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Chemistry (Ch) Graduate Courses (2017-18)

Ch 101. Chemistry Tutorials. 3 units (1-0-2): third term. Small group study and discussion on special areas of chemistry, chemical engineering, molecular biology, or biophysics. Instructors drawn from advanced graduate students and postdoctoral staff will lead weekly tutorial sessions and assign short homework assignments, readings, or discussions. Tutorials to be arranged with instructors before registration. Instructors: Gray, Okumura, Stoltz, Tirrell.
Ch 102. Introduction to Inorganic Chemistry. 9 units (3-0-6): third term. Structure and bonding of inorganic species with special emphasis on spectroscopy, ligand substitution processes, oxidation-reduction reactions, organometallic and biological inorganic chemistry. Instructor: Agapie.
Bi/Ch 110. Introduction to Biochemistry. 12 units (4-0-8): first term. Lectures and recitation introducing the molecular basis of life processes, with emphasis on the structure and function of proteins. Topics will include the derivation of protein structure from the information inherent in a genome, biological catalysis, the intermediary metabolism that provides energy to an organism, and the use of DNA manipulations, cloning, and expression of proteins in foreign hosts to study protein structure and function. Instructors: Campbell, Parker.
Bi/Ch 111. Biochemistry of Gene Expression. 12 units (4-0-8): second term. Lectures and recitation on the molecular basis of biological structure and function. Emphasizes the storage, transmission, and expression of genetic information in cells. Specific topics include DNA replication, recombination, repair and mutagenesis, transcription, RNA processing, and protein synthesis. Instructors: Campbell, Parker.
Ch 112. Inorganic Chemistry. 9 units (3-0-6): first term. Introduction to group theory, ligand field theory, and bonding in coordination complexes and organotransition metal compounds. Systematics of bonding, reactivity, and spectroscopy of commonly encountered classes of transition metal compounds. Instructor: Agapie.
Bi/Ch 113. Biochemistry of the Cell. 12 units (4-0-8): third term. Lectures and recitation on the biochemistry of basic cellular processes in the cytosol and organelles, with emphasis on membrane and protein trafficking. Specific topics include protein secretion, virus entry, endocytosis, endoplasmic reticulum dynamics, nuclear trafficking, autophagy, apoptosis, and mitochondrial dynamics. The relationship of these processes to human disease will be discussed. Not offered 2017-18. Instructor: Chan.
Ch 117. Introduction to Electrochemistry. 9 units (3-0-6): second term. Discussion of the structure of electrode-electrolyte interface, the mechanism by which charge is transferred across it, and experimental techniques used to study electrode reactions. Topics change from year to year but usually include diffusion currents, polarography, coulometry, irreversible electrode reactions, the electrical double layer, and kinetics of electrode processes. Instructor: See.
Ch 120 ab. Nature of the Chemical Bond. Ch 120 a: 9 units (3-0-6), first term: Ch 120 b: (1-1-7), second term. Modern ideas of chemical bonding, with an emphasis on qualitative concepts useful for predictions of structures, energetics, excited states, and properties. Part a: The quantum mechanical basis for understanding bonding, structures, energetics, and properties of materials (polymers, ceramics, metals alloys, semiconductors, and surfaces), including transition metal and organometallic systems with a focus on chemical reactivity. The emphasis is on explaining chemical, mechanical, electrical, and thermal properties of materials in terms of atomistic concepts. Part b: The student does an individual research project using modern quantum chemistry computer programs to calculate wavefunctions, structures, and properties of real molecules. Instructor: Goddard.
Ch 121 ab. Atomic-Level Simulations of Materials and Molecules. Ch 121 a: 9 units (3-0-6) second term: Ch 121 b (1-1-7) third term. Atomistic-based methods for predicting the structures and properties of molecules and solids and simulating the dynamical properties. The course will highlight theoretical foundations and applications of atomistic simulations to current problems in such areas as biological systems (proteins, DNA, carbohydrates, lipids); polymers (crystals, amorphous systems, copolymers); semiconductors (group IV, III-V, surfaces, defects); inorganic systems (ceramics, zeolites, superconductors, and metals); organometallics, and catalysis (heterogeneous and homogeneous). Part a covers the basic methods with hands-on applications to systems of interest using modern software. The homework for the 1st 5 weeks emphasizes computer-based solutions. For the exams and 2nd 5 weeks of the homework each student selects a short research project and uses atomistic simulations to solve it. For part b each student selects a more extensive research project and uses atomistic simulations to solve it. Instructor: Goddard.
