Spring 2022

- CHEMICAL AND BIOLOGICAL ENGR -

• 421 Green and Catalytic Chemistry (UGRD)

Concepts of heterogeneous and homogeneous catalysis applied to current industrial processes associated with fuel production and manufacturing of chemicals. In particular, available routes for conversions using alternative, more sustainable feedstocks and processes will be discussed in the context of green chemistry and engineering principles. These case studies will serve as platforms to the fundamentals of heterogeneous acid and metal catalysis, including techniques of catalyst synthesis and characterization, as well as understanding of how reactions occur on surfaces.

Instructors: Michele L. Sarazen
Cross listed classes: CHM 421 | ENE 421

- CHEMISTRY -

• 202 General Chemistry II (UGRD)

Continuation of 201. Principles of chemistry; introduction to chemical bonding and solid state structure; chemical kinetics, descriptive inorganic chemistry; laboratory manipulations, preparations, and analysis. Fulfills medical school entrance requirements in general chemistry and qualitative analysis.

Instructors: Andrew B. Bocarsly | Sonja A. Francis | Robert P. L'Esperance

• 215 Advanced General Chemistry: Honors Course (UGRD)

Selected topics from general chemistry are presented from an advanced point of view. Emphasis is on the conceptual development of electronic structure and bonding, on applications of thermodynamics to chemical equilibrium, and on kinetics. A unified approach to molecular science is developed. The course is intended for serious students of science or engineering.

Instructors: Paul J. Chirik | Sonja A. Francis | Robert P. L'Esperance

• 251 Chemistry Research Experience II (UGRD)

The Chemistry Research Experience sequence provide sophomore students with an in lab research experience. The sequence comprises two semesters with CHM 250 as a prerequisite for CHM 251, a credit bearing P/D/F course. Students will gain an introduction to chemical research within the laboratory of a Chemistry faculty mentor. Students are expected to spend 6 hours per week engaged in research and attend weekly meetings as outlined by the mentoring faculty. At the end of the semester, students will present an oral presentation summarizing their results.

Instructors: Robert P. L'Esperance | Susan K. VanderKam

• 304 Organic Chemistry II: Foundations of Chemical Reactivity and Synthesis (UGRD)

This course begins by discussing the chemical consequences of conjugation and the Diels-Alder reaction. After a coverage of aromaticity and the chemistry of benzene, we then move into the heart of the course: the nature and reactivity of the carbonyl group, a subject that is central to both mainstream organic chemistry and biochemistry. Throughout this course, an effort will be made to demystify the art of chemical synthesis. This course is appropriate for chemistry majors, premedical students, and other students with an interest in organic chemistry and its central position in the life sciences.

Instructors: Sandra L. Knowles | Jenny S. Martinez | Erik J. Sorensen

• 306 Physical Chemistry: Chemical Thermodynamics and Kinetics (UGRD)

At the center of this course is the recognition of Gibbs Free Energy as a fundamental quantity describing physical processes. From this, we will develop concepts of thermodynamics and kinetics, and illustrate them with examples from chemistry.

Instructors: Michael T. Kelly

• 373 Analytical Methods and Experimental Design (UGRD)

Fundamental principles of modern analytical tools including spectroscopy, chromatography & electrochemical methods will be introduced. These techniques will be used to design experiments. Data treatments using statistical methods for proper reporting of information with precision, accuracy, and uncertainty will be covered. Relationships between physical parameters will also be discussed from a statistical point of view. Computational Chemistry will be integrated into data analysis.

Instructors: Michael T. Kelly | Chia-Ying Wang

• 406 Advanced Physical Chemistry: Chemical Dynamics and Thermodynamics (UGRD)

This course is an introduction to statistical thermodynamics, kinetics, and molecular reaction dynamics. Following a review of classical thermodynamics, the statistical mechanics of molecular systems is developed. Discussions of transport properties, chemical kinetics, and reaction dynamics form the rest of the course.

Instructors: William M. Jacobs | Chia-Ying Wang

• 412 Inorganic Chemistry: Structure and Materials (UGRD)

Structural principles and bonding theories are discussed for various classes of main group inorganic and transition metal coordination compounds. The topics include an introduction to group theory, vibrational spectroscopy, molecular orbital theory, electronic structure of d-orbitals, and ligand field theory. Additional topics will include topics in the areas of solid-state chemistry, inorganic materials chemistry, and nanoscience.

