Jeffrey Babicz

All Publications

• Deciphering decomposition pathways of high explosives with cryogenic X-ray Raman spectroscopy. Proceedings of the National Academy of Sciences of the United States of America Paredes Mellone, O. A., Nielsen, M. H., Babicz, J. T., Vinson, J., Willey, T. M., Sokaras, D. 2025; 122 (23): e2426320122

  Abstract

  We employed cryogenic X-ray Raman spectroscopy to investigate the early-stage decomposition of the high explosive molecule hexanitrohexaazaisowurtzitane (CL-20). By systematically varying the radiation dose under cryogenic conditions, we induced the decomposition of the molecule using ionizing radiation and observed the evolution of spectral features at the carbon, nitrogen, and oxygen K edges. Through extensive first-principles calculations, we identified key intermediates in the early stages of the decomposition process, resulting from C-C and C-N bond cleavage which leads to the opening of the internal cage structure. A detailed analysis of spectral trends and fingerprints provided evidence supporting N-NO2 homolytic cleavage as the primary initial decomposition pathway. The combination of advanced core-level spectroscopy methods and state-of-the-art theoretical calculations enabled a comprehensive characterization of the molecular changes induced by controlled radiation dose exposures. Our findings establish a benchmark for understanding the decomposition chemistry of high-explosive materials, offering important insights into their stability and reactivity under extreme conditions.

  View details for DOI 10.1073/pnas.2426320122

  View details for PubMedID 40460126

• Spectroscopy and crystallography define carotenoid oxygenases as a new subclass of mononuclear non-heme FeII enzymes. The Journal of biological chemistry DeWeese, D. E., Everett, M. P., Babicz, J. T., Daruwalla, A., Solomon, E. I., Kiser, P. D. 2025: 108444

  Abstract

  Carotenoid cleavage dioxygenases (CCDs) are non-heme FeII enzymes that catalyze the oxidative cleavage of alkene bonds in carotenoids, stilbenoids, and related compounds. How these enzymes control the reaction of O2 with their alkene substrates is unclear. Here, we apply spectroscopy in conjunction with X-ray crystallography to define the iron coordination geometry of a model CCD, CAO1, in its resting state and following substrate binding and coordination sphere substitutions. Resting CAO1 exhibits a five-coordinate (5C), square pyramidal FeII center that undergoes steric distortion towards a trigonal bipyramidal geometry in the presence of piceatannol. Titrations with the O2-analog, nitric oxide (NO), show a >100-fold increase in iron-NO affinity upon substrate binding, defining a crucial role for the substrate in activating the FeII site for O2 reactivity. The importance of the 5C FeII structure for reactivity was probed through mutagenesis of the second-sphere Thr151 residue of CAO1, which occludes ligand binding at the sixth coordination position. A T151G substitution resulted in the conversion of the iron center to a six-coordinate (6C) state and a 135-fold reduction in apparent catalytic efficiency towards piceatannol compared to the wild-type enzyme. Substrate complexation resulted in partial 6C to 5C conversion, indicating solvent dissociation from the iron center. Additional substitutions at this site demonstrated a general functional importance of the occluding residue within the CCD superfamily. Taken together, these data suggest an ordered mechanism of CCD catalysis occurring via substrate-promoted solvent replacement by O2. CCDs thus represent a new class of mononuclear non-heme FeII enzymes.

  View details for DOI 10.1016/j.jbc.2025.108444

  View details for PubMedID 40147775

• Determination of Thiol Protonation States by Sulfur X-ray Spectroscopy in Biological Systems JOURNAL OF PHYSICAL CHEMISTRY LETTERS Ribson, R. D., Follmer, A. H., Babicz, J. T., Alfaro, V., Hadt, R. G., Hunter, M. S., Wilson, M. A., Sokaras, D., Alonso-Mori, R. 2025; 16 (9): 2401-2408

  Abstract

  Cysteine is one of the most functionally diverse of the proteinogenic amino acids, owing to its reactive thiol side chain that can undergo deprotonation to form a strongly nucleophilic thiolate. However, few techniques can directly interrogate sulfur charge and covalency in cysteine, particularly in proteins. X-ray spectroscopies provide an element specific probe of sulfur. We demonstrate the sensitivity of S Kβ and Kα X-ray emission spectroscopy (XES) to cysteine ionization and compare it to S K-edge X-ray absorption spectroscopy (XAS) in the physiologically relevant biomolecules l-cysteine and N-acetyl-l-cysteine at room temperature in solution phase. Kβ XES and K-edge XAS are most sensitive to chemical changes at the cysteine thiol and can be used to evaluate the composition of thiol/thiolate mixtures. These results provide a foundation for assessing the pKa of functionally significant cysteine residues in proteins and open the door to time-resolved studies of cysteine-dependent enzymes.

