Chemistry

Ch 1 ab. General Chemistry. 6 units (3-0-3) first term; 9 units (4-0-5) second term. Lectures and recitations dealing with the principles of chemistry. First term: 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 equilibria, oxidation and reduction, thermodynamics, kinetics, introduction to organic chemistry and the chemistry of life. Graded pass/fail. Instructors: Lewis, Heath, MacMillan. Additional information concerning this course can be found at http://www.its.caltech.edu/~chem1.

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. Instructors: Lewis, Bellan, D. Newman. Satisfies the menu requirement of the Caltech core curriculum.

Ch 3 a. Fundamental Techniques of Experimental Chemistry. 6 units (0-5-1); 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. Enrollment first term will be limited to students who have gained advanced placement into Ch 41 or Ch 21, or by permission of the instructor. Graded pass/fail. Instructor: Staff.

Ch 3 b. Experimental Procedures of Synthetic Chemistry. 8 units (1-6-1); third term. Prerequisites: Ch 1 a, Ch 1 b, and Ch 3 a. Instruction in fundamental synthesis, separation, and characterization procedures used in chemical research. Instructor: Staff.

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. 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 emphasizes spectroscopic methods of analysis; Ch 4 b stresses applications of chromatography in addition to more classical separation techniques. Ch 4 a, first term; Ch 4 b, second term only. Instructor: Staff.

Ch 5 ab. Advanced Techniques of Synthesis and Analysis. Ch 5 a 12 units (1-9-2); Ch 5 b 9 units (1-6-2); second, third terms. Prerequisite: Ch 4 ab. Modern synthetic chemistry. Specific experiments may change from year to year. Multistep syntheses of natural products, coordination complexes, and organometallic complexes will be included. Experiments to illustrate the fundamental principles of inorganic and organometallic chemistry. Methodology will include advanced techniques of synthesis and instrumental characterization. Instructors: Peters, Dougherty.

Ch 6 ab. Application of Physical Methods to Chemical Problems. 10 units (0-6-4); second, third terms. Prerequisites: Ch 1, Ch 4 ab, and Ch 21 or equivalents (may be taken concurrently). Introduction to the application of modern physical methods to chemical problems, with emphasis in the area of molecular spectroscopy. Techniques including X-ray crystallography, laser Raman spectroscopy, microwave spectroscopy, electron spin resonance, ultraviolet photoelectron spectroscopy, and Fourier transform ion cyclotron resonance spectroscopy are used to examine the structure, properties, and reaction dynamics of molecules in the gas phase, in solution, and at surfaces. Instructors: Okumura, Beauchamp, Collier.

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 the powerful contemporary methods for polypeptide and oligonucleotide synthesis. Experiments will address nucleic acid and 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: Dervan.

Ch 10 abc. Frontiers in Chemistry. 3 units (2-0-1); first, second terms. 8 units (1-6-1); third term. Open for credit to freshmen and sophomores. Prerequisites: Ch 10 c prerequisites are Ch 10 ab, Ch 3 a, 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: Barton, Dervan.

Ch 14. Chemical Equilibrium and Analysis. 6 units (2-0-4); third term. A systematic treatment of ionic equilibria in solution. Topics covered include acid-base equilibria in aqueous and nonaqueous solutions, complex ion formation, chelation, oxidation-reduction reactions, and some aspects of reaction mechanisms. Instructors: Rees, Brandow.

Ch 15. Chemical Equilibrium and Analysis Laboratory. 10 units (0-6-4); first term. Prerequisites: Ch 1 ab, Ch 3 a, Ch 14, 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: Brandow.

Ch 21 abc. The Physical Description of Chemical Systems. 9 units (3-0-6); first, second, third terms. Prerequisites: Ch 1 ab, Ph 2 ab, Ma 2 ab. Atomic and molecular quantum mechanics, spectroscopy, thermodynamics, statistical mechanics, and chemical kinetics. Instructors: McKoy, Blake, Okumura.

Ch 24 ab. Introduction to Biophysical Chemistry. 9 units (3-0-6); second, third terms. Prerequisites: Ma 1 abc, Ph 1 abc, Ch 21 a or Ph 2 ab. Fundamental physical chemistry, with emphasis on those topics most important in biology. Thermodynamics and its applications to aqueous solutions and living systems, membrane potentials and the thermodynamics of transport, reaction kinetics and mechanisms, transport properties, applications of molecular spectroscopy in biology, and statistical mechanics with applications to biological polymers. Instructors: Rees, S. Chan.

