Courses

CHEM 100(F) LEC Chemistry Matters

Chemistry matters! From fueling the world's economy to preventing the next pandemic to forecasting future climate change, chemistry touches all aspects of daily life. This course provides an introduction to chemical principles and applications for students with little or no high school chemistry background. Through the lens of contemporary issues and applications (e.g. energy, environment, materials, medicine, etc.), students will be introduced to concepts fundamental to studying matter at the molecular level. Particular emphasis will be placed on skills essential for students to understand chemistry in these contexts, including quantitative reasoning and the development of chemical literacy and intuition. Laboratory meetings will be used to reinforce lecture material through experimentation at the bench and active learning exercises. [ more ]

CHEM 101(F, S) LEC Concepts of Chemistry

This course broadens and deepens the foundation in chemistry of students who have had one or more years of chemistry at the high school level. Most students begin study of chemistry at Williams with this course. Familiarity with stoichiometry, basic concepts of equilibria, the model of an atom, Lewis structures and VSEPR, and gas laws is expected. Principal topics for this course include modern atomic theory, molecular structure and bonding, states of matter, chemical equilibrium (acid-base and solubility), and an introduction to atomic and molecular spectroscopies. Laboratory periods will largely focus on experiment design, data analysis, literature, scientific writing, and other skills critical to students' development as scientists. The course is of interest to students who anticipate professional study in chemistry, related sciences, or one of the health professions, as well as to those who want to explore the fundamentals of chemistry as part of their general education. This course may be taken pass/fail; however, students who are considering graduate study in science or in the health professions should elect to take this course for a grade. [ more ]

CHEM 114 LEC The Science Behind Materials: Shaping the Past and Future of Society

Last offered Spring 2022

We are surrounded by materials. They have fulfilled human needs since ancient times. From Phoenician glass to flexible OLED displays, materials have impacted society and changed the way humans lead their lives. What makes materials the way they are? Why are some brittle while others are ductile? How can we design materials with specific properties that will solve tomorrow's problems? To answer these questions, we have to think about materials at the atomic scale, looking at how their smallest building blocks organize into specific structures. In this course, we will explore the relationships between structure, processing, and properties for a range of materials including metals, ceramics, polymers, and composites. We will talk about some of the cutting-edge research that materials scientists are working on today, concluding with an outlook to potential applications of emerging technologies. [ more ]

CHEM 115 LEC AIDS: The Disease and Search for a Cure

Last offered Fall 2023

Since the discovery of the human immunodeficiency virus (HIV-1) in 1983, modern techniques of molecular biology have revealed much about its structure and life cycle. The intensity of the scientific investigation directed at HIV-1 is unprecedented in history. We now know more about this virus than any other pathogen. However, the early optimism concerning the prospects for an effective AIDS vaccine has not yet materialized, and HIV strains that are resistant to drug therapies are common. We are now four decades into the AIDS pandemic, and the World Health Organization estimates that there are more than 38 million HIV-infected persons worldwide. After an introduction to chemical structure, we examine the molecular biology of the HIV virus, the molecular targets of anti-HIV drugs, and the prospects for a cure. We look at how HIV-1 interacts with the human immune system and discuss strategies for developing an effective HIV vaccine. [ more ]

CHEM 117 LEC Roses are Red, Violets are Blue: The Origins, Perception, and Impact of Color

Last offered Spring 2021

Have you ever been tickled pink? Felt blue? Seen red?, Been green with envy? The course will consider color, starting with the physical and chemical origins of color (the electromagnetic spectrum, the absorption and emission of electromagnetic radiation, refraction, diffraction, incandescence, fluorescence, phosphorescence, iridescence). We will develop an understanding of chemical bonding and how that influences color. We will cover how we measure and describe color from a scientific perspective as well as how we can generate materials and devices with different color properties (liquid crystal displays, light emitting diodes for instance). From there we will discuss pigments used in works of art and textiles over time, the characteristics that make certain pigments suitable for particular applications. If we have time, we will touch on the historical and cultural impacts and meanings of different pigments and hues, the biological perception of color, and some color theory. [ more ]

