E. Alp | Argonne National Laboratory (original) (raw)
Papers by E. Alp
Physical Review Letters, 2003
We demonstrate an interferometer for hard x rays with two back-reflecting sapphire crystal mirror... more We demonstrate an interferometer for hard x rays with two back-reflecting sapphire crystal mirrors -a prototype x-ray Fabry-Pérot interferometer. A finesse of 15 and 0:76 eV broad Fabry-Pérot transmission resonances are measured by the time response of the interferometer. Interference patterns are observed directly in spectral dependences of reflectivity.
Physical Review Letters, 1995
The phonon density of states was measured by observing the nuclear resonant fluorescence of 57 Fe... more The phonon density of states was measured by observing the nuclear resonant fluorescence of 57 Fe versus the energy of incident x rays from a synchrotron radiation beam. An energy resolution of 6 meV was achieved by use of high-resolution crystal optics for the incident beam. Extremely low background levels were obtained via time discrimination of the nuclear fluorescent radiation.
Physical Review Letters, 2000
A coherently excited nuclear state in a rotating sample acquires a phase shift during its time ev... more A coherently excited nuclear state in a rotating sample acquires a phase shift during its time evolution that is proportional to its angular momentum and the rotation angle. As a consequence, the radiative decay of the excited state proceeds into the rotated direction, and the time spectrum of the nuclear decay is mapped onto an angular scale. This effect has been observed in nuclear resonant scattering of synchrotron radiation from a 57 Fe metal foil rotating at 18 kHz.
Physical Review Letters, 2001
A high-resolution inelastic neutron-scattering experiment has been carried out on a saturated sol... more A high-resolution inelastic neutron-scattering experiment has been carried out on a saturated solution of lithium in deuterated ammonia to investigate the vibrational dynamics at low wave-vector transfer. The response function of the system, dominated by the deuterium dynamics, showed clear coherent contributions arising from collective excitations. Density-fluctuation modes were visible up to the highest measured wavevector transfer, 0.8 Å Ϫ1 , with an associated dispersion relation characterized by a remarkably anomalous behavior around twice the Fermi momentum. The nature of the anomaly is ascribed to electron correlation effects and closely resembles the Kohn anomaly as observed in the phonon spectrum of solid metals.
Journal of Applied Physics, 2013
The phonon dispersion was measured at room temperature along (0,0,L) in the tetragonal phase of L... more The phonon dispersion was measured at room temperature along (0,0,L) in the tetragonal phase of LaFeAsO using inelastic x-ray scattering. Spin-polarized first-principles calculations imposing various types of antiferromagnetic order are in better agreement with the experimental results than nonmagnetic calculations, although the measurements were made well above the magnetic ordering temperature, TN . Splitting observed between two A1g phonon modes at 22 and 26 meV is only observed in spin-polarized calculations. Magneto-structural effects similar to those observed in the AFe2As2 materials are confirmed present in LaFeAsO. The presence of Fe-spin is necessary to find reasonable agreement of the calculations with the measured spectrum well above TN . On-site Fe and As force constants show significant softening compared to nonmagnetic calculations, however an investigation of the real-space force constants associates the magnetoelastic coupling with a complex renormalization instead of softening of a specific pairwise force.
Angewandte Chemie International Edition, 2013
The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe−S clusters that facili... more The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe−S clusters that facilitate the transfer of an electron to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H 2 . Here, we have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe-4S] ferredoxin as well as a model complex resembling the [2Fe] H catalytic domain of the H-cluster. To enrich the hydrogenase with 57 Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with 56 Felabeled Fe−S clusters was activated in vitro using 57 Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe] H subcluster with 57 Fe, which NRVS confirms by detecting 57 Fe−CO and 57 Fe−CN normal modes from the H-cluster nonprotein ligands. The NRVS and iron quantification results also suggest that the hydrogenase contains a second 57 Fe−S cluster. Electron paramagnetic resonance (EPR) spectroscopy indicates that this 57 Fe-enriched metal center is not the [4Fe-4S] H subcluster of the H-cluster. This finding demonstrates that the CpI hydrogenase retained an 56 Fe-enriched [4Fe-4S] H cluster during in vitro maturation, providing unambiguous evidence of stepwise assembly of the H-cluster. In addition, this work represents the first NRVS characterization of [FeFe] hydrogenases.
