Master of Science
Chemistry and Biochemistry
Faculty
A. Mattson, Professor and Department Head; Ph.D., Northwestern University; metal-free catalyst design, methodology development, complex molecule synthesis.
J. M. Argüello, Professor; Ph.D., Universidad Nacional de Río Cuarto, Argentina; transmembrane ion transport, metal-ATPases structure-function, bacterial metal homeostasis, role os metals in bacterial pathogenesis.
S. C. Burdette, Professor; Ph.D., Massachusetts Institute of Technology; synthesis of fluorescent sensors for iron, photoactive chelators for delivery of metal ions in cells, applications of azobenzene derivatives with unusual optical properties, polymers to detect metal contaminants in the environment.
B.E. Bursten, Professor; Ph.D., University of Wisconsin–Madison; correlation of theoretical electronic structural data with the bonding and reactivity patterns of transition metal and heavy-element complexes
R. E. Dempski, Professor; Ph.D., Massachusetts Institute of Technology; molecular mechanism of human zinc transporter, structure-function of light activated channel, optogenetics.
J. P. Dittami, Professor; Ph.D., Rensselaer Polytechnic Institute; medicinal chemistry, organic synthesis, new synthetic methods development.
A. Gericke, Professor; Dr rer nat., University of Hamburg; biophysical characterization of lipid-mediated protein function, development of vibrational spectroscopic tools to characterize biological tissue.
R. L. Grimm, Associate Professor; Ph.D., California Institute of Technology; growth and characterization by surface science and by photoelectrochemistry of non-traditional semiconductor materials related to solar energy capture, catalysis, and conversion.
G. A. Kaminski, Associate Professor; Ph.D., Yale University; computational physical and biophysical chemistry, force field development, protein structure and binding, host-guest complex formation, solvation effects.
J. MacDonald, Associate Professor; Ph.D., University of Minnesota; porous crystalline materials composed of organic & coordination compounds, polymorphism of pharmaceutical drugs, crystallization of proteins, surpramolecular assembly on surfaces.
P. Musacchio, Assistant Professor; Ph.D., Princeton University; catalysis, methodology development, complex molecule synthesis.
C. Perez Olsen, Assistant Professor; Ph.D., University of Washington; characterization of membrane composition by mass spectrometry, quantification of lipid flux with stable isotope tracers, genetic dissection of the regulatory pathways of membrane maintenance.
S. F. Scarlata, Professor, Ph.D., University Illinois Urbana-Champaign; Mechanisms of cell signaling using fluorescence imaging and correlation methods, how mechanical deformation affects calcium fluxes in cells.
Research Interests
The four major areas of research in the department are:
- Biochemistry and Biophysics. Within this area there is active research on a number of topics including heavy metal transport and metal homeostasis of both plants and bacteria, computational biochemistry/biophysics of membrane proteins, enzyme structure and function, and G protein and calcium signaling, membrane protein domains and mechanotransduction.
- Molecular Design and Synthesis. Within this area there is active research on topics encompassing organic synthesis and medicinal chemistry, supramolecular materials, metal ion sensors and chelators, polymorphism in pharmaceutical drugs, spectroscopy and photophysical properties of molecules, catalysis for C-H functionalization, and more.
- Nanotechnology and Materials. This research area encompasses such projects as photonic and nonlinear optical materials, nanoporous and microporous crystals of organic and coordination compounds, molecular interactions at surfaces, and others.
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Sustainability and Green Chemistry. This focus addresses the efficiency in which we use natural resources, utilizing and producing less environmentally hazardous chemicals, discovering new pathways for chemical syntheses, discovering catalytic reagents to supplant stoichiometric reagents, as well as carbon-negative materials and processes.
Programs of Study
The Department of Chemistry and Biochemistry offers the M.S. and Ph.D. in both Chemistry and Biochemistry. Major areas of research in the department align with the research interests above.”
Admission Requirements
A Bachelor of Science degree with demonstrated proficiency in chemistry or biochemistry is required for entrance to Chemistry and Biochemistry graduate programs.
