Research 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.

Academic Appointments

Administrative Appointments

  • Courtesy faculty, Dept. of Chemical and Systems Biology, Stanford University (2013 - Present)
  • Faculty Affiliate, Stanford Neuroscience Institute (2013 - Present)
  • Executive Committee Member, Stanford ChEM-H (2012 - Present)
  • Cofounder, Board Member, SiteOne Therapeutics, Inc (2011 - Present)
  • Founder, Center for Molecular Analysis and Design at Stanford (2009 - Present)
  • Founding Member, NSF Center for Selective C–H Functionalization (2009 - Present)
  • Permanent Member, NIH study section, Synthetic & Biological Chemistry A (2009 - 2013)
  • Member, Bio-X (2004 - Present)
  • Member, American Chemical Society (1992 - Present)

Honors & Awards

  • John A. and Cynthia Fry Gunn University Fellow in Undergraduate Education, Stanford University (2011–2020)
  • Dean’s Award for Distinguished Achievements in Teaching, Stanford University (2008)

Boards, Advisory Committees, Professional Organizations

  • Scientist Consultant, Pfizer Inc. (2004 - Present)
  • Scientist Consultant, Gilead Sciences (2007 - Present)
  • Founder and Board Member, SiteOne Therapeutics (2010 - Present)

Professional Education

  • Postdoc, Massachusetts Institute of Technology, Chemistry (1999)
  • PhD, California Institute of Technology, Chemistry (1997)
  • BS, University of California, Berkeley, Chemistry (1992)

Stanford Advisees

All Publications

  • Site-selective bromination of sp3 C–H bonds Chem.Sci Sathyamoorthi, S., Banerjee, S., Du Bois, J., Burns, N. Z., Zare, R. N. 2018; 9: 100-104


    A method for converting sp3 C-H to C-Br bonds using an N-methyl sulfamate directing group is described. The reaction employs Rh2(oct)4 and a mixture of NaBr and NaOCl and is performed in aqueous solution open to air. For all sulfamates examined, oxidation occurs with high selectivity at the γ-carbon, affording a uniquely predictable method for C-H bond halogenation. Results from a series of mechanistic experiments suggest that substrate oxidation likely proceeds by a radical chain process. Initial formation of an N-halogenated sulfamate followed by Rh-mediated homolysis generates an N-centered radical, which serves as the active oxidant.

    View details for DOI 10.1039/C7SC04611A

    View details for PubMedCentralID PMC5873043

  • Intermolecular sp3 C-H Amination of Complex Molecules. Angewandte Chemie (International ed. in English) Chiappini, N. D., Mack, J. B., Du Bois, J. n. 2018


    A general and operationally convenient method for intermolecular amination of sp3 C-H bonds is described. This technology allows for efficient functionalization of complex molecules, including numerous pharmaceutical targets. The combination of pivalonitrile as solvent, Al2O3 as an additive, and phenyl sulfamate as a nitrogen source affords differential reaction performance and substrate scope. Mechanistic data strongly implicate a pathway for catalyst decomposition that initiates with solvent oxidation, thus providing rationale for the marked influence of pivalonitrile on this reaction process.

    View details for PubMedID 29484792

  • Ruthenium-Catalyzed C-H Hydroxylation in Aqueous Acid Enables Selective Functionalization of Amine Derivatives. Journal of the American Chemical Society Mack, J. B., Gipson, J. D., Du Bois, J., Sigman, M. S. 2017; 139 (28): 9503-9506


    The identification, optimization, and evaluation of a new catalytic protocol for sp3C-H hydroxylation is described. Reactions are performed in aqueous acid using a bis(bipyridine)Ru catalyst to enable oxidation of substrates possessing basic amine functional groups. Tertiary and benzylic C-H hydroxylation is strongly favored over N-oxidation for numerous amine derivatives. With terpene-derived substrates, similar trends in reactivity toward tertiary and benzylic C-H bonds are observed. Hydroxylation of chiral tertiary centers is enantiospecific in spite of the ionizing strength of the reaction medium. Preliminary kinetics experiments show a marked difference in reactivity between isomeric cis- and trans-Ru catalysts suggesting that the catalyst is configurationally stable under the reaction conditions.

