Chemistry Academic Year 2023 – 2024 Jump To: Jump To: General Information Address Frick Laboratory Phone 609-258-4116 Website Department of Chemistry Program Offerings: Ph.D. Director of Graduate Studies: Erik Sorensen Graduate Program Administrator: Patti Wallack Overview The Department of Chemistry provides facilities for students intending to work toward the degree of Doctor of Philosophy (Ph.D.). The Department of Chemistry is a vital, expanding hub of scientific inquiry with deep historic roots and a ready grasp on the future. Housed in the world-class Frick Chemistry Laboratory, faculty and students work at the frontiers of science where the lines between chemistry and other disciplines merge. They conduct collaborative, interdisciplinary research with the potential to produce anything from new molecules and forms of energy to advanced models of catalysis and innovative materials. They also are immersed in the classic pursuit of chemistry -- to examine the composition of substances and investigate their properties and reactions. Graduate students are invited and encouraged to pursue individualized programs. Their experience is enhanced by strong faculty mentoring and access to world-leading intellectual and physical resources. 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 defense of a student’s original research proposal as well as a defense of the thesis dissertation. The chief objectives of the requirements are stimulation of interesting discussion based upon original inquiry and coordination of information by candidates in a number of fields that challenge their interests. A Master of Science is offered to select industry-sponsored candidates who are employees of companies that are members of the Industrial Associates Program. The program may be completed on a part-time basis under one of the following three plans: two consecutive academic years with full-time study one term each year; two consecutive academic years with half-time study both terms of each year; two consecutive academic years with full-time study one term of one year and half-time study in two other terms during the two-year period. For additional information about eligibility and application procedures for the Master of Science, please contact the department directly. Apply Application deadline December 1, 11:59 p.m. Eastern Standard Time (This deadline is for applications for enrollment beginning in fall 2024) Program length Ph.D. 5 years, M.S. 2 years Fee $75 GRE General Test - optional/not required; Subject Test in Chemistry or Physics - optional/not required Additional departmental requirements Ph.D. applicants are required to select an area of research interest when applying. The M.S. degree is only open to employees of firms with active membership in the department’s industrial associates program. Program Offerings Ph.D. Program Offering: Ph.D. Courses Departmental Coursework Requirement Students are required to take six courses and to perform satisfactorily, obtaining a minimum of a 3.0 average. Students may choose P/D/F enrollment for one of these six courses. Students may pursue coursework in the following subfields: chemical biology, inorganic chemistry, catalysis, and organic synthesis, physical experimental, theoretical and computational, or materials chemistry. Course selections and enrollment decisions are made in consultation with their faculty adviser to best meet their needs and research interests. Additional pre-generals requirements Departmental Breadth Requirement The Department of Chemistry requires that students demonstrate a breadth of knowledge in the field of chemistry. The breadth requirement is generally completed by successfully passing the qualifying exams in a minimum of three of the following subfields: organic chemistry, inorganic chemistry, physical chemistry, biochemistry, and chemical physics. Students, with approval by the DGS, may also satisfy the breadth requirement by replacing one or more examination with equivalent graduate-level coursework. This coursework would count within the six courses mandated by the course requirement. General exam The general examination consists of two written proposals and the student’s oral defense of each. The first proposal is based on the student’s chosen area of thesis research. The second consists of an independent research proposal that is in the student’s general area of research but which is not a part of the student’s thesis research. These proposals are considered together with a review of the student’s overall academic record and research progress. Of students who pass the general examination, only those who have shown some degree of distinction in their work proceed toward the doctorate. Qualifying for the M.A. The Master of Arts (M.A.) degree is normally an incidental degree awarded on the way to full Ph.D. candidacy and is earned after a student successfully completes the general examination. It may also be awarded to students who, for various reasons, leave the Ph.D. program, provided that this requirement has been met. Teaching Students are required to teach at least six contact hours per week for one term or three contact hours per week for two terms; this requirement is most often fulfilled during the second year of enrollment. Post-Generals requirements Third Year Seminar In the third year of study, students present a thirty-minute seminar on their research progress. To foster understanding of the different chemical disciplines, third-year students are required to attend all such seminars. Out-of-Field Proposal Prior to the defense of the thesis at the Final Public Oral, the student must generate an original research proposal, not directly related to the thesis research, and defend the proposal before the advisory committee. While this milestone should be completed well in advance of the Final Public Oral, it must be completed no later than two weeks in advance. The “out of field” research proposal must be written and circulated among the advisory committee before the oral presentation date. The student is responsible for organizing the committee members to meet for this oral exam and informing the Graduate Administrator prior to the date agreed upon. The student is required to circulate a final version of the proposal for the committee to review a minimum of two weeks in advance of the oral exam. The committee records a grade for the written proposal and its oral