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Nuclear resonant vibrational spectroscopy (NRVS) is an excellent synchrotron-based vibrational spectroscopy. Its isotope specificity and other advantages are particularly good to study, for example, iron center(s) inside complicated molecules such as enzymes. In order to investigate some small energy shifts, the energy scale variation from scan to scan must be corrected via an in-situ measurement or with other internal reference peak(s) inside the spectra to be calibrated. On the other hand, the energy re-distribution within each scan also needs attention for a sectional scan which has a different scanning time per point in different sections and is often used to measure weak NRVS signals. In this publication, we: (1) evaluated the point-to-point energy re-distribution within each NRVS scan or within an averaged scan with a time-scaled (not energy-scaled) function; (2) discussed the errorbar contributed from the improper "distribution" of ΔEi or the averaged ΔE within one scan (Eerr1) vs. that due to the different ΔEi from different scans (Eerr2). It is well illustrated that the former (Eerr1) is as important as, or sometimes even more important than, the latter (Eerr2); and (3) provided a procedure to re-calibrate the published NRVS-derived PVDOS spectra in case of need. This article establishes the concept that, at least for sectional NRVS scans, the energy positions should be corrected according to the time scanned rather than be scaled with a universal constant, as in a conventional calibration procedure. [ABSTRACT FROM AUTHOR]

Nuclear resonant vibrational spectroscopy (NRVS) is an excellent modern vibrational spectroscopy, in particular, for revealing site-specific information inside complicated molecules, such as enzymes. There are two different concepts about the energy calibration for a beamline or a monochromator (including a high resolution monochromator): the absolute energy calibration and the practical energy calibration. While the former pursues an as-fine-as-possible and as-repeatable-as-possible result, the latter includes the environment influenced variation from scan to scan, which often needs an in situ calibration measurement to track. However, an in situ measurement often shares a weak beam intensity and therefore has a noisy NRVS spectrum at the calibration sample location, not leading to a better energy calibration/correction in most cases. NRVS users for a long time have noticed that there are energy drifts in the vibrational spectra's zero-energy positions from scan to scan (Δ Ei), but their trend has not been explored and utilized in the past. In this publication, after providing a brief introduction to the critical issue(s) in practical NRVS energy calibrations, we have evaluated the trend and the mechanism for these zero-energy drifts (Δ Ei) and explored their link to the energy scales (αi) from scan to scan. Via detailed analyses, we have established a new stepwise procedure for carrying out practical energy calibrations, which includes the correction for the scan-dependent energy variations using Δ Ei values rather than running additional in situ calibration measurements. We also proved that one additional instrument-fixed scaling constant (α0) exists to convert such "calibrated" energy axis (E′) to the real energy axis (Ereal). The "calibrated" real energy axis (Ereal) has a preliminary error bar of ±0.1% (the 2 σ E divided by the vibrational energy position), which is 4–8 times better than that from the current practical energy calibration procedure. [ABSTRACT FROM AUTHOR]

To study metalloenzymes in detail, we developed a new experimental setup allowing the controlled preparation of catalytic intermediates for characterization by various spectroscopic techniques. The in situ monitoring of redox transitions by infrared spectroscopy in enzyme lyophilizate, crystals, and solution during gas exchange in a wide temperature range can be accomplished as well. Two O2‐tolerant [NiFe]‐hydrogenases were investigated as model systems. First, we utilized our platform to prepare highly concentrated hydrogenase lyophilizate in a paramagnetic state harboring a bridging hydride. This procedure proved beneficial for 57Fe nuclear resonance vibrational spectroscopy and revealed, in combination with density functional theory calculations, the vibrational fingerprint of this catalytic intermediate. The same in situ IR setup, combined with resonance Raman spectroscopy, provided detailed insights into the redox chemistry of enzyme crystals, underlining the general necessity to complement X‐ray crystallographic data with spectroscopic analyses. [ABSTRACT FROM AUTHOR]

Abstract: A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe−H/D bending modes in CrHydA1 [FeFe]‐hydrogenase Cys‐to‐Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H‐cluster from a ‐SH to ‐OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H‐cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe−H/D normal modes. We observed a significant shift to higher frequency in an Fe−H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)‐substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the ‐OH group of C169S with the bridgehead ‐NH‐ moiety of the active site, as compared to that of the ‐SH group of C169 in the native enzyme. [ABSTRACT FROM AUTHOR]

The reaction of protein-bound iron-sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2(NO)4(Cys)2]) and Roussin's Black Salt (RBS, [Fe4(NO)7S3]. In the latter case, the absence of 32S/34S shifts in the Fe−S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates. [ABSTRACT FROM AUTHOR]

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

We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Iron-sulfur protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the crystal structure. [ABSTRACT FROM AUTHOR]

There are several practical and intertangled issues which make the experiments of nuclear resonant vibrational spectroscopy (NRVS) on biological samples difficult to perform. The sample temperature is one of the most important issues. In NRVS the real sample temperatures can be very different from the readings on the temperature sensors. In this study the following have been performed: (i) citing and analyzing various existing NRVS data to assess the real sample temperatures during the NRVS measurements and to understand their trends with the samples' loading conditions; (ii) designing several NRVS measurements with (Et4N)[FeCl4] to verify these trends; and (iii) proposing a new sample-loading procedure to achieve significantly lower real sample temperatures and to balance among the intertangled experimental issues in biological NRVS measurements. [ABSTRACT FROM AUTHOR]

Nuclear resonant vibrational spectroscopy (NRVS) is a relatively new spectroscopic method which measures site-specific vibrational information and is useful in many research areas. It has an almost zero background and is suitable for measuring weak signals but needs a lot of scans to complete one real spectrum. Due to various reasons, some NRVS scans have occasional spike(s), which can introduce fake peak(s) when the averaged spectrum is converted into partial vibrational density of state (PVDOS) and can mislead the deduction of the corresponding structural information from it. For better use of the NRVS spectra with occasional spikes, people have to identify and smooth the sporadic spiky points while leaving all other points untouched. In this publication, we used the concept of machine learning and created a fully automated procedure for screening and smoothing the occasional spiky points in NRVS spectra. The procedure uses the statistical information obtained from the particular NRVS scan to be processed itself and needs neither an external parameter nor the information from other NRVS scans. A corresponding R subroutine code is also presented to batch process large numbers of measured NRVS scans. This work is the first attempt toward organizing an automatic de-spiking process for NRVS scans without using an external parameter. [ABSTRACT FROM AUTHOR]