    View details for DOI 10.1021/jacs.7b05469

    View details for PubMedID 28660763

  • Mechanistic analysis of a copper-catalyzed C-H oxidative cyclization of carboxylic acids. Chemical science Banerjee, S. n., Sathyamoorthi, S. n., Du Bois, J. n., Zare, R. N. 2017; 8 (10): 7003–8


    We recently reported that carboxylic acids can be oxidized to lactone products by potassium persulfate and catalytic copper acetate. Here, we unravel the mechanism for this C-H functionalization reaction using desorption electrospray ionization, online electrospray ionization, and tandem mass spectrometry. Our findings suggest that electron transfer from a transient benzylic radical intermediate reduces Cu(ii) to Cu(i), which is then re-oxidized to Cu(ii) in the catalytic cycle. The resulting benzylic carbocation is trapped by the pendant carboxylate group to give the lactone product. Formation of the putative benzylic carbocation is supported by Hammett analysis. The proposed mechanism for this copper-catalyzed oxidative cyclization process differs from earlier reports of analogous reactions, which posit a substrate carboxylate radical as the reactive oxidant.

    View details for PubMedID 29147527

    View details for PubMedCentralID PMC5642147

  • Copper-Catalyzed Oxidative Cyclization of Carboxylic Acids ORGANIC LETTERS Sathyamoorthi, S., Du Bois, J. 2016; 18 (24): 6308-6311


    A method for converting C-H to C-O bonds through oxidative cyclization of carboxylic acids to generate lactone products is described. The reaction employs catalytic amounts of Cu(OAc)2 and potassium persulfate as the terminal oxidant and is performed open to air in an aqueous acetic acid solvent system. Preliminary mechanistic studies suggest that substrate oxidation likely proceeds by sulfate radical anion and that the Cu catalyst has no influence on the product-determining step. These conclusions differ from related investigations that propose the intermediacy of a carboxylate radical.

    View details for DOI 10.1021/acs.orglett.6b03176

    View details for Web of Science ID 000390180300024

    View details for PubMedID 27978696

  • Asymmetric synthesis of batrachotoxin: Enantiomeric toxins show functional divergence against Na-V SCIENCE Logan, M. M., Toma, T., Thomas-Tran, R., Du Bois, J. 2016; 354 (6314): 865-869


    The steroidal neurotoxin (-)-batrachotoxin functions as a potent agonist of voltage-gated sodium ion channels (NaVs). Here we report concise asymmetric syntheses of the natural (-) and non-natural (+) antipodes of batrachotoxin, as well both enantiomers of a C-20 benzoate-modified derivative. Electrophysiological characterization of these molecules against NaV subtypes establishes the non-natural toxin enantiomer as a reversible antagonist of channel function, markedly different in activity from (-)-batrachotoxin. Protein mutagenesis experiments implicate a shared binding side for the enantiomers in the inner pore cavity of NaV These findings motivate and enable subsequent studies aimed at revealing how small molecules that target the channel inner pore modulate NaV dynamics.

    View details for DOI 10.1126/science.aag2981

    View details for Web of Science ID 000388531900035

    View details for PubMedID 27856903

  • Manganese(II)/Picolinic Acid Catalyst System for Epoxidation of Olefins ORGANIC LETTERS Moretti, R. A., Du Bois, J., Stack, T. D. 2016; 18 (11): 2528-2531


    An in situ generated catalyst system based on Mn(CF3SO3)2, picolinic acid, and peracetic acid converts an extensive scope of olefins to their epoxides at 0 °C in <5 min, with remarkable oxidant efficiency and no evidence of radical behavior. Competition experiments indicate an electrophilic active oxidant, proposed to be a high-valent Mn = O species. Ligand exploration suggests a general ligand sphere motif contributes to effective oxidation. The method is underscored by its simplicity and use of inexpensive reagents to quickly access high value-added products.

