Colin D. Abernethy

BSc (Hons), Durham University, England. PhD, The University of New Brunswick, Canada. Current research interests include the synthesis of new early transition-metal nitride compounds and the development of practical exercises for undergraduate chemistry teaching laboratories. Author of publications in the fields of inorganic and physical chemistry, as well as chemical education. Recipient of research grants from The Royal Society, Nuffield Foundation, Research Corporation for the Advancement of Science, and American Chemical Society. Received postdoctoral research fellowships at the University of Texas at Austin and at Cardiff University, Wales. Previously taught at: Strathclyde University, Scotland; Western Kentucky University; and Keene State College, New Hampshire. SLC, 2010–

Undergraduate Courses 2021-2022

Chemistry

Biochemistry

Advanced, Small seminar—Fall

This course is concerned with the chemical basis of biology. We will begin by examining the structure and function of the main classes of biologically important molecules: amino acids, peptides, and proteins; carbohydrates; and lipids. We will then look at enzyme activity, including the mechanisms, kinetics, and regulation of enzyme-mediated reactions. This will be followed by an overview of nucleic acids (DNA and RNA) and their role within eukaryotic cells. The study of biological membranes will then lead to an investigation of bioenergetics and metabolic processes within cells.

Faculty

First-Year Studies: Chemistry for Contrarians: A Nontraditional Science Course for Liberal Arts Students

Open, FYS—Year

For anyone who wants to know how the world (and the universe) works at a fundamental level, modern science has (almost) all the answers; however, painful memories of school science classes and seemingly impenetrable scientific jargon often put people off from engaging with this area of study. In this course, we will take two very different approaches to engage with chemistry and related areas of physics and biology. I hope to convince you that science is, ultimately, about people—how we learn about and change our beliefs concerning the physical world. Fall semester: Gaming Our Way to Scientific Literacy. In recent years, a number of educational board and card games have been designed to aid students in learning the vocabulary and concepts of the physical and life sciences. The manufacturers of these games claim that they are scientifically accurate and offer a novel way for nontraditional learners to develop a working knowledge of basic science. We will study a number of important core topics in subatomic and atomic physics, chemistry, and biochemistry. To enliven our classes, we will use the following games as the center of each unit of study: Subatomic: An Atom Building Game™; Periodic: A Game of the Elements™; Covalence: A Molecule Building Game™; Ion: A Compound Building Game™; Peptide: A Protein Building Game™; and Cytosis: A Cell Biology Game™. In each case, we will look at how the developers have integrated current scientific knowledge into their games. By playing, we will determine how effective these games are in helping us to learn scientific concepts and to gain confidence using scientific vocabulary. Spring Semester: Reading and Writing the Biography of Chemistry. During the spring semester, we will read the stories of some chemical elements and important chemical compounds—not just their discovery but also their cultural and historical significance. We will discover how different cultures affect attitudes toward various chemicals and their use and how, in return, important chemicals have affected culture and transformed lives. During the fall semester, students will meet with the instructor weekly for individual conferences. In the spring, we will meet weekly or every other week, depending on students’ needs and the progress of their conference projects.

Faculty

General Chemistry I

Open, Small Lecture—Fall

Chemistry is the study of the properties, composition, and transformation of matter. Chemistry is central to the production of the materials required for modern life; for example, the synthesis of pharmaceuticals to treat disease, the manufacture of fertilizers and pesticides required to feed an ever-growing population, and the development of efficient and environmentally benign energy sources. This course provides an introduction to the fundamental concepts of modern chemistry. We will begin by examining the structure and properties of atoms, which are the building blocks of the elements and the simplest substances in the material world around us. We will then explore how atoms of different elements can bond with each other to form an infinite variety of more complex substances, called compounds. This will lead us to an investigation of several classes of chemical reactions: the processes by which substances are transformed into new materials with different physical properties. Along the way, we will learn how and why the three states of matter (solids, liquids, and gases) differ from one another and how energy may be either produced or consumed by chemical reactions. In weekly laboratory sessions, we will perform experiments to illustrate and test the theories presented in the lecture part of the course. These experiments will also serve to develop practical skills in both synthetic and analytic chemical techniques.

