Chemistry (CHEM)

Professor David Beratan, Chair (5311 French Family Science Center); Professor Dewey McCafferty, Director of Graduate Studies (B219 LSRC); Professors Agre, Baldwin, Beratan, Bonk, Crumbliss, McCafferty, McLendon, Palmer, Reichert, Shaw, Simon, Toone, Warren, Widenhoefer, Yang; Associate Professors Craig, Fitzgerald, Liu, MacPhail, Oas; Assistant Professors Akhremitchev, Coltart, Franz, Hong, Zhou; Professors Emeriti Arnett,Chesnut, Hobbs, Lochmuller, McPhail, Quin, Smith, Wells, and Wilder

The Department of Chemistry offers graduate work leading to the PhD degree. While students are normally admitted only to the PhD program, some students do ultimately pursue an MS degree. Entering graduate students should normally have taken an undergraduate degree in chemistry, along with related work in mathematics and physics. Graduate courses are offered in the fields of analytical, biological, inorganic, organic, physical, and theoretical chemistry, and there are active research programs in each of these areas. In addition, chemistry graduate students are also involved in a variety of interdisciplinary research programs, including biological chemistry, toxicology, pharmacology, and molecular biophysics.

Students will complete 22 units of graded course work by the end of the fall semester of the second year of residence. Normally, students will complete a minimum of 12 units during their first semester, along with the research orientation seminar (CHEM 377). Courses from outside the department may be substituted for chemistry graduate courses, with permission of the director of graduate studies.

275. Advanced Studies. (1) Analytical chemistry, (2) inorganic chemistry, (3) organic chemistry, and (4) physical chemistry. Open to especially well-prepared undergraduates by consent of director of undergraduate studies. Instructor: Staff. 3 units.

302. Spectrochemical Analysis. Advanced topics in spectroscopic analysis, emphasizing absorption, emission, and luminescence techniques and applications to biomolecules. Prerequisite: Chemistry 301 or consent of instructor. Instructor: Staff. 2 units.

304. Separation Science. Fundamental separation chemistry, practical aspects of chromatographic methods, larger scale processes. Prerequisite: Chemistry 301 or consent of instructor. Instructor: Staff. 2 units.

306. Biomolecular Mass Spectrometry. Advanced topics in the mass spectral characterization of biopolymers with an emphasis on protein and DNA analysis. Fundamental and practical aspects of the ionization processes and the instrumentation associated with MALDI- and ESI-Mass spectrometry discussed along with applications of these techniques to structural problems in chemistry and biochemistry. Prerequisite: Chemistry 301 or consent of instructor. Instructor Fitzgerald. 2 units.

309. Special Topics in Analytical Chemistry. An advanced treatment of important areas in modern analysis. Topics may include: electrochemistry, small computer applications, magnetic resonance, and problem-solving approaches. 1 to 4 units. Instructor: Staff. Variable credit.

311. Biological Chemistry. Chemistry of the major classes of biological molecules, including nucleic acids, amino acids and proteins, carbohydrates and lipids. Topics include structure, reactivity and synthesis, and the interaction of biological molecules. Instructors: Hong, McCafferty, Shaw, and Toone. 4 units.

312. Chemistry and Biology of Nucleosides, Nucleotides, and Nucleic Acids. Synthesis, biosynthesis, and reactivity of nucleic acids and their polymers. Mechanisms of DNA and RNA coding, decoding, transmission, and in vitro evolution. Covalent and reversible interactions of nucleic acids with small molecules and macromolecules. Instructors: Hong, McCafferty, Shaw, and Toone. 4 units.

314. Chemical Genomics. Information transfer, restructuring, and decoding in biological systems. Gene expression and evolution of function. Functional consequences of gene expression. Instructors: Shaw and Toone. Variable credit.

