School of Humanities and Sciences
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Hans Andersen
David Mulvane Ehrsam and Edward Curtis Franklin Professor in Chemistry, Emeritus
BioProfessor Emeritus Hans C. Andersen applies statistical mechanics to develop theoretical understanding of the structure and dynamics of liquids and new computer simulation methods to aid in these studies.
He was born in 1941 in Brooklyn, New York. He studied chemistry as an undergraduate, then physical chemistry as a doctoral candidate at the Massachusetts Institute of Technology (B.S. 1962, Ph.D. 1966). At MIT he first learned about using a combination of mathematical techniques and the ideas of statistical mechanics to investigate problems of chemical and physical interest. This has been the focus of his research ever since. He joined the Stanford Department of Chemistry as Assistant Professor in 1968, and became Professor of Chemistry in 1980. He was named David Mulvane Ehrsam and Edward Curtis Franklin Professor in Chemistry in 1994. Professor Andersen served as department chairman from 2002 through 2005. Among many honors, his work has been recognized in the Theoretical Chemistry Award and Hildebrand Award in Theoretical and Experimental Chemistry of Liquids from the American Chemical Society, as well as the Dean's Award for Distinguished Teaching and Walter J. Gores Award for Excellence in Teaching at Stanford. He has been elected a member of the National Academy of Sciences, and a fellow of both the American Academy of Arts and Sciences and American Association for the Advancement of Science.
Professor Andersen’s research program has used both traditional statistical mechanical theory and molecular dynamics computer simulation. Early in his career, he was one of the developers of what has come to be known as the Weeks-Chandler-Andersen theory of liquids, which is a way of understanding the structure, thermodynamics, and dynamics of simple dense liquids. Later, he developed several new simulation techniques – now in common use – for exploring the behavior of liquids, such as simulation of a system under constant pressure and/or temperature. He used computer simulations of normal and supercooled liquids to study the temperature dependence of molecular motion in liquids, crystallization in supercooled liquids, and the structure of amorphous solids.
Professor Andersen also developed and analyzed a class of simple lattice models, called facilitated kinetic Ising models, which were then widely used by others to provide insight into the dynamics of real liquids. He simulated simple models of rigid rod polymers to understand the dynamics of this type of material. More recently, in collaboration with Professor Greg Voth of the University of Chicago, he has applied statistical mechanical ideas to the development of coarse grained models of liquids and biomolecules. Such models can be used to simulate molecular systems on long time scales. He has also used mode coupling theory to describe and interpret experiments on rotational relaxation in supercooled liquids and nematogens, in collaboration with Professor Michael Fayer of the Stanford Chemistry Department. -
Steven Banik
Assistant Professor of Chemistry
BioSteven Banik’s research interests center on rewiring mammalian biology and chemical biotechnology development using molecular design and construction. Projects in the Banik lab combine chemical biology, organic chemistry, protein engineering, cell and molecular biology to precisely manipulate the biological machines present in mammalian cells. Projects broadly aim to perform new functions that shed light on regulatory machinery and the potential scope of mammalian biology. A particular focus is the study of biological mechanisms that can be coopted by synthetic molecules (both small molecules and proteins). These concepts are applied to develop new therapeutic strategies for treating aging-related disorders, genetic diseases, and cancer.
Prior to joining the faculty at Stanford, Steven was a NIH and Burroughs CASI postdoctoral fellow advised by Prof. Carolyn Bertozzi at Stanford. His postdoctoral research developed approaches for targeted protein degradation from the extracellular space with lysosome targeting chimeras (LYTACs). He received his Ph.D. from Harvard University in 2016, where he worked with Prof. Eric Jacobsen on synthetic methods for the selective, catalytic difluorination of organic molecules and new approaches for generating and controlling reactive cationic intermediates in asymmetric catalysis. -
Zhenan Bao
K. K. Lee Professor and Professor, by courtesy, of Materials Science and Engineering and of Chemistry
On Partial Leave from 04/01/2024 To 06/30/2024BioZhenan Bao joined Stanford University in 2004. She is currently a K.K. Lee Professor in Chemical Engineering, and with courtesy appointments in Chemistry and Material Science and Engineering. She was the Department Chair of Chemical Engineering from 2018-2022. She founded the Stanford Wearable Electronics Initiative (eWEAR) and is the current faculty director. She is also an affiliated faculty member of Precourt Institute, Woods Institute, ChEM-H and Bio-X. Professor Bao received her Ph.D. degree in Chemistry from The University of Chicago in 1995 and joined the Materials Research Department of Bell Labs, Lucent Technologies. She became a Distinguished Member of Technical Staff in 2001. Professor Bao currently has more than 700 refereed publications and more than 80 US patents with a Google Scholar H-index 211.
Bao is a member of the US National Academy of Engineering, the American Academy of Arts and Sciences and the National Academy of Inventors. Bao was elected a foreign member of the Chinese Academy of Science in 2021. She is a Fellow of AAAS, ACS, MRS, SPIE, ACS POLY and ACS PMSE.
Bao is a member of the Board of Directors for the Camille and Dreyfus Foundation from 2022. She served as a member of Executive Board of Directors for the Materials Research Society and Executive Committee Member for the Polymer Materials Science and Engineering division of the American Chemical Society. She was an Associate Editor for the Royal Society of Chemistry journal Chemical Science, Polymer Reviews and Synthetic Metals. She serves on the international advisory board for Advanced Materials, Advanced Energy Materials, ACS Nano, Accounts of Chemical Reviews, Advanced Functional Materials, Chemistry of Materials, Chemical Communications, Journal of American Chemical Society, Nature Asian Materials, Materials Horizon and Materials Today. She is one of the Founders and currently sits on the Board of Directors of C3 Nano Co. and PyrAmes, both are silicon valley venture funded companies.
