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2016-17 Catalog: Chemistry

Ch 1 ab

General Chemistry

6 units   |  9 units
Lectures and recitations dealing with the principles of chemistry. First term: Chemical bonding - electronic structure of atoms, periodic properties, ionic substances, covalent bonding, Lewis representations of molecules and ions, shapes of molecules, Lewis acids and bases, Bronsted acids and bases, hybridization and resonance, bonding in solids. Second term: Chemical dynamics - spectroscopy, chemical equilibria, oxidation and reduction, thermodynamics, kinetics, introduction to organic chemistry and the chemistry of life. Graded pass/fail.
Instructors: Lewis (a), Reisman, Miller (b)
Ch/APh 2

Introduction to Energy Sciences

9 units (4-0-5)   |  third term
Prerequisites: Ch 1 ab, Ph 1 ab, Ma 1 ab.
Energy production and transduction in biological, chemical, and nuclear reactions. Bioenergetics: energy sources and storage; components of biological energy flows: pumps, motors, and solar cells; circuitry of biological energy flows and biological energy transduction pathways. Chemistry of energy production and utilization: fossil fuel utilization and energy conversion pathways; artificial photosynthesis, solar cells, and solar energy conversion. Principles of nuclear energy production: nuclear energy decay processes, fission and fusion reactions, and reactor principles. Not offered on a pass/fail basis. Satisfies the menu requirement of the Caltech core curriculum. Not offered 2016-17.
Ch 3 a

Fundamental Techniques of Experimental Chemistry

6 units (1-3-2)   |  first, second, third terms
Introduces the basic principles and techniques of synthesis and analysis and develops the laboratory skills and precision that are fundamental to experimental chemistry. Freshmen who have gained advanced placement into Ch 41 or Ch 21, or who are enrolled in Ch 10, are encouraged to take Ch 3 a in the fall term. Freshmen who enter in academic years 2017, 2018, and 2019 must take Ch 3 a in their first nine terms of residence in order to be graded pass/fail. Freshmen entering in academic year 2020 and thereafter must take Ch 3 a in their first six terms of residence in order to be graded pass/fail.
Instructor: Mendez
Ch 3 x

Experimental Methods in Solar Energy Conversion

6 units (1-3-2)   |  first, second, third terms
Introduces concepts and laboratory methods in chemistry and materials science centered on the theme of solar energy conversion and storage. Students will perform experiments involving optical spectroscopy, electrochemistry, laser spectroscopy, nanoparticle synthesis, photochemistry, and photoelectrochemistry, culminating in the construction and testing of dye-sensitized solar cells. Pass/fail grading conditions are the same as for Ch 3a above.
Instructor: Mendez
Ch 4 ab

Synthesis and Analysis of Organic and Inorganic Compounds

9 units (1-6-2)
Prerequisites: Ch 1 (or the equivalent) and Ch 3 a or Ch 3 x. Ch 4 a is a prerequisite for Ch 4 b. Previous or concurrent enrollment in Ch 41 is strongly recommended.
Introduction to methods of synthesis, separation, purification, and characterization used routinely in chemical research laboratories. Ch 4 a focuses on the synthesis and analysis of organic molecules; Ch 4 b focuses on the synthesis and analysis of inorganic and organometallic molecules. Ch 4 a, second term; Ch 4 b, third term.
Instructor: Mendez
Ch 5 ab

Advanced Techniques of Synthesis and Analysis

Ch 5 a 12 units (1-9-2), second term   |  Ch 5 b 12 units (1-9-2), first term
Prerequisites: Ch 4 ab. Ch 102 strongly recommended for Ch 5 b.
Modern synthetic chemistry. Specific experiments may change from year to year. Experiments illustrating the multistep syntheses of natural products (Ch 5 a), coordination complexes, and organometallic complexes (Ch 5 b) will be included. Methodology will include advanced techniques of synthesis and instrumental characterization. Terms may be taken independently.
Instructors: Grubbs (a), Agapie (b)
Ch 6 ab

