| 1. |
- Chapman, Henry N., et al.
(författare)
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Femtosecond diffractive imaging with a soft-X-ray free-electron laser
- 2006
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Ingår i: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 2:12, s. 839-843
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Tidskriftsartikel (refereegranskat)abstract
- Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).
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| 2. |
- Ekeberg, Tomas, 1983-, et al.
(författare)
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Three-dimensional structure determination with an X-ray laser
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus.
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| 3. |
- Kroll, Thomas, et al.
(författare)
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Effect of 3d/4p Mixing on 1s2p Resonant Inelastic X-ray Scattering : Electronic Structure of Oxo-Bridged Iron Dimers
- 2021
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 143:12, s. 4569-4584
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Tidskriftsartikel (refereegranskat)abstract
- 1s2p resonant inelastic X-ray scattering (1s2p RIXS) has proven successful in the determination of the differential orbital covalency (DOC, the amount of metal vs ligand character in each d molecular orbital) of highly covalent centrosymmetric iron environments including heme models and enzymes. However, many reactive intermediates have non-centrosymmetric environments, e.g., the presence of strong metal-oxo bonds, which results in the mixing of metal 4p character into the 3d orbitals. This leads to significant intensity enhancement in the metal K-pre-edge and as shown here, the associated 1s2p RIXS features, which impact their insight into electronic structure. Binuclear oxo bridged high spin Fe(III) complexes are used to determine the effects of 4p mixing on 1s2p RIXS spectra. In addition to developing the analysis of 4p mixing on K-edge XAS and 1s2p RIXS data, this study explains the selective nature of the 4p mixing that also enhances the analysis of L-edge XAS intensity in terms of DOC. These 1s2p RIXS biferric model studies enable new structural insight from related data on peroxo bridged biferric enzyme intermediates. The dimeric nature of the oxo bridged Fe(III) complexes further results in ligand-to-ligand interactions between the Fe(III) sites and angle dependent features just above the pre-edge that reflect the superexchange pathway of the oxo bridge. Finally, we present a methodology that enables DOC to be obtained when L-edge XAS is inaccessible and only 1s2p RIXS experiments can be performed as in many metalloenzyme intermediates in solution.
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| 4. |
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| 5. |
- Kroll, Thomas, et al.
(författare)
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Resonant Inelastic X-ray Scattering on Ferrous and Ferric bis-imidazole Porphyrin and Cytochrome c : Nature and Role of the Axial Methionine-Fe Bond
- 2014
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:52, s. 18087-18099
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Tidskriftsartikel (refereegranskat)abstract
- Axial Cu–S(Met) bonds in electron transfer (ET) active sites are generally found to lower their reduction potentials. An axial S(Met) bond is also present in cytochrome c (cyt c) and is generally thought to increase the reduction potential. The highly covalent nature of the porphyrin environment in heme proteins precludes using many spectroscopic approaches to directly study the Fe site to experimentally quantify this bond. Alternatively, L-edge X-ray absorption spectroscopy (XAS) enables one to directly focus on the 3d-orbitals in a highly covalent environment and has previously been successfully applied to porphyrin model complexes. However, this technique cannot be extended to metalloproteins in solution. Here, we use metal K-edge XAS to obtain L-edge like data through 1s2p resonance inelastic X-ray scattering (RIXS). It has been applied here to a bis-imidazole porphyrin model complex and cyt c. The RIXS data on the model complex are directly correlated to L-edge XAS data to develop the complementary nature of these two spectroscopic methods. Comparison between the bis-imidazole model complex and cyt c in ferrous and ferric oxidation states show quantitative differences that reflect differences in axial ligand covalency. The data reveal an increased covalency for the S(Met) relative to N(His) axial ligand and a higher degree of covalency for the ferric states relative to the ferrous states. These results are reproduced by DFT calculations, which are used to evaluate the thermodynamics of the Fe–S(Met) bond and its dependence on redox state. These results provide insight into a number of previous chemical and physical results on cyt c.
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| 6. |
- Lundberg, Marcus, et al.