Bao was a recipient of the VinFuture Prize Female Innovator 2022, ACS Award of Chemistry of Materials 2022, MRS Mid-Career Award in 2021, AICHE Alpha Chi Sigma Award 2021, ACS Central Science Disruptor and Innovator Prize in 2020, ACS Gibbs Medal in 2020, the Wilhelm Exner Medal from the Austrian Federal Minister of Science in 2018, the L'Oreal UNESCO Women in Science Award North America Laureate in 2017. She was awarded the ACS Applied Polymer Science Award in 2017, ACS Creative Polymer Chemistry Award in 2013 ACS Cope Scholar Award in 2011. She is a recipient of the Royal Society of Chemistry Beilby Medal and Prize in 2009, IUPAC Creativity in Applied Polymer Science Prize in 2008, American Chemical Society Team Innovation Award 2001, R&D 100 Award, and R&D Magazine Editors Choice Best of the Best new technology for 2001. -
Stacey Bent
Vice Provost, Graduate Edu & Postdoc Affairs, Jagdeep & Roshni Singh Professor in the School of Engineering, Professor of Energy Science Eng, Sr Fellow at Precourt & Professor, by courtesy, of Electrical Eng, Materials Sci Eng & Chemistry
BioThe research in the Bent laboratory is focused on understanding and controlling surface and interfacial chemistry and applying this knowledge to a range of problems in semiconductor processing, micro- and nano-electronics, nanotechnology, and sustainable and renewable energy. Much of the research aims to develop a molecular-level understanding in these systems, and hence the group uses of a variety of molecular probes. Systems currently under study in the group include functionalization of semiconductor surfaces, mechanisms and control of atomic layer deposition, molecular layer deposition, nanoscale materials for light absorption, interface engineering in photovoltaics, catalyst and electrocatalyst deposition.
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Carolyn Bertozzi
Baker Family Director of Sarafan ChEM-H, Anne T. and Robert M. Bass Professor in the School of Humanities and Sciences and Professor, by courtesy, of Chemical and Systems Biology and of Radiology
BioProfessor Carolyn Bertozzi's research interests span the disciplines of chemistry and biology with an emphasis on studies of cell surface sugars important to human health and disease. Her research group profiles changes in cell surface glycosylation associated with cancer, inflammation and bacterial infection, and uses this information to develop new diagnostic and therapeutic approaches, most recently in the area of immuno-oncology.
Dr. Bertozzi completed her undergraduate degree in Chemistry at Harvard University and her Ph.D. at UC Berkeley, focusing on the chemical synthesis of oligosaccharide analogs. During postdoctoral work at UC San Francisco, she studied the activity of endothelial oligosaccharides in promoting cell adhesion at sites of inflammation. She joined the UC Berkeley faculty in 1996. A Howard Hughes Medical Institute Investigator since 2000, she came to Stanford University in June 2015, among the first faculty to join the interdisciplinary institute ChEM-H (Chemistry, Engineering & Medicine for Human Health). She is now the Baker Family Director of Stanford ChEM-H.
Named a MacArthur Fellow in 1999, Dr. Bertozzi has received many awards for her dedication to chemistry, and to training a new generation of scientists fluent in both chemistry and biology. She has been elected to the Institute of Medicine, National Academy of Sciences, and American Academy of Arts and Sciences; and received the Lemelson-MIT Prize, the Heinrich Wieland Prize, the ACS Award in Pure Chemistry, and the Chemistry of the Future Solvay Prize, among others.
The Bertozzi Group develops chemical tools to study the glycobiology underlying diseases such as cancer, inflammation, tuberculosis and most recently COVID-19. She is the inventor of "bioorthogonal chemistry", a class of chemical reactions compatible with living systems that enable molecular imaging and drug targeting. Her group also developed new therapeutic modalities for targeted degradation of extracellular biomolecules, such as antibody-enzyme conjugates and Lysosome Targeting Chimeras (LYTACs). As well, her group studies NGly1 deficiency, a rare genetic disease characterized by loss of the human N-glycanase.
Several of the technologies developed in the Bertozzi lab have been adapted for commercial use. Actively engaged with several biotechnology start-ups, Dr. Bertozzi cofounded Redwood Bioscience, Enable Biosciences, Palleon Pharmaceuticals, InterVenn Bio, OliLux Bio, Grace Science LLC and Lycia Therapeutics. She is also a member of the Board of Directors of Lilly. -
Steven Boxer
Camille Dreyfus Professor of Chemistry
Current Research and Scholarly InterestsPlease visit my website for complete information:
http://www.stanford.edu/group/boxer/ -
John Brauman
J.G. Jackson and C.J. Wood Professor of Chemistry, Emeritus
BioJohn Brauman’s research has advanced the understanding of the factors that determine the rates and products of chemical reactions. His primary areas of effort have involved the spectroscopy, photochemistry, reaction dynamics, and reaction mechanisms of gas-phase ions.
John I. Brauman was born in Pittsburgh, PA in 1937. He attended the Massachusetts Institute of Technology (S.B. 1959) and the University of California at Berkeley (Ph.D. 1963). Following a National Science Foundation Postdoctoral Fellowship at the University of California, Los Angeles, he accepted a position at Stanford University where he is now J. G. Jackson - C. J. Wood Professor of Chemistry Emeritus, and serves as Associate Dean of Research. He was previously Department Chair and Associate Dean for Natural Sciences.
