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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 , remote control of mass spectrometers from the classroom as well as a real mass spectrometry laboratory.

Prerequisites: , 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
The student will learn to master some techniques relevant for understanding the mathematical structure of quantum mechanics, as used in Quantum Chemistry I 09-701. The following subjects are treated: Fourier series and Fourier transforms; eigenfunction expansion; eigenvalue problems and matrix diagonalization; hydrogen atom radial equation; differentials and line integrals (useful for thermodynamics). Undergraduates who have taken 09-231, Mathematical Methods for Chemists, may not enroll in this course. It is also not an acceptable chemistry elective for the major or minor in chemistry.

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.

09-620 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.

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.

09-707  Nanoparticles

12 units
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 Chemistry and Sustainability

12 units
This course aims to educate students in the foundations of systematic leadership for building a sustainable world. Many sustainability challenges are associated with commercial chemicals and with operational modes of the chemical enterprise. For scientists, effectiveness in solving the technical challenges and redirecting cultural behavior is the defining substance of sustainability leadership. The course aims to challenge students to analyze and understand the root causes of unsustainability, especially in the technological dimension, to imagine a more sustainable world and to begin to define personal leadership missions. Students will be introduced to sustainability ethics as the foundation stone of transformative sustainability leadership, to the Collins "Sustainability Compass" and "Code of Sustainability Ethics" and to the Robért/Broman "Framework for Strategic Sustainable Development (FSSD)"as powerful guiding tools. The Collins "Bookcase of Green Science Challenges" organizes the technical content. It systematizes the major chemical sustainability challenges of our time: clean synthesis, renewable feed-stocks, safe energy, elemental pollutants, persistent molecular toxicants and endocrine disruptors. Focal areas will be the technical, toxicological and cultural histories of elemental and molecular pollutants and endocrine disruptor (ED) science—EDs represent the single greatest sustainability challenge of everyday chemicals. The graded substance will take the form of take-home work. Students will primarily read key books and articles and will summarize and personally evaluate the material in essay assignments.

The course is intended for upper level undergraduates and graduates. There are no other prerequisites. The class is limited to 25 students.

09-711 Physical Organic Chemistry

12 units
This course introduces students to the study of structure and reactivity of organic compounds from a physical and theoretical standpoint. Students will learn the fundamentals of molecular orbital theory along with some practical applications to aromaticity and anti-aromaticity. Methods are described for the study of reaction mechanisms by means of physical methods such as kinetics, isotope effects, substituent effects, and solvent effects. Important reactive intermediates are described, along with detection methods.  This course may be suitable for upper level undergraduates in chemistry with the appropriate background in organic chemistry and physical chemistry.

09-712 Communication Issues in Scientific Research

Mini: 3 units
The design and presentation of scientific plans and results to the scientific community are very important aspects of the work of any chemist, who needs to disseminate the results of research by publishing papers and to write research proposal to raise funds. This course will cover skills that are important for the design and writing of scientific documents, such as research reports, papers and research proposals. The course will also cover aspects of responsible research conduct in recording the results of lab 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 in the format specified for an NSF Graduate Research Fellowship as well as for their participation in class discussions and in review of proposals written by others.

This mini-course is intended for graduate students in Chemistry in their first three years in graduate school. Undergraduate students who plan to apply for an NSF Graduate Research Fellowship will be able to enroll in the course. Postdoctoral fellows are welcome to audit the course.

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.

09-716 Bioactive Natural Products

Mini 4: 6 units
This mini-course is aimed at students with an interest in natural products research. Natural products are used as active components in medicinal products, as model compounds for further development into medicinally active drugs, as ingredients in food and for flavor and fragrances, among other very useful and interesting applications. An overview of the structural variety and activity of natural products will be presented along with their isolation and structural determination. Overall, the course will offer an introduction to the work that is customary in natural product research. This course will cover: Strategies to select the plant or marine material for study; main groups of natural products derived from plants; representative natural products derived from marine organisms; preparation of extracts and selection of active fractions, screening strategies; separation and purification of active components; bench-top bioassays and chemical assays and structure elucidation (especially 2D-NMR spectroscopy) Student's performance will be assessed by weekly assignments on the topics discussed in lecture and by two exams.