![Research paper thumbnail of Dynamics of Rhodobacter capsulatus [2Fe-2S] Ferredoxin VI and Aquifex aeolicus Ferredoxin 5 via Nuclear Resonance Vibrational Spectroscopy (NRVS) and Resonance Raman Spectroscopy †](https://attachments.academia-assets.com/44076940/thumbnails/1.jpg)
](Biochemistry, 2008
We have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe 2 S 2 (Cys) ... more We have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe 2 S 2 (Cys) 4 sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe-S stretching modes peaking around 335 cm -1 , and additional features observed as high as the B 2u mode at ∼421 cm -1 . Both forms of Rc FdVI have also been investigated by resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B 3u mode at ∼288 cm -1 , attributed to an asymmetric combination of the two FeS 4 breathing modes, is often the strongest resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS 4 breathing. NRVS and RR analysis of isotope shifts with 36 S-substituted into bridging S 2ions in Rc FdVI allowed quantitation of S 2motion in different normal modes. We observed the symmetric Fe-Fe stretching mode at ∼190 cm -1 in both NRVS and RR spectra. At still lower energies, the NRVS presents a complex envelope of bending, torsion, and protein modes, with a maximum at 78 cm -1 . The 57 Fe partial vibrational densities of states (PVDOS) were interpreted by normalmode analysis with optimization of Urey-Bradley force fields. Progressively more complex D 2h Fe 2 S 2 S′ 4 , C 2h Fe 2 S 2 (SCC) 4 , and C 1 Fe 2 S 2 (Cys) 4 models were optimized by comparison with the experimental spectra. After modification of the CHARMM22 all-atom force field by the addition of refined Fe-S force constants, a simulation employing the complete protein structure was used to reproduce the PVDOS, with better results in the low frequency protein mode region. This process was then repeated for analysis of data on the reduced FdVI. Finally, the degree of collectivity was used to quantitate the delocalization of the dynamic properties of the redox-active Fe site. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins. † This work was funded by NIH Grants GM-65440 (to S.P.C.), EB-001962 (to S.P.C.), and GM-45303 (to T.I.), and the DOE Office of Biological and Environmental Research (to S.P.C.). Use of the APS is supported by the DOE Office of Basic Energy Sciences, Office of Science. SPring-8 is funded by JASRI.
Physical Review Letters, 2003
We demonstrate an interferometer for hard x rays with two back-reflecting sapphire crystal mirror... more We demonstrate an interferometer for hard x rays with two back-reflecting sapphire crystal mirrors -a prototype x-ray Fabry-Pérot interferometer. A finesse of 15 and 0:76 eV broad Fabry-Pérot transmission resonances are measured by the time response of the interferometer. Interference patterns are observed directly in spectral dependences of reflectivity.
Physical Review Letters, 1995
The phonon density of states was measured by observing the nuclear resonant fluorescence of 57 Fe... more The phonon density of states was measured by observing the nuclear resonant fluorescence of 57 Fe versus the energy of incident x rays from a synchrotron radiation beam. An energy resolution of 6 meV was achieved by use of high-resolution crystal optics for the incident beam. Extremely low background levels were obtained via time discrimination of the nuclear fluorescent radiation.
Physical Review Letters, 2000
A coherently excited nuclear state in a rotating sample acquires a phase shift during its time ev... more A coherently excited nuclear state in a rotating sample acquires a phase shift during its time evolution that is proportional to its angular momentum and the rotation angle. As a consequence, the radiative decay of the excited state proceeds into the rotated direction, and the time spectrum of the nuclear decay is mapped onto an angular scale. This effect has been observed in nuclear resonant scattering of synchrotron radiation from a 57 Fe metal foil rotating at 18 kHz.
Physical Review Letters, 2001
A high-resolution inelastic neutron-scattering experiment has been carried out on a saturated sol... more A high-resolution inelastic neutron-scattering experiment has been carried out on a saturated solution of lithium in deuterated ammonia to investigate the vibrational dynamics at low wave-vector transfer. The response function of the system, dominated by the deuterium dynamics, showed clear coherent contributions arising from collective excitations. Density-fluctuation modes were visible up to the highest measured wavevector transfer, 0.8 Å Ϫ1 , with an associated dispersion relation characterized by a remarkably anomalous behavior around twice the Fermi momentum. The nature of the anomaly is ascribed to electron correlation effects and closely resembles the Kohn anomaly as observed in the phonon spectrum of solid metals.
