Two-Color Valence-to-Core X-ray Emission Spectroscopy Tracks Cofactor Protonation State in a Class I Ribonucleotide Reductase

Proton transfer reactions are of central importance to a wide variety of biochemical processes, though determining proton location and monitoring proton transfers in biological systems is often extremely challenging. Herein, we use two-color valence-to-core X-ray emission spectroscopy (VtC XES) to identify protonation events across three oxidation states of the O2 -activating, radical-initiating manganese-iron heterodinuclear cofactor in a class I-c ribonucleotide reductase. This is the first application of VtC XES to an enzyme intermediate and the first simultaneous measurement of two-color VtC spectra. In contrast to more conventional methods of assessing protonation state, VtC XES is a more direct probe applicable to a wide range of metalloenzyme systems. These data, coupled to insight provided by DFT calculations, allow the inorganic cores of the MnIV FeIV and MnIV FeIII states of the enzyme to be assigned as MnIV (μ-O)2 FeIV and MnIV (μ-O)(μ-OH)FeIII , respectively.

X-ray reflectivity of chemically vapor-deposited diamond single crystals in the Laue geometry

The absolute X-ray reflectivity of chemically vapor-deposited (CVD) single-crystal diamond plates was measured in the Laue geometry in the double-crystal non-dispersive setting with an asymmetric Si beam-conditioner crystal. The measurements were supplemented by rocking-curve topography. The measured reflectivity curves are examined in the framework of the Darwin-Hamilton approach using a set of two independent parameters: the characteristic thickness of mosaic blocks and their average angular misorientation. Owing to strong extinction effects, the width of the reflectivity curves does not directly represent the average misorientation of the blocks. Two different sets of parameters were found for the 111 asymmetric reflection in the two different scattering configurations (beam compression and beam expansion). Analysis of the rocking-curve topographs shows that this discrepancy can be attributed to inhomogeneity of the diamond crystal microstructure.

X-ray emission spectroscopy: an effective route to extract site occupation of cations

Cation site occupation is an important determinant of materials properties, especially in a complex system with multiple cations such as in ternary spinels. In this work, we show that XES provides not only the site occupation information as EXAFS, but also additional information on the oxidation states of the cations at each site. Additionally, we show that XES is a superior and a far more accurate method than EXAFS.

Lifshitz transition from valence fluctuations in YbAl3

In mixed-valent Kondo lattice systems, such as YbAl₃, interactions between localized and delocalized electrons can lead to fluctuations between two different valence configurations with changing temperature or pressure. The impact of this change on the momentum-space electronic structure is essential for understanding their emergent properties, but has remained enigmatic. Here, by employing a combination of molecular beam epitaxy and in situ angle-resolved photoemission spectroscopy we show that valence fluctuations can lead to dramatic changes in the Fermi surface topology, even resulting in a Lifshitz transition. As the temperature is lowered, a small electron pocket in YbAl₃ becomes completely unoccupied while the low-energy ytterbium (Yb) 4f states become increasingly itinerant, acquiring additional spectral weight, longer lifetimes, and well-defined dispersions. Our work presents a unified picture of how local valence fluctuations connect to momentum-space concepts such as band filling and Fermi surface topology in mixed valence systems.

How the electronic structure of a mixed-valence system changes with respect to local chemical environment remains elusive. Here, Chatterjee et al. show that valence fluctuations of YbAl₃ can lead to dramatic changes in the Fermi surface topology in reciprocal space.

Observation of a Charge Density Wave Incommensuration Near the Superconducting Dome in Cu_{x}TiSe_{2}

X-ray diffraction was employed to study the evolution of the charge density wave (CDW) in Cu_{x}TiSe_{2} as a function of copper intercalation in order to clarify the relationship between the CDW and superconductivity. The results show a CDW incommensuration arising at an intercalation value coincident with the onset of superconductivity at around x=0.055(5). Additionally, it was found that the charge density wave persists to higher intercalant concentrations than previously assumed, demonstrating that the CDW does not terminate inside the superconducting dome. A charge density wave peak was observed in samples up to x=0.091(6), the highest copper concentration examined in this study. The phase diagram established in this work suggests that charge density wave incommensuration may play a role in the formation of the superconducting state.

