Graduate Course Descriptions

Chemistry Graduate Course Descriptions

CH 521 Advanced Organic Chemistry     3 CR
Explores the effects of structure and environment on reaction rates and equilibria and the use of statistical and quantum mechanics in organic chemical reactions. Topics include organic reaction mechanism, Huckel theory, orbital symmetry, photochemistry and standard concepts of physical organic chemistry. Prerequisite: CH-222 Organic Chemistry II or equivalent

CH 522 Organic Chemistry     3 CR
Surveys three general classes of reactions, namely reduction, oxidation and the formation of carbon-carbon bonds. Each reaction will be used as a tool in chemical synthesis. For the chem-bioinformatic track emphasis will be given to biomolecules. Prerequisite: CH-222 Organic Chemistry II or equivalent

CH 523 Spectroscopic Methods in Organic Chemistry     3 CR
Identification and structure determination of organic molecules by modern spectroscopic techniques. Emphasis on IR, NMR, CMR and mass spectrometry. Hands-on work in NMR and FT-IR. Prerequisites: CH-222 Organic Chemistry II and CH-351 Instrumental Analysis or equivalent

CH 524 Special Topics in Organic Chemistry     3 CR
Heterocyclic Chemistry; Medicinal Chemistry; Polymer Chemistry; Supramolecular Chemistry; Organometallic Chemistry; Radical and Photochemistry; Combinatorial Chemistry.

CH 526 Medicinal Chemistry and Pharmacology     3 CR
A basic neuropharmacology - neurochemistry course in which principles underlying the actions of neural transmission, neurotransmitters and medications are addressed. Chemicals that affect the CNS are presented, including routes of drug administration, pharmacokinetics, pharmacodynamics drug-receptor interactions, and drug metabolism. In addition, mechanisms of action, therapeutic effects, adverse effects and therapeutic indications are noted for major classes of drugs and for commonly used drugs within each class.

CH 530 Physical Chemistry II     3 CR
Explores advanced kinetics and quantum mechanics. Prerequisite: Physical Chemistry or equivalent

CH 531 Advanced Physical Chemistry I: Molecular Structure     3 CR
Topics in quantum chemistry, molecular structure, group theory and applications of these topics to spectroscopy. Prerequisite: CH-332 Physical Chemistry II or equivalent

CH 532 Advanced Physical Chemistry II: Molecular Dynamics     3 CR
Topics in statistical thermodynamics, collision theory, and reaction dynamics and mechanism. Prerequisite: CH-332 Physical Chemistry II or equivalent

CH 533 Bio-Physical Chemistry     3 CR
This course provides a rigorous introduction to the application of physical theory and methods to the study of biomolecular systems. Topics covered will include a review of classical and quantum theory and a review of protein, nucleic acid, carbohydrate and lipid structure and function. More advanced material will emphasize the application of physical theory, especially thermodynamic and kinetic theory, to understand biomolecular structure and function, with an emphasis on understanding protein folding, protein-ligand binding and enzyme catalysis. Students will also learn about the use of physical methods such as spectroscopy, NMR and crystallography to study biomolecular structure and function. The course will also introduce students to the use of computational methods to model and simulate biomolecules, with an emphasis on protein modeling and simulating proteins.

CH 534 Special Topics in Physical Chemistry     3 CR
Topics include: Magnetic Resonance Spectroscopy; Statistical Mechanics; Mathematical and Computer Concepts in Chemistry.

CH 541 Advanced Biochemistry     3 CR
Explores the integration of the basic chemistry of biomolecules into living systems. Topics include bioenergetics and metabolic pathways; biosynthesis and biodegredation of amino acids, proteins, nucleotides and DNA; chemical communication; hormones and the cell cycle. Prerequisite: CH-342 Biochemistry II or equivalent

CH 545 Bioinformatics   3 CR
This hands-on course provides an introduction to the theory and application of bioinformatics methods and algorithms to solve biological research problems. A variety of practical and theoretical topics will be covered, with an emphasis on applying bioinformatics methods to solve real world problems. Thus, while students will be introduced to the theoretical underpinnings of bioinformatics, emphasis will be on students learning how to search and mine databases, calculate and analyze protein and nucleic acid sequence alignments, analyze genes and phylogenetic trees, compare and classify molecular structures, and analyze data from genomics and proteomics experiments. Students will also learn how to use known protein and nucleic sequences and structures to model and analyze unknown protein and nucleic acid structures. Finally, the course introduces students to the use of bioinformatics programs to predict protein function and analyze protein interaction networks.