Faculty

General Chemistry II

Intermediate, Small Lecture—Spring

This course is a continuation of General Chemistry I. We will begin with a detailed study of both the physical and chemical properties of solutions, which will enable us to consider the factors that affect both the rates and direction of chemical reactions. We will then investigate the properties of acids and bases and the role that electricity plays in chemistry. The course will conclude with introductions to nuclear chemistry and organic chemistry. Weekly laboratory sessions will allow us to demonstrate and test the theories described in the lecture segment of the course.

Faculty

Previous Courses

Chemistry

Atoms, Molecules, and Reactions: An Introduction to Physical Chemistry

Open, Seminar—Fall

In this course, we will think about the most fundamental question in chemistry: Why do chemical reactions happen? To answer this, we will first discuss the Second Law of Thermodynamics, which determines whether any change in the universe can occur. Before we can apply the Second Law of Thermodynamics to chemical systems, we will need to investigate the structure of atoms and the ways in which individual atoms can bond to one another to form molecular structures of increasing complexity. Once we have mastered the modern, quantum mechanical theories of chemical bonding, we will be able to look at different types of chemical reactions, their rates, and the ways in which chemical equilibria may be established and influenced. In the laboratory section of the course, we will put these ideas into practice: building molecules with different structures and then exploring their physical properties and chemical reactivity. Chemistry plays a pivotal role in all the natural sciences. Accordingly, this course will be useful for any students with an interest in the physical, biological, and medicinal sciences and for pre-engineering students.

Faculty

Biochemistry

Advanced, Seminar—Fall

This course is concerned with the chemical basis of biology. We will begin by examining the structure and function of the main classes of biologically important molecules: amino acids, peptides, and proteins; carbohydrates; and lipids. We will then look at enzyme activity, including the mechanisms, kinetics, and regulation of enzyme-mediated reactions. This will be followed by an overview of nucleic acids (DNA and RNA) and their role within eukaryotic cells. The study of biological membranes will then lead to an investigation of bioenergetics and metabolic processes within cells.

Faculty

Elemental Epics: Stories of Love, War, Madness, and Murder From the Periodic Table of the Elements

Open, Lecture—Spring

The Periodic Table displays the chemical elements according to the structure of their atoms and, consequently, their chemical properties. The Periodic Table also represents a treasure trove of fascinating stories that span both natural and human history. Many of the elements on the table have influenced key historical events and shaped individual lives. In this course, we will tour the Periodic Table and learn how the stories of the discovery and investigation of the elements fuse science with human drama—from murders to cures for deadly diseases and from new technologies to the fall of civilizations.

Faculty

General Chemistry I

Open, Lecture—Fall

Chemistry is the study of the properties, composition, and transformation of matter. Chemistry is central to the production of the materials required for modern life; for example, the synthesis of pharmaceuticals to treat disease, the manufacture of fertilizers and pesticides required to feed an ever-growing population, and the development of efficient and environmentally benign energy sources. This course provides an introduction to the fundamental concepts of modern chemistry. We will begin by examining the structure and properties of atoms, which are the building blocks of the elements and the simplest substances in the material world around us. We will then explore how atoms of different elements can bond with each other to form an infinite variety of more complex substances called compounds. This will lead us to an investigation of several classes of chemical reactions, the processes by which substances are transformed into new materials with different physical properties. Along the way, we will learn how and why the three states of matter (solids, liquids, and gases) differ from one another and how energy may be either produced or consumed by chemical reactions. In weekly laboratory sessions, we will perform experiments to illustrate and test the theories presented in the lecture part of the course. These experiments will also serve to develop practical skills in both synthetic and analytic chemical techniques.