Instructors: Susan K. VanderKam

• 500A Responsible Conduct of Research in Chemistry (Half-Term) (GRAD)

Discussion and evaluation of the role professional researchers play in dealing with the reporting of research, responsible authorship, human and animal studies, misconduct and fraud in science, intellectual property, and professional conduct in scientific relationships. Participants are expected to read the materials and cases prior to each meeting. Successful completion is based on regular attendance and active participation in discussion. This half-term course is designed to satisfy federal funding agencies' requirements for training in the ethical practice of scientists. Required for graduate students and post-docs.

Instructors: Michael T. Kelly

• 500B Responsible Conduct of Research in Chemistry (Half-Term) (GRAD)

Instructors: Michael T. Kelly

• 500C Responsible Conduct of Research in Chemistry (Half-Term) (GRAD)

Discussion and evaluation of the role professional researchers play in dealing wtih the reporting of research, responsible authorship, human and animal studies, misconduct and fraud in science, intellectual property, and professional conduct in scientific relationships. Participants are expected to read the materials and cases prior to each meeting. Successful completion is based on regular attendance and active participation in discussion. This half-term course is designed to satisfy federal funding agencies' requirements for training in the ethical practice of scientists. Required for chemistry graduate students/post-docs.

Instructors: Michael T. Kelly

• 502 Advanced Quantum Chemistry (GRAD)

Selected advanced topics in quantum mechanics including: time-dependent quantum mechanics, angular momentum theory, scattering theory, and radiation-matter interactions.

Instructors: Herschel A. Rabitz

• 504 Molecular Spectroscopy (GRAD)

Basic principles and modern aspects of spectroscopy are discussed. Topics include light-matter interactions (quantum mechanics & statistical mechanics), linear and non-linear spectroscopy, time-resolved spectroscopy, single-molecule spectroscopy, and nano-optics. Application examples include problems in gas-phase chemical physics, solid-state and condensed-matter physics, organic and organo-metallic chemistry, biology and spectroscopy in complex environments.

Instructors: Chia-Ying Wang | Marissa L. Weichman | Haw Yang

• 516 Biophysical Chemistry II (GRAD)

Broad introduction to major contemporary techniques used to study structures, functions, and interactions of biological macromolecules, including quantitative theory of molecular interactions. Aims to convey to students with diverse backgrounds and interests the utility of various experimental methods for solving molecular problems. Emphasis is on applications, practical aspects, and experimental design, and on the strengths and limitations of individual methods and complementarities among them.

Instructors: Jannette Carey | Venu Gopal Vandavasi

• 534 Modern Methods for Organic Synthesis (GRAD)

This course exposes you to many types of carbon-based molecular structures, the transformations they undergo, and many kinds of chemical reactions and strategies that are important to the field of organic synthesis. Recent advances in asymmetric catalysis, cascade and other complexity-generating structural transformations, and powerful strategies for chemical synthesis that evolved from ideas about the structural origins of important, biologically active molecules such as steroid hormones, cofactors, and alkaloids are addressed.

Instructors: Robert R. Knowles | David W. MacMillan

• 536 Topics in Organic Chemistry: Methods for Complex Organic Synthesis (GRAD)

This course provides an overview of contemporary methods in synthetic organic chemistry for first year graduate students and advanced undergraduates. Special emphasis is placed on understanding the mechanisms, scope, limitations, and selectivities of some of the most important synthetic methodologies developed in the 21st century. Selected topics include advances in cross coupling, olefin metathesis, pi acid catalysis, organocatalysis, photocatalysis, pi allyl chemistry, hydrogenation, C-H activation and hydrogen-bonding catalysis.

Instructors: David W. MacMillan

• 539 Introduction to Chemical Instrumentation (GRAD)

This course covers the application of selected analytical instrumentation to modern chemical/biochemical research, including materials science and environmental and medicinal chemistry. Primary emphasis: NMR methods; advantages and applications of cryoprobe-assisted high sensitivity 13C-NMR spectroscopy; data processing and spectrum analysis; integration with mass spectrometry; X-ray diffraction; IR, UV, and EPR spectroscopy; chiroptical techniques. Practical problem solving exercises for identification and characterization of molecular structure and dynamics using in-house examples are a significant part of the curriculum.

Instructors: István Pelczer

• 541 Chemical Biology II (GRAD)

The course provides an in depth treatment of biopolymer chemistry and natural products biosynthesis. Topics include: nucleic acid and protein chemistry; biopolymer engineering; the logic and enzymology of natural product biosynthesis with a focus on non-ribosomal peptide synthetases and polyketide synthases.

