Department of Chemistry

Chair

Robert J. Cava

Associate Chair

Michael H. Hecht

Director of Graduate Studies

Andrew B. Bocarsly

Professor

Steven L. Bernasek

Andrew B. Bocarsly

Roberto Car

Robert J. Cava

G. Charles Dismukes

John T. Groves

Michael H. Hecht

Maitland Jones Jr.

David W. C. MacMillan

Robert A. Pascal Jr.

Herschel A. Rabitz

Clarence E. Schutt

Jeffrey Schwartz

Giacinto Scoles

Martin F. Semmelhack

Zoltán G. Soos

Erik J. Sorensen

Thomas G. Spiro

Salvatore Torquato

Visiting Professor

Henny W. Zandbergen

Associate Professor

Jannette L. Carey

Annabella Selloni

Assistant Professor

Stefan Bernhard

Chulbom Lee

Joshua D. Rabinowitz, also Lewis-Sigler Institute for Integrative Genomics

Wolfgang Richter

Lecturer with Rank of Professor

Edward Stiefel

Lecturer

Henry L. Gingrich

Robert P. L’Esperance

Alison Williams

Associated Faculty

Emily A. Carter, Mechanical and Aerospace Engineering

Frederick M. Hughson, Molecular Biology

François Morel, Geosciences

Satish C. B. Myneni, Geosciences

Yigong Shi, Molecular Biology

Jeffry B. Stock, Molecular Biology

 

The Department of Chemistry provides facilities for students intending to work toward the degree of Doctor of Philosophy (Ph.D.) and for students doing postdoctoral research.

Entering graduate students are normally expected to have met the standard requirements for the bachelor’s degree with specialization in chemistry, including a minimum of one year each in organic chemistry, inorganic chemistry, and physical chemistry, or a related subject. The department advises its students to have acquired in advance of graduate work a good fundamental training in mathematics and physics, including at least one year each of physics and calculus.

Departmental qualifying examinations are offered in the fields of biochemistry, chemical physics, inorganic chemistry, organic chemistry, and physical chemistry in the fall of each year. Graduate students are expected to pass an examination in three of these fields, or to complete course work during their first year of study in order to compensate for their deficiencies.

The general examination consists of the oral defense of a research proposal together with a review of the student’s overall academic record. Of students who pass the general examination, only those who have shown some degree of distinction in their work proceed toward the doctorate.

The Ph.D. is awarded primarily on the basis of a thesis describing original research in one area of chemistry. Graduate students begin this research during their first year of graduate work; it becomes one of their most important activities in the second year, and thereafter they devote almost all of their time to it. The final public oral examination consists of the candidate’s defense of one original research proposal, as well as a defense of the thesis dissertation. The chief objective of the system is to stimulate interesting discussion based upon original inquiry and coordination of information by the candidate in a number of fields that challenge his or her interest.

Normally, students are required to teach at least six contact hours per week for one term during the second year of enrollment.

Materials Chemistry

Graduate students interested in pursuing thesis work in the growing area of materials-related chemistry should be aware of the many opportunities for research in this area that exist in the chemistry department and across campus. Collaborative research in materials science and engineering is facilitated through the programs of the Princeton Institute for the Science and Technology of Materials (PRISM), a multidisciplinary research institute that addresses the molecular basis of material science. The institute is made up of faculty from seven departments in the sciences and engineering at Princeton, and provides opportunities for collaborative thesis research for graduate students admitted to any of the participating departments. It houses specialized shared research instrumentation, laboratory space, and an environment for collaborative research projects, and it sponsors a program of seminars and visiting scientists that address important areas of materials science and engineering. For further information, see the PRISM section of this catalog.

Molecular Biophysics

The discipline of molecular biophysics focuses on the applications of chemistry, engineering, mathematics, and physics to problems of biological systems, principally at the molecular level. The program mission is to provide students having backgrounds in these disciplines with exposure to contemporary biological problems that can benefit from the application of tools and approaches from the physical sciences and mathematics. The program itself does not admit students directly, nor does it award degrees; hence all program students must meet the requirements for admission and degree completion in their home department. Any student may join the program by participating in its activities. Students who wish to be considered for program support must meet additional requirements. For more information, consult the program Web site at www.princeton.edu/~chemdept/mbp.