CHEM 200(S) LEC Advanced Chemical Concepts

This course treats an array of topics in modern chemistry, emphasizing broad concepts that connect and weave through the various subdisciplines of the field--biochemistry, inorganic chemistry, organic chemistry, and physical chemistry. It provides the necessary background in chemical science for students who are planning advanced study or a career in chemistry, biological science, geoscience, environmental science, or a health profession. Topics include coordination complexes, thermodynamics, electrochemistry, and kinetics. Laboratory sections will give students hands-on experience involving synthesis, characterization, and reactivity studies of coordination and organic complexes; spectroscopic analyses; thermodynamics; electrochemistry; and kinetics. Students will hone their skills in the presentation of results through written reports and worksheets. [ more ]

CHEM 201(F) LEC Organic Chemistry: Introductory Level

This course provides the necessary background in organic chemistry for students who are planning advanced study or a career in chemistry, the biological sciences, or the health professions. It initiates the systematic study of the common classes of organic compounds with emphasis on theories of structure and reactivity. Specific topics include basic organic structures and bonding, delocalization and conjugation, acidity & basicity, nucleophilic addition and substitution reactions, stereochemistry and molecular energetics. The theory and interpretation of infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy, as well as the fundamentals of molecular modeling as applied to organic molecules are presented. The coordinated laboratory work includes organic synthesis, purification and separation techniques, as well as characterization by IR and NMR spectroscopy. [ more ]

CHEM 242(S) LEC Organic Chemistry: Intermediate Level

This course is a continuation of CHEM 156/201 and it concludes the systematic study of the common classes of organic compounds with emphasis on theories of structure and reactivity. Specific topics include radical chemistry, an introduction to mass spectrometry and ultraviolet spectroscopy, the theory and chemical reactivity of conjugated and aromatic systems, the concepts of kinetic and thermodynamic control, an extensive treatment of the chemistry of the carbonyl group, alcohols, ethers, polyfunctional compounds, the concept of selectivity, the fundamentals of organic synthesis, an introduction to carbohydrates, carboxylic acids and derivatives, acyl substitution reactions, amines, and an introduction to amino acids, peptides, and proteins. The coordinated laboratory work includes application of the techniques learned in the introductory level laboratory, along with new functional group analyses, to the separation and identification of several unknown samples. Skills in analyzing NMR, IR, and MS data are practiced and further refined. [ more ]

CHEM 319 SEM Integrative Bioinformatics, Genomics, and Proteomics Lab

Last offered Spring 2023

What can computational biology teach us about cancer? In this lab-intensive experience for the Genomics, Proteomics, and Bioinformatics program, computational analysis and wet-lab investigations will inform each other, as students majoring in biology, chemistry, computer science, mathematics/statistics, and physics contribute their own expertise to explore how ever-growing gene and protein data-sets can provide key insights into human disease. In this course, we will take advantage of one well-studied system, the highly conserved Ras-related family of proteins, which play a central role in numerous fundamental processes within the cell. The course will integrate bioinformatics and molecular biology, using database searching, alignments and pattern matching, and phylogenetics to reconstruct the evolution of gene families by focusing on the gene duplication events and gene rearrangements that have occurred over the course of eukaryotic speciation. By utilizing high through-put approaches to investigate genes involved in the inflammatory and MAPK signal transduction pathways in human colon cancer cell lines, students will uncover regulatory mechanisms that are aberrantly altered by siRNA knockdown of putative regulatory components. This functional genomic strategy will be coupled with independent projects using phosphorylation-state specific antisera to test our hypotheses. Proteomic analysis will introduce the students to de novo structural prediction and threading algorithms, as well as data-mining approaches and Bayesian modeling of protein network dynamics in single cells. Flow cytometry and mass spectrometry may also be used to study networks of interacting proteins in colon tumor cells. [ more ]

CHEM 321(F) LEC Biochemistry I: Structure and Function of Biological Molecules

This course introduces the foundational concepts of biochemistry with an emphasis on the structure and function of biological macromolecules. Specifically, the structure of proteins and nucleic acids are examined in detail in order to determine how their chemical properties and their biological behavior result from those structures. Other topics covered include catalysis, enzyme kinetics, mechanism and regulation; the molecular organization of biomembranes; and the flow of information from nucleic acids to proteins. In addition, the principles and applications of the methods used to characterize macromolecules in solution and the interactions between macromolecules are discussed. The laboratory provides a hands-on opportunity to study macromolecules and to learn the fundamental experimental techniques of biochemistry including electrophoresis, chromatography, and principles of enzymatic assays. [ more ]