Degree Requirements
Each Ph.D. student must take at least three core courses in their self-identified home track (biochemistry, inorganic, organic, physical), at least three elective courses either from an approved list of classes or pre-approved by the CBC graduate committee, as well as seminar courses. Entering Ph.D. students who have deficiencies in specific areas (inorganic, organic, physical, or biochemistry), as revealed by entrance interviews, will take appropriate courses to correct these deficiencies. Students entering with a M.S. degree may petition for a reduced course load.
Chemistry and Biochemistry Research Laboratories
The Chemistry and Biochemistry Research Laboratories are located in Goddard Hall and at Gateway Park. Department facilities and instrumentation in individual research laboratories include 500 and 400 MHz FT-NMR, GC-MS, GC, HPLC, capillary electrophoresis, DSC (differential scanning calorimeter), TGA (thermogravometric analysis), polarizing optical stereomicroscope, FT-IR, UV-VIS absorption, fluorescence and phosphorescence spectroscopy; powder and single crystal X-ray diffractometers, X-ray photoelectron spectrometer, cyclic voltammetry, impedence spectroscopy, ellipsometer, quartz crystal microbalance, grazing incidence IR, atomic force microscope (AFM), and other surface-related facilities. Additional equipment in the biochemistry area include: centrifugues, ultra-centrifugues, PCR, phospho imager, scintillation counter, FPLC, bacteria and eukaryotic cell culture and plant growth facilities.
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M.S. in Chemistry or Biochemistry, -
Ph.D. in Chemistry or Biochemistry, Ph.D.
Classes
CH 516: Chemical Spectroscopy
Department
The emphasis is on using a variety of spectroscopic data to arrive at molecular structures, particularly of organic molecules. Major emphasis is on inland C-NMR, IR and MS. There is relatively little emphasis on theory or on sampling handling techniques.
CH 520: Cell Signaling
Department
Cell signaling defines the way cells respond to changes in their environment including, heat, nutrients, drugs, hormones, and other factors. These external factors allow cells to grow, divide, migrate and proliferate depending on the stimulus, and inappropriate responses lead to cancer and other diseases. This course is directed for advanced undergraduates and graduate level course that is a combination of on-line lectures, discussions, and review of recent literature. Students who previously took the CH 555 version of this course cannot take CH 520 for credit.
CH 536: Theory and Applications of NMR Spectroscopy
Department
This course emphasizes the fundamental aspects of 1D 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.
CH 538: Medicinal Chemistry
Department
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).
Prerequisites
A good foundation in organic chemistry, e.g., CH 2310 Organic Chemistry I and CH 2320 Organic Chemistry II
CH 540: Regulation of Gene Expression
Department
This course covers the biochemical mechanisms involved in regulation of gene expression: modifications of DNA structures that influence transcription rates, transcriptional regulation, post-transcriptional processing of RNA including splicing and editing, nuclear/cytoplasmic transport, regulation of translation, and factors that control the half-lives of both mRNA and protein. During the course, common experimental methods are explored, including a discussion of the information available from each method.
CH 541: Membrane Biophysics
Department
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 an introduction to 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. Topics will be developed assuming a good understanding of protein and lipid chemistry, enzyme kinetics, cell biology, and electricity.
CH 542: Drugs in the Brain
Department
This class will introduce the concepts of basic neuropharmacology and the action of major neurotransmitter families in the brain. The mechanisms of action of the major psychoactive drugs families including cannabis, opioids, and psychedelics will be covered. The effects of pharmaceutical treatments for anxiety and depression on brain chemistry will be discussed as well.
Recommended Background
Fundamental understanding of introductory biochemistry (CH4110, CH4120, and/or CH4130).
CH 543: Organometallic Chemistry and Catalysis
Department
Organometallic chemistry and catalytic reactions have fundamentally changed the way drugs and polymeric materials are made today. Furthermore, they have enabled the synthesis and application of new electronic materials (e.g. in OLEDs and molecular wires) and materials mimicking natural processes (e.g. self-healing and anti-bacterial coatings). This course will establish principles to understand the reactivity of organometallic compounds of transition and main groups metals. Furthermore, metal-free catalysis will be introduced. Pulling on influences from both inorganic and organic chemistry, the class will provide insight into catalysis approaches that have revolutionized synthetic chemistry, enabling highly efficient, sustainable production of compounds that are used in such different areas as drug discovery, protein analysis, and performance plastics. Case studies will be drawn from the current literature and applications that are widely used in industrial and academic settings and will include work that has led to recent Nobel prizes in the area. Recommended preparation includes the organic chemistry sequence (CH2310, CH2320, and CH2330) and CH3410. The course is recommended for both graduate and advanced undergraduate students.