Faculty

General Chemistry I: An Introduction to Chemistry and Biochemistry

Open, Lecture—Fall

This course is the first part of a two-semester sequence that provides a broad foundation for the scientific discipline of chemistry, introducing its fundamental principles and techniques and demonstrating the central role of chemistry in biology and medicine. We first look at basic descriptions of elemental properties, the periodic table, solid and molecular structures, and chemical bonding. We then relate these topics to the electronic structure of atoms. The mole as a unit is introduced so that a quantitative treatment of stoichiometry can be considered. After this introduction, we go on to consider physical chemistry, which provides the basis for a quantitative understanding of (i) the kinetic theory of gases (which is developed to consider the nature of liquids and solids); (ii) equilibria and the concepts of the equilibrium constant and of pH; (iii) energy changes in chemical reactions and the fundamental principles of thermodynamics; (iv) the rates of chemical reactions and the concepts of the rate-determining step and activation energy. Practical work in the laboratory periods of this course introduces the use and handling of basic chemical equipment and illustrates the behavior of simple chemical substances. In addition to the two regular class meetings and laboratory session each week, there will be an hour-long weekly group conference. This lecture course will be of interest to students interested in the study of chemistry or biology and to those planning on a career in medicine and related health.

Faculty

General Chemistry II

Intermediate, Lecture—Spring

This course is a continuation of General Chemistry I. We will begin with a detailed study of both the physical and chemical properties of solutions. This will enable us to consider the factors that affect both the rates and the direction of chemical reactions. We will then investigate the properties of acids and bases and the role that electricity plays in chemistry. The course will conclude with introductions to nuclear chemistry and organic chemistry. Weekly laboratory sessions will allow us to demonstrate and test the theories described in the lecture segment of the course.

Faculty

General Chemistry II: An Introduction to Chemistry and Biochemistry

Intermediate, Lecture—Spring

This course is the second part of a two-semester sequence that provides a broad foundation for the scientific discipline of chemistry, introducing its fundamental principles and techniques and demonstrating the central role of chemistry in biology and medicine. The course begins with a review of the important concepts discussed in General Chemistry I. The main types of organic compounds are then introduced by reference to simple systems and to specific compounds of industrial, biological, and medical importance. The more important reactions of each of these types are described and explained in terms of the structure of the functional groups involved. We go on to explore the chemical basis of life, the essential molecular components of biological cells, and the essential chemical processes that occur within them. The biological roles of amino acids, proteins, carbohydrates, and lipids are introduced. Practical work in the laboratory periods of this course introduces important chemical reactions and common methods of chemical detection and identification. In addition to the two regular class meetings and laboratory session each week, there will be an hour-long weekly group conference. This lecture course will be of interest to students interested in the study of chemistry or biology and to those planning on a career in medicine and related health.

Faculty

Inorganic Chemistry

Open, Seminar—Spring

In this course, we will investigate the properties of the chemical elements and some of their most important compounds. In so doing, we will discover the trends in structure, bonding, and reactivity that emerge as we move from one element to the next in the periodic table. Included in our survey will be discussions of the important roles that inorganic substances play in our everyday lives, particularly in the fields of bioinorganic chemistry, industrial materials, and nanotechnology. In the laboratory section of the course, we will prepare important examples of inorganic compounds and then investigate their reactivity. This will involve learning how to work with highly reactive and air-sensitive materials using vacuum-line and glove-box techniques. Chemistry plays a pivotal role in all of the natural sciences. Accordingly, this course will be useful for any students with an interest in the physical, biological, and medicinal sciences and for pre-engineering students.

