Chemistry and Chemical Biology

Faculty of the Department of Chemistry and Chemical Biology

Stuart L. Schreiber, Morris Loeb Professor of Chemistry and Chemical Biology (Chair)
James E. Davis, Senior Lecturer on Chemistry and Chemical Biology and Molecular and Cellular Biology (Head Tutor)
James G. Anderson, Philip S. Weld Professor of Atmospheric Chemistry ( )
David A. Evans, Abbott and James Lawrence Professor of Chemistry (on leave 2002-2003)
Bretislav Friedrich, Lecturer on 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, Professor of Chemistry and Physics (on leave fall term)
Dudley R. Herschbach, Frank B. Baird, Jr. Research Professor of Science (on leave 2001-02)
Richard H. Holm, Higgins Professor of Chemistry (on leave fall term)
Eric N. Jacobsen, Harvard College Professor and the Sheldon Emery Professor of Chemistry
William Klemperer, Erving Research Professor of Chemistry (on leave 2001-02)
Jeremy R. Knowles, Amory Houghton Professor of Chemistry and Biochemistry (on leave 2002-03)
Charles M. Lieber, Mark Hyman, Jr. Professor of Chemistry (on leave spring term)
David R. Liu, Assistant Professor of Chemistry and Chemical Biology
Andrew G. Myers, Professor of Chemistry and Chemical Biology
Hongkun Park, Assistant Professor of Chemistry and Chemical Biology
Garry Procter, Lecturer on Chemistry and Chemical Biology
David R. Reichman, Assistant Professor of Chemistry and Chemical Biology
Matthew D. Shair, Professor of Chemistry and Chemical Biology
Eugene I. Shakhnovich, Professor of Chemistry and Chemical Biology
Richard J. Staples, Lecturer on Chemistry and Chemical Biology
Gregory L. Verdine, Harvard College Professor and Professor of Chemistry
George M. Whitesides, Mallinckrodt Professor of Chemistry and Chemical Biology
Xiaoliang Sunney Xie, Professor of Chemistry and Chemical Biology
Xiaowei Zhuang, Assistant Professor of Chemistry and Chemical Biology and of Physics

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

Yorke Edward Rhodes, Visiting Professor of Chemistry and Chemical Biology (New York University)
Claude Wintner, Visiting Scholar in Chemistry and Chemical Biology, Visiting Professor of Chemistry and Chemical Biology (Haverford College)

Affiliates of the Department

Stephen C. Harrison, Higgins Professor of Biochemistry
David R. Nelson, Mallinckrodt Professor of Physics and Professor of Applied Physics
Don C. Wiley, John L. Loeb Professor of Biochemistry and Biophysics, Tutor in Biochemical Sciences (on leave 2001-02)

Depending on their prior preparation, students will choose one of three possible entries to studies in this Department. Students with an average or weak background in chemistry should enroll in Chemistry 5 and 7; students with a strong background in chemistry should enroll in Chemistry 10; students with outstanding chemical preparation may enroll at once in Chemistry 17 or 20. Most well prepared students who wish to pursue honors level concentration in chemistry or closely allied fields will elect the (10)+20+30+40+135 track. Others who start with 5+7+17+27 may join the other track by taking 135 and 40. Most students of life sciences, especially those preparing for medical school, will take 5+7 or 10 followed by 17 and 27. Students may not take both Chemistry 17 and 20 for credit. Since there is little or no overlap in content between Chemistry 27 and 30, students interested in a strong background in both bio-organic and theoretical organic chemistry may take both courses. The Science A Core requirement may be satisfied by taking any one of Chemistry 5, 7, 10, 17, or 20.