Physical and Biophysical Chemistry Laboratory

10 units (1-6-3)   |  second, third terms
Prerequisites: Ch 1, Ch 4 ab, and Ch 21 or Ch 24 or equivalents (may be taken concurrently).
Introduction to modern physical methods in chemistry and biology. Techniques include laser spectroscopy, microwave spectroscopy, electron spin resonance, nuclear magnetic resonance, mass spectrometry, FT-IR, fluorescence, scanning probe microscopies, and UHV surface methods. The two terms can be taken in any order.
Instructor: Weitekamp
Ch 7

Advanced Experimental Methods in Bioorganic Chemistry

9 units (1-6-2)   |  third term
Prerequisites: Ch 41 abc, and Bi/Ch 110, Ch 4 ab. Enrollment by instructor's permission. Preference will be given to students who have taken Ch 5 a or Bi 10.
This advanced laboratory course will provide experience in powerful contemporary methods used in chemical biology, including polypeptide synthesis and the selective labeling and imaging of glycoproteins in cells. Experiments will address amino acid protecting group strategies, biopolymer assembly and isolation, and product characterization. A strong emphasis will be placed on understanding the chemical basis underlying the successful utilization of these procedures. In addition, experiments to demonstrate the application of commercially available enzymes for useful synthetic organic transformations will be illustrated.
Instructor: Hsieh-Wilson
Ch 8

Experimental Procedures of Synthetic Chemistry

9 units (1-6-2)   |  first term
Prerequisites: Ch 1 ab and Ch 3 a or Ch 3 x. Previous or concurrent enrollment in Ch 41 is strongly recommended.
Introduction to the synthesis of organic and organometallic compounds, and to methods of separation, purification, and spectroscopic characterization used in chemical research.
Instructor: Mendez
Ch/ChE 9

Chemical Synthesis and Characterization for Chemical Engineering

9 units (1-6-2)   |  third term
Prerequisites: Ch 1 ab and Ch 3 a or Ch 3 x. Previous or concurrent enrollment in Ch 41 is strongly recommended.
Instruction in synthesis, separation, purification, and physical and spectroscopic characterization procedures of model organic and inorganic materials, with emphasis on chemical reactions such as polymerization, catalysis, and light absorption and emission. Enrollment priority given to chemical engineering majors.
Instructor: Mendez
Ch 10 abc

Frontiers in Chemistry

3 units (2-0-1) first, second terms   |  8 units (1-6-1) third term
Prerequisites: Ch 10 c prerequisites are Ch 10 ab, Ch 3 a or Ch 3 x, and either Ch 1 ab, Ch 41 ab, or Ch 21 ab, and instructor's permission.
Ch 10 ab is a weekly seminar by a member of the chemistry department on a topic of current research; the topic will be presented at an informal, introductory level. The other weekly session will acquaint students with the laboratory techniques and instrumentation used on the research topics. Ch 10 c is a research-oriented laboratory course, which will be supervised by a chemistry faculty member. Weekly class meetings will provide a forum for participants to discuss their research projects. Graded pass/fail.
Instructors: Dervan, Hoelz
Ch 14

Chemical Equilibrium and Analysis

9 units (2-3-4)   |  third term
This course will cover acid-base equilibria, complex ion formation, chelation, oxidation-reduction reactions, and partitioning equilibria. These topics will serve as the basis for introducing separation techniques such is gas and liquid chromatography and the hyphenated techniques associated with them (GC-MS, LC-MS, etc.) Laboratory activities will be integrated with the course topics.
Instructor: Dalleska
Ch 15

Chemical Equilibrium and Analysis Laboratory

10 units (0-6-4)   |  first term
Prerequisites: Ch 1 ab, Ch 3 a or Ch 3 x, or instructor's permission.
Laboratory experiments are used to illustrate modern instrumental techniques that are currently employed in industrial and academic research. Emphasis is on determinations of chemical composition, measurement of equilibrium constants, evaluation of rates of chemical reactions, and trace-metal analysis.
Instructor: Not offered 2016-17
Ch 21 abc

