Graduate Chemistry Course Descriptions
Chemistry 501 - Organic Chemistry
This core organic chemistry course introduces reaction mechanisms and organic synthesis to students with varying undergraduate backgrounds in chemistry. Critical skills toward solving mechanism are developed as the underlying organic principles (kinetics, strain, stereoelectronics, stereochemistry and conformational analysis) are elaborated. These principles will be used to predict and understand reactivity and stereochemistry in more sophisticated reactions. Some of the common carbon-carbon bond forming reactions and functional group manipulations are discussed. This course draws on many synthetic examples from the chemical literature to illustrate mechanism, synthetic utility and to exercise predictive skills.
Chemistry 502 - Synthetic Organic Chemistry
The aim of this course is to cultivate knowledge of modern organic synthesis. The application of organic reactions to the synthesis of complex molecules, including natural products, will be studied. In addition to synthetic strategies, detailed reaction mechanism, reaction scope and issues in catalysis will be discussed. The course material will draw heavily on the Nicolaou text, but will also engage the student with recent synthetic literature. Most students will have taken CHE 501 prior to taking this course.
Chemistry 503 - Inorganic Chemistry
This course is intended to provide students with a broad background in inorganic chemistry. The fundamental concepts of coordination chemistry will be developed, including the structure, electronic properties, and reactivity of transition metal complexes. Elements of group theory will be introduced to describe the fundamental underpinnings of spectroscopic and crystallographic characterization methods. Fundamentals of organometallic chemistry and catalytic reaction mechanisms will be covered. The course will conclude with introductions to bioinorganic chemistry and solid-state inorganic chemistry.
Chemistry 504 - Physical Methods of Inorganic Chemistry
This course will survey modern physical methods of characterization and study of inorganic and organometallic compounds. Topics include NMR, IR and UV/visible spectroscopy, ESR, and mass spectrometry. Examples of applications of these methods in the current literature will be presented.
Chemistry 505 - Physical Chemistry I
This course will begin with a review of the fundamentals of classical thermodynamics with emphasis on the connections between thermodynamics and microscopic structure. The subject matter will then be developed from a molecular and statistical point of view. The usefulness of thermodynamics and associated statistical methods in understanding molecular events in chemical reactions will be stressed. The kinetics of chemical processes will be treated for reactions in both gaseous and condensed phases in the last third with an emphasis on current reaction dynamics (theory and experiment).
Chemistry 506 - Physical Chemistry II
“Bands and Bonds”.
These days quantum chemistry programs are not only used by theoreticians but also in many experimental groups in order to assist research. This course is designed to give the students an overview of computational methods applied both to molecules and to solids. The molecular orbital (MO) model and its application to molecules will be introduced. Periodic systems can be modeled by using either the linear combinations of atomic orbitals (LCAO), or the nearly free electron approach. Results from both will be compared. Practical computational exercises will be given. In addition, the students will learn how to predict the general electronic structure of a system without performing any computations.
Chemistry 507 - Analytical Chemistry
This course will be a survey comprising two topics: (1) electroanalytical chemistry, including potentiometry, voltammetry, coulometry and coulometric titrations. (2) spectroscopy; including atomic, molecular absorption, emission detectors and signal-to-noise theory. spectroscopy, including atomic absorption and emission spectroscopy, molecular absorption and emission spectroscopy, detectors and signal-to-noise theory, and various analytical aspects of non-optical spectroscopy. An introduction to relevant instrumentation on these two topics will be discussed.
Chemistry 508 - Statistics & Instrumentation
PRINCIPLES AND EXAMPLES from the following areas will be presented.
Modern Separation Processes. Gas-Liquid Chromatography, Gas-Solid Chromatography, High Performance Liquid Chromatography, Supercritical Fluid Chromatography, Capillary Electrophoresis and Capillary Electrochromatography.
Statistical analysis will be discussed from the viewpoint of proper interpretation of ones experimental data.