CH 547 Computational Chemistry & Molecular Modeling
This is an advanced course in computational chemistry and molecular modeling. The course will cover classical theory and its application to molecular modeling and simulation. Most of the course, however, will be devoted to quantum theory and its application to molecular modeling and simulation. Students will learn about semi-empirical and ab initio methods, their algorithmic implementations, and the ways they can be applied to solve molecular problems. The course will balance theoretical instruction with project-based problem solving and students will get the opportunity to use sophisticated, research-quality computational chemistry software.

CH 549 Special Topics in Biochemistry     3 CR
Topics include: Medicinal Chem & Pharmacology; Electrically Excitable Cells; Computer Aided access to Proteins and Data Bases; Cell Motility; Chemical Concepts in Genetic Engineering.

CH 550 Instrumental Analysis     3 CR
Explores theory and practice of instrumental methods of analysis: spectrophotometric, electroanalytical, and chromatographic methods of separation and quantification. Prerequisites: CH-252 Analytical Chemistry and CH-331 Physical Chemistry or equivalent

CH 551 Advanced Analytical Instrumentation I: Spectroscopy     3 CR
Fundamentals and practical aspects of analytical spectroscopy. Special emphasis will be given to theory and instrumentation; methods and applications will be covered. Prerequisite: CH-351 Instrumental Analysis or equivalent

CH 552 Advanced Analytical Instrumentation II: Chromatography     3 CR
Fundamentals and practical aspects of analytical separation and chromatography. Special emphasis will be given to theory and instrumentation; methods and applications will be covered. Prerequisite: CH-351 Instrumental Analysis or equivalent

CH 553 Inorganic Chemistry     3 CR
The physical and chemical properties of the elements and their compounds are correlated with their positions in the periodic table. Bonding theory and coordination chemistry are emphasized. This undergraduate-graduate level course also has an undergraduate course number of CH 355. Three credits will be given for the completion of this course with a grade “B” or better. For the chem-bioinformatics track emphasis will be given to biomolecules.

CH 554 Special Topics in Analytical Chemistry     3 CR
Topics include: Data Acquisition and LIMS; Aquatic Chemistry; GC-MS: Theory, Instrumentation and Method; Thermal Analysis; Applications of Super Critical Fluids.

CH 555 Theoretical Inorganic Chemistry     3 CR
An advanced theoretical study of bonding and spectroscopy of inorganic compounds. Topics include crystal field, ligand field and molecular orbital theories of inorganic complexes; magnetic susceptibility and electronic, infrared and raman spectroscopy. Prerequisite: CH-355 Advanced Inorganic Chemistry

CH 556 Chemical Applications of Group Theory     3 CR
Basic principles of group theoretical methods. Topics include molecular symmetry, normal coordinate analysis, molecular bonding and energy levels and theoretical basis for selection rules. Prerequisite: CH-355 Advanced Inorganic Chemistry

CH 559 Special Topics in Inorganic Chemistry     3 CR
Topics include: Electronic Spectra of Transition Metal Complexes; Reactions of Transition Metal Complexes; Ionic Liquids; Bioinorganic Chemistry.

CH 561 Environmental Chemistry     3 CR
Focuses on the chemical aspects of the human environment. The course will examine the sources, reactions, transport, effects, and fates of chemical species in water, soil, air and living environments and the effects of technology thereon. Prerequisite: CH-221 Organic Chemistry I and MA-151 Introductory Calculus or equivalent

CH 565 Environmental Sampling and Analysis     3 CR
Discusses methods and protocols of environmental sampling and analysis in water, air and biological matrices. Addresses EPA quality assurance and quality control plan. Laboratory and field work include sampling of sur and groundwater, chemical and biological analyses of water, monitoring, treated effluent quality control, and detection of hazardous contaminants. Prerequisite: CH-561 Environmental Chemistry or equivalent

CH 567 Design of Experiments     3 CR
The objective of this course is to teach students the statistical tools used by scientists to design, conduct, and analyze experiments effectively and efficiently. Also to teach students how to obtain information for characterization and optimization of systems. In this process the students will learn how to use Minitab software to conduct their analysis. Prerequisite: All students are assumed to have an introductory level of statistics

CH 569 Special Topics in Environmental Chemistry     3 CR
Topics include: Water and Wastewater Treatment Systems; Hazardous Waste Management; Environmental Regulations; Environmental Hydrology and Water Resource Management; Atmospheric Chemistry and Air pollution; Chemical Toxicology.