Ch 41 abc. Organic Chemistry. 9 units (3-0-6); first, second, third terms. Prerequisite: Ch 1 ab or instructor’s permission. The synthesis, structures, and mechanisms of reactions of organic compounds. Instructors: Grubbs, Hsieh-Wilson, Stoltz.

Ch 80. Chemical Research. 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.

Ch 81. Independent Reading in Chemistry. Units by arrangement. Prerequisite: 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 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. Graded pass/fail. Instructor: Bikle.

Ch/ChE 91. Scientific Writing. 3 units (1-0-2); third term. Training in the writing of scientific research papers. Each student must complete a 3,000-word paper styled after an article in the Journal of the American Chemical Society on a subject of chemical or biochemical relevance. The manuscript may be based on a paper submitted by the student for a previous class or on a SURF report, but it must be the student’s original writing and be within the intellectual scope of the chemistry and chemical engineering division. Each student will work individually with a faculty member under the supervision of the course instructor. Fulfills the Institute scientific writing requirement. Instructor: Weitekamp.

Ch 102. Introduction to Inorganic Chemistry. 9 units (3-0-6); third term. Prerequisite: Ch 41 ab. Structure and bonding of inorganic species with special emphasis on spectroscopy, ligand substitution processes, oxidation-reduction reactions, and biological inorganic chemistry. Letter grades only. Instructor: Peters.

Bi/Ch 110. Introduction to Biochemistry. 12 units (4-0-8). For course description, see Biology.

Bi/Ch 111. Biochemistry of Gene Expression. 12 units (4-0-8). For course description, see Biology.

Ch 112. Inorganic Chemistry. 9 units (3-0-6); first term. Prerequisite: 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: Bercaw.

Bi/Ch 113. Biochemistry of the Cell. 12 units (4-0-8). For course description, see Biology.

Ch 117. Introduction to Electrochemistry. 6 units (2-0-4); 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. Instructors: Lewis, staff.

Ch 120 abc. Nature of the Chemical Bond. 9 units (3-0-6) first term; 6 units (2-0-4) second term; 6 units (1-1-4) third term. Prerequisite: general exposure to quantum mechanics (e.g., Ph 2 ab, Ph 12 abc, or equivalent). Modern ideas of chemical bonding, with an emphasis on qualitative concepts and how they are used to make 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). The emphasis is on explaining chemical, mechanical, electrical, and thermal properties of materials in terms of atomistic concepts. Part b: The quantum mechanical basis for understanding transition metal systems with a focus on chemical reactivity. There will be an emphasis on organometallic complexes, on homogeneous catalysis, and on heterogeneous catalysis. Part c: The student does an individual research project using modern quantum chemistry computer programs to calculate wavefunctions, structures, and properties of real molecules. Part b not offered 2005–06. Instructor: Goddard.

Ch 121 ab. Atomic Level Simulations of Materials and Molecules. 9 units (3-1-5) second, third terms. Prerequisites: Ma 2 ab, Ph 2 ab, Ch 1 ab, or equivalent. Recommended: Ch 41 abc, Ch 21 a. Methods for predicting the structures and properties of molecules and solids. The course will highlight theoretical foundations and applications to current problems in the following areas: 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); and organometallics and catalysis (heterogeneous and homogeneous). Both terms will involve the use of computers for building and calculating systems of interest. Part a covers the basic methods. Part b will focus on simulations applied to problems in petroleum chemistry. Ch 120 a is recommended but not required for Ch 121 a. Part b not offered 2005–06. Instructor: Goddard.

Ch 122 abc. Methods for the Determination of the Structure of Molecules. 9 units (3-0-6); first, second, third terms. Prerequisite: Ch 21 abc or instructor’s permission. Modern methods used in the determination of the structure of molecules, including X-ray, electron, and neutron diffraction; mass spectrometry; optical, infrared, Raman, microwave, Mössbauer, nuclear magnetic, and electron spin resonance spectroscopy. The emphasis will be on nuclear magnetic resonance (first term), and diffraction methods and mass spectrometry (third term). All three terms can be taken independently. Ch 122 a will be offered first term. Instructor: Day.

Ch 125 abc. The Elements of Quantum Chemistry. 9 units (3-0-6); first, second, third terms. Prerequisite: 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: Kuppermann, McKoy.

Ch 126. Molecular Spectra and Molecular Structure. 9 units (3-0-6); third term. Prerequisite: Ch 21 and Ch 125 a taken concurrently, 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. Instructors: Collier, Zewail.

Ge/Ch 127. Nuclear Chemistry. 9 units (3-0-6). For course description, see Geological and Planetary Sciences.

Ge/Ch 128. Cosmochemistry. 9 units (3-0-6). For course description, see Geological and Planetary Sciences.

Ch 130. Spectroscopy. 9 units (3-0-6); third term. Discussion of various topics in lasers and their applications. Group theory with applications to molecular structure and spectroscopy will also be discussed. Not offered 2005–06.

Bi/Ch 132. Biophysics of Macromolecules. 9 units (3-0-6). For course description, see Biology.

Ch 135 ab. Chemical Dynamics. 9 units (3-0-6); part a, third term; part b, second term. Prerequisites: Ch 21 abc and Ch 41 abc, or equivalent, or instructor’s permission. Part a: introduction to the dynamics of chemical reactions. Topics include scattering cross sections, rate constants, intermolecular potentials, reactive scattering, nonadiabatic processes, statistical theories of unimolecular reactions, and the application of laser and molecular beam techniques to the study of reaction mechanisms. Part b: the quantum description of chemical reactions. The scattering matrix. The calculation of reaction cross sections, probabilities, and rate constants. Collision lifetimes and resonances. Classical trajectories. The two terms can be taken independently. Not offered 2005–06.

Ch/ChE 140 ab. Principles and Applications of Semiconductor Photoelectrochemistry. 6 units (4-0-2); second, third terms. Prerequisite: APh/EE 9 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. The course will meet for four one-hour lectures per week and will be in a tutorial format with instruction predominantly from graduate students and postdoctoral fellows with expertise in the field. Instructor: Lewis. Given in alternate years; offered 2005–06.

Ch 142. Frontiers in Chemical Biology. 4 units (2-0-2); second term. Prerequisite: Bi/Ch 110 or instructor’s permission. A discussion of enzyme structure and function, and ligand-protein-nucleic acid interactions. Not offered 2005–06.

Ch 143. Basic FT NMR Spectroscopy. 9 units (3-2-4); second term. Prerequisite: Ch 41 abc. The course will cover NMR basics and applications, with emphasis on FT NMR and the principles of multipulse NMR techniques used in structural analysis, including determination of relaxation times, INEPT, DEPT, NOSEY, and COSY. A number of NMR techniques will be illustrated with the Chapman-Russell FT NMR Problems videodisc-based computer program, which features on-screen spectra at a variety of magnetic fields with, and without, decoupling, 2-D spectra, and so on. The practical use of NMR will be further demonstrated by laboratory exercises using modern pulse FT NMR techniques with high-field spectrometers for structural analysis. Instructor: J. D. Roberts.

Ch 144 ab. Advanced Organic Chemistry. 9 units (3-0-6); first term. Prerequisite: 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. In 2005–06, only part a will be offered (first term). Instructor: Dougherty.

Ch 145. Bioorganic Chemistry of Proteins. 9 units (3-0-6); first term. Prerequisites: Ch 41 abc and Bi/Ch 110. This course aims to define the information that can be derived on the structure and function of enzymes through the use of affinity labeling reagents, mechanism-based inactivators, and transition-state analog inhibitors. While the focus will be on selected classes of enzymes, the material covered is intended to give insight into general rules for the investigation of enzyme mechanisms and inhibitor design. Not offered 2005–06.

Ch 146. Bioorganic Chemistry of Nucleic Acids. 9 units (3-0-6); third term. Prerequisite: 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). Given in alternate years; not offered 2005–06.

Ch/ChE 147. Polymer Chemistry. 9 units (3-0-6); second term. Prerequisite: Ch 41 abc. 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). For course description, see Chemical Engineering.

Ch 153. Advanced Inorganic Chemistry. 9 units (2-0-7); second term. Prerequisites: Ch 112 and Ch 21 abc or concurrent registration. Topics in modern inorganic chemistry. Electronic structure, spectroscopy, and photochemistry with emphasis on examples from the modern research literature. Instructor: Gray.

Ch 154 ab. Organometallic Chemistry. 9 units (3-0-6); second, third terms. Prerequisite: 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. Instructor: Bercaw. Part b not offered 2005–06.

ChE/Ch 155. Chemistry of Catalysis. 9 units (3-0-6). For course description, see Chemical Engineering.

Ch 163. Lectures-Seminars in Physical Chemistry. 6 units (2-0-4); third term. Not offered 2005–06.

ChE/Ch 164. Introduction to Statistical Thermodynamics. 9 units (3-0-6). For course description, see Chemical Engineering.

Ch 165. Nonequilibrium Statistical Mechanics. 9 units (3-0-6); third term. Prerequisite: 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. Principles of Three-Dimensional Protein Structure. 9 units (3-3-3). For course description, see Biochemistry and Molecular Biophysics.

ESE/Ge/Ch 171. Atmospheric Chemistry I. 9 units (3-0-6).For course description, see Environmental Science and Engineering.

ESE/Ge/Ch 172. Atmospheric Chemistry II. 9 units (3-0-6). For course description, see Environmental Science and Engineering.

ESE/Ch/Ge 175 ab. Environmental Organic Chemistry. 9 units (3-0-6). For course description, see Environmental Science and Engineering.

Ch 180. Chemical Research. Units by arrangement. Offered to M.S. candidates in chemistry. Graded pass/fail.

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. Instructor: Barton. Given in alternate years; offered 2005–06.

Ch 213 abc. Advanced Ligand Field Theory. 12 units (1-0-11); first, second, third terms. Prerequisite: 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. Instructors: Gray, staff.

Ch 221. Electron Transfer Reactions in Chemistry and Biology. 6 units; second term. Prerequisite: Ch 21 abc. Fundamentals of electron transfer reactions. Molecular (statistical) theory, dielectric continua, electronic matrix elements, Franck-Condon principle, relevant thermodynamics, reorganization energy, quantum effects, charge transfer spectra, solvent dynamics. Reactions in solution at metal electrode-liquid, modified electrode-liquid, semiconductor electrode-liquid, and liquid-liquid interfaces. STM theory. Reactions in photosynthetic reaction centers and in other proteins. Not offered 2005–06.

Ch 227 ab. Advanced Topics in Chemical Physics. 9 units (3-0-6); part a second term; part b third term. Prerequisite: Ch 125 abc or Ph 125 abc or equivalent. The general quantum mechanical theory of molecular collisions will be presented in detail. Quasi-classical, semi-classical, and other approximations. Applications to inelastic and reactive molecule-molecule and inelastic electron-molecule collisions. Part a not offered 2005–06. Instructor: Heath.

Ch 228. Dynamics and Complexity in Physical and Life Sciences. 9 units (3-0-6); third term. This course is concerned with the dynamics of molecular systems, with particular focus on complexity, the elementary motions that lead to functions in chemical and biological assemblies. It will address principles of dynamics as they relate to the nature of the chemical bond. An overview of modern techniques, such as those involving lasers, NMR, and diffraction, for unraveling dynamics in complex systems. Applications from areas of physics, chemistry, and biology—from coherence and chaos to molecular recognition and self-assembly. Instructor: Zewail.

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 2005–06.

Ch 242 ab. Chemical Synthesis. 9 units (3-0-6); first, second terms. Prerequisite: 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, MacMillan.

Ch 244 a. Topics in Chemical Biology. 9 units; second term. Current topics at the interface of chemistry and biology. Not offered 2005–06.

Ch 247 a. Organic Reaction Mechanisms. 6 units (2-0-4); third term. A mechanistic view of free-radical reactions using examples from biological systems. Topics: initiation, termination, and propagation of radical reactions in vivo, mechanisms of lipid damage, spin labeling, photosynthesis, oxygen radicals and oxygen toxicity, and radical reactions in proteins and nucleic acids. Not offered 2005–06.

Ch 250. Advanced Topics in Chemistry. Units and term to be arranged. Content will vary from year to year; topics are chosen according to interests of students and staff. Visiting faculty may present portions of this course. Instructors: MacMillan, Stoltz.

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.