Journal of Applied Physics, 2013
The phonon dispersion was measured at room temperature along (0,0,L) in the tetragonal phase of L... more The phonon dispersion was measured at room temperature along (0,0,L) in the tetragonal phase of LaFeAsO using inelastic x-ray scattering. Spin-polarized first-principles calculations imposing various types of antiferromagnetic order are in better agreement with the experimental results than nonmagnetic calculations, although the measurements were made well above the magnetic ordering temperature, TN . Splitting observed between two A1g phonon modes at 22 and 26 meV is only observed in spin-polarized calculations. Magneto-structural effects similar to those observed in the AFe2As2 materials are confirmed present in LaFeAsO. The presence of Fe-spin is necessary to find reasonable agreement of the calculations with the measured spectrum well above TN . On-site Fe and As force constants show significant softening compared to nonmagnetic calculations, however an investigation of the real-space force constants associates the magnetoelastic coupling with a complex renormalization instead of softening of a specific pairwise force.
Angewandte Chemie International Edition, 2013
The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe−S clusters that facili... more The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe−S clusters that facilitate the transfer of an electron to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H 2 . Here, we have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe-4S] ferredoxin as well as a model complex resembling the [2Fe] H catalytic domain of the H-cluster. To enrich the hydrogenase with 57 Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with 56 Felabeled Fe−S clusters was activated in vitro using 57 Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe] H subcluster with 57 Fe, which NRVS confirms by detecting 57 Fe−CO and 57 Fe−CN normal modes from the H-cluster nonprotein ligands. The NRVS and iron quantification results also suggest that the hydrogenase contains a second 57 Fe−S cluster. Electron paramagnetic resonance (EPR) spectroscopy indicates that this 57 Fe-enriched metal center is not the [4Fe-4S] H subcluster of the H-cluster. This finding demonstrates that the CpI hydrogenase retained an 56 Fe-enriched [4Fe-4S] H cluster during in vitro maturation, providing unambiguous evidence of stepwise assembly of the H-cluster. In addition, this work represents the first NRVS characterization of [FeFe] hydrogenases.
Biochemistry, 2008
We have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe 2 S 2 (Cys) ... more We have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe 2 S 2 (Cys) 4 sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe-S stretching modes peaking around 335 cm -1 , and additional features observed as high as the B 2u mode at ∼421 cm -1 . Both forms of Rc FdVI have also been investigated by resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B 3u mode at ∼288 cm -1 , attributed to an asymmetric combination of the two FeS 4 breathing modes, is often the strongest resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS 4 breathing. NRVS and RR analysis of isotope shifts with 36 S-substituted into bridging S 2ions in Rc FdVI allowed quantitation of S 2motion in different normal modes. We observed the symmetric Fe-Fe stretching mode at ∼190 cm -1 in both NRVS and RR spectra. At still lower energies, the NRVS presents a complex envelope of bending, torsion, and protein modes, with a maximum at 78 cm -1 . The 57 Fe partial vibrational densities of states (PVDOS) were interpreted by normalmode analysis with optimization of Urey-Bradley force fields. Progressively more complex D 2h Fe 2 S 2 S′ 4 , C 2h Fe 2 S 2 (SCC) 4 , and C 1 Fe 2 S 2 (Cys) 4 models were optimized by comparison with the experimental spectra. After modification of the CHARMM22 all-atom force field by the addition of refined Fe-S force constants, a simulation employing the complete protein structure was used to reproduce the PVDOS, with better results in the low frequency protein mode region. This process was then repeated for analysis of data on the reduced FdVI. Finally, the degree of collectivity was used to quantitate the delocalization of the dynamic properties of the redox-active Fe site. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins. † This work was funded by NIH Grants GM-65440 (to S.P.C.), EB-001962 (to S.P.C.), and GM-45303 (to T.I.), and the DOE Office of Biological and Environmental Research (to S.P.C.). Use of the APS is supported by the DOE Office of Basic Energy Sciences, Office of Science. SPring-8 is funded by JASRI.