Chemistry 510 - Advanced Inorganic Chemistry Topics
This course will review the structure and properties of inorganic materials that are relevant for real world applications such as electronics, energy conversion, gas storage, and catalysis. Specifically, the course will include discussion of ceramics, layered compounds, porous materials, semiconductors, superconductors, and magnetic materials. Elements of solid-state chemistry and physics will be discussed, and important characterization techniques such as X-ray diffraction and electron microscopy will be addressed. The role of finite size will be discussed with reference to recent advances in nanoscience and nanotechnology.
Chemistry 514A - Special Topics in Organic Chemistry: Bio-Organic Chemistry
This course will present some of the recent developments in bioorganic chemistry on various topics such as protein structure and design, nucleic acid structure and design, peptide nucleic acids, peptoids, betapeptides, non-natural oligomers, ribozymes, and catalytic antibodies. Basic understanding of the biorelevant molecules will be provided as a foundation, followed by a discussion of recent papers focusing on the structure, function, and design aspects.
Chemistry 514B - Special Topics in Organic Chemistry: Structural Identification
This is a spectroscopic course targeted for structural characterization in organic chemistry.
Chemistry 514C - Special Topics in Organic Chemistry: Organometallics in organic Synthesis
This course will survey the recent advances of organometallic reactions in modern organic synthesis.
Chemistry 514D - Special Topics in Organic Chemistry: Polymer Chemistry
Synthetic polymers have become an integral part of our lives and can be found in many everyday and advanced materials: rubber tires, bullet-proof vests, paints, fibers, contact lenses, drug delivery vehicles and many others. This course will cover the basics of polymer synthesis, including traditional polymerization techniques, such as free-radical and anionic chain polymerizations, and step-growth polymerization. Newer methods of polymer synthesis, such as ring-opening metathesis polymerization and living free-radical polymerizations will also be discussed. Students will be introduced to the methods of preparation of advanced polymer structures, such as block, star and brush copolymers, semi-conducting and biodegradable polymers. Fundamentals of structure and physical properties of polymers, and methods of characterization will also be covered.
Chemistry 516 - Special Topics in Analytical Chemistry: Environmental Chemistry
This course will focus on the role of Analytical Chemistry in the investigations on the fate and transport of chemical pollutants in the environment. In this regard, we will discuss the fundamentals of environmental sampling, sample preparation, and trace analysis using modern instrumental techniques (LC/MS, GC/MS, ICP/MS, etc). Topics will also include a discussion of the physico-chemical factors that affect the persistence, mobility, and distribution of pollutants in soil, water, atmosphere, and biota. In addition, we will be discussing recent research articles from the Journal of Environmental Science and Technology to familiarize the students with current and emerging issues that are relevant to environmental chemistry. Ultimately, the students will not only learn how to select the most appropriate analytical tool for a particular environmental investigation, based on knowledge of the chemical and physical properties of pollutants, but they will also become knowledgeable on the impacts of chemical pollutants on wildlife, human health, and the environment as a whole.
Chemistry 520 - Organometallic Chemistry
Survey of organometallic chemistry, with the emphasis on transition metals. The course covers structure and bonding of organometallic compounds, synthesis, reaction mechanisms, and selected applications in synthetic organic chemistry and catalysis.
Chemistry 523A - Bioinorganic Chemistry
This course will cover current topics of interest in bioinorganic chemistry. Topics to be covered include metalloenzymes and biomimetic chemistry, metallodrugs and metal ion complexes used as imaging agents in medicine.
Chemistry 525 - Electrochemical Technology I
This course will provide an intermediate level discussion of electroanalytical and physical electrochemical topics. Included are potentiostatic, potentiodynamic, galvanostatic and coulostatic methodologies. Analysis of literature publications using one or more of these approaches will be emphasized.
