CHEM 5020a, Fundamentals of Transition Metal Chemistry  James Mayer

This half-term course covers the structures and properties of coordination compounds, and strategies for the design and analysis of new compounds. Elements of chelating ligands, spectroscopic methods, and magnetism are addressed. Prerequisites: two terms of organic chemistry and one term of inorganic chemistry (CHEM 252 or equivalent).  ½ Course cr
TTh 9am-10:15am

CHEM 5030b, Fundamentals of Organometallic Chemistry  Nilay Hazari

A half-term survey of the main principles of organometallic chemistry that enables students to understand basic concepts in the field. It prepares students for CHEM 504, the second half of this course. Prerequisites: two terms of organic chemistry and one term of inorganic chemistry (CHEM 252) or equivalent experience.  ½ Course cr
MW 9am-10:15am

CHEM 5060a, Bioinorganic Spectroscopy  Gary Brudvig

This course is an advanced introduction to biological inorganic chemistry with an emphasis on the methods used to characterize the active sites of metalloproteins. The major physical methods used in the determination of molecular structure, bonding, and physical properties of metal ions in proteins are introduced. Prerequisite: a general knowledge of biochemistry and familiarity with both inorganic coordination chemistry and physical chemistry.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5070a, Bioinorganic Mechanisms  Gary Brudvig

This course is an advanced introduction to biological inorganic chemistry. An overview of the relevant geometric and electronic structures of metalloprotein active sites is presented and related to each protein’s function. The objective is to define and understand the function of metals in biology in terms of structure. Prerequisite: CHEM 506 or permission of the instructor. It is assumed that students have a general knowledge of biochemistry and are familiar with both inorganic coordination chemistry and physical chemistry.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5080a, Materials Chemistry I: Structures and Properties  Hailiang Wang

This course is an advanced introduction to materials chemistry. It aims to serve senior undergraduates who are interested in learning and applying chemical principles for materials research and applications. Fundamental principles in solid-state chemistry, including crystal structures and chemical interactions, are taught. Ionics, metal, semiconductor, and polymer materials, including their synthesis, structures, properties, and applications, are discussed. Prerequisites: general chemistry, inorganic chemistry, and physical chemistry, or equivalent experience.  ½ Course cr
MW 9am-10:15am

CHEM 5090a, Materials Chemistry II: Characterization Techniques  Hailiang Wang

This course aims to serve graduate and senior undergraduate students from various academic departments who are interested in learning advanced chemistry for performing materials-related research. Material characterization techniques including X-ray/electron diffraction, electron microscopy and integrated spectroscopy, scanning probe microscopy, X-ray spectroscopy (both lab and synchrotron based), and vibrational spectroscopy (including in-situ techniques) are introduced and discussed, with the focus on understanding fundamental structure-property correlations. Prerequisites: Undergraduate level general chemistry, inorganic chemistry, and physical chemistry, or equivalent level of knowledge.  ½ Course cr
MW 9am-10:15am

CHEM 5100b, Materials Chemistry III: Electrochemistry for Energy and Environment  Hailiang Wang

This course aims to serve graduate and senior undergraduate students from various academic departments who are interested in learning electrochemistry and its related materials chemistry for performing energy and environmental research. The most important task of this course is to discuss and understand how the properties of electrochemical energy storage and conversion devices are fundamentally determined by their chemistry. Battery and electrocatalytic reactions that are of current research focus are introduced and discussed in detail. State-of-the-art materials development, structural characterization, electrochemical reaction studies, mechanistic investigation, and reactor engineering related to these reactions are also be covered. Prerequisites: undergraduate-level general chemistry (CHEM 161 and CHEM 165 or CHEM 163 and CHEM 167), inorganic chemistry (CHEM 252), and thermodynamics/physical chemistry (CHEM 332) or equivalent level of knowledge.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5110b, Fundamentals of Chemical Crystallography and Diffraction  Brandon Mercado

