Professional Education


  • Doctor of Philosophy, Stanford University, Chemistry (2020)
  • Master of Science, Seoul National University, Chemistry (2011)
  • Bachelor of Science, Seoul National University, Chemistry (2009)

Stanford Advisors


All Publications


  • A Thioether-Ligated Cupric Superoxide Model with Hydrogen Atom Abstraction Reactivity. Journal of the American Chemical Society Bhadra, M. n., Transue, W. J., Lim, H. n., Cowley, R. E., Lee, J. Y., Siegler, M. A., Josephs, P. n., Henkel, G. n., Lerch, M. n., Schindler, S. n., Neuba, A. n., Hodgson, K. O., Hedman, B. n., Solomon, E. I., Karlin, K. D. 2021

    Abstract

    The central role of cupric superoxide intermediates proposed in hormone and neurotransmitter biosynthesis by noncoupled binuclear copper monooxygenases like dopamine-β-monooxygenase has drawn significant attention to the unusual methionine ligation of the CuM ("CuB") active site characteristic of this class of enzymes. The copper-sulfur interaction has proven critical for turnover, raising still-unresolved questions concerning Nature's selection of an oxidizable Met residue to facilitate C-H oxygenation. We describe herein a model for CuM, [(TMGN3S)CuI]+ ([1]+), and its O2-bound analog [(TMGN3S)CuII(O2•-)]+ ([1·O2]+). The latter is the first reported cupric superoxide with an experimentally proven Cu-S bond which also possesses demonstrated hydrogen atom abstraction (HAA) reactivity. Introduction of O2 to a precooled solution of the cuprous precursor [1]B(C6F5)4 (-135 °C, 2-methyltetrahydrofuran (2-MeTHF)) reversibly forms [1·O2]B(C6F5)4 (UV/vis spectroscopy: λmax 442, 642, 742 nm). Resonance Raman studies (413 nm) using 16O2 [18O2] corroborated the identity of [1·O2]+ by revealing Cu-O (446 [425] cm-1) and O-O (1105 [1042] cm-1) stretches, and extended X-ray absorption fine structure (EXAFS) spectroscopy showed a Cu-S interatomic distance of 2.55 Å. HAA reactivity between [1·O2]+ and TEMPO-H proceeds rapidly (1.28 × 10-1 M-1 s-1, -135 °C, 2-MeTHF) with a primary kinetic isotope effect of kH/kD = 5.4. Comparisons of the O2-binding behavior and redox activity of [1]+ vs [2]+, the latter a close analog of [1]+ but with all N atom ligation (i.e., N3S vs N4), are presented.

    View details for DOI 10.1021/jacs.1c00260

    View details for PubMedID 33684290

  • Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c. Nature communications Reinhard, M. E., Mara, M. W., Kroll, T., Lim, H., Hadt, R. G., Alonso-Mori, R., Chollet, M., Glownia, J. M., Nelson, S., Sokaras, D., Kunnus, K., Driel, T. B., Hartsock, R. W., Kjaer, K. S., Weninger, C., Biasin, E., Gee, L. B., Hodgson, K. O., Hedman, B., Bergmann, U., Solomon, E. I., Gaffney, K. J. 2021; 12 (1): 1086

    Abstract

    The dynamics of photodissociation and recombination in heme proteins represent an archetypical photochemical reaction widely used to understand the interplay between chemical dynamics and reaction environment. We report a study of the photodissociation mechanism for the Fe(II)-S bond between the heme iron and methionine sulfur of ferrous cytochrome c. This bond dissociation is an essential step in the conversion of cytochrome c from an electron transfer protein to a peroxidase enzyme. We use ultrafast X-ray solution scattering to follow the dynamics of Fe(II)-S bond dissociation and 1s3p (Kbeta) X-ray emission spectroscopy to follow the dynamics of the iron charge and spin multiplicity during bond dissociation. From these measurements, we conclude that the formation of a triplet metal-centered excited state with anti-bonding Fe(II)-S interactions triggers the bond dissociation and precedes the formation of the metastable Fe high-spin quintet state.

    View details for DOI 10.1038/s41467-021-21423-w

    View details for PubMedID 33597529

  • Kbeta X-ray Emission Spectroscopy as a Probe of Cu(I) Sites: Application to the Cu(I) Site in Preprocessed Galactose Oxidase. Inorganic chemistry Lim, H., Baker, M. L., Cowley, R. E., Kim, S., Bhadra, M., Siegler, M. A., Kroll, T., Sokaras, D., Weng, T., Biswas, D. R., Dooley, D. M., Karlin, K. D., Hedman, B., Hodgson, K. O., Solomon, E. I. 2020

