Graduate Bulletin

Spring 2018

Chemistry Department

The Department of Chemistry, within the College of Arts and Sciences, offers courses of study leading to the degrees of Master of Arts in Teaching Chemistry, Master of Science, and Doctor of Philosophy. Students in the M.A.T. program must register through the School of Professional Development. A student in the Ph.D. program may choose dissertation research in any one of the diverse areas of chemistry represented by the interests of the program faculty, or may choose an interdisciplinary topic under the guidance of a faculty member in another program. Coordinated activities exist with several programs, and include optional concentrations in chemical physics and chemical biology. 

Areas of Current Research

Synthetic Chemistry
The synthesis of new molecular compounds distinguishes chemistry from other scientific disciplines. Although many disciplines study the properties of materials and natural phenomena, only chemistry concerns itself with the preparation of new molecular arrangements. The success of past synthetic efforts can readily be appreciated by observing the vast array of new materials that have improved the quality of our lives.

The Chemistry Department at Stony Brook is very fortunate to have many strong synthetic programs in both organic and inorganic chemistry. Among the studies underway are the search for inventive synthetic reactions to produce new molecules, the synthesis of new molecular structures to evaluate our theories of chemical bonding, and the synthesis of new compounds with unusual physical properties (molecular engineering). A major focus in the program lies in the areas of bio-organic and bio-inorganic chemistry. Synthetic chemistry is being applied to the understanding of receptor-substrate interactions as well as of enzyme function, the preparation of artificial enzymes, the mechanism of mutagenesis and carcinogenesis, and the preparation of new compounds for the treatment of diseases.

Organometallic Chemistry
Organometallic chemistry is an interdisciplinary field bringing together many aspects of inorganic and organic chemistry. A wide range of organometallic systems are under study using a variety of synthetic, structural, mechanistic, and theoretical techniques. Synthetic and structural research is focused on such problems as the chemistry of unsaturated metal-carbon bonds in metal carbene and carbyne complexes, the stabilization of highly reactive organic moieties through metal complexation, the chemistry of transition metal carbonyl cluster compounds, and the development of useful synthetic reagents. Homogeneous catalysis studies include investigations of the carbonylations of fluoroolefins, small-ring heterocycles, alkenylamides, and similar molecules, and catalytic applications of compounds with unsaturated metal-carbon bonds. Theoretical work includes ab initio and qualitative molecular orbital studies of organometallic compounds and of the chemisorption of organic molecules onto metal surfaces and molecular mechanics minimizations of ligand geometries.

Structural and Mechanistic Organic Chemistry
The structures of a wide range of organic molecules are examined at Stony Brook using many techniques, including automated high-field FT-NMR spectroscopy (1H, 13C, 19F, etc.) and X-ray crystallography. Molecular modeling programs, such as Gaussian and Macromodel, are operated on color graphics workstations in order to rationalize and predict the conformations and reactivities of molecules under study. Variable-temperature 1H and 13C NMR spectroscopy is used to investigate conformational changes in macrocycles and other synthetic hosts for guest metal ions and organic molecules. VT-NMR is also used to investigate proton transfer in polyamines and intermolecular exchange of guest ions between polydentate ligands. Stereochemical probes are used to examine mechanisms of organic reactions such as pericyclic and biomimetic processes. Reaction mechanisms are also studied by determining activation volumes using reactors in the high-pressure laboratory that can attain pressures higher than 200,000 psi.

Institute of Chemical Biology & Drug Discovery at Stony Brook (ICB&DD)
The primary objective of the ICB&DD, directed by Distinguished Professor Iwao Ojima, is to serves as a world-class “Center of Excellence” in chemical biology and drug discovery at Stony Brook. The rapid and impressive advancement of chemical biology in the last decade clearly demonstrates that solutions for the vast majority of medical problems rely on the understanding of the molecular basis of diseases, therapeutic targets, drug actions, and drug resistance. The ICB&DD promotes highly productive interdisciplinary and collaborative research among chemists, biologists, medicinal chemists, pharmacologists, and physicians to attack major and significant biomedical problems to find solutions including the discovery of novel therapeutic drugs.

Biological Chemistry
A significant number of the faculty are using their chemical expertise to explore the chemical and physical details of biological phenomena. Research programs span biological chemistry, enzyme mechanisms, protein folding, membrane structure and function, biophysics and structural biology. Techniques such as high resolution NMR, stop-flow kinetics, fluorescence and Raman spectroscopy are used to probe protein structure, function, and folding. Novel biosynthetic and chemical strategies are being used to generate small molecules for use in probing enzyme mechanisms and exploring ligand-receptor interactions.