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 Division 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 are urged to consult a member of the Chemistry Department in planning their work for the first year. Advice may be obtained in the Head Tutor’s Office, Science Center 114.
Chemistry 5. Introduction to Principles of Chemistry
Catalog Number: 7171
James E. Davis
Half course (fall term). M., W., F., at 9, one hour per week of discussion, and three hours per week of laboratory. EXAM GROUP: 2
Introduction to the structure and properties of atoms, molecules, and ions, stoichiometry; thermochemistry; electronic structure of atoms; periodic properties of the elements; chemical bonding; molecular geometry and bonding theories; gases; intermolecular forces, liquids, and solids; properties of solutions.
Note: Chemistry 5–7 is the mainstream general chemistry sequence for students with typical high school chemistry backgrounds (one year) or for students with no previous study of chemistry. Calculus is not necessary for Chemistry 5, but a strong background in high school algebra is essential. Students who lack this algebra background should take Math Ar or Math Xa before attempting Chemistry 5. Students with very strong high school chemistry backgrounds may enroll instead in Chemistry 10, 17, or 20; see those course descriptions for details.

Chemistry 7. Principles of Chemistry
Catalog Number: 5118
Hongkun Park and Charles M. Lieber
Half course (spring term). M., W., F., at 9, one hour per week of discussion, and three hours per week of laboratory. EXAM GROUP: 2
Evolution of the elements; nuclear chemistry; rates and mechanisms of chemical reactions; chemical kinetics; chemical equilibrium; acids and bases; additional aspects of aqueous equilibria; instrumental analysis; chemistry of the environment; chemical thermodynamics; electrochemistry; modern materials; chemistry of the nonmetals; metals and metallurgy; chemistry of coordination compounds; the chemistry of life.
Prerequisite: Chemistry 5 or equivalent, in particular: chemical equilibrium, the first and second law of thermodynamics, and elements of acid-base chemistry. A few simple operations of the calculus are developed and used. Fluency in precalculus secondary school mathematics is assumed. Exposure to secondary school physics will be helpful.

Chemistry 10. Accelerated Course: Foundations of Chemistry
Catalog Number: 1376
Roy G. Gordon and Dudley R. Herschbach
Half course (fall term). Lectures M., W., F., at 9, discussion section, and laboratory work averaging four hours a week, to be arranged. EXAM GROUP: 2
Physical principles in chemistry: atomic and molecular structure, thermodynamics, and chemical kinetics. Applications to reaction equilibria and mechanisms; electrochemistry; photochemistry; environmental chemistry, life sciences and materials chemistry; selected commonplace, exotic, and poetic phenomena. Laboratory work stresses the principles and techniques of quantitative chemistry.
Note: Open to students with strong secondary school courses in chemistry, physics and mathematics, and who are currently enrolled in Mathematics 1a (or equivalent preparation). To be admitted to Chemistry 10, students must obtain a satisfactory score on the Harvard Chemistry Placement Examination, given during freshman week, or must obtain permission of the instructor. Students who do not take this examination or do not achieve a satisfactory score should take Chemistry 5 and 7. Chemistry 10 may not be counted toward a degree in addition to Chemistry 5 or 7.

Chemistry 17. Principles of Organic Chemistry
Catalog Number: 5085
Claude Wintner (Haverford College)
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. 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.
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 Chemistry 7, or 10. Others may enter only by permission of the instructor.

Chemistry 20. Organic Chemistry
Catalog Number: 0876
Andrew G. Myers
Half course (spring term). Lectures, M., W., F., at 9, and a discussion section to be arranged. EXAM GROUP: 2
An introduction to structure, bonding, and mechanism of organic reactions; chemical transformation of the common functional groups in aliphatic and aromatic compounds; synthesis; determination of structure; 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.
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 Chemistry 7, 9, or 10. Others may enter only by permission of the instructor.

