School of Humanities and Sciences
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Justin Du Bois
Henry Dreyfus Professor of Chemistry and Professor, by courtesy, of Chemical and Systems Biology
BioResearch and Scholarship
Research in the Du Bois laboratory spans reaction methods development, natural product synthesis, and chemical biology, and draws on expertise in molecular design, molecular recognition, and physical organic chemistry. An outstanding goal of our program has been to develop C–H bond functionalization processes as general methods for organic chemistry, and to demonstrate how such tools can impact the logic of chemical synthesis. A second area of interest focuses on the role of ion channels in electrical conduction and the specific involvement of channel subtypes in the sensation of pain. This work is enabled in part through the advent of small molecule modulators of channel function.
The Du Bois group has described new tactics for the selective conversion of saturated C–H to C–N and C–O bonds. These methods have general utility in synthesis, making possible the single-step incorporation of nitrogen and oxygen functional groups and thus simplifying the process of assembling complex molecules. To date, lab members have employed these versatile oxidation technologies to prepare natural products that include manzacidin A and C, agelastatin, tetrodotoxin, and saxitoxin. Detailed mechanistic studies of metal-catalyzed C–H functionalization reactions are performed in parallel with process development and chemical synthesis. These efforts ultimately give way to advances in catalyst design. A long-standing goal of this program is to identify robust catalyst systems that afford absolute control of reaction selectivity.
In a second program area, the Du Bois group is exploring voltage-gated ion channel structure and function using the tools of chemistry in combination with those of molecular biology, electrophysiology, microscopy and mass spectrometry. Much of this work has focused on studies of eukaryotic Na and Cl ion channels. The Du Bois lab is interested in understanding the biochemical mechanisms that underlie channel subtype regulation and how such processes may be altered following nerve injury. Small molecule toxins serve as lead compounds for the design of isoform-selective channel modulators, affinity reagents, and fluorescence imaging probes. Access to toxins and modified forms thereof (including saxitoxin, gonyautoxin, batrachotoxin, and veratridine) through de novo synthesis drives studies to elucidate toxin-receptor interactions and to develop new pharmacologic tools to study ion channel function in primary cells and murine pain models.
Maria Theresa Dulay
Senior Research Scientist, Basic Life
Senior Research Scientist, Basic Life, Rad/Molecular Imaging Program at Stanford
BioReceived PhD from University of Texas at Austin, Department of Chemistry with Marye Anne Fox
NIH Postdoctoral Fellow at Stanford University in Richard N. Zare's research lab, Department of Chemistry
David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry
BioMy research group studies complex molecular systems by using ultrafast multi-dimensional infrared and non-linear UV/Vis methods. A basic theme is to understand the role of mesoscopic structure on the properties of molecular systems. Many systems have structure on length scales large compare to molecules but small compared to macroscopic dimensions. The mesoscopic structures occur on distance scales of a few nanometers to a few tens of nanometers. The properties of systems, such as water in nanoscopic environments, room temperature ionic liquids, functionalized surfaces, liquid crystals, metal organic frameworks, water and other liquids in nanoporous silica, polyelectrolyte fuel cell membranes, vesicles, and micelles depend on molecular level dynamics and intermolecular interactions. Our ultrafast measurements provide direct observables for understanding the relationships among dynamics, structure, and intermolecular interactions.
Bulk properties are frequently a very poor guide to understanding the molecular level details that determine the nature of a chemical process and its dynamics. Because molecules are small, molecular motions are inherently very fast. Recent advances in methodology developed in our labs make it possible for us to observe important processes as they occur. These measurements act like stop-action photography. To focus on a particular aspect of a time evolving system, we employ sequences of ultrashort pulses of light as the basis for non-linear methods such as ultrafast infrared two dimensional vibrational echoes, optical Kerr effect methods, and ultrafast IR transient absorption experiments.
