Jeffrey Babicz

All Publications

• Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage. Journal of the American Chemical Society Babicz, J. T., Rogers, M. S., DeWeese, D. E., Sutherlin, K. D., Banerjee, R., Bottger, L. H., Yoda, Y., Nagasawa, N., Saito, M., Kitao, S., Kurokuzu, M., Kobayashi, Y., Tamasaku, K., Seto, M., Lipscomb, J. D., Solomon, E. I. 2023

  Abstract

  The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.

  View details for DOI 10.1021/jacs.3c02242

  View details for PubMedID 37414058

• Mechanisms of O2 Activation by Mononuclear Non-Heme Iron Enzymes. Biochemistry Solomon, E. I., DeWeese, D. E., Babicz, J. T. 2021

  Abstract

  Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (alpha-ketoglutarate or pterin) to activate O2 to form FeIV═O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the FeIV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.

  View details for DOI 10.1021/acs.biochem.1c00370

  View details for PubMedID 34266238

• Direct coordination of pterin to FeII enables neurotransmitter biosynthesis in the pterin-dependent hydroxylases. Proceedings of the National Academy of Sciences of the United States of America Iyer, S. R., Tidemand, K. D., Babicz, J. T., Jacobs, A. B., Gee, L. B., Haahr, L. T., Yoda, Y., Kurokuzu, M., Kitao, S., Saito, M., Seto, M., Christensen, H. E., Peters, G. H., Solomon, E. I. 2021; 118 (15)

  Abstract

  The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the FeII active site to form a highly reactive FeIV = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-FeIV = O intermediate and characterized its structure as a FeII-peroxy-pterin species using absorption, Mossbauer, resonance Raman, and nuclear resonance vibrational spectroscopies. From parallel characterization of the pterin cofactor and tryptophan substrate-bound ternary FeII active site before the O2 reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of FeIV = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the FeII site in both the ternary complex and the peroxo intermediate. Reaction coordinate calculations predict a 14 kcal/mol reduction in the oxygen activation barrier due to the direct binding of the pterin carbonyl to the FeII site, as this interaction provides an orbital pathway for efficient electron transfer from the pterin cofactor to the iron center. This direct coordination of the pterin cofactor enables the biological function of the pterin-dependent hydroxylases and demonstrates a unified mechanism for oxygen activation by the cofactor-dependent nonheme iron enzymes.

  View details for DOI 10.1073/pnas.2022379118

  View details for PubMedID 33876764

• Nuclear Resonance Vibrational Spectroscopic Definition of the Fe(IV)2 Intermediate Q in Methane Monooxygenase and Its Reactivity. Journal of the American Chemical Society Jacobs, A. B., Banerjee, R., Deweese, D. E., Braun, A., Babicz, J. T., Gee, L. B., Sutherlin, K. D., Böttger, L. H., Yoda, Y., Saito, M., Kitao, S., Kobayashi, Y., Seto, M., Tamasaku, K., Lipscomb, J. D., Park, K., Solomon, E. I. 2021

  Abstract

  Methanotrophic bacteria utilize the nonheme diiron enzyme soluble methane monooxygenase (sMMO) to convert methane to methanol in the first step of their metabolic cycle under copper-limiting conditions. The structure of the sMMO Fe(IV)2 intermediate Q responsible for activating the inert C-H bond of methane (BDE = 104 kcal/mol) remains controversial, with recent studies suggesting both "open" and "closed" core geometries for its active site. In this study, we employ nuclear resonance vibrational spectroscopy (NRVS) to probe the geometric and electronic structure of intermediate Q at cryogenic temperatures. These data demonstrate that Q decays rapidly during the NRVS experiment. Combining data from several years of measurements, we derive the NRVS vibrational features of intermediate Q as well as its cryoreduced decay product. A library of 90 open and closed core models of intermediate Q is generated using density functional theory to analyze the NRVS data of Q and its cryoreduced product as well as prior spectroscopic data on Q. Our analysis reveals that a subset of closed core models reproduce these newly acquired NRVS data as well as prior data. The reaction coordinate with methane is also evaluated using both closed and open core models of Q. These studies show that the potent reactivity of Q toward methane resides in the "spectator oxo" of its Fe(IV)2O2 core, in contrast to nonheme mononuclear Fe(IV)═O enzyme intermediates that H atoms abstract from weaker C-H bonds.

