motion, oscillations, elasticity, random walks, diffusion, and fluids. Examples and problem set questions will be drawn from the life sciences and medicine.
Note: This course, when taken for a letter grade, meets the General Education requirement for Science of the Physical Universe or the Core area requirement for Science A.
Prerequisite: Physical Sciences 1 (or Chemistry 7), Mathematics 1b, or the equivalent.

Physical Sciences 3. Electromagnetism, Waves, Imaging, and Information
Catalog Number: 5262
John Huth and Logan S. McCarty
Half course (spring term). Tu., Th., 9:30–11, and a weekly section and lab to be arranged. EXAM GROUP: 11, 12
This course is an introduction to light and sound waves, electromagnetism, and information. Case studies in Physical Science 3 will emphasize biological systems. Topics covered include: wave propagation in various media, imaging techniques of relevance to biological applications, electric fields, magnetic fields, electric forces, electrical circuits, and the transmission and processing of information in electronic and biological systems.
Note: This course is part of an integrated introduction to the physical sciences intended for students who plan to pursue a concentration in the life sciences and/or satisfy pre-medical requirements in Physics. May not ordinarily be taken for credit in addition to Physics 1b, 11b, or 15b. This course, when taken for a letter grade, meets the General Education requirement for Science of the Physical Universe or the Core area requirement for Science A.
Prerequisite: Physical Sciences 2 (or Physics 1a or 11a), Mathematics 1b, or equivalent.

Primarily for Undergraduates

Because of the sequence of prerequisites for chemistry courses, the Department strongly recommends some work in mathematics as well as chemistry in the first year. Freshmen contemplating this program are urged to consult a member of the Chemistry Department in planning their work for the first year. Advice may be obtained in the Associate Director of Undergraduate Studies’ Office, Science Center 114.

Chemistry 17. Principles of Organic Chemistry
Catalog Number: 5085
Alan Saghatelian
Half course (fall term). M., W., F., at 11, and a discussion section to be arranged. EXAM GROUP: 4
An introduction to structure, bonding, and reaction mechanisms of organic compounds; chemical transformation of the common functional groups; principles of organic synthesis.
Note: The Chemistry 17/27 sequence is intended primarily for students in the life sciences, whereas the 20/30 sequence is intended primarily for Chemistry concentrators and other students concentrating in the physical sciences. Either sequence satisfies the organic chemistry requirement for medical school. Students may not count both Chemistry 17 and Chemistry 20 for degree credit. On the other hand, Chemistry 27 and Chemistry 30 cover different material, so students may choose to take both courses for degree credit; students should ordinarily take the third half course only after completing either the 17/27 or 20/30 sequence. This course, when taken for a letter grade, meets the Core area requirement for Science A.
Prerequisite: Open to freshmen with a score of 750 or higher in the College Boards or the Chemistry Placement Examination; to students who scored 4 or 5 on the Chemistry Advanced Placement Examination; and to students who achieved a grade of B or higher in either Physical Sciences 1, Chemistry 7, or 15. Others may enter only by permission of the instructor.

Chemistry 20. Organic Chemistry
Catalog Number: 0876
Ryan M. Spoering
Half course (spring term). M., W., F., at 9, and a discussion section to be arranged. EXAM GROUP: 2
An introduction to structure and bonding in organic molecules; mechanisms of organic reactions; chemical transformations of the functional groups of organic chemistry; synthesis; determination of chemical structures: infrared and NMR spectroscopy.
Note: The Chemistry 17/27 sequence is intended primarily for students in the life sciences, whereas the 20/30 sequence is intended primarily for Chemistry concentrators and other students concentrating in the physical sciences. Either sequence satisfies the organic chemistry requirement for medical school. The content of Chemistry 17 is similar to that of Chemistry 20, so students may not count both courses toward the degree. On the other hand, Chemistry 27 and Chemistry 30 cover different material, so students may choose to take both courses for degree credit; students should ordinarily take the third half course only after completing either the 17/27 or 20/30 sequence. This course, when taken for a letter grade, meets the Core area requirement for Science A.
Prerequisite: Open to freshmen with a score higher than 750 in the College Boards or the Chemistry Placement Examination; to students who scored 5 on the Chemistry Advanced Placement Examination; and to students who achieved a grade of B or higher in either Physical Sciences 1, Chemistry 7, or 15. Others may enter only by permission of the instructor.

