Normal mode analysis of Pyrococcus furiosus rubredoxin via nuclear resonance vibrational spectroscopy (NRVS) and resonance raman spectroscopy

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S(cys))(4) site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). The oxidized form has also been investigated by resonance Raman spectroscopy. In the oxidized Rd NRVS, strong asymmetric Fe-S stretching modes are observed between 355 and 375 cm(-1); upon reduction these modes shift to 300-320 cm(-1). This is the first observation of Fe-S stretching modes in a reduced Rd. The peak in S-Fe-S bend mode intensity is at approximately 150 cm(-1) for the oxidized protein and only slightly lower in the reduced case. A third band occurs near 70 cm(-1) for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The (57)Fe partial vibrational density of states (PVDOS) were interpreted by normal mode analysis with optimization of Urey-Bradley force fields. The three main bands were qualitatively reproduced using a D(2)(d) Fe(SC)(4) model. A C(1) Fe(SCC)(4) model based on crystallographic coordinates was then used to simulate the splitting of the asymmetric stretching band into at least 3 components. Finally, a model employing complete cysteines and 2 additional neighboring atoms was used to reproduce the detailed structure of the PVDOS in the Fe-S stretch region. These results confirm the delocalization of the dynamic properties of the redox-active Fe site. Depending on the molecular model employed, the force constant K(Fe-S) for Fe-S stretching modes ranged from 1.24 to 1.32 mdyn/A. K(Fe-S) is clearly diminished in reduced Rd; values from approximately 0.89 to 1.00 mdyn/A were derived from different models. In contrast, in the final models the force constants for S-Fe-S bending motion, H(S-Fe-S), were 0.18 mdyn/A for oxidized Rd and 0.15 mdyn/A for reduced Rd. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.     

Crystal monochromator with a resolution beyond 10(8)

Monochromatization with crystal diffraction has been achieved to a resolution (lambda/delta lambda) beyond 10(8). The monchromator is specifically designed for 23.880 keV synchrotron radiation (lambda = 51.9 pm) for applications involving nuclear resonant scattering from 119Sn. The design uses asymmetrically cut silicon (12 12 12) crystal reflections from two single-crystalline monoliths oriented in a dispersive geometry. A transmitted energy bandwidth of 140 +/- 20 mu eV was measured, corresponding to a resolution of 1.7 x 10(8). Methods of improving efficiency, wavelength stability and resolution are discussed.     

Time-domain interferometry using synchrotron radiation applied to diffusion in ordered alloys

Time-domain interferometry of synchrotron radiation (TDI) has recently been used as a tool for investigating diffusion in glasses. This work deals with an extension of this technique to ordered structures. In a TDI experiment performed on the B2 alloy CoGa at the APS the intensity scattered into Bragg directions showed no detectable quasielastic signal. Experimental lower limits of the elastic contribution are given. They are in accordance with the coherent scattering function derived in this paper. This result indicates that TDI can be applied to diffusion in crystalline solids, e.g. intermetallic alloys, by using diffuse scattering. Requirements and limitations of diffuse scattering experiments are discussed. Received 21 September 2000 and Received in final form 13 December 2000     

3D Motions of Iron in Six‐Coordinate {FeNO}7 Hemes by Nuclear Resonance Vibration Spectroscopy

The vibrational spectrum of a six‐coordinate nitrosyl iron porphyrinate, monoclinic [Fe(TpFPP)(1‐MeIm)(NO)] (TpFPP=tetra‐para‐fluorophenylporphyrin; 1‐MeIm=1‐methylimidazole), has been studied by oriented single‐crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in‐plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in‐plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in‐plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out‐of‐plane Fe‐N‐O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v₅₀ as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe‐X‐O (X=N, C, and O) complexes is correlated with the Fe?XO bond lengths. The nature of highest frequency band at ≈560 cm^?1 has also been examined in two additional new derivatives. Previously assigned as the Fe?NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.     

Electrochemical Investigations of the Anticancer Drug Idarubicin Using Multiwalled Carbon Nanotubes Modified Glassy Carbon and Pyrolytic Graphite Electrodes

The effect of surface modifications on the electrochemical behavior of the anticancer drug idarubicin was studied at multiwalled carbon nanotubes modified glassy carbon and edge plane pyrolytic graphite electrodes. The surface morphology of the modified electrodes was characterized by scanning electron microscopy. The modified electrodes were constructed for the determination of idarubicin using adsorptive stripping differential pulse voltammetry. The experimental parameters such as supporting electrolyte, pH, accumulation time and potential, amount of carbon nanotubes for the sensitive assay of idarubicin were studied as details. Under the optimized conditions, idarubicin gave a linear response in the range 9.36×10^?8–1.87×10^?6 M for modified glassy carbon and 9.36×10^?8–9.36×10^?7 M for modified edge plane pyrolytic graphite electrodes. The detection limits were found as 1.87×10^?8 M and 3.75×10^?8 M based on modified glassy carbon and edge plane pyrolytic graphite electrodes, respectively. Interfering species such as ascorbic acid, dopamine, and aspirin showed no interference with the selective determination of idarubicin. The analyzing method was fully validated and successfully applied for the determination of idarubicin in its pharmaceutical dosage form. The possible oxidation mechanism of idarubicin was also discussed. The results revealed that the modified electrodes showed an obvious electrocatalytic activity toward the oxidation of idarubicin by a remarkable enhancement in the current response compared with bare electrodes.     

Structural and electronic characterization of non-heme Fe(II)-nitrosyls as biomimetic models of the Fe(B) center of bacterial nitric oxide reductase

The detoxification of nitric oxide (NO) by bacterial NO reductase (NorBC) has gained much attention as this reaction provides a paradigm as to how NO can be detoxified anaerobically in cells. However, a clear mechanistic picture of how the heme/non-heme active site of NorBC activates NO is lacking, mostly as a result of insufficient knowledge about the properties of the non-heme iron(II)-NO adduct. Here we report the first biomimetic model complexes for this species that closely resemble the coordination environment found in the protein, using the ligands BMPA-Pr and TPA. The systematic investigation of these compounds allowed us to gain key insight into the electronic structure and geometric properties of high-spin non-heme iron(II)-NO adducts. In particular, we show how small changes in the ligand environment of iron could be used by NorBC to greatly modulate the properties, and hence, the reactivity of this species.     

Atomic vibrational dynamics of amorphous Fe-Mg alloy thin films

The atomic vibrational dynamics of ⁵⁷Fe in 800-Å thick amorphous Fe_xMg_1−x alloy thin films (0.3≤x≤0.7) has been investigated at room temperature by nuclear resonant inelastic X-ray scattering (NRIXS) of 14.4125 keV synchrotron radiation. The amorphous phase has been successfully stabilized by codeposition of Fe and Mg in ultrahigh vacuum onto a substrate held at −140 °C during deposition. The amorphous structure of the samples was confirmed by X-ray diffraction and conversion electron Mössbauer spectroscopy. The ⁵⁷Fe-projected partial vibrational density of states, g(E), has been obtained from the measured NRIXS vibrational excitation probability, together with thermodynamic quantities such as the probability of recoilless absorption (f-factor), the average kinetic energy per Fe atom, the average force constant, and the vibrational entropy per Fe atom. A plot of g(E)/E² versus E proves the existence of non-Debye-like vibrational excitations with a peak at E_bp∼3-5 meV (boson peak). Both the boson peak height and E_bp were found to depend linearly on the composition x. Above the boson peak, g(E)/E² exhibits an exponential decrease.     

Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.