Experimental and theoretical correlations between vanadium K-edge X-ray absorption and Kβ emission spectra

A series of vanadium compounds was studied by K-edge X-ray absorption (XAS) and K[Formula: see text] X-ray emission spectroscopies (XES). Qualitative trends within the datasets, as well as comparisons between the XAS and XES data, illustrate the information content of both methods. The complementary nature of the chemical insight highlights the success of this dual-technique approach in characterizing both the structural and electronic properties of vanadium sites. In particular, and in contrast to XAS or extended X-ray absorption fine structure (EXAFS), we demonstrate that valence-to-core XES is capable of differentiating between ligating atoms with the same identity but different bonding character. Finally, density functional theory (DFT) and time-dependent DFT calculations enable a more detailed, quantitative interpretation of the data. We also establish correction factors for the computational protocols through calibration to experiment. These hard X-ray methods can probe vanadium ions in any oxidation or spin state, and can readily be applied to sample environments ranging from solid-phase catalysts to biological samples in frozen solution. Thus, the combined XAS and XES approach, coupled with DFT calculations, provides a robust tool for the study of vanadium atoms in bioinorganic chemistry.

Structural origin of the anomalous temperature dependence of the local magnetic moments in the CaFe2As2 family of materials

We report a combination of Fe Kβ x-ray emission spectroscopy and density functional reduced Stoner theory calculations to investigate the correlation between structural and magnetic degrees of freedom in CaFe2(As1-xPx)2. The puzzling temperature behavior of the local moment found in rare earth-doped CaFe2As2 [H. Gretarsson et al., Phys. Rev. Lett. 110, 047003 (2013)] is also observed in CaFe2(As1-xPx)2. We explain this phenomenon based on first-principles calculations with scaled magnetic interaction. One scaling parameter is sufficient to describe quantitatively the magnetic moments in both CaFe2(As1-xPx)2 (x=0.055) and Ca0.78La0.22Fe2As2 at all temperatures. The anomalous growth of the local moments with increasing temperature can be understood from the observed large thermal expansion of the c-axis lattice parameter combined with strong magnetoelastic coupling. These effects originate from the strong tendency to form As-As dimers across the Ca layer in the CaFe2As2 family of materials. Our results emphasize the dual local-itinerant character of magnetism in Fe pnictides.

Study of iron dimers reveals angular dependence of valence-to-core X-ray emission spectra

Transition-metal Kβ X-ray emission spectroscopy (XES) is a developing technique that probes the occupied molecular orbitals of a metal complex. As an element-specific probe of metal centers, Kβ XES is finding increasing applications in catalytic and, in particular, bioinorganic systems. For the continued development of XES as a probe of these complex systems, however, the full range of factors which contribute to XES spectral modulations must be explored. In this report, an investigation of a series of oxo-bridged iron dimers reveals that the intensity of valence-to-core features is sensitive to the Fe-O-Fe bond angle. The intensity of these features has a well-known dependence on metal-ligand bond distance, but a dependence upon bond angle has not previously been documented. Herein, we explore the angular dependence of valence-to-core XES features both experimentally and computationally. Taken together, these results show that, as the Fe-O-Fe angle decreases, the intensity of the Kβ″ feature increases and that this effect is modulated by increasing amounts of Fe np mixing into the O 2s orbital at smaller bond angles. The relevance of these findings to the identification of oxygenated intermediates in bioinorganic systems is highlighted, with special emphasis given to the case of soluble methane monooxygenase.