Chemistry 27. Organic Chemistry of Life
Catalog Number: 5978
George M. Whitesides
Half course (spring term). M., W. , 2:30-4, and a discussion section, and a five-hour laboratory each week to be arranged. EXAM GROUP: 7, 8
Chemical principles that govern the processes driving living systems are illustrated with examples drawn from biochemistry, cell biology, and medicine. The course deals with organic chemical reactivity (reaction mechanisms, structure-reactivity relationships), with matters specifically relevant to the life sciences (chemistry of proteins, nucleic acids, drugs, natural products, cofactors, signal transduction), and with applications of chemical biology to medicine and biotechnology. An understanding of organic reactions and their "arrow" pushing mechanisms is required.
Note: Chemistry 27 and 30 may both be taken for degree credit. See note for Chemistry 17. This course, when taken for a letter grade, meets the Core area requirement for Science A.
Prerequisite: Chemistry 17 or Chemistry 30 or Chemistry 20 with permission of the instructor.

Chemistry 30. Organic Chemistry
Catalog Number: 6587
Tobias Ritter
Half course (fall term). Lectures M., W., F., at 9, and laboratory, four to six hours a week, to be arranged. EXAM GROUP: 2
Continuation of Chemistry 20. Fundamental principles and advanced topics in organic chemistry. Carbonyl chemistry and pericyclic reactions are covered in particular detail, using principles of stereochemistry, stereoelectronic theory, and molecular orbital theory as a foundation. Students learn about strategies in multi-step organic synthesis and are given an introduction into organometallic chemistry. Laboratory: an introduction to organic chemistry laboratory techniques and experimental organic synthesis.
Note: Chemistry 27 and 30 may both be taken for degree credit. See note for Chemistry 17. This course, when taken for a letter grade, meets the Core area requirement for Science A.
Prerequisite: Chemistry 20 or equivalent.

Chemistry 40. Inorganic Chemistry
Catalog Number: 8201
Cynthia M. Friend
Half course (spring term). M., W., F., at 9. EXAM GROUP: 2
An introduction to basic concepts of inorganic chemistry. Develops principles of chemical bonding and molecular structure on a basis of symmetry, applying these concepts to coordination chemistry (highlighting synthesis), organometallic chemistry (applications to catalysis), materials synthesis, and bioinorganic processes.
Prerequisite: Chemistry 17 or 20.

Chemistry 60. Foundations of Physical Chemistry
Catalog Number: 5181
Roy G. Gordon
Half course (spring term). Tu., Th., 11:30–1. EXAM GROUP: 13, 14
A compact introduction to major principles of physical chemistry (statistical mechanics, thermodynamics, and chemical kinetics ), concurrently providing mathematical and physical foundations for these subjects and preparation for Chemistry 160 and 161, or Chemistry 105.
Prerequisite: Physical Sciences 1 or equivalent; completion or concurrent enrollment in Mathematics 21a or Applied Mathematics 21a; completion or concurrent enrollment in Physics 11a or equivalent.

*Chemistry 91r. Introduction to Research
Catalog Number: 4366
Gregory C. Tucci, and members of the Department
Half course (fall term; repeated spring term). Spring: Tu., Th., at 1.
Reading and/or laboratory work related to one of the research projects under way in the department.
Note: Open to a limited number of chemistry concentrators who are accepted as research students without having taken Chemistry 98. Written permission of the sponsor must be filed at the Office of the Associate Director of Undergraduate Studies in Chemistry. Any student enrolling in this course must register the name of his or her research mentor with the course head whose signature must appear on each student’s study card.

*Chemistry 98r. Introduction to Research—Junior Year
Catalog Number: 3124
Gregory C. Tucci, and members of the Department
Half course (fall term; repeated spring term). Hours to be arranged.
Research under the direction of, or approved by, a member of the faculty of the Department of Chemistry.
Note: Open with permission of the instructor to junior chemistry majors who have satisfactorily completed the non-credit Introduction to Research Tutorial in the spring term of the sophomore year. In that non-credit spring term tutorial, taught Tu., Th., 1-2:30, students will attend introductory lectures and research seminars in order to acquaint themselves with departmental research programs. In the junior year, students who complete the non-credit tutorial and obtain placement in a research laboratory will undertake research as Chemistry 98r. Written permission of the research adviser must be filed at the office of the Associate Director of Undergraduate Studies in Chemistry. Any student enrolling in this course must register the name of his or her research mentor with the course head whose signature must appear on each student’s study card.