We are using ultrafast 2D IR vibrational echo spectroscopy and other multi-dimensional IR methods, which we have pioneered, to study dynamics of molecular complexes, water confined on nm lengths scales with a variety of topographies, molecules bound to surfaces, ionic liquids, and materials such as metal organic frameworks and porous silica. We can probe the dynamic structures these systems. The methods are somewhat akin to multidimensional NMR, but they probe molecular structural evolution in real time on the relevant fast time scales, eight to ten orders of magnitude faster than NMR. We are obtaining direct information on how nanoscopic confinement of water changes its properties, a topic of great importance in chemistry, biology, geology, and materials. For the first time, we are observing the motions of molecular bound to surfaces. In biological membranes, we are using the vibrational echo methods to study dynamics and the relationship among dynamics, structure, and function. We are also developing and applying theory to these problems frequently in collaboration with top theoreticians.
We are studying dynamics in complex liquids, in particular room temperature ionic liquids, liquid crystals, supercooled liquids, as well as in influence of small quantities of water on liquid dynamics. Using ultrafast optical heterodyne detected optical Kerr effect methods, we can follow processes from tens of femtoseconds to ten microseconds. Our ability to look over such a wide range of time scales is unprecedented. The change in molecular dynamics when a system undergoes a phase change is of fundamental and practical importance. We are developing detailed theory as the companion to the experiments.
We are studying photo-induced proton transfer in nanoscopic water environments such as polyelectrolyte fuel cell membranes, using ultrafast UV/Vis fluorescence and multidimensional IR measurements to understand the proton transfer and other processes and how they are influenced by nanoscopic confinement. We want to understand the role of the solvent and the systems topology on proton transfer dynamics.
Associate Professor of Photon Science and, by courtesy, of Chemistry
Current Research and Scholarly InterestsThe research team Professor Gaffney leads focuses on time resolved studies of chemical reactions. Recent advances in ultrafast x-ray lasers, like the LCLS at SLAC National Accelerator Laboratory, enable chemical reactions to be observed on the natural time and length scales of the chemical bond – femtoseconds and Ångströms. The knowledge gained from x-ray and optical laser studies will be used to spark new approaches to photo-catalysis and chemical synthesis.
David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry and Professor of Photon Science at SLAC
BioCombining inorganic, biophysical and structural chemistry, Professor Keith Hodgson investigates how structure at molecular and macromolecular levels relates to function. Studies in the Hodgson lab have pioneered the use of synchrotron x-radiation to probe the electronic and structural environment of biomolecules. Recent efforts focus on the applications of x-ray diffraction, scattering and absorption spectroscopy to examine metalloproteins that are important in Earth’s biosphere, such as those that convert nitrogen to ammonia or methane to methanol.
Keith O. Hodgson was born in Virginia in 1947. He studied chemistry at the University of Virginia (B.S. 1969) and University of California, Berkeley (Ph.D. 1972), with a postdoctoral year at the ETH in Zurich. He joined the Stanford Chemistry Department faculty in 1973, starting up a program of fundamental research into the use of x-rays to study chemical and biological structure that made use of the unique capabilities of the Stanford Synchrotron Radiation Lightsource (SSRL). His lab carried out pioneering x-ray absorption and x-ray crystallographic studies of proteins, laying the foundation for a new field now in broad use worldwide. In the early eighties, he began development of one of the world's first synchrotron-based structural molecular biology research and user programs, centered at SSRL. He served as SSRL Director from 1998 to 2005, and SLAC National Accelerator Laboratory (SLAC) Deputy Director (2005-2007) and Associate Laboratory Director for Photon Science (2007-2011).
Today the Hodgson research group investigates how molecular structure at different organizational levels relates to biological and chemical function, using a variety of x-ray absorption, diffraction and scattering techniques. Typical of these molecular structural studies are investigations of metal ions as active sites of biomolecules. His research group develops and utilizes techniques such as x-ray absorption and emission spectroscopy (XAS and XES) to study the electronic and metrical details of a given metal ion in the biomolecule under a variety of natural conditions.
A major area of focus over many years, the active site of the enzyme nitrogenase is responsible for conversion of atmospheric di-nitrogen to ammonia. Using XAS studies at the S, Fe and Mo edge, the Hodgson group has worked to understand the electronic structure as a function of redox in this cluster. They have developed new methods to study long distances in the cluster within and outside the protein. Studies are ongoing to learn how this cluster functions during catalysis and interacts with substrates and inhibitors. Other components of the protein are also under active study.
