Chemistry and Biochemistry

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, CRISPR, 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 spectro-fluorimetry, and real-time quantitative PCR. Methods of data analysis, common statistical approaches and technical writing will be emphasized throughout the course.

Through lectures, problem sets, reading and discussion, and presentations this course will help elucidate for students the processes that allow regulated gene expression, mechanisms used in each type of regulation, and methods and techniques used for investigation of regulatory mechanisms. Readings from the current original research literature will explore the growing use of model systems and “omics” level approaches to enhance our ever expanding understanding of the gene regulatory mechanisms. The development of cell-based therapeutics and genetic engineering as they relate to gene regulation will be introduced.

The CH 1010 course is an introduction to chemistry using the fundamental structures of atoms as a starting point. Emphasis is placed on discussing how all properties of matter as well as bonding mechanisms arise from atomic structure. Lewis structures and molecular orbitals are used to understand bonding, and the intermolecular forces present in chemicals systems are used as a prelude to reactivity patterns covered in future courses.

Bonding theories introduced earlier in the sequence are applied to chemical reactions, including reduction/oxidation reactions, to demonstrate patterns in reactivity. Solution thermodynamics, concentration scales, and colligative properties are discussed in the context of balanced chemical reactions both in aqueous solution and in the gas phase.

This course will examine the dynamic nature of solutions at the molecular level, and will develop an understanding of the mathematical aspects of molecular dynamics and equilibrium. Reaction kinetics will be outlined in detail leading into exploration of various fundamentals and examples of equilibrium processes in the gas phase as well as in solution, including acid-base chemistry and precipitation. Principles of thermodynamics will be introduced (entropy, free energy), and relationships with equilibrium will be explored. Case studies in current topics will be emphasized throughout the course.

We will examine the nature of molecular motions and their interaction with electromagnetic radiation, which provides us with all of our structural information about molecules. In addition, students will be introduced to the fundamentals of mass spectrometry and electrochemistry. The concepts of these techniques will be discussed in the context of structural organic chemistry and polymer characterization

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.

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.

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.

Laboratory experience in standard methods for the preparation and purification of organic compounds. The course will provide sufficient training in laboratory technique so that no previous laboratory experience beyond that of general chemistry is required. This course may be taken concurrently or following lecture courses in organic chemistry. Recommended for pre-medical students and students majoring in disciplines outside of chemistry and biochemistry that desire laboratory experience in basic methods of organic synthesis.

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.

This laboratory course emphasizes principles, techniques, and instrumentation employed in modern physical chemistry with a view towards applications throughout the molecular sciences. Investigations include chemical thermodynamics and phase equilibria; gas-phase, solution-phase, and interfacial reaction kinetics and dynamics; and molecular modeling of small molecules. Emphasis includes data collection, interpretation, error analysis, and write-up.

The emphasis in CH 2660 is on fundamental techniques essential for the synthesis, purification, and characterization of organic compounds. These techniques include setting up, running and monitoring reactions, isolation and purification by solvent extraction, crystallization, distillation, and chromatographic techniques, followed by determination of physical properties and characterization by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy Micro-synthetic methods and multi-step synthesis are introduced. This course differs from CH 2360 by providing in-depth experience with spectroscopic characterization of molecular structure and hands-on training operating core instruments in addition to methods of organic synthesis. This course is required for students majoring in chemistry, and is recommended for students majoring in biochemistry and disciplines outside of chemistry that desire a strong background in methods of organic synthesis and characterization.

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.

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. This course will be offered in 2022-23, and in alternating years thereafter.

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.

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.

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. This course is normally for students in their third year.

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 fundamental concepts of protein architecture and dynamics are presented with an emphasis on the functional outcomes of chemistry coordinated in three dimensional space. Catalytic mechanics and enzyme function are outlined in detail. Current methods in the determination of enzyme structure and function will be discussed, and students will use common tools in macromolecular analysis and structural modeling. Case studies in enzyme dysfunction, disease, and current research will be used throughout the course.