*Chemistry 99r. Tutorial—Senior Year
Catalog Number: 4508
Gregory C. Tucci, and members of the Department
Half course (fall term; repeated spring term). Hours to be arranged.
Research under the direction of, or approved by, a member of the faculty of the Department of Chemistry.
Note: Open to seniors accredited by the Department as honors candidates. Students enrolled in Chem 99r have the option of writing a thesis. Written permission of the research adviser must be filed at the office of the Associate Director of Undergraduate Studies in Chemistry. Any student enrolling in this course must register the name of his or her research mentor with the course head whose signature must appear on each student’s study card.

Cross-listed Courses

Earth and Planetary Sciences 107. Environmental Geochemistry
Earth and Planetary Sciences 133. Atmospheric Chemistry
*Freshman Seminar 22j. Seeing by Spectroscopy
Life Sciences 1b. An Integrated Introduction to the Life Sciences: Genetics, Genomics, and Evolution
MCB 52. Molecular Biology
MCB 176. Biochemistry of Membranes

For Undergraduates and Graduates

*Chemistry 100. Experimental Chemistry and Chemical Biology
Catalog Number: 7796
Ryan M. Spoering
Half course (spring term). F., at 4, and two five-hour labs each week. EXAM GROUP: 9
A laboratory course where students carry out research. Projects will be drawn directly from faculty covering a range of methodologies in chemistry and chemical biology. Students will discuss their progress and write formal reports.
Note: Open to freshmen, sophomores, juniors, and seniors, regardless of concentration, and suitable for students either with or without extensive laboratory experience.
Prerequisite: Chemistry 30 or Chemistry 27, and permission of the instructor.

[Chemistry 105. Mechanisms of Organic Reactions: Physical-Organic Chemistry]
Catalog Number: 3181
Instructor to be determined
Half course (fall term). Hours to be arranged.
The study of the relation between structure of carbon compounds and their reactivity and properties. Thermodynamics, electronic structure, reaction mechanisms, reactive intermediates, catalysis, structure-reactivity relations, influence of solvents on reactivity.
Note: Expected to be given in 2010–11.
Prerequisite: Chemistry 7, or Physical Sciences 1, Chemistry 17/20 and Chemistry 27/30 with a grade of B- or better.

Chemistry 135. Experimental Synthetic Chemistry
Catalog Number: 3406 Enrollment: Limited to 45.
Allen Dennis Aloise
Half course (spring term). M., at 1. EXAM GROUP: 6
An introduction to experimental problems encountered in the synthesis, isolation, purification, characterization, and identification of inorganic and organic compounds. Each student works on a different sequence of reactions, encouraging technical proficiency and simulating actual research.
Note: Preference given to concentrators in Chemistry. Recommended as an efficient preparation for research in experimental inorganic and organic chemistry and related sciences such as biochemistry and pharmacology. Normally follows Chemistry 27 or 30 and is strongly recommended as preparation for Chemistry 98r and 99r.

Chemistry 158. Nanoscience and Nanotechnology
Catalog Number: 7504
Charles M. Lieber
Half course (spring term). Tu., Th., 2–3:30. EXAM GROUP: 16, 17
A survey of nanoscience and nanotechnology. Topics include: bottom-up versus top-down paradigms; synthesis and fabrication of zero-, one-and two-dimensional materials; physical properties of nanostructures, including electronic and optical properties; hierarchical organization in two and three dimensions; functional devices circuits and nanosystems; applications with emphasis on nano-bio interface and electronics.
Note: For advanced undergraduate and graduate students.
Prerequisite: Chemistry 40, or equivalent.

Chemistry 160. Physical Chemistry
Catalog Number: 3420
Alán Aspuru-Guzik
Half course (fall term). Tu., Th., 11:30–1. EXAM GROUP: 13, 14
An introduction to modern theories of the structure of matter, including the principles of quantum mechanics, the electronic structure of atoms and molecules, chemical bonding, and atomic and molecular spectra.
Prerequisite: Applied Mathematics 21a and 21b, Mathematics 21a and 21b, or equivalent preparation in calculus and differential equations; Physical Sciences 1 or equivalent preparation in chemical bonding and fundamental principles; Physical Sciences 2 or Physics 11a, and Physical Sciences 3 or Physics 11b.