Chemistry 27. Organic Chemistry of Life
Catalog Number: 5978
David R. Liu
Half course (spring term). M., W., F., at 11, and a discussion section, and a five hour laboratory each week to be arranged. EXAM GROUP: 4
Sequel to Chemistry 17. Organic chemical principles of molecular science that govern the processes occurring in living systems are illustrated with examples drawn from biochemistry, cell biology, and medicine. The course deals with generalities of organic chemical reactivity (reaction mechanisms, structure-reactivity and structure-property relationships), with matters specifically relevant to the life sciences (chemistry of proteins, nucleic acids, natural products, cofactors, signal transduction), and with applications of chemical biology in medicine and biotechnology (drug design and mechanism, metabolism). It requires an understanding of organic reactions and their mechanisms, with considerable focus on “arrow pushing”.
Note: Chemistry 27 and 30 may both be taken for degree credit. See note for Chemistry 17.
Prerequisite: Chemistry 17; Chemistry 30; or Chemistry 20 with permission of the instructor.

Chemistry 30. Organic Chemistry
Catalog Number: 6587
Yorke Rhodes
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 including reactions involving carbanions, carbonium ions, carbenes and free radicals; and an introduction to biologically important classes of compounds including carbohydrates, amino acids, peptides, nucleic acids and other heterocyclic compounds. Laboratory: an introduction to the practice of organic chemistry and the identification of unknown compounds.
Note: Chemistry 27 and 30 may both be taken for dergee credit. See note for Chemistry 17.
Prerequisite: Chemistry 20 or Chemistry 27.

Chemistry 40. Inorganic Chemistry
Catalog Number: 8201
William Klemperer and Richard H. Holm
Half course (spring term). M., W., F., at 12. EXAM GROUP: 5
An introduction to basic concepts of inorganic chemistry. Topics include synthesis, bonding, thermodynamics, stereochemistry, and reactivity of inorganic compounds of the main group and the transition elements.
Prerequisite: Chemistry 17 or 20.

Chemistry 60. Foundations of Physical Chemistry
Catalog Number: 5181
Eric J. Heller
Half course (fall term). Tu., Th., 10–11:30. EXAM GROUP: 12, 13
This course is designed to be a compact introduction to major principles of physical chemistry (chemical kinetics, thermodynamics, and statistical mechanics), concurrently providing mathematical and physical foundations for these subjects and mathematical preparation for Chemistry 160 and 161, or Chemistry 105.
Prerequisite: Chemistry 5, 7 or 10 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
James E. Davis (fall term), Dudley R. Herschbach (spring term) and members of the Department
Half course (fall term; repeated spring term). Hours to be arranged.
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 Head Tutor in Chemistry. Any student enrolling in this course must register the name of his or her research mentor with the course head, James E. Davis, and Dr. Davis’ signature must appear on each student’s study card.

*Chemistry 98r. Introduction to Research—Junior Year
Catalog Number: 3124
James E. Davis (fall term), Dudley R. Herschbach (spring term) 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 approval 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 Head Tutor in Chemistry. Any student enrolling in this course must register the name of his or her research mentor with the course head, James E. Davis, and Dr. Davis’ signature must appear on each student’s study card.

*Chemistry 99r. Tutorial — Senior Year
Catalog Number: 4508
James E. Davis (fall term), Dudley R. Herschbach (spring term) 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. Written permission of the research adviser must be filed at the office of the Head Tutor in Chemistry. Any student enrolling in this course must register the name of his or her research mentor with the course head, James E. Davis, and Dr. Davis’ signature must appear on each student’s study card.

Cross-listed Courses

Biological Sciences 52 (formerly Biological Sciences 10). Introductory Molecular Biology
Earth and Planetary Sciences 107. Environmental Geochemistry
[MCB 112. Structure and Function of Proteins and Nucleic Acids]
MCB 176. Biochemistry of Membranes

For Undergraduates and Graduates

Chemistry 105. Mechanisms of Organic Reactions
Catalog Number: 3181
George M. Whitesides
Half course (spring term). M., W., F., at 10. EXAM GROUP: 3
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.
Prerequisite: Chemistry 5 and 7, or 10; and Chemistry 20 and 30 with a grade of B- or better. Chem 60 or MCB 61 highly recommended.