CHEM 322(S) LEC Biochemistry II: Metabolism

This lecture course provides an in-depth presentation of the complex metabolic reactions that are central to life. Emphasis is placed on the biological flow of energy including alternative modes of energy generation (aerobic, anaerobic, photosynthetic); the regulation and integration of the metabolic pathways including compartmentalization and the transport of metabolites; and biochemical reaction mechanisms including the structures and mechanisms of coenzymes. This comprehensive study also includes the biosynthesis and catabolism of small molecules (carbohydrates, lipids, amino acids, and nucleotides). Laboratory experiments introduce the principles and procedures used to study enzymatic reactions, bioenergetics, and metabolic pathways. [ more ]

CHEM 324 LEC Enzyme Kinetics and Reaction Mechanisms

Last offered Fall 2023

Enzymes are complex biological molecules capable of catalyzing chemical reactions with very high efficiency, stereo-selectivity and specificity. The study of enzymatically-catalyzed reactions gives insight into the study of organic reaction mechanisms in general, and into the topic of catalysis especially. This course explores the methods and frameworks for determining enzymatic reaction mechanisms. These methods are based on a firm foundation of organic reaction mechanisms and chemical kinetics. We will investigate the major types of biochemical reactions, focusing on their catalytic mechanisms and how those mechanisms can be elucidated. We will lay the foundation for this mechanistic consideration with discussion of transition state theory, structure-reactivity relationships, steady state and pre-steady kinetics, use of isotopes, genetic modification, and other tools for probing enzymatic reactions. We will also examine the catalytic roles of a variety of vitamins and cofactors. [ more ]

CHEM 326 SEM Chemical and Synthetic Biology

Last offered Spring 2024

This course surveys the rapidly evolving, interdisciplinary and interconnected fields of chemical and synthetic biology. Chemical biology uses precise molecular-level manipulations to influence living systems from the bottom up, often by introducing components that are foreign to nature. Synthetic biology takes advantage of existing molecular technology and adopts an engineering mindset to reprogram life. Students will achieve literacy through immersion in chemical and synthetic biology. We will prioritize broad exposure to these fields, their vocabulary, culture, practices and ideas, through extensive engagement with the primary literature that expert practitioners use to teach themselves. The course model is instructor-facilitated peer-to-peer instruction, emphasizing skills important for autonomous and collaborative work in real-world scientific and professional fields. Topics we will cover include synthetic genomes, metabolic engineering, chemical synthesis and manipulation of biomacromolecules, directed evolution, and reworking of the central dogma of biology. [ more ]

CHEM 335(S) LEC Inorganic/Organometallic Chemistry

This course covers fundamental aspects of the chemistry of main group elements and transition metals, and highlights how these properties are key to understanding the roles of these elements in applications such as the catalysis of synthetic organic transformations, the functions of enzymatic processes, the production of commodity chemicals such as plastics, and the actions of metal-based drugs such as cis-platin. The course introduces concepts of symmetry and group theory, and their systematic application to the study of the structure, bonding, and spectroscopy of inorganic and organometallic compounds. The course also covers the kinetics and mechanism of selected inorganic and organometallic reactions. Class discussions will involve exploration of the primary literature and review articles around recent developments and applications in inorganic chemistry, such as finding molecular solutions to water oxidation, the capture of solar energy, to cancer treatments and the optimization of industrial-scale reactions. [ more ]

CHEM 336(F) LEC Materials Chemistry

Materials have defined much of what is possible in our daily lives. Materials scientists are at the center of imagining and delivering progress, as they improve existing materials and develop new ones to meet today's needs. Materials science focuses on the relationships between the structure, processing, properties, and performance of materials. In this course, we will explore how the properties and potential applications of a solid are related to its atomic and molecular structure, as well as to its organization on larger length scales than are traditionally considered in chemistry. We will cover a variety of different types of materials including metals, ceramics, polymers, and composites. We will examine some of the latest developments in materials science, including new strategies for the synthesis of materials on different length scales, as well as a variety of potential applications of emerging technologies. [ more ]

