Graduate Course Descriptions

30100: Advanced Inorganic Chemistry
30200: Synthesis and Physical Methods in Inorganic Chemistry
30400: Organometallic Chemistry
30500: Nanoscale Materials
30600: Chemistry of the Elements
30700: Metal Catalysis in Polymer Synthesis
30900: Bioinorganic Chemistry
31100: Supramolecular Chemistry
32100: Physical Organic Chemistry I: Structure and Mechanism
32200: Organic Synthesis and Structure
32300: Tactics of Organic Synthesis
32400: Physical Organic Chemistry II: Special Topics
32500: Bioorganic Chemistry
32900: Polymer Chemistry
33000: Complex Chemical Systems
33500: Chemistry of Enzyme Catalysis
33100: New Synthetic Reactions and Catalysts
33200: Chemical Biology I
33300: Chemical Biology II
33600: Biological Chemistry of Materials: Principles and Applications
35000: Introduction to Research
36100: Wave Mechanics and Spectroscopy
36200: Quantum Mechanics
36300: Statistical Thermodynamics
36400: Advanced Statistical Mechanics
36500: Chemical Dynamics
36800: Advanced Computational Chemistry
36900: Materials Chemistry
37100: Advanced Spectroscopies
38700: Biophysical Chemistry
40000: Research in Related Departments and Institutes
4xx00: Research
5000x: Advanced Training for Teachers and Researchers in Chemistry


Note: The syllabus for each course depends substantially on the faculty member teaching the course; therefore courses taught from one year to the next may cover different subject matter.

Chemistry 30100: Advanced Inorganic Chemistry
Group Theory and its applications in inorganic chemistry are developed. These concepts are used in surveying the chemistry of inorganic compounds from the standpoint of quantum chemistry, chemical bonding principles, and the relationship between stucture and reactivity.
Generally offered Autumn quarter.
Chemistry 30200: Synthesis and Physical Methods in Inorganic Chemistry

This course covers theoretical and practical aspects of important physical methods for the characterization of inorganic molecules.  Topics may include NMR, IR, RAMAN, EPR, and electronic and photoelectron spectroscopy; electrochemical methods; and single-crystal X-ray diffraction.