Faculty

Organic Chemistry I (Guided Inquiry)

Open, Seminar—Fall

Organic chemistry is the study of chemical compounds whose molecules are based on a framework of carbon atoms, typically in combination with hydrogen, oxygen, and nitrogen. Despite this rather limited set of elements, there are more organic compounds known than there are compounds that do not contain carbon. Adding to the importance of organic chemistry is the fact that very many of the chemical compounds that make modern life possible—such as pharmaceuticals, pesticides, herbicides, plastics, pigments, and dyes—can be classed as organic. Organic chemistry, therefore, impacts many other scientific subjects; and knowledge of organic chemistry is essential for detailed understanding of materials science, environmental science, molecular biology, and medicine. This course gives an overview of the structures, physical properties, and reactivity of organic compounds. We will see that organic compounds can be classified into families of similar compounds based upon certain groups of atoms that always behave in a similar manner no matter what molecule they are in. These functional groups will enable us to rationalize the vast number of reactions that organic reagents undergo. Topics covered in this course include: the types of bonding within organic molecules; fundamental concepts of organic reaction mechanisms (nucleophilic substitution, elimination, and electrophilic addition); the conformations and configurations of organic molecules; and the physical and chemical properties of alkanes, halogenoalkanes, alkenes, alkynes and alcohols. In the laboratory section of the course, we will develop the techniques and skills required to synthesize, separate, purify, and identify organic compounds. Organic Chemistry is a key requirement for pre-med students and is strongly encouraged for all others who are interested in the biological and physical sciences. In addition, the Guided Inquiry exercises conducted in class will sharpen your analytical skills and teach you how to think like a scientist. Depending on the COVID-19 situation, the lab portion of this course may proceed as normal, be postponed until later in the semester, or offered as a separate one- or two-credit course (Practical Organic Chemistry) in the spring.

Faculty

Organic Chemistry I: A Guided Inquiry Seminar

Open, Seminar—Fall

Research has shown that students learn much more effectively when they are actively engaged and when ideas and concepts are developed by the students themselves rather than simply being presented by a professor or read in a textbook. This course is designed as a series of interactive Guided Inquiry exercises. During each seminar, you will be presented with data and important observations regarding the topic being studied. The class will work in small groups to answer a series of directed questions designed to lead each student toward the development of a target concept or idea. These classroom activities are designed to follow the scientific process as much as possible. You will be asked to make predictions based on the model that has been developed by the class. Further data or information will then be provided that can be used to check your predictions. In this way, you will simultaneously learn both the course content and the key critical thinking skills that constitute scientific thought and exploration. After each topic has been developed in class, you will be asked to read the relevant section of the textbook and then answer a series of problems to reinforce your understanding of the material. You should consider taking this course if you enjoy highly interactive seminars, working in small groups, and figuring out problems yourself rather than simply listening to a professor while taking notes in class. Organic chemistry is the study of chemical compounds whose molecules are based on a framework of carbon atoms, typically in combination with hydrogen, oxygen, and nitrogen. Despite this rather limited set of elements, there are more organic compounds known than there are compounds that do not contain carbon. Adding to the importance of organic chemistry is the fact that very many of the chemical compounds that make modern life possible—such as pharmaceuticals, pesticides, herbicides, plastics, pigments, and dyes—can be classed as organic. Organic chemistry, therefore, impacts many other scientific subjects; and knowledge of organic chemistry is essential for a detailed understanding of materials science, environmental science, molecular biology, and medicine. This course gives an overview of the structures, physical properties, and reactivity of organic compounds. We will see that organic compounds can be classified into families of similar compounds based upon certain groups of atoms that always behave in a similar manner no matter what molecule they are in. These functional groups will enable us to rationalize the vast number of reactions that organic re-agents undergo. Topics covered in this course include: the types of bonding within organic molecules; fundamental concepts of organic reaction mechanisms (nucleophilic substitution, elimination, and electrophilic addition); the conformations and configurations of organic molecules; and the physical and chemical properties of alkanes, halogenoalkanes, alkenes, alkynes, and alcohols. In the laboratory section of the course, we will develop the techniques and skills required to synthesize, separate, purify, and identify organic compounds. Organic Chemistry is a key requirement for pre-med students and is strongly encouraged for all others who are interested in the biological and physical sciences. In addition, the Guided Inquiry exercises will sharpen your analytical skills and teach you how to think like a scientist. Your experiences working as part of a team in this course will help you in future situations where the ability to collaborate to solve problems is a critical measure of success.