Brauman’s work has been recognized in the National Medal of Science, National Academy of Sciences Award in Chemical Sciences, Linus Pauling Medal, Dean's Award for Distinguished Teaching from Stanford University, among many other honors. He is a member of the National Academy of Sciences, American Academy of Arts and Sciences, American Philosophical Society, a Fellow of the American Association for the Advancement of Science, Fellow of the American Chemical Society, and Honorary Fellow of the California Academy of Sciences. He received the 2017 ACS Parsons Award in recognition of his service to public science communication and policy, which includes roles as Deputy Editor for Physical Sciences and Editorial Board Chair for Science magazine, and Home Secretary of the National Academy of Sciences.
Research in the Brauman Group centered on structure and reactivity. Brauman has studied ionic reactions in the gas phase, including acid-base chemistry, the mechanisms of proton transfers, nucleophilic displacement, and addition-elimination reactions. His work has explored the shape of the potential surfaces and the dynamics of reactions on these surfaces. He has made contributions to the field of electron photodetachment spectroscopy of negative ions, measurements of electron affinities, the study of dipole-supported electronic states, and multiple photon infrared activation of ions. He has also studied mechanisms of solution and gas phase organic reactions as well as organometallic reactions and the behavior of biomimetic organometallic species. -
Megan Brennan
Lecturer
BioDr. Megan Brennan's interests include the development of organic chemistry lab courses that give students hands-on opportunities to explore chemistry while reinforcing and building upon concepts learned in lecture classes. She aims for her labs to bring chemistry to life, and to afford students a chance to have fun and experience a taste of scientific discovery.
While studying chemistry at Lafayette College (B.S. 2002), Dr. Brennan worked on the preparation of triazaphenanthrenes and the Oxa–Pictet–Spengler reaction of 1-(3-furyl)alkan-2-ols. She completed her doctoral work at Stanford (Ph.D. 2008), conducting her thesis research in palladium asymmetric allylic alkylation under the advisement of Professor Barry Trost. During her postdoctoral research with Professor Scott Miller at Yale University, she investigated the use of peptides containing a thiazole side chain for use in acyl anion chemistry. She joined the teaching staff at University of California, Berkeley in 2010 before coming returning to Stanford in 2011 to spearhead the development of a new summer organic chemistry sequence, a comprehensive course designed for pre-meds, offering an entire year of organic chemistry in nine weeks.
Dr. Brennan also acts as the liaison to the chemistry majors, to promote events with faculty in both the academic and social aspect: providing an environment that allows students to be comfortable and able to learn, while helping them take advantage of every opportunity that Stanford offers.
Dr. Brennan's current research is in the development classroom experiments that bring cutting edge industrial and academic research into the undergraduate laboratory experience. -
Noah Burns
Associate Professor of Chemistry
Current Research and Scholarly InterestsResearch in our group explores the boundaries of modern organic synthesis to enable the more rapid creation of the highest molecular complexity in a predictable and controllable fashion. We are particularly inspired by natural products not only because of their importance as synthetic targets but also due to their ability to serve as invaluable identifiers of unanswered scientific questions.
One major focus of our research is selective halogenation of organic molecules. Dihalogenation and halofunctionalization encompass some of the most fundamental transformations in our field, yet methods capable of accessing relevant halogenated motifs in a chemo-, regio-, and enantioselective fashion are lacking.
We are also interested in the practical total synthesis of natural products for which there is true impetus for their construction due to unanswered chemical, medicinal, biological, or biophysical questions. We are specifically engaged in the construction of unusual lipids with unanswered questions regarding their physical properties and for which synthesis offers a unique opportunity for study. -
Lynette Cegelski
Professor of Chemistry
Current Research and Scholarly InterestsOur research program is inspired by the challenge and importance of elucidating chemical structure and function in complex biological systems and the need for new strategies to treat infectious diseases. The genomics and proteomics revolutions have been enormously successful in generating crucial "parts lists" for biological systems. Yet, for many fascinating systems, formidable challenges exist in building complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell factories. We have introduced uniquely enabling problem-solving approaches integrating solid-state NMR spectroscopy with microscopy and biochemical and biophysical tools to determine atomic- and molecular-level detail in complex macromolecular assemblies and whole cells and biofilms. We are uncovering new chemistry and new chemical structures produced in nature. We identify small molecules that influence bacterial assembly processes and use these in chemical genetics approaches to learn about bacterial cell wall, amyloid and biofilm assembly.
Translationally, we have launched a collaborative antibacterial drug design program integrating synthesis, chemical biology, and mechanistic biochemistry and biophysics directed at the discovery and development of new antibacterial therapeutics targeting difficult-to-treat bacteria. -
James K. Chen
Jauch Professor and Professor of Chemical and Systems Biology, of Developmental Biology and of Chemistry
Current Research and Scholarly InterestsOur laboratory combines chemistry and developmental biology to investigate the molecular events that regulate embryonic patterning, tissue regeneration, and tumorigenesis. We are currently using genetic and small-molecule approaches to study the molecular mechanisms of Hedgehog signaling, and we are developing chemical technologies to perturb and observe the genetic programs that underlie vertebrate development.