Physical Chemistry

9 units (3-0-6)   |  first, second, third terms
Prerequisites: Ch 1 ab, Ph 2 a or Ph 12 a, Ma 2; Ma 3 is recommended.
Atomic and molecular quantum mechanics, spectroscopy, thermodynamics, statistical mechanics, and chemical kinetics.
Instructors: Chan (a), Cai (b), Beauchamp (c)
Ch 24

Introduction to Biophysical Chemistry: Spectroscopy

9 units (3-0-6)   |  second term
Prerequisites: Ch 1 ab, Ph 2 a or Ph 12 a, Ma 2 and Ch 21 a.
Develops the basic principles of the interaction of light with matter, including spectroscopic and scattering methods of macromolecular structure determination, with emphasis on biochemical and biophysical applications.
Instructor: Heath
Ch 25

Introduction to Biophysical Chemistry: Thermodynamics

9 units (3-0-6)   |  third term
Prerequisites: Ch 1 ab, Ph 2 a or Ph 12 a, Ma 2; Ch 21 a and Ch 24 recommended.
Develops the basic principles of solution thermodynamics, transport processes, and reaction kinetics, with emphasis on biochemical and biophysical applications.
Instructor: Rees
Ch 41 abc

Organic Chemistry

9 units (3-0-6)   |  first, second, third terms
Prerequisites: Ch 1 ab or instructor's permission.
The synthesis, structure, and mechanisms of reactions of organic compounds.
Instructors: Grubbs (a), Hsieh-Wilson (b), Fu (c
Ch 80

Chemical Research

Offered to B   |  S
Prerequisites: consent of research supervisor.
Experimental and theoretical research requiring a report containing an appropriate description of the research work.
Ch 81

Independent Reading in Chemistry

Units by arrangement
Prerequisites: instructor's permission.
Occasional advanced work involving reading assignments and a report on special topics. No more than 12 units in Ch 81 may be used as electives in the chemistry option.
Ch 82/182

Senior Thesis Research

9 units   |  first, second, third terms
Prerequisites: instructor's permission.
Three terms of Ch 82/182 are to be completed during the junior and/or senior year of study. Ch 182 is taken only by students pursuing a joint B.S./M.S. degree in Chemistry. At the end of the third term, students enrolled in Ch 82 will present a thesis of approximately 20 pages (excluding figures and references) to the mentor and the Chemistry Curriculum and Undergraduate Studies Committee. The thesis must be approved by both the research mentor and the CUSC. Students enrolled in Ch 182 will present a Masters Thesis, as described in requirements for the Masters degree. An oral thesis defense will be arranged by the CUSC in the third term for all enrollees. The first two terms of Ch 82/182 will be taken on a pass/fail basis, and the third term will carry a letter grade.
Instructor: Staff
Ch 90

Oral Presentation

3 units (2-0-1)   |  second term
Training in the techniques of oral presentation of chemical and biochemical topics. Practice in the effective organization and delivery of technical reports before groups. Strong oral presentation is an essential skill for successful job interviews and career advancement. Graded pass/fail.
Instructor: Bikle
Ch/ChE 91

Scientific Writing

3 units (2-0-1)   |  first, second terms
Training in the writing of scientific research papers for chemists and chemical engineers. Fulfills the Institute scientific writing requirement.
Instructor: Parker
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
Prerequisites: Ch 41 ab.
Structure and bonding of inorganic species with special emphasis on spectroscopy, ligand substitution processes, oxidation-reduction reactions, organometallic and biological inorganic chemistry
Instructor: Agapie
ChE/Ch/E/Bi 107