CHEM 338 TUT Bioinorganic Chemistry: Metals in Living Systems

Last offered Spring 2021

Bioinorganic chemistry is an interdisciplinary field that examines the role of metals in living systems. Metals are key components of a wide range of processes, including oxygen transport and activation, catalytic reactions such as photosynthesis and nitrogen-fixation, and electron-transfer processes. Metals furthermore perform regulatory roles and stabilize the structures of proteins. In medical applications, they are central to many diagnostic and therapeutic tools, and some metals are highly toxic. The course begins with a review and survey of the principles of coordination chemistry: topics such as structure and bonding, spectroscopic methods, electrochemistry, kinetics and reaction mechanisms. Building on this fundamental understanding of the nature of metals, we will explore the current literature in fields of interest in small groups, presenting our findings to the class periodically. [ more ]

CHEM 342 LEC Synthetic Organic Chemistry

Last offered Spring 2024

The origins of organic chemistry are to be found in the chemistry of living things and the emphasis of this course is on the chemistry of naturally-occurring compounds. This course presents the logic and practice of chemical total synthesis while stressing the structures, properties and preparations of terpenes, polyketides and alkaloids. Modern synthetic reactions are surveyed with an emphasis on the stereochemical and mechanistic themes that underlie them. To meet the requirements for the semester's final project, each student chooses an article from the recent synthetic literature and then analyzes the logic and strategy involved in the published work in a final paper. A summary of this paper is also presented to the class in a short seminar. There will be no laboratory component in 2022. Instead, one of the three class meetings each week will focus on discussion and presentation of reactions, mechanisms, and syntheses from the chemical literature. [ more ]

CHEM 344(S) LEC Physical Organic Chemistry

The structure of a molecule is inherently linked to its reactivity, and these correlations form the basis for understanding organic reaction mechanisms. This course advances the understanding from previous organic courses through a detailed examination of the concepts that underlie these structure/reactivity relationships, including molecular strain and stability, acid/base chemistry, steric and electronic effects, and aromaticity. These concepts will also be explored in the context of specific classes of reaction mechanisms. Classical and modern experimental and theoretical tools used to elucidate reaction mechanisms will also be presented, including reaction kinetics, isotope effects, and linear free energy relationships. By studying the primary literature, we will see how these experiments have been applied to the elucidation of reaction mechanism, while also learning to design a set of experiments for study of mechanisms of contemporary interest. [ more ]

CHEM 345 LEC Supramolecular Organic Chemistry

Last offered Fall 2022

Supramolecular chemistry is the study of chemical systems, often with practical applications, that are composed of two or more molecular components held together by non-covalent interactions. More specifically, we will focus on the use of "synthetic influence" over organic compounds and reactions to make tailor-made building blocks that will produce functional molecular assemblies. The various analytical methodologies used to probe these relatively weaker and more dynamic chemical systems will be studied. We will also examine (and be inspired by) the supramolecular chemistry found in nature, as the field was originally defined by the host-guest interactions used to explain receptor-substrate binding in many biological systems. Today, the field has intersected with numerous disciplines which we will explore; these include analytical molecular recognition and sensing, self-assembly molecular engineering, catalysis, and organic-based molecular devices, among others. We will also explore more complex supramolecular topics such as dynamic covalent chemistry and the mechanical bond. Students will be expected to delve into the chemical literature and analyze the research of pioneering chemists in the field (past and present) by choosing one prominent journal article, culminating in a final literature review paper. [ more ]

Taught by: Michael Ihde

Catalog details

CHEM 348(S) LEC Polymer Chemistry

From synthetic to natural macromolecules, we encounter polymers everywhere and every day. This course explores the multitude of synthetic techniques available and discusses how structure defines function. Topics include polymer types, concept of molecular weight, structure-property relationships and polymer synthesis methods including condensation and chain (anionic, cationic, radical) polymerizations. Fundamentals of composition and physical properties of polymers, and methods of characterization are also covered. Examples of polymer functionalization, self-assembly, and surface modification are also discussed. [ more ]

CHEM 361(S) LEC Quantum Chemistry and Chemical Dynamics

This course introduces quantum mechanics, which serves as the basis for understanding molecular structure and spectroscopy. We will begin by discussing the Schrodinger wave equation and then apply this to understanding the translational, vibrational, and rotational structure of molecules. This leads to a discussion of atomic/molecular electronic structure and spectroscopy. Computational methods will be taught to illustrate key quantum mechanical concepts, interpret experimental data, and extend hypotheses. Applications will be chosen from contemporary research fields, including photochemistry, laser spectroscopy, environmental/atmospheric chemistry, organometallic chemistry, and physical organic chemistry. [ more ]