At the start of the fall term the program director meets with incoming first-year graduate students in each participating department (applied and computational mathematics, chemical engineering, chemistry, computer science, molecular biology, and physics) to introduce the program. Interested students may discuss their preparedness, and recommendations are made for course work that can provide needed cross-disciplinary background.

A survey course, CHM 550, “Contemporary Problems in Molecular Biophysics,” is offered each spring term. This course, organized by the director, is open to all students and is required of students who will be candidates for program support. Each member of the training faculty discusses in an informal setting ongoing research in the interdisciplinary area. At the end of the term, each student prepares a written report on one seminar of particular personal interest, relating the topic to the current state of knowledge in the specific research area and to the discipline of molecular biophysics in general. Student reports are expected to culminate in a proposal for a research project that is theoretically sound and practically realistic. This document later serves as one point in evaluation of the student’s candidacy for program support.

The program supports a topical seminar series each year. Students in the survey course work together to identify a research area that will be the theme for the series of invited seminars in the following academic year. The invitation program is organized over the summer under the guidance of the program director.

By the end of the second year, students must pass the general examination in their home departments before being considered for program support. Candidates are interviewed by the program director and a committee of the training faculty. Criteria for support include: evaluation of the student’s preparedness and motivations for pursuing a biophysical approach to the thesis problem; the suitability of the thesis problem to the training goals of the program; and the student’s participation and performance in the survey course. Students in the program must take the course in scientific ethics offered in the Department of Molecular Biology.

Students carrying out thesis research in molecular biophysics are assigned a thesis advisory committee in consultation with the thesis adviser and the program director. This committee meets with the student at the start of each year until completion of the Ph.D. The roles of the committee include: recommending specific course work to complete the student’s cross-disciplinary training; evaluating the student’s progress on the thesis project; suggesting complementary biophysical approaches to meet the project goals; and advising the student about career paths related to the discipline.

Graduate Courses of Interest. Students may find the following courses useful.

Chemistry

503 Introduction to Statistical Mechanics

504 Molecular Spectroscopy

506 Chemical Bonding

512 Chemical Kinetics

515, 516 Biophysical Chemistry I, II

538 Topics in Biological Chemistry

539 Introduction to Chemical Instrumentation

542 Principles of Macromolecular Structure

543 Advanced Topics in Structural Biology

Molecular Biology

505 Molecular Biology of Prokaryotes

506 Molecular Biology of Eukaryotes

Physics

511 Thermodynamics, Kinetic Theory, and Statistical Mechanics

557 Electronic Methods in Experimental Physics

561, 562 Biophysics

A typical curriculum might include (in addition to any core departmental courses) CHM 538 or a survey course in biochemistry, followed by CHM 542, dealing with macromolecular structure, and CHM 515, CHM 543, or PHY 562, dealing with diffraction and spectroscopic methods applied to macromolecules and membranes. Competency in the techniques of molecular biology and genetics at the level of MOL 340, 350 should be mastered. The student’s general examination includes questions dealing with molecular biophysics.

Program in Neuroscience

Students may participate in the interdisciplinary Program in Neuroscience. The program encourages the serious study of molecular, cellular, developmental, and systems neuroscience as it interfaces with cognitive and behavioral research. For more information, see the program description.

Seminars in Chemistry

The department conducts an active seminar program featuring outside speakers in the various fields of chemistry. Through visiting professorships and the special lectureships sponsored by the FMC Corporation, Wyeth, and Bristol-Myers Squibb, authorities from around the world are brought to the Princeton Department of Chemistry for periods ranging from one week to one full academic year. Most of the research groups in the department hold regular research seminars.

Equipment and Facilities

The department’s activities are centered in the Frick Chemical Laboratory and the adjoining Hoyt Laboratory. Frick also houses the Chemistry Library, comprising an extensive collection of periodicals as well as standard reference works, texts, and monographs. Facilities include professionally staffed machine, electronics, and glassblowing shops; a recently renovated student machine shop; a central chemistry stockroom; darkrooms; and cold and constant-temperature rooms. Nearby are facilities of the engineering, mathematics, molecular biology, physics, and psychology departments.