315. Advanced Biomedical Imaging Seminar. For grad students in BME, Chem, MSTP focusing on imaging from three distinct perspectives: (i) technology (x-ray based, magnetic resonance, optical, and sonographic modalities), (ii) design and synthesis of imaging probes (cellular, vascular, targeted probes), and (iii) imaging paradigm (anatomical , functional, metabolic, etc.). Recent publications on diverse topics: molecular imaging, contrast agent development, cellular imaging, nanotechnology, hardware design, image guided therapy, interventional imaging and drug delivery, and data analysis and reduction. MatLab, and ImageJ extensively used in course. Choice of topics determined at beginning of each semester to reflect projects of members of seminar series. Course can be taken up to 3 times, as content will change to address varying perspectives. Consent of instructor required. Instructor: Mukundan. Variable credit. C-L: Biomedical Engineering 315

316. Techniques in Biochemistry. Purification and study of biological molecules including macromolecules. Chromatography, spectroscopy (IR, UV/vis, fluorescence, CD), electrophoretic methods, immunological methods, analytical ultracentrifugation, and their application to the study of biomolecules. Instructors: Fitzgerald, Hong, McCafferty, Shaw, and Toone. 2 units.

318. Chemical Biology. The application of chemical concepts and methods to solving problems in molecular and cell biology, with emphasis on the use of small molecules to elucidate and control information transfer in biological systems. Provides relevant background on both useful chemical tools and new biological targets. Instructors: Hong, Toone, McCafferty. 4 units.

320. Physical Methods in Inorganic Chemistry. Physical methods covered include paramagnetic NMR, EPR, magnetism, NQR, Mossbauer spectroscopy, photoelectron spectroscopy, and x-ray analysis. Instructor: Palmer. 2 units.

322. Chemical Applications of Group Theory Including Spectroscopy. Topics covered include symmetry, point groups, group theory, character tables, electronic absorption spectroscopy, infrared spectroscopy, Raman spectroscopy, and microwave spectroscopy. Instructors: Palmer, Simon, and Warren. 2 units.

324. Bioinorganic Chemistry. Topics covered include metal activated enzymes in hydrolysis, oxygencarriers, nitrogen fixation, iron storage and transport, photosynthesis, protein electron transfer, and DNA mediated electron transfer. Instructors: Crumbliss and Franz. 2 units.

326. Inorganic Reaction Mechanisms. A discussion of the mechanism of coordination reactions in solution. Examples include redox reactions and linear free energy relationships. Instructor: Crumbliss. 2 units.

328. Synthesis and Synthetic Methods in Inorganic/Organometallic Chemistry. A discussion of inorganic synthetic methods including supramolecular chemistry and organometallic reactions. Instructor: Widenhoefer. 2 units.

329. Special Topics in Inorganic Chemistry. Lectures, oral reports, and discussions on advanced topics and recent advances in the field of inorganic chemistry. Topics may include: bioinorganic chemistry, fluxional molecules, homogeneous catalysis, synthesis and properties of selected groups of compounds, and new physical methods. 1 to 4 units. Instructor: Staff. Variable credit.

331. Organic Chemistry. Bonding and structure, stereochemistry, conformational analysis, substitution, addition, and elimination reactions, carbon reactive intermediates, concerted reactions, photochemistry, carbon alkylation, carbonyl addition nucleophilic substitution, electrophilic additions, reduction, cycloadditions, rearrangements, main group organometallics, oxidation. Instructors: Baldwin, Coltart, Craig, Hong, Toone, and Widenhoefer. 4 units.

333. Nuclear Magnetic Resonance. Structural elucidation of organic and inorganic compounds by NMR. Fundamentals of data acquisition (pulse sequences, detection), multidimensional techniques, study of dynamic processes and their application to the determination of structure. Instructors: Baldwin and Widenhoefer. Variable credit.

336. Bioorganic Chemistry. Basic enzymology, mechanisms of enzymatic reactions, cofactors, oxidoreductases, C1 chemistry, carbon-carbon bond formation, carboxylation/decarboxylation, heme, pyridoxal enzymes, thiamine enzymes. Prerequisite: Chemistry 331 or equivalent. Instructor: Toone. 4 units. C-L: Biochemistry 336

338. Organometallic Chemistry. Bonding electron counting and structure. Ligand substitution, oxidative addition/reductive elimination, transmetallation, CO and olefin insertion, beta-hydride elimination, methathesis and attack on coordinated ligands. Cross-coupling, Heck coupling, catalytic hydrogenation, olefin polymerization, carbocyclization hydroformylation and related carbonylation chemistry, Wacker oxidation. Transition metal carbene complexes; transition metal oxo complexes. Instructors: Widenhoefer. 2 units.