Chemistry 161. Statistical Thermodynamics
Catalog Number: 3575
Eugene I. Shakhnovich
Half course (spring term). Tu., Th., 11:30–1. EXAM GROUP: 13, 14
An introduction to statistical mechanics, thermodynamics, and chemical kinetics with applications to problems in chemistry and biology. Topics include: thermodynamics and statistical properties of gases, liquids and crystals, critical phenomena, elements of non-equilibrium statistical mechanics with applications to Chemistry and Biophysics such as theories for biopolymers and chemical reactions. The course has two tracks - Chem 161is the basic track. Chem 240 is the advanced track. Each course will have separate sections and homework.
Prerequisite: Chemistry 160 and Applied Mathematics 21a, or equivalent. Or permission of instructor.

Chemistry 163. Frontiers in Biophysics
Catalog Number: 3635
Xiaoliang Sunney Xie
Half course (fall term). M., W., 1–2:30. EXAM GROUP: 6, 7
Emerging physical tools are changing the way biological problems are addressed. This interdisciplinary course will introduce new experimental advances, microscopy and spectroscopy in particular, together with underlying principles, in molecular and cellular biophysics.
Note: Primarily for advanced undergraduate students and graduate students with either biological or physical backgrounds.
Prerequisite: Chemistry 160, Chemistry 161, or permission of the instructor.

[*Chemistry 164r. Quantum Chemistry via density functionals: theory and applications]
Catalog Number: 8277
Instructor to be determined
Half course (fall term). Hours to be arranged.
What are "density functionals," where do they come from, and why do they work? This course provides a solid introduction to modern DFT methods (and time-dependent DFT), with applications to various chemical problems. Practical calculations on problems of interest to the student’s research subject are encouraged.
Note: Expected to be given in 2010–11.
Prerequisite: Chemistry 160, or equivalent.

*Chemistry 165. Experimental Physical Chemistry
Catalog Number: 0667
Cynthia M. Friend
Half course (spring term). Mon., 3:00-4:00, and sections on Wed., 1-5, or 6-10 pm. EXAM GROUP: 8
Hands-on introduction to physical methods and techniques used widely in chemistry and chemical physics research laboratories. Computer-based methods of data acquisition and analysis are used throughout.
Note: Recommended as an efficient preparation for research in experimental chemistry, chemical physics, engineering sciences, and related disciplines.
Prerequisite: Chemistry 7, or Physical Sciences 1, or equivalent; Applied Mathematics 21a or Mathematics 21a; one full course in physics or equivalent.

*Chemistry 185 (formerly *Chemistry 285). Molecular Pathophysiology and Pharmacology of Human Disease
Catalog Number: 4005
Gregory L. Verdine and Vicki L. Sato
Half course (spring term). Th., 2–5. EXAM GROUP: 16, 17, 18
This course will address both the molecular basis of human disease, and the biological and chemical foundation of therapeutic intervention. The course will include lectures by prominent experts, and analysis of the primary literature.
Note: May not be taken concurrently with MCB 185. May not be taken for credit if MCB 185 or Chem 285 has already been taken. Credit can not also be received for MCB 185.
Prerequisite: Chemistry 20/30 or 17/27, Life Sciences 52 or their equivalents.

[Chemistry 192. Principles of Drug Discovery and Development]
Catalog Number: 9628 Enrollment: Limited to 20.
Instructor to be determined
Half course (spring term). Hours to be arranged.
This interdisciplinary course will examine the process of drug discovery and development through disease-driven examples. Topics include: the efficacy/toxicity balance, the differences between drugs and inhibitors, the translation of cellular biochemistry to useful medicine.
Note: Expected to be given in 2010–11. May not be taken concurrently with MCB 192. May not be taken for credit if MCB 192 has already been taken.
Prerequisite: MCB 52 and one year of organic chemistry. MCB 54 is recommended.

Cross-listed Courses

[Earth and Planetary Sciences 187 (formerly Earth and Planetary Sciences 137). Biogeochemical Processes]
MCB 199. Statistical Thermodynamics and Quantitative Biology

Primarily for Graduates

Chemistry 201. Organic Synthesis and Genomic Medicine
Catalog Number: 7505
Stuart L. Schreiber
Half course (fall term). Tu., Th., 10–11:30. EXAM GROUP: 12, 13
Organic Synthesis and Genomic Medicine, teaches advanced students in chemistry and chemical biology the principles that underlie modern synthetic organic chemistry and genome biology, and the coordination of the two disciplines, especially using chemical biology, towards genomic medicine. For example, the course will explore how synthetic organic chemistry could provide a general mechanism to exploit the dramatic insights being gained from modern human genetics in order to develop safe and effective therapeutics for currently intractable diseases.
Prerequisite: Chemistry 17/27, Chemistry 20/30, or the equivalent