  View details for DOI 10.1021/acs.jpclett.4c03247

  View details for Web of Science ID 001433819500001

  View details for PubMedID 40012333

  View details for PubMedCentralID PMC11892467

• Experimental electronic structures of the FeIV=O bond in S=1 heme vs. nonheme sites: Effect of the porphyrin ligand. Proceedings of the National Academy of Sciences of the United States of America Braun, A., Gee, L. B., Waters, M. D., Jose, A., Baker, M. L., Mara, M. W., Babicz, J. T., Ehudin, M. A., Quist, D. A., Zhou, A., Kroll, T., Titus, C. J., Lee, S. J., Nordlund, D., Sokaras, D., Yoda, Y., Kobayashi, Y., Tamasaku, K., Hedman, B., Hodgson, K. O., Karlin, K. D., Que, L., Solomon, E. I. 2025; 122 (8): e2420205122

  Abstract

  High-valent FeIV=O species are common intermediates in biological and artificial catalysts. Heme and nonheme S=1 FeIV=O sites have been synthesized and studied for decades but little quantitative experimental comparison of their electronic structures has been available, due to the lack of direct methods focused on the iron. This study allows a rigorous determination of the electronic structure of a nonheme FeIV=O center and its comparison to an FeIV=O heme site using 1s2p resonant inelastic X-ray scattering (RIXS) and Fe L-edge X-ray absorption spectroscopy (XAS). Further, variable temperature magnetic circular dichroism (VT-MCD) of the ligand field transitions, combined with nuclear resonance vibrational spectroscopy of the two S=1 FeIV=O systems show that the equatorial ligand field decreases from a nonheme to a heme FeIV=O site. Alternatively, RIXS and Fe L-edge XAS combined with MCD show that the Fe dπ orbitals are unperturbed in the FeIV=O heme relative to the nonheme site because the strong axial Fe-O bond uncouples the Fe dπ orbitals from the porphyrin π-system. As a consequence, the thermodynamics and kinetics of the H-atom abstraction reactions are actually very similar for heme compound II and nonheme FeIV=O active sites.

  View details for DOI 10.1073/pnas.2420205122

  View details for PubMedID 39982745

• The Liquid Jet Endstation for Hard X-ray Scattering and Spectroscopy at the Linac Coherent Light Source. Molecules (Basel, Switzerland) Antolini, C., Sosa Alfaro, V., Reinhard, M., Chatterjee, G., Ribson, R., Sokaras, D., Gee, L., Sato, T., Kramer, P. L., Raj, S. L., Hayes, B., Schleissner, P., Garcia-Esparza, A. T., Lim, J., Babicz, J. T., Follmer, A. H., Nelson, S., Chollet, M., Alonso-Mori, R., van Driel, T. B. 2024; 29 (10)

  Abstract

  The ability to study chemical dynamics on ultrafast timescales has greatly advanced with the introduction of X-ray free electron lasers (XFELs) providing short pulses of intense X-rays tailored to probe atomic structure and electronic configuration. Fully exploiting the full potential of XFELs requires specialized experimental endstations along with the development of techniques and methods to successfully carry out experiments. The liquid jet endstation (LJE) at the Linac Coherent Light Source (LCLS) has been developed to study photochemistry and biochemistry in solution systems using a combination of X-ray solution scattering (XSS), X-ray absorption spectroscopy (XAS), and X-ray emission spectroscopy (XES). The pump-probe setup utilizes an optical laser to excite the sample, which is subsequently probed by a hard X-ray pulse to resolve structural and electronic dynamics at their intrinsic femtosecond timescales. The LJE ensures reliable sample delivery to the X-ray interaction point via various liquid jets, enabling rapid replenishment of thin samples with millimolar concentrations and low sample volumes at the 120 Hz repetition rate of the LCLS beam. This paper provides a detailed description of the LJE design and of the techniques it enables, with an emphasis on the diagnostics required for real-time monitoring of the liquid jet and on the spatiotemporal overlap methods used to optimize the signal. Additionally, various scientific examples are discussed, highlighting the versatility of the LJE.

  View details for DOI 10.3390/molecules29102323

  View details for PubMedID 38792184

• 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