Ch 122. Structure Determination by X-ray Crystallography. 9 units (3-0-6): first term. This course provides an introduction to small molecule X-ray crystallography. Topics include symmetry, space groups, diffraction by crystals, the direct and reciprocal lattice, Patterson and direct methods for phase determination, and structure refinement. It will cover both theoretical and applied concepts and include hands-on experience in data collection, structure solution and structure refinement. Instructor: Takase.
Ch 125 abc. The Elements of Quantum Chemistry. 9 units (3-0-6): first, second, third terms. A first course in molecular quantum mechanics consisting of a quantitative treatment of quantum mechanics with applications to systems of interest to chemists. The basic elements of quantum mechanics, the electronic structure of atoms and molecules, the interactions of radiation fields and matter, scattering theory, and reaction rate theory. Part c not offered 2017-18. Instructors: Okumura (a), Miller/Chan (b).
Ch 126. Molecular Spectra and Molecular Structure. 9 units (3-0-6): third term. Quantum mechanical foundations of the spectroscopy of molecules. Topics include quantum theory of angular momentum, rovibrational Hamiltonian for polyatomic molecules, molecular symmetry and permutation-inversion groups, electronic spectroscopy, interaction of radiation and matter. Not offered 2017-18.
Ge/Ch 127. Nuclear Chemistry. 9 units (3-0-6): first term. A survey course in the properties of nuclei, and in atomic phenomena associated with nuclear-particle detection. Topics include rates of production and decay of radioactive nuclei; interaction of radiation with matter; nuclear masses, shapes, spins, and moments; modes of radioactive decay; nuclear fission and energy generation. Given in alternate years; offered 2017-18. Instructor: Burnett.
Ge/Ch 128. Cosmochemistry. 9 units (3-0-6): first term. Examination of the chemistry of the interstellar medium, of protostellar nebulae, and of primitive solar-system objects with a view toward establishing the relationship of the chemical evolution of atoms in the interstellar radiation field to complex molecules and aggregates in the early solar system that may contribute to habitability. Emphasis will be placed on identifying the physical conditions in various objects, timescales for physical and chemical change, chemical processes leading to change, observational constraints, and various models that attempt to describe the chemical state and history of cosmological objects in general and the early solar system in particular. Given in alternate years; offered 2017-18. Instructor: Blake.
Bi/Ch 132. Biophysics of Macromolecules. 9 units (3-0-6): first term. Introduction to biophysical methods in molecular and cellular biology. Biomolecule structure and dynamics, single molecule microscopy, in situ sequencing, single cell genomics, proteomics, mass spectrometry, x-ray diffraction, electron microscopy and microfluidics. Not offered 2017-18. Instructor: Beauchamp.
Ch 135. Chemical Dynamics. 9 units (3-0-6): second term. Introduction to the kinetics and dynamics of chemical reactions. Topics include scattering cross sections, rate constants, intermolecular potentials, classical two-body elastic scattering, reactive scattering, nonadiabatic processes, statistical theories of unimolecular reactions, photochemistry, laser and molecular beam methods, theory of electron transfer, solvent effects, condensed phase dynamics, surface reactions, isotope effects. Not offered 2017-18.
Ch/ChE 140 ab. Principles and Applications of Semiconductor Photoelectrochemistry. 9 units (3-0-6): second, third terms. The properties and photoelectrochemistry of semiconductors and semiconductor/liquid junction solar cells will be discussed. Topics include optical and electronic properties of semiconductors; electronic properties of semiconductor junctions with metals, liquids, and other semiconductors, in the dark and under illumination, with emphasis on semiconductor/liquid junctions in aqueous and nonaqueous media. Problems currently facing semiconductor/liquid junctions and practical applications of these systems will be highlighted. Part b not offered 2017-18. Instructor: Lewerenz (a).
Ch 143. NMR Spectroscopy for Structural Identification. 9 units (3-0-6): third term. This course will address both one-dimensional and two-dimensional techniques in NMR spectroscopy which are essential to elucidating structures of organic and organometallic samples. Dynamic NMR phenomena, multinuclear, paramagnetic and NOE effects will also be covered. An extensive survey of multipulse NMR methods will also contribute to a clear understanding of two-dimensional experiments. (Examples for Varian NMR instrumentation will be included.) Not offered 2017-18.
Ch 144 ab. Advanced Organic Chemistry. 9 units (3-0-6): second term. An advanced survey of selected topics in modern organic chemistry. Topics vary from year to year and may include structural and theoretical organic chemistry; materials chemistry; macromolecular chemistry; mechanochemistry; molecular recognition/supramolecular chemistry; reaction mechanisms; reactive intermediates; pericyclic reactions; and photochemistry. Instructors: Dougherty (a), Robb (b).