(författare)
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Metal-ligand Covalency of Iron Complexes from High-Resolution Resonant Inelastic X-ray Scattering
- 2013
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Ingår i: Journal of the American Chemical Society. - Washington : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 135:45, s. 17121-17134
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Tidskriftsartikel (refereegranskat)abstract
- Data from Kα resonant inelastic X-ray scattering (RIXS) have been used to extract electronic structure information, i.e., the covalency of metal–ligand bonds, for four iron complexes using an experimentally based theoretical model. Kα RIXS involves resonant 1s→3d excitation and detection of the 2p→1s (Kα) emission. This two-photon process reaches similar final states as single-photon L-edge (2p→3d) X-ray absorption spectroscopy (XAS), but involves only hard X-rays and can therefore be used to get high-resolution L-edge-like spectra for metal proteins, solution catalysts and their intermediates. To analyze the information content of Kα RIXS spectra, data have been collected for four characteristic σ-donor and π-back-donation complexes: ferrous tacn [FeII(tacn)2]Br2, ferrocyanide [FeII(CN)6]K4, ferric tacn [FeIII(tacn)2]Br3 and ferricyanide [FeIII(CN)6]K3. From these spectra metal–ligand covalencies can be extracted using a charge-transfer multiplet model, without previous information from the L-edge XAS experiment. A direct comparison of L-edge XAS and Kα RIXS spectra show that the latter reaches additional final states, e.g., when exciting into the eg (σ*) orbitals, and the splitting between final states of different symmetry provides an extra dimension that makes Kα RIXS a more sensitive probe of σ-bonding. Another key difference between L-edge XAS and Kα RIXS is the π-back-bonding features in ferro- and ferricyanide that are significantly more intense in L-edge XAS compared to Kα RIXS. This shows that two methods are complementary in assigning electronic structure. The Kα RIXS approach can thus be used as a stand-alone method, in combination with L-edge XAS for strongly covalent systems that are difficult to probe by UV/vis spectroscopy, or as an extension to conventional absorption spectroscopy for a wide range of transition metal enzymes and catalysts.
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| 7. |
- Seibert, M. Marvin, et al.
(författare)
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Single mimivirus particles intercepted and imaged with an X-ray laser
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7332, s. 78-81
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Tidskriftsartikel (refereegranskat)abstract
- X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
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| 8. |
- Thapper, Anders, et al.
(författare)
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The Unperturbed Oxo-Sulfido Functional Group cis-Mo(VI)OS, Related to that in the Xanthine Oxidase Family of Molybdoenzymes: Synthesis, Structural Characterization and Reactivity Aspects
- 1999
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 38:18, s. 4104-4114
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Tidskriftsartikel (refereegranskat)abstract
- The oxo-sulfido functional group cis-MoVIOS is essential to the activity of the xanthine oxidase family of enzymes but has proven elusive to synthesis in molecules containing no other four-electron ligands. A direct route to molecules containing this group has been achieved. The reaction system [MoO2(OSiPh3)2]/L in dichloromethane yields the complexes [MoVIO2(OSiPh3)2L] (L = phen (1), Me4phen (2), 4,4'-Me2bpy (3), 5,5'-Me2bpy (4), 2 py (5)) (74-96%), which are shown to have a distorted octahedral structure of crystallographically imposed C2 symmetry (1, 5) with cis oxo and trans silyloxy ligands. The related reaction system [MoO3S]2-/2Ph3SiCl/L in acetonitrile affords the complexes [MoVIOS(OSiPh3)2L] (L = phen (6), Me4phen (7), 4,4'-Me2bpy (8), 5,5'-Me2bpy (9)) (36-69%). From the collective results of elemental analysis, mass spectrometry, 1H NMR, and X-ray structure determinations (6, 7), complexes 6-9 are shown to contain the cis-MoVIOS group in molecules with the same overall stereochemistry as dioxo complexes 1-5. The crystal structures of 6 and 7 exhibit O/S disorder, which was modeled in refinements with 50% site occupancies. The Mo=O (1.607(5) (6), 1.645(5) (7) Å) and Mo=S (2.257(3) (6), 2.203(2) (7) Å) bond distances obtained in this way are somewhat shorter and longer, respectively, than expected. Distances obtained by molybdenum EXAFS analysis using the GNXAS protocol for 6-9 (Mo=O 1.71-1.72 Å; Mo=S 2.18-2.19 Å) are considered more satisfactory and are in good agreement with EXAFS values for xanthine oxidase. Molybdenum K-edge data for 1 and 6-9 are reported. Reaction of 7 with Ph3P in dichloromethane results in sulfur abstraction and formation of [MoVOCl(OSiPh3)2(Me4phen)] (10), which has a distorted octahedral structure with cis O/Cl and cis silyloxy ligands. Sulfur rather than oxygen abstraction is favored by relative Mo=O/Mo=S bond strengths. Complexes 6-9 should allow exploration of the biologically significant cis-MoVIOS group.
