| 1. |
- Gopakumar, Geethanjali, 1992-, et al.
(författare)
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X-ray Induced Fragmentation of Protonated Cystine
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Protein structure determination using high-intensity X-ray sources induces damage in the protein. Disulfide bridges, formed between two cysteine amino acid residues stabilize the protein structure. Owing to the higher absorption cross-section of sulfur for X-ray photons, and a large number of electrons released from sulfur atoms, these disulfide bridges are hot spots for a higher level of noise in structural studies. But it is yet to be understood how exactly the damage occurs through the interaction of the disulfide bridges with photons. Here we study the fragmentation of protonated cystine in the gas phase, which is the dimer of cysteine, by irradiation with X-rays across the sulfur L-edge using an electrospray ionization source (ESI) in combination with an ion trap. This is complemented with the calculation of the sulfur NEXAFS spectrum on the level of Restricted Open-Shell Configuration Interaction (ROCIS) and Density Functional Theory (DFT) calculations for molecular orbital visualization as well as Molecular Dynamics (MD) simulations for the fragmentation of triply charged cystine ions. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons by combining the experiments and simulations. The disulfide bridge breaks for resonant excitation at lower energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments formed subsequently break into smaller fragments.
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| 2. |
- Lejaeghere, Kurt, et al.
(författare)
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Reproducibility in density functional theory calculations of solids.
- 2016
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 351:6280, s. 1415-1422
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Tidskriftsartikel (refereegranskat)abstract
- The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.
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| 3. |
- Långberg, Marie, et al.
(författare)
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Characterization of Native Oxide and Passive Film on Austenite/Ferrite Phases of Duplex Stainless Steel Using Synchrotron HAXPEEM
- 2019
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Ingår i: Journal of the Electrochemical Society. - : Electrochemical Society. - 0013-4651 .- 1945-7111. ; 166:11, s. C3336-C3340
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Tidskriftsartikel (refereegranskat)abstract
- A new measurement protocol was used for microscopic chemical analysis of surface oxide films with lateral resolution of 1 mu m. The native air-formed oxide and an anodic passive film on austenite and ferrite phases of a 25Cr-7Ni super duplex stainless steel were investigated using synchrotron hard X-ray photoemission electron microscopy (HAXPEEM). Pre-deposited Pt-markers, in combination with electron backscattering diffraction mapping (EBSD), allowed analysis of the native oxide on individual grains of the two phases and the passive film formed on the same area after electrochemical polarization of the sample. The results showed a certain difference in the composition of the surface films between the two phases. For the grains with (001) crystallographic face // sample surface, the native oxide film on the ferrite contained more Cr oxide than the austenite. Anodic polarization up to 1000 mV/(Ag/AgCl) in 1M NaCl solution at room temperature resulted in a growth of the Cr- and Fe-oxides, diminish of Cr-hydroxide, and an increased proportion of Fe3+ species. by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 License (CC BY, http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse of the work in any medium, provided the original work is properly cited.
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| 4. |
- Långberg, Marie, 1988-, et al.
(författare)
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Lateral variation of the native passive film on super duplex stainless steel resolved by synchrotron hard X-ray photoelectron emission microscopy
- 2020
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Ingår i: Corrosion Science. - Stockholm, : Elsevier BV. - 0010-938X .- 1879-0496. ; 174
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Tidskriftsartikel (refereegranskat)abstract
- A native passive film on 25Cr-7Ni super duplex stainless steel was analyzed using synchrotron hard X-ray photoemission electron microscopy, focusing on variations between individual grains of ferrite and austenite phases. The film consists of an oxide inner layer and an oxyhydroxide outer layer, in total 2.3 nm thick. The Cr content is higher in the outer than the inner layer, ca. 80 % on average. The Cr content is higher on ferrite than austenite, whereas the thickness is rather uniform. The grain orientation has a small but detectable influence, ferrite (111) grains have a lower Cr content than other ferrite grains.
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| 5. |
- Grånäs, Oscar, 1979-, et al.
(författare)
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Femtosecond fragmentation of CS2 after sulfur 1s ionization : interplay between Auger cascade decay, charge delocalization, and nuclear motion
- 2020
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Ingår i: Journal of Physics B. - : IOP PUBLISHING LTD. - 0953-4075 .- 1361-6455. ; 53:24
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Tidskriftsartikel (refereegranskat)abstract
- We present a combined experimental and theoretical study of the fragmentation of molecular CS2 after sulfur 1s Auger cascade decay, consisting of electron-multi-ion coincidence spectra of charged fragments and theoretical simulations combining density functional theory and molecular dynamics. On the experimental side, a procedure for a complete determination of all sets of ions formed is described. For many of the fragmentation channels, we observed a higher charge in one of the sulfur atoms than the other atoms. Based on these observations and the theoretical simulations where the time scale of the nuclear motion and decay is taken into account, we propose that KLL Auger decay after the 1s core hole creation, via 2p double hole states, results in highly charged and strongly repulsive states with one localized core hole. These localized core holes are sufficiently long-lived that some will decay after fragmentation of the molecular ion, thereby efficiently impeding charge exchange between the fragments.