Accurate and precise structure models of small molecules provide critical insight into the function and properties of materials. This course introduces the principles of chemical crystallography, focusing on structure determination by X-ray diffraction. Key topics include diffraction geometry, symmetry elements, space group theory, and solving “the phase problem.” With the growing role of electron crystallography in structural analysis, the course will also introduce Microcrystal Electron Diffraction (MicroED) as a complementary technique for determining structures from nanocrystalline materials. By the end of the course, students will have a solid foundation in diffraction principles, including an understanding of how and why crystals produce diffraction patterns. They will develop an appreciation for the chemical significance of these patterns and the distinct advantages and challenges of using X-rays versus electrons to probe crystalline materials. Prerequisite: inorganic chemistry, CHEM 502, or permission of the instructor.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5120b, Crystal Structure Refinement in Chemical Crystallography  Brandon Mercado

Determining the connectivity of atoms in unknown compounds is a fundamental challenge in chemistry. This course focuses on the practical aspects of structure modeling and refinement from diffraction data, covering topics such as visualizing electron density, handling molecular disorder, addressing twinning, and preparing results for publication. In addition to single crystal X-ray diffraction, students will explore electron crystallography techniques, with a focus on Microcrystal Electron Diffraction (MicroED) for structure determination of nanometer to micron-sized crystals. By the end of the course, students will have hands-on experience in interpreting and refining structural data across multiple diffraction methods. They will be equipped to critically evaluate both their own structure models and those published in the literature and structural databases, gaining the expertise needed for high-quality crystallographic analysis. Prerequisite: CHEM 511 or permission of the instructor.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5140b, Molecular Materials: Design, Synthesis, and Properties  Amymarie Bartholomew

Materials synthesized from molecular building blocks have an extraordinary range of properties (porosity, magnetism, conductivity, and combinations thereof, etc.), which depend on the molecular components and the manner in which they are assembled. This course introduces ways to understand and predict the properties of molecularly derived materials from their constituent molecules and their covalent, ionic, or spatial interactions upon assembly. The course also introduces techniques used to synthesize and study molecular materials, with the goal of providing students with a holistic understanding of research in this field. Prerequisite: Fundamentals of Transition Metal Chemistry (CHEM 402) or permission of the instructor.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5160a, Organic Structure and Energetics  William Jorgensen

The course covers concepts in physical organic chemistry including molecular structure and bonding, conformational energetics, electronic effects, thermochemistry, ring strain, noncovalent interactions, molecular recognition, and host-guest chemistry. Prerequisites: two terms of organic chemistry and two terms of physical chemistry, or related courses, or permission of the instructor.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5170a, Kinetics and Thermodynamics in Organic Systems  Scott Miller

The course generally follows CHEM 516. This module covers concepts in physical organic chemistry including acid-base chemistry, advanced issues in stereochemistry, kinetics, and thermodynamics, as well as experiments and techniques employed in mechanistic analysis. Issues in catalysis are addressed throughout. Prerequisites: CHEM 516, two terms of introductory organic chemistry, and two terms of physical chemistry. Permission of the instructor may be sought for potential exceptions.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5200a, Chemical Biology of Nucleic Acids  Sarah Slavoff

This course provides a chemical perspective on fundamental concepts and applications in the chemical biology of nucleic acids. Covered topics include nucleic acid synthesis, functional and modified nucleic acids, sequencing, CRISPR/Cas9, and analytical methods. Prerequisites: two terms of organic chemistry.  ½ Course cr
TTh 9am-10:15am

CHEM 5210a, Protein Design and Catalysis  Jason Crawford

The lecture component of this course largely focuses on protein function, catalysis, and the chemistry and biology of diverse small molecule products. The course also serves to support students in writing an effective NSF style research proposal in chemical biology and communicating its contents to a diverse scientific audience. Prerequisites: Two semesters of undergraduate organic chemistry (CHEM 174/175 and/or CHEM 220/221). A basic understanding of biochemistry and molecular biology is also assumed, but you can “catch up” by carefully and thoroughly reading the course materials and recommended books.  ½ Course cr
TTh 9am-10:15am

CHEM 5240a, Chemical Biology of Drug Discovery  David Spiegel

This course explores the design and enablement of medicines derived from a convergence of concepts and techniques from chemistry and biology. Topics include: small molecule drug discovery concepts and tools, drug metabolism, protein therapeutics, hybrid chemical/biologic drugs, and bi-functional molecules. Modern approaches for target discovery and validation are also discussed. The course is not organized around a textbook. Rather, material covered in lectures is the focus of the course and supplementary reading is recommended, mostly from modern research literature. Reading lists are distributed at the outset of the module. Prerequisites: two terms of undergraduate organic chemistry, biochemistry, and molecular biology.  ½ Course cr
MW 9am-10:15am