defense. Grading is on a scale from Excellent to Fail. Dissertation and FPO The Ph.D. is awarded after the candidate’s doctoral dissertation has been accepted and the final public oral examination sustained. Faculty Chair Paul J. Chirik Associate Chair Robert R. Knowles Director of Graduate Studies Erik J. Sorensen Director of Undergraduate Studies Robert P. L'Esperance Professor Andrew B. Bocarsly Roberto Car Robert Joseph Cava Paul J. Chirik John T. Groves Michael H. Hecht Todd K. Hyster Robert R. Knowles David W. MacMillan Tom Muir Joshua D. Rabinowitz Herschel A. Rabitz Gregory D. Scholes Annabella Selloni Martin F. Semmelhack Mohammad R. Seyedsayamdost Erik J. Sorensen Salvatore Torquato Haw Yang Associate Professor Jannette Carey Leslie M. Schoop Assistant Professor William M. Jacobs Ralph E. Kleiner Alice Kunin Jose B. Roque Erin E. Stache Marissa L. Weichman Associated Faculty Bonnie L. Bassler, Molecular Biology Emily C. Davidson, Chemical and Biological Eng Kelsey B. Hatzell, Mechanical & Aerospace Eng Frederick M. Hughson, Molecular Biology Bruce E. Koel, Chemical and Biological Eng Alexei V. Korennykh, Molecular Biology A. James Link, Chemical and Biological Eng Cameron A. Myhrvold, Molecular Biology Satish C. Myneni, Geosciences Sabine Petry, Molecular Biology Michele L. Sarazen, Chemical and Biological Eng Jeffry B. Stock, Molecular Biology Martin Helmut Wühr, Molecular Biology Senior Lecturer Robert P. L'Esperance Susan K. VanderKam Lecturer Corey Clapp Sonja A. Francis Michael T. Kelly Sandra L. Knowles Ana Mostafavi István Pelczer Chia-Ying Wang For a full list of faculty members and fellows please visit the department or program website. Permanent Courses Courses listed below are graduate-level courses that have been approved by the program’s faculty as well as the Curriculum Subcommittee of the Faculty Committee on the Graduate School as permanent course offerings. Permanent courses may be offered by the department or program on an ongoing basis, depending on curricular needs, scheduling requirements, and student interest. Not listed below are undergraduate courses and one-time-only graduate courses, which may be found for a specific term through the Registrar’s website. Also not listed are graduate-level independent reading and research courses, which may be approved by the Graduate School for individual students. CBE 526 - Surface Science: Processes and Probes (also CHM 527/MSE 526) An introduction to processes at surfaces and interfaces. Experimental methods of surface science. Electron spectroscopy, ion scattering, and scanning probe microscopy. Atomic structure of surfaces and adsorbed layers. Thermodynamics of surface processes. Adsorption and molecular dynamics of gas-surface reactions. Kinetics of adsorption, desorption, diffusion, and reactions. Liquid interfaces. Heterogeneous catalysts. Etching. Film growth and epitaxy. Applications to energy and environmental science and technology. CHM 500A - Responsible Conduct of Research in Chemistry (Half-Term) Discussion and evaluation of the role professional researchers play in dealing with the reporting of research, responsible authorship, human and animal studies, misconduct and fraud in science, intellectual property, and professional conduct in scientific relationships. Participants are expected to read the materials and cases prior to each meeting. Successful completion is based on regular attendance and active participation in discussion. This half-term course is designed to satisfy federal funding agencies' requirements for training in the ethical practice of scientists. Required for graduate students and post-docs. CHM 500B - Responsible Conduct of Research in Chemistry (Half-Term) Discussion and evaluation of the role professional researchers play in dealing with the reporting of research, responsible authorship, human and animal studies, misconduct and fraud in science, intellectual property, and professional conduct in scientific relationships. Participants are expected to read the materials and cases prior to each meeting. Successful completion is based on regular attendance and active participation in discussion. This half-term course is designed to satisfy federal funding agencies' requirements for training in the ethical practice of scientists. Required for chemistry graduate students & post-docs. CHM 500C - Responsible Conduct of Research in Chemistry (Half-Term) Discussion and evaluation of the role professional researchers play in dealing wtih the reporting of research, responsible authorship, human and animal studies, misconduct and fraud in science, intellectual property, and professional conduct in scientific relationships. Participants are expected to read the materials and cases prior to each meeting. Successful completion is based on regular attendance and active participation in discussion. This half-term course is designed to satisfy federal funding agencies' requirements for training in the ethical practice of scientists. Required for chemistry graduate students/post-docs. CHM 501 - Basic Principles of Quantum Mechanics 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 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 CBE 524/MSE 514) Statistical mechanics provides the basis for understanding the equilibrium and nonequilibrium properties of matter in terms of the microscopic details of molecular interactions and structure. The course aims to provide students with working knowledge of the fundamentals and applications of statistical mechanics. CHM 504 - Molecular Spectroscopy This course will cover selected topics in molecular spectroscopy with an emphasis on the basic principles. An additional focus will be placed on strong radiation field interactions with molecules going into a regime where the spectra and dynamics of the molecules are influenced by the radiation. CHM 509 - Topics in Physical Chemistry Topics covered vary from year to year and are selected from 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 510 - Topics in Physical Chemistry (also PHY 544) Topics covered vary from year to year and are selected from 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 515 - Biophysical Chemistry I Broad introduction to major contemporary techniques used to study structures, functions, and interactions of biological macromolecules. Emphasis on applications, practical aspects, and experimental design rather than theory, and on