Additional projects include the study of iron in dioxygen activation and oxidation within the binuclear iron-containing enzyme methane monooxygenase and in cytochrome oxidase. Lab members are also investigating the role of copper in electron transport and in dioxygen activation. Other studies include the electronic structure of iron-sulfur clusters in models and enzymes.
The research group is also focusing on using the next generation of x-ray light sources, the free electron laser. Such a light source, called the LCLS, is also located at SLAC. They are also developing new approaches using x-ray free electron laser radiation to image noncrystalline biomolecules and study chemical reactivity on ultrafast time scales.
Professor of Chemistry, Emerita
BioProfessor Wray Huestis’ research concerns the molecular mechanisms whereby cells control their shape, motility, deformability and the structural integrity of their membranes. Metabolic control of interprotein and protein-lipid interactions is studied by a variety of biochemical, spectroscopic and radiochemical techniques, including fluorescence and EPR spectrometry, autoradiography and electron microscopy. The role of lipid metabolism and transport in regulating the fluid dynamics of cell suspensions (red blood cells, platelets, lymphocytes) is examined using circulating cells and cells grown in culture. Cell-cell and cell-liposome interactions are studied using model membrane systems with widely differing physical properties. Complexes of liposomes and encapsulated viruses are used as selective vectors to deliver water-soluble compounds across the membranes of intact cells. The particular projects described in the listed publications have as a common goal an understanding of the molecular workings of the cell membrane.
Associate Professor of Chemistry and Senior Fellow at the Precourt Institute for Energy
BioAssociate Professor of Chemistry Matthew Kanan develops new catalysts and chemical reactions for applications in renewable energy conversion and CO2 utilization. His group at Stanford University has recently developed a novel method to create plastic from carbon dioxide and inedible plant material rather than petroleum products, and pioneered the study of “defect-rich” heterogeneous electro-catalysts for converting carbon dioxide and carbon monoxide to liquid fuel.
Matthew Kanan completed undergraduate study in chemistry at Rice University (B.A. 2000 Summa Cum Laude, Phi Beta Kappa). During doctoral research in organic chemistry at Harvard University (Ph.D. 2005), he developed a novel method for using DNA to discover new chemical reactions. He then moved into inorganic chemistry for his postdoctoral studies as a National Institutes of Health Postdoctoral Research Fellow at the Massachusetts Institute of Technology, where he discovered a water oxidation catalyst that operates in neutral water. He joined the Stanford Chemistry Department faculty in 2009 to continue research into energy-related catalysis and reactions. His research and teaching have already been recognized in selection as one of Chemistry & Engineering News’ first annual Talented 12, the Camille Dreyfus Teacher-Scholar Award, Eli Lilly New Faculty Award, and recognition as a Camille and Henry Dreyfus Environmental Mentor, among other honors.
The Kanan Lab addresses fundamental challenges in catalysis and synthesis with an emphasis on enabling new technologies for scalable CO2 utilization. The interdisciplinary effort spans organic synthesis, materials chemistry and electrochemistry.
One of the greatest challenges of the 21st century is to transition to an energy economy with ultra-low greenhouse gas emissions without compromising quality of life for a growing population. The Kanan Lab aims to help enable this transition by developing catalysts and chemical reactions that recycle CO2 into fuels and commodity chemicals using renewable energy sources. To be implemented on a substantial scale, these methods must ultimately be competitive with fossil fuels and petrochemicals. With this requirement in mind, the group focuses on the fundamental chemical challenge of making carbon–carbon (C–C) bonds because multi-carbon compounds have higher energy density, greater value, and more diverse applications that one-carbon compounds. Both electrochemical and chemical methods are being pursued. For electrochemical conversion, the group studies how defects known as grain boundaries can be exploited to improve CO2/CO electro-reduction catalysis. Recent work has unveiled quantitative correlations between grain boundaries and catalytic activity, establishing a new design principle for electrocatalysis, and developed grain boundary-rich copper catalysts with unparalleled activity for converting carbon monoxide to liquid fuel. For chemical CO2 conversion, the group is developing C–H carboxylation and CO2 hydrogenation reactions that are promoted by simple carbonate salts. These reactions provide a way to make C–C bonds between un-activated substrates and CO2 without resorting to energy-intensive and hazardous reagents. Among numerous applications, carbonate-promoted carboxylation enables the synthesis of a monomer used to make polyester plastic from CO2 and a feedstock derived from agricultural waste.