CHEM 5280b, Natural Products Synthesis  Timothy Newhouse

Survey of natural products syntheses, with an emphasis on those that contain unique strategies, transformations, or reagents. Key transformations are introduced in the context of various syntheses. Retrosynthetic analysis and synthetic planning are discussed. Prerequisites: undergraduate organic chemistry and one term of a graduate course in organic chemistry, or permission of the instructor.  ½ Course cr
TTh 9am-10:15am

CHEM 5290b, Total Synthesis  Seth Herzon

This course is conducted as a seminar. The content focuses on modern strategies and tactics in natural product synthesis with a focus on alkaloids, terpenes, and polyketides. One objective of the course is to introduce strategy level decision making considering multiple approaches to retrosynthetic disconnection. Additionally, a wide variety of methodologies are described and discussed with respect to how they can be implemented in total synthesis. The course draws from primary sources in order for students to develop critical reading and writing skills. Prerequisite: one chemistry course at the 500 level or permission of the instructor.  ½ Course cr
TTh 9am-10:15am

CHEM 5320a, Synthetic Methods in Organic Chemistry I  Jon Ellman

Compound synthesis is essential to the discovery and development of new chemical entities with a desired property, whether for fundamental study or a more applied goal such as a new pharmaceutical, agrochemical, or material. In this course we emphasize key transformations and principles to provide a framework for the efficient design and synthesis of organic compounds. Prerequisites: two terms of organic chemistry and one term of introductory inorganic chemistry, or related course, or permission of the instructor.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5330a, Synthetic Methods in Organic Chemistry II  Jon Ellman

Compound synthesis is essential to the discovery and development of new chemical entities with a desired property, whether that be for fundamental study or for a more applied goal such as a new pharmaceutical, agrochemical, or material. In this course we emphasize key transformations and principles to provide a framework for the efficient design and synthesis of organic compounds. This course builds on the knowledge learned in CHEM 532. Prerequisite: CHEM 532 or permission of the instructor.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5350b, Fundamental Medicinal Chemistry  William Jorgensen

The course covers basic concepts of medicinal chemistry including drug structures, properties of drugs, methods of drug discovery, protein-ligand interactions, enzyme inhibition, assays, drug targets, anti-infective agents, virtual and high-throughput screening, structures to avoid (PAINS), structure-based drug design, and metabolism. Prerequisites: undergraduate organic and physical chemistry, or permission of the instructor.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5360b, Computer Simulations of Organic and Biomolecular Systems  William Jorgensen

The course covers methods and applications of statistical mechanics and molecular dynamics to model fluid systems including biomolecules in aqueous solution. Topics covered include force fields, Monte Carlo and molecular dynamics theory, simulation of water and other liquids, free-energy methods and applications, QM/MM simulations, protein dynamics, and molecular recognition and design. Prerequisites: undergraduate organic and physical chemistry, or permission of the instructor.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5600La, Advanced Instrumentation Laboratory I  Patrick Vaccaro

A laboratory course introducing physical chemistry tools used in the experimental and theoretical investigation of large and small molecules. Modules include electronics, vacuum technology, optical spectroscopy and lasers, and computer programming.  ½ Course cr
F 2:30pm-3:20pm

CHEM 5680b, Advanced Quantum Mechanics  Tianyu Zhu

Topics in quantum mechanics that are essential for understanding modern chemistry, physics, and biophysics. Topics include the interaction of radiation with matter and the use of quantized radiation fields and may include time-dependent quantum theory, scattering, semiclassical methods, angular momentum, density matrices, and electronic structure methods. Prerequisite: introductory quantum mechanics or permission of the instructor.  ½ Course cr
TTh 9am-10:15am

