CHEM 113Chemistry and Crime: From Sherlock Holmes to Modern Forensic Science

Last offered Fall 2017

In this course, designed for students who do not plan to major in the natural sciences, we use a case-oriented approach to explore selected topics of forensic science. These include: (1) the scientific and technological foundation for the examination of physical, chemical, and biological items of evidence, and (2) the scope of expert qualifications and testimony, the legal status of scientific techniques, and the admissibility of the results in evidence. The analysis of trace evidence, including glass, soil, gunpowder residues and bullet fragments, and inorganic and heavy metal poisons are discussed through an understanding of the basic concepts of chemistry and analytical chemistry. Forensic toxicology and pharmacology are applied to the analysis of alcohol, poisons, and drugs based upon the principles of organic chemistry and biochemistry. The characterization of blood and other body fluids necessitate an understanding of serology and molecular genetics. The cases which stimulate the exploration of these areas include: the John and Robert Kennedy assassinations, the Jeffrey MacDonald case (Fatal Vision), the Wayne Williams case, the deaths of celebrities Marilyn Monroe, John Belushi, and Janis Joplin, the authenticity of the Shroud of Turin, the Casey Anthony case, the Tylenol poisonings, and the identity of Anastasia. Interactive demonstration sessions provide an appreciation of scientific experimentation in general and the work of a crime lab in particular. It includes an analysis of evidence and provides an opportunity to learn forensic techniques such as chromatography (for ink, drug, and fire accelerant analysis), spectroscopy (for alcohol and drug analysis), and electrophoresis (for DNA fingerprinting). [ more ]

CHEM 115AIDS: The Disease and Search for a Cure

Last offered Fall 2018

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 known pathogen. However, the early optimism concerning the prospects for an effective AIDS vaccine has now waned and HIV strains that are resistant to drug therapies are common. We are now three decades into the AIDS pandemic and the World Health Organization estimates that there are more than 34 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 prospects for developing an effective HIV vaccine. [ more ]

CHEM 116Chemistry and Physics of Cooking

Last offered Spring 2016

Cooking is a creative and artistic process, but it is based on fundamental chemical and physical principles. In this course, which is intended for students who do not plan to major in the natural sciences, we explore these scientific principles and their application to the kitchen. We draw on edible examples such as chemical bonding and intermolecular forces (salting, emulsification, and spherification), acid-base chemistry (leavening, making jam, and macaroni and cheese), kinetics and thermodynamics (cooking styles and times), states of matter (carbonation, ices, foams, and gels), types of chemical reactions (baking bread, grilling vegetables, tenderizing meat), and energy transfer (kitchen equipment and gadgets). The kitchen is a laboratory--in the classroom, we carry out experiments to demonstrate and to test these scientific concepts. This course also considers the science behind contemporary ideas in cooking known as "modernist cuisine" and/or "molecular gastronomy". Bon appetit! [ more ]

CHEM 151(F)Introductory Chemistry

This course provides an introduction to chemistry for those students with little or no high school chemistry. Students will be introduced to concepts fundamental to studying matter at the molecular level. Principal topics include introductions to the nature of atoms and molecules, stoichiometry, solubility rules and equilibria, gas laws, chemical equilibrium, acid-base reactions, periodic relationships, chemical bonding, molecular structure, intermolecular forces, oxidation-reduction reactions, and related applications. Laboratory work comprises a system of qualitative analysis and quantitative techniques. The course provides preparation for further study of organic chemistry, biochemistry, physical and inorganic chemistry and is intended for students who are anticipating professional study in chemistry, in related sciences, or in one of the health professions, as well as for those students who are interested in exploring the fundamental ideas of chemistry as part of their general education. [ more ]

CHEM 153(F)Concepts of Chemistry

This course broadens and deepens the foundation in chemistry of students who have had typically one year 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, and the model of an atom is expected. Principal topics for this course include kinetic theory of gases, 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 work includes synthesis, qualitative and quantitative chemical analysis, and molecular modeling. 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 fundamental ideas of chemistry as part of their general education. [ more ]

CHEM 155(F)Principles of Modern Chemistry

This course is designed for students with strong preparation in secondary school chemistry, including a laboratory experience, such as provided by an Advanced Placement chemistry course (or equivalent) with a corresponding score of 5 of the AP Chemistry Exam (or a 7 on the IB Exam, or equivalent). Topics include chemical thermodynamics, kinetics, structure and bonding, coordination chemistry, electrochemistry and spectroscopy and their application to fields such as materials science, industrial, environmental, biological, and medicinal chemistry. Laboratory work includes synthesis, characterization, and reactivity of coordination complexes, electrochemical analysis, materials chemistry, qualitative analysis, and molecular modeling. This course is of interest for students who are anticipating professional study in chemistry, related sciences, or one of the health professions, as well as for students who want to explore the fundamental ideas of chemistry as part of their general education. [ more ]