Chemistry 527 - Analytical Surface Spectroscopy
This course is meant to introduce methods of surface analysis and their applications within a framework which includes a problem solving approach to complex real world systems. The course will be divided into three areas; formal lecture material, teamwork based problems sets, assignments and oral presentation/research review paper. The grading will be based on two exams (both take home), problem sets (a shared team grade which the class will assign) and the presentation and review paper. The material to be covered in lecture will cover electron spectroscopies, optical spectroscopies and ion spectroscopy as they are applied to the determination of surface chemistry. The applications of these methods will be developed through the problem sets and the review papers. Topics such as catalysis, corrosion, adhesion, semiconductor materials, biomaterials, electrochemical surfaces, polymers, membranes and other as of interest to the class will be discussed.
Chemistry 528 - Analytical Microseperations
This course covers fundamental principles and analytical applications of microseparation techniques in the liquid phase. Emphasis is given to the fundamentals in capillary electrophoresis (CE), capillary electrochromatography (CEC), and capillary liquid chromatography (CLC). Topics discussed include theories of the separation processes and instrumentation.
Chemistry 530 - Analytical Mass Spectrometry
This course covers modern analytical mass spectrometry techniques and their application to solving research problems. Part of the course will focus on instrumentation - mass analyzers, ionization sources, detectors, inlet systems, etc. The analytical advantages of each method will be explored, as will an understanding of the fundamental principles which underlie each methodology. In addition, we will examine sophisticated experimental methods, such as tandem mass spectrometry (MS/MSO for structural elucidation, on-line separations, mass spectrometry (GC/MS, LC/MS, CE/MS, etc.) in which the mass spectrometer serves as a detector for separations techniques, and quantification. Another portion of the course will be dedicated to mass spectral interpretation. Topics such as isotope distribution and fragmentation patterns (for organic compounds as well as biological compounds) as useful tools in mass spectral interpretation will be covered. Throughout the course, the broad-ranging applications for mass spectrometry will be underscored, from forensics to geological/archaeological dating to biomolecule sequencing to studying atmospheric chemistry.
Chemistry 512 - Mini Courses in Physical Chemistry (1 crd)
- NMR in Life Sciences: A one semester NMR lecture course with emphasis on protein NMR spectroscopy and NMR-based metabonomics. CHE 512 will combine a comprehensive theoretical treatment of high resolution NMR spectroscopy with an exposition of the experimental techniques applicable to biological macromolecules. The "Product Operator Formalism" will be presented with particular emphasis in order to enable the participants to understand sophisticated multidimensional NMR experiments. This course also teaches the methodological foundations to pursue NMR-based structural biology.
- Practical Crystallography for Chemistry and Materials Science: Goals of the Course: How to see atoms using Crystallography, How to grow crystals, How to get a working knowledge of X-ray crystallographic techniques. Topics covered: Crystal lattices, The geometry of X-ray diffraction: single crystals and powders, Atomic structure and the intensity of reflected X-ray beams, Crystallization techniques, Use of an optical microscope, X-ray data collection, Symmetry elements and their effect on the diffraction pattern, From X-ray intensities to atomic structure Interpretation and presentation of results, The use of crystallographic databases: Practical experience with searching the Cambridge Structural Database and the Inorganic Database.
- Computation of NMR Parameters: In this 5-week unit we will learn about the basic mechanisms for NMR nuclear magnetic shielding and spin-spin coupling from a theoretical point of view. The mini-course includes "hands-on" exercises for computations of NMR parameters with quantum chemistry software. Students will be provided with access to computers and step-by-step instructions for using the software. For instance, we will verify by computations that C-H coupling constants for ethane, ethene, ethyne, and benzene are proportional to the carbon hybridization s-character.
