Stanford Advisors

All Publications

  • Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad FeIV═O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction. Journal of the American Chemical Society Srnec, M., Iyer, S. R., Dassama, L. M., Park, K., Wong, S. D., Sutherlin, K. D., Yoda, Y., Kobayashi, Y., Kurokuzu, M., Saito, M., Seto, M., Krebs, C., Bollinger, J. M., Solomon, E. I. 2020


    The alpha-ketoglutarate (alphaKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV═O intermediate in the alphaKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the FeIV═O complex in taurine dioxygenase (TauD), the alphaKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate FeIV═O complexes in two different substrate orientations (one more along [sigma channel] and another more perpendicular [pi channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the pi channel by the significantly larger oxyl character present in the ppi orbital oriented toward the substrate, which leads to an earlier transition state along the C-H coordinate.

    View details for DOI 10.1021/jacs.0c08903

    View details for PubMedID 33103886

  • Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate-dependent nonheme ferrous enzymes. Proceedings of the National Academy of Sciences of the United States of America Goudarzi, S., Iyer, S. R., Babicz, J. T., Yan, J. J., Peters, G. H., Christensen, H. E., Hedman, B., Hodgson, K. O., Solomon, E. I. 2020


    Determining the requirements for efficient oxygen (O2) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)-dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O2) and a sequential mechanism (cofactor binding and reaction with O2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the FeII), αKG binding to FeII-DAOCS results in ∼45% five-coordinate sites that selectively react with O2 relative to the remaining six-coordinate sites. However, this reaction produces an FeIII species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to FeII-DAOCS produces five-coordinate sites that rapidly react with O2 to form an FeIV=O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.

    View details for DOI 10.1073/pnas.1922484117

    View details for PubMedID 32094179

  • Geometric and Electronic Structural Contributions to Fe/O2 Reactivity. Bulletin of Japan Society of Coordination Chemistry Solomon, E. I., Iyer, S. R. 2019; 73: 3–14


    While two classes of non-heme iron enzymes use ferric centers to activate singlet organic substrates for the spin forbidden reaction with 3O2, most classes use high spin ferrous sites to activate dioxygen. These FeII active sites do not exhibit intense absorption bands and have an integer spin ground state thus are mostly EPR inactive. We have developed new spectroscopic methodologies that provide geometric and electronic structural insight into the ferrous centers and their interactions with cosubstrates for dioxygen activation and into the nature of the intermediates generated in these reactions. First, we present our variable-temperature variable-field magnetic circular dichroism (VTVH MCD) methodology to experimentally define the geometric and electronic structure of the high spin ferrous active site. Then, we focus on using Nuclear Resonance Vibrational Spectroscopy (NRVS, performed at SPring-8) to define geometric structure and VTVH MCD to define the electronic structure of the FeIII-OOH and FeIV=O intermediates generated in O2 activation and the spin state dependence of their frontier molecular orbitals (FMOs) in controlling reactivity. Experimentally validated reaction coordinates are derived for the anticancer drug bleomycin in its cleavage of DNA and for an alpha- ketoglutarate dependent dioxygenase in its selective halogenation over the thermodynamically favored hydroxylation of substrate.

    View details for DOI 10.4019/bjscc.73.3

    View details for PubMedID 32391114

  • O2 Activation by Nonheme FeII alpha-Ketoglutarate-Dependent Enzyme Variants: Elucidating the Role of the Facial Triad Carboxylate in FIH. Journal of the American Chemical Society Iyer, S. R., Chaplin, V. D., Knapp, M. J., Solomon, E. I. 2018


    FIH [factor inhibiting HIF (hypoxia inducible factor)] is an alpha-ketoglutarate (alphaKG)-dependent nonheme iron enzyme that catalyzes the hydroxylation of the C-terminal transactivation domain (CAD) asparagine residue in HIF-1alpha to regulate cellular oxygen levels. The role of the facial triad carboxylate ligand in O2 activation and catalysis was evaluated by replacing the Asp201 residue with Gly (D201G), Ala (D201A), and Glu (D201E). Magnetic circular dichroism (MCD) spectroscopy showed that the (FeII)FIH variants were all 6-coordinate (6C) and the alphaKG plus CAD bound FIH variants were all 5-coordinate (5C), mirroring the behavior of the wild-type ( wt) enzyme. When only alphaKG is bound, all FIH variants exhibited weaker FeII-OH2 bonds for the sixth ligand compared to wt, and for alphaKG-bound D201E this is either extremely weak or the site is 5C, demonstrating that the Asp201 residue plays an important role in the wt enzyme in ensuring that the (FeII/alphaKG)FIH site remains 6C. Variable-temperature, variable-field (VTVH) MCD spectroscopy showed that all of the alphaKG- and CAD-bound FIH variants, though 5C, have different ground-state geometric and electronic structures, which impair their oxygen activation rates. Comparison of O2 consumption to substrate hydroxylation kinetics revealed uncoupling between the two half reactions in the variants. Thus, the Asp201 residue also ensures fidelity between CAD substrate binding and oxygen activation, enabling tightly coupled turnover.

    View details for PubMedID 30148961

  • Leveraging teacher partnerships to facilitate effective high school visits and mentorship Iyer, S., Schwartz, J. AMER CHEMICAL SOC. 2018
  • A chameleon catalyst for nonheme iron-promoted olefin oxidation CHEMICAL COMMUNICATIONS Iyer, S. R., Javadi, M. M., Feng, Y., Hyun, M. Y., Oloo, W. N., Kim, C., Que, L. 2014; 50 (89): 13777-13780


    We report the chameleonic reactivity of two nonheme iron catalysts for olefin oxidation with H2O2 that switch from nearly exclusive cis-dihydroxylation of electron-poor olefins to the exclusive epoxidation of electron-rich olefins upon addition of acetic acid. This switching suggests a common precursor to the nucleophilic oxidant proposed to Fe(III)-η(2)-OOH and electrophilic oxidant proposed to Fe(V)(O)(OAc), and reversible coordination of acetic acid as a switching pathway.

    View details for DOI 10.1039/c4cc06164k

    View details for Web of Science ID 000343988200034

    View details for PubMedID 25251577

  • Cyclohexene as a substrate probe for the nature of the high-valent iron-oxo oxidant in Fe(TPA)-catalyzed oxidations NEW JOURNAL OF CHEMISTRY Oloo, W. N., Feng, Y., Iyer, S., Parmelee, S., Xue, G., Que, L. 2013; 37 (11): 3411-3415

    View details for DOI 10.1039/c3nj00524k

    View details for Web of Science ID 000325763700008

  • Microwave observation of (KBr)-K-41-Br-79 and (KBr)-K-41-Br-81 from laser-ablated potassium bromide JOURNAL OF MOLECULAR SPECTROSCOPY Timp, B. A., Doran, J. L., Lyer, S., Grabow, J., Leopold, K. R. 2012; 271 (1): 20-24