Professional Education


  • Doctor of Philosophy, University of California Davis (2016)
  • Bachelor of Arts, University of California Davis (2011)
  • Bachelor of Science, University of California Davis (2011)

Stanford Advisors


All Publications


  • High-Frequency Fe-H Vibrations in a Bridging Hydride Complex Characterized by NRVS and DFT ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Pelmenschikov, V., Gee, L. B., Wang, H., MacLeod, K., McWilliams, S. F., Skubi, K. L., Cramer, S. P., Holland, P. L. 2018; 57 (30): 9367–71

    Abstract

    High-spin iron species with bridging hydrides have been detected in species trapped during nitrogenase catalysis, but there are few general methods of evaluating Fe-H bonds in high-spin multinuclear iron systems. An 57 Fe nuclear resonance vibrational spectroscopy (NRVS) study on an Fe(μ-H)2 Fe model complex reveals Fe-H stretching vibrations for bridging hydrides at frequencies greater than 1200 cm-1 . These isotope-sensitive vibrational bands are not evident in infrared (IR) spectra, showing the power of NRVS for identifying hydrides in this high-spin iron system. Complementary density functional theory (DFT) calculations elucidate the normal modes of the rhomboidal iron hydride core.

    View details for PubMedID 29847703

  • Sterically Stabilized Terminal Hydride of a Diiron Dithiolate INORGANIC CHEMISTRY Carlson, M. R., Gray, D. L., Richers, C. P., Wang, W., Zhao, P., Rauchfuss, T. B., Pelmenschikov, V., Pham, C. C., Gee, L. B., Wang, H., Cramer, S. P. 2018; 57 (4): 1988–2001

    Abstract

    The kinetically robust hydride [t-HFe2(Me2pdt)(CO)2(dppv)2]+ ([t-H1]+) (Me2pdt2- = Me2C(CH2S-)2; dppv = cis-1,2-C2H2(PPh2)2) and related derivatives were prepared with 57Fe enrichment for characterization by NMR, FT-IR, and NRVS. The experimental results were rationalized using DFT molecular modeling and spectral simulations. The spectroscopic analysis was aimed at supporting assignments of Fe-H vibrational spectra as they relate to recent measurements on [FeFe]-hydrogenase enzymes. The combination of bulky Me2pdt2- and dppv ligands stabilizes the terminal hydride with respect to its isomerization to the 5-16 kcal/mol more stable bridging hydride ([μ-H1]+) with t1/2(313.3 K) = 19.3 min. In agreement with the nOe experiments, the calculations predict that one methyl group in [t-H1]+ interacts with the hydride with a computed CH···HFe distance of 1.7 Å. Although [t-H571]+ exhibits multiple NRVS features in the 720-800 cm-1 region containing the bending Fe-H modes, the deuterated [t-D571]+ sample exhibits a unique Fe-D/CO band at ∼600 cm-1. In contrast, the NRVS spectra for [μ-H571]+ exhibit weaker bands near 670-700 cm-1 produced by the Fe-H-Fe wagging modes coupled to Me2pdt2- and dppv motions.

    View details for DOI 10.1021/acs.inorgchem.7b02903

    View details for Web of Science ID 000426014800033

    View details for PubMedID 29384371

    View details for PubMedCentralID PMC5821139

  • NRVS for Fe in Biology: Experiment and Basic Interpretation. Methods in enzymology Gee, L. B., Wang, H., Cramer, S. P. 2018; 599: 409–25

    Abstract

    For over 20 years, nuclear resonance vibrational spectroscopy (NRVS) has been used to study vibrational dynamics of iron-containing materials. With the only selection rule being iron motion, 57Fe NRVS has become an excellent tool to study iron-containing enzymes. Over the past decade, considerable progress has been made in the study of complex metalloenzymes using NRVS. Iron cofactors in heme-containing globins; [2Fe2S], [3Fe4S], [4Fe4S] proteins; the [NiFe] and [FeFe] hydrogenases; and nitrogenases have been explored in a fashion not possible through traditional vibrational spectroscopy. In this chapter, we discuss the basics of NRVS, a strategy to perform NRVS, and a discussion of the application of NRVS on rubredoxin and [FeFe] hydrogenase.