Faculty

Organic Chemistry I: An Interactive Guided Inquiry Seminar Course

Open, Seminar—Fall

Research has shown that students learn much more effectively when they are actively engaged and when ideas and concepts are developed by the students themselves rather than simply being presented by a professor or read in a textbook. This course is designed as a series of interactive Guided Inquiry exercises. During each seminar, you will be presented with data and important observations regarding the topic being studied. The class will work in small groups to answer series of directed questions designed to lead each student to the development of a target concept or idea. These classroom activities are designed to follow the scientific process as much as possible. You will be asked to make predictions based on the model that has been developed by the class. Further data or information will then be provided that can be used to check your predictions. In this way, you will simultaneously learn course content and the keycritical thinking skills that constitute scientific thought and exploration. After each topic has been developed in class, you will be asked to read the relevant section of the textbook and then answer a series of problems to reinforce your understanding of the material. No prior knowledge of chemistry is required. Students will be able to take this course and Organic Chemistry II (Guided Inquiry) in the spring semester and then take General Chemistry or other chemistry courses in subsequent years. You should consider taking this course if you enjoy highly interactive seminars, working in small groups, and figuring out problems yourself rather than simply listening to a professor while taking notes in class. Organic chemistry is the study of chemical compounds whose molecules are based on a framework of carbon atoms, typically in combination with hydrogen, oxygen, and nitrogen. Despite this rather limited set of elements, there are more organic compounds known than there are compounds that do not contain carbon. Adding to the importance of organic chemistry is the fact that very many of the chemical compounds that make modern life possible—such as pharmaceuticals, pesticides, herbicides, plastics, pigments, and dyes—can be classed as organic. Organic chemistry, therefore, impacts many other scientific subjects; and knowledge of organic chemistry is essential for a detailed understanding of materials science, environmental science, molecular biology, and medicine. This course gives an overview of the structures, physical properties, and reactivityof organic compounds. We will see that organic compounds can be classified into families of similar compounds based upon certain groups of atoms that always behave in a similar manner no matter what molecule they are in. These functional groups will enable us to rationalize the vast number of reactions that organic re-agents undergo. Topics covered in this course include: the types of bonding within organic molecules; fundamental concepts of organic reaction mechanisms (nucleophilic substitution, elimination, and electrophilic addition); the conformations and configurations of organic molecules; and the physical and chemical properties of alkanes, halogenoalkanes, alkenes, alkynes and alcohols. In the laboratory section of the course, we will develop the techniques and skills required to synthesize, separate, purify, and identify organic compounds. Organic Chemistry is a key requirement for pre-med students and is strongly encouraged for all others who are interested in the biological and physical sciences. In addition, the Guided Inquiry exercises will sharpen your analytical skills and teach you how to think like a scientist. Your experiences working as part of a team in this course will help you in future situations where the ability to collaborate to solve problems is a critical measure of success.

Faculty

Organic Chemistry II (Guided Inquiry)

Intermediate, Seminar—Spring

This course is a continuation of Organic Chemistry I (Guided Inquiry). This semester, we will explore the physical and chemical properties of additional families of organic molecules. The reactivity of aromatic compounds, aldehydes and ketones, carboxylic acids and their derivatives (acid chlorides, acid anhydrides, esters, and amides), enols and enolates, and amines will be discussed. We will also investigate the methods by which large, complicated molecules can be synthesized from simple starting materials. Modern methods of organic structural determination—such as mass spectrometry, 1H and 13C nuclear magnetic resonance spectroscopy, and infrared spectroscopy—will also be introduced. In the laboratory section of this course, we will continue to develop the techniques and skills required to synthesize, separate, purify, and identify organic compounds. Organic Chemistry II (Guided Inquiry) is a key requirement for pre-med students and is strongly encouraged for all others who are interested in the biological and physical sciences.