    Abstract

    Cu(I) active sites in metalloproteins are involved in O2 activation, but their O2 reactivity is difficult to study due to the Cu(I) d10 closed shell which precludes the use of conventional spectroscopic methods. Kbeta X-ray emission spectroscopy (XES) is a promising technique for investigating Cu(I) sites as it detects photons emitted by electronic transitions from occupied orbitals. Here, we demonstrate the utility of Kbeta XES in probing Cu(I) sites in model complexes and a metalloprotein. Using Cu(I)Cl, emission features from double-ionization (DI) states are identified using varying incident X-ray photon energies, and a reasonable method to correct the data to remove DI contributions is presented. Kbeta XES spectra of Cu(I) model complexes, having biologically relevant N/S ligands and different coordination numbers, are compared and analyzed, with the aid of density functional theory (DFT) calculations, to evaluate the sensitivity of the spectral features to the ligand environment. While the low-energy Kbeta2,5 emission feature reflects the ionization energy of ligand np valence orbitals, the high-energy Kbeta2,5 emission feature corresponds to transitions from molecular orbitals (MOs) having mainly Cu 3d character with the intensities determined by ligand-mediated d-p mixing. A Kbeta XES spectrum of the Cu(I) site in preprocessed galactose oxidase (GOpre) supports the 1Tyr/2His structural model that was determined by our previous X-ray absorption spectroscopy and DFT study. The high-energy Kbeta2,5 emission feature in the Cu(I)-GOpre data has information about the MO containing mostly Cu 3dx2-y2 character that is the frontier molecular orbital (FMO) for O2 activation, which shows the potential of Kbeta XES in probing the Cu(I) FMO associated with small-molecule activation in metalloproteins.

    View details for DOI 10.1021/acs.inorgchem.0c02495

    View details for PubMedID 33136386

  • X-ray Absorption Spectroscopy as a Probe of Ligand Noninnocence in Metallocorroles: The Case of Copper Corroles INORGANIC CHEMISTRY Lim, H., Thomas, K. E., Hedman, B., Hodgson, K. O., Ghosh, A., Solomon, E. I. 2019; 58 (10): 6722–30
  • Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O-2 activation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Appel, M. J., Meier, K. K., Lafrance-Vanasse, J., Lim, H., Tsai, C., Hedman, B., Hodgson, K. O., Tainer, J. A., Solomon, E. I., Bertozzi, C. R. 2019; 116 (12): 5370–75
  • A Six-Coordinate Peroxynitrite Low-Spin Iron(III) Porphyrinate Complex-The Product of the Reaction of Nitrogen Monoxide (center dot NO(g)) with a Ferric-Superoxide Species JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sharma, S. K., Schaefer, A. W., Lim, H., Matsumura, H., Moenne-Loccoz, P., Hedman, B., Hodgson, K. O., Solomon, E. I., Karlin, K. D. 2017; 139 (48): 17421–30

    Abstract

    Peroxynitrite (-OON═O, PN) is a reactive nitrogen species (RNS) which can effect deleterious nitrative or oxidative (bio)chemistry. It may derive from reaction of superoxide anion (O2•-) with nitric oxide (·NO) and has been suggested to form an as-yet unobserved bound heme-iron-PN intermediate in the catalytic cycle of nitric oxide dioxygenase (NOD) enzymes, which facilitate a ·NO homeostatic process, i.e., its oxidation to the nitrate anion. Here, a discrete six-coordinate low-spin porphyrinate-FeIII complex [(PIm)FeIII(-OON═O)] (3) (PIm; a porphyrin moiety with a covalently tethered imidazole axial "base" donor ligand) has been identified and characterized by various spectroscopies (UV-vis, NMR, EPR, XAS, resonance Raman) and DFT calculations, following its formation at -80 °C by addition of ·NO(g) to the heme-superoxo species, [(PIm)FeIII(O2•-)] (2). DFT calculations confirm that 3 is a six-coordinate low-spin species with the PN ligand coordinated to iron via its terminal peroxidic anionic O atom with the overall geometry being in a cis-configuration. Complex 3 thermally transforms to its isomeric low-spin nitrato form [(PIm)FeIII(NO3-)] (4a). While previous (bio)chemical studies show that phenolic substrates undergo nitration in the presence of PN or PN-metal complexes, in the present system, addition of 2,4-di-tert-butylphenol (2,4DTBP) to complex 3 does not lead to nitrated phenol; the nitrate complex 4a still forms. DFT calculations reveal that the phenolic H atom approaches the terminal PN O atom (farthest from the metal center and ring core), effecting O-O cleavage, giving nitrogen dioxide (·NO2) plus a ferryl compound [(PIm)FeIV═O] (7); this rebounds to give [(PIm)FeIII(NO3-)] (4a).The generation and characterization of the long sought after ferriheme peroxynitrite complex has been accomplished.

    View details for PubMedID 29091732

  • Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy SCIENCE Mara, M. W., Hadt, R. G., Reinhard, M., Kroll, T., Lim, H., Hartsock, R. W., Alonso-Mori, R., Chollet, M., Glownia, J. M., Nelson, S., Sokaras, D., Kunnus, K., Hodgson, K. O., Hedman, B., Bergmann, U., Gaffney, K. J., Solomon, E. I. 2017; 356 (6344): 1276-+

    Abstract

    The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe-S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free-electron laser, determining that the Fe-S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints. The 4 kcal/mol is comparable with calculations of stabilization effects in other systems, demonstrating how biological systems use an entatic state for modest yet accessible energetics to modulate chemical function.