CH 544: Elucidation of Organic Reaction Mechanisms
Department
In this advanced course, students will develop skill sets to independently understand, explain, and predict reactions of organic molecules. Principles of modern physical organic chemistry, such as bonding, hybridization, molecular orbital theory, non-covalent interactions, stereochemistry, and conformational analysis, will be introduced alongside experimental techniques related to thermodynamics and kinetics to provide scientists with tools to understand existing reaction pathways and study new reactions. The interplay between mechanistic hypotheses and experimental observations will be demonstrated using case studies from the primary literature. Recommended for graduate students and undergraduates who have completed the sequence in organic chemistry (CH2310, CH2320, and CH2330).
CH 545: Plant Natural Products
Department
This class will cover the chemistry of a number of families of plant-derived natural products, including, terpenoids, phenolic compounds, and alkaloids. The coverage of aspects of the chemistry involving these natural products may include biosynthesis, chemical synthesis, and medicinal chemistry applications. The historical and current roles of select natural products, such as tetrahydrocannabinol, taxol, heroin, and quinine, in society may also be discussed. This class will be offered in 2020-2021 and alternating years thereafter.
Recommended Background
A fundamental understanding of organic chemistry, such as that obtained in an introductory organic chemistry sequence (CH2310, CH2320, and CH2330).
CH 546: Natural Product Isolation and Analysis
Department
In this laboratory class, students will learn strategies to isolate and characterize natural products. Techniques used during this course may include solvent extraction, supercritical fluid extraction, NMR spectroscopy, IR spectroscopy, mass spectrometry, gas chromatography, and liquid chromatography. This class will be offered in 2021-2022 and alternating years thereafter.
Recommended Background
Introductory chemistry laboratory experience.
CH 554/CHE 554: Molecular Modeling
Department
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.
CH 555: Advanced Topics
A course of advanced study in selected areas whose content and format varies to suit the interest and needs of faculty and students. This course may be repeated for different topics covered.
This course is 1-3 credits as arranged.
CH 560: Current Topics in Biochemistry
Department
In this seminar course, a different topic is selected each semester. Current articles are read and analyzed.
CH 561: Functional Genomics
Department
In this seminar course, students will present and critically analyze selected, recent publications in functional genomics. The course will conclude with a written project, either a mini-grant proposal or an analysis of publicly available data in a research manuscript format. The course will be offered in alternate years, and is offered by special arrangement only based on expressed student interest.
CH 571: Seminar
Department
Reports on current advances in the various branches of chemistry.
CH 598: Directed Research
Department
CH 599: M.S. Thesis
Department
CH 699: Ph.D. Dissertation
Department
CH 4110: Biochemistry I
Department
The principles of protean 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.
CH 4120: Biochemistry II
Department
Oriented around biological membranes, this term 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.
CH 4130: Biochemistry III
Department
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.
CH 4140: Metabolism and Disease
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.
Specific concepts that we will discuss are: Glucose and glycogen metabolism; Gluconeogenesis; Citric Acid Cycle; Lipid, amino acid and nucleotide metabolisms; Mammalian Fuel Metabolism: Integration and Regulation.
Recommended Background
Familiarity with organic chemistry topics including functional groups, nucleophilic addition and substitution reactions, stereochemistry, and carbonyl chemistry. General knowledge of cellular architecture is also recommended. See CH 2310, CH 2320, CH 2330, and BB2550 or equivalent.
CH 4330: Organic Synthesis
Department
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.
CH 4420: Inorganic Chemistry II
Department
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 catalysis by metal complexes.
Recommended Background
CH 2310 and CH 2320, or equivalent.
CH 4520: Chemical Statistical Mechanics
Department
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.