Chemistry 205. Advanced Physical Organic Chemistry
Catalog Number: 6636
Eric N. Jacobsen
Half course (spring term). Tu., Th., 10–11:30. EXAM GROUP: 12, 13
An in-depth perspective on mechanistic organic chemistry, with analysis of fundamental organic and organotransition metal reaction mechanisms, reactive intermediates, catalysis, stereochemistry,non-covalent interactions, and molecular recognition. Classical and modern tools of physical-organic chemistry, including reaction kinetics, computer modeling, isotope effects, and linear free-energy relationships will be evaluated in the context of literature case studies.
Prerequisite: Chem 206 or an equivalent upper-level course in organic chemistry, and Chem 160/161 or an equivalent sequence in physical chemistry; or permission of the instructor.

*Chemistry 206. Advanced Organic Chemistry
Catalog Number: 1063
Matthew D. Shair
Half course (fall term). M., W., F., at 10. EXAM GROUP: 3
A discussion of the important classes of organic reactions will be presented along with an analysis of mechanism. Topics include rearrangements, pericyclic reactions, carbonyl additions, enolate-based transformations, and photochemically induced reactions. An introduction to FMO theory and stereoelectronic effects will be provided.
Prerequisite: Chemistry 30 or permission of instructor.

Chemistry 207. Advanced Organic Synthesis and Reactions - (New Course)
Catalog Number: 86638
Matthew D. Shair
Half course (fall term). M., W., F., at 10. EXAM GROUP: 3
This course presents reactivity principles of organic molecules. Topics include frontier molecular orbital theory, stereoelectronic effects, conformational analysis, cationic, anionic, radical, and carbene intermediates. These reactivity principles are used in a presentation of target-oriented synthesis. Strategies and tactics for asssembling complex organic molecules are presented.
Prerequisite: Undergraduates must take Chem 30 as a prerequisite.

[*Chemistry 215 (formerly Chemistry 115). Advanced Organic Chemistry: Synthesis of Complex Molecules]
Catalog Number: 0480
Instructor to be determined
Half course (fall term). Hours to be arranged.
An integrated course in complex synthetic problem solving that focuses on the development of principles and strategies for synthesis design with a concurrent, comprehensive review of modern synthetic transformations.
Note: Expected to be given in 2010–11.
Prerequisite: A grade of A in Chemistry 30.

Chemistry 217. Practical Applications of NMR Spectroscopy and Mass Spectrometery in Chemistry
Catalog Number: 1061
Andrew G. Myers
Half course (spring term). Tu., Th., 1–2:30. EXAM GROUP: 15, 16
The goal of this course is to introduce students to analytical techniques that enable the characterization and study of molecules. While emphasis will be placed on the analysis of small molecules with nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), the course will also extend to the study of biomolecules and should prove useful for both pure chemists and chemical biologists.
Prerequisite: Chem 27/30 or equivalent; familiarity with the basic interpretation of 1D 1H NMR.

*Chemistry 240. Statistical Thermodynamics
Catalog Number: 5215
Eugene I. Shakhnovich
Half course (spring term). Tu., Th., 11:30–1. EXAM GROUP: 13, 14
An introduction to statistical mechanics, thermodynamics, and chemical kinetics with applications to problems in chemistry and biology. Topics include: thermodynamics and statistical properties of gases, liquids and crystals, critical phoenomena, elements of non-equilibrium statistical mechanics with applications to Chemistry and Biophysics such as theories for biopolymers and chemical reactions. The course has two tracks. Chem 161 is the basic track. Chem 240 is the advanced track. Each will have separate sections and homework.
Prerequisite: Chemistry 160 and Chemistry 161, or permission of instructor.

[*Chemistry 241. Chemical Kinetics]
Catalog Number: 1122
Instructor to be determined
Half course (spring term). Hours to be arranged.
The rates of chemical processes from both experimental and theoretical points of view; reactions in molecular beams, gases, liquids, solids and at interfaces; applications in chemistry, materials science, atmospheric science and biology.
Note: Expected to be given in 2010–11.
Prerequisite: Introductory physical chemistry (Chemistry 60, Molecular and Cellular Biology 199, or equivalent); introductory quantum mechanics (Chemistry 160, Physics 143a, or equivalent).