The following three courses, CH 4110, CH 4120, and CH 4130, are a three-term sequence intended to provide a strong emphasis in biochemistry.

Oriented around biological membranes, this course begins with a description of lipids and proteins forming biomembranes. Permeability and the mechanism of transmembrane mass transport are presented. Transport of electrons and redox equivalents is explained within the context of aerobic production of ATP and plant photosynthesis. Finally the transport of information across biomembranes in signal transduction and neurotransmission are discussed.

The following three courses, CH 4110, CH 4120, and CH 4130, are a three-term sequence intended to provide a strong emphasis in biochemistry.

This course presents the structure and function of DNA. Precursors and biomolecules that give rise to DNA, the mechanism of DNA replication, RNA synthesis, and protein synthesis are described in detail. In addition to mechanistic studies, regulation of these processes is covered as well as those of genetic mutation, DNA repair, and epigenetics.

The following three courses, CH 4110, CH 4120, and CH 4130, are a three-term sequence intended to provide a strong emphasis in biochemistry.

This course presents a thorough analysis of the most relevant metabolic processes in cells. The catabolism of sugars and lipids will be presented in the context of energy generation and storage. Nucleotide and amino acid metabolism will discussed as building blocks for large biomolecules. Throughout the course the links between metabolism, hereditary pathologies, as well as risk of metabolic imbalances such as diabetes and obesity will be presented.

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.

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. This course will be offered in 2021-22, and in alternating years thereafter.

Modern synthetic methods as applied to the construction of societally relevant target molecules will be the focus of this course. Discussions may emphasize the logic and strategy in synthetic approaches toward active pharmaceutical ingredients, agrochemicals, fine chemicals, materials, and other targets of interest. The analysis of current examples from the primary literature will draw attention to the most state-of-the-art synthetic tactics. Recommended for graduate students and undergraduates who have a basic understanding of the principles governing organic reactions, such as those covered in CH2310, CH2320, and CH2330. This course will be offered in 2022-23 and alternate years thereafter.

The principles and applications of group theory as a tool in chemistry are presented with an emphasis on systems in inorganic chemistry. Topics covered include the development of symmetry group representations and character tables, applications of group theory in quantum-mechanical wavefunctions, molecular vibrations, ligand field theory, and molecular orbital theory. Particular emphasis will be placed on transition metal complexes, including classical coordination complexes, metal carbonyl complexes, and organotransition metal complexes.

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 2021-22, and in alternating years thereafter.

Advanced topics in identification of organic species and determination of molecular structure by spectroscopic methods. Methods covered include !H- and 13 C-NMR, mass spectrometry and infrared and UV-visible spectroscopy. This course is concerned only with interpretation of spectra and does not cover techniques obtaining them; there is no laboratory.

This course emphasizes the fundamental aspects of ID and 2D nuclear magnetic resonance spectroscopy (NMR). The theory of pulsed Fourier transform NMR is presented through the use of vector diagrams. A conceptual nonmathematical approach is employed in discussion of NMR theory. The course is geared toward an audience which seeks an understanding of NMR theory and an appreciation of the practical applications of NMR in chemical analysis. Students are exposed to hands-on NMR operation. Detailed instructions are provided and each student is expected to carry out his or her own NMR experiments on a Bruker AVANCE 400 MHz NMR spectrometer.

This course will focus on the medicinal chemistry aspects of drug discovery from an industrial pharmaceutical Research and Development perspective. Topics will include Chemotherapeutic Agents (such as antibacterial, antiviral and antitumor agents) and Pharmacodynamic Agents (such as antihypertensive, antiallergic, antiulcer and CNS agents).

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This course trains students in the area of molecular modeling using a variety of quantum mechanical and force field methods. The approach will be toward practical applications, for researchers who want to answer specific questions about molecular geometry, transition states, reaction paths and photoexcited states. No experience in programming is necessary; however, a background at the introductory level in quantum mechanics is highly desirable. Methods to be explored include density functional theory, ab initio methods, semiempirical molecular orbital theory, and visualization software for the graphical display of molecules.