CHCHE Courses (2019-20)

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General Chemistry

Ch 1 a 6 units (3-0-3) first term; Ch 1 b 9 units (4-0-5) second term  | 
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, thermodynamics, kinetics, chemical equilibria, electrochemistry, and introduction to organic chemistry. Graded pass/fail.
Instructors: Lewis (a), Robb, Miller (b)

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

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, photochemistry, and photoelectrochemistry, culminating in the construction and testing of dyesensitized solar cells. Freshmen who enter in academic years 2017, 2018, and 2019 must take Ch 3x 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 3x in their first six terms of residence in order to be graded pass/fail.
Instructor: Mendez

Synthesis and Analysis of Organic and Inorganic Compounds

9 units (1-6-2)  | 
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

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  | 
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. Part b not offered 2019-20.
Instructors: Grubbs (a), Agapie (b)

Physical and Biophysical Chemistry Laboratory

9 units (1-5-3)  |  second, third terms
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. Part b not offered 2019-20.
Instructor: Okumura

Advanced Experimental Methods in Bioorganic Chemistry

9 units (1-6-2)  |  third term
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

Experimental Procedures of Synthetic Chemistry for Premedical Students

9 units (1-6-2)  |  first term
Open to non-pre-medical students, as space allows. Introduction to methods of extraction, synthesis, separation and purification, and spectroscopic characterization of Aspirin, Tylenol, and medical test strips.
Instructor: Mendez

Chemical Synthesis and Characterization for Chemical Engineering

9 units (1-6-2)  |  third term
Instruction in synthesis, separation, purification, and physical and spectroscopic characterization procedures of model organic and organometallic compounds. Specific emphasis will be focused on following the scientific method in the study of model organic and inorganic materials. Enrollment priority given to chemical engineering majors.
Instructor: Mendez

Frontiers in Chemistry

1 unit (1-0-0) first, second terms; 6 units (1-4-1) third term  | 
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. 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

Introduction to Chemical Engineering

1 unit (1-0-0)  |  second term
A series of weekly seminars given by chemical engineering faculty or an outside speaker, on a topic of current research. Topics will be presented at an informal, introductory level. Graded pass/fail.

Chemical Equilibrium and Analysis

9 units (3-0-6)  |  second 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 as 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: Rees

Chemical Equilibrium and Analysis Laboratory

10 units (0-6-4)  |  third term
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: Dalleska

Introduction to Chemical Engineering Computation

9 units (1-4-4)  |  first term
Introduction to the solution of engineering problems through the use of the computer. Elementary programming in Python is taught, and applied to solving chemical engineering problems in data analysis, process simulation, and optimization. No previous knowledge of computer programming is assumed.
Instructor: Flagan

Physical Chemistry

9 units (3-0-6)  |  first, second, third terms
Atomic and molecular quantum mechanics, spectroscopy, chemical dynamics, statistical mechanics, and thermodynamics.
Instructors: Chan (a), Wei (b), Beauchamp (c)

Introduction to Biophysical Chemistry: Thermodynamics

9 units (3-0-6)  |  third term
Develops the basic principles of solution thermodynamics, transport processes, and reaction kinetics, with emphasis on biochemical and biophysical applications. Not offered 2019-20

Organic Chemistry

9 units (4-0-5)  |  first, second, third terms
The synthesis, structure, and mechanisms of reactions of organic compounds.
Instructors: Grubbs (a), Hsieh-Wilson (b), Reisman (c)

Separation Processes

9 units (3-0-6)  |  second term
Equilibrium staged separations. Membrane separations. Absorption. Distillation. Liquid-liquid extraction. Introduction to mass transfer.
Instructor: Seinfeld

Chemical Engineering Thermodynamics

9 units (3-0-6)  |  second, third terms
A comprehensive treatment of classical thermodynamics with engineering and chemical applications. First and second laws. Applications to closed and open systems. Equations of state. Thermochemical calculations. Properties of real fluids. Power generation and refrigeration cycles. Multicomponent systems, excess properties, fugacities, activity coefficients, and models of nonideal solutions. Chemical potential. Phase and chemical reaction equilibria.
Instructors: Gavalas, Ismagilov

Special Topics in Chemical Engineering

Units by arrangement  |  terms to be arranged
Special problems or courses arranged to meet the emerging needs of undergraduate students. May be repeated for credit, as content may vary. Grading scheme at instructor's discretion.
Instructor: to be determined

Chemical Research

Units in accordance with work accomplished.  | 
Offered to B. S. candidates in chemistry. Units in accordance with work accomplished. Prerequisite: consent of research supervisor. Experimental and theoretical research requiring a report containing an appropriate description of the research work.