Bis(imino)pyridine Iron Dinitrogen Compounds Revisited: Differences in Electronic Structure Between Four- and Five-Coordinate Derivatives

The electronic structures of the four- and five-coordinate aryl-substituted bis(imino)pyridine iron dinitrogen complexes, ((iPr)PDI)FeN(2) and ((iPr)PDI)Fe(N(2))(2) ((iPr)PDI = 2,6-(2,6-(i)Pr(2)-C(6)H(3)-N=CMe)(2)C(5)H(3)N), have been investigated by a combination of spectroscopic techniques (NMR, Mössbauer, X-ray Absorption and X-ray Emission) and DFT calculations. Homologation of the imine methyl backbone to ethyl or isopropyl groups resulted in the preparation of the new bis(imino)pyridine iron dinitrogen complexes, ((iPr)RPDI)FeN(2) ((iPr)RPDI = 2,6-(2,6-(i)Pr(2)-C(6)H(3)-N=CR)(2)C(5)H(3)N; R = Et, (i)Pr), that are exclusively four coordinate both in the solid state and in solution. The spectroscopic and computational data establish that the ((iPr)RPDI)FeN(2) compounds are intermediate spin ferrous derivatives (S(Fe) = 1) antiferromagnetically coupled to bis(imino)pyridine triplet diradical dianions (S(PDI) = 1). While this ground state description is identical to that previously reported for ((iPr)PDI)Fe(DMAP) (DMAP = 4-N,N-dimethylaminopyridine) and other four-coordinate iron compounds with principally σ-donating ligands, the d-orbital energetics determine the degree of coupling of the metal-chelate magnetic orbitals resulting in different NMR spectroscopic behavior. For ((iPr)RPDI)Fe(DMAP) and related compounds, this coupling is strong and results in temperature independent paramagnetism where a triplet excited state mixes with the singlet ground state via spin orbit coupling. In the ((iPr)RPDI)FeN(2) family, one of the iron SOMOs is essentially d(z2) in character resulting in poor overlap with the magnetic orbitals of the chelate, leading to thermal population of the triplet state and hence temperature dependent NMR behavior. The electronic structures of ((iPr)RPDI)FeN(2) and ((iPr)PDI)Fe(DMAP) differ from ((iPr)PDI)Fe(N(2))(2), a highly covalent molecule with a redox non-innocent chelate that is best described as a resonance hybrid between iron(0) and iron(II) canonical forms as originally proposed in 2004.

Bis(imino)pyridine iron dinitrogen compounds revisited: differences in electronic structure between four- and five-coordinate derivatives

The electronic structures of the four- and five-coordinate aryl-substituted bis(imino)pyridine iron dinitrogen complexes, ((iPr)PDI)FeN(2) and ((iPr)PDI)Fe(N(2))(2) ((iPr)PDI = 2,6-(2,6-(i)Pr(2)-C(6)H(3)-N=CMe)(2)C(5)H(3)N), have been investigated by a combination of spectroscopic techniques (NMR, Mössbauer, X-ray Absorption, and X-ray Emission) and DFT calculations. Homologation of the imine methyl backbone to ethyl or isopropyl groups resulted in the preparation of the new bis(imino)pyridine iron dinitrogen complexes, ((iPr)RPDI)FeN(2) ((iPr)RPDI = 2,6-(2,6-(i)Pr(2)-C(6)H(3)-N=CR)(2)C(5)H(3)N; R = Et, (i)Pr), that are exclusively four coordinate both in the solid state and in solution. The spectroscopic and computational data establish that the ((iPr)RPDI)FeN(2) compounds are intermediate spin ferrous derivatives (S(Fe) = 1) antiferromagnetically coupled to bis(imino)pyridine triplet diradical dianions (S(PDI) = 1). While this ground state description is identical to that previously reported for ((iPr)PDI)Fe(DMAP) (DMAP = 4-N,N-dimethylaminopyridine) and other four-coordinate iron compounds with principally σ-donating ligands, the d-orbital energetics determine the degree of coupling of the metal-chelate magnetic orbitals resulting in different NMR spectroscopic behavior. For ((iPr)RPDI)Fe(DMAP) and related compounds, this coupling is strong and results in temperature independent paramagnetism where a triplet excited state mixes with the singlet ground state via spin orbit coupling. In the ((iPr)RPDI)FeN(2) family, one of the iron singly occupied molecular orbitals (SOMOs) is essentially d(z(2)) in character resulting in poor overlap with the magnetic orbitals of the chelate, leading to thermal population of the triplet state and hence temperature dependent NMR behavior. The electronic structures of ((iPr)RPDI)FeN(2) and ((iPr)PDI)Fe(DMAP) differ from ((iPr)PDI)Fe(N(2))(2), a highly covalent molecule with a redox noninnocent chelate that is best described as a resonance hybrid between iron(0) and iron(II) canonical forms as originally proposed in 2004.

