Nuclear resonance energy analysis of inelastic x-ray scattering

Glass-Like Phonon Dynamics and Thermal Transport in a GeTe Nano-Composite at Low Temperature

In this work, the experimental evidence of glass-like phonon dynamics and thermal conductivity in a nanocomposite made of GeTe and amorphous carbon is reported, which is of interest for microelectronics, and specifically phase change memories. It is shown that, the total thermal conductivity is reduced by a factor of three at room temperature with respect to pure GeTe, due to the reduction of both electronic and phononic contributions. This latter, similarly to glasses, is small and weakly increasing with temperature between 100 and 300 K, indicating a mostly diffusive thermal transport and reaching a value of 0.86(7) Wm-1K-1 at room temperature. A thorough investigation of the nanocomposite's phonon dynamics reveals the appearance of an excess intensity in the low energy vibrational density of states, reminiscent of the Boson peak in glasses. These features can be understood in terms of an enhanced phonon scattering at the interfaces, due to the presence of elastic heterogeneities, at wavelengths in the 2-20 nm range. The findings confirm recent simulation results on crystalline/amorphous nanocomposites and open new perspectives in phonon and thermal engineering through the direct manipulation of elastic heterogeneities.

Fate of oxygen species from O2 activation at dimetal cofactors in an oxidase enzyme revealed by 57Fe nuclear resonance X-ray scattering and quantum chemistry

Oxygen (O₂) activation is a central challenge in chemistry and catalyzed at prototypic dimetal cofactors in biological enzymes with diverse functions. Analysis of intermediates is required to elucidate the reaction paths of reductive O₂ cleavage. An oxidase protein from the bacterium Geobacillus kaustophilus, R2lox, was used for aerobic in-vitro reconstitution with only ⁵⁷Fe(II) or Mn(II) plus ⁵⁷Fe(II) ions to yield [FeFe] or [MnFe] cofactors under various oxygen and solvent isotopic conditions including ^16/18O and H/D exchange. ⁵⁷Fe-specific X-ray scattering techniques were employed to collect nuclear forward scattering (NFS) and nuclear resonance vibrational spectroscopy (NRVS) data of the R2lox proteins. NFS revealed Fe/Mn(III)Fe(III) cofactor states and Mössbauer quadrupole splitting energies. Quantum chemical calculations of NRVS spectra assigned molecular structures, vibrational modes, and protonation patterns of the cofactors, featuring a terminal water (H₂O) bound at iron or manganese in site 1 and a metal-bridging hydroxide (μOH^-) ligand. A procedure for quantitation and correlation of experimental and computational NRVS difference signals due to isotope labeling was developed. This approach revealed that the protons of the ligands as well as the terminal water at the R2lox cofactors exchange with the bulk solvent whereas ¹⁸O from ¹⁸O₂ cleavage is incorporated in the hydroxide bridge. In R2lox, the two water molecules from four-electron O₂ reduction are released in a two-step reaction to the solvent. These results establish combined NRVS and QM/MM for tracking of iron-based oxygen activation in biological and chemical catalysts and clarify the reductive O₂ cleavage route in an enzyme.

Differential Protonation at the Catalytic Six-Iron Cofactor of [FeFe]-Hydrogenases Revealed by 57Fe Nuclear Resonance X-ray Scattering and Quantum Mechanics/Molecular Mechanics Analyses

[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined ⁵⁷Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga. Selective ⁵⁷Fe labeling at only [4Fe4S] or [FeFe], or at both subcomplexes was achieved by protein expression with a ⁵⁷Fe salt and in vitro maturation with a synthetic diiron site precursor containing ⁵⁷Fe. H-cluster states were populated under infrared spectroscopy control. NRVS spectral analyses facilitated assignment of the vibrational modes of the cofactor species. This approach revealed the H-cluster structure of the oxidized state (Hox) with a bridging carbon monoxide at [FeFe] and ligand rearrangement in the CO-inhibited state (Hox-CO). Protonation at a cysteine ligand of [4Fe4S] in the oxidized state occurring at low pH (HoxH) was indicated, in contrast to bridging hydride binding at [FeFe] in a one-electron reduced state (Hred). These findings are direct evidence for differential protonation either at the four-iron or diiron subcomplex of the H-cluster. NFS time-traces provided Mössbauer parameters such as the quadrupole splitting energy, which differ among cofactor states, thereby supporting selective protonation at either subcomplex. In combination with data for reduced states showing similar [4Fe4S] protonation as HoxH without (Hred') or with (Hhyd) a terminal hydride at [FeFe], our results imply that coordination geometry dynamics at the diiron site and proton-coupled electron transfer to either the four-iron or the diiron subcomplex discriminate catalytic and regulatory functions of [FeFe]-hydrogenases. We support a reaction cycle avoiding diiron site geometry changes during rapid H₂ turnover.

Tracking the Connection between Disorder and Energy Landscape in Glasses Using Geologically Hyperaged Amber

Fossil amber offers the unique opportunity to investigate an amorphous material that has been exploring its energy landscape for more than 110 million years of natural aging. By applying different X-ray scattering methods to amber before and after annealing the sample to erase its thermal history, we identify a link between the potential energy landscape and the structural and vibrational properties of glasses. We find that hyperaging induces a depletion of the vibrational density of states in the terahertz region, also ruling the sound dispersion and attenuation properties of the corresponding acoustic waves. Critically, this is accompanied by a densification with structural implications different in nature from that caused by hydrostatic compression. Our results, rationalized within the framework of fluctuating elasticity theory, reveal how upon approaching the bottom of the potential energy landscape (9% decrease in the fictive temperature) the elastic matrix becomes increasingly less disordered (6%) and longer-range correlated (22%).