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Christopher Chidsey
Associate Professor of Chemistry, Emeritus
Current Research and Scholarly InterestsThe Chidsey group research interest is to build the chemical base for molecular electronics. To accomplish this, we synthesize the molecular and nanoscopic systems, build the analytical tools and develop the theoretical understanding with which to study electron transfer between electrodes and among redox species through insulating molecular bridges
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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 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, and to leverage that understanding for the modulation of biological processes. Her current research focuses on deciphering the molecular recognition mechanisms of multidrug transporters implicated in drug resistance, rational engineering and repurposing of natural products, and control of transcription factors relevant to sickle cell disease.
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Joseph M. DeSimone
Sanjiv Sam Gambhir Professor of Translational Medicine, Professor of Chemical Engineering and, by courtesy, of Chemistry, of Materials Science and Engineering, and of Operations, Information and Technology at the Graduate School of Business
BioJoseph M. DeSimone is the Sanjiv Sam Gambhir Professor of Translational Medicine and Chemical Engineering at Stanford University. He holds appointments in the Departments of Radiology and Chemical Engineering with courtesy appointments in the Department of Chemistry and in Stanford’s Graduate School of Business.
The DeSimone laboratory's research efforts are focused on developing innovative, interdisciplinary solutions to complex problems centered around advanced polymer 3D fabrication methods. In Chemical Engineering and Materials Science, the lab is pursuing new capabilities in digital 3D printing, as well as the synthesis of new polymers for use in advanced additive technologies. In Translational Medicine, research is focused on exploiting 3D digital fabrication tools to engineer new vaccine platforms, enhanced drug delivery approaches, and improved medical devices for numerous conditions, with a current major focus in pediatrics. Complementing these research areas, the DeSimone group has a third focus in Entrepreneurship, Digital Transformation, and Manufacturing.
Before joining Stanford in 2020, DeSimone was a professor of chemistry at the University of North Carolina at Chapel Hill and of chemical engineering at North Carolina State University. He is also Co-founder, Board Chair, and former CEO (2014 - 2019) of the additive manufacturing company, Carbon. DeSimone is responsible for numerous breakthroughs in his career in areas including green chemistry, medical devices, nanomedicine, and 3D printing. He has published over 350 scientific articles and is a named inventor on over 200 issued patents. Additionally, he has mentored 80 students through Ph.D. completion in his career, half of whom are women and members of underrepresented groups in STEM.
In 2016 DeSimone was recognized by President Barack Obama with the National Medal of Technology and Innovation, the highest U.S. honor for achievement and leadership in advancing technological progress. He has received numerous other major awards in his career, including the U.S. Presidential Green Chemistry Challenge Award (1997); the American Chemical Society Award for Creative Invention (2005); the Lemelson-MIT Prize (2008); the NIH Director’s Pioneer Award (2009); the AAAS Mentor Award (2010); the Heinz Award for Technology, the Economy and Employment (2017); the Wilhelm Exner Medal (2019); the EY Entrepreneur of the Year Award (2019 U.S. Overall National Winner); and the Harvey Prize in Science and Technology (2020). He is one of only 25 individuals elected to all three branches of the U.S. National Academies (Sciences, Medicine, Engineering). DeSimone received his B.S. in Chemistry in 1986 from Ursinus College and his Ph.D. in Chemistry in 1990 from Virginia Tech. -
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. -
Keith Hodgson
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. -
Wray Huestis
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.
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Matthew Kanan
Professor of Chemistry
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. -
Hemamala Karunadasa
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. -
Chaitan Khosla
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. -
Eric Kool
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 -
Fang Liu
Assistant Professor of Chemistry
Current Research and Scholarly InterestsThe group will develop scalable and controllable processes to produce low dimensional materials and their artificial structures, and unravel their novel static and dynamical properties of broad interest to future photonic, electronic and energy technologies. The topics will include: a) Unraveling time-resolved dynamics in light-induced electronic response of two dimensional (2D) materials artificial structures. b) Fabrication of 1D atomically thin nanoribbon arrays and characterization of the electronic and magnetic properties for the prominent edge states. c) Lightwave manipulation with 2D superlattices. These research projects will provide participating students with broad interdisciplinary training across physics, chemistry, and materials science.
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Thomas Markland
Associate Professor of Chemistry
Current Research and Scholarly InterestsOur research centers on problems at the interface of quantum and statistical mechanics. Particular themes that occur frequently in our research are hydrogen bonding, the interplay between structure and dynamics, systems with multiple time and length-scales and quantum mechanical effects. The applications of our methods are diverse, ranging from chemistry to biology to geology and materials science. Particular current interests include proton and electron transfer in fuel cells and enzymatic systems, atmospheric isotope separation and the control of catalytic chemical reactivity using electric fields.
Treatment of these problems requires a range of analytic techniques as well as molecular mechanics and ab initio simulations. We are particularly interested in developing and applying methods based on the path integral formulation of quantum mechanics to include quantum fluctuations such as zero-point energy and tunneling in the dynamics of liquids and glasses. This formalism, in which a quantum mechanical particle is mapped onto a classical "ring polymer," provides an accurate and physically insightful way to calculate reaction rates, diffusion coefficients and spectra in systems containing light atoms. Our work has already provided intriguing insights in systems ranging from diffusion controlled reactions in liquids to the quantum liquid-glass transition as well as introducing methods to perform path integral calculations at near classical computational cost, expanding our ability to treat large-scale condensed phase systems. -
Todd Martinez
David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry and Professor of Photon Science
Current Research and Scholarly InterestsAb initio molecular dynamics, photochemistry, molecular design, mechanochemistry, graphical processing unit acceleration of electronic structure and molecular dynamics, automated reaction discovery, ultrafast (femtosecond and attosecond) chemical phenomena
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W. E. Moerner
Harry S. Mosher Professor
Current Research and Scholarly InterestsLaser spectroscopy and microscopy of single molecules to probe biological systems, one biomolecule at a time. Primary thrusts: fluorescence microscopy far beyond the optical diffraction limit (PALM/STORM/STED), methods for 3D optical microscopy in cells, and trapping of single biomolecules in solution for extended study. We explore protein localization patterns in bacteria, structures of amyloid aggregates in cells, signaling proteins in the primary cilium, and dynamics of DNA and RNA.
