Chemistry & Biochemistry
Cat. I The theme of CH 1010 is that all matter in the universe is composed of atoms bonded together in a limited number of ways. Molecularity is one of a small number of fundamental themes of chemistry (and of all science); it is important for us to address it immediately because it permeates all of chemistry. Specific concepts that we will discuss are: Introduction to the Molecular View Types of Compounds: The Periodic Table Chemical Calculations Types of Reactions The Quantum Structure of the Atom
Cat. I We will examine the origin and strength of electrical forces within molecules (covalent bonds), between positive and negative ions in a lattice (ionic bonds), and between atoms or molecules of a pure substance (intermolecular forces). Energy changes accompanying the rupture or formation of such bonds will be discussed. Specific concepts that we will discuss are: Molecular Structure and Shape Gases Solids Intra-and Intermolecular Forces Liquids Energy (First Law of Thermodynamics)
Cat. I We will examine the nature of dynamic equilibrium at the molecular level, and will develop an understanding of the mathematical aspects of equilibrium. Phase equilibrium, further aspects of thermodynamics (entropy, free energy), equilibrium of chemical reactions in the gas phase, and equilibrium of chemical reactions in solution will be discussed. Specific concepts that we will discuss are: Phase Equilibrium Chemical Equilibrium of Gas Phase Reactions Solutions Chemical Equilibrium of Reactions in Solution Entropy and Free Energy
Cat.I We will examine the nature of molecular motions and their interaction with light, which provides us with all of our structural information about molecules. Various types of molecular spectroscopy will be discussed. Then we will turn to the dynamics of interactions between molecules, examining the rates of chemical reactions, and discussing the detailed molecular pathways by which they occur. Specific concepts that we will discuss are: NMR Spectroscopy Vibrational Spectroscopy Electronic Spectroscopy Dynamics of Physical Processes (Diffusion, phase changes, phase distribution) Dynamics of Chemical Processes
Cat. I A systematic survey of the major reaction types and functional groups in organic chemistry. The course will provide a representative collection of characteristic reactions and transformations of a variety of types of organic molecules. Most of the examples will be drawn from aliphatic chemistry. Some theoretical models will be introduced with a view toward establishing a general overview of the material. The course is intended for chemists, chemical engineers, pre-medical students and all those interested in the biosciences. A familiarity with the material presented in the general chemistry courses is assumed.
Cat. I Modern theories of aromaticity, including a general assessment of delocalized bonding. The chemistry of some significant functional groups not surveyed in Organic Chemistry I, and the meaning of acidity and basicity in organic chemistry, will be more fully explored. The course will provide an introduction to the systematic synthesis of polyfunctional organic compounds. Recommended background: CH 2310. The course is intended for chemists, chemical engineers and bio-science majors.
Cat. I This course fully explores three most important analytical methods in organic chemistry: infrared spectroscopy, mass spectrometry, and nuclear magnetic resonance spectroscopy. It will continue the coverage of aromatic chemistry. New topics to be introduced include structures, properties, and reactivities of aldehydes and ketones, carboxylic acids and their derivatives, amines, and the interaction among polyfunctional compounds. It reinforces the retrosynthetic analysis and multistep synthesis of organic compounds and revisits reaction mechanisms and stereochemistry of all the new functional groups studied. Recommended background: CH2310 and CH2320. The course is intended for biochemists, chemists, chemical engineers and bioscience majors.
Cat. I Laboratory experience in the preparation, purification, and characterization of organic substances. The course will also contain sufficient training in laboratory technique and data handling so that no previous laboratory experience beyond that of general chemistry will be assumed. (To be taken concurrently or following studies in organic chemistry.) Recommended for chemical engineers, pre-medical students, BB majors, and other nonchemists desiring chemical laboratory experience. One lecture and three three-hour labs.
Cat. I This laboratory course focuses on the application of modern instrumental methods of analysis to chemical, biochemical and environmental problems. Practical experience is gained in quantitative electrochemistry, ultraviolet-visible spectrophotometry, fluorometry and bioluminescence, high performance liquid chromatography, and capillary electrophoresis. Principles of experimental design and execution are developed as student teams select a chemical, biochemical or environmental problem, formulate an approach, conduct the analysis, and present findings to the class. Methods of data analysis and common statistical approaches are emphasized throughout the course. Recommended background: CH 1010, CH 1020, CH 1030, CH 1040.