Ch 145. Bioorganic Chemistry of Proteins. 9 units (3-0-6): first term. An advanced survey of current and classic topics in bioorganic chemistry/chemical biology. The content will vary from year to year and may include the structure, function, and synthesis of peptides and proteins; enzyme catalysis and inhibition; cellular metabolism; chemical genetics; genomics and proteomics; posttranslational modifications; chemical tools to study cellular dynamics; and enzyme evolution. Instructor: Ondrus.
Ch 146. Bioorganic Chemistry of Nucleic Acids. 9 units (3-0-6): . The course will examine the bioorganic chemistry of nucleic acids, including DNA and RNA structures, molecular recognition, and mechanistic analyses of covalent modification of nucleic acids. Topics include synthetic methods for the construction of DNA and RNA; separation techniques; recognition of duplex DNA by peptide analogs, proteins, and oligonucleotide-directed triple helical formation; RNA structure and RNA as catalysts (ribozymes). Not offered 2017-18.
Ch/ChE 147. Polymer Chemistry. 9 units (3-0-6): second term. An introduction to the chemistry of polymers, including synthetic methods, mechanisms and kinetics of macromolecule formation, and characterization techniques. Instructor: Grubbs.
ChE/Ch 148. Polymer Physics. 9 units (3-0-6): third term. An introduction to the physics that govern polymer structure and dynamics in liquid and solid states, and to the physical basis of characterization methods used in polymer science. The course emphasizes the scaling aspects of the various physical properties. Topics include conformation of a single polymer chain under different solvent conditions; dilute and semi-dilute solutions; thermodynamics of polymer blends and block copolymers; rubber elasticity; polymer gels; linear viscoelasticity of polymer solutions and melts; glass transition and crystallization. Not offered 2017-18. Instructor: Wang.
Ch 149. Tutorial in Organic Chemistry. 6 units (2-0-4): first term. Discussion of key principles in organic chemistry, with an emphasis on reaction mechanisms and problem-solving. This course is intended primarily for first-year graduate students with a strong foundation in organic chemistry. Meets during the first three weeks of the term. Graded pass/fail. Instructors: Fu, Stoltz.
Ch 153 ab. Advanced Inorganic Chemistry. 9 units (3-0-6): second, third terms. Ch 153 a: Topics in modern inorganic chemistry. Electronic structure, spectroscopy, and photochemistry with emphasis on examples from the modern research literature. Ch 153 b: Applications of physical methods toward the characterization of inorganic and bioinorganic species. A range of spectroscopic approaches will be covered. Part b Not offered 2017-18. Instructors: Gray, Winkler (a).
Ch 154 ab. Organometallic Chemistry. 9 units (3-0-6): second, third terms. A general discussion of the reaction mechanisms and the synthetic and catalytic uses of transition metal organometallic compounds. Second term: a survey of the elementary reactions and methods for investigating reaction mechanisms. Third term: contemporary topics in inorganic and organometallic synthesis, structure and bonding, and applications in catalysis. Part b not offered 2017-18. Instructor: Peters (a).
ChE/Ch 155. Chemistry of Catalysis. 9 units (3-0-6): third term. Discussion of homogeneous and heterogeneous catalytic reactions, with emphasis on the relationships between the two areas and their role in energy problems. Topics include catalysis by metals, metal oxides, zeolites, and soluble metal complexes; utilization of hydrocarbon resources; and catalytic applications in alternative energy approaches. Not offered 2017-18.
ChE/Ch 164. Introduction to Statistical Thermodynamics. 9 units (3-0-6): second term. An introduction to the fundamentals and simple applications of statistical thermodynamics. Foundation of statistical mechanics; partition functions for various ensembles and their connection to thermodynamics; fluctuations; noninteracting quantum and classical gases; heat capacity of solids; adsorption; phase transitions and order parameters; linear response theory; structure of classical fluids; computer simulation methods. Instructor: Wang.
ChE/Ch 165. Chemical Thermodynamics. 9 units (3-0-6): first term. An advanced course emphasizing the conceptual structure of modern thermodynamics and its applications. Review of the laws of thermodynamics; thermodynamic potentials and Legendre transform; equilibrium and stability conditions; metastability and phase separation kinetics; thermodynamics of single-component fluid and binary mixtures; models for solutions; phase and chemical equilibria; surface and interface thermodynamics; electrolytes and polymeric liquids. Instructor: Wang.
Ch 166. Nonequilibrium Statistical Mechanics. 9 units (3-0-6): third term. Transport processes in dilute gases; Boltzmann equation; Brownian motion; Langevin and Fokker-Planck equations; linear response theory; time-correlation functions and applications; nonequilibrium thermodynamics. Not offered 2017-18.