CHEM 5720b, Introduction to Statistical Mechanics I  Victor Batista

An introduction to modern statistical mechanics, starting with fundamental concepts of quantum statistical mechanics to establish a microscopic derivation of statistical thermodynamics. Topics include ensembles; Fermi, Bose, and Boltzmann statistics; density matrices; mean-field theories; phase transitions; chemical reaction dynamics; time-correlation functions; Monte Carlo simulations; and molecular dynamics simulations. Prerequisite: physical chemistry, multivariable calculus, or equivalent experience.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5730b, Introduction to Statistical Mechanics II  Victor Batista

An introduction to modern statistical mechanics, starting with fundamental concepts of quantum statistical mechanics to establish a microscopic derivation of statistical thermodynamics. Topics include ensembles; Fermi, Bose, and Boltzmann statistics; density matrices; mean-field theories; phase transitions; chemical reaction dynamics; time-correlation functions; Monte Carlo simulations; and molecular dynamics simulations. Prerequisite: physical chemistry, multivariable calculus, or equivalent experience.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5760a, Fundamentals for Physical Chemistry  Mark Johnson

This course reinforces the principles of physics that are most relevant to experimental and theoretical physical chemistry. These include classical electricity and magnetism (with emphasis on the nature of light and the interaction of light with matter), optics, lasers, angular momentum, and atomic structure, including the spin-orbit interaction. The basic theme of the course is to provide students with physical intuition that can bridge the observations of everyday experience to the abstract concepts required for the correct, quantum-mechanical description of atomic-scale phenomena. Prerequisites: two terms of undergraduate physical chemistry (CHEM 328 or CHEM 332, and CHEM 333; or equivalents); and physics course work covering classical mechanics and electrostatics.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5780a, Molecules and Radiation I: Matrix Methods in Quantum Mechanics  Kurt Zilm

This course is an efficient entry to the study of molecular spectroscopy and provides a broad foundation for chemical physicists, biophysicists, and engineers. It covers a general treatment of the quantum mechanics of spectroscopy and specific applications for time-dependent systems. This course focuses on matrix mechanics, perturbation theory, and angular momentum. Prerequisite: previous exposure to quantum mechanics at the level of physical chemistry, or permission of the instructor.  ½ Course cr
MWF 9:25am-10:15am

CHEM 5800b, Foundations and Applications of Nonlinear Spectroscopy  Staff

Nonlinear spectroscopy encompasses a broad range of techniques, including coherent Raman and pump-probe experiments, that provide rich insight into the structure and dynamics of matter through interactions with multiple and/or intense light fields. The versatility and power of these methods are evident in the wide range of contexts where they are used to investigate the behavior of molecules, macromolecules, materials, and beyond. This course offers a comprehensive introduction to the theoretical framework and experimental approaches of modern nonlinear spectroscopy. Topics include response functions, lineshapes, dynamics, spectral simulations, as well as experimental considerations and implementations, among others. The goal of the course is to develop core concepts that can be applied to the design and interpretation of spectroscopic experiments more generally. Prerequisite: CHEM 5780 or equivalent exposure to matrix mechanics and time-dependent perturbation theory. Though not required, CHEM 5790 is recommended and may be taken concurrently.  ½ Course cr
MW 9am-10:15am

CHEM 5880b, Optical Spectroscopy: Applications in Biophysics  E. Chui-Ying Yan

The course covers basic theory of fluorescence and vibrational spectroscopies and their applications in biophysics. Emphasis is placed on quantitative interpretation of experimental data to gain structural and dynamic information to address biological questions at the molecular level. Topics include fluorescence correlation spectroscopy (FCS); Forster resonance energy transfer (FRET); fluorescence anisotropy; and Raman, infrared, and non-linear optical spectroscopies. Discussions of applications focus on current and classic literature. This course provides foundational knowledge for advanced courses on molecular optical imaging. Prerequisite: undergraduate upper-level physical chemistry or permission of the instructor.  ½ Course cr
MW 9am-10:15am

CHEM 5900a, Ethical Conduct and Scientific Research  Paul Cooper

A survey of ethical questions relevant to the conduct of research in the sciences with particular emphasis on chemistry. A variety of issues, including plagiarism, the falsification of data, and financial malfeasance, are discussed, using as examples recent cases of misconduct by scientists. Enrollment is restricted to graduate students in chemistry.  0 Course cr
M 5:10pm-6pm