The chemistry department has an extensive collection of modern, shared instrumentation. This includes Fourier transform NMR spectrometers at 600, 500, 300, and 270 MHz, some with multinuclear, variable temperature, and solid-state capabilities; all of these are readily accessible for student operation. There are also state-of-the-art mass, electron spin resonance, Fourier transform infrared, and ultraviolet-visible spectrometers. Several less-sophisticated instruments are also available for routine samples. Additionally, a picosecond laser facility is housed within the department. A new X-ray diffractometer is available for crystal structure determination, as is a complete molecular graphics facility and instrumentation for preparation and characterization of biological samples. Computer capabilities are also extensive and include a wide-ranging network of dedicated workstations throughout the department. These machines satisfy most of the normal computing requirements for the department’s research groups, but larger programs can be handled by massive computing resources on campus.

The Ph.D.-level staff members of the chemistry department’s instrument facility play an important role in repairing equipment, operating sophisticated instrumentation, and planning experiments that would require modifications to existing equipment.

In addition to departmental facilities, individual research laboratories contain specialized equipment such as lasers, computers, NMR spectrometers, ultra-high vacuum apparatus, and photon-counting facilities. Virtually every research group is involved in collaborative projects within the department and with other departments such as engineering, materials science, molecular biology, and physics.

Courses

CHM 501 Introduction to Quantum Chemistry

Roberto Car

Basic development of quantum theory and the Schroedinger equation. Single-particle potential problems, an introduction to angular momentum theory, and operator concepts and electron structure.

CHM 502 Advanced Quantum Chemistry

Herschel A. Rabitz

Typical topics covered include advanced aspects of angular momentum theory, scattering, time-dependent processes, and interaction of radiation with matter. Specialized topics are included at the discretion of the instructor.

CHM 503 Introduction to Statistical Mechanics (also CHE 524)

Pablo G. Debenedetti, Salvatore Torquato

Understanding equilibrium and nonequilibrium properties of matter in terms of the microscopic details of molecular interactions and structure. Topics include Gibbs ensembles, the microscopic basis of the laws of classical thermodynamics, noninteracting systems, virial expansion, distribution function theory, Monte Carlo and molecular dynamics simulation techniques, critical phenomena, percolation theory, renormalization group methods, and Boltzmann equation and applications.

CHM 504 Molecular Spectroscopy

Staff

A survey of atomic and molecular energy levels and the Hamiltonians that describe them. The interaction of radiation with matter, including multiphoton effects. Examples include electronic and nuclear spectroscopy of molecules and crystals, electron spin resonance, microwave spectroscopy, and the uses of lasers in modern spectroscopic research.

CHM 506 Chemical Bonding

Staff

Theories of the chemical bond and intermolecular interactions and quantum mechanical methods and their use in predicting and interpreting chemical phenomena are studied. Illustrative examples are drawn from organic, inorganic, physical, and biological chemistry.

CHM 507 Solid-State Chemistry

Annabella Selloni

Crystal types and binding energies; crystal structure and symmetry; reciprocal lattice, Brillouin zones, energy bands, and Fermi surfaces; impurity states; energy transport in ionic, molecular, and semiconducting crystals; magnetism and spin waves; and chemistry and photochemistry in the solid state.

CHM 509, 510 Topics in Physical Chemistry (also MSE 509, 520)

Staff

Topics covered vary from year to year and are selected from among the following: state-selected chemical processes; high-resolution spectroscopy; energy transfer and redistribution; laser-induced chemistry; surface chemistry; electronic properties of conjugated polymers; nonlinear optical materials; physical electrochemistry; heterogeneous reaction dynamics; spectroscopy and dynamics of clusters; and chaotic systems.

CHM 511 The Chemistry and Physics of Nanomaterials (see MSE 513)

CHM 512 Chemical Kinetics

Steven L. Bernasek

Discussion of reaction rate theory, molecular dynamics, and experimental techniques.