Nonresonant inelastic x-ray scattering and energy-resolved Wannier function investigation of d-d excitations in NiO and CoO

Nonresonant inelastic x-ray scattering measurements on NiO and CoO show that strong dipole-forbidden d-d excitations appear within the Mott gap at large wave vectors. These dominant excitations are highly anisotropic, and have [001] nodal directions for NiO. Theoretical analyses based on a novel, energy-resolved Wannier function (within the local density approximation+Hubbard U) show that the anisotropy reflects the local exciton wave functions and local point-group symmetry. The sensitivity to weak symmetry breaking in particle-hole wave functions suggests a wide application to strongly correlated systems.

Spatial distribution of competing ions around DNA in solution

The competition of monovalent and divalent cations for proximity to negatively charged DNA is of biological importance and can provide strong constraints for theoretical treatments of polyelectrolytes. Resonant x-ray scattering experiments have allowed us to monitor the number and distribution of each cation in a mixed ion cloud around DNA. These measurements provide experimental evidence to support a general theoretical prediction: the normalized distribution of each ion around polyelectrolytes remains constant when ions are mixed at different ratios. In addition, the amplitudes of the scattering signals throughout the competition provide a measurement of the surface concentration parameter that predicts the competition behavior of these cations. The data suggest that ion size needs to be taken into account in applying Poisson-Boltzmann treatments to polyelectrolytes such as DNA.

Imaging density disturbances in water with a 41.3-attosecond time resolution

We show that the momentum flexibility of inelastic x-ray scattering may be exploited to invert its loss function, allowing real time imaging of density disturbances in a medium. We show the disturbance arising from a point source in liquid water, with a resolution of 41.3 attoseconds (4.13 x 10(-17) s) and 1.27 A (1.27 x 10(-8) cm). This result is used to determine the structure of the electron cloud around a photoexcited chromophore in solution, as well as the wake generated in water by a 9 MeV gold ion. We draw an analogy with pump-probe techniques and suggest that energy-loss scattering may be applied more generally to the study of attosecond phenomena.

Counterion distribution around DNA probed by solution X-ray scattering

Counterion atmospheres condensed onto charged biopolymers strongly affect their physical properties and biological functions, but have been difficult to quantify experimentally. Here, monovalent and divalent counterion atmospheres around DNA double helices in solution are probed using small-angle x-ray scattering techniques. Modulation of the ion scattering factors by anomalous (resonant) x-ray scattering and by interchanging ion identities yields direct measurements of the scattering signal due to the spatial correlation of surrounding ions to the DNA. The quality of the data permit, for the first time, quantitative tests of extended counterion distributions calculated from atomic-scale models of biologically relevant molecules.

Flash-cooling and annealing of protein crystals

Flash-cooling and annealing of macromolecular crystals have been investigated using in situ X-ray imaging, diffraction-peak lineshape measurements and conventional crystallographic diffraction. The dominant mechanisms by which flash-cooling creates disorder are suggested and a fixed-temperature annealing protocol for reducing this disorder is demonstrated that should be more reliable and flexible than existing protocols. Flash-cooling tetragonal lysozyme crystals degrades diffraction resolution and broadens the distributions of lattice orientations (mosaicity) and lattice spacings. The diffraction resolution strongly correlates with the width of the lattice-spacing distribution. Annealing at fixed temperatures of 253 and 233 K consistently reduces the lattice-spacing spread and improves the resolution for annealing times up to approximately 30s. X-ray images show that this improvement arises from the formation of well ordered domains with characteristic sizes >10 microm and narrower mosaicities than the crystal as a whole. Flash-cooled triclinic crystals of lysozyme, which have a smaller water content than the tetragonal form, diffract to higher resolution with smaller mosaicities and exhibit pronounced ordered domain structure even before annealing. It is suggested that differential thermal expansion of the protein lattice and solvent may be the primary cause of flash-cooling-induced disorder. Mechanisms by which annealing at T << 273 K reduce this disorder are discussed.