    View details for PubMedID 28642436

    View details for PubMedCentralID PMC5706643

  • Hydroxo-Bridged Dicopper(II,III) and -(III,III) Complexes: Models for Putative Intermediates in Oxidation Catalysis JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Halvagar, M. R., Solntsev, P. V., Lim, H., Hedman, B., Hodgson, K. O., Solomon, E. I., Cramer, C. J., Tolman, W. B. 2014; 136 (20): 7269-7272

    Abstract

    A macrocyclic ligand (L(4-)) comprising two pyridine(dicarboxamide) donors was used to target reactive copper species relevant to proposed intermediates in catalytic hydrocarbon oxidations by particulate methane monooxygenase and heterogeneous zeolite systems. Treatment of LH4 with base and Cu(OAc)2·H2O yielded (Me4N)2[L2Cu4(μ4-O)] (1) or (Me4N)[LCu2(μ-OH)] (2), depending on conditions. Complex 2 was found to undergo two reversible 1-electron oxidations via cyclic voltammetry and low-temperature chemical reactions. On the basis of spectroscopy and theory, the oxidation products were identified as novel hydroxo-bridged mixed-valent Cu(II)Cu(III) and symmetric Cu(III)2 species, respectively, that provide the first precedence for such moieties as oxidation catalysis intermediates.

    View details for DOI 10.1021/ja503629r

    View details for Web of Science ID 000336416600021

    View details for PubMedID 24821432

    View details for PubMedCentralID PMC4046753

  • Excited-state proton-relay dynamics of 7-hydroxyquinoline controlled by solvent reorganization in room temperature ionic liquids PHYSICAL CHEMISTRY CHEMICAL PHYSICS Lim, H., Jeong, H., Park, S., Lee, J. Y., Jang, D. 2012; 14 (1): 218-224

    Abstract

    The excited-state triple proton relay of 7-hydroxyquinoline (7HQ) along a hydrogen-bonded methanol chain in room temperature ionic liquids (RTILs) has been investigated using picosecond time-resolved fluorescence spectroscopy. The rate constant of the proton relay in a methanol-added RTIL is found to be slower by an order of magnitude than that in bulk methanol and to have unity in its kinetic isotope effect. These suggest that the excited-state tautomerization dynamics of 7HQ in methanol-added RTILs is mainly controlled by the solvent reorganization dynamics to form a cyclically hydrogen-bonded complex of 7HQ·(CH(3)OH)(2) upon absorption of a photon due to high viscosity values of RTILs. Because the cyclic complex of 7HQ·(CH(3)OH)(2) at the ground state is unstable in RTILs, the collision-induced slow formation of the cyclic complex should take place upon excitation prior to undergoing subsequent intrinsic proton transfer rapidly.

    View details for DOI 10.1039/c1cp22329a

    View details for Web of Science ID 000297593800025

    View details for PubMedID 22073404

  • Excited-State Double Proton Transfer of 7-Azaindole Dimers in a Low-Temperature Organic Glass PHOTOCHEMISTRY AND PHOTOBIOLOGY Lim, H., Park, S., Jang, D. 2011; 87 (4): 766-771

    Abstract

    The excited-state double proton transfer of model DNA base pairs, 7-azaindole (7AI) dimers, is explored in a low-temperature organic glass of n-dodecane using picosecond time-resolved fluorescence spectroscopy. Reaction mechanisms are found to depend on the conformations of 7AI dimers at the moment of excitation; whereas planar conformers tautomerize rapidly (<10 ps), twisted conformers undergo double proton transfer to form tautomeric dimers on the time scale of 250 ps at 8 K. The proton transfer is found to consist of two orthogonal steps: precursor-configurational optimization and intrinsic proton transfer via tunneling. The rate is almost isotope independent at cryogenic temperatures because configurational optimization is the rate-determining step of the overall proton transfer. This optimization is assisted by lattice vibrations below 150 K or by librational motions above 150 K.

    View details for DOI 10.1111/j.1751-1097.2011.00923.x

    View details for Web of Science ID 000292864200004

    View details for PubMedID 21413991

  • Excited-State Double Proton Transfer Dynamics of Model DNA Base Pairs: 7-Hydroxyquinoline Dimers JOURNAL OF PHYSICAL CHEMISTRY A Lim, H., Park, S., Jang, D. 2010; 114 (43): 11432-11435

    Abstract

    The excited-state double proton transfer of model DNA base pairs, 7-hydroxyquinoline dimers, in benzene has been investigated using picosecond time-resolved fluorescence spectroscopy. Upon excitation, whereas singly hydrogen-bonded noncyclic dimers do not go through tautomerization within the relaxation time of 1400 ps, doubly hydrogen-bonded cyclic dimers undergo excited-state double proton transfer on the time scale of 25 ps to form tautomeric dimers, which subsequently undergo a conformational change in 180 ps to produce singly hydrogen-bonded tautomers. The rate constant of the double proton transfer reaction is temperature-independent, showing a large kinetic isotope effect of 5.2, suggesting that the rate is governed mostly by tunneling.

    View details for DOI 10.1021/jp106301q

    View details for Web of Science ID 000283471900009

    View details for PubMedID 20939620