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| 9. |
- Wilson, Samuel, et al.
(författare)
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Iron L-edge X-ray Absorption Spectroscopy of Oxy-Picket Fence Porphyrin : Electronic Structure of the Fe-O2 Bond
- 2013
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 135:3, s. 1124-1136
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structure of the Fe-O-2 center in oxy-hemoglobin and oxy-myoglobin is a long-standing issue in the field of bioinorganic chemistry. Spectroscopic studies have been complicated by the highly delocalized nature of the porphyrin, and calculations require interpretation of multi-determinant wave functions for a highly covalent metal site. Here, iron L-edge X-ray absorption spectroscopy, interpreted using a valence bond configuration interaction multiplet model, is applied to directly probe the electronic structure of the iron in the biomimetic Fe-O-2 heme complex [Fe(pfp)-(1-Melm)O-2] (pfp ("picket fence porphyrin") = meso-tetra(alpha,alpha,alpha,alpha-o-pivalamidophenyl)porphyrin or TpivPP). This method allows separate estimates of sigma-donor, pi-donor, and pi-acceptor interactions through ligand-to-metal charge transfer and metal-to-ligand charge transfer mixing pathways. The L-edge spectrum of [Fe(pfp)(1-MeIm)O-2] is further compared to those of [Fe-II(pfp)(1-MeIm)(2)], [Fe-II(pfp)], and [Fe-III(tpp)(ImH)(2)]Cl (tpp = meso-tetraphenylporphyrin) which have Fe-II S = 0, Fe-II S = 1, and Fe-III S = 1/2 ground states, respectively. These serve as references for the three possible contributions to the ground state of oxy-pfp. The Fe-O-2 pfp site is experimentally determined to have both significant sigma-donation and a strong pi-interaction of the O-2 with the iron, with the latter having implications with respect to the spin polarization of the ground state.
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| 10. |
- Yan, James J., et al.
(författare)
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Resonant inelastic X-ray scattering determination of the electronic structure of oxyhemoglobin and its model complex
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:8, s. 2854-2859
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structure of the heme oxy-iron center in oxyhemoglobin and oxymyoglobin has been the subject of debate for decades. Various experimental and computational methods have been used to study this system, leading to conflicting conclusions. This study uses X-ray spectroscopy to directly probe the iron center in the highly delocalized oxyhemoglobin and its model compound to define the electronic structure and understand the differences between the protein and the model. This study settles a longstanding debate in bioinorganic chemistry and provides insight into heme iron–oxygen binding, the key first step in many biocatalytic processes.Hemoglobin and myoglobin are oxygen-binding proteins with S = 0 heme FeO28 active sites. The electronic structure of these sites has been the subject of much debate. This study utilizes Fe K-edge X-ray absorption spectroscopy (XAS) and 1s2p resonant inelastic X-ray scattering (RIXS) to study oxyhemoglobin and a related heme FeO28 model compound, [(pfp)Fe(1-MeIm)(O2)] (pfp = meso-tetra(α,α,α,α-o-pivalamido-phenyl)porphyrin, or TpivPP, 1-MeIm = 1-methylimidazole) (pfpO2), which was previously analyzed using L-edge XAS. The K-edge XAS and RIXS data of pfpO2 and oxyhemoglobin are compared with the data for low-spin FeII and FeIII [Fe(tpp)(Im)2]0/+ (tpp = tetra-phenyl porphyrin) compounds, which serve as heme references. The X-ray data show that pfpO2 is similar to FeII, while oxyhemoglobin is qualitatively similar to FeIII, but with significant quantitative differences. Density-functional theory (DFT) calculations show that the difference between pfpO2 and oxyhemoglobin is due to a distal histidine H bond to O2 and the less hydrophobic environment in the protein, which lead to more backbonding into the O2. A valence bond configuration interaction multiplet model is used to analyze the RIXS data and show that pfpO2 is dominantly FeII with 6–8% FeIII character, while oxyhemoglobin has a very mixed wave function that has 50–77% FeIII character and a partially polarized Fe–O2 Ï€-bond.
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