*Chemistry 242. Quantum Mechanics for Physical Chemistry
Catalog Number: 2971
Cesar Rodriguez-Rosario; Semion Saikin; Roel Sanchez-Carrera; Dmitrij Rappoport
Half course (fall term). Tu., Th., 2:30–4. EXAM GROUP: 16, 17
Review of the fundamental principles of quantum mechanics: Hilbert spaces, operator algebra, Schrodinger, Heisenberg and interaction pictures. Approximate methods of solution of the Schrodinger equation: Perturbation, mean-field theories and the variational principle. Theory of chemical bonding: Effective Hamiltonian theories and molecular orbital theory. Symmetry and spectroscopy: Electronic, vibrational and NMR spectroscopy. Time-dependent quantum phenomena and its applications to chemical reaction dynamics: transition state theory and Marcus theory of electron transfer. Theory and applications of modern molecular electronic structure: Hartree Fock theory, density functional theory and Moller-Plesset Perturbation theory.
Prerequisite: Chemistry 160 or Physics 143, Physics 11 or 12, and Applied Mathematics 105a and 105b, or Mathematics 21, or equivalent.

[*Chemistry 243. Applied Quantum Mechanics]
Catalog Number: 3622
Instructor to be determined
Half course (spring term). M., W., 2–3:30.
The course will cover the application of quantum mechanical principles to contemporary problems in chemistry and physics. The topics covered in the course will include: chemical bonding and the Born-Oppenheimer Approximation, atom/molecule-photon interaction (including second quantization and the dressed-state approach), Quantum Optics, and solid-state and nano-science (band theory, Fermi liquid theory, and electron transport).
Note: Expected to be given in 2010–11. Intended for graduate and advanced undergraduate students in chemistry, physics, and applied physics.
Prerequisite: Two semesters of quantum mechanics (Chemistry 160 / Chemistry 242, or Physics 143a / 143b, or equivalent).

Chemistry 254. Advanced Inorganic Chemistry - (New Course)
Catalog Number: 32665
Theodore A. Betley
Half course (spring term). M., W., F., at 10. EXAM GROUP: 3
Application of group theory towards understanding reactivity patterns in transition element chemistry with an emphasis on synthesis, structure, bonding, and reaction mechanisms. Advanced problems of interest to inorganic chemistry will be discussed in the context of catalysis, organometallics, and bioinorganic processes.

[Chemistry 267. Surface and Interfacial Phenomena]
Catalog Number: 0571
Instructor to be determined
Half course (spring term). Tu., Th., 10–11:30.
General principles governing surface and interfacial phenomena are developed using treatment of surface electronic and geometric structure as a foundation. The course will treat both theoretical and experimental tools for the investigation of surface structure. Selected spectroscopic techniques will also be treated, with emphasis on surface phenomena. The latter part of the course will develop principles of absorption, reaction, and growth phenomena illustrated through current literature topics.
Note: Expected to be given in 2010–11. Recommended for graduate and advanced undergraduate students in Chemistry, Applied Physics, and related areas with interest in Materials Chemistry and Engineering, Surface Chemistry, Applied Physics, and other areas dependent onproperties and behavior of interfaces.
Prerequisite: Chemistry 160 and 161 or equivalent; Applied Mathematics 21a or Mathematics 21a; one full course in physics or equivalent.

*Chemistry 270. Chemical Biology
Catalog Number: 7754
Gavin MacBeath
Half course (fall term). Tu., Th., 1–2:30. EXAM GROUP: 15, 16
Applying chemical approaches to problems in biology. Topics include: protein engineering and directed evolution; RNA catalysis and gene regulation; chemical genetics, genomics, and proteomics; drug action and resistance; rational and combinatorial approaches to drug discovery; metabolic engineering.
Prerequisite: A strong background in organic chemistry and biochemistry.

[*Chemistry 280 (formerly Chemistry 180). Macromolecular Structure and Function]
Catalog Number: 6449
Instructor to be determined
Half course (spring term). Hours to be arranged.
Explores the relationship between the structure and function of biological macromolecules. Emphasis is placed on the chemical principles governing recognition and catalysis in biological systems, using examples drawn from the scientific literature.
Note: Expected to be given in 2010–11.

