| 1. |
- Ahlberg Gagnér, Viktor, 1989, et al.
(författare)
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Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments. © 2019, The Author(s).
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| 2. |
- Al-Khalili, A, et al.
(författare)
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Dissociative recombination cross section and branching ratios of protonated dimethyl disulfide and N-methylacetamide
- 2004
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 121:12, s. 5700-5708
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Tidskriftsartikel (refereegranskat)abstract
- Dimethyl disulfide (DMDS) and N-methylacetamide are two first choice model systems that represent the disulfide bridge bonding and the peptide bonding in proteins. These molecules are therefore suitable for investigation of the mechanisms involved when proteins fragment under electron capture dissociation (ECD). The dissociative recombination cross sections for both protonated DMDS and protonated N-methylacetamide were determined at electron energies ranging from 0.001 to 0.3 eV. Also, the branching ratios at 0 eV center-of-mass collision energy were determined. The present results give support for the indirect mechanism of ECD, where free hydrogen atoms produced in the initial fragmentation step induce further decomposition. We suggest that both indirect and direct dissociations play a role in ECD.
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| 3. |
- Allum, F., et al.
(författare)
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A localized view on molecular dissociation via electron-ion partial covariance
- 2022
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Ingår i: Communications Chemistry. - : Springer Science and Business Media LLC. - 2399-3669. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Inner-shell photoelectron spectroscopy provides an element-specific probe of molecular structure, as core-electron binding energies are sensitive to the chemical environment. Short-wavelength femtosecond light sources, such as Free-Electron Lasers (FELs), even enable time-resolved site-specific investigations of molecular photochemistry. Here, we study the ultraviolet photodissociation of the prototypical chiral molecule 1-iodo-2-methylbutane, probed by extreme-ultraviolet (XUV) pulses from the Free-electron LASer in Hamburg (FLASH) through the ultrafast evolution of the iodine 4d binding energy. Methodologically, we employ electron-ion partial covariance imaging as a technique to isolate otherwise elusive features in a two-dimensional photoelectron spectrum arising from different photofragmentation pathways. The experimental and theoretical results for the time-resolved electron spectra of the 4d(3/2) and 4d(5/2) atomic and molecular levels that are disentangled by this method provide a key step towards studying structural and chemical changes from a specific spectator site. Coincidence experiments at free-electron lasers enable time resolved site-specific investigations of molecular photochemistry at high signal rates, but isolating individual dissociation processes still poses a considerable technical challenge. Here, the authors use electron-ion partial covariance imaging to isolate otherwise elusive chemical shifts in UV-induced photofragmentation pathways of the prototypical chiral molecule 1-iodo-2-methylbutane.
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| 4. |
- Andersson, Jonas, et al.
(författare)
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Parametrization of energy sharing distributions in direct double photoionization of He
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- We present experimental results on the characteristic sharing of available excess energy, ranging from 11–221eV, between two electrons in single-photon direct double ionization of He. An effective parametrization of the sharing distributions is presented along with an empirical model that describes the complete shape of the distribution based on a single experimentally determinable parameter. The measured total energy sharing distributions are separated into two distributions representing the shake-off and knock-out parts by simulating the sharing distribution curves expected from a pure wave collapse after a sudden removal of the primary electron. In this way, empirical knock-out distributions are extracted and both the shake-off and knock-out distributions are parametrized. These results suggest a simple method that can be applied to other atomic and molecular systems to experimentally study important aspects of the direct double ionization process.
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| 5. |
- Andersson, Jonas, et al.
(författare)
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Triple ionization of atomic Cd involving 4p(-1) and 4s(-1) inner-shell holes
- 2015
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Ingår i: Physical Review A. - 1050-2947 .- 1094-1622. ; 92:2
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Tidskriftsartikel (refereegranskat)abstract
- The triple ionization spectrum of atomic Cd formed upon the removal of a 4p or a 4s inner-shell electron and subsequent Auger decays has been obtained at 200 eV photon energy. By using a versatile multielectron coincidence detection technique based on a magnetic bottle spectrometer in combination with multiconfiguration Dirac-Fock calculations, Auger cascades leading to tricationic final states have been analyzed and final-state configurations have been identified. The most prominent Auger cascades leading to the ground state of Cd3+ have been identified in good agreement with theory.
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| 6. |
- Andersson, Patrik U, 1970, et al.
(författare)
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Formation of Highly Rovibrationally Excited Ammonia from Dissociative Recombination of NH4
- 2010
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Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 1:17, s. 2519-2523
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Tidskriftsartikel (refereegranskat)abstract
- The internal energy distribution of ammonia formed in the dissociative recombination (DR) of NH4+ with electrons has been studied by an imaging technique at the ion storage ring CRYRING. The DR process resulted in the formation of NH3 + H (0.90 ± 0.01), with minor contributions from channels producing NH2 + H2 (0.05 ± 0.01) and NH2 + 2H (0.04 ± 0.02). The formed NH3 molecules were highly internally excited, with a mean rovibrational energy of 3.3 ± 0.4 eV, which corresponds to 70% of the energy released in the neutralization process. The internal energy distribution was semiquantitatively reproduced by ab initio direct dynamics simulations, and the calculations suggested that the NH3 molecules are highly vibrationally excited while rotational excitation is limited. The high internal excitation and the translational energy of NH3 and H will influence their subsequent reactivity, an aspect that should be taken into account when developing detailed models of the interstellar medium and ammonia-containing plasmas.
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| 7. |
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| 8. |
- Andersson, Åke, et al.
(författare)
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Indication of 310-Helix Structure in Gas-Phase Neutral Pentaalanine
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:4, s. 938-45
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 310-helix with two β-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.
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| 9. |
- Andersson, Åke, et al.
(författare)
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IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase
- 2021
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:34, s. 7449-7456
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Tidskriftsartikel (refereegranskat)abstract
- We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multi-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm(-1). Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.
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| 10. |
- Andersson, Åke, et al.
(författare)
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Single-photon hot-electron ionization of C70
- 2023
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Ingår i: Physical Review A. - 2469-9926 .- 2469-9934. ; 107:1
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Tidskriftsartikel (refereegranskat)abstract
- Gas phase C70 molecules have been ionized with single photons of energies between 16 and 70 eV, and the electron spectra measured with velocity map imaging in coincidence with the ions. The doubly ionized and unfragmented species was present at photon energies of 22 eV and up, and triply charged ions were present from 55 eV. The low-kinetic-energy parts of the spectra are explained with thermal emission of transient hot electrons. We propose a generally applicable mechanism, named resonance ionization shadowing, for the creation of hot electrons by absorption of above-threshold energy photons.
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