[Chemistry 115. Advanced Organic Chemistry: Synthesis of Complex Molecules]
Catalog Number: 0480
Andrew G. Myers
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 2002–03.
Prerequisite: Chemistry 105 or a grade of A in Chemistry 30.

Chemistry 117. Diversity-Oriented Synthesis
Catalog Number: 2774
Matthew D. Shair
Half course (fall term). Tu., Th., at 10. EXAM GROUP: 12
This course will cover reactions and strategies used in the synthesis of complex molecules. Special emphasis will be placed on reactions and strategies that are useful in diversity-oriented syntheses. Areas covered will include: conformational analysis, important C-C bond forming reactions, asymmetric synthesis, asymmetric catalysis, functional group manipulation, tandem reactions, multicomponent reactions, and strategies for ring formation. The application of diversity-oriented synthesis to the discovery of new reactions, catalysts, and molecules with novel biological properties will also be included.

Chemistry 135. Experimental Synthetic Chemistry
Catalog Number: 3406 Enrollment: Limited to 64. Preference given to concentrators in Chemistry, Biochemical Sciences, and Biology, in that order.
Garry Procter
Half course (spring term). Lectures M., at 1, and laboratory, eight to nine hours a week, Tu., 2–10 p.m., W., 1–9 p.m., or Th., 2–10 p.m. 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 chosen to encourage the development of technical proficiency and to simulate actual research.
Note: 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 98 and 99.

Chemistry 150. Inorganic Chemistry II. Transition Elements
Catalog Number: 6491
Richard H. Holm
Half course (fall term). Tu., Th., at 10, and a discussion section to be arranged. EXAM GROUP: 12
An introduction to the chemistry of the transition elements and bioinorganic chemistry. Topics include electronic structure, physical methods, stereochemistry, kinetics, and mechanisms of inorganic reactions. Liberal use will be made of elementary theory and quantum chemistry.
Prerequisite: Chemistry 40 or 160, or permission of the instructor.

[Chemistry 153. Organotransition Metal Chemistry]
Catalog Number: 1848
Eric N. Jacobsen
Half course (spring term). Hours to be arranged.
An introduction to organotransition metal chemistry. Topics include organometallic reaction mechanisms and the application of transition metal complexes in organic synthesis and in homogeneous catalysis.
Note: Expected to be given in 2002–03. Intended primarily for graduate students and advanced undergraduates in chemistry.
Prerequisite: Chemistry 30 or equivalent, and Chemistry 40 or equivalent. Concurrent enrollment in Chemistry 115 and/or Chemistry 206 is recommended.

Chemistry 154. Crystal Symmetry, Diffraction, and Structure Analysis
Catalog Number: 8873
Richard J. Staples
Half course (spring term). M., W., F., at 9; laboratory one afternoon per week. EXAM GROUP: 2
Theory of the internal symmetry and arrangement of atoms in crystals; development and use of space groups. Geometrical and physical aspects of the diffraction process, with emphasis on comprehensive interpretation of x-ray diffraction effects from single crystals. Methods of crystal structure analysis. Laboratory includes searching and utilizing the CSD database, as well as the data collection and crystal structure solution of a new single crystal.
Note: Given in alternate years.
Prerequisite: Familiarity with atomic structure, basic symmetry principles, linear algebra, and electromagnetic waves.

[Chemistry 158. Materials Chemistry]
Catalog Number: 7504
Charles M. Lieber
Half course (fall term). Hours to be arranged.
An introduction to inorganic and organic materials. Topics include: structure of crystalline solids; electronic structure and conduction in materials; crystal chemistry; synthesis of bulk, thin film, and nanoscale materials; structure-property relationships, including superconductivity, magnetism and giant magneto resistance, nonlinear optical materials, mesoporous structures, and monostructures.
Note: Expected to be given in 2002–03. Primarily intended for advanced undergraduates and graduates.
Prerequisite: Chemistry 40 or equivalent.