*Chemistry 301hf (formerly Chemistry 299hf). Scientific Teaching and Communications: Practicum
Catalog Number: 9903
Matthew D. Shair 2280, Ryan M. Spoering 5625, and Gregory C. Tucci 5020
Half course (throughout the year). Tu., 4–6. EXAM GROUP: 18
This course will teach graduate students how to communicate scientific concepts in the classroom. Students will focus on becoming effective teachers in discussion sections and in the laboratory. The course will emphasize hands-on experience in teaching and explaining scientific concepts.
Note: Required of all first-year graduate students in the Department of Chemistry and Chemical Biology.

Cross-listed Courses

Applied Physics 291. Electron Microscopy Laboratory
Biophysics 242r. Special Topics in Biophysics
Earth and Planetary Sciences 200. Atmospheric Chemistry and Physics
Engineering Sciences 268. Environmental Chemical Kinetics
[Physics 218. Modern Dynamical Systems]

Graduate Courses of Reading and Research

A student intending to elect one of the following research courses should consult the instructor as far in advance as possible.

*Chemistry 300. Research and Reading
Catalog Number: 6307
Members of the Department
Individual work under the supervision of members of the Department.

*Chemistry 300p. Physical Chemistry Seminar
Catalog Number: 3043
Eugene I. Shakhnovich 3147
Full course (indivisible). Friday at 5:00 pm.
Weekly physical chemistry seminar and discussion with a member of the faculty of the Department of Chemistry and Chemical Biology.
Note: Required for first year physical chemistry and chemical physics graduate students and is strongly recommended for second year physical chemistry and chemical physics graduate students.

*Chemistry 302. Organometallic Chemistry
Catalog Number: 1413
Eric N. Jacobsen 1040

*Chemistry 303. Organic Chemistry
Catalog Number: 1043
David A. Evans 7774

*Chemistry 304. Theoretical Atomic, Molecular, and Chemical Physics
Catalog Number: 0532
Eric J. Heller 1074 (on leave fall term)

*Chemistry 311. Physical Chemistry
Catalog Number: 2640
Charles M. Lieber 3102

*Chemistry 315. Photochemistry and Kinetics
Catalog Number: 5964
James G. Anderson 6057 (on leave 2009-10)

*Chemistry 318. Organic Chemistry
Catalog Number: 4295
George M. Whitesides 7447

*Chemistry 323. Organic Chemistry
Catalog Number: 2477
Stuart L. Schreiber 2166

*Chemistry 325. Physical Chemistry
Catalog Number: 8530
Cynthia M. Friend 7446

*Chemistry 330. Physical Chemistry
Catalog Number: 1454
Adam E. Cohen 5761

*Chemistry 331. Chemical Biology
Catalog Number: 1408
Gregory L. Verdine 1980

*Chemistry 336. Physical and Inorganic Chemistry and Materials Science
Catalog Number: 5266
Roy G. Gordon 1353

*Chemistry 340. Inorganic Chemistry
Catalog Number: 7987
Theodore A. Betley 5760

*Chemistry 350. Theoretical Physical Chemistry
Catalog Number: 8285
Eugene I. Shakhnovich 3147

*Chemistry 386. Theoretical Chemistry
Catalog Number: 5300
Alán Aspuru-Guzik 5539

*Chemistry 387. Organic Chemistry
Catalog Number: 4674
Matthew D. Shair 2280

*Chemistry 388. Organic Chemistry
Catalog Number: 1979
Andrew G. Myers 8278

*Chemistry 389. Physical Chemistry
Catalog Number: 5111
Xiaoliang Sunney Xie 2290

*Chemistry 390. Organic Chemistry and Chemical Biology
Catalog Number: 7469
David R. Liu 2717

*Chemistry 391. Physical Chemistry
Catalog Number: 9897
Hongkun Park 2485

*Chemistry 393. Physical Chemistry
Catalog Number: 1273
Xiaowei Zhuang 3991 (on leave 2009-10)

*Chemistry 394. Chemical Biology and Proteomics
Catalog Number: 8697
Gavin MacBeath 4347

*Chemistry 396. Organic Chemistry
Catalog Number: 2293
Daniel E. Kahne 5065

*Chemistry 397. Organic Chemistry
Catalog Number: 3972
Suzanne Walker (Medical School) 5087

*Chemistry 398. Organic and Organometallic Chemistry
Catalog Number: 1013
Tobias Ritter 5540

*Chemistry 399. Biochemistry and Chemical Biology
Catalog Number: 4050
Alan Saghatelian 5541