BMB/Bi/Ch 170. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3-0-6): first term. Detailed analysis of the structures of the four classes of biological molecules and the forces that shape them. Introduction to molecular biological and visualization techniques. Instructor: Clemons.
ESE/Ge/Ch 171. Atmospheric Chemistry I. 9 units (3-0-6): third term. A detailed course about chemical transformation in Earth's atmosphere. Kinetics, spectroscopy, and thermodynamics of gas-phase chemistry of the stratosphere and troposphere; sources, sinks, and lifetimes of trace atmospheric species; stratospheric ozone chemistry; oxidation mechanisms in the troposphere. Instructors: Seinfeld, Wennberg.
ESE/Ge/Ch 172. Atmospheric Chemistry II. 3 units (3-0-0): first term. A lecture and discussion course about active research in atmospheric chemistry. Potential topics include halogen chemistry of the stratosphere and troposphere; aerosol formation in remote environments; coupling of dynamics and photochemistry; development and use of modern remote-sensing and in situ instrumentation. Graded pass/fail. Not offered 2017-18.
BMB/Bi/Ch 173. Biophysical/Structural Methods. 9 units (3-0-6): second term. Basic principles of modern biophysical and structural methods used to interrogate macromolecules from the atomic to cellular levels, including light and electron microscopy, X-ray crystallography, NMR spectroscopy, single molecule techniques, circular dichroism, surface plasmon resonance, mass spectrometry, and molecular dynamics and systems biological simulations. Instructors: Clemons, Jensen, and other guest lecturer.
BMB/Bi/Ch 174. Molecular Machines in the Cell. 9 units (3-0-6): third term. Detailed analysis of specific macromolecular machines and systems that illustrate the principles and biophysical methods taught in BMB/Bi/Ch 170 and BMB/Bi/Ch 173. Instructors: Clemons, Hoelz, Shan and various guest lecturers (subject to change each year).
ESE/Ch 175. Physical Chemistry of Engineered Waters. 9 units (3-0-6): second term. This course will cover selected aspects of the chemistry of engineered water systems and related water treatment processes. Lectures cover basic principles of physical-organic and physical-inorganic chemistry relevant to the aquatic environment under realistic conditions. Specific topics include acid-base chemistry, metal-ligand chemistry, redox reactions, photochemical transformations, biochemical transformations, heterogeneous surface reactions, catalysis, and gas-transfer dynamics. The primary emphasis during the winter term course will be on the physical chemistry of engineered waters. Instructor: Hoffmann.
ESE/Ch 176. Physical Organic Chemistry of Natural Waters. 9 units (3-0-6): third term. This course will cover selected aspects of the chemistry of natural and engineered aquatic systems. Lectures cover basic principles of physical-organic and physical-inorganic chemistry relevant to the aquatic environment under realistic conditions. Specific topics that are covered include the principles of equilibrium chemistry in natural water, acid-base chemistry of inorganic and organic acids including aquated carbon dioxide, metal-ligand chemistry, ligand substitution kinetics, kinetics and mechanisms of organic and inorganic redox reactions, photochemical transformations of chemical compounds, biochemical transformations of chemical compounds in water and sediments, heterogeneous surface reactions and catalysis. Thermodynamic, transport, kinetics and reaction mechanisms are emphasized. The primary emphasis during the spring term course will be on the organic chemistry of natural waters emphasizing the fate and behavior of organic compounds and persistent organic pollutants in the global environment. Instructor: Hoffmann.
BMB/Ch 178. Macromolecular Function: Kinetics, Energetics, and Mechanisms. 9 units (3-0-6): first term. Discussion of the energetic principles and molecular mechanisms that underlie enzyme's catalytic proficiency and exquisite specificity. Principles of allosteric regulation, selectivity, enzyme evolution, and computational enzyme design. Practical kinetics sections discuss how to infer molecular mechanisms from rate/equilibrium measurements and their application to more complex biological systems, including steady-state and pre-steady-state kinetics, kinetic simulations, and kinetics at the single molecule resolution. Instructor: Shan.
Ch 180. Chemical Research. Units by arrangement: . Offered to M. S. candidates in chemistry. Graded pass/fail.
BMB/Ch 202 abc. Biochemistry Seminar Course. 1 unit: first, second, third terms. A course that includes a seminar on selected topics from outside faculty on recent advances in biochemistry. Students will participate in the seminar along with a formal discussion section with visiting faculty. Students will meet with the Biochemistry seminar speaker in the discussion section for an hour, and then attend the Biochemistry seminar at 4 p.m. BMB Seminars take place 1-2 times per month (usually on Thursdays).