Chemistry 160. Physical Chemistry
Catalog Number: 3420
Cynthia M. Friend
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; one full course in physics (with an honor grade, if in Physics 1); Chemistry 10 or equivalent.

Chemistry 161. Statistical Thermodynamics
Catalog Number: 3575
David R. Reichman
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.
Prerequisite: Chemistry 160 and Applied Mathematics 21a, or equivalent.

Chemistry 162. Molecular Spectroscopy
Catalog Number: 0924
William Klemperer and Xiaoliang Sunney Xie
Half course (spring term). Tu., Th., 11:30–1. EXAM GROUP: 16, 17
Modern molecular spectroscopy applied to the study of the structure and dynamics in gas and condensed phase systems. Topics include electronic, vibrational, rotational and nuclear hyperfine energy levels of polyatomic molecules, their interactions with electromagnetic radiation, selection rules and relaxation processes. The fundamental principles are illustrated by spectroscopic approaches, such as absorption, fluorescence, scattering, magnetic resonance, as well as nonlinear processes and photochemistry.
Prerequisite: Chemistry 160 and 161; or Physics 143 and 181; (or equivalent preparation). Concurrent registration in Chemistry 161 or Physics 181 acceptable.

Chemistry 163. Molecular Biophysics and Biophysical Chemistry: Structure and Conformational Dynamics of Bio-macromolecules
Catalog Number: 3635
Xiaowei Zhuang
Half course (fall term). M., W., F., at 10. EXAM GROUP: 3
An introduction to the structure and conformational dynamics of bio-macromolecules including proteins and nucleic acids. Emphasis will be placed on the molecular interactions responsible for the macromolecular structure and the experimental techniques used to probe the macromolecular structure and conformational dynamics. The relation of structure and dynamics to function will also be discussed.
Prerequisite: Biological Sciences 10 or 52 or 56; Chemistry 160 or Physics 15; or permission of instructor.

[Chemistry 164r. Molecular Biophysics and Biophysical Chemistry: Theory and Simulations of Macromolecules]
Catalog Number: 5588
Eugene I. Shakhnovich
Half course (fall term). Hours to be arranged.
Introduction to the principles of macromolecular structure, folding and dynamics, with emphasis on structure-function relationship. Principles of protein folding and molecular evolution. Molecular dynamics and other simulation approach to protein dynamics, enzymatic function and folding. Empirical and knowledge-based energy functions for structure prediction and design. Examples include: prediction of protein structure using ab initio and bioinformatics approaches, theory of random and designed heteropolymers with application to protein folding and design, molecular recognition, rational drug design.
Note: Expected to be given in 2002–03. It is suggested that students enroll in Biophysics 164 when this course is bracketed. Cannot be taken for credit by students who have completed Biophysics 164r.
Prerequisite: Biological Sciences 11 and one of the following: Chemistry 160, Biochemistry 61, Physics 143, or permission of instructor.

Chemistry 165. Experimental Physical Chemistry
Catalog Number: 0667
Bretislav Friedrich
Half course (spring term). Lectures: F., 1–2:30; laboratories M., or Tu., 1–5. EXAM GROUP: 6, 7
The course aims at providing an introduction to the methods and techniques used in current physical chemistry/chemical physics research laboratories and at developing scientific writing and oral presentation skills. Nine out of a total of eleven laboratory assignments are experiments conducted directly in the Research Groups of the Chemistry Department using their state-of-the art equipment. These involve: molecular beams; mass spectrometry; Fourier transform infrared and nuclear magnetic resonance spectroscopies; laser ablation; laser spectroscopy; cavity ring-down spectroscopy; scanning tunneling and atomic force microscopy; kinetics. Computer-based methods of data acquisition & analysis are used throughout.
Note: Recommended as an efficient preparation for research in experimental physical chemistry/chemical physics and related sciences.
Prerequisite: Chemistry 160 or Physics 143a

Chemistry 167. Surface and Interfacial Phenomena
Catalog Number: 7480
Cynthia M. Friend
Half course (fall term). Tu., Th., 2:30–4. EXAM GROUP: 16, 17
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 adsorption, reaction, and growth phenomena illustrated through current literature topics.
Note: Primarily for graduates and advanced undergraduates in Chemistry, Physics, and Applied Sciences.
Prerequisite: Chemistry 160 or equivalent.