Generally offered Spring quarter.
Chemistry 30400: Organometallic Chemistry
The preparation and properties of organometallic compounds, notably those of the transition elements, their reactions, and the concepts of homogeneous catalysis are discussed.
Generally offered Autumn quarter.
Chemistry 30500: Nanoscale Materials
This course will provide an overview of nanoscale phenomena in metals, semiconductors and magnetic materials. It will cover the fundamental aspects of quantum confinement in semiconductors and metals, superparamagnetism in nanoscale magnets, electronic properties of nanowires and carbon nanotubes, surface plasmon resonances in nanomaterials, photonic crystals, etc. Special attention will be paid to preparative aspects of nanomaterials, colloidal and gas-phase syntheses of nanoparticles, nanowires and nanotubes. Engineered nanomaterials and their assemblies are considered promising candidates for a variety of applications, from solar cells, electronic circuits, light-emitting devices and data storage to catalysts, biological tags, cancer treatments and drug delivery. The course will cover state of the art in these and other areas. Finally, the course will provide an overview of the experimental techniques used for structural characterization of inorganic nanomaterials: electron microscopy, X-ray diffractometry, small-angle X-ray scattering, STM, AFM, Raman spectroscopy, etc.
Special topics course.
Chemistry 30600: Chemistry of the Elements
The descriptive chemistries of the main-group elements and the transition metals are surveyed from a synthetic perspective, and reaction chemistry of inorganic molecules is systematically developed.
Generally offered Winter quarter.
Chemistry 30700: Metal Catalysis in Polymer Synthesis
This course focuses on the application of metal catalysts in polymer synthesis. The scope, mechanisms, stereocontrol aspects, and applications of Ziegler-Natta, metallocene/single-site, ring-opening metathesis, ATRP, and other metal catalyzed/mediated polymerization reactions are discussed. Key underlying concepts from organometallic chemistry and polymer science are introduced as appropriate, and the properties and applications of important polymers produced by metal catalysis are discussed.
Offered Infrequently
Chemistry 30900: Bioinorganic Chemistry
This course focuses on the various roles of metals in biology. Topics include coordination chemistry of bioinorganic units, substrate binding and activation, electron-transfer proteins, atom and group transfer chemistry, metal homeostasis, ion channels, metals in medicine, and model systems.
Generally offered Autum quarter.
Chemistry 31100: Supramolecular Chemistry
This course develops the concepts of supramolecular chemistry (both organic and metal-based systems) and its applications. Coordination chemistry is introduced as a background to metal-based supramolecular systems. The chemistry and physical properties of transition metal complexes are presented, including crystal field theory, molecular orbital theory, magnetism, and electronic spectra. The mechanisms by which molecular motors operate are presented and reference is made to synthetic systems that attempt to emulate biological molecular motors.
Chemistry 32100: Physical Organic Chemistry I: Structure and Mechanism
The chemical bond, stereochemistry, acids and bases, linear free energy relationships. Approaches to the study of reaction mechanisms, including thermochemistry, kinetics, isotope effects, solvent and substituent effects.
Generally offered Autumn quarter.
Chemistry 32200: Organic Synthesis and Structure
A close consideration of the mechanism, applicability and limitations of the major reactions in organic synthesis. Stereochemical control in synthesis. Advanced nmr techniques for structure elucidation.
Generally offered Autumn quarter.
Chemistry 32300: Tactics of Organic Synthesis
A dissection of the most important syntheses of complex natural and unnatural products. Synthesis planning and methodology. The logic of synthesis. Biogenesis.
Generally offered Winter quarter.
Chemistry 32400: Physical Organic Chemistry II: Special Topics
Recent topics have included nuclear magnetic resonance and electron spin resonance spectroscopy, photochemistry, cycloaddition reactions, transition state theory, and molecular orbital theory in organic chemistry.
Generally offered Winter quarter.
Chemistry 32500: Bioorganic Chemistry
A goal of this course is to relate chemical phenomena with biological activities. The course will cover two main areas: chemical modifications of biological macromolecules and their potential effects, and the application of spectroscopic methods to elucidate the structure and dynamics of biologically relevant molecules.
Generally offered Spring quarter.
Chemistry 32600: Protein Fundamentals
The focus of this course is on the physico-chemical phenomena that define protein structure and function. Topics include (1) the interactions/forces that define polypeptide conformation; (2) the principles of protein folding, structure, and design; and (3) the concepts of molecular recognition and enzyme catalysts.
Generally offered Autumn quarter.
Chemistry 32900: Polymer Chemistry
This course introduces a broad range of polymerization reactions and discusses their mechanisms and kinetics. New concepts of polymerization and new materials of current interest are introduced and discussed. The physical properties of polymers, ranging from thermal properties to electrical and optical properties in both a solution state and a solid state are discussed, with the emphasis on structure/property relationship.
Offered infrequently.
Chemistry 33000: Complex Chemical Systems
This course describes chemical systems in which nonlinear kinetics lead to unexpected (emergent) behavior of the system. Autocatalytic and spatiotemporal pattern forming systems are covered, and their importance in the development and function of living systems are discussed.
Offered infrequently.
Chemistry 33100: New Synthetic Reactions and Catalysts
This course presents recent highlights of new synthetic reactions and catalysts for efficient organic synthesis. Mechanistic details as well as future possibilities will be discussed.
Generally offered Spring quarter.
Chemistry 33200: Chemical Biology I & Chemistry 33300: Chemical Biology II
These courses emphasize the concepts of physical organic chemistry--including mechanism, molecular orbital theory, thermodynamics and kinetics--in a survey of modern research topics in chemical biology. Topics will be taken from the recent literature and will include the roles of proteins in signal transduction pathways, the biosynthesis of natural products, strategies to engineer cells with novel functions, the role of spatial and temporal inhomogeneities in cell function, and organic synthesis and protein engineering for the development of molecular tools to characterize cellular activities. Students should have an undergraduate-level knowledge of organic chemistry and biochemistry.