Cat. I The experiments to be performed this term have been chosen to illustrate important principles and experimental techniques of physical chemistry. Students will gain experience with many of the instruments that they are likely to use in any chemical laboratory setting. These include optical spectrometers, vacuum lines, molecular modeling workstations and calorimeters. Recommended background: CH 2640 and CH 3510.
Cat. I The emphasis in CH 2660 is on basic techniques essential for the synthesis, isolation, and characterization of organic compounds. These include isolation and purification by solvent extraction, crystallization, distillation, and chromatographic techniques, followed by the determination of physical properties and characterization by infrared and nuclear magnetic resonance spectroscopy. Micro-synthetic procedures are introduced. Mastery of the techniques and manipulations emphasized in CH 2640 and CH 2650 would be advantageous.
Cat. I The synthesis, isolation, and characterization of inorganic compounds are emphasized. Syntheses of main group compounds, classical transition metal complexes, and organotransition metal compounds are included. In addition to reinforcing and building on standard techniques of synthesis and characterization, several new techniques are introduced: synthesis under inert atmosphere, measurement of magnetic susceptibility by NMR, and cyclic voltammetry. Some exposure to 13C NMR is also provided. The final experiment of the course requires the student to design a synthesis for a compound selected from a list provided, based on strategies learned in the course.
Cat. II This course will review and further develop concepts introduced in CH 2310, CH 2320, and CH 2330. These concepts will include oxidation states of organic compounds, acidity and basicity, and stereochemistry and conformational analysis. Chemical reactivity will be emphasized and will include functional group interconversion and ionic and free radical carbon-carbon bond formation. Recommended background: CH 2310, CH 2320, and CH 2330. This course is intended for students planning to take advanced courses in organic and/or medicinal chemistry and for chemists, biochemists, chemical engineers, and bioscience majors who desire a stronger background in organic chemistry. Offered in 2014-15 and in alternating years thereafter.
Cat. I This course provides the fundamental understanding of atomic, molecular and solid state structures and properties. Orbital structures of atoms, symmetry of molecules and point groups are used to understand chemical bonding and reactions. Various acid-base concepts are explored to analyze the acidity of cations and basicity of anions, solubility and precipitations of inorganic compounds, and metal-ligand binding affinities. Redox properties are discussed using Pourbaix diagrams. Thermodynamic stabilities of inorganic species are discussed using acid-base and redox concepts and thermochemical analyses are used to analyze chemical reactivity at atomic, molecular, and solid state level.
Cat. I The content of this course will be the development of the principles of classical thermodynamics. The laws of thermodynamics will be developed by using a series of increasingly complex model systems and a universal equation of state is formulated which incorporates the relationships illustrated by these model systems. Using this equation it will be possible to appreciate that thermodynamic laws are applicable to all systems of matter, regardless of their complexity. Finally, the principles developed are applied to problems of a chemical nature, focusing on predicting the spontaneity of chemical reactions. The material in this course will be of greatest interest to those students enrolled in the basic sciences including biology, chemistry, and physics, and in applied fields such as chemical engineering, materials science and biotechnology. Recommended background: Students should be familiar with the material covered in the general chemistry sequence CH 1010-1040, and calculus including multi variables.
Cat. I An introduction to quantum mechanics with applications to atomic and molecular species. The course will be developed systematically beginning with the postulates of quantum mechanics. The Schroedinger equation will be applied to systems such as the particle in a box, the rigid rotor, the harmonic oscillator and the hydrogen atom. Emphasis will be given to a quantum mechanical description of multielectron atoms, molecular bonding and spectroscopy. Recommended background: a solid foundation in elementary physics and calculus. This course is normally for students in their third year.
Cat. I This course deals in a general way with the interactions between energy and molecules, and considers how energetic and structural considerations affect the outcome of molecular interactions. The manipulation of kinetic data and results is stressed. Selected topics from both organic and inorganic chemistry are analyzed in terms of reaction thermodynamics, rates and mechanisms. Students are expected to be familiar with thermodynamics, equilibria, reaction rates and the Periodic Table of the elements. The following three courses, CH 4110, CH 4120, and CH 4130, are a three-term sequence intended to provide a strong emphasis in biochemistry. As background for this sequence, CH 1010, CH 1020, CH 1030, CH 1040, CH 2310, CH 2320, and CH 2330, or their equivalents, are recommended.
