Natural Sciences
Showing 51-100 of 299 Results
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James Collman
George A. and Hilda M. Daubert Professor of Chemistry, Emeritus
BioProfessor Emeritus James Collman has made landmark contributions to inorganic chemistry, metal ion biochemistry, homogeneous catalysis, and transition metal organometallic chemistry. He pioneered numerous now-popular research tools to reveal key structural and functional details of metalloenzymes essential to respiration and energy, and hemoglobin and myoglobin, essential to oxygen transport in the blood.
Born 1932 in Beatrice, Nebraska, James P. Collman studied chemistry at U. Nebraska–Lincoln (B.S. 1954, M.S. 1956). His doctoral work at U. Illinois at Urbana-Champaign (Ph.D., 1958) focused on Grignard reagents. As a faculty member at U. North Carolina, he demonstrated aromatic reactivity in metal acetylacetonates, and he developed metal complexes that hydrolyze peptide bonds under physiological conditions. He came to Stanford University as Professor of Chemistry in 1967. Among many honors, Prof. Collman’s was elected to the National academy of Sciences in 1975, and named California Scientist of the Year in 1983.
At Stanford, Prof. Collman invented a new paradigm for studying biological systems using functional synthetic analogs of metal-containing enzyme systems, free from the protein coatings that can affect metalloprotein chemical properties. This strategy allowed him to elucidate the intrinsic reactivity of the metal center as well as the effects of protein-metal interactions on biological function.
One focal point of this research has involved heme-proteins such as the oxygen (O2) carrier hemoglobin (Hb), and the O2-storing protein myoglobin (Mb). Prof. Collman was the first to prepare and characterize stable, functional analogues of the Hb and Mb active sites, which contain an iron derivative of the large flat “porphyrin” ligand. In his “picket fence” porphyrin, groups installed on the periphery block side reactions, which would otherwise degrade the structure. This protected iron complex manifests the unique magnetic, spectroscopic and structural characteristics of the O2-binding Hb and Mb sites, and exhibits very similar O2-binding affinities.
The Collman Group also prepared functional mimics of the O2-binding/reducing site in a key respiration enzyme, cytochrome c oxidase, CcO, which converts O2 to H2O during biosynthesis of the energy storage molecule ATP. This enzyme must be very selective: partial O2 reduction products are toxic. Prof. Collman invented a powerful synthetic strategy to create analogs of the CcO active site and applied novel electrochemical techniques to demonstrate that these models catalyze the reduction of O2 to water without producing toxic partially-reduced species. He was able to mimic slow, rate-limiting electron delivery by attaching his CcO model to a liquid-crystalline membrane using “click chemistry.” He demonstrated that hydrogen sulfide molecules and heterocycles reversibly bind to the metal centers at CcO’s active site, connecting a synthetic enzyme model to simple molecules that reversibly inhibit respiration. These respiration inhibitors exhibit physiological properties, affecting blood clotting and controlling the effects of the hormone, nitric oxide, NO.
In addition, Prof. Collman performed fundamental studies of organometallic reactions. He also prepared and characterized homodinuclear and heterodinuclear complexes having metal-metal multiple bonds, and made the first measurements of the rotational barriers found in multiple metal-metal bonds.
Prof. Collman’s impactful textbook “Principles and Applications of Organotransition Metal Chemistry” has seen multiple editions. His book “Naturally Dangerous: Surprising Facts About Food, Health, and the Environment” explains the science behind everyday life, and received favorable reviews in Nature and The Washington Post. -
Bianxiao Cui
Job and Gertrud Tamaki Professor of Chemistry
Current Research and Scholarly InterestsOur objective is to develop new biophysical methods to advance current understandings of cellular machinery in the complicated environment of living cells. Currently, we are focusing on four research areas: (1) Membrane curvature at the nano-bio interface; (2) Nanoelectrode arrays (NEAs) for scalable intracellular electrophysiology; (3) Electrochromic optical recording (ECORE) for neuroscience; and (4) Optical control of neurotrophin receptor tyrosine kinases.
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Yi Cui
Fortinet Founders Professor, Professor of Materials Science and Engineering, of Energy Science and Engineering, of Photon Science, Senior Fellow at Woods, at Precourt and Professor, by courtesy, of Chemistry
BioCui studies fundamentals and applications of nanomaterials and develops tools for their understanding. Research Interests: nanotechnology, batteries, electrocatalysis, wearables, 2D materials, environmental technology (water, air, soil), cryogenic electron microscopy.
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Hongjie Dai
The J.G. Jackson and C.J. Wood Professor of Chemistry, Emeritus
BioProfessor Dai’s research spans chemistry, physics, and materials and biomedical sciences, leading to materials with properties useful in electronics, energy storage and biomedicine. Recent developments include near-infrared-II fluorescence imaging, ultra-sensitive diagnostic assays, a fast-charging aluminum battery and inexpensive electrocatalysts that split water into oxygen and hydrogen fuels.