[Chemistry 170. Chemical Biology]
Catalog Number: 7754
David R. Liu
Half course (fall term). Hours to be arranged.
This course explores many of the most interesting recent advances in applying chemical approaches to problems in chemistry and biology. Topics include: protein design and engineering, molecular evolution, DNA damage and repair, novel natural proteins, metabolic engineering, drug action and resistance, rational and combinatorial approaches to drug discovery, chemical genetics, and genomics. Lectures are supplemented with problem sets, discussion sections, and additional readings from the scientific literature.
Note: Expected to be given in 2002–03.
Prerequisite: A strong background in organic chemistry, including basic biochemistry.

Chemistry 180. Macromolecular Structure and Function
Catalog Number: 6449
Gregory L. Verdine
Half course (spring term). Tu., Th., 10–11:30. EXAM GROUP: 12, 13
This course will explore in detail the relationship between the structure and function of biological macromolecules. Emphasis will be placed on the chemical principles governing recognition and catalysis in biological systems, using examples drawn from the scientific literature. Topics will include conformational analysis of nucleic acids and proteins, binding of biological macromolecules to each other and small molecules, and the molecular basis for catalysis. Areas of biologic emphasis will include gene regulation, signal transduction and chemical genetics.

Engineering Sciences 168. Aquatic Chemistry
Catalog Number: 5874
Scot T. Martin
Half course (fall term). Tu., Th., 1–2:30. EXAM GROUP: 15, 16
Applications of organic, inorganic, and physical chemistry to describe and quantify processes occurring in natural waters. Thermodynamics and kinetics of aqueous solutions, acid-base chemical transformations, role of dissolved carbon dioxide, gas-water exchange, complexation of aqueous metal ions, precipitation and dissolution, oxidation and reduction, electrical aspects of solid-solution interfaces, particle aggregation, trace metal cycling, and photochemistry.
Prerequisite: Chemistry 5 and 7 or equivalent.

Cross-listed Courses

Biophysics 164r (formerly Biophysics 151r). Molecular Biophysics and Biophysical Chemistry: Theory and Simulation of Macromolecules

Primarily for Graduates

*Chemistry 206. Advanced Organic Chemistry
Catalog Number: 1063
David A. Evans
Half course (fall term). M., W., F., at 10. EXAM GROUP: 3
An in-depth discussion of the important classes of organic reactions will be provided. The discussion will include an introduction to FMO theory, streoelectronic effects, conformational analysis, and enantioselective reaction variants. Reaction families that will be surveyed include the major classes of cycloadditions, olefin and carbonyl addition processes, and sigmatropic rearrangements. The generation, structure, and reactivity of commonly encountered reactive intermediates such as enolates, metalloenamines, carbenes, carbonim ions, and free radicals will be integrated into the lectures. Weekly problem assignments designed to improve “electron-pushing” skills will be provided. Small study groups headed by experienced graduate student mentors will emphasize the development of problem-solving skills.
Prerequisite: Chemistry 105, a prior course in mechanistic organic chemistry, or permission of instructor.

Chemistry 240. Statistical Mechanics
Catalog Number: 5215
David R. Reichman
Half course (fall term). Tu., Th., 11:30–1. EXAM GROUP: 13, 14
Equilibrium and nonequilibrium statistical mechanics, with a strong emphasis on interacting systems, including the thermodynamics and structure of gases, liquids, and crystals, critical phenomena, and the theory of transport processes.
Prerequisite: Chemistry 160 and 161, or permission of instructor.