CHM 513 Electronic Properties of Materials

Roberto Car

An introduction to the electronic theory of materials. The course assumes basic knowledge of quantum mechanics at the single particle level. Topics include elementary electronic structure theory of crystalline solids, clusters, and nanostructures; defects, surfaces, and disordered materials; electric transport in bulk materials, nanostructures, and molecular wires; and optical properties and electron spectroscopies.

CHM 514 Molecular and Biomolecular Imaging (also MOL 512)

Staff

This course presents a united treatment of spectroscopic methods applied to imaging. The theoretical and experimental foundations of magnetic resonance and laser methods is emphasized. Medical, biochemical, and materials science applications are presented.

CHM 515 Biophysical Chemistry I

Joshua D. Rabinowitz

Introduction to contemporary techniques used to study the structures, functions, and interactions of biological macromolecules. Methods include spectroscopies (UV, CD, fluorescence, and NMR); X-ray diffraction; hydrodynamic and transport methods; and principles and practice of ligand-binding analysis. Focus is on applications rather than theory to convey the utility of each method for solving molecular problems, and on the strengths and limitations of individual methods and the complementarities among them. Suitable for beginning graduate or advanced undergraduate students in chemistry, engineering, molecular biology, and physics. There are no formal prerequisites.

CHM 516 Biophysical Chemistry II

Jannette L. Carey

Introduction to basic principles of macromolecular structure, stability, and interactions: protein structure; protein thermodynamics and folding; nucleic acid structure and stability; and principles of intermolecular recognition. Special emphasis is on understanding the molecular origins of cooperativity in macromolecular systems, and the relationships between structure and stability and covalent and noncovalent properties and processes. Suitable for beginning graduate or advanced undergraduate students in chemistry, engineering, molecular biology, and physics. There are no formal prerequisites.

CHM 521 Organometallic Chemistry

Jeffrey Schwartz

Familiarizes the student with basic principles of structural reactivity of transition metal organometallic chemistry.

CHM 522 Advanced Inorganic Chemistry

Andrew B. Bocarsly

Advanced topics in inorganic chemistry, including solid-state and bioinorganic chemistry, band theory, and reaction mechanisms.

CHM 523 Coordination Chemistry

Andrew B. Bocarsly

Chemistry of transition metal complexes and ligand field and molecular orbital theory.

CHM 524 Topics in Inorganic Chemistry

Staff

Topics covered vary from year to year and are selected from among the following: inorganic spectroscopy and applications to chemical bonding in transition metal complexes; homogeneous catalysis based on transition metal systems; noninnocent ligand and fluxional processes; organic synthesis via organometallic reagents and the mechanisms of these reactions; metal clusters; stereochemistry of inorganic reactions; and bioinorganic chemistry.

CHM 527 Physics and Chemistry of Minerals and Materials (see GEO 501)

CHM 530 Synthetic Organic Chemistry

Erik J. Sorensen

Methods for introduction and modification of functional groups, formation and cleavage of bonds; selection and employment of protecting groups; control of stereochemistry; manipulation of polyfunctional molecules; design and use of selective reagents; and multistage syntheses are studied. These areas of study are illustrated with examples of outstanding achievements in the total synthesis of complex molecules.

CHM 531 Advanced Organic Chemistry

Chulbom Lee

Geared toward graduate students interested in synthetic organic chemistry, the course covers general strategies for the stereocontrolled formation of carbon-carbon bonds as well as basic concepts in physical organic chemistry that shed light on regio- and stereo-control in organic reactions.

CHM 532 Mechanistic and Physical Organic Chemistry

Staff

The ways in which molecules are changed into other molecules are studied. Some topics include mechanisms of acid and base catalyzed reactions, nucleophilic and electrophilic displacements and substitutions, addition and elimination reactions, condensations, inter- and intra-molecular rearrangements, electrocyclic ring openings and closings, and sigmatropic shifts.

CHM 534 Modern Methods for Organic Synthesis

Chulbom Lee, Erik J. Sorensen

A mechanism-based course on modern synthetic methodologies for beginning graduate students and advanced undergraduates. The class discusses various types of organic reactions, their mechanisms, the reactive intermediates involved in these transformations, and the scope and limitations of each method. The initial goal is to become fluent in the language of organic chemistry; the broader objective is to understand the fundamental principles underlying each transformation. The course is expected to provide sufficient foundation to comprehend and use the research literature in chemical synthesis.