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Robert Pecora
Professor of Chemistry, Emeritus
Current Research and Scholarly InterestsThe development of the basic principles behind the dynamic light scattering (DLS) technique and its application to a wide variety of liquid systems is one of Pecora's outstanding contributions to physical chemistry. DLS is now an indispensable tool in the repertoire of polymer, colloid and biophysical chemists. It is generally accepted to be one of the best methods for measuring the mutual diffusion coefficients and, in dilute systems, the hydrodynamic sizes of polymers and particulates in solution or suspension. It is widely used, among other things, for studying size distributions of polymer and colloid dispersions; for testing theories of polymer dynamics in dilute and concentrated systems; and for studying interactions between macromolecules and colloidal particles in liquid dispersions. The basic work that established the foundation of this technique was done in the 1960s. Pecora has revisited this area over the years-formulating theories, for instance, of scattering from hollow spheres, large cylindrically symmetric molecules and wormlike chains.
An experimental program began in the early seventies resulted in a now classic series of studies on the rotational dynamics of small molecules in liquids. This work, utilizing mainly depolarized DLS and carbon 13 nuclear magnetic relaxation, has had a wide impact in the area of liquid state dynamics.
It was also during this period that the theoretical foundation for the fluorescence correlation spectroscopy technique (FCS) was formulated. Because of recent advances in equipment and materials, this technique has recently been revived and is now a powerful tool in biophysics.
The experimental and theoretical techniques developed for the study of the dynamics of relatively simple small molecule liquids have been used to investigate more complex systems such as the rotation of small molecule solvents in glassy and amorphous polymers. The resonance- enhanced depolarized light scattering technique was also developed in this period.
Extensive studies using depolarized dynamic light scattering (using the Fabry-Perot interferometer) as well as photon correlation spectroscopy, NMR, FCS and small angle X-ray scattering to the dynamics of oligonucleotides have determined the hydrodynamic diameter of DNA and the internal bending angles of the bases. They also provided support for relations relating hydrodynamic parameters to molecular dimensions for short rodlike molecules and “polyelectrolyte effects” on the translational and rotational motions of these highly charged molecules.
A major area of experimental and theoretical study has been the study of the dynamics of rigid and semirigid rodlike polymers in both dilute and semidilute dispersions. The work on translation and rotation of poly (-benzyl-L-glutamate) in semidilute solution is a foremost early work in this area.
The Pecora group has synthesized and studied the dynamics of model
rigid rod/sphere composite liquids. Studies of the translation of dilute spheres through solutions of the rods as functions of the rod and sphere sizes and the rod concentrations have provided the stimulus for more experiment and theoretical work in this area. Transient electric birefringence decay studies of the rotation of dilute rigid rod polymers in suspensions of comparably sized spherical particles have revealed scaling laws for the rod rotation.
A unique feature of part of this work on rigid and semirigid rodlike polymers is the utilization of genetic engineering techniques to construct a monodisperse, homologous series of DNA restriction fragments. These biologically-produced fragments have served as well-characterized model macromolecules for solution studies of the dynamics of semirigid rodlike polymers.
The well-regarded book of Pecora and Berne on dynamic light scattering, first published in 1976, has become a major reference work. It is now a Dover paperback. -
Jianghong Rao
Professor of Radiology (Molecular Imaging Program at Stanford) and, by courtesy, of Chemistry
Current Research and Scholarly InterestsProbe chemistry and nanotechnology for molecular imaging and diagnostics
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Grant M. Rotskoff
Assistant Professor of Chemistry
BioGrant Rotskoff studies the nonequilibrium dynamics of living matter with a particular focus on self-organization from the molecular to the cellular scale. His work involves developing theoretical and computational tools that can probe and predict the properties of physical systems driven away from equilibrium. Recently, he has focused on characterizing and designing physically accurate machine learning techniques for biophysical modeling. Prior to his current position, Grant was a James S. McDonnell Fellow working at the Courant Institute of Mathematical Sciences at New York University. He completed his Ph.D. at the University of California, Berkeley in the Biophysics graduate group supported by an NSF Graduate Research Fellowship. His thesis, which was advised by Phillip Geissler and Gavin Crooks, developed theoretical tools for understanding nonequilibrium control of the small, fluctuating systems, such as those encountered in molecular biophysics. He also worked on coarsegrained models of the hydrophobic effect and self-assembly. Grant received an S.B. in Mathematics from the University of Chicago, where he became interested in biophysics as an undergraduate while working on free energy methods for large-scale molecular dynamics simulations.