Undergraduate Research

Units by arrangement, instructor's permission required  | 
Research in chemical engineering offered as an elective in any term. Graded pass/fail.
Instructor: Staff

Independent Reading in Chemistry

Units by arrangement  | 
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.

Senior Thesis Research

9 units  |  first, second, third terms
Three terms of Ch 82 are to be completed during the junior and/or senior year of study. 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. An oral thesis defense will be arranged by the CUSC in the third term for all enrollees. The first two terms of Ch 82 will be taken on a pass/fail basis, and the third term will carry a letter grade.
Instructors: Okumura, staff

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. Class size limited to 12 students.
Instructor: Bikle

Senior Thesis

9 units (0-4-5)  |  first, second, third terms
A research project carried out under the direction of a chemical engineering faculty member. The project must contain a significant design component. Students must submit a proposal outlining the proposed project, and clearly identifying its design component to the faculty mentor for the thesis and the chemical engineering option representative, by the beginning of the first term of the thesis for review and approval. In addition, students must submit a midterm progress report in each term, end-of-term progress reports at the end of the first two terms, and a thesis draft in the third term. A grade will not be assigned prior to completion of the thesis, which normally takes three terms. A P grade will be given for the first two terms and then changed to the appropriate letter grade at the end of the course.

Scientific Writing

3 units (2-0-1)  |  first, second, third terms
Training in the writing of scientific research papers for chemists and chemical engineers. Fulfills the Institute scientific writing requirement.
Instructors: Parker, Weitekamp

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.
Instructor: Staff

Chemical Reaction Engineering

9 units (3-0-6)  |  second term
Elements of chemical kinetics and chemically reacting systems. Homogeneous and heterogeneous catalysis. Chemical reactor analysis.
Instructor: Davis

Introduction to Inorganic Chemistry

9 units (4-0-5)  |  third term
Structure and bonding of inorganic species with special emphasis on spectroscopy, ligand substitution processes, oxidation-reduction reactions, organometallic, biological inorganic chemistry, and solid-state chemistry.
Instructors: Hadt, See

Transport Phenomena

9 units (3-0-6)  |  first, second, third terms
A rigorous development of the basic differential equations of conservation of momentum, energy, and mass in fluid systems. Solution of problems involving fluid flow, heat transfer, and mass transfer.
Instructors: Kornfield, Shapiro, Flagan

Intermediate Organic Chemistry

9 units (4-0-5)  |  second term
A survey of selected topics beyond introductory organic chemistry, including reaction mechanisms and catalysis.
Instructor: Fu

Dynamics and Control of Chemical Systems

9 units (3-0-6)  |  third term
Analysis of linear dynamic systems. Feedback control. Stability of closed-loop control systems. Root locus, Frequency response, and Nyquist analysis. Feedforward, cascade, and multivariable control systems.
Instructor: Seinfeld

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, and the intermediary metabolism that provides energy to an organism.
Instructor: Clemons

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

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.
Instructors: Agapie, Hadt

Design, Invention, and Fundamentals of Microfluidic Systems

9 units (3-0-6)  |  second term
This course combines three parts. First, it will cover fundamental aspects of kinetics, mass-transport, and fluid physics that are relevant to microfluidic systems. Second, it will provide an understanding of how new technologies are invented and reduced to practice. Finally, students in the course will work together to design microfluidic systems that address challenges in Global Health, with an emphasis on students' inventive contributions and creativity. Students will be encouraged and helped, but not required, to develop their inventions further by working with OTT and entrepreneurial resources on campus. Participants in this course benefit from enrollment of students with diverse backgrounds and interests. For chemical engineers, suggested but not required courses are ChE 101 (Chemical Reaction Engineering) and ChE 103 abc (Transport Phenomena). Students are encouraged to contact the instructor to discuss enrollment.
Instructor: Ismagilov