Generally offered Winter and Spring quarter.
Chemistry 33500: Chemistry of Enzyme Catalysis
The course will cover a series of topics illustrating and exploring aspects of the chemistry of enzyme catalysis, and will use case studies based on the primary scientific literature – both classic & current papers. For each class, there will be primary scientific papers assigned that the student will be expected to have studied in depth prior to class, including ‘reading around’ on the same & related topics; suggestions for supplementary reading will be given. Classes will be conducted as discussion sessions, guided by the Instructor – all students will be expected to be prepared to answer questions from the instructor, and to take active part in class discussions. Participation in class will count for a portion of the grade for each student.
Chemistry 33600: Biological Chemistry of Materials: Principles and Applications
This course will focus on principles of bioconjugation techniques; Preparation of immobilized-enzymes/proteins: adsorption, occlusion, cross-linking and covalent binding. Applications of cofactor-dependent enzymes: building of enzymatic electrodes and biofuel cells. Development of immuonosensors based on ELISA, electrochemistry, optics, carbon nanotubes and piezoelectric methods. Principles and design of DNA/RNA based sensors (Ribozymes, SELEX, Aptamers DNAzymes, Molecular Beacons). Amplification methods for nucleic acids detection in test tube and in cells. Preparation and characterization of nanoparticles in nucleic acids and proteins sensing processes.
Offered Spring quarter 2015.
Chemistry 35000: Introduction to Research
Individual laboratory or theoretical work under the supervision of a staff member. The student must make arrangements with a staff member, who will assign and supervise the work.
Generally offered Autumn, Winter and Spring quarters.
Chemistry 36100: Wave Mechanics and Spectroscopy
The introductory concepts, general principles, and applications of wave mechanics to spectroscopy are presented.
Generally offered Autumn quarter.
Chemistry 36200: Quantum Mechanics
A formal development of quantum mechanics is presented including operators, matrix mechanics, and perturbation methods. The theory is applied to the description of the electronic structure of atoms and molecules.
Generally offered Winter quarter.
Chemistry 36300: Statistical Thermodynamics
PQ: CHEM 26100-26200. This course  covers the thermodynamics and introductory statistical mechanics of systems at equilibrium.
A. Dinner. Autumn.
Chemistry 36400: Advanced Statistical Mechanics
PQ: CHEM 36300 or equivalent. Topics may include statistics of quantum mechanical systems, weakly and strongly interacting classical systems, phase transitions and critical phenomena, systems out of equilibrium, and polymers.
K. Freed. Winter.
Chemistry 36500: Chemical Dynamics
This course develops a molecular-level description of chemical kinetics, reaction dynamics, and energy transfer in both gases and liquids. Topics will include potential energy surfaces, collision dynamics and scattering theory, reaction rate theory, collisional and radiationless energy transfer, molecule-surface interactions, Brownian motion, time correlation functions, and computer simulations.
Generally offered Spring quarter.
Chemistry 36800: Advanced Computational Chemistry
Numerical analysis. Molecular mechanics and molecular dynamics simulations. Calculations of the geometric and electronic structure of molecules.
Generally offered Spring quarter.
Chemistry 36900: Materials Chemistry
This course covers structural aspects of colloidal systems, surfactants, polymers, diblock copolymers, and self-assembled monolayers. We also cover the electronic properties associated with organic conducting polymers, organic light-emitting devices, and transistors. More novel topics of molecular electronics, nanotubes, quantum dots, and magnetic systems are also covered. The aim of the course is to provide a broad perspective of the various contributions of chemistry to the development of functional materials.
Chemistry 37100: Advanced Spectroscopies
This is a linear and nonlinear spectroscopy course. It includes notions on matter-radiation interaction, absorption, scattering and oscillator strength, applied mostly with the optical range while briefly touching upon microwave (NMR, ESR) and X-rays at the extreme. It will cover nonlinear optical processes such as coherent Raman, harmonic and sum-frequency, induced transparency, slow light, and X-ray generation. It will also cover the coherent and incoherent dynamical probes such as pump-probe, echos and two-dimensional spectroscopy.
Generally offered Spring quarter.
Chemistry 38700: Biophysical Chemistry
This course develops a physicochemical description of biological systems. Topics include macromolecules, fluid-phase lipid-bilayer structures in aqueous solution, biomembrane mechanics, control of biomolecular assembly, computer simulation of biomolecular systems.
Offered infrequently.
Chemistry 40000: Research in Related Departments and Institutes
For students who have been accepted as candidates for the Ph.D. degree in the Department of Chemistry but who prefer to fulfill the dissertation requirement by carrying out research in one of the related departments or institutes. The programs of all such students must be approved in advance both by the Department of Chemistry and by the chief administrative officer of the department or institute in which the research is to be done.
Offered all quarters.
Chemistry 4xx00: Research
A specific 40000 level number is assigned to each member of the faculty. Students doing research with a specific faculty member will normally register for the specific assigned course number
Offered all quarters.
Chemistry 50000, 50001, 50002: Advanced Training for Teachers and Researchers in Chemistry – I, II, III.
This course will extend the traditional two-week departmental TA training into a full year, covering both the materials that are critical to becoming an excellent TA and the skills to produce well-rounded PhD candidates. At the end of this course, students are expected to develop an enhanced understanding and talent of critical thinking, an enriched knowledge base that is critical in solving real-world problems, an improved ability in the consideration and use of innovative pedagogical tools, the ability to transition into independent research, and effective skills in preparing high-quality written reports and oral presentations, as well as to begin thinking about career development skills.
Offered all quarters.