Inorganic Chemistry
Inorganic chemistry, being concerned with the synthesis, structure, and dynamics of the compounds formed by the more than 100 natural and synthetic elements, covers an extremely vast research area. New compounds and new synthetic methods are among the goals of inorganic chemistry research. Such compounds range from materials important in technology to catalysts for industrial chemical processes, small molecules present in outer space, and metal complexes that serve as models for biological materials. The methodologies used in inorganic chemistry include a wide variety of spectroscopic techniques, kinetic methods, procedures for the elucidation of geometric and electronic structures, and theory. The breadth and depth of inorganic chemistry are well represented at Stony Brook, as seen by the following examples of current research: thermally and photochemically activated dynamic processes, in particular, electron transfer reactions; synthetic and structural studies of active site analogs of metalloenzymes such as the zinc proteins that regulate gene transcription and the high-potential iron-sulfur proteins; activation of small molecules by transition metal complexes and homogeneous catalysis; chemistry of unsaturated carbon-metal bonds in mononuclear compounds and in extended molecular assemblies; molecular orbital calculations and molecular mechanics methods applied to transition metal cluster compounds and related organometallic substances; NMR studies of zeolites and supported catalysts.

Magnetic Resonance
Magnetic resonance in the Chemistry Department ranges from studies in physiology to studies in chemical physics. Topics under investigation include the use of liquid and solid state nuclear magnetic resonance (NMR) spectroscopy and micro-imaging techniques with stable spin 1/2 and quadrupolar nuclides to study inorganic, organic, biological, and living systems. Projects in progress employ a range of single and N-dimensional NMR spectroscopic techniques and novel imaging techniques to elucidate chemical processes and determine the structures of biological and organic molecules in solution.

Novel NMR methods are being developed for the determination of the structures of micro- and macromolecules as they exist in disordered solids and to study the structure and dynamics of molecules in the liquid crystalline state and those absorbed on solid surfaces. Pulsed electron paramagnetic resonance (EPR) techniques are being developed to study metalloenzymes, organic conductors, and other molecules.

The Stony Brook NMR Facility http://www.stonybrook.edu/commcms/nmr/ is a campus-wide facility that serves the educational and research needs of the University community. With spectrometers located at two different sites, the Chemistry Department and the Center for Molecular Medicine (CMM), the NMR facility offers instrument access to students, post-docs and investigators on diverse research fields including structural biology, chemistry, biophysics, and material sciences. The facility has been updated recently with new Bruker spectrometers, and has a total of nine instruments operating from 300 to 850 MHz proton frequencies.

Macromolecules
With development of state-of-the-art X-ray diffraction and small-angle X-ray scattering (SAXS) at the State University of New York’s X3 Beamline at the National Synchrotron Light Source at Brookhaven National Laboratory, the polymer and biomacromolecular physics group, being members of the participating research team (PRT), possesses one of the most powerful X-ray scattering facilities in the country. The experiments at Stony Brook make use of a wide variety of complementary techniques such as SAXS, laser light scattering, photon correlation spectroscopy, fluorescence photobleaching recovery, holographic relaxation spectroscopy, transient electric birefringence, and various forms of nuclear magnetic resonance spectroscopy. Stony Brook scientists can perform measurements to determine the structure and dynamical behavior of advanced polymeric materials, supramolecular systems, and biomacromolecules. Time-dependent processes can be studied using stop-flow, steady-flow, pressure-jump, and temperature-jump experiments together with time-resolved capabilities using intense radiation sources such as pulsed lasers and the synchrotron radiation. Unparalleled opportunities exist for interdisciplinary research using unique and novel instrumentation in polymer materials, polymer physics, colloid science, and biophysical chemistry.

Photon-Molecule Interactions
Recent developments in the use of lasers for the investigation of molecular structure and dynamics have led to a revolution in the fields of molecular spectroscopy and dynamics. Intimate details about the structure and interactions of atoms and molecules can now be studied to an extent never before possible. In this program the systems being studied by laser spectroscopy range from atoms and diatomic molecules to molecular crystals and polymers. In these systems various properties are being investigated, including nonlinear interactions with the radiation field, excited state electronic structure, radiationless transitions, ionization mechanisms, crystal field interactions, and photochemical reactions, as well as electron and energy transfer processes. Luminescence spectroscopy, luminescence excitation, multiphoton ionization, multiphoton photoelectron spectroscopy, Raman spectroscopy, and vacuum ultraviolet spectroscopy are among the techniques being used and developed for the ever greater understanding of atomic and molecular systems.