Solid State NMR Spectroscopy For Materials Chemistry

9 units (3-3-3)  |  second term
Principles and applications of solid state NMR spectroscopy will be addressed with focus on structure and dynamics characterization of organic and inorganic solids. NMR characterization methods in the areas of heterogeneous catalysts, batteries, energy storage materials, etc. will be reviewed. More specific topics include NMR methods in solid state such as magic angle spinning (MAS), cross-polarization (CP), NMR of quadrupole nuclei, multiple pulse and multi-dimensional solid state NMR experiments, dynamics NMR. Hands-on experience will be provided via separate laboratory sessions using solid NMR spectrometers at Caltech Solid State NMR facility.
Instructor: Hwang

Electronic Materials Processing

9 units (3-0-6)  |  third term
Introduction into the gas-phase processing techniques used in the fabrication of electronic materials and devices. Kinetic theory of gases. Surface chemistry and gas-surface interaction dynamics. Film deposition techniques: physical and chemical vapor deposition, atomic layer epitaxy, liquid-phase epitaxy, molecular beam epitaxy. Introduction into plasmas and their role in patterned etching and layer deposition. Charging damage during plasma processing. Determination of key parameters that control the ion energy and flux to the wafer surface. Not offered 2019–20.

Introduction to Electrochemistry

9 units (3-0-6)  |  first term
Discussion of the fundamentals and applications of electrochemistry with an emphasis on the structure of electrode-electrolyte interfaces, the mechanism by which charge is transferred across it, experimental techniques used to study electrode reactions, and application of electrochemical techniques to study materials chemistry. Topics may vary but usually include diffusion, cyclic voltammetry, coulometry, irreversible electrode reactions, the electrical double layer, and kinetics of electrode processes.
Instructor: See

Introduction to the Design of Chemical Systems

9 units (3-0-6)  |  second term
Short-term, open-ended projects that require students to design a chemical process or product. Each team generates and filters ideas, identifies use cases and objectives, evaluates and selects a design strategy, develops a project budget, schedules milestones and tasks, and writes a proposal with supporting documentation. Each project must meet specified requirements for societal impact, budget, duration, person hours, environmental impact, safety, and ethics.
Instructor: Vicic

Nature of the Chemical Bond

Ch 120 a: 9 units (3-0-6), third term; Ch 120 b: (1-1-7), first 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

Optimal Design of Chemical Systems

9 units (1-6-2)  |  third term
Short-term, open-ended projects that require students to design and build a chemical process or manufacture a chemical product. Each team selects a project after reviewing a collection of proposals. Students use chemical engineering principles to design, build, test, and optimize a system, component, or product that fulfills specified performance requirements, subject to constraints imposed by budget, schedule, logistics, environmental impact, safety, and ethics.
Instructor: Vicic

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  | 
Application of Atomistic-based methods [Quantum Mechanics (QM) and Molecular Dynamics (MD)] for predicting the structures and properties of molecules and solids and simulating the dynamical properties. This course emphasizes hands-on use of modern commercial software (such as Jaguar for QM, VASP for periodic QM, and LAMMPS for MD) for practical applications and is aimed at experimentalists and theorists interested in understanding structures, properties, and dynamics in such areas as biological systems (proteins, DNA, carbohydrates, lipids); polymers (crystals, amorphous systems, co-polymers); semiconductors (group IV, III-V, surfaces, defects); inorganic systems (ceramics, zeolites, superconductors, and metals); organo-metallics, and catalysis (heterogeneous, homogeneous, and electrocatalysis). Ch121a covers the basic methods with hands-on applications to systems of interest using modern software. The homework for the first 5 weeks emphasizes computer based solutions. For the second 5 weeks of the homework each student proposes a short research project and uses atomistic simulations to solve it. Ch121b each student selects a more extensive research project and uses atomistic simulations to solve it.
Instructor: Goddard

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

The Elements of Quantum Chemistry

9 units (3-0-6)  |  first, second, third terms
A treatment of quantum mechanics with application to molecular and material systems. The basic elements of quantum mechanics, the electronic structure of atoms and molecules, the interactions of radiation fields and matter, and time dependent techniques relevant to spectroscopy will be covered. The course sequence prepares students for Ch 225 and 226. Part (c) not offered 2019-20.
Instructors: Cushing (a), Weitekamp (b)