CHM 536 Topics in Organic Chemistry

Staff

Topics covered vary from year to year and are selected from among the following: structure, synthesis, reactions, stereochemistry, and biosynthesis of naturally occurring substances, including polyketides, alkaloids, terpenoids, and antibiotics; and the structure and reactivity of reaction intermediates such as carbonium ions, carbanions, radicals, carbenes, and excited states.

CHM 537 Organometallic Reagents in Organic Synthesis

Staff

An advanced course dealing with the applications of organo-transition metal reagents in organic synthesis. Emphasis is placed on systems already in use. Discussion is held concerning the scope and limitations of the methods in terms of mechanism . A prior course in organometallic chemistry (CHM 521) is recommended.

CHM 538 Topics in Biological Chemistry

Staff

The chemical mechanisms of enzyme-catalyzed reactions are studied. The nature and sequence of events at enzyme active sites, emphasizing the participation of prosthetic groups and amino acid side chains in catalysis are also studied. Topics discussed include the use of kinetic, spectroscopic, and structural data as well as substrate analog and isotopic substitution studies for analysis of enzyme mechanisms.

CHM 539 Introduction to Chemical Instrumentation

Robert A. Pascal Jr.

The operation and application of instrumentation used in modern chemical research is covered. Emphasis is on proton and carbon NMR. Pulsed-Fourier transform and 2D-NMR techniques are described. The course also has a laboratory section, in which students get hands-on exposure to FT-NMR and other spectrometers.

CHM 542 Principles of Macromolecular Structure

Staff

Structures and properties of biological macromolecules. The forces and interactions that direct biological polymers to adapt particular 3-dimensional structures are discussed from both a structural and a thermodynamic perspective. Special emphasis is on recent experimental work, probing the folding and stability of proteins as well as the design of novel proteins.

CHM 543 Advanced Topics in Structural Biology

Staff

Structural biology of human diseases. A critical discussion of protein structures of medical interest such as antibodies, histocompatibility complexes, growth factors, receptors, T-cell activation, G-coupled receptors, viruses, and bacterial toxins. The structural basis of signal transduction is treated in terms of high-resolution crystal structures of kinases and phosphatases. Special emphasis is on methods used to obtain and interpret results by using X-ray crystallography.

CHM 544 Metals in Biology (also ENV 544)

John T. Groves, Edward I. Stiefel

A survey of the bioinorganic chemistry of the 25 elements whose bioinorganic chemistry is relevant to the environment (biochemical cycles), agriculture, and health. In-depth coverage of key transition metal ions, including manganese, iron, copper, and molybdenum focuses on redox roles in anaerobic and aerobic systems and metalloenzymes that activate small molecules and ions, including hydrogen, nitrogen, nitrate, nitric oxide, oxygen, superoxide, and hydrogen peroxide. Appreciation of the structure and diversity of metalloenzyme systems is critical to understanding life at the molecular level.

CHM 550 Contemporary Problems in Molecular Biophysics (also MOL 550)

Jannette L. Carey

Members of the training faculty in molecular biophysics present their current research related to the discipline in seminar format. Emphasis is on developing the background and interdisciplinary context of ongoing projects. This survey course is an effective way for students to act on their interest in the interdisciplinary area, gain exposure to its many facets, and decide if they wish to be considered candidates for training grant support.

Pertinent Courses in Allied Departments

Chemical Engineering

448 Introduction to Nonlinear Dynamics

533 Molecular Recognition and Biomolecular Engineering

536 Glasses and Supercooled Liquids

544 Solid-State Properties of Polymers

Computer Science

551 Introduction to Computational Molecular Biology

Electrical Engineering

540 Organic Materials for Photonics and Electronics

Geosciences

418 Environmental Aqueous Geochemistry

470 Environmental Chemistry of Soils

537 Atmospheric Chemistry

Mechanical and Aerospace Engineering

501 Mathematical Methods of Engineering Analysis I

Molecular Biology

504 Cellular Biochemistry

Physics

501 Electricity and Magnetism

505, 506 Quantum Mechanics I, II