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 the synthesis, structural and functional aspects of nucleic acids and carbohydrates, and their applications in chemistry, biology and medicine. Later in the course, students will have the opportunity to explore cutting-edge research in this exciting new field that bridges chemistry with biology. Students will be required to keep abreast of the current literature. In addition to standard homework assignments and examinations, students will have the opportunity to work in teams to tackle contemporary problems at the forefront of chemistry and biology. The difference between the 09-518 (9-unit) and 09-718 (12-unit) is that this latter is a graduate level course. Students signed up for 09-718 will be required to turn in an original research proposal at the end of the course, in addition to all the other assignments.

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 Metals in Biology: Function and Reactivity

Fall: 12 units
Metal ions play important roles in many biological processes, including photosynthesis, respiration, global nitrogen cycle, carbon cycle, antibiotics biosynthesis, gene regulation, bio-signal sensing, and DNA/RNA repair, just to name a few. Usually, metal ions are embedded in protein scaffold to form active centers of proteins in order to catalyze a broad array of chemical transformations, which are essential in supporting the biological processes mentioned above. These metal containing proteins, or metalloproteins, account for half of all proteins discovered so far. In this course, the relation between the chemical reactivity and the structure of metalloproteins will be discussed in detail. The main focus is to illustrate the geometric and electronic structure of metal centers and their interactions with the protein environment in governing the chemical reactivity of metalloproteins. The applications of these principles in designing biomimetic/bioinspried inorganic catalysts and in engineering metalloproteins bearing novel chemical reactivity will also be discussed. The basic principles of the frequently utilized physical methods in this research area will also be introduced, which include optical absorption spectroscopy, Infrared (IR) and Raman spectroscopies, Mossbauer spectroscopy, electron paramagnetic resonance (EPR), X-ray absorption and diffraction techniques.

09-722 Kinetics and Mechanisms of Enzymatic Reactions

12 units
Major attention is devoted to kinetic methods of investigation of mechanisms of homogeneous chemical and enzymatic reactions. A mini course on kinetics and mechanisms of chemical reactions in solution is integrated followed by basics of kinetics of enzymatic reactions. The relationships between electronic structures, catalytic properties, and oxidation reactivity of biologically relevant metal complexes will be provided. Multiple roles of metal complexes in chemical and biochemical oxidations will be presented. Electrochemical and redox properties, electronic structures of metal complexes will be reviewed. Mechanistic pathways of action of hydrolases, kinases, hydrogenases, oxidases, peroxidases, cytochrome P-450, and other metalloenzymes will be described. (Undergraduate course: 09-522, 9-units) 3 hrs. lec.

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 Environmental Chemistry

9 units
Environmental pollutants are common consequences of human activities. These chemicals have a wide range of deleterious effects on the environment and people. This course will introduce students to a range of major environmental pollutants, with a particular focus on persistent organic pollutants. We will use chemical principles including thermodynamics, kinetics, photochemistry, organic reaction mechanisms, and structure-activity relationships to understand the environmental fate of major classes of pollutants. The transport of chemicals through the environment and their partitioning between air, water, soil, and people will be described. The major environmental reaction pathways (oxidation, photolysis, hydrolysis, reduction, metabolism) of common pollutants will be explored. This will provide students with the necessary knowledge to predict the chemical fate of environmental pollutants, and improve their understanding of the environmental impacts of their everyday chemical use and exposure. Specific topics include water quality, photochemical smog, organic aerosols, atmospheric chemistry and global climate change, toxicity of pesticides, and heterogeneous and multiphase atmospheric chemistry.

Prerequisites: Organic Chemistry I (09-217 or 09-219)

Co-requisites: Thermodynamics (09-214, 09-345 or 09-347 or 33-341 or 27-215 or 24-324 or equivalent) OR with permission of instructor.

09-725 Transition Metal 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.