Born in 1966 in Shaoyang, China, Hongjie Dai began his formal studies in physics at Tsinghua U. (B.S. 1989) and applied sciences at Columbia U. (M.S. 1991). He obtained his Ph.D. from Harvard U and performed postdoctoral research with Dr. Richard Smalley. He joined the Stanford faculty in 1997, and in 2007 was named Jackson–Wood Professor of Chemistry. Among many awards, he has been recognized with the ACS Pure Chemistry Award, APS McGroddy Prize for New Materials, Julius Springer Prize for Applied Physics and Materials Research Society Mid-Career Award. He has been elected to the American Academy of Arts and Sciences, National Academy of Sciences (NAS), National Academy of Medicine (NAM) and Foreign Member of Chinese Academy of Sciences.
The Dai Laboratory has advanced the synthesis and basic understanding of carbon nanomaterials and applications in nanoelectronics, nanomedicine, energy storage and electrocatalysis.
Nanomaterials
The Dai Lab pioneered some of the now-widespread uses of chemical vapor deposition for carbon nanotube (CNT) growth, including vertically aligned nanotubes and patterned growth of single-walled CNTs on wafer substrates, facilitating fundamental studies of their intrinsic properties. The group developed the synthesis of graphene nanoribbons, and of nanocrystals and nanoparticles on CNTs and graphene with controlled degrees of oxidation, producing a class of strongly coupled hybrid materials with advanced properties for electrochemistry, electrocatalysis and photocatalysis. The lab’s synthesis of a novel plasmonic gold film has enhanced near-infrared fluorescence up to 100-fold, enabling ultra-sensitive assays of disease biomarkers.
Nanoscale Physics and Electronics
High quality nanotubes from his group’s synthesis are widely used to investigate the electrical, mechanical, optical, electro-mechanical and thermal properties of quasi-one-dimensional systems. Lab members have studied ballistic electron transport in nanotubes and demonstrated nanotube-based nanosensors, Pd ohmic contacts and ballistic field effect transistors with integrated high-kappa dielectrics.
Nanomedicine and NIR-II Imaging
Advancing biological research with CNTs and nano-graphene, group members have developed π–π stacking non-covalent functionalization chemistry, molecular cellular delivery (drugs, proteins and siRNA), in vivo anti-cancer drug delivery and in vivo photothermal ablation of cancer. Using nanotubes as novel contrast agents, lab collaborations have developed in vitro and in vivo Raman, photoacoustic and fluorescence imaging. Lab members have exploited the physics of reduced light scattering in the near-infrared-II (1000-1700nm) window and pioneered NIR-II fluorescence imaging to increase tissue penetration depth in vivo. Video-rate NIR-II imaging can measure blood flow in single vessels in real time. The lab has developed novel NIR-II fluorescence agents, including CNTs, quantum dots, conjugated polymers and small organic dyes with promise for clinical translation.
Electrocatalysis and Batteries
The Dai group’s nanocarbon–inorganic particle hybrid materials have opened new directions in energy research. Advances include electrocatalysts for oxygen reduction and water splitting catalysts including NiFe layered-double-hydroxide for oxygen evolution. Recently, the group also demonstrated an aluminum ion battery with graphite cathodes and ionic liquid electrolytes, a substantial breakthrough in battery science. -
Laura M.K. Dassama
Assistant Professor of Chemistry and of Microbiology and Immunology
BioLaura Dassama is a chemical biologist who uses principles from chemistry and physics to understand complex biological phenomena. Her group’s primary goal is to use detailed understanding of the factors that enable interactions between biological molecules to provide insights that allow functional control of those molecules. Her research projects aim to 1) discover the drivers of biomolecular interactions and 2) leverage that information to modulate disease relevant proteins.
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Casey Decosto
Ph.D. Student in Chemistry, admitted Autumn 2021
BioCassandra (Casey) Mendoza Decosto (she/they) is a proud first-generation Filipina American from Los Angeles, California. A Pasadena City College alumna who transferred to CSU-Los Angeles, she previously studied singlet-oxygen photochemistry with Prof. Matthias Selke. Now, as a Chemistry Ph.D. candidate in Prof. Laura Dassama’s lab, she leverages bioinformatic and biochemical approaches to discover novel proteins that drive metabolite trafficking, membrane remodeling, and antibiotic evasion in bacterial pathogens such as Treponema pallidum. As a CBI ChEM-H and EDGE fellow, Casey works to increase educational and research access on and off campus through programs like Stanford’s Community College Outreach Program (CCOP).
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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. -
Michael Fayer
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. -
Kelly Gaffney
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.