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, density matricies, linear and nonlinear interactions of radiation and matter. Not offered 2019-20.
Instructor: Blake

Chemical Engineering Laboratory

9 units (1-6-2)  |  first term
Short-term projects that require students to work in teams to design systems or system components. Projects typically include unit operations and instruments for chemical detection. Each team must identify specific project requirements, including performance specifications, costs, and failure modes. Students use chemical engineering principles to design, implement, and optimize a system (or component) that fulfills these requirements, while addressing issues and constraints related to environmental impact, safety, and ethics. Students also learn professional ethics through the analysis of case studies.
Instructor: Vicic

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 2019-20.
Instructor: Burnett

Chemical Engineering Design Laboratory

9 units (1-6-2)  |  second term
Short-term, open-ended research projects targeting chemical processes in microreactors. Projects include synthesis of chemical products or nanomaterials, detection and destruction of environmental pollutants, and other gas phase conversions. Each student is required to construct and troubleshoot his/her own microreactor, then experimentally evaluate and optimize independently the research project using chemical engineering principles. Where possible, cost analysis of the optimized process is performed.
Instructors: Giapis, Vicic


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 2019-20.
Instructor: Blake

Introduction to Biophotonics

9 units (3-0-6)  |  first term
This course will cover basic optics and introduce modern optical spectroscopy principles and microscopy techniques. Topics include molecular spectroscopy; linear and nonlinear florescence microscopy; Raman spectroscopy; coherent microscopy; single-molecule spectroscopy; and super-resolution imaging. Not offered 2019-20.
Instructor: Wei

Biomolecular Engineering Laboratory

9 units (1-5-3)  |  third term
Design, construction, and characterization of engineered biological systems. Students will propose and execute research projects in biomolecular engineering and synthetic biology. Emphasis will be on projects that apply rational or library-based design strategies to the control of system behavior.
Instructors: Davis, Vicic

Chemical Dynamics

9 units (3-0-6)  |  third 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 2019-20.
Instructor: Okumura

Principles and Applications of Semiconductor Photoelectrochemistry

9 units (3-0-6)  |  second term
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 a Not offered 2019-20
Instructor: Lewis (b)

Data Science for Chemical Systems

9 units (1-2-6)  |  second term
Through short lectures, in-class activities, and problem sets, students learn and use methods in data science to complete projects focused on (i) descriptive and predictive analyses of chemical processes and (ii) Quantitative Structure Property Relationships (QSPR). Topics covered may include six sigma; SPC & SQC; time-series analysis; data preprocessing; dimensionality reduction; supervised, reinforcement, and unsupervised learning; decision tree & clustering methods; univariate and multivariate regression; and visualization. Python is the programming language of instruction.
Instructor: Vicic

Challenges in Data Science for Chemical Systems

9 units (1-0-8)  |  third term
Student groups complete a one-term, data-science project that addresses an instructor-approved chemical engineering challenge. The project may be an original research idea; related to work by a research group at the Institute; an entry in a relevant national/regional contest; a response to an industry relationship; or other meaningful opportunity. There is no lecture, but students participate in weekly progress updates. A student may not select a project too similar to research completed to fulfill requirements for ChE 80 or ChE 90abc.
Instructor: Vicic

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 2019-20.

Advanced Organic Chemistry

9 units (3-0-6)  |  first 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. Not offered 2019-20.

Chemical Biology of Proteins

9 units (3-0-6)  |  first term
An advanced survey of current and classic topics in chemical biology. Content draws largely from current literature and varies from year-to-year. Topics may include the structure, function, and synthesis of peptides and proteins; enzyme catalysis and inhibition; cellular metabolism; chemical genetics; proteomics; posttranslational modifications; chemical tools to study cellular dynamics; and enzyme evolution.
Instructor: Ondrus

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 2019-20.