    View details for DOI 10.1021/acs.orglett.6b00518

    View details for Web of Science ID 000377319000003

    View details for PubMedID 27191036

  • Mutant cycle analysis with modified saxitoxins reveals specific interactions critical to attaining high-affinity inhibition of hNa(V)1.7 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Thomas-Tran, R., Du Bois, J. 2016; 113 (21): 5856-5861


    Improper function of voltage-gated sodium channels (NaVs), obligatory membrane proteins for bioelectrical signaling, has been linked to a number of human pathologies. Small-molecule agents that target NaVs hold considerable promise for treatment of chronic disease. Absent a comprehensive understanding of channel structure, the challenge of designing selective agents to modulate the activity of NaV subtypes is formidable. We have endeavored to gain insight into the 3D architecture of the outer vestibule of NaV through a systematic structure-activity relationship (SAR) study involving the bis-guanidinium toxin saxitoxin (STX), modified saxitoxins, and protein mutagenesis. Mutant cycle analysis has led to the identification of an acetylated variant of STX with unprecedented, low-nanomolar affinity for human NaV1.7 (hNaV1.7), a channel subtype that has been implicated in pain perception. A revised toxin-receptor binding model is presented, which is consistent with the large body of SAR data that we have obtained. This new model is expected to facilitate subsequent efforts to design isoform-selective NaV inhibitors.

    View details for DOI 10.1073/pnas.1603486113

    View details for Web of Science ID 000376779900044

    View details for PubMedID 27162340

    View details for PubMedCentralID PMC4889396

  • Synthesis of the Paralytic Shellfish Poisons (+)-Gonyautoxin 2, (+)-Gonyautoxin 3, and (+)-11,11-Dihydroxysaxitoxin JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Mulcahy, J. V., Walker, J. R., Merit, J. E., Whitehead, A., Du Bois, J. 2016; 138 (18): 5994-6001


    The paralytic shellfish poisons are a collection of guanidine-containing natural products that are biosynthesized by prokaryote and eukaryote marine organisms. These compounds bind and inhibit isoforms of the mammalian voltage-gated Na(+) ion channel at concentrations ranging from 10(-11) to 10(-5) M. Here, we describe the de novo synthesis of three paralytic shellfish poisons, gonyautoxin 2, gonyautoxin 3, and 11,11-dihydroxysaxitoxin. Key steps include a diastereoselective Pictet-Spengler reaction and an intramolecular amination of an N-guanidyl pyrrole by a sulfonyl guanidine. The IC50's of GTX 2, GTX 3, and 11,11-dhSTX have been measured against rat NaV1.4, and are found to be 22 nM, 15 nM, and 2.2 μM, respectively.

    View details for DOI 10.1021/jacs.6b02343

    View details for Web of Science ID 000375889100041

    View details for PubMedID 27138488

  • Rh2(II,III) Catalysts with Chelating Carboxylate and Carboxamidate Supports: Electronic Structure and Nitrene Transfer Reactivity. Journal of the American Chemical Society Varela-Álvarez, A., Yang, T., Jennings, H., Kornecki, K. P., MacMillan, S. N., Lancaster, K. M., Mack, J. B., Du Bois, J., Berry, J. F., Musaev, D. G. 2016; 138 (7): 2327-2341


    Dirhodium-catalyzed C-H amination is hypothesized to proceed via Rh2-nitrene intermediates in either the Rh2(II,II) or Rh2(II,III) redox state. Herein, we report joint theoretical and experimental studies of the ground electronic state (GES), redox potentials, and C-H amination of [Rh2(II,III)(O2CCH3)4(L)n](+) (1_L) (L = none, Cl(-), and H2O), [Rh2(esp)2](+) (2), and Rh2(espn)2Cl (3) (esp = α,α,α',α'-tetramethyl-1,3-benzenedipropanoate and espn = α,α,α',α'-tetramethyl-1,3-benzenedipropanamidate). CASSCF calculations on 1_L yield a wave function with two closely weighted configurations, (δ*)(2)(π1*)(2)(π2*)(1) and (δ*)(2)(π1*)(1)(π2*)(2), consistent with reported EPR g values [ Chem. Phys. Lett. 1986 , 130 , 20 - 23 ]. In contrast, EPR spectra of 2 show g values consistent with the DFT-computed (π*)(4)(δ*)(1) GES. EPR spectra and Cl K-edge XAS for 3 are consistent with a (π*)(4)(δ*)(1) GES, as supported by DFT. Nitrene intermediates 2N_L and 3N_L are also examined by DFT (the nitrene is an NSO3R species). DFT calculations suggest a doublet GES for 2N_L and a quartet GES for 3N_L. CASSCF calculations describe the GES of 2N as Rh2(II,II) with a coordinated nitrene radical cation, (π*)(4)(δ*)(2)(πnitrene,1)(1)(πnitrene,2)(0). Conversely, the GES of 3N is Rh2(II,III) with a coordinated triplet nitrene, (π*)(4)(δ*)(1)(πnitrene,1)(1)(πnitrene,2)(1). Quartet transition states ((4)TSs) are found to react via a stepwise radical mechanism, whereas (2)TSs are found to react via a concerted mechanism that is lower in energy compared to (4)TSs for both 2N_L and 3N_L. The experimental (determined by intramolecular competition) and (2)TS-calculated kinetic isotopic effect (KIE) shows a KIE ∼ 3 for both 2N and 3N, which is consistent with a concerted mechanism.