- Biomineralization: Nature already creates many elaborate structures at room temperature and in mild physiological environments compared to present chemical syntheses under extreme conditions. Recent progress has revealed new insights into the control of crystal growth of biominerals by biological macromolecules and by organic and inorganic small molecules. This course will discuss the mechanisms of crystallization from solutions and future research directions in understanding hard tissue diseases, both natural (bones and teeth) and pathological (e.g. kidney stones). The finding that nano-sized crystallites and protein co/self assemblies may be involved in the in vivo nucleation and growth of biological minerals opens up a whole new approach to our understanding of biomineralization and the in vitro mimicking of these processes.
- Basic Practical NMR Spectroscopy: This module is designed to teach the users of the Varian NMR spectrometers how to use the VNMR menus to acquire and process data. The users will also be taught the importance of proper procedures for locking, shimming, optimization of NMR parameters and phasing of NMR spectra, as well as its presentation. The following experiments will be covered: 1D proton, 1D carbon, DEPT, COSY and HSQC.
- Computer Modeling of Biological Systems I: The course is the first part of a three-segment cycle of lectures devoted to computer modeling of biological systems such as proteins and nucleic acids. The cycle of lectures is designed for seniors and graduate students who are interested in studying biological systems at the molecular level. The goal is to provide a general overview of computational quantum chemistry (Part I), molecular mechanics (Part II), and a combined QM/MM method (Part III) as applied to molecules of biological interest. The courses are in the form of a computational laboratory, based on Windows PC workstations, Q-Chem/AMBER software for calculations and Spartan/Accelrys software for visualization. The calculations for the courses will be performed using the computing resources of UB’s Center for Computational Research. All materials used in the courses are located on a web-server (www.ccr.buffalo.edu/display/~mfrein/Computer+Modeling+of+Biological+Systems) in PDF format. In Part I of the cycle, students will learn how to apply modern quantum-chemical programs to calculate molecular properties of amino acids and nucleic-acid base pairs, such as optimal geometries, dipole moments, atomic charges, electrostatic potentials, electronic densities, and molecular oscillations. Students will also calculate hydrogen bonding interactions, chemical reactions and electronic properties in clusters of amino acids and nucleic-acid base pairs. Results of the calculations will be compared with available experimental data.
- Computer Modeling of Biological Systems II: Part II of the cycle is devoted to molecular-mechanical calculations of biopolymers such as proteins and nucleic acids. Applying modern molecular-mechanical programs, students will calculate molecular dynamics of biopolymers using stochastic boundary conditions and periodic boundary conditions in the gas phase and in water solution. After dynamics, students will calculate properties of biopolymers obtained from molecular-mechanical trajectories. Results of the calculations will be compared with available experimental data.
- Computer Modeling of Biological Systems III: Part III of the cycle is design as an introduction to a QM/MM method, which combines quantum-mechanical calculations and molecular-mechanical dynamics. Students will calculate molecular properties of biopolymer fragments, such as protein active-sites or nucleic-acid elements, inside biopolymer environment including water solution. The calculations will be applied to study the interaction between a drug molecule and a protein or nucleic-acid receptor. Results of the calculations will be compared with available experimental data.
- Advanced Practical NMR Spectroscopy: This module will cover all aspects of nD NMR, shaped pulses, triple-resonance experiments and basic user programming. Setup, calibration, acquisition and processing of both gradient and non-gradient indirect detection experiments, coherence selection and gradient suppression, selective 1D experiments and water suppression techniques will be covered.
- Mathematica for Chemistry: Mathematica is a popular mathematical software package with many powerful features. It’s use in chemistry will be illustrated by a number of hands on examples in five weekly three hour sessions. Examples will include the use of algebra (calculus), numerical methods and graphics. Students will submit a project report for a grade.
- Electron Structure Theory: This course treats selected concepts and methods of modern molecular electronic structure computation. The intent is to present the underlying mathematical and physical ideas correctly, but usually without proofs. The course is intended mainly for students who want to further develop, rather than just apply, computational chemistry methods, but it is appropriate also for those simply curious about the inner workings of existing computer programs.