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| 6. |
- Grånäs, Oscar, 1979-, et al.
(författare)
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Ultrafast modification of the electronic structure of a correlated insulator
- 2022
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Ingår i: Physical Review Research. - : American Physical Society. - 2643-1564. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- A nontrivial balance between Coulomb repulsion and kinematic effects determines the electronic structure of correlated electron materials. The use of electromagnetic fields strong enough to rival these native microscopic interactions allows us to study the electronic response as well as the time scales and energies involved in using quantum effects for possible applications. We use element-specific transient x-ray absorption spectroscopy and high-harmonic generation to measure the response to ultrashort off-resonant optical fields in the prototypical correlated electron insulator NiO. Surprisingly, fields of up to 0.22 V/angstrom lead to no detectable changes in the correlated Ni 3d orbitals contrary to previous predictions. A transient directional charge transfer is uncovered, a behavior that is captured by first-principles theory. Our results highlight the importance of retardation effects in electronic screening and pinpoints a key challenge in functionalizing correlated materials for ultrafast device operation.
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| 7. |
- Kissavos, Andreas E., et al.
(författare)
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Thermodynamics of ordered and disordered phases in the binary Mo-Ru system
- 2007
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 75:18
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Tidskriftsartikel (refereegranskat)abstract
- We have performed ab initio calculations of the mixing enthalpy for the Mo-Ru alloy system. Both completely random alloys on the fcc, bcc, and hcp lattices as well as ordered and partially ordered structures based on the hcp lattice and a sigma phase have been examined. Further, we have performed a ground-state search for the Ru-rich region using ab initio derived effective interactions, and find a series of structures below the tie line of the simple compounds. Using the structures from this ground-state search, we are able to make an estimation of the contribution to the total energy due to ordering effects in this system. We find unusually large deviations between calculated and experimental values of the mixing enthalpy for Ru-rich hcp alloys. Our calculations indicate, in agreement with experiment, that there are ordering trends in the system. However, even under assumption of maximal order theoretical results differ substantially from the experiment. Possible reasons for the disagreement are discussed.
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| 8. |
- Peters, L., et al.
(författare)
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Correlation effects and orbital magnetism of Co clusters
- 2016
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Ingår i: PHYSICAL REVIEW B. - 2469-9950. ; 93:22
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Tidskriftsartikel (refereegranskat)abstract
- Recent experiments on isolated Co clusters have shown huge orbital magnetic moments in comparison with their bulk and surface counterparts. These clusters hence provide the unique possibility to study the evolution of the orbital magnetic moment with respect to the cluster size and how competing interactions contribute to the quenching of orbital magnetism. We investigate here different theoretical methods to calculate the spin and orbital moments of Co clusters, and assess the performances of the methods in comparison with experiments. It is shown that density-functional theory in conventional local density or generalized gradient approximations, or even with a hybrid functional, severely underestimates the orbital moment. As natural extensions/corrections, we considered the orbital polarization correction, the LDA+U approximation as well as the LDA+DMFT method. Our theory shows that of the considered methods, only the LDA+DMFT method provides orbital moments in agreement with experiment, thus emphasizing the importance of dynamic correlations effects for determining fundamental magnetic properties of magnets in the nanosize regime.
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| 9. |
- Ueda, K., et al.
(författare)
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Adsorption and Reaction of CO and NO on Ir(111) under Near Ambient Pressure Conditions
- 2016
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Ingår i: Topics in Catalysis. - : Springer Science and Business Media LLC. - 1022-5528 .- 1572-9028. ; 59:5-7, s. 487-496
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Tidskriftsartikel (refereegranskat)abstract
- The adsorption and reaction of CO and NO on Ir(111) have been studied by near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) together with low-energy electron diffraction, scanning tunneling microscopy, and mass spectroscopy (MS). Under both ultrahigh vacuum (UHV) and NAP conditions CO molecules occupy on-top sites of the Ir(111) surface at room temperature (RT) by forming two-dimensional clusters. Exposure to NO under UHV conditions at RT induces partially dissociative adsorption, while NAP NO exposure leads to a Ir(111) surface that is covered by molecular NO. We conducted in-operando NAP-XPS/MS observation of the NO + 13CO reaction under a NAP condition as a function of temperature. Below 210 °C adsorption of NO is inhibited by CO, while above 210 °C the CO inhibition is released due to partial desorption of CO and dissociative adsorption of NO starts to occur leading to associative formation of N2. Under the most active condition studied here the Ir surface is covered by a dense co-adsorption layer consisting of on-top CO, atomic N and O, which suggests that this reaction is not a NO-dissociation-limited process but a N2/CO2 formation-limited process.
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