CHEM 363(F) LEC Environmental Fate of Organic Chemicals

This course introduces students to the methods used to assess the risks posed by organic chemicals to human, animal, and ecosystem health. Our goal is to develop a quantitative understanding for how specific features of organic molecular structure directly dictate a given molecule's environmental fate. We will begin by using thermodynamic principles to estimate the salient physiochemical properties of molecules (e.g., vapor pressure, solubility, charging behavior, etc.) that impact the distribution, or partitioning, of organic chemicals between air, water, soils, and biota. Then, using quantitative structure activity relationships, we will predict the degradation kinetics resulting from natural nucleophilic, photochemical, and biological processes that determine chemical lifetime in the environment. [ more ]

CHEM 364 LEC Instrumental Methods of Analysis

Last offered Spring 2024

Instrumental methods of analysis provide scientists with different lenses to observe and elucidate fundamental chemical phenomena and to measure parameters and properties at the atomic, molecular, and bulk scales. This course introduces a framework for learning about a variety of instrumental techniques that typically include chromatography, mass spectrometry, thermal methods, atomic and molecular absorption and emission spectroscopy, X-ray diffraction, and optical and electron microscopies. Students complete laboratory projects and gain hands-on experience and project planning skills to study molecules and materials of interest. This practical experience is complemented by lectures that cover the theory and broader applications of these techniques. Students also explore the primary literature and highlight recent advances in instrumental methods that address today's analytical questions. The skills learned are useful in a wide variety of scientific areas and will prepare you well for research endeavors. [ more ]

CHEM 366(F) LEC Thermodynamics and Statistical Mechanics

The thermodynamic laws provide us with our most powerful and general scientific principles for predicting the direction of spontaneous change in physical, chemical, and biological systems. This course develops the concepts of energy, entropy, free energy, temperature, heat, work, and chemical potential within the framework of classical and statistical thermodynamics. The principles developed are applied to a variety of problems: chemical reactions, phase changes, energy technology, industrial processes, and environmental science. Laboratory experiments provide quantitative and practical demonstrations of the theory of real and ideal systems studied in class. [ more ]

CHEM 367(S) LEC Biophysical Chemistry

In this course, physical chemistry concepts are presented from the viewpoint of their practical application to a set of biochemical problems, which are explored side-by-side in the lecture and highly-integrated lab program. Major emphasis is placed on quantitative thermodynamic models of equilibrium processes, and students will learn how to develop and apply mathematical models to data. The main topics covered include: 1) conformations of biological macromolecules and the forces that stabilize them; 2) spectroscopic techniques for the study of structure and function; and 3) macromolecular interactions and binding. [ more ]

CHEM 368 TUT Computational Chemistry and Molecular Spectroscopy

Last offered Spring 2024

This tutorial provides an introduction to the principles of computational quantum mechanics and their application to problems of chemical interest such as chemical bonding, chemical reactivity, and molecular spectroscopy. Emphasis is placed upon modern electronic structure calculations, their fundamentals, practical considerations, interpretation, and applications to current research questions. Under guidance in sessions and through independent work, students will use computational methods to explore assigned weekly research problems. The research results will be presented to and discussed with the tutorial partner at the end of each week. [ more ]

Taught by: TBA

Catalog details

CHEM 493(F) HON Senior Research and Thesis

Individual research projects in a field of interest to the student are carried out under the direction of a faculty member and culminate in a thesis; this is part of a full-year thesis (493-494). Students in this program are strongly encouraged to keep 1:10 p.m. to 2:25 p.m. on Friday free for departmental colloquia. [ more ]

CHEM 494(S) HON Senior Research and Thesis

Individual research projects in a field of interest to the student are carried out under the direction of a faculty member and culminate in a thesis; this is part of a full-year thesis (493-494). Students in this program are strongly encouraged to keep 1:10 p.m. to 2:25 p.m. on Friday free for departmental colloquia. [ more ]

CHEM 497(F) IND Independent Study, for Seniors: Chemistry

Chemistry independent study for seniors. Individual research projects in a field of interest to the student are carried out under the direction of a faculty member. [ more ]

CHEM 498(S) IND Independent Study, for Seniors: Chemistry

Chemistry independent study for seniors. Individual research projects in a field of interest to the student are carried out under the direction of a faculty member. [ more ]