Research Summary
My research focuses on theoretical and computational approaches to "mesoscale" biophysics. Many of the cellular phenomena that we consider the hallmarks of living systems occur at the scale of hundreds or thousands of proteins. Processes like the self-assembly of organelle-sized structures, the dynamics of cell division, and the transduction of signals from the environment to the machinery of the cell are not macroscopic phenomena—they are the result of a fluctuating, nonequilibrium dynamics. Experimentally probing mesoscale systems remains extremely difficult, though it is continuing to benefit from advances in cryo-electron microscopy and super-resolution imaging, among many other techniques. Predictive and explanatory models that resolve the essential physics at these intermediate scales have the power to both aid and enrich the understanding we are presently deriving from these experimental developments.
Major parts of my research include:
1. Dynamics of mesoscale biophysical assembly and response.— Biophysical processes involve chemical gradients and time-dependent external signals. These inherently nonequilibrium stimuli drive supermolecular organization within the cell. We develop models of active assembly processes and protein-membrane interactions as a foundation for the broad goal of characterizing the properties of nonequilibrium biomaterials.
2. Machine learning and dimensionality reduction for physical models.— Machine learning techniques are rapidly becoming a central statistical tool in all domains of scientific research. We apply machine learning techniques to sampling problems that arise in computational chemistry and develop approaches for systematically coarse-graining physical models. Recently, we have also been exploring reinforcement learning in the context of nonequilibrium control problems.
3. Methods for nonequilibrium simulation, optimization, and control.— We lack well-established theoretical frameworks for describing nonequilibrium states, even seemingly simple situations in which there are chemical or thermal gradients. Additionally, there are limited tools for predicting the response of nonequilibrium systems to external perturbations, even when the perturbations are small. Both of these problems pose key technical challenges for a theory of active biomaterials. We work on optimal control, nonequilibrium statistical mechanics, and simulation methodology, with a particular interest in developing techniques for importance sampling configurations from nonequilibrium ensembles. -
Jennifer Schwartz Poehlmann
Senior Lecturer of Chemistry
BioReaching out to Stanford’s diverse body of students and beyond to share the excitement of scientific discovery has been a growing passion for Dr. Jennifer Schwartz Poehlmann. In addition to coordinating and co-teaching Stanford’s freshmen chemistry sequence, she takes a leadership role in developing training programs for teaching assistants and enhancing classroom and lab experiences for undergraduates, while also providing STEM learning opportunities for incoming freshmen and local high school students.
Jennifer Schwartz Poehlmann studied chemistry at Washington University in Saint Louis Missouri (A.B. 2002) before coming to Stanford University as a graduate student (Ph.D. 2008). Her thesis work under Prof. Edward Solomon addressed structural contributions to reactivity in active sites of non-heme di-iron enzymes, including ferritins. She joined the Stanford Center (now Vice Provost) for Teaching and Learning as a Teaching Fellow in 2008. In 2009, she became Lecturer and Introductory Course Coordinator for the Department of Chemistry, and in 2011 was promoted to Senior Lecturer. She has received multiple awards for her teaching and training work, including the Walter J. Gores Award for Excellence in Teaching, Dean’s Award for Achievements in Teaching, Hoagland Award Fund for Innovations in Undergraduate Teaching, and Society of Latino Engineers and School of Engineering’s Professor of the Year Award.
Teaching
Dr. Schwartz coordinates and co-teaches the introductory course sequence of Chem31A, 31B, and 33 for about 450 students each year. She has also created a set of companion courses (Chem31A-C, 31B-C, and 33-C) designed to provide motivated students an opportunity to build stronger study habits and problem solving tools that help them persevere in the sciences regardless of prior science background. In parallel, she has been involved in the creation and teaching of the Leland Scholars Program, which facilitates the transition to college for incoming freshman intending to study in STEM or pre-health fields.
Instructor Training
Dr. Schwartz has always believed that well-prepared and enthusiastic teachers inspire and motivate learning, yet excellent teaching requires training, feedback, reflection and support. She has worked both within the department and more broadly to help ensure that teaching assistants throughout the university receive the training, practice and mentorship they need to grow and excel as educators. She previously directed the Department of Chemistry’s TA Training program and, with the Vice Provost for Teaching and Learning, co-founded and directs the Mentors in Teaching Program, MinT, which provides training and resources to teaching mentors from more than 15 departments on campus. Through MinT, advanced graduate students learn effective ways to mentor TAs, through mid-quarter feedback, classroom observation, establishment of teaching goals, and workshops that enable new TAs to better engage with students in the classroom.
Enhanced Learning Experiences
Dr. Schwartz has been heavily involved in the development of hands-on, guided-inquiry lab activities that are now fully integrated into lab/lecture courses throughout the introductory general and organic chemistry sequence. Through the “Inspiring Future Scientists in Chemistry” Outreach Program, she is also helping to bring the excitement of exploring real-world chemistry into local high schools. She works with local high school teachers to design lab experiences that reinforce and compliment the chemistry concepts in the California State curriculum. Stanford Chemistry students take these activities to local high schools, providing hundreds of students the opportunity to work with enthusiastic young scientists while getting hands-on experience in chemistry. The program aims to demonstrate how chemistry relates to the ‘real world’ and to promote an appreciation for both science and higher education. -
Edward I. Solomon
Monroe E. Spaght Professor of Chemistry and Professor of Photon Science
On Leave from 04/01/2024 To 06/30/2024Current Research and Scholarly InterestsProf. Solomon's work spans physical-inorganic, bioinorganic, and theoretical-inorganic chemistry, focusing on spectroscopic elucidation of the electronic structure of transition metal complexes and its contribution to reactivity. He has advanced our understanding of metal sites involved in electron transfer, copper sites involved in O2 binding, activation and reduction to water, structure/function correlations over non-heme iron enzymes, and correlation of biological to heterogeneous catalysis.