Instructors: Ralph E. Kleiner | Mohammad R. Seyedsayamdost
Cross listed classes: QCB 541

• 542 Principles of Macromolecular Structure: Protein Folding, Structure and Design (GRAD)

This course is taught from the scientific literature. We begin the semester with several classic papers on protein folding. As the semester progresses, we read about protein structure, stability, and folding pathways. The latter part of the semester focuses on recent papers describing new research aimed toward the construction of novel proteins from "scratch." These papers cover topics ranging from evolution in vitro to computational and rational design. The course ends by discussing the possibility of creating artificial proteomes in the laboratory, and further steps toward synthetic biology.

Instructors: Michael H. Hecht
Cross listed classes: MOL 542

• 544 Metals in Biology: From Stardust to DNA (GRAD)

Life processes depend on over 25 elements whose bioinorganic chemistry is relevant to the environment (biogeochemical cycles), agriculture, and health. CHM 544 surveys the bioinorganic chemistry of the elements. In-depth coverage of key transition metal ions including manganese, iron, copper, and molybdenum focuses on redox roles in anaerobic and aerobic systems and metalloenzymes that activate small molecules and ions, including hydrogen, nitrogen, nitrate, nitric oxide, oxygen, superoxide, and hydrogen peroxide. Appreciation of the structure and reactivity of metalloenzyme systems is critical to understanding life at the molecular level.

Instructors: John T. Groves
Cross listed classes: ENV 544

- GEOSCIENCES -

• 418 Environmental Aqueous Geochemistry (UGRD)

Application of quantitative chemical principles to the study of natural waters. Includes equilibrium computations, carbonate system, gas exchange, precipitation/dissolution of minerals, coordination of trace metals, redox reactions in water and sediments.

Instructors: Anne M. Kraepiel-Morel
Cross listed classes: CHM 418

- INTEGRATED SCIENCE CURRICULUM -

• 233 An Integrated, Quantitative Introduction to the Natural Sciences II (UGRD)

An integrated, mathematically and computationally sophisticated introduction to physics and chemistry, drawing on examples from biological systems. This year long, four course sequence is a multidisciplinary course taught across multiple departments with the following faculty: T. Gregor, J. Shaevitz (PHY); O. Troyanskaya (COS); J. Akey (EEB); E. Wieschaus, M. Wuhr (MOL); S. Biswas, J. Gadd, A., Kalra, O. Kimchi, A. Mayer, H. McNamara, C. Yuste (LSI). Five hours of lecture, one three-hour experimental lab, one three-hour computational lab.

Instructors: Gregory D. Scholes | Joshua W. Shaevitz | Olga G. Troyanskaya | Cara Mary Weisman
Cross listed classes: CHM 233 | COS 233 | MOL 233 | PHY 233

• 234 An Integrated, Quantitative Introduction to the Natural Sciences II (UGRD)

An integrated, mathematically and computationally sophisticated introduction to physics and chemistry, drawing on examples from biological systems. This year long, four course sequence is a multi-disciplinary course taught across multiple departments with the following faculty: T. Gregor, J. Shaevitz (PHY); O. Troyanskaya (COS); J. Akey (EEB); E. Wieschaus, M. Wuhr (MOL); J. Gadd, B. Husic, O. Kimchi, A. Mayer, H. McNamara (LSI). Five hours of lecture, one three-hour experimental lab, one three-hour computational lab.

Instructors: Gregory D. Scholes | Joshua W. Shaevitz | Olga G. Troyanskaya | Cara Mary Weisman
Cross listed classes: CHM 234 | COS 234 | MOL 234 | PHY 234

- MOLECULAR BIOLOGY -

• 345 Biochemistry (UGRD)

This course focuses on the fundamental biochemical principles that underlie cellular function. An emphasis will be placed on protein structure, function, and regulation. Additional topics covered will include metabolism and catalysis, and cutting-edge methodologies for studying macromolecules in health and disease systems.

Instructors: Ana Mostafavi | Nieng Yan
Cross listed classes: CHM 345

- MATERIALS SCIENCE AND ENGR -

• 504 Monte Carlo and Molecular Dynamics Simulation in Statistical Physics & Materials Science (GRAD)

This course examines methods for simulating matter at the atomistic scale with emphasis on the concepts that underline modern computational methodologies for classical many-body systems at or near statistical equilibrium. The course covers Monte Carlo and Molecular Dynamics (from basics to advanced techniques), and includes an introduction to ab-initio Molecular Dynamics and the use of Machine Learning techniques in molecular simulations.

Instructors: Roberto Car
Cross listed classes: CHM 560 | PHY 512 | CBE 520