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1.
Struct Dyn ; 6(5): 054101, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31531387

RESUMO

We have performed a full-dimensional theoretical study of vibrationally resolved photoelectron emission from the valence shell of the water molecule by using an extension of the static-exchange density functional theory that accounts for ionization as well as for vibrational motion in the symmetric stretching, antisymmetric stretching, and bending modes. At variance with previous studies performed in centrosymmetric molecules, where vibrationally resolved spectra are mostly dominated by the symmetric stretching mode, in the present case, all three modes contribute to the calculated spectra, including intermode couplings. We have found that diffraction of the ejected electron by the various atomic centers is barely visible in the ratios between vibrationally resolved photoelectron spectra corresponding to different vibrational states of the remaining H2O+ cation (the so-called v-ratios), in contrast to the prominent oscillations observed in K-shell ionization of centrosymmetric molecules, including those that only contain hydrogen atoms around the central atoms, e.g., CH4. To validate the conclusions of our work, we have carried out synchrotron radiation experiments at the SOLEIL synchrotron and determined photoelectron spectra and v-ratios for H2O in a wide range of photon energies, from threshold up to 150 eV. The agreement with the theoretical predictions is good.

2.
Langmuir ; 35(36): 11859-11871, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31453695

RESUMO

The surface chemistry of gold nanoparticles produced by the pulsed laser ablation in liquids method is investigated by X-ray photoelectron spectroscopy (XPS). The presence of surface oxide expected on these systems is investigated using synchrotron radiation in conditions close to their original state in solvent but free from substrate or solvent effects which could affect the interpretation of spectroscopic observations. For that purpose we performed the experiment on a controlled free-standing nanoparticle beam produced by combination of an atomizer and an aerodynamic lens system. These results are compared with those obtained by the standard situation of deposited nanoparticles on silicon substrate. An accurate analysis based on Bayesian statistics concludes that the existence of oxide in the free-standing conditions cannot be solely confirmed by the recorded core-level 4f spectra. If present, our data indicate an upper limit of 2.15 ± 0.68% of oxide. However, a higher credence to the hypothesis of its existence is brought by the structureless valence profile of the free-standing beam. Moreover, the cross-comparison with the deposited nanoparticles case clearly evidences an important misleading substrate effect. Experiment with free-standing nanoparticles is then demonstrated to be the right way to further investigate oxidation states on Au nanoparticles.

3.
J Phys Chem A ; 123(5): 1062-1068, 2019 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-30609369

RESUMO

Recent thorough experimental activity aiming to generate high harmonics in the SF6 molecules requires the knowledge of, on one hand, accurate valence-shell photoionization cross sections and phases, from a threshold up to a few tens of eV, where resonances are likely to appear, and, on the other hand, the effect of the nuclear vibrational dynamics on the process. In this work, we have experimentally determined and theoretically evaluated vibrationally resolved photoionization cross sections of SF6 up to 80 eV photon energies, with an emphasis on the E2T1u channel, for which vibrational progressions are fully resolved in the experiment. Our results reveal the presence of shape resonances due to excitation to SF6 virtual states lying just above the ionization threshold, in agreement with previous synchrotron radiation work and theoretical calculations. More interestingly, our calculations also disclose resonance features at photoelectron energies as high as 40-50 eV, which are due to the transient confinement of the ejected electron in the octahedral cage formed by the peripheral F atoms. In the vicinity of all resonances, including those due to confinement, the calculated ionization phases experience an excursion of about π or π/2 and significantly depend on the final vibrational state of the remaining cation. Both effects should be taken into account to correctly interpret ongoing high-harmonic generation work in SF6. A similar behavior is expected for other symmetric molecules containing a central atom, such as BF3, CF4, and the like.