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Daniel Stack
Associate Professor of Chemistry
On Leave from 04/01/2024 To 06/30/2024BioResearch in the Stack group focuses on the mechanism of dioxygen activation and the subsequent oxidative reactivity with primarily copper complexes ligated by imidazoles or histamines. Specifically, the group is interested in substrate hydroxylations and full dioxygen reduction. The remarkable specificity and energy efficiency of metalloenzymes provide the inspiration for the work. Trapping and characterizing immediate species, primarily at low temperatures, provide key mechanistic insights especially through substrate reactivity along with spectroscopic and metrical correlation to DFT calculations. Our objective is to move these efficient enzymatic mechanisms into small synthetic complexes, not only to reproduce biological reactivity, but more importantly to move the oxidative mechanism beyond that possible in the protein matrix.
Daniel Stack was born, raised and attended college in Portland Oregon. He received his B.A. from Reed College in 1982 (Phi Beta Kappa), working with Professor Tom Dunne on weak nickel-pyrazine complexes. In Boston, he pursued his doctoral study in synthetic inorganic chemistry at Harvard University (Ph.D., 1988) with Professor R. H. Holm, investigating site-differentiated synthetic analogues of biological Fe4S4 cubanes. As an NSF Postdoctoral Fellow with Professor K. N. Raymond at the University of California at Berkeley, he worked on synthesizing new, higher iron affinity ligands similar to enterobactin, a bacterial iron sequestering agent. He started his independent career in 1991 at Stanford University primarily working on oxidation catalysis and dioxygen activation, and was promoted to an Associate Professor in 1998. His contributions to undergraduate education have been recognized at the University level on several occasions, including the Dinkelspiel Award for Outstanding Contribution to Undergraduate Education in 2003.
Areas of current focus include:
Copper Dioxygen Chemistry
Our current interests focus on stabilizing species formed in the reaction of dioxygen with Cu(I) complexes formed with biologically relevant imidazole or histamine ligation. Many multi-copper enzymes ligated in this manner are capable of impressive hydroxylation reactions, including oxidative depolymerization of cellulose, methane oxidation, and energy-efficient reduction of dioxygen to water. Oxygenation of such complexes at extreme solution temperatures (-125°C) yield transient Cu(III) containing complexes. As Cu(III) is currently uncharacterized in any biological enzyme, developing connections between the synthetic and biological realms is a major focus.
Surface Immobilization of Catalysts in Mesoporous Materials
In redox active biological metal sites, the ligation environment is coupled tightly to the functional chemistry. Yet, the metal sites are also site-isolated, creating species that may only have a transient existence in a homogeneous solution. Site isolation of synthetic complexes can be achieved synthetically by supporting the metal complex on a solid matrix. Movement of these complexes into silica based materials or onto electroactive carbon electrodes represent a new direction for the group in the development of bio-inspired metal-based catalysts. -
Alice Ting
Professor of Genetics, of Biology and, by courtesy, of Chemistry
Current Research and Scholarly InterestsWe develop chemogenetic and optogenetic technologies for probing and manipulating protein networks, cellular RNA, and the function of mitochondria and the mammalian brain. Our technologies draw from protein engineering, directed evolution, chemical biology, organic synthesis, high-resolution microscopy, genetics, and computational design.
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Barry Trost
Job and Gertrud Tamaki Professor in the School of Humanities and Sciences, Emeritus
BioBorn in Philadelphia, Pennsylvania, Barry Trost began his university training at the University of Pennsylvania (BA, 1962) and completed his Ph.D. in Chemistry at the Massachusetts Institute of Technology (1965). He moved directly to the University of Wisconsin, where he was promoted to Professor of Chemistry and subsequently Vilas Research Professor. He joined the faculty at Stanford as Professor of Chemistry in 1987 and became Tamaki Professor of Humanities and Sciences in 1990. In addition to serving multiple visiting professorships, Professor Trost was presented with a Docteur honoris causa of the Université Claude-Bernard (Lyon I), France, and in 1997 a Doctor Scientiarum Honoris Causa of the Technion, Haifa, Israel. In recognition of his innovations and scholarship in the field of organic synthesis, Professor Trost has received the ACS Award in Pure Chemistry, ACS Award for Creative Work in Synthetic Organic Chemistry, Arthur C. Cope Scholar Award, and the Presidential Green Chemistry Challenge Award, among many others. Professor Trost has been elected a Fellow of the American Academy of Arts and Sciences, American Chemical Society, and American Association for the Advancement of Science, and a member of the National Academy of Sciences, and served as Chairman of the NIH Medicinal Chemistry Study Section. He has held over 125 special university lectureships and presented over 270 Plenary Lectures at national and international meetings. He has published two books and over 950 scientific articles. He edited a major compendium entitled Comprehensive Organic Synthesis consisting of nine volumes and serves on the editorial board for Science of Synthesis and Reaxys.
The Trost Group’s research program revolves around the theme of synthesis, including target molecules with potential applications as novel catalysts, as well as antibiotic and antitumor therapies. The work comprises two major activities: 1) developing the tools, i.e., the reactions and reagents, and 2) creating the proper network of reactions to make complex targets readily available from simple starting materials.
Efforts to develop "chemists' enzymes" – non-peptidic transition metal based catalysts that can perform chemo-, regio-, diastereo-, and especially enantioselective reactions – focus close attention to the question of atom economy to minimize waste, energy, and consumption of raw materials.