    View details for DOI 10.1016/bs.mie.2017.11.002

    View details for PubMedID 29746248

  • Direct Observation of an Iron-Bound Terminal Hydride in [FeFe]-Hydrogenase by Nuclear Resonance Vibrational Spectroscopy JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Reijerse, E. J., Pham, C. C., Pelmenschikov, V., Gilbert-Wilson, R., Adamska-Venkatesh, A., Siebel, J. F., Gee, L. B., Yoda, Y., Tamasaku, K., Lubitz, W., Rauchfuss, T. B., Cramer, S. P. 2017; 139 (12): 4306–9

    Abstract

    [FeFe]-hydrogenases catalyze the reversible reduction of protons to molecular hydrogen with extremely high efficiency. The active site ("H-cluster") consists of a [4Fe-4S]H cluster linked through a bridging cysteine to a [2Fe]H subsite coordinated by CN- and CO ligands featuring a dithiol-amine moiety that serves as proton shuttle between the protein proton channel and the catalytic distal iron site (Fed). Although there is broad consensus that an iron-bound terminal hydride species must occur in the catalytic mechanism, such a species has never been directly observed experimentally. Here, we present FTIR and nuclear resonance vibrational spectroscopy (NRVS) experiments in conjunction with density functional theory (DFT) calculations on an [FeFe]-hydrogenase variant lacking the amine proton shuttle which is stabilizing a putative hydride state. The NRVS spectra unequivocally show the bending modes of the terminal Fe-H species fully consistent with widely accepted models of the catalytic cycle.

    View details for DOI 10.1021/jacs.7b00686

    View details for Web of Science ID 000398247100018

    View details for PubMedID 28291336

    View details for PubMedCentralID PMC5545132

  • Is trehalose an effective quenching agent of Azotobacter vinelandii Mo-nitrogenase turnover? INORGANICA CHIMICA ACTA Gee, L. B., Scott, A. D., Dapper, C. H., Newton, W. E., Cramer, S. P. 2016; 453: 74–77
  • Synchrotron-based Nickel Mossbauer Spectroscopy INORGANIC CHEMISTRY Gee, L. B., Lin, C., Jenney, F. E., Adams, M. W., Yoda, Y., Masuda, R., Saito, M., Kobayashi, Y., Tamasaku, K., Lerche, M., Seto, M., Riordan, C. G., Ploskonka, A., Power, P. P., Cramer, S. P., Lauterbach, L. 2016; 55 (14): 6866–72

    Abstract

    We used a novel experimental setup to conduct the first synchrotron-based (61)Ni Mössbauer spectroscopy measurements in the energy domain on Ni coordination complexes and metalloproteins. A representative set of samples was chosen to demonstrate the potential of this approach. (61)NiCr2O4 was examined as a case with strong Zeeman splittings. Simulations of the spectra yielded an internal magnetic field of 44.6 T, consistent with previous work by the traditional (61)Ni Mössbauer approach with a radioactive source. A linear Ni amido complex, (61)Ni{N(SiMe3)Dipp}2, where Dipp = C6H3-2,6-(i)Pr2, was chosen as a sample with an "extreme" geometry and large quadrupole splitting. Finally, to demonstrate the feasibility of metalloprotein studies using synchrotron-based (61)Ni Mössbauer spectroscopy, we examined the spectra of (61)Ni-substituted rubredoxin in reduced and oxidized forms, along with [Et4N]2[(61)Ni(SPh)4] as a model compound. For each of the above samples, a reasonable spectrum could be obtained in ∼1 d. Given that there is still room for considerable improvement in experimental sensitivity, synchrotron-based (61)Ni Mössbauer spectroscopy appears to be a promising alternative to measurements with radioactive sources.

    View details for DOI 10.1021/acs.inorgchem.5b03004

    View details for Web of Science ID 000380181400011

    View details for PubMedID 27387959

  • Characterization of the [3Fe-4S](0/1+) cluster from the D14C variant of Pyrococcus furiosus ferredoxin via combined NRVS and DFT analyses DALTON TRANSACTIONS Lauterbach, L., Gee, L. B., Pelmenschikov, V., Jenney, F. E., Kamali, S., Yoda, Y., Adams, M. W., Cramer, S. P. 2016; 45 (17): 7215–19

    Abstract

    The D14C variant of Pyrococcus furiosus ferredoxin provides an extraordinary framework to investigate a [3Fe-4S] cluster at two oxidation levels and compare the results to its physiologic [4Fe-4S] counterpart in the very same protein. Our spectroscopic and computational study reveals vibrational property changes related to the electronic and structural aspects of both Fe-S clusters.

    View details for DOI 10.1039/c5dt04760a

    View details for Web of Science ID 000375001000005

    View details for PubMedID 27063792

    View details for PubMedCentralID PMC4940129

  • Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration JOURNAL OF INORGANIC BIOCHEMISTRY Maiuri, M., Delfino, I., Cerullo, G., Manzoni, C., Pelmenschikov, V., Guo, Y., Wang, H., Gee, L. B., Dapper, C. H., Newton, W. E., Cramer, S. P. 2015; 153: 128–35

    Abstract

    We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.

    View details for DOI 10.1016/j.jinorgbio.2015.07.005

    View details for Web of Science ID 000367563200013

    View details for PubMedID 26343576

    View details for PubMedCentralID PMC4917305

  • Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy NATURE COMMUNICATIONS Ogata, H., Kraemer, T., Wang, H., Schilter, D., Pelmenschikov, V., van Gastel, M., Neese, F., Rauchfuss, T. B., Gee, L. B., Scott, A. D., Yoda, Y., Tanaka, Y., Lubitz, W., Cramer, S. P. 2015; 6: 7890

    Abstract

    The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the (57)Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique 'wagging' mode involving H(-) motion perpendicular to the Ni(μ-H)(57)Fe plane was studied using (57)Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)(57)Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe-CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)(57)Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)(57)Fe(CO)3](+) and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H(-) binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe-H moieties in other important natural and synthetic catalysts.