    View details for DOI 10.1021/jacs.5b12790

    View details for PubMedID 26820386

  • Inhibition of Sodium Ion Channel Function with Truncated Forms of Batrachotoxin ACS Chem. Neurosci. Toma, T., Logan, M. M., Maynard, F., Devlin, A. S., Du Bois, J. 2016; 7 (10): 1463-1468
  • Saxitoxin. Angewandte Chemie (International ed. in English) Thottumkara, A. P., Parsons, W. H., Du Bois, J. 2014; 53 (23): 5760-5784


    The paralytic agent (+)-saxitoxin (STX), most commonly associated with oceanic red tides and shellfish poisoning, is a potent inhibitor of electrical conduction in cells. Its nefarious effects result from inhibition of voltage-gated sodium channels (Na(V)s), the obligatory proteins responsible for the initiation and propagation of action potentials. In the annals of ion channel research, the identification and characterization of Na(V)s trace to the availability of STX and an allied guanidinium derivative, tetrodotoxin. The mystique of STX is expressed in both its function and form, as this uniquely compact dication boasts more heteroatoms than carbon centers. This Review highlights both the chemistry and chemical biology of this fascinating natural product, and offers a perspective as to how molecular design and synthesis may be used to explore Na(V) structure and function.

    View details for DOI 10.1002/anie.201308235

    View details for PubMedID 24771635

  • Organocatalytic C-H hydroxylation with Oxone (R) enabled by an aqueous fluoroalcohol solvent system CHEMICAL SCIENCE Adams, A. M., Du Bois, J. 2014; 5 (2): 656-659

    View details for DOI 10.1039/c3sc52649f

    View details for Web of Science ID 000328954200028

  • Selective Intermolecular Amination of C-H Bonds at Tertiary Carbon Centers ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Roizen, J. L., Zalatan, D. N., Du Bois, J. 2013; 52 (43): 11343-11346


    C-H insertion: A method for intermolecular amination of tertiary CH bonds is described that uses limiting amounts of substrate and a convenient phenol-derived nitrogen source. Structure-selectivity and mechanistic studies suggest that steric interaction between the substrate and active oxidant is the principal determinant of product selectivity.

    View details for DOI 10.1002/anie.201304238

    View details for Web of Science ID 000330735800022

    View details for PubMedID 24000186

  • Marked difference in saxitoxin and tetrodotoxin affinity for the human nociceptive voltage-gated sodium channel (Nav1.7) [corrected]. Proceedings of the National Academy of Sciences of the United States of America Walker, J. R., Novick, P. A., Parsons, W. H., McGregor, M., Zablocki, J., Pande, V. S., Du Bois, J. 2012; 109 (44): 18102-18107


    Human nociceptive voltage-gated sodium channel (Na(v)1.7), a target of significant interest for the development of antinociceptive agents, is blocked by low nanomolar concentrations of (-)-tetrodotoxin(TTX) but not (+)-saxitoxin (STX) and (+)-gonyautoxin-III (GTX-III). These findings question the long-accepted view that the 1.7 isoform is both tetrodotoxin- and saxitoxin-sensitive and identify the outer pore region of the channel as a possible target for the design of Na(v)1.7-selective inhibitors. Single- and double-point amino acid mutagenesis studies along with whole-cell electrophysiology recordings establish two domain III residues (T1398 and I1399), which occur as methionine and aspartate in other Na(v) isoforms, as critical determinants of STX and gonyautoxin-III binding affinity. An advanced homology model of the Na(v) pore region is used to provide a structural rationalization for these surprising results.