Synthetic efficiency raises the question of metal catalyzed cycloadditions to rings other than six-membered. A general strategy is evolving for a "Diels-Alder" equivalent for formation of five, seven, nine, etc. membered carbo- and heterocyclic rings.
An exciting new direction derives from the molecular gymnastics acetylenes undergo in the presence of transition metals. Additional specific goals include cycloisomerization to virtually all types of ring sizes and systems with particularly versatile juxtaposition of functionality.
Palladium and ruthenium catalysts represent a major part of the lab's efforts, in order to invent new synthetic processes together with new opportunities for selectivity complementary to that obtained using other metal complexes. Main group chemistry, especially involving silicon, zinc, and sulfur, also offers many opportunities for new reaction design. Rational design of novel catalysts for asymmetric additions to carbonyl and imine groups are an exciting thrust.From these new synthetic tools evolve new synthetic strategies towards complex natural products. Targets include β-lactam antibiotics, ionophores, steroids and related compounds (e.g., Vitamin D metabolites), alkaloids, nucleosides, carbohydrates, and macrolide, terpenoid, and tetracyclic antitumor and antibiotic agents. -
Robert Waymouth
Robert Eckles Swain Professor of Chemistry and Professor, by courtesy, of Chemical Engineering
BioRobert Eckles Swain Professor in Chemistry Robert Waymouth investigates new catalytic strategies to create useful new molecules, including bioactive polymers, synthetic fuels, and sustainable plastics. In one such breakthrough, Professor Waymouth and Professor Wender developed a new class of gene delivery agents.
Born in 1960 in Warner Robins, Georgia, Robert Waymouth studied chemistry and mathematics at Washington and Lee University in Lexington, Virginia (B.S. and B.A., respectively, both summa cum laude, 1982). He developed an interest in synthetic and mechanistic organometallic chemistry during his doctoral studies in chemistry at the California Institute of Technology under Professor R.H. Grubbs (Ph.D., 1987). His postdoctoral research with Professor Piero Pino at the Institut fur Polymere, ETH Zurich, Switzerland, focused on catalytic hydrogenation with chiral metallocene catalysts. He joined the Stanford University faculty as assistant professor in 1988, becoming full professor in 1997 and in 2000 the Robert Eckles Swain Professor of Chemistry.
Today, the Waymouth Group applies mechanistic principles to develop new concepts in catalysis, with particular focus on the development of organometallic and organic catalysts for the synthesis of complex macromolecular architectures. In organometallic catalysis, the group devised a highly selective alcohol oxidation catalyst that selectively oxidizes unprotected polyols and carbohydrates to alpha-hyroxyketones. In collaboration with Dr. James Hedrick of IBM, we have developed a platform of highly active organic catalysts and continuous flow reactors that provide access to polymer architectures that are difficult to access by conventional approaches.
The Waymouth group has devised selective organocatalytic strategies for the synthesis of functional degradable polymers and oligomers that function as "molecular transporters" to deliver genes, drugs and probes into cells and live animals. These advances led to the joint discovery with the Wender group of a general, safe, and remarkably effective concept for RNA delivery based on a new class of synthetic cationic materials, Charge-Altering Releasable Transporters (CARTs). This technology has been shown to be effective for mRNA based cancer vaccines. -
Paul Wender
Francis W. Bergstrom Professor and Professor, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly InterestsMolecular imaging, therapeutics, drug delivery, drug mode of action, synthesis
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Yan Xia
Associate Professor of Chemistry
Current Research and Scholarly InterestsPolymer Chemistry, Microporous Polymer Membranes, Responsive Polymers, Degradable Polymers, Polymers with Unique Mechanical Behaviors, Polymer Networks, Organic Electronic Materials
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Richard Zare
Marguerite Blake Wilbur Professor of Natural Science and Professor, by courtesy, of Physics
Current Research and Scholarly InterestsMy research group is exploring a variety of topics that range from the basic understanding of chemical reaction dynamics to the nature of the chemical contents of single cells.
Under thermal conditions nature seems to hide the details of how elementary reactions occur through a series of averages over reagent velocity, internal energy, impact parameter, and orientation. To discover the effects of these variables on reactivity, it is necessary to carry out studies of chemical reactions far from equilibrium in which the states of the reactants are more sharply restricted and can be varied in a controlled manner. My research group is attempting to meet this tough experimental challenge through a number of laser techniques that prepare reactants in specific quantum states and probe the quantum state distributions of the resulting products. It is our belief that such state-to-state information gives the deepest insight into the forces that operate in the breaking of old bonds and the making of new ones.
Space does not permit a full description of these projects, and I earnestly invite correspondence. The following examples are representative:
The simplest of all neutral bimolecular reactions is the exchange reaction H H2 -> H2 H. We are studying this system and various isotopic cousins using a tunable UV laser pulse to photodissociate HBr (DBr) and hence create fast H (D) atoms of known translational energy in the presence of H2 and/or D2 and using a laser multiphoton ionization time-of-flight mass spectrometer to detect the nascent molecular products in a quantum-state-specific manner by means of an imaging technique. It is expected that these product state distributions will provide a key test of the adequacy of various advanced theoretical schemes for modeling this reaction.
Analytical efforts involve the use of capillary zone electrophoresis, two-step laser desorption laser multiphoton ionization mass spectrometry, cavity ring-down spectroscopy, and Hadamard transform time-of-flight mass spectrometry. We believe these methods can revolutionize trace analysis, particularly of biomolecules in cells.
