Ph.D. Chemistry

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

GEO 568 Advanced Aqueous Chemistry (also

CHM 528

) This course focuses on selected topics in aqueous chemistry of the natural systems, including: chemistry of inorganic and organic species in aqueous solutions- hydration, hydrolysis, coordination chemistry of metal-ligand complexes, chemical equilibria in fresh and saline water; mineral dissolution and alteration, recrystallization and evolution of secondary phases, dissolution kinetics; nucleation and precipitation of minerals, biological control in mineral precipitation, precipitation kinetics; electron transfer in aquatic systems, redox equilibria and kinetics; chemistry of water-solid/air interfaces.

MSE 504 Monte Carlo and Molecular Dynamics Simulation in Statistical Physics & Materials Science (also

CHM 560

/

PHY 512

/

CBE 520

) 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 513 Introduction to Nanotechnology (also

CHM 511

/

MAE 516

) The first part of the course contains fundamental chemical concepts and basic ideas needed to calculate the difference between the bulk properties of matter and the properties of aggregates. The second part describes the tools needed to probe matter at the nanoscale level. The third part discusses examples of nanoscale materials (clusters, monolayers, fullerenes, biomolecules) and their applications.

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

PHY 570

/

EEB 517

/

CHM 517

/

MOL 515

) 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.