In addition to CO2 chemistry, the Kanan group is pursuing new strategies to control selectivity in molecular catalysis for fine chemical synthesis. Of particular interest in the use of electrostatic interactions to discriminate between competing reaction pathways based on their charge distributions. This effort uses ion pairing or interfaces to control the local electrostatic environment in which a reaction takes place. The group has recently shown that local electric fields can control regioselectivity in isomerization reactions catalyzed by gold complexes.
Associate Professor of Chemistry and Senior Fellow at the Precourt Institute for Energy
BioProfessor Hema Karunadasa works with colleagues in materials science, earth science, and applied physics to drive the discovery of new materials with applications in clean energy. Using the tools of synthetic chemistry, her group designs materials that couple the structural tunability of organic molecules with the diverse electronic and optical properties of extended inorganic solids. This research targets materials such as sorbents for capturing environmental pollutants, phosphors for solid-state lighting, and absorbers for solar cells.
Hemamala Karunadasa studied chemistry and materials science at Princeton University (A.B. with high honors 2003; Certificate in Materials Science and Engineering 2003), where her undergraduate thesis project with Professor Robert J. Cava examined geometric magnetic frustration in metal oxides. She moved from solid-state chemistry to solution-state chemistry for her doctoral studies in inorganic chemistry at the University of California, Berkeley (Ph.D. 2009) with Professor Jeffrey R. Long. Her thesis focused on heavy atom building units for magnetic molecules and molecular catalysts for generating hydrogen from water. She continued to study molecular electrocatalysts for water splitting during postdoctoral research with Berkeley Professors Christopher J. Chang and Jeffrey R. Long at the Lawrence Berkeley National Lab. She further explored molecular catalysts for hydrocarbon oxidation as a postdoc at the California Institute of Technology with Professor Harry B. Gray. She joined the Stanford Chemistry Department faculty in September 2012. Her research explores solution-state routes to new solid-state materials.
Professor Karunadasa’s lab at Stanford takes a molecular approach to extended solids. Lab members gain expertise in solution- and solid-state synthetic techniques and structure determination through powder- and single-crystal x-ray diffraction. Lab tools also include a host of spectroscopic and electrochemical probes, imaging methods, and film deposition techniques. Group members further characterize their materials under extreme environments and in operating devices to tune new materials for diverse applications in renewable energy.
Please visit the lab website for more details and recent news.
Wells H. Rauser and Harold M. Petiprin Professor and Professor of Chemistry and, by courtesy, of Biochemistry
Current Research and Scholarly InterestsResearch in this laboratory focuses on problems where deep insights into enzymology and metabolism can be harnessed to improve human health.
For the past two decades, we have studied and engineered enzymatic assembly lines called polyketide synthases that catalyze the biosynthesis of structurally complex and medicinally fascinating antibiotics in bacteria. An example of such an assembly line is found in the erythromycin biosynthetic pathway. Our current focus is on understanding the structure and mechanism of this polyketide synthase. At the same time, we are developing methods to decode the vast and growing number of orphan polyketide assembly lines in the sequence databases.
For more than a decade, we have also investigated the pathogenesis of celiac disease, an autoimmune disorder of the small intestine, with the goal of discovering therapies and related management tools for this widespread but overlooked disease. Ongoing efforts focus on understanding the pivotal role of transglutaminase 2 in triggering the inflammatory response to dietary gluten in the celiac intestine.
George A. and Hilda M. Daubert Professor of Chemistry
Current Research and Scholarly Interests• Design of cell-permeable reagents for profiling, modifying, and controlling RNAs
• Developing fluorescent probes of DNA repair pathways, with applications in cancer, aging, and neurodegenerative disease
• Discovery and development of small-molecule modulators of DNA repair enzymes, with focus on cancer and inflammation