09-729 Introduction To Sustainable Energy Science

Fall
This course focuses on the chemistry aspects of sustainable energy science. It introduces the major types of inorganic and molecular materials for various important processes of energy conversion and storage, such as photovoltaics, fuel cells, water splitting, solar fuels, batteries, and CO₂ reduction. All the energy processes heavily rely on innovations in materials. This course is intended to offer perspectives on the materials/physical chemistry that are of importance in energy processes, in particular, how the atomic and electronic structures of materials impact the energy harvesting and conversion. In current energy research, intense efforts are focused on developing new strategies for achieving sustainable energy through renewable resources as opposed to the traditional oil/coal/gas compositions. This course offers students an introduction to the current energy research frontiers with a focus on solar energy conversion/storage, electrocatalysis and artificial photosynthesis. The major types of materials to be covered include metals, semiconductors, two-dimensional materials, and hybrid perovskites, etc. The material functions in catalysis, solar cells, fuel cells, batteries, supercapacitors, hydrogen production and storage are also discussed in the course. The lectures are power-point presentation style with sufficient graphical materials to aid students to better understand the course materials. Demo experiments are designed to facilitate student learning.

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.

09-733 Chemistry and Light

12 units
This course covers the optical and electronic processes in inorganic and organic molecules found in modern "organic" optoelectronics. After an introduction into the field of optoelectronics we will look at the molecular structure of small molecules and polymers commonly employed as chromophores for such applications. It is the objective of this course for the student to understand the electronic structure of these molecules from electrochemical and spectroscopical techniques. The last part will emphasize the fabrication and characterization of organic LEDs, solar cells, photodetectors, chemical sensors, electrochromic devices etc.

09-734 Chemical Approaches to Energy Conversion and Storage

12 units
Solar energy and electrical energy from renewable resources need to be stored to resolve intermittency issues. Energy can be stored through charge transfer, changes in chemical bonding, or in electric polarization. This course will introduce students to general aspects of energy-storage technologies using these strategies, integrating scientific and engineering perspectives to discuss thermodynamics, mechanisms of energy storage, and fundamental aspects of efficiency, capacity, and power delivery. Then we will explore current and experimental technologies, covering supercapacitors, batteries, and water-splitting catalysts. By the end of the course, students will be able to apply chemical principles to understand energy-storage technologies and gain knowledge of important classes of these systems.

09-735 Applied Topics in Macromolecular and Biophysical Techniques

Fall: 9 or 12 units
Applications of physical chemistry are widespread. Physical chemical principles are fundamental to the methods used to sequence human genome, obtain high resolution structures of proteins and complex nucleic acids e.g., ribosome, and further provides the framework to predict how molecules fold in 3-dimension, how the different domains interact (inter- and intra-molecular interactions) to perform biological functions. The principles that were discussed in theory in undergraduate physical chemistry classes, will be applied in order to understand the molecular structures and dynamics in nucleic acids and proteins, and to more advanced molecular motors. In the last decade major advances have been made through single-molecule studies that provide finer details of macromolecules in action. This course aims to teach and apply physical chemistry as related to biological problems.

Prerequisites: 09-214 or 09-345 or 09-347 AND 03-121 or 03-231 or 03-232, or permission from the instructor.

09-736 Transition Metal Catalysis for Organic and Polymer Synthesis

12 units
Transition metal catalysts are invaluable in small molecule and polymer synthesis. The course will begin with a brief overview of organometallic chemistry and a discussion of fundamental organometallic reactions. Following this, a survey of some selected topics for the formation of small molecules and polymers will be presented. Some topics to be highlighted include: (1) Hydrogenation (2) Palladium Catalyzed Cross-Coupling (3) Epoxidation (4) Olefin Metathesis (5) Olefin Polymerization.

09-737 Medicinal Chemistry and Drug Development

Mini 2: 6 units
Modern medicine is increasingly practiced at the molecular level. Biomedical research provides fundamental knowledge about the mechanisms by which diseases arise and progress, leading to strategies for curing the disease (or at least alleviating the symptoms). Organic chemistry is the study of molecular structures and reactivity, so it is well positioned and, in fact, essential to the development of new drugs to either improve existing treatments or allow treatment of emerging or orphan diseases. This course will introduce students to the concepts, strategies and methods involved in the discovery and development of new drugs, from the standpoint of organic chemistry.

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.

09-760 The Molecular Basis of Polymer Mechanics

Spring
This course is a graduate level course designed to prepare students for graduate research in polymer science. Based around a laboratory component, students will learn the lab skills needed to synthesize and fully characterize novel polymer materials. The classroom component will teach the theory behind the measurements made in lab, as well as an understanding of the best experiments to learn about the properties of the material. Emphasis will be placed on current literature and technical communication (written and oral).

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

09-932 Graduate Teaching II

3 units