Dynamic response of tetragonal lysozyme crystals to changes in relative humidity: implications for post-growth crystal treatments

The dynamic response of tetragonal lysozyme crystals to dehydration has been characterized in situ using a combination of X-ray topography, high-resolution diffraction line-shape measurements and conventional crystallographic diffraction. For dehydration from 98% relative humidity (r.h.) to above 89%, mosaicity and diffraction resolution show little change and X-ray topographs remain featureless. Lattice constants decrease rapidly but the lattice-constant distribution within the crystal remains very narrow, indicating that water concentration gradients remain very small. Near 88% r.h., the c-axis lattice parameter decreases abruptly, the steady-state mosaicity and diffraction resolution degrade sharply and topographs develop extensive contrast. This transformation exhibits metastability and hysteresis. At fixed r.h. < 88% it is irreversible, but the original order can be almost completely restored by rehydration. These results suggest that this transformation is a first-order structural transition involving an abrupt loss of crystal water. The front between transformed and untransformed regions may propagate inward from the crystal surface and the resulting stresses along the front may degrade mosaicity. Differences in crystal size, shape and initial perfection may produce the observed variations in degradation timescale. Consequently, the success of more general post-growth treatments may often involve identifying procedures that either avoid lattice transitions, minimize disorder created during such transitions or maintain the lattice in an ordered metastable state.

Macromolecular impurities and disorder in protein crystals

The mechanisms by which macromolecular impurities degrade the diffraction properties of protein crystals have been investigated using X-ray topography, high-resolution diffraction line shape measurements, crystallographic data collection, chemical analysis, and two-photon excitation fluorescence microscopy. Hen egg-white lysozyme crystals grown from solutions containing a structurally unrelated protein (ovotransferrin) and a related protein (turkey egg-white lysozyme) can exhibit significantly broadened mosaicity due to formation of cracks and dislocations but have overall B factors and diffraction resolutions comparable to those of crystals grown from uncontaminated lysozyme. Direct fluorescence imaging of the three-dimensional impurity distribution shows that impurities incorporate with different densities in sectors formed by growth on different crystal faces, and that impurity densities in the crystal core and along boundaries between growth sectors can be much larger than in other parts of the crystal. These nonuniformities create stresses that drive formation of the defects responsible for the mosaic broadening. Our results provide a rationale for the use of seeding to obtain high-quality crystals from heavily contaminated solutions and have implications for the use of crystallization for protein purification. Proteins 1999;36:270-281.

X-ray topographic studies of protein crystal perfection and growth

The effects of solution variations during growth on the perfection of tetragonal lysozyme crystals have been characterized using X-ray topography and high angular and wavevector resolution reciprocal-space scans. X-ray images of crystals grown under nearly uniform conditions show little contrast or evidence of defects, and mosaic widths of these crystals are comparable with those reported for microgravity-grown crystals. Images of crystals for which solution conditions (temperature, pH or salt concentration) are changed after an initial period of uniform growth can show extensive contrast, indicating the presence of disorder. The X-ray mosaic widths of these crystals can be significantly broadened, but their radial widths are at most very slightly broadened, indicating that image contrast is primarily due to mosaicity. Comparison of X-ray images with mosaic scans indicates that regions grown after the change in solution conditions have broader mosaicities and are more disordered; that regions grown immediately after the change tend to have broader mosaicities than subsequent growth regions; and that the pre-change growth region is largely unaffected by solution changes. The observed disorder may arise from solution change-related transient growth instabilities, from transient liquid-liquid phase separation that can occur during the change, and from post-change relaxation of the lattice constant of the pre-change growth regions. These results suggest that solution variations during growth, including those typical of macroseeding, vapor-diffusion growth and other widely used techniques, may be an important source of disorder in some protein crystals.