  View details for DOI 10.1021/jacs.1c05436

  View details for PubMedID 34570980

• Valence-Dependent Electrical Conductivity in a 3D Tetrahydroxyquinone-Based Metal-Organic Framework. Journal of the American Chemical Society Chen, G., Gee, L. B., Xu, W., Zhu, Y., Lezama-Pacheco, J. S., Huang, Z., Li, Z., Babicz, J. T., Choudhury, S., Chang, T., Reed, E., Solomon, E. I., Bao, Z. 2020

  Abstract

  Electrically conductive metal-organic frameworks (cMOFs) have become a topic of intense interest in recent years because of their great potential in electrochemical energy storage, electrocatalysis, and sensing applications. Most of the cMOFs reported hitherto are 2D structures, and 3D cMOFs remain rare. Herein we report FeTHQ, a 3D cMOF synthesized from tetrahydroxy-1,4-quinone (THQ) and iron(II) sulfate salt. FeTHQ exhibited a conductivity of 3.3 ± 0.55 mS cm-1 at 300 K, which is high for 3D cMOFs. The conductivity of FeTHQ is valence-dependent. A higher conductivity was measured with the as-prepared FeTHQ than with the air-oxidized and sodium naphthalenide-reduced samples.

  View details for DOI 10.1021/jacs.0c09379

  View details for PubMedID 33315385

• 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. n., Iyer, S. R., Babicz, J. T., Yan, J. J., Peters, G. H., Christensen, H. E., Hedman, B. n., Hodgson, K. O., Solomon, E. I. 2020

  Abstract

  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

• Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Snyder, B. R., Bols, M. L., Rhoda, H. M., Vanelderen, P., Bottger, L. H., Braun, A., Yan, J. J., Hadt, R. G., Babicz, J. T., Hu, M. Y., Zhao, J., Alp, E., Hedman, B., Hodgson, K. O., Schoonheydt, R. A., Sels, B. F., Solomon, E. I. 2018; 115 (48): 12124–29

  View details for DOI 10.1073/pnas.1813849115

  View details for Web of Science ID 000451351000043

• Spectroscopic and Electronic Structure Study of ETHE1: Elucidating the Factors Influencing Sulfur Oxidation and Oxygenation in Mononuclear Nonheme Iron Enzymes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Goudarzi, S., Babicz, J. T., Kabil, O., Banerjee, R., Solomon, E. I. 2018; 140 (44): 14887–902

  View details for DOI 10.1021/jacs.8b09022

  View details for Web of Science ID 000449887800049

• Kinetic and spectroscopic investigation of oxygen activation at a single iron center via Gibbs free energy coupling: Generation of an active alkane oxidation catalyst Cunningham, L., Babicz, J., Tucker, W., McCracken, J., Rybak-Akimova, E., Solomon, E., Caradonna, J. AMER CHEMICAL SOC. 2018

  View details for Web of Science ID 000447609101690

• Correlating the structures and activities of the resting oxidized and native intermediate states of a small laccase by paramagnetic NMR JOURNAL OF INORGANIC BIOCHEMISTRY Machczynski, M. C., Babicz, J. T. 2016; 159: 62-69

  Abstract

  Multicopper oxidases (MCO) are the fastest and most efficient known catalysts of the oxygen-reduction reaction. When all four copper ions are oxidized during catalysis, the native intermediate state (NI) decays in seconds to the resting oxidized state (RO), which returns to the catalytic cycle via reduction, but at a much slower rate than NI. We report the long-lived (months at 4°C) NI state of the small laccase (SLAC) MCO and the subsequent characterization of both its RO and NI states by paramagnetic (1)H NMR. We find that the RO state of the trinuclear cluster (TNC) is best described as an isolated Type-3 dicopper site, antiferromagnetically coupled by a hydroxo group with -2J=500cm(-1). The NI state is more complicated; we develop a theoretical treatment for the case in which all three copper ions in the TNC are coupled, and find that the results are consistent with three coupling constants of -2J=300, 240, and 160cm(-1). These couplings result in a ground doublet state, a low-lying excited doublet state at 121cm(-1), and a quartet excited state at 411cm(-1), in good agreement with DFT models in which the Type-2 copper has a terminal hydroxo ligand.

  View details for DOI 10.1016/j.jinorgbio.2016.02.002

  View details for Web of Science ID 000378021000009

  View details for PubMedID 26918900