4.
J Chem Phys ; 149(14): 144302, 2018 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-30316287

RESUMO

Ionization of the I 3d, 4s, and 4p orbitals in methyl iodide (CH3I) has been studied by using synchrotron radiation to measure the total ion yield and by recording photoelectron spectra with linearly polarized radiation in two polarization orientations. The complete photoelectron spectrum of CH3I has been recorded at several photon energies, and bands due to the C 1s, I 3d, 4s, 4p, and 4d atomic-like orbitals, as well as the molecular orbitals, have been observed and assigned. In the vicinity of the I 3d5/2 and 3d3/2 ionization thresholds at 626.8 and 638.3 eV, respectively, the ion yield displays weak structure in the pre-edge region due to transitions into valence or Rydberg states, and, at higher energies, a shoulder and a broad maximum attributed to the I 3d5/2 → εf and the I 3d3/2 → εf shape resonances, respectively. The absorption spectrum calculated using time-dependent density functional theory, within the Tamm-Dancoff approximation, has allowed assignments to be proposed for the valence and Rydberg states. The Stieltjes imaging technique has been used to simulate the absorption spectrum above the ionization threshold and indicates that transitions into the f(l = 3) continuum channel dominate. This conclusion has been corroborated by a Continuum Multiple Scattering-Xα (CMS-Xα) calculation. The asymmetric broadening of the photoelectron bands associated with the I 3d orbital, due to post collision interaction, is taken into account in our experimental analysis. Experimentally derived photoelectron anisotropy parameters for the I 3d orbital are in good agreement with the theoretical predictions obtained with the CMS-Xα approach. The I 3d shake-up/shake-off photoelectron spectrum has been recorded, and assignments have been proposed for several of the satellites. The M4N45N45 and M5N45N45 Auger electron yields have been measured, and that for the M5N45N45 decay exhibits a maximum due to interchannel coupling between the 3d5/2 and 3d3/2 continua. The photoelectron band associated with the I 4p orbital has an unusual appearance. Based upon previous theoretical work for the analogous Xe 4p orbital, it appears that the initial I 4p-1 hole state decays rapidly through Coster-Kronig and super-Coster-Kronig transitions. This leads to a redistribution of the spectral intensity associated with the I 4p orbital and results in a photoelectron spectrum containing a single structured band together with an extended continuum. Another continuum is observed on the high binding energy side of the peak due to the 4s orbital, and we assign this to super-Coster-Kronig transitions into the 4p-14d-1 continuum.

5.
Sci Data ; 5: 180201, 2018 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-30277481

RESUMO

Fluctuation X-ray scattering (FXS) is an emerging experimental technique in which solution scattering data are collected using X-ray exposures below rotational diffusion times, resulting in angularly anisotropic X-ray snapshots that provide several orders of magnitude more information than traditional solution scattering data. Such experiments can be performed using the ultrashort X-ray pulses provided by a free-electron laser source, allowing one to collect a large number of diffraction patterns in a relatively short time. Here, we describe a test data set for FXS, obtained at the Linac Coherent Light Source, consisting of close to 100 000 multi-particle diffraction patterns originating from approximately 50 to 200 Paramecium Bursaria Chlorella virus particles per snapshot. In addition to the raw data, a selection of high-quality pre-processed diffraction patterns and a reference SAXS profile are provided.


Assuntos
Phycodnaviridae , Espalhamento a Baixo Ângulo , Difração de Raios X
6.
J Chem Phys ; 149(9): 094304, 2018 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-30195315

RESUMO

Auger electron spectra following excitation or ionization of the I 3d level in CH3I have been recorded with horizontally or vertically plane polarized synchrotron radiation. These spectra have enabled the Auger electron angular distributions, as characterized by the ß parameter, to be determined. The I 3d photoionization partial cross section of CH3I has been calculated with the continuum multiple scattering approach, and the results show that in the photon energy range over which Auger spectra were measured, the I 3d cross section exhibits an atomic-like behavior and is dominated by transitions into the εf continuum channel. In this limit, the theoretical value of the alignment parameter (A20) characterizing the core ionized state in an atom becomes constant, independent of photon energy. This theoretical value has been used to obtain the Auger electron intrinsic anisotropy parameters (α2) from the ß parameters extracted from our normal (non-resonant) molecular Auger spectra. The resulting anisotropy parameters for the M45N45N45 transitions in CH3I have been compared to those calculated for the corresponding transitions in xenon, and the experimental and theoretical results are in good agreement. Anisotropy parameters have also been measured for the M45N1N45, M45N23N45, and M45N45O23 transitions. For the M45N1N45 and M45N23N45 Auger decays in CH3I, the experimentally derived angular distributions do not exhibit the strong dependence on the final ionic state that is predicted for these transitions in xenon. Resonantly excited Auger spectra have been recorded at 620.4 and 632.0 eV, coinciding with the I 3d5/2 → σ* and 3d3/2 → σ* transitions, respectively. The resulting Auger electron angular distributions for the M4N45N45 and M5N45N45 decays were found to exhibit a higher anisotropy than those for the normal process. This is due to the larger photo-induced alignment in the neutral core excited state. For a particular Auger transition, the Auger electron kinetic energy measured in the resonantly excited spectrum is higher than that in the normal spectrum. This shift, due to the screening provided by the electron excited into the σ* orbital, has been rationalized by calculating orbital ionization energies of I 3d excited and I 3d ionized states in CH3I.