CHEM 156(S)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. The fundamentals of molecular modeling as applied to organic molecules are presented. Specific topics include basic organic structure and bonding, isomerism, stereochemistry, molecular energetics, the theory and interpretation of infrared and nuclear magnetic spectroscopy, substitution and elimination reactions, and the addition reactions of alkenes and alkynes. The coordinated laboratory work includes purification and separation techniques, structure-reactivity studies, organic synthesis, IR and NMR spectroscopy, and the identification of unknown compounds. [ more ]

CHEM 251(F)Organic Chemistry: Intermediate Level

This course is a continuation of Chemistry 156 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 255(F)Organic Chemistry: Intermediate Level--Special Laboratory Section

This course is a continuation of CHEM 156 and contains the same material as CHEM 251 except for the laboratory program described below: The aim of this advanced laboratory section is to enrich and enhance the laboratory experiences of motivated students of recognized ability by providing a laboratory program that more closely resembles the unpredictable nature and immediacy of true chemical research. Students synthesize, isolate, and characterize (using a range of modern physical and spectroscopic techniques) a family of unknown materials in a series of experiments constituting an integrated, semester-long investigation. A flexible format is employed in which the students are responsible for helping to plan the course of their laboratory work based upon discussions with the instructor about the previous week's experimental results. Students are drawn from CHEM 156 with placement based upon student selection and nomination by the CHEM 156 instructor. Participants attend their regular CHEM 251 lecture but attend the special laboratory section instead of a CHEM 251 laboratory section. [ more ]

CHEM 256(S)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 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, kinetics, and nuclear chemistry. Laboratory work includes experiments involving synthesis, characterization, and reactivity studies of coordination and organic complexes, spectroscopic analyses, thermodynamics, electrochemistry, kinetics, and nuclear chemistry. [ more ]

CHEM 319Integrative Bioinformatics, Genomics, and Proteomics Lab

Last offered Fall 2016

What can computational biology teach us about cancer? In this capstone 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, phylogenetics, and recombinant DNA techniques 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 MAPK signal transduction pathway 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 will be used to study networks of interacting proteins in colon tumor cells. [ more ]

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

This course introduces the basic 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)Biochemistry II: Metabolism

This lecture course provides an in-depth presentation of the complex metabolic reactions which 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(S)Enzyme Kinetics and Reaction Mechanisms

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(F)Chemical and Synthetic Biology

Chemistry provides invaluable tools for investigating and manipulating biological systems. Recent advances increasingly allow us to exploit the complex technological capabilities evolved by living things. This course will survey the highly interdisciplinary and interconnected fields of chemical and synthetic biology. These disciplines bring chemical tools and frameworks to bear on living systems and address problems in basic science, medicine, chemical production, biotechnology and more. Chemical biology uses precise molecular-level manipulations to influence living systems from the bottom up, often by introducing components that are completely foreign to nature. Synthetic biology takes advantage of existing molecular technology and adopts an engineering mindset to reprogram living systems. Both fields are quite new, rapidly evolving, and full of promise--as well as hype! In this course, we will aim to: 1) develop our own conceptions of chemical and synthetic biology and their interplay; 2) learn the fundamental techniques for using chemistry to manipulate biology; and 3) critically assess the progress, shortcomings and challenges for these areas. Our format will include student-driven presentation and discussion of primary literature case studies along with instructor-presented content. Topics we may cover include bioconjugation, chemical synthesis of biomacromolecules, synthetic organisms, metabolic engineering, directed evolution, and comprehensive reworking of the central dogma. [ more ]

CHEM 335(F)Inorganic/Organometallic Chemistry

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

CHEM 336(S)Materials Chemistry

Materials Science focuses on the study of bulk physical properties such as hardness, electrical conductivity, optical behavior, and elasticity. Materials chemists bridge the gap between traditional synthetic chemists and materials scientists, by working to understand the relationships between bulk physical properties, length scale (mesoscale, nanoscale), and molecular structure. This course will cover a variety of different types of materials and their properties including solids (insulators, semiconductors, conductors, superconductors, magnetic materials), soft materials (polymers, gels, liquid crystals), nanoscale structures, and organic electronics. We'll examine some of the latest developments in materials chemistry, including new strategies for the synthesis and preparation of materials on different length scales, as well as a variety of potential applications of emerging technologies. [ more ]

CHEM 338Bioinorganic Chemistry: Metals in Living Systems

Last offered Spring 2017

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 perform regulatory roles and stabilize the structures of proteins. In medical applications, the metals are central to many diagnostic and therapeutic tools. To understand the role metals in these biological processes, we will cover 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, students explore topics of current interest in the field. [ more ]