Protonation State of MnFe and FeFe Cofactors in a Ligand-Binding Oxidase Revealed by X-ray Absorption, Emission, and Vibrational Spectroscopy and QM/MM Calculations

Enzymes with a dimetal-carboxylate cofactor catalyze reactions among the top challenges in chemistry such as methane and dioxygen (O₂) activation. Recently described proteins bind a manganese-iron cofactor (MnFe) instead of the classical diiron cofactor (FeFe). Determination of atomic-level differences of homo- versus hetero-bimetallic cofactors is crucial to understand their diverse redox reactions. We studied a ligand-binding oxidase from the bacterium Geobacillus kaustophilus (R2lox) loaded with a FeFe or MnFe cofactor, which catalyzes O₂ reduction and an unusual tyrosine-valine ether cross-link formation, as revealed by X-ray crystallography. Advanced X-ray absorption, emission, and vibrational spectroscopy methods and quantum chemical and molecular mechanics calculations provided relative Mn/Fe contents, X-ray photoreduction kinetics, metal-ligand bond lengths, metal-metal distances, metal oxidation states, spin configurations, valence-level degeneracy, molecular orbital composition, nuclear quadrupole splitting energies, and vibrational normal modes for both cofactors. A protonation state with an axial water (H₂O) ligand at Mn or Fe in binding site 1 and a metal-bridging hydroxo group (μOH) in a hydrogen-bonded network is assigned. Our comprehensive picture of the molecular, electronic, and dynamic properties of the cofactors highlights reorientation of the unique axis along the Mn-OH₂ bond for the Mn1(III) Jahn-Teller ion but along the Fe-μOH bond for the octahedral Fe1(III). This likely corresponds to a more positive redox potential of the Mn(III)Fe(III) cofactor and higher proton affinity of its μOH group. Refined model structures for the Mn(III)Fe(III) and Fe(III)Fe(III) cofactors are presented. Implications of our findings for the site-specific metalation of R2lox and performance of the O₂ reduction and cross-link formation reactions are discussed.

Role of disorder in the thermodynamics and atomic dynamics of glasses

We measured the density of vibrational states (DOS) and the specific heat of various glassy and crystalline polymorphs of SiO2. The typical (ambient) glass shows a well-known excess of specific heat relative to the typical crystal (α-quartz). This, however, holds when comparing a lower-density glass to a higher-density crystal. For glassy and crystalline polymorphs with matched densities, the DOS of the glass appears as the smoothed counterpart of the DOS of the corresponding crystal; it reveals the same number of the excess states relative to the Debye model, the same number of all states in the low-energy region, and it provides the same specific heat. This shows that glasses have higher specific heat than crystals not due to disorder, but because the typical glass has lower density than the typical crystal.

Phonon spectroscopy in a Bi2Te3 nanowire array

The lattice dynamics in an array of 56 nm diameter Bi2Te3 nanowires embedded in a self-ordered amorphous alumina membrane were investigated microscopically using (125)Te nuclear inelastic scattering. The element specific density of phonon states is measured on nanowires in two perpendicular orientations and the speed of sound is extracted. Combined high energy synchrotron radiation diffraction and transmission electron microscopy was carried out on the same sample and the crystallinity was investigated. The nanowires grow almost perpendicular to the c-axis, partly with twinning. The average speed of sound in the 56 nm diameter Bi2Te3 nanowires is ~7% smaller with respect to bulk Bi2Te3 and a decrease in the macroscopic lattice thermal conductivity by ~13% due to nanostructuration and to the reduced speed of sound is predicted.

Temperature gradient analyzers for compact high-resolution X-ray spectrometers

Compact high-resolution X-ray spectrometers with a one-dimensional temperature gradient at the analyzer crystal are considered. This gradient, combined with the use of a position-sensitive detector, makes it possible to relax the usual Rowland-circle condition, allowing increased space at the sample position for a given energy resolution or arm radius. Thus, for example, it is estimated that approximately meV resolution is possible with a 3 m analyzer arm and 200 mm clearance between the sample and detector. Simple analytic formulae are provided, supported by excellent agreement with ray-tracing simulations. One variation of this method also allows the detector position sensitivity to be used to determine momentum transfer, effectively improving momentum resolution without reducing (slitting down) the analyzer size. Application to medium-resolution ( approximately 10-100 meV) inelastic X-ray scattering spectrometers with large angular acceptance is discussed, where this method also allows increased space at the sample. In some cases the application of a temperature gradient can improve the energy resolution even with a single-element detector.

Longitudinal coherence function in X-ray imaging of crystals

The longitudinal coherence function at the Advanced Photon Source beamline 34-ID-C has been measured by a novel method and the coherence length (xi(L)) determined to be, xi(L) = 0.66 +/- 0.02 microm. Three dimensional Coherent X-ray Diffraction (CXD) patterns were measured for multiple Bragg reflections from two Zinc Oxide (ZnO) nanorods with differing aspect ratios. The visibility of fringes corresponding to the 002 crystal direction for each reflection were found to be different and used to map the coherence function of the incident radiation. Partial coherence was found to be associated with amplitude 'hot' spots in three dimensional reconstructions of the crystal structure.