CH 571 Polymer Chemistry     3 CR
Introduction to polymer chemistry through a study of step and chain polymerization and copolymerization as well as block and graft copolymers. Polymerization techniques in solution, emulsion, and microemulsion. Polymer structure and characterization with an overview of the properties of commercial polymers. Prerequisite: CH-222 Organic Chemistry II or equivalent

CH 590/CH 590L ChemInformatics: Sources and Technology     3 CR
Information is a vital key to success in today's chemical and pharmaceutical industries. The premier chemical information resources will be reviewed with emphasis on Chemical Abstracts Service (CAS). Chemical information retrieval applications will be highlighted including STN International and Scifinder, in addition to select Internet resources. Students will gain an appreciation for chemical database design and content as well as formulating effective queries for text & structure-based searches. Personal laptop with internet connectivity is required.

CH 595 Advanced Integrated Laboratory     3 CR
The central theme for this laboratory is inorganic coordination chemistry. Students will be required to work on unified projects rather than a series of unrelated experiments. Projects will involve synthesis and analysis of a complex or a pair of isomers. Emphasis will be on analytical and instrumental methods that are fundamental for the characterization of inorganic compounds. Six hours of laboratory work per week.

CH 597 Molecular modeling and drug design     3 CR
This course provides a guided introduction to molecular modeling and computer-enabled drug design. The course will emphasize the practical application of advanced software to analyze, model, simulate and design drugs and their target interactions. While the course will explore the theoretical aspects of molecular modeling and drug design, considerable classroom time will be devoted to applied modeling and design using available software tools and resources. Topics covered will include an introduction to drug discovery, a review of biochemistry and basic physical theory, molecular database searching, molecular visualization and analysis, conformational analysis, protein-ligand docking, virtual screening, ADME/Tox prediction, molecular dynamics and Monte Carlo simulations and QSAR.

CH 598 Comprehensive Exam     0 CR
Chemistry graduate students (non-thesis track) are required to pass a comprehensive test (after the completion of 33 Crs in course work for the Molecular Biochemistry track and 35 Crs in course work for the Chem-Bioinformatics track)) in fulfillment of the MS degree.

CH 599 Thesis     3 + 3 CR
Original research under the supervision of faculty member(s) leading to a written thesis. 

Computer Science Graduate Course Descriptions for Chem-Bioinformatics Track

CS 504 Intro to Programming and Using Scripting     3 CR
This course will provide an introduction to structured programming and elementary data structures using the Javascript language [or any other scripting or dynamic language such as Python, Perl, PHP, LUA or Ruby]. Topics covered include basic programming concepts, control statements, loops and branching structures, string processing, and debugging.

CS 550 Dynamic Web Page Development     3 CR
This course enables students to develop low-bandwidth visual effects for web pages. A variety of software will be employed to develop web sites and media for the web. Topics include: (1) web animation and interactivity using Macromedia Flash®, (2) vector-based graphic construction and digital compression using Macromedia Fireworks®, a graphic optimizing tool, and (3) dynamic web page construction using Macromedia Dreamweaver®, a visual HTML editor. Prerequisite: CS 500.

CS 551 Introduction to Object-Oriented Programming with Java     3 CR
Introduction to fundamental concepts of object-oriented analysis (OOA), design (OOD) and programming (OOP), and how object-oriented languages differ from procedural languages. Notation is used to teach the concepts of abstraction, encapsulation, modularity, hierarchy and polymorphism. This course is designed for both programmers and analysts. Java is used to implement these objected-oriented concepts. Prerequisite: CS 501.

CS 603 Database Design     3 CR
Goals and techniques in the design, implementation and maintenance of large database management systems: physical and logical organization, file structures, indexing, entity relationship model, hierarchical, network and relational models, normalization, query languages and database logic. Prerequisite: CS 501

CS 615/348 Programming in Unix     3 CR
To be completed by CS faculty member. Discusses main issues of Unix OS programming and administration. In particular, it explores a popular Unix text editor Emacs, Unix file system, process manipulation, regular expressions and their use, filters, and system administration and security. Prerequisite: CS611 or permission of the instructor