    View details for DOI 10.1073/pnas.1206952109

    View details for PubMedID 23077250

    View details for PubMedCentralID PMC3497785

  • Fluorescent Saxitoxins for Live Cell Imaging of Single Voltage-Gated Sodium Ion Channels beyond the Optical Diffraction Limit CHEMISTRY & BIOLOGY Ondrus, A. E., Lee, H. D., Iwanaga, S., Parsons, W. H., Andresen, B. M., Moerner, W. E., Du Bois, J. 2012; 19 (7): 902-912


    A desire to better understand the role of voltage-gated sodium channels (Na(V)s) in signal conduction and their dysregulation in specific disease states motivates the development of high precision tools for their study. Nature has evolved a collection of small molecule agents, including the shellfish poison (+)-saxitoxin, that bind to the extracellular pore of select Na(V) isoforms. As described in this report, de novo chemical synthesis has enabled the preparation of fluorescently labeled derivatives of (+)-saxitoxin, STX-Cy5, and STX-DCDHF, which display reversible binding to Na(V)s in live cells. Electrophysiology and confocal fluorescence microscopy studies confirm that these STX-based dyes function as potent and selective Na(V) labels. The utility of these probes is underscored in single-molecule and super-resolution imaging experiments, which reveal Na(V) distributions well beyond the optical diffraction limit in subcellular features such as neuritic spines and filopodia.

    View details for DOI 10.1016/j.chembiol.2012.05.021

    View details for Web of Science ID 000307261100016

    View details for PubMedID 22840778

  • Metal-Catalyzed Nitrogen-Atom Transfer Methods for the Oxidation of Aliphatic C-H Bonds ACCOUNTS OF CHEMICAL RESEARCH Roizen, J. L., Harvey, M. E., Du Bois, J. 2012; 45 (6): 911-922


    For more than a century, chemists have endeavored to discover and develop reaction processes that enable the selective oxidation of hydrocarbons. In the 1970s, Abramovitch and Yamada described the synthesis and electrophilic reactivity of sulfonyliminoiodinanes (RSO(2)N═IPh), demonstrating the utility of this new class of reagents to function as nitrene equivalents. Subsequent investigations by Breslow, Mansuy, and Müller would show such oxidants to be competent for alkene and saturated hydrocarbon functionalization when combined with transition metal salts or metal complexes, namely those of Mn, Fe, and Rh. Here, we trace our own studies to develop N-atom transfer technologies for C-H and π-bond oxidation. This Account discusses advances in both intra- and intermolecular amination processes mediated by dirhodium and diruthenium complexes, as well as the mechanistic foundations of catalyst reactivity and arrest. Explicit reference is given to questions that remain unanswered and to problem areas that are rich for discovery. A fundamental advance in amination technology has been the recognition that iminoiodinane oxidants can be generated in situ in the presence of a metal catalyst that elicits subsequent N-atom transfer. Under these conditions, both dirhodium and diruthenium lantern complexes function as competent catalysts for C-H bond oxidation with a range of nitrogen sources (e.g., carbamates, sulfamates, sulfamides, etc.), many of which will not form isolable iminoiodinane equivalents. Practical synthetic methods and applications thereof have evolved in parallel with inquiries into the operative reaction mechanism(s). For the intramolecular dirhodium-catalyzed process, the body of experimental and computational data is consistent with a concerted asynchronous C-H insertion pathway, analogous to the consensus mechanism for Rh-carbene transfer. Other studies reveal that the bridging tetracarboxylate ligand groups, which shroud the dirhodium core, are labile to exchange under standard reaction conditions. This information has led to the generation of chelating dicarboxylate dinuclear rhodium complexes, exemplified by Rh(2)(esp)(2). The performance of this catalyst system is unmatched by other dirhodium complexes in both intra- and intermolecular C-H amination reactions. Tetra-bridged, mixed-valent diruthenium complexes function as effective promoters of sulfamate ester oxidative cyclization. These catalysts can be crafted with ligand sets other than carboxylates and are more resistant to oxidation than their dirhodium counterparts. A range of experimental and computational mechanistic data amassed with the tetra-2-oxypyridinate diruthenium chloride complex, [Ru(2)(hp)(4)Cl], has established the insertion event as a stepwise pathway involving a discrete radical intermediate. These data contrast dirhodium-catalyzed C-H amination and offer a cogent model for understanding the divergent chemoselectivity trends observed between the two catalyst types. This work constitutes an important step toward the ultimate goal of achieving predictable, reagent-level control over product selectivity.

    View details for DOI 10.1021/ar200318q

    View details for Web of Science ID 000305321100013

    View details for PubMedID 22546004