Faculty

Organic Chemistry II: A Guided Inquiry Seminar

Intermediate, Seminar—Spring

This course is a continuation of Organic Chemistry I: A Guided Inquiry Seminar. This semester, we will explore the physical and chemical properties of additional families of organic molecules. The reactivity of aromatic compounds, aldehydes and ketones, carboxylic acids and their derivatives (acid chlorides, acid anhydrides, esters, and amides), enols and enolates, and amines will all be discussed. We will also investigate the methods by which large, complicated molecules can be synthesized from simple starting materials. Modern methods of organic structural determination—such as mass spectrometry, 1 H and 13 C nuclear magnetic resonance spectroscopy, and infrared spectroscopy—will also be introduced. In the laboratory section of this course, we will continue to develop the techniques and skills required to synthesize, separate, purify, and identify organic compounds. Organic Chemistry II is a key requirement for pre-med students and is strongly encouraged for all others who are interested in the biological and physical sciences.

Faculty

Organic Chemistry II: An Interactive Guided Inquiry Seminar Course

Intermediate, Seminar—Spring

This course is a continuation of Organic Chemistry I (Guided Inquiry). This semester, we will explore the physical and chemical properties of additional families of organic molecules. The reactivity of aromatic compounds, aldehydes and ketones, carboxylic acids and their derivatives (acid chlorides, acid anhydrides, esters, and amides), enols and enolates, and amines will be discussed. We will also investigate the methods by which large, complicated molecules can be synthesized from simple starting materials. Modern methods of organic structural determination—such as mass spectrometry, 1 H and 13 C nuclear magnetic resonance spectroscopy, and infrared spectroscopy—will also beintroduced. In the laboratory section of this course, we will continue to develop the techniques and skills required to synthesize, separate, purify, and identify organic compounds. Organic Chemistry II is a key requirement for pre-med students and is strongly encouraged for all others who are interested in the biological and physical sciences.

Faculty

Organic Chemistry III: An Introduction to Organic Synthesis

Advanced, Seminar—Spring

This advanced course is a continuation of the study of Organic Chemistry beyond the topics studied in Organic Chemistry I & II. We will commence the semester by investigating the exceptional stability of aromatic molecules and their main modes of reaction: electrophilic aromatic substitution and nucleophilic aromatic substitution. We will then look at the ways in which organic molecules can rearrange and fragment during reactions. Once those topics have been mastered, we will be able to learn the principles of retrosynthetic analysis: the method used to devise efficient strategies for the synthesis of complex organic molecules. Conference work for this course will be the development of a synthetic route to prepare an important pharmaceutical compound.

Faculty

Practical Organic Chemistry

Intermediate, Seminar—Spring

This course, the accompanying laboratory for this year’s Organic Chemistry (Guided Inquiry) I & II course sequence, consists of a series of virtual laboratory experiences and group exercises that are designed to illustrate and explore many of the principles of organic chemistry described in the seminar courses. Students will be introduced to the important practical techniques used in synthetic organic chemistry, including the separation, purification, and identification of compounds. Opportunities for in-person laboratory activities will also be offered for those students able and willing to participate.

Faculty

Spectroscopy and Chemical Structure Determination

Intermediate, Seminar—Fall

Every time a chemist conducts a reaction or isolates a compound, his or her first task is to identify the molecular structure of what has been made or isolated. To help do this, chemists have a powerful array of modern instrumental techniques that are used to quickly and accurately determine the structures of compounds. One of the most challenging (and entertaining!) parts of chemistry is to use the information obtained from these techniques to assign structures to unknown compounds (a bit like Sherlock Holmes using clues to solve a murder mystery). In this course, we focus on the three most widely used techniques: mass spectrometry, infrared spectroscopy, and nuclear magnetic resonance spectroscopy. All of these techniques provide valuable information about the structures of molecules, and all are used on a day-to-day basis by most chemists. In the laboratory, we will gain hands-on experience in a variety of one- and two-dimensional NMR techniques and infrared spectroscopy. Once we have a sound understanding of each of those techniques, we will become chemical detectives and use the information that the techniques provide to solve chemical puzzles in order to elucidate the identities and structures of unknown molecules.

Faculty