341. Quantum Chemistry. Foundations and approximate methods in quantum chemistry, with an emphasis on their applications to molecular structure and modeling. Instructors: Akhremitchev, Beratan, Liu, MacPhail, Simon, Warren, and Yang. 4 units.

342. Quantum Mechanics. Special emphasis on chemical applications. Topics include: linear algebra, the uncertainty relations, angular momentum, perturbation theory, time-dependent phenomena, molecules in electromagnetic fields, group theory, and electron correlation. Prerequisite: Chemistry 341 or consent of instructor. Instructors: Akhremitchev, Beratan, Liu, MacPhail, Simon, and Yang. 4 units.

343. Statistical Thermodynamics. Introduction to statistical thermodynamics, with an emphasis on ideal systems and selected model approaches to more complex systems, for example, lattice models. Instructors: Beratan, MacPhail, and Yang. 2 units.

344. Statistical Mechanics. Fundamentals of quantum and classical statistical mechanics using the ensemble approach. Introduction of modern techniques and applications including the renormalization group treatment of phase transitions and linear response theory of time-dependent statistical mechanics. Prerequisite: Chemistry 343 or consent of instructor. Instructors: Beratan, MacPhail, and Yang. 4 units.

346. Biophysical Chemistry. The interrelationships between structure, function, and mechanisms of biological macromolecules. Principles of dynamics, including kinetics, reactivity and transport, and structure, including thermodynamics, NMR, fluorescence, and CD spectroscopy. Instructors: Akhremitchev, Beratan, Oas, Shaw, Simon, and Warren. 4 units.

349A. Special Topics in Physical Chemistry. Presentation of one or more topics of interest such as advanced methods in crystallography, light scattering and small angle X-ray diffraction application of ESR spectroscopy to chemical problems, electronic spectroscopy of proteins group theory intermolecular forces, liquid crystals, methods or determining the rates of elementary steps in reaction kinetics, physical chemistry of aerosols, physical-chemical methods of polymer characterization, structure and bonding in metal-enzymes, statistical mechanics of fluids, topics in structural chemistry, and triplet excitons. Variable credit. Instructor: Staff. Variable credit.

349B. Special Topics in Physical Chemistry. Presentation of one or more topics of interest such as advanced methods in crystallography, light scattering and small angle X-ray diffraction application of ESR spectroscopy to chemical problems, electronic spectroscopy of proteins group theory intermolecular forces, liquid crystals, methods or determining the rates of elementary steps in reaction kinetics, physical chemistry of aerosols, physical-chemical methods of polymer characterization, structure and bonding in metal-enzymes, statistical mechanics of fluids, topics in structural chemistry, and triplet excitons. Variable credit. Instructor: Staff. Variable credit.

375. Research. Instruction in methods used in the investigation of original problems. Individual work and conferences. 1 to 6 units each. Instructors: All members of the graduate staff. Variable credit.

376. Research. Instruction in methods used in the investigation of original problems. Individual work and conferences. 1 to 6 units each. Instructors: All members of the graduate staff. Variable credit.

377. Research Orientation Seminar. A survey of departmental research. Required of all entering graduate students in chemistry. Consent of director of graduate studies required. Instructors: All members of the graduate staff. 1 unit.

380. Graduate Training Internship. Designed to allow graduate student in Chemistry to engage in internship lab work and doctoral study with external agencies and institutions for credit, when determined necessary for degree completion. Laboratory work and analysis can be conducted at external institution with permission of immediate faculty supervisor. Permission of instructor required. Instructor: Staff. 1 unit.

2008-09 Bulletin of the Duke University Graduate School

2008-09 Bulletin of the
Duke University Graduate School