Ch 212. Bioinorganic Chemistry. 9 units (3-0-6): third term. Current topics in bioinorganic chemistry will be discussed, including metal storage and regulation, metalloenzyme structure and reactions, biological electron transfer, metalloprotein design, and metal-nucleic acid interactions and reactions. Not offered 2017-18.
Ch 213 abc. Advanced Ligand Field Theory. 12 units (1-0-11): first, second, third terms. A tutorial course of problem solving in the more advanced aspects of ligand field theory. Recommended only for students interested in detailed theoretical work in the inorganic field. Instructor: Gray.
Ch 227 ab. Advanced Topics in Chemical Physics. 9 units (3-0-6): third term. The goal of this course is to utilize approaches derived from the chemico-physical to understand what are often considered complex biological problems. The course is a literature driven course with a strong emphasis on student participation. Not offered 2017-18.
Ch 228. Dynamics and Complexity in Physical and Life Sciences. 9 units (3-0-6): third term. This course is concerned with the structure-dynamics-function of complex systems, from materials to chemical and biological functions. We will address principles of elementary dynamics as they relate to the nature of the structures involved. An overview of modern techniques, such as those involving lasers, NMR, diffraction and imaging will be overviewed. Applications include areas in physics, chemistry and biology, covering phenomena of interest, from coherence and chaos to molecular recognition and self-assembly. Course requirement, which includes writing a "science paper" and presentation, will be outlined in the first meeting. Not offered 2017-18.
BMB/Ch 230. Macromolecular Structure Determination with Modern X-ray Crystallography Methods. 12 units (2-4-6): third term. Advanced course in macromolecular crystallography integrating lecture and laboratory treatment of diffraction theory, crystallization (proteins, nucleic acids and macromolecular complexes), crystal characterization, X-ray sources and optics, crystal freezing, X-ray diffraction data collection (in-house and synchrotron), data reduction, multiple isomorphous replacement, single- and multi-wavelength anomalous diffraction phasing techniques, molecular replacement, electron density interpretation, structure refinement, structure validation, coordinate deposition and structure presentation. In the laboratory component, one or more proteins will be crystallized and the structure(s) determined by several methods, in parallel with lectures on the theory and discussions of the techniques. Instructor: Hoelz.
Ch/Bi 231. Advanced Topics in Biochemistry. 6 units (2-0-4): third term. Transcriptional regulation in eukaryotes. Topics: the subunit structure of eukaryotic RNA polymerases and their role in transcriptional reactions; the composition of eukaryotic promoters, including regulatory units; general and specific transcription factors; developmental regulatory circuits and factors; structural motifs involved in DNA binding and transcriptional initiation and control. Not offered 2017-18.
Ch 242 ab. Chemical Synthesis. 9 units (3-0-6): first, second terms. An integrated approach to synthetic problem solving featuring an extensive review of modern synthetic reactions with concurrent development of strategies for synthesis design. Part a will focus on the application of modern methods of stereocontrol in the construction of stereochemically complex acyclic systems. Part b will focus on strategies and reactions for the synthesis of cyclic systems. Instructors: Stoltz (a), Virgil (b).
Ch 247. Organic Reaction Mechanisms. 9 units (3-0-6): second term. This course will discuss and uncover useful strategies and tactics for approaching complex reaction mechanisms prevalent in organic reactions. Topics include: cycloaddition chemistry, rearrangements, radical reactions, metal-catalyzed processes, photochemical reactions among others. Recommended only for students interested in advanced study in organic chemistry or related fields. Not offered 2017-18.
Ch 250. Advanced Topics in Chemistry. 3 units: third term. Content will vary from year to year; topics are chosen according to the interests of students and staff. Visiting faculty may present portions of this course. In Spring 2016 the class will be a seminar course in pharmaceutical chemistry with lectures by industrial researchers from both discovery (medicinal chemistry) and development (process chemistry) departments. Not offered 2017-18.
Ch 251. Advanced Topics in Chemical Biology. 9 units (3-0-6): second term. Content will vary from year to year; advanced topics in chemical biology are chosen according to the interests of students and staff. Visiting faculty may lead portions of this course. In Winter 2018, the seminar course will be interactive classroom learning covering both fundamental discoveries and applied technologies in nucleic acids and genome sciences. Instructors: Dervan, Ondrus.
Ch 280. Chemical Research. Hours and units by arrangement: . By arrangement with members of the faculty, properly qualified graduate students are directed in research in chemistry.