Social Media for Scientists

9 units (3-0-6)   |  first, third terms
An introduction to the use of social media for scientific communication. Social media platforms are discussed in the context of their use to professionally engage scientific communities and general audiences. Topics will include ethics, privacy, reputation management, ownership and the law, and will focus on the use and impact of social media for personal and professional career development. Lectures will include presentations by invited experts in various specialties, a number of which will have worldwide recognition.
Instructor: Davis
Bi/Ch 110

Introduction to Biochemistry

12 units (4-0-8)   |  first term
Prerequisites: Ch 41 abc or instructor's permission.
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
Prerequisites: Bi/Ch 110; Bi 8 and Bi 122 recommended.
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
Prerequisites: Ch 102 or instructor's permission.
Introduction to group theory, ligand field theory, and bonding in coordination complexes and organotransition metal compounds. Systematics of synthesis, bonding, and reactivities of commonly encountered classes of transition metal compounds.
Instructor: Agapie
Bi/Ch 113

Biochemistry of the Cell

12 units (4-0-8)   |  third term
Prerequisites: Bi/Ch 110; Bi 9 recommended or consent of instructor.
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.
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: Lewis
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
Prerequisites: general exposure to quantum mechanics (e.g., Ch 21 a).
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
Prerequisites: Ch 21 a or Ch 125 a.
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
Prerequisites: Ch 21 abc or instructor's permission.
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
Prerequisites: Ch 21 abc or an equivalent brief introduction to quantum mechanics.
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.
Instructors: Okumura (a), part b and c not offered 2016-17
Ch 126

Molecular Spectra and Molecular Structure

9 units (3-0-6)   |  third term
Prerequisites: Ch 21 and Ch 125 a/Ph 125 a or instructor's permission.
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.
Instructor: Blake
Ge/Ch 127

Nuclear Chemistry

9 units (3-0-6)   |  first term
Prerequisites: instructor's permission.
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; not offered 2016-17.
Instructor: Burnett
Ge/Ch 128

Cosmochemistry

9 units (3-0-6)   |  third term
Prerequisites: instructor's permission.
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; not offered 2016-17.
Bi/Ch 132

Biophysics of Macromolecules

9 units (3-0-6); first term   |  Recommended prerequisite: Bi/Ch 110
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.
Instructors: Beauchamp, Cai
Ch 135

Chemical Dynamics

9 units (3-0-6)   |  second term
Prerequisites: Ch 21 abc and Ch 41 abc, or equivalent, or instructor's permission.
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.
Instructors: Okumura, Marcus
Ch/ChE 140 ab

Principles and Applications of Semiconductor Photoelectrochemistry

9 units (3-0-6)   |  second, third terms
Prerequisites: APh/EE 9 ab or instructor's permission.
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.
Instructors: Lewerenz (a), part b not offered 2016-17
Ch 143

NMR Spectroscopy for Structural Identification

9 units (3-0-6)   |  third term
Prerequisites: Ch 41 abc.
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.)
Instructor: Virgil
Ch 144 ab

Advanced Organic Chemistry

9 units (3-0-6)   |  second term
Prerequisites: Ch 41 abc; Ch 21 abc recommended.
An advanced survey of selected topics in modern physical organic chemistry. Topics vary from year to year and may include structural and theoretical organic chemistry; molecular recognition/supramolecular chemistry; reaction mechanisms and the tools to study them; reactive intermediates; materials chemistry; pericyclic reactions; and photochemistry. Part b not offered 2016-17.
Instructor: Dougherty (a)
Ch 145

Bioorganic Chemistry of Proteins

9 units (3-0-6)   |  first term
Prerequisites: Ch 41 abc; Bi/Ch 110 recommended.
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; carbohydrates and glycobiology; chemical genetics; genomics and proteomics; posttranslational modifications; chemical tools to study cellular dynamics; and enzyme evolution. Not offered 2016-17.
Ch 146

Bioorganic Chemistry of Nucleic Acids

9 units (3-0-6)
Prerequisites: Ch 41 ab.
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 2016-17.
Ch/ChE 147