CHEM 341Toxicology and Cancer

Last offered Spring 2018

What is a poison and what makes it poisonous? Paracelcus commented in 1537: "What is not a poison? All things are poisons (and nothing is without poison). The dose alone keeps a thing from being a poison." Is the picture really this bleak; is modern technology-based society truly swimming in a sea of toxic materials? How are the nature and severity of toxicity established, measured and expressed? Do all toxic materials exert their effect in the same manner, or can materials be poisonous in a variety of different ways? Are the safety levels set by regulatory agencies low enough for a range of common toxic materials, such as mercury, lead, and certain pesticides? How are poisons metabolized and how do they lead to the development of cancer? What is cancer and what does it take to cause it? What biochemical defense mechanisms exist to counteract the effects of poisons?
This course attempts to answer these questions by surveying the fundamentals of modern chemical toxicology and the induction and progression of cancer. Topics will range from description and quantitation of the toxic response, including risk assessment, to the basic mechanisms underlying toxicity, mutagenesis, carcinogenesis, and DNA repair.
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CHEM 342Synthetic Organic Chemistry

Last offered Spring 2019

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. Laboratory sessions introduce students to techniques for synthesis and purification of natural products and their synthetic precursors. [ more ]

CHEM 343Medicinal Chemistry

Last offered Fall 2014

This course explores the design, development, and function of pharmaceuticals. Fundamental concepts of organic chemistry are extended to the study of pharmacodynamics--the interactions between drugs and their targets that elicit a biological effect--and pharmacokinetics-the study of how the body absorbs, distributes, metabolizes, and eliminates drugs. The path of drug development is traced from discovery of an initial lead, through optimization of structure, to patenting and production. Mechanisms by which drugs target cell membranes, nucleic acids, and proteins are discussed. Drug interactions with enzyme and receptor targets are studied extensively. Specific drug classes selected for detailed analysis may include opiate analgesics, aspirin and other NSAIDs, antibacterial agents, cholinergic & adrenergic agents, CNS agents, as well as antiviral, antiulcer, and anticholesterol drugs. [ more ]

CHEM 344(S)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 348(F)Polymer Chemistry

From synthetic to natural macromolecules, we encounter polymers everywhere and everyday. This course explores the multitude of synthetic techniques available and discusses how structure defines function. Topics include condensation and chain (anionic, cationic, radical) polymerizations, dendrimers, controlling molecular weight, ring opening, and biopolymer syntheses. Fundamentals of composition and physical properties of polymers, and methods of characterization are also covered. [ more ]

CHEM 361(F)Quantum Chemistry and Chemical Dynamics

This course provides an introduction to quantum mechanics which serves as the basis for understanding atomic and molecular structure as well as spectroscopic methods. This leads to a discussion of chemical kinetics and molecular reaction dynamics in the gas phase and in solution.Computational chemistry methods are used to illustrate chemical concepts, to interpret experimental data, and to extend hypotheses. Applications of these principles are chosen from contemporary research fields, including polymer chemistry, photochemistry, atmospheric chemistry, and solid and liquid state chemistry. Quantitative laboratory experiments and consultation with the scientific literature provide the background necessary for carrying out an independent theoretical or experimental project. [ more ]

CHEM 364(S)Instrumental Methods of Analysis

This course provides the student an understanding of the applicability of current laboratory instrumentation both to the elucidation of fundamental chemical phenomena and to the measurement of certain atomic and molecular parameters. Student will gain knowledge and understanding of the theory and practical use of a variety of instrumental techniques; including, but not limited to, chromatography, mass spectrometry, thermal methods, electroanalytical techniques, atomic and molecular absorption and emission spectroscopy, X-ray diffraction, and optical and electron microscopies, with examples drawn from the current literature. Analytical chemical and instrumental techniques will be developed in the lecture and extensively applied within the laboratory. These skills are useful in a wide variety of scientific areas. Through exploration of primary literature and review articles we will discuss recent developments in instrumental methods and advances in the approaches used to address modern analytical questions. [ more ]

CHEM 366(S)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)Biophysical Chemistry

This course is designed to provide a working knowledge of basic physical chemistry to students primarily interested in the biochemical, biological, or medical professions. Topics of physical chemistry are presented from the viewpoint of their application to biochemical problems. Three major areas of biophysical chemistry are discussed: 1) the conformation of biological macromolecules and the forces that stabilize them; 2) techniques for the study of biological structure and function including spectroscopic, hydrodynamic, electrophoretic, and chromatographic; 3) the behavior of biological macromolecules including ligand interaction and conformational transitions. [ more ]

CHEM 368 TComputational Chemistry and Molecular Spectroscopy

Last offered Spring 2019

This course 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 the laboratory session 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 394(S)Junior Research and Thesis: Chemistry

Chemistry junior research and thesis. [ more ]

Taught by: TBA

Catalog details

CHEM 493(F)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)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)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)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 ]