Soft X-Ray Spectroscopy
The National Synchrotron Light Source at Brookhaven National Laboratory, located only 15 miles from Stony Brook, provides unique opportunities for frontier research in chemistry. The synchrotron and associated devices are unequaled sources of high-intensity X-ray and vacuum ultraviolet radiation. One area of current research uses soft X-rays, photons with energies of 100 to 1000 eV, to investigate the excitation and relaxation of core electrons in molecules. Because core electrons, e.g., the 1s electrons of carbon, are tightly bound to individual atoms, the excitation energy is essentially localized on a particular atom in the molecule. This localization has the potential for producing photochemistry with far greater atomic site specificity than can be achieved by excitation of valence electronics with visible and ultraviolet light.

Surface Chemistry
Catalysis, corrosion, and friction are a few examples of familiar processes that occur on solid surfaces. The field of surface chemistry tries to unravel and understand the basic chemical principles that underly such phenomena. At Stony Brook we are actively researching how the electronic and geometric structure of a surface affects its chemical selectivity and reactivity during surface-mediated processes such as catalysis and the chemical vapor deposition of metals from organometallic precursors. In addition, we are interested in understanding the interactions between energetic ions and surfaces in both atmospheric and metal-etching reactions. An arsenal of sophisticated techniques is available to prove both the geometric and electronic structures of a reacting surface on an atomic level. Techniques such as Auger electron spectroscopy (AES) and high-resolution, electron energy loss spectroscopy (HREELS) are used to determine the composition of a surface, while ultraviolet and X-ray photons are commonly used to eject photoelectrons from a surface (which are energy analyzed) yielding electronic structure information. Another technique, low-energy electron diffraction (LEED), exploits the wave nature of electrons and is used to help determine the geometric structure of a surface. These techniques, routinely used at Stony Brook, are complemented by the powerful extended- and near-edge X-ray absorption fine-structure techniques (EXAFS and NEXAFS), available at the National Synchrotron Light Source at nearby Brookhaven National Laboratory.

Theoretical Chemistry
Theoretical investigations of a wide variety of chemical phenomena are underway at Stony Brook. Research programs in electronic structure theory are concerned with the development of formalism and computational techniques. Applications include determination of the geometry, spectral shifts, and reaction pathways of molecules chemisorbed onto metal surfaces; calculation of the structure of molecules in highly excited Rydberg states; and evaluation of probability amplitudes for multiphoton excitation and calculation of Born corrections, Born couplings, and orbital stresses in small molecules. In the field of statistical mechanics, analysis and numerical simulation are combined to obtain properties of liquids and ionic solutions from the properties of their constituent molecules and their interactions. Much of this work is focused on the calculation of pair correlation functions, transport properties and dielectric phase diagrams, solvent effects, and rates of electron transfer reactions. Other current work includes theory of photon-molecule interactions, quantum ensembles, Jahn-Teller dynamics, and lifetimes of quasistationary molecular states. In addition, students often do theoretical work closely related to active experimental programs under the joint guidance of a theorist and an experimentalist.

Nuclear and Isotope Chemistry
Nuclear chemistry research at Stony Brook has focused on reactions induced by heavy ion beams. Beams are obtained from accelerators located at Stony Brook, Berkeley, Chicago, Michigan, and France. The reactions produce very hot and rapidly rotating atomic nuclei that are studied by observation of particles and fragments that are emitted. Their energies and angles of emission allow for a reconstruction of the properties of the hot emitting nuclei and the mechanism of their production.

Isotope chemistry deals with the small differences in physical and chemical properties of matter that have their origin in the mass difference of isotopes of an element. Although the effects are small, they can be measured with high precision. In general, the effects are quantum effects, and measurement of isotope effects has proven to be a unique method for the study of molecular and intermolecular forces. Isotope effect studies have found application in chemical physics, organic chemistry and biochemistry, geochemistry, and anthropology. Practical applications are found in isotope separation processes. Our present efforts are concentrated on the systematization of isotope chemistry.