7.
Sci Adv ; 4(8): eaat3962, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30151427

RESUMO

Autoionizing resonances are paradigmatic examples of two-path wave interferences between direct photoionization, which takes a few attoseconds, and ionization via quasi-bound states, which takes much longer. Time-resolving the evolution of these interferences has been a long-standing goal, achieved recently in the helium atom owing to progress in attosecond technologies. However, already for the hydrogen molecule, similar time imaging has remained beyond reach due to the complex interplay between fast nuclear and electronic motions. We show how vibrationally resolved photoelectron spectra of H2 allow one to reconstruct the associated subfemtosecond autoionization dynamics by using the ultrafast nuclear dynamics as an internal clock, thus forgoing ultrashort pulses. Our procedure should be general for autoionization dynamics in molecules containing light nuclei, which are ubiquitous in chemistry and biology.

8.
J Phys Chem Lett ; 9(13): 3604-3611, 2018 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-29902010

RESUMO

We report an investigation of lead halide perovskite CH3NH3PbBr3 nanocrystals and associated ligand molecules by combining several different state-of-the-art experimental techniques, including synchrotron radiation-based XPS and VUV PES of free-standing nanocrystals isolated in vacuum. By using this novel approach for perovskite materials, we could directly obtain complete band alignment to vacuum of both CH3NH3PbBr3 nanocrystals and the ligands widely used in their preparation. We discuss the possible influence of the ligand molecules to apparent perovskite properties, and we compare the electronic properties of nanocrystals to those of bulk material. The experimental results were supported by DFT calculations.

9.
Rev Sci Instrum ; 89(3): 035112, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29604777

RESUMO

The Laser Applications in Materials Processing (LAMP) instrument is a new end-station for soft X-ray imaging, high-field physics, and ultrafast X-ray science experiments that is available to users at the Linac Coherent Light Source (LCLS) free-electron laser. While the instrument resides in the Atomic, Molecular and Optical science hutch, its components can be used at any LCLS beamline. The end-station has a modular design that provides high flexibility in order to meet user-defined experimental requirements and specifications. The ultra-high-vacuum environment supports different sample delivery systems, including pulsed and continuous atomic, molecular, and cluster jets; liquid and aerosols jets; and effusive metal vapor beams. It also houses movable, large-format, high-speed pnCCD X-ray detectors for detecting scattered and fluorescent photons. Multiple charged-particle spectrometer options are compatible with the LAMP chamber, including a double-sided spectrometer for simultaneous and even coincident measurements of electrons, ions, and photons produced by the interaction of the high-intensity X-ray beam with the various samples. Here we describe the design and capabilities of the spectrometers along with some general aspects of the LAMP chamber and show some results from the initial instrument commissioning.

10.
Sci Data ; 3: 160060, 2016 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-27479754

RESUMO

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.


Assuntos
Mimiviridae , Difração de Raios X , Algoritmos , Simulação por Computador , Cristalografia por Raios X , Coleta de Dados , Elétrons , Processamento de Imagem Assistida por Computador , Imagem Tridimensional , Lasers , Modelos Teóricos , Tamanho da Partícula , Espalhamento de Radiação , Raios X
11.
Sci Data ; 3: 160061, 2016 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-27479842

RESUMO

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.


Assuntