Graduate Program
Graduate Courses
All courses with numbers of 09-700 or higher are full-semester graduate courses for 12 units. Some courses (typically 9 unit) with lower numbers also count for graduate credit and those are also listed. The department also offers some half-semester graduate courses marked as 6 units (typically 09-600 numbers). Note that 12 units is equivalent to what may be familiar as a 4 credit course at other universities. Chemical Research (09-861) units may vary from 0 to 48 units for Ph.D. students at different stages in the program.
- 09-543 Mass Spectrometry: Fundamentals, Instrumentation, and Techniques
- 09-560 Molecular Modeling and Computational Chemistry
- 09-603 Mathematical Analysis for Chemistry
- 09-604 An Introduction to Chemical Kinetics
- 09-611 Chemical Thermodynamics
- 09-612 An Introduction to Quantum Chemistry
- 09-614 Modern Optical Spectroscopy
- 09-700 Introduction to Chemical Research
- 09-701 Quantum Chemistry I
- 09-702 Statistical Mechanics and Dynamics
- 09-703 Advanced Statistical Mechanics
- 09-704 Chemical Kinetics
- 09-705 Chemosensors and Biosensors
- 09-707 Nanoparticles
- 09-708 Quantum Chemistry II
- 09-709 Molecular Quantum Chemistry
- 09-710 Introduction to Environmentally Benign Chemistry
- 09-711 Physical Organic Chemistry
- 09-712 Ethics and Communication Issues in Scientific Research
- 09-714 Advanced Organic Chemistry
- 09-715 Physical Chemistry of Macromolecules
- 09-717 Organotransition Metal Chemistry: Principles and Applications
- 09-718 Bioorganic Chemistry: Nucleic Acids and Carbohydrates
- 09-719 Bioorganic Chemistry: Peptides, Proteins and Combinatorial Chemistry
- 09-720 Physical Inorganic Chemistry
- 09-721 Bioinorganic Chemistry
- 09-722 Oxidation and Inorganic Chemistry
- 09-723 Proximal Probe Techniques: New Tools For Nanoscience And Nanotechnology
- 09-724 Global Atmospheric Chemistry: Fundamentals and Data Analysis Methods
- 09-725 Transition Metal Chemistry
- 09-731 Radiochemistry
- 09-732 Nuclear Chemistry
- 09-741 Organic Chemistry of Polymers
- 09-742 Physical Chemistry of Polymers
- 09-745 Polymer Rheology
- 09-746 Linear Viscoelasticity
- 09-751 NMR Techniques, Instrumentation and Signal Processing
- 09-752 Advanced Magnetic Resonance Spectroscopy
- 09-801 Special Topics in Physical Chemistry
- 09-802 Introduction to Biophysical Chemistry
- 09-803 Chemistry of Gene Expression
- 09-811 Special Topics in Organic Chemistry
- 09-821 Special Topics in Inorganic Chemistry
- 09-831 Special Topics in Nuclear Chemistry
- 09-841 Modern Spectroscopy
- 09-851 Independent Study
- 09-852 Special Topics in NMR Spectroscopy
- 09-861 Chemical Research
- 09-871 Doctoral Dissertation
- 09-911 Graduate Seminar
- 09-931 Graduate Teaching I
- 09-932 Graduate Teaching II
09-543 Mass Spectrometry: Fundamentals, Instrumentation, and Techniques
Spring: 6 units
This course is intended for students of chemistry, biological sciences and material science who are interested in understanding fundamentals, instrumentation and techniques used in mass spectrometry. RRKM theory, ionization techniques, various scan modes (SIM, SRM, MS-MS,?) and basic interpretation are covered. The operating principles of various ion sources, mass analyzers and detectors are covered. Applications are focused in the area of proteomic analysis such as protein identification and peptide sequencing using MALDI and electrospray ionization. Hyphenated techniques such as GC-MSn, LC-MSn and CE-MSn are covered. This course may use a NSF funded Internet based Virtual Mass Spectrometry Laboratory, remote control of mass spectrometers from the classroom as well as a real mass spectrometry laboratory. Prerequisites: 09-214, 09-345 or 33-341, and 15-100 or permission of instructor.
09-560 Molecular Modeling and Computational Chemistry
12 units
Computer modeling is playing an increasingly important role in chemical research. This course provides an overview of computational chemistry techniques including molecular mechanics, molecular dynamics and both semi-empirical and ab initio electronic structure theory. Sufficient theoretical background is provided for students to understand the uses and limitations of each technique. An integral part of the course is hands on experience with state-of-the-art computational chemistry tools running on graphics workstations. Prerequisites: (15-111 or 15-200) and 09-344 and 09-345.
09-603 Mathematical Analysis for Chemistry
Fall: 6 units
This course surveys those techniques of mathematical analysis that are most relevant to chemical applications. Topics include multidimensional calculus, differential equations, integral transforms, and linear algebra. This course is meant as a mathematical primer for courses in quantum mechanics, thermodynamics and kinetics. Examples are taken from each of these subject areas.
09-604 An Introduction to Chemical Kinetics
Spring: 6 units
Rate laws and reaction mechanisms. Solving kinetics problems using the Laplace transform method. Transient and steady-state methods. Potential energy surfaces and reaction paths. Basic concepts of statistical mechanics and theories of reaction rates. Bimolecular and unimolecular reactions. Reactions in solution. Prerequisite: 09-603 or permission of instructor.
09-611 Chemical Thermodynamics
Fall: 6 units
A focused course on chemical thermodynamics. The basic thermodynamic functions will be introduced and discussed. The formal basis for thermochemistry will be presented. Single component phase equilibrium will be considered. The thermodynamic basis of solutions will be developed and applied to separation methods. The fundamental basis of chemical equilibrium will be developed and applied to a wide variety of reactions. Finally, a few special topics such as self-assembled systems will be presented. Prerequisite: 09-603 or permission of instructor.
09-612 An Introduction to Quantum Chemistry
Spring: 6 units
Introduction to quantum principles. The main topics to be covered include Schroedinger equation, particle in a box, the harmonic oscillator, and rigid rotor. Applications to vibrational, rotational, and electronic spectroscopy. Prerequisite: 09-603 or permission of instructor.
09-614 Modern Optical Spectroscopy
Mini 3: 6 units
This is a course exclusively in optical methods, both time resolved and steady state. In addition to methodology, spectral interpretation in terms of group theory will be discussed. The time-dependent formalism of quantum mechanics will also be introduced. Molecules in gas phase and condensed phase will be discussed. Frequent use will be made of the current literature. Background consisting of undergraduate physical chemistry is assumed.
09-700 Introduction to Chemical Research
3 units
A survey of the areas of research and problems currently being investigated by the faculty of the Department of Chemistry. Fundamental concepts in Transition Metal Chemistry are reviewed in this course followed by presentations of results obtained in current research that is based on these concepts. The class covers coordination numbers and stereochemistry, electronic structure, physical properties, and aspects of chemical reactivity of transition elements and their complexes. In lectures and class discussions, we identify general problems pursued in transition metal chemistry, discuss the choice and relevance of the questions posed by researchers, present modern methods and techniques used to answer the questions and the type of information that can be obtained using these methods. Special emphasis is given to examples drawn from supramolecular chemistry, molecular materials, and mineralogy.
09-701 Quantum Chemistry I
12 units
Introduction to quantum mechanics. The main topics to be covered will include wave packets, interference, the uncertainty principle, Ehrenfest's theorem, the Schroedinger equation and its solution for finite and infinite square wells and barriers, the harmonic oscillator, the rigid rotor, the hydrogen atom and time-independent perturbations.
09-702 Statistical Mechanics and Dynamics
12 units
Application of statistical mechanics to chemical systems. Calculation of Themodynamic functions, phase transitions and chemical equilibrium. Calculation of transport properties of gases and liquids. Elementary theory of chemical kinetics.
09-703 Advanced Statistical Mechanics
12 units
Quantum statistical mechanics: ideal Fermi and Bose systems. Structure and dynamics of classical liquids. Monte Carlo and Molecular dynamics computer simulations. Brownian dynamics and time-correlation function formalism. Modern theories of chemical reactions.
09-704 Chemical Kinetics
12 units
Rate laws. Analysis of linear chemical networks by Laplace transform and matrix formalism. Transient and steady-state methods. Stability of chemical systems. Theories of reaction rates. Molecular energetics. Applications to reactions in solution, electrolytes, electron and proton transfer reactions, heterogeneous systems.
09-705 Chemosensors and Biosensors
Fall: 12 units
Chemosensors and biosensors rely on "recognition" and "signaling" elements to transduce a molecular-scale binding event into an observable signal. Students in this course will be introduced to current research and technology for detecting chemical and biological analytes in a variety of contexts, including environmental testing, biological probing and medical diagnostics. Recognition elements ranging from small organic molecules to antibodies will be presented, while various detection modes, including fluorescence, gravimetric and colorimetric, that illustrate different signaling elements will be discussed and compared. Issues to be addressed include sensitivity, selectivity and efficiency. Each sensor will be analyzed in terms of the physical chemistry, organic chemistry and/or biochemistry underlying its function.
This course discusses the chemistry, physics, and biology aspects of several major types of nanoparticles, including metal, semiconductor, magnetic, carbon, and polymer nanostructures. For each type of nanoparticles, we select pedagogical examples (e.g. Au, Ag, CdSe, etc.) and introduce their synthetic methods, physical and chemical properties, self assembly, and various applications. Apart from the nanoparticle materials, other topics to be briefly covered include microscopy and spectroscopy techniques for nanoparticle characterization, and nanolithography techniques for fabricating nano-arrays. The course is primarily descriptive with a focus on understanding major concepts (such as plasmon, exciton, polaron, etc.). The lectures are power point presentation style with sufficient graphical materials to aid students to better understand the course materials. Overall, this course is intended to provide an introduction to the new frontiers of nanoscience and nanotechnology. Students will gain an understanding of the important concepts and research themes of nanoscience and nanotechnology, and develop their abilities to pursue highly disciplinary nanoscience research. The course should be of interest and accessible to advanced undergraduates and graduate students in fields of chemistry, materials science, and biology as well. Students enrolled in this course should be comfortable with introductory chemistry and physics. Prerequisites: For 09-507: 09-105, Introduction to Modern Chemistry and 09-106, Modern Chemistry II. For graduate version: undergraduates require permission of instructor.
09-708 Quantum Chemistry II
12 units
Time-dependent processes. Evolution of quantum states. Interaction of radiation with matter: the physical basis of chemical spectroscopy. Density matrix and coherence. Magnetic resonance. Time-domain spectroscopy. Energy transfer and relaxation.
09-709 Molecular Quantum Chemistry
12 units
Theory of the electronic structure of molecules. Hydrogen molecule. Valence bond and molecular orbital theory. Hartree-Fock approximation. Electron correlation. Configuration interaction. Many-body perturbation theory.
09-710 Introduction to Environmentally Benign Chemistry
12 units
Examples of primary and secondary prevention. The special role of catalysis in green chemistry. Overview of energy sources, resources and associated pollution. Introduction to combustion and approaches to greening of combustion. Options for green energy sources. Anthropogenic atmospheric pollution, atmospheric chemistry of the CFC's and nitrogen oxides in the atmosphere. Extension of macrocyclic concept of recyclability to the molecular level in oxidation chemistry. Biocatalysis as a route to new chemicals. Introduction to bioremediation.
09-711 Physical Organic Chemistry
12 units
The study of the structure and reactivity of organic molecules from a physical and theoretical standpoint. Introduction to molecular orbital theory and the study of mechanisms of pericyclic, electron-transfer, photochemical and heterolytic reactions by the use of physical methods such as kinetics, isotope effects, substituent effects and spectroscopic methods.
09-712 Ethics and Communication Issues in Scientific Research
Mini 2: 3 units
The design and presentation of scientific plans and results to the science community are very important aspects of the work of any chemist who needs to disseminate the results of research by publishing papers and to raise funds in order to support a research program. This course will cover several ethical principles and writing skills that are important for the design and implementation of research proposals. The course will also cover aspects of responsible research conduct in designing and conducting experiments and recording and analyzing the results of those experiments. The organization and presentation of data and research ideas for communication to the scientific community will be discussed. Students will learn about the scientific review process to which original manuscripts and proposals are subjected. Students enrolled in the course will be evaluated based on the quality of writing of a short original proposal and their participation in class discussions and in review panels. This mini-course is intended for graduate students in chemistry or closely related disciplines.
09-714 Advanced Organic Chemistry
Spring: 12 units
This course will expose the students to modern methods of organic chemistry including insights into the basis and mechanisms of chemical reactions. Topics include but are not limited to: spectroscopic analysis and structure determination, synthetic methods, organic reaction mechanisms, physical organic chemistry, Frontier molecular orbital (FMO) theory. Other topics and the extent of coverage will be determined based on the interests of the class. Upon completion of the course students should be able to design reaction schemes and evaluate the suitability of modern reagents towards synthesis of complex organic molecules and determine their structures from spectral data.
09-715 Physical Chemistry of Macromolecules
12 units
This course addresses the fundamentals of polymer science with the emphasis on physicochemical consequences of chain nature of macromolecules and on the behavior of polymers in condensed state (polymers as soft condense matter). The topics to be covered include: chain structure and molecular weight; molecular weight distribution; step growth and addition polymerization mechanisms; chain conformation and behavior of polymers in solution; concentrated solutions and phase separation behavior; rubber elasticity; introduction to polymer viscoelasticity and rheology; mechanical behavior of polymers; glass transition and crystallization; multicomponent polymeric materials; liquid crystalline polymers; polymers at surfaces and interfaces; self-assembly and nanostructure formation in synthetic and biological systems; conducting and semiconducting polymers. Graduate students taking the course for 12 units will be required to write a term paper on a selected topic.
09-717 Organotransition Metal Chemistry: Principles and Applications
12 units
The first half of the course focuses on the fundamentals of structure and bonding in organotransition complexes and how these rules can be used to explain, and predict, chemical reactivity. The latter half of the course covers applications, and more specifically, homogenous catalysts for industrial processes and organic sythesis.
09-718 Bioorganic Chemistry: Nucleic Acids and Carbohydrates
12 units
This course will introduce students to new developments in chemistry and biology, with emphasis on synthetic and functional aspects of nucleic acids and proteins, and their applications. Later in the course, students will get to explore some of the ongoing research in functional genomics. Prerequisites: 09-217 and 09-218
09-719 Bioorganic Chemistry: Peptides, Proteins and Combinatorial Chemistry
12 units
This course will introduce students to new developments in chemistry and biology, with emphasis on synthetic and functional aspects of proteins, peptides and small molecules. Basic concepts of bioorganic chemistry will be presented in the context of the current literature and students will have the opportunity to learn about the experimental methods that are used. An introduction to combinatorial chemistry in the context of drug design will also be presented. Prerequisites: 09-217 and 09-218
09-720 Physical Inorganic Chemistry
12 units
This course develops the principles of magnetochemistry and inorganic spectroscopy. Electronic absorption, magnetic circular dichroism, resonance raman, NMR, EPR, Mössbauer, magnetization and x-ray methods will be introduced with application toward the determination of electronic structures of transition metal complexes.
09-721 Bioinorganic Chemistry
12 units
This course addresses the basis for the selection and regulation of metal atoms and ligand systems and the interactions with their corresponding protein environments. The chemistry of catalytic processes in metalloenzymes, and atom transfer and electron transport in metalloproteins will be reviewed. The array of physical methods required for study will be introduced, with application toward the determination of electronic and molecule structure and enzymatic mechanisms.
09-722 Oxidation and Inorganic Chemistry
12 units
The roles of metal complexes in oxidation processes (inorganic, organic, biological) will be presented. Special attention will be given to processes involving the activation of molecular oxygen from a mechanistic viewpoint. The electronic structures of metal complexes of dioxygen and its reduced species, superoxide, peroxide and oxide are reviewed, as are the relationships between electronic structure and oxidation reactivity.
09-723 Proximal Probe Techniques: New Tools For Nanoscience And Nanotechnology
12 units
Proximal probe techniques are revolutionizing physical and biological sciences, owing to their ability to explore and manipulate matter at the nanoscale, and to operate in various environments (including liquids). Proximal probe techniques rely on the use of nanoscale probes, positioned and scanned in the immediate vicinity of the material surface. Their development is often viewed as a first step towards nanotechnology, since they demonstrate the feasibility of building purposeful structures one atom or one (macro)molecule at a time. This course is designed for the students of chemistry, biology physics and engineering, who are interested in the fundamentals of proximal probe techniques and in their applications in various areas, converging into a rapidly developing, interdisciplinary field of nanoscience. It will provide thorough physical background of such basic techniques as Atomic Force Microscopy (AFM), Scanning Tunneling Microscopy (STM), and Near-Field Scanning Optical Microscopy (NSOM) and of their variants.
09-724 Global Atmospheric Chemistry: Fundamentals and Data Analysis Methods
12 units
The existing 9-unit course comprises three units, the first being introductory meteorology, the second stratospheric chemistry and ozone depletion, and the third being global tropospheric chemistry. This course is taught in alternate spring terms (odd years). Evaluation is dominated by one exam (in meteorology) and two projects (nominally in stratospheric and tropospheric chemistry, optionally both stratospheric) which are presented as short (15 minute) talks, with two page written summaries required of individuals in group projects. A 12 unit version would include a final paper in addition to these projects. (Formerly offered as 09-620)
09-725 Transition Metal Chemistry
12 units
Fundamental concepts in Transition Metal Chemistry are reviewed in this course followed by presentations of results obtained in current research that is based on these concepts. The class covers coordination numbers and stereochemistry, electronic structure, physical properties, and aspects of chemical reactivity of transition elements and their complexes. In lectures and class discussions, we identify general problems pursued in transition metal chemistry, discuss the choice and relevance of the questions posed by researchers, present modern methods and techniques used to answer the questions and the type of information that can be obtained using these methods. Special emphasis is given to examples drawn from supramolecular chemistry, molecular materials, and mineralogy.
09-731 Radiochemistry
12 units
Introduction to nuclear systematics and properties, nuclear transformations, radioactivity, nuclear reactions, fission, interactions of radiation with matter, experimental techniques and applications. This course offers a general survey suitable for chemists, biologists, physicists and engineers.
09-732 Nuclear Chemistry
12 units
Nuclear models; radioactive decay processes; nuclear reactions: theory and experiment; nuclear processes as chemical probes: Mössbauer effect, angular correlations, hyperfine interactions.
09-741 Organic Chemistry of Polymers
12 units
A survey of synthesis and reactions of high polymers, kinetics and mechanisms of step-growth and chain-growth polymerization via radical, ionic and coordinate intermediates, polymers for special applications (biomedical, ceramic, microelectronic, information storage).
09-742 Physical Chemistry of Polymers
12 units
An advanced graduate course that applies statistical mechanics to the study of the equilibrium and dynamic properties of polymers. The structure and dynamics of single polymer chains, solutions and bulk polymers are discussed.
09-745 Polymer Rheology
12 units
Course contents include basic concepts (forces, displacements, stress, tensor, strain, etc.), linear and nonlinear elastic solids, linear viscous fluid, linear viscoelastic fluid and solid and certain topics in nonlinear viscoelastic behavior. Emphasis is on concepts, illustrated with examples based on the properties of real materials.
09-746 Linear Viscoelasticity
12 units
The mathematical model for linear viscoelasticity is developed and compared with the behavior observed for polymeric materials. Emphasis is on the interpretation of experimental results in terms of fundamental material properties and discussion of the latter in terms of molecular concepts for a variety of amorphous and crystalline polymers.
09-751 NMR Techniques, Instrumentation and Signal Processing
12 units
This course is intended for students of chemistry, biology and physics who are interested in deeper understanding of the instrumentation and signal processing in NMR spectroscopy and imaging. The introductory part deals with the basic ideas behind high resolution NMR in liquids. The second part of the course is devoted to the description and brief analysis of major components of the NMR instrument. The third and last part is devoted exclusively to the digital processing of the NMR signals by computers. The relations between the time domain and the frequency domain are thoroughly discussed and the principles of manipulation of spectra by a computer are given.
09-752 Advanced Magnetic Resonance Spectroscopy
12 units
This course discusses nuclear magnetic resonance spectroscopy using the language of spin quantum mechanics, density matrix and product operator formalisms. Coherence tranfer and phase cycling protocols are analyzed with a view at practical applications in homo- and hetero-nuclear multidimensional spectroscopy and rotating frame experiments. Relaxation and population transfer processes are discussed and its implications for the elucidation of molecular structure are emphasized. Examples stemming from molecular biophysics will be presented.
Special Topics courses are given routinely and cover selected areas of current research interests.
09-801 Special Topics in Physical Chemistry
12 units
09-802 Introduction to Biophysical Chemistry
Intermittent: 12 units
All biological processes are governed by the same thermodynamic and kinetic factors that control chemical reactions. This course will introduce students to how fundamental concepts and cutting-edge techniques from physical chemistry are being applied to improve our understanding of modern biology. Chemistry 09-802 is an introductory class on macromolecular organization, chemical kinetics, and thermodynamics with emphasis to biological applications. Topics of interest will be entropy, free energy, kinetics of complex biological reactions, the non covalent forces that determine protein and nucleic acid stability (the hydrophobic effect, electrostatic interactions and the hydrogen bond), the folding and misfolding kinetics in solution. Issues of particular interest will be allosteric mechanisms; ligand binding and finally single-molecule techniques will be discussed. (No prior knowledge of any single-molecule techniques is needed).
Prerequisite: One semester of undergraduate physical chemistry or general physics. Any experience in biochemistry will be helpful, but not mandatory.
09-803 Chemistry of Gene Expression
Fall: 12 units
This course examines the chemical basis of biological reactions required for the propagation of genetic information stored in DNA and the organic chemistry principles behind the structure and function of nucleic acids. Main topics of lectures and class discussion will include the chemical and biochemical syntheses, properties and analyses of natural and modified nucleic acids to investigate cellular processes such as transcription, RNA splicing, other RNA regulation and translation; an introduction to the enzymatic strategies that accelerate these chemical reactions and a comparison of protein enzymes, ribozymes and other nucleic acid based enzymes in contemporary chemistry and biology. Students will learn to critically evaluate current scientific efforts that examine various aspects of chemistry and biological chemistry, the relationship between the structure and function of biomolecular systems, propose experiments to examine biological chemistry research problems and communicate these ideas and participate in scientific discussions and debates.
09-811 Special Topics in Organic Chemistry
12 units
09-821 Special Topics in Inorganic Chemistry
12 units
09-831 Special Topics in Nuclear Chemistry
12 units
09-841 Modern Spectroscopy
12 units
This course emphasizes the use of modern optical methods in the study of molecular properties and reactivity. Basic topics such as the use of group theory in the analysis of vibrational, rotational and electronic spectra are covered in detail. In addition, recently developed techniques such as time-resolved and nonlinear spectroscopies are discussed as are applications of optical methods to problems in chemistry, biology and materials science.
09-851 Independent Study
Units variable
09-852 Special Topics in NMR Spectroscopy
12 units
09-861 Chemical Research
Units variable
09-871 Doctoral Dissertation
5 units
09-911 Graduate Seminar
1 unit
Recent advances in chemistry discussed by graduate students.
09-931 Graduate Teaching I
3 units