The principles of protein structure are presented. Mechanisms of enzymatic catalysis, including those requiring coenzymes, are outlined in detail. The structures and biochemical properties of carbohydrates are reviewed. Bioenergetics, the role of ATP, and its production through glycolysis and the TCA cycle are fully considered.
Oriented around biological membranes, this course begins with a discussion of electron transport and the aerobic production of ATP, followed by a study of photosynthesis. The study of the biosynthesis of lipids and steroids leads to a discussion of the structure and function of biological membranes. Finally, the membrane processes in neurotransmission are discussed. Recommended background: CH 4110.
This course presents a thorough analysis of the biosynthesis of DNA (replication), RNA (transcription) and proteins (translation), and of their biochemical precursors. Proteins and RNAs have distinct lifetimes within the living cell; thus the destruction of these molecules is an important biochemical process that is also discussed. In addition to mechanistic studies, regulation of these processes is covered.
Cat. I The experiments in this laboratory course have been designed to acquaint the students with the basic skills necessary to perform biochemical studies. The course will cover, for instance, protein purification, subcellular fractionation, enzyme kinetics (Km, Vmax, specific activity, effector-protein interaction, etc.), exclusion and ion exchange chromatography, and electrophoresis. Recommended background: CH 4120.
Cat. II This course will focus on different areas of biophysics with special emphasis on membrane phenomena. The biomedical-biological importance of biophysical phenomena will be stressed. The course will begin with the introduction of the molecular forces relevant in biological media and subsequently develop the following topics: Membrane Structure and Function; Channels, Carriers and Pumps; Nerve Excitation and related topics; and Molecular Biophysics of Motility. Recommended background: prior knowledge of Biochemistry (CH 4110, CH 4120), Mechanics (PH 1110) and Electricity (PH 1120). This course will be offered in 2013-14 and in alternating years thereafter.
Cat. I This laboratory course focuses on modern DNA technologies and general applications of gene manipulation. Topics include gene amplification and recombination, promoter and plasmid engineering, gene expression and analysis, model systems, genomics and transgenics. Experiments in this course are integrated into an overall genetic engineering project throughout the term that will involve techniques such as electrophoresis, quantitative spectrofluorimetry, and real-time quantitative PCR. Methods of data analysis, common statistical approaches and technical writing will be emphasized throughout the course. Recommended background: CH 4110, CH 4120, CH 4130.
Cat. I This course will cover the biochemical mechanisms involved in regulation of gene expression, modifications of DNA structures that influence transcription rates, transcriptional regulation by protein binding, post-transcriptional modifications of RNA including splicing and editing, regulation of translation including ribosome binding and initiation of translation, and factors that control the half-lives of both mRNA and protein. During the course, common experimental methods will be explored, including a discussion of the information available from each method. Recommended background CH 4110, CH 4120, CH 4130, BB 4010
A discussion of selected modern synthetic methods including additions, condensations and cyclizations. Emphasis is placed on the logic and strategy of organic synthesis. Recommended background: CH 2310, CH 2320 and CH 2330, or the equivalent. This course will be offered in 2014-15 and in alternate years thereafter.
Complexes of the transition metals are discussed. Covered are the electronic structures of transition metal atoms and ions, and the topological and electronic structures of their complexes. Symmetry concepts are developed early in the course and used throughout to simplify treatments of electronic structure. The molecular orbital approach to bonding is emphasized. The pivotal area of organotransition metal chemistry is introduced, with focus on complexes of carbon monoxide, metal-metal interactions in clusters, and catlysis by metal complexes. Recommended background: CH 2310 and CH 2320, or equivalent. This course will be offered in 2011-12 and in alternate years thereafter.
This course deals with how the electronic, translational, rotational and vibrational energy levels of individual molecules, or of macromolecular systems are statistically related to the energy, entropy and free energy of macroscopic systems, taking into account the quantum mechanical properties of the component particles. Ensembles, partition functions, and Boltzmann, Fermi/Dirac and Bose- Einstein statistics are used. A wealth of physical chemical phenomena, including material related to solids, liquids, gases, spectroscopy and chemical reactions are made understandable by the concepts learned in this course. This course will be offered in 2011-12 and in alternate years thereafter.