CHEM 5920b, Biochemical Rates and Mechanisms I  J Patrick Loria

An advanced treatment of enzymology. Topics include transition state theory and derivation of steady-state and pre-steady-state rate equations. The role of entropy and enthalpy in accelerating chemical reactions is considered, along with modern methods for the study of enzyme chemistry. These topics are supplemented with in-depth analysis of the primary literature. Prerequisites: CHEM 332 or equivalent, two terms of organic chemistry, and MATH 115.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5930b, Biochemical Rates and Mechanisms II  J Patrick Loria

This course focuses on the role of molecular motions in enzyme function, and on biochemical and spectroscopic methods to interrogate these motions. Examples explore motions ranging from picoseconds to milliseconds and how the timescales and amplitudes of these motions impact catalysis and allostery. Prerequisite: CHEM 592 or permission of the instructor.  ½ Course cr
TTh 11:35am-12:50pm

CHEM 5940b, Resonant and Non-Resonant Interaction of Light with Matter  Mark Johnson

This course considers the interaction of light with individual molecules and collections of molecules in solutions and solids from the perspective of a classical radiation field interacting with the energy levels that arise from quantized motions. We begin with the generation of light by accelerated charges as described by Maxwell’s equations for the electric and magnetic fields. We then consider the polarization states of light, how the oscillating electric field drives the motions of electrons, and how this results in scattering when off-resonant and then evolves into shifts in level populations as the frequency approaches that of the eigenenergies between levels. Classical analogies to quantum mechanical behavior are stressed in the context of the damped-driven electron in a harmonic potential (the so-called Drude model). The kinetics of absorption and emission are discussed in the context of the Einstein treatment that leads to light amplification and laser action. Finally, we develop the “selection rules” that describe what transitions can occur depending on the light polarization and the character of the electronic and nuclear motions. Prerequisite: an upper-level undergraduate physics course in electricity and magnetism or CHEM 576.  ½ Course cr
MW 11:35am-12:50pm

CHEM 5950b, Molecular Spectroscopy and Dynamics  Mark Johnson

This course covers the traditional treatment of molecular spectroscopy, including angular momentum coupling and selection rules for electric dipole excitations in atoms and diatomic molecules. It also explores vector aspects of the interaction of light with molecules in the molecular frame, which involves consideration of the polarization states of the light beam. Polyatomic molecules expand the complexity of the interactions through introduction of normal modes and anharmonic couplings both within the ground electronic state and between electronic states. That background is then leveraged to explore intra- and inter-molecular energy flow in molecules when isolated in the gas phase or immersed in solvent. Prerequisite: one graduate-level course in quantum mechanics and/or one semester of molars.  ½ Course cr
MW 11:35am-12:50pm

CHEM 6000a, Research Seminar  Staff

Presentation of a student’s research results to the student’s adviser and fellow research group members. Extensive discussion and literature review are normally a part of the series.
HTBA

CHEM 7200a, Current Topics in Organic Chemistry  Jon Ellman

A seminar series based on invited speakers in the general area of organic chemistry.
HTBA

CHEM 7300a, Theoretical Chemistry Seminar  Tianyu Zhu

A seminar series based on invited speakers in the areas of theoretical chemistry.
HTBA

CHEM 7400a, Seminar in Chemical Biology  Jon Ellman

Seminar in Chemical Biology for graduate level students None
HTBA

CHEM 7500a, Biophysical and Physical Chemistry Seminar  J Patrick Loria

A seminar series based on invited speakers in the areas of biophysical and physical chemistry.
HTBA

CHEM 7600a, Seminar in Inorganic Chemistry  Nilay Hazari

Seminar for graduate students in the inorganic research area of chemistry - invited speakers of this discipline None
HTBA

CHEM 9800a, Introduction to Research for Long Rotations  Staff

During the fall term, first year chemistry graduate students in long rotations are introduced to research during their first laboratory rotation. At the end of the first rotation, students in the course present an oral presentation on their research. The presentation is no longer than ten minutes with a question-and-answer period of no longer than five minutes. Enrollment requires that a student be a first-year graduate student participating in long rotations.
HTBA

CHEM 9900a, Research  Staff

Individual research for Ph.D. degree candidates in the Department of Chemistry, under the direct supervision of one or more faculty members.
HTBA