strengths and limitations of individual methods and complementarities among them. Intended to convey to students with diverse backgrounds and interests the utility of each method for solving molecular problems. CHM 516 - Biophysical Chemistry II Comprehensive introduction to major contemporary techniques used to study the structures, functions, and interactions of biological macromolecules, with an emphasis on applications rather than theory. Particular stress is laid on the strengths and limitations of individual methods and the complimentarities among them. Methods covered include spectroscopies (UV, florescense, CD, and NMR), X-ray diffraction, hydrodynamic and transport methods (sedimentation and diffusion), and miscellaneous methods. CHM 521 - Organometallic Chemistry Familiarizes the student with basic principles of structural reactivity of transition metal organometallic chemistry. CHM 522 - Advanced Inorganic Chemistry (also MSE 592) Advanced topics in inorganic chemistry, including solid-state and bioinorganic chemistry, band theory, and reaction mechanisms. CHM 523 - Coordination Chemistry Chemistry of transition metal complexes and ligand field and molecular orbital theory. CHM 524 - Topics in Inorganic Chemistry Topics covered vary from year to year and are selected from 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 529 - Topics in Inorganic Chemistry Topics covered vary from year to year. The subject matter will be selected from among the following, related to the inorganic chemistry of solids: point group and space group symmetry, irreproducible representations, structure-property relations, crystallography, methods in X-ray, neutron and electron diffraction science, the structures of solids and molecules, the electronic structure of molecular and non-molecular solids, the optical, electronic and magnetic properties of molecular and non-molecular solids and their relation to crystal structure. CHM 530 - Synthetic Organic Chemistry 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 532 - Mechanistic and Physical Organic Chemistry 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 intramolecular rearrangements, electrocyclic ring openings and closings, and sigmatropic shifts. CHM 534 - Modern Methods for Organic Synthesis A mechanism-based course on modern synthetic methodologies for beginning graduate students and advanced undergraduates. The class will discuss 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 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 Topics covered vary from year to year and are selected from 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 538 - Topics in Biological Chemistry 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 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 the students get hands-on exposure to FT-NMR and other spectrometers. CHM 541 - Chemical Biology II (also QCB 541) A chemically and quantitatively rigorous treatment of metabolism and protein synthesis, with a focus on modern advances and techniques. Topics include metabolic pathways and their regulation; metabolite and flux measurement; mathematical modeling of metabolism; amino acid, peptide and protein chemistry; protein engineering and selected applications thereof. CHM 542 - Principles of Macromolecular Structure: Protein Folding, Structure and Design (also MOL 542) 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 placed on recent experimental work probing the folding and stability of proteins as well as on the design of novel proteins. CHM 544 - Metals in Biology: From Stardust to DNA (also ENV 544) A course in inorganic physiology and biochemistry, presenting the chemical principles adopted by nature to perform biological functions. Topics include metal ion function in protein and nucleic acid structure, metalloenzyme mechanisms, metal regulation of gene expression, biological energy conversion via ion pumping, storage and mobilization of the elements, and biomineralization. CHM 599 - Curriculum Practical Training in Chemistry This course is designed for a student to pursue an internship, practicum or other form of employment directly related to the student MSE 504 - Monte Carlo and Molecular Dynamics Simulation in Statistical Physics & Materials Science (also CBE 520/CHM 560/PHY 512) This course examines methods for simulating matter at the molecular and electronic scale. Molecular dynamics, Monte Carlo and electronic structure methods will be covered with emphasis on hands-on experience in writing and/or exercising simulation codes for atomistic and electronic structure simulation. MSE 512 - Phase Transformations in Materials: Theory and Simulation (also CHM 511) This special topics course focuses on the theory and simulation of phase transformations in materials. Through a combination of traditional lectures, peer-to-peer instruction and several computational projects, the physics of nucleation, growth and coarsening behavior of both solid-like and liquid-like multicomponent materials are explored. Computational approaches covered in the class include Langevin equations, Monte Carlo, diffuse interface (phase field), and the level set methods. MSE 515 - Random Heterogeneous Materials (also APC 515/CHM 559) Foams, composites, porous media, and biological media are all examples of random heterogeneous materials. The relationship between the macroscopic (transport, mechanical, electromagnetic and chemical) properties and microstructure of random media is formulated. Topics include correlation functions; percolation theory; fractal concepts; sphere packings; Monte Carlo techniques; and image analysis; homogenization theory; effective-medium theories; cluster and perturbation expansions; variational bounding techniques; topology optimization methods; and cross-property relations. Biological and cosmological applications will be discussed. QCB 515 - Method and Logic in Quantitative Biology (also CHM 517/EEB 517/MOL 515/PHY 570) Close reading of published papers illustrating the principles, achievements and difficulties that lie at the interface of theory and experiment in biology. Two important papers, read in advance by all students, will be considered each week; emphasis will be on student discussion, not formal lectures. Topics include: cooperativity, robust adaptation, kinetic proofreading, sequence analysis, clustering, phylogenetics, analysis of fluctuations, maximum likelihood methods.