Polymer Chemistry

9 units (3-0-6)  |  first term
An introduction to the chemistry of polymers, including synthetic methods, mechanisms and kinetics of macromolecule formation, and characterization techniques.
Instructor: Robb

Polymer Physics

9 units (3-0-6)  |  third term
An introduction to the physics that govern the structure and dynamics of polymeric liquids, 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, a chain under different solvent conditions; dilute and semi-dilute solutions; thermodynamics of polymer blends and block copolymers; polyelectrolytes; rubber elasticity; polymer gels; linear viscoelasticity of polymer solutions and melts. Not offered 2019-20.
Instructor: Wang

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, Ondrus

Physical and Chemical Rate Processes

12 units (3-0-9)  |  second, third terms
The foundations of heat, mass, and momentum transfer for single and multiphase fluids will be developed. Governing differential equations; laminar flow of incompressible fluids at low and high Reynolds numbers; forced and free convective heat and mass transfer, diffusion, and dispersion. Emphasis will be placed on physical understanding, scaling, and formulation and solution of boundary-value problems. Applied mathematical techniques will be developed and used throughout the course.
Instructor: Brady

Heterogeneous Kinetics and Reaction Engineering

9 units (3-0-6)  |  first term
Survey of heterogeneous reactions on metal and oxide catalysts. Langmuir-Hinshelwood versus Eley-Rideal reaction mechanisms. Reaction, diffusion, and heat transfer in heterogeneous catalytic systems. Characterization of porous catalysts.
Instructor: Giapis

Advanced Inorganic Chemistry

9 units (3-0-6)   |  second (Ch 153 a), third (Ch 153 c offered in 2019-20, alternating with Ch 153 b in subsequent years) 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 to the characterization of inorganic and bioinorganic species, with an emphasis on the practical application of Moessbauer, EPR, and pulse EPR spectroscopies. Ch 153 c: Theoretical and spectroscopic approaches to understanding the electronic structure of transition metal ions. Topics in the 153bc alternate sequence may include saturation magnetization and zero-field splitting in magnetic circular dichroism and molecular magnetism, hyperfine interactions in electron paramagnetic resonance spectroscopy, Moessbauer and magnetic Moessbauer spectroscopy, vibronic interactions in electronic absorption and resonance Raman spectroscopy, and bonding analyses using x-ray absorption and/or emission spectroscopies.
Instructors: Gray, Winkler (a), Hadt/Peters (c)

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 2019-20.
Instructors: Peters, Agapie (a)

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 2019-20.

Aerosol Physics and Chemistry

9 units (3-0-6)  |  second term
Fundamentals of aerosol physics and chemistry; aerodynamics and diffusion of aerosol particles; condensation and evaporation; thermodynamics of particulate systems; nucleation; coagulation; particle size distributions; optics of small particles. Not offered 2019-20.
Instructors: Seinfeld, Flagan

Introduction to Biomolecular Engineering

12 units (3-0-9)  |  first term
The course introduces rational design and evolutionary methods for engineering functional protein and nucleic acid systems. Rational design topics include molecular modeling, positive and negative design paradigms, simulation and optimization of equilibrium and kinetic properties, design of catalysts, sensors, motors, and circuits. Evolutionary design topics include evolutionary mechanisms and tradeoffs, fitness landscapes, directed evolution of proteins, and metabolic pathways. Some assignments require programming (Python is the language of instruction).
Instructors: Arnold, Pierce

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

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

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. Not offered in 2019-20.

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. Offered 2019-20.
Instructors: Seinfeld, Wennberg

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 2019-20.
Instructors: Seinfeld, Wennberg

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 lectures

Advanced Topics in Biochemistry and Biophysics

6 units (3-0-3)  |  first term
Discussion of research fields in biochemistry and molecular biophysics at Caltech.
Instructors: Clemons, Hoelz, Shan and various guest lecturers

Special Topics in Transport Phenomena

9 units (3-0-6)  |  first term
May be repeated for credit. Advanced problems in heat, mass, and momentum transfer. Introduction to mechanics of complex fluids; physicochemical hydrodynamics; microstructured fluids; colloidal dispersions and active matter. Other topics may be discussed depending on class needs and interests.
Instructor: Brady

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

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

Macromolecular Function: Kinetics, Energetics, and Mechanisms

9 units (3-0-6)  |  second term
Discussion of the energetic principles and molecular mechanisms that underlie enzyme's catalytic proficiency and exquisite specificity. Principles of allosteric regulation, selectivity, and enzyme evolution. 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-steadystate kinetics, kinetic simulations, and kinetics at the single molecule resolution.
Instructor: Shan

Chemical Research

Units by arrangement  | 
Offered to M.S. candidates in chemistry. Graded pass/fail.