Chemistry 241. Chemical Kinetics
Catalog Number: 6976
Dudley R. Herschbach
Half course (spring term). Tu., Th., 10–11:30. EXAM GROUP: 12, 13
Theory of bimolecular gas phase reactions, success of those theories when applied to reactions of free radicals, unimolecular and thermomolecular rate theories, thermochemistry, energy transfer and recent advances in molecular beam and laser chemistry.
Note: Given in alternate years.

Chemistry 242. Quantum Mechanics I
Catalog Number: 2971
William Klemperer and Hongkun Park
Half course (fall term). M., W., F., at 12. EXAM GROUP: 5
Principles of quantum mechanics, Particle in a potential well, Identical particles, Angular momentum, time-independent perturbation theory, Chemical bonding in molecules.
Prerequisite: Chemistry 160 or Physics 143, Physics 11 or 12, and Applied Mathematics 105a and 105b, or Mathematics 21, or equivalent.

[Chemistry 243. Quantum Mechanics II]
Catalog Number: 0566
Hongkun Park
Half course (spring term). Hours to be arranged.
Time-dependent perturbation theory, Matter-photon interaction and spectorscopy, Scattering theory and its application, Electronic motion in low-dimensional structures, Electron-electron interaction.
Note: Expected to be given in 2002–03. Given in alternate years.
Prerequisite: Chemistry 242.

[Chemistry 244. Quantum Chemistry]
Catalog Number: 8295
Roy G. Gordon
Half course (spring term). Hours to be arranged.
Quantum mechanics applied to molecules and solids. Hartree-Fock, configuration-interaction, perturbation, coupled cluster, density functional, Monte-Carlo and semi-empirical theories. Use of computer programs for these methods.
Note: Expected to be given in 2002–03.
Prerequisite: Chemistry 242.

Chemistry 245. Single-molecule Biophysics
Catalog Number: 0944
Xiaoliang Sunney Xie
Half course (fall term). W., F., at 11. EXAM GROUP: 4
The emerging single-molecule methodology of biophysics, including the principles of single-molecule studies and the experimental approaches, such as the patch clamp technique, atomic force microscopy, optical tweezers, near field microscopy, and confocal and nonlinear optical microscopy. Applications to various biological problems will be discussed.
Prerequisite: Introductory level biochemistry and physical chemistry including quantum mechanics and statistical mechanics; or permission of instructor.

Cross-listed Courses

Applied Physics 291. Electron Microscopy Laboratory
Earth and Planetary Sciences 200. Atmospheric Chemistry and Physics
[Earth and Planetary Sciences 202. Introduction to the Dynamics of Atmospheres and Oceans]
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. Reading
Catalog Number: 6307
Members of the Department
Individual work under the supervision of members of the Department.

*Chemistry 301. Inorganic Chemistry
Catalog Number: 3748
Richard H. Holm 7015 (on leave fall term)

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

*Chemistry 303. Organic Chemistry
Catalog Number: 1043
David A. Evans 7774 (on leave 2002-2003)

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

*Chemistry 307. Organic Chemistry
Catalog Number: 5101
Elias J. Corey 1369

*Chemistry 311. Physical Chemistry
Catalog Number: 2640
Charles M. Lieber 3102 (on leave spring term)

*Chemistry 313. Organic Chemistry
Catalog Number: 0183
Yoshito Kishi 3852

*Chemistry 315. Photochemistry and Kinetics
Catalog Number: 5964
James G. Anderson 6057

*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 327. Theoretical Chemistry
Catalog Number: 6064
Martin Karplus 1361

*Chemistry 330. Physical Chemistry and Chemical Physics
Catalog Number: 4327
Dudley R. Herschbach 1381 (on leave 2001-02)

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

*Chemistry 377. Physical Chemistry, Including Molecular Spectroscopy
Catalog Number: 5506
William Klemperer 1391 (on leave 2001-02)

*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 392. Physical Chemistry
Catalog Number: 6980
David R. Reichman 2569

*Chemistry 393. Physical Chemistry
Catalog Number: 1273
Xiaowei Zhuang 3991