Polymer Chemistry

9 units (3-0-6), second term
Prerequisites: Ch 41 abc.
An introduction to the chemistry of polymers, including synthetic methods, mechanisms and kinetics of macromolecule formation, and characterization techniques. Course will be offered second term. Not offered 2016-17.
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.
Instructor: Wang
Ch 149

Tutorial in Organic Chemistry

6 units (2-0-4)   |  first term
Prerequisites: Ch 41 abc and instructor's permission.
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
Prerequisites: Ch 112 and Ch 21 abc or concurrent registration.
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.
Instructors: Gray, Winkler (a), Peters (b)
Ch 154 ab

Organometallic Chemistry

9 units (3-0-6)   |  second, third terms
Prerequisites: Ch 112 or equivalent.
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 2016-17.
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 2016-17.
ChE/Ch 164

Introduction to Statistical Thermodynamics

9 units (3-0-6)   |  second term
Prerequisites: Ch 21 abc or instructor's permission.
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.
Instructors: Wang, Miller
ChE/Ch 165

Chemical Thermodynamics

9 units (3-0-6)   |  first term
Prerequisites: ChE 63 ab or instructor's permission.
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
Prerequisites: Ch 21 abc or equivalent.
Transport processes in dilute gases; Boltzmann equation; Brownian motion; Langevin and Fokker-Planck equations; linear response theory; time-correlation functions and applications; nonequilibrium thermodynamics.
Instructor: Marcus
BMB/Bi/Ch 170

Biochemistry and Biophysics of Macromolecules and Molecular Assemblies

9 units (3- 0-6)   |  first term
Prerequisites: Bi/Ch 110. 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
Prerequisites: Ch 1 or equivalent.
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, Sanders
ESE/Ge/Ch 172

Atmospheric Chemistry II

3 units (3-0-0)   |  first term
Prerequisites: ESE/Ge/Ch 171 or equivalent.
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 2016-17.
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 lecturers
BMB/Bi/Ch 174

Molecular Machines in the Cell

9 units (3-0-6)   |  third term
Prerequisites: Bi/Ch 110, BMB/Bi/Ch 170, BMB/Bi/Ch 173.
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 Inorganic Chemistry of Natural Waters

9 units (3-0-6)   |  second term
Prerequisites: Ch 1 or instructor's permission.
This course will cover selected aspects of the chemistry of natural and engineered aquatic systems. Lectures cover basic principles of physical-organic and physical-inorganicchemistry 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 winter term course will be on the inorganic chemistry of natural 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
Prerequisites: Bi/Ch 110 or equivalent.
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. Students 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
Prerequisites: Ch 112 and Bi/Ch 110 or equivalent.
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 2016-17.
Ch 213 abc

Advanced Ligand Field Theory

12 units (1-0-11)   |  first, second, third terms
Prerequisites: Ch 21 abc or concurrent registration.
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
Prerequisites: Ch 125 abc or Ph 125 abc or equivalent.
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. Part b not offered 2015-16.
Instructors: Heath (a), part b not offered 2016-17
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 2016-2017.
BMB/Ch 230

Macromolecular Structure Determination with Modern X-ray Crystallography Methods

12 units (2-4-6)   |  third term
Prerequisites: BMB/Bi/Ch 170 and consent of instructor.
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 2016-17.
Ch 242 ab

Chemical Synthesis

9 units (3-0-6)   |  first, second terms
Prerequisites: Ch 41 abc.
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), Reisman (b)
Ch 247

Organic Reaction Mechanisms

9 units (3-0-6)   |  second term
Prerequisites: Ch 41 abc, Ch 242 a recommended.
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 2016-17.
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 2016-17.
Ch 251

Advanced Topics in Chemical Biology

9 units (3-0-6)   |  second term
Prerequisites: Ch 145 or 146 or consent of the instructor.
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 2017, 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.
Published Date: July 28, 2022