Molecular Imaging

9 units (3-0-6)  |  second term
This course will cover the basic principles of biological and medical imaging technologies including magnetic resonance, ultrasound, nuclear imaging, fluorescence, bioluminescence and photoacoustics, and the design of chemical and biological probes to obtain molecular information about living systems using these modalities. Topics will include nuclear spin behavior, sound wave propagation, radioactive decay, photon absorption and scattering, spatial encoding, image reconstruction, statistical analysis, and molecular contrast mechanisms. The design of molecular imaging agents for biomarker detection, cell tracking, and dynamic imaging of cellular signals will be analyzed in terms of detection limits, kinetics, and biological effects. Participants in the course will develop proposals for new molecular imaging agents for applications such as functional brain imaging, cancer diagnosis, and cell therapy. Not offered 2019-20.
Instructor: Shapiro

Special Problems in Chemical Engineering

Up to 9 units by arrangement  |  any term
Special courses of readings or laboratory instruction. The student should consult a member of the faculty and prepare a definite program of reading, computation, theory and/or experiment. The student must submit a summary of progress at midterm and, at the end of the quarter, a final assignment designed in consultation with the instructor. This course may be credited only once. Grading: either grades or pass/fail, as arranged with the instructor.
Instructor: Staff

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).

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 2019-20.

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

Advanced Quantum Chemistry

9 units (3-0-6)  |  second term
The electronic structure of atoms and molecules, the interactions of radiation fields and matter, scattering theory, and reaction rate theory
Instructor: Chan/Miller

Optical and Nonlinear Spectroscopy

9 units (3-0-6)  |  third term
Quantum mechanical foundations of optical spectroscopy as applied to chemical and material systems. Topics include optical properties of materials, nonlinear and quantum optics, and multidimensional spectroscopy.
Instructors: Blake, Cushing

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

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), Reisman, Virgil (b)

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 2019-20.

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.
Instructors: Stoltz, Reeves

Advanced Topics in Chemical Biology

9 units (3-0-6)  |  second term
Advanced Topics in Chemical Biology. Hours and units to be arranged. Content will vary from year to year; topics are chosen according to the interests of students and staff. Not offered 2019-20.

Advanced Topics in Chemical Physics

Hours and units to be arranged  | 
Content will vary from year to year; topics are chosen according to the interests of students and staff. Not offered 2019-20.

Advanced Topics in Biochemistry

6 units (2-0-4)  |  third term
Hours and units to be arranged. Content will vary from year to year; topics are chosen according to the interests of students and staff. Not offered 2019-20.

Integrative Projects in Microbial Science and Engineering

6 units (3-0-3)  |  second term
A project-based course designed to train students to integrate biological, chemical, physical and engineering tools into innovative microbiology research. Students and faculty will brainstorm to identify several "grand challenges" in microbiology. Small teams, comprised of students from different graduate programs and disciplinary backgrounds (e.g. a chemical engineer, a computer scientist and a biologist) and a faculty member, will work to compose a project proposal addressing one of the grand challenges, integrating tools and concepts from across disciplines. Student groups will present draft proposals and receive questions and critiques from other members of the class at check-in points during the academic term. While there will not be an experimental laboratory component, project teams may tour facilities or take field trips to help define the aims and approaches of their projects. At the end of the course, teams will deliver written proposals and presentations that will be critiqued by students and faculty.
Instructor: CEMI Faculty

Rotations in Chemistry

Variable units as arranged with the advising faculty member  |  first, second, third terms
By arrangement with members of the faculty, properly qualified graduate students will have the opportunity to engage in a short-term research project culminating in a presentation to their peers enrolled in the course and participating laboratories. (Pass-Fail only).

Chemical Research

Hours and units by arrangement  | 
By arrangement with members of the faculty, properly qualified graduate students are directed in research in chemistry.

Chemical Engineering Research

Offered to Ph.D candidates in chemical engineering. Main lines of research now in progress are covered in detail in section two.
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