    View details for DOI 10.1038/ncomms8890

    View details for Web of Science ID 000360344600002

    View details for PubMedID 26259066

    View details for PubMedCentralID PMC4531378

  • Docking and Migration of Carbon Monoxide in Nitrogenase: The Case for Gated Pockets from Infrared Spectroscopy and Molecular Dynamics BIOCHEMISTRY Gee, L. B., Leontyev, I., Stuchebrukhov, A., Scott, A. D., Pelmenschikov, V., Cramer, S. P. 2015; 54 (21): 3314–19

    Abstract

    Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.

    View details for DOI 10.1021/acs.biochem.5b00216

    View details for Web of Science ID 000355779600007

    View details for PubMedID 25919807

    View details for PubMedCentralID PMC4522414

  • Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O-2-tolerant NAD(+)-reducing [NiFe] hydrogenase CHEMICAL SCIENCE Lauterbach, L., Wang, H., Horch, M., Gee, L. B., Yoda, Y., Tanaka, Y., Zebger, I., Lenz, O., Cramer, S. P. 2015; 6 (2): 1055–60

    Abstract

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function the various metal cofactors present in the enzyme. Here all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe-CO and Fe-CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe-CO modes. The present approach explores the complex vibrational signature of the Fe-S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.

    View details for DOI 10.1039/c4sc02982h

    View details for Web of Science ID 000348147100024

    View details for PubMedID 25678951

    View details for PubMedCentralID PMC4321745

  • Synthesis and vibrational spectroscopy of Fe-57-labeled models of [NiFe] hydrogenase: first direct observation of a nickel-iron interaction CHEMICAL COMMUNICATIONS Schilter, D., Pelmenschikov, V., Wang, H., Meier, F., Gee, L. B., Yoda, Y., Kaupp, M., Rauchfuss, T. B., Cramer, S. P. 2014; 50 (88): 13469–72

    Abstract

    A new route to iron carbonyls has enabled synthesis of (57)Fe-labeled [NiFe] hydrogenase mimic (OC)3(57)Fe(pdt)Ni(dppe). Its study by nuclear resonance vibrational spectroscopy revealed Ni-(57)Fe vibrations, as confirmed by calculations. The modes are absent for [(OC)3(57)Fe(pdt)Ni(dppe)](+), which lacks Ni-(57)Fe bonding, underscoring the utility of the analyses in identifying metal-metal interactions.

    View details for DOI 10.1039/c4cc04572f

    View details for Web of Science ID 000343965300010

    View details for PubMedID 25237680

    View details for PubMedCentralID PMC4191989

  • Differences in peripheral endocannabinoid modulation of scratching behavior in facial vs. spinally-innervated skin NEUROPHARMACOLOGY Spradley, J., Davoodi, A., Gee, L., Carstens, M., Carstens, E. 2012; 63 (4): 743–49

    Abstract

    Cannabinoids suppress nocifensive behaviors in rodents. We presently investigated peripheral endocannabinoid modulation of itch- and pain-related behaviors elicited from facial vs. spinally-innervated skin of rats. Intradermal (id) injection of the pruritogen serotonin (5-HT) elicited significantly more hindlimb scratch bouts, and longer cumulative time scratching, when injected in the rostral back compared to the cheek. Pretreatment of skin with inhibitors of degrading enzymes for the endocannabinoids anandamide (URB597) or 2-arachidonoylglycerol (JZL184) significantly reduced scratching elicited by 5-HT in the rostral back. These effects were prevented by co-treatment with antagonists of the CB₁ (AM251) or CB₂ receptor (AM630), implicating both receptor subtypes in endocannabinoid suppression of scratching in spinally-innervated skin. Conversely, pretreatment with either enzyme inhibitor, or with AM630 alone, increased the number of scratch bouts elicited by id 5-HT injection in the cheek. Moreover, pretreatment with JZL184 also significantly increased pain-related forelimb wipes directed to the cheek following id injection of the algogen, allyl isothiocyanate (AITC; mustard oil). Thus, peripheral endocannabinoids have opposite effects on itch-related scratching behaviors in trigeminally- vs. spinally-innervated skin. These results suggest that increasing peripheral endocannabinoid levels represents a promising therapeutic approach to treat itch arising from the lower body, but caution that such treatment may not relieve, and may even exacerbate, itch and pain arising from trigeminally-innervated skin of the face or scalp.

    View details for DOI 10.1016/j.neuropharm.2012.05.032

    View details for Web of Science ID 000306637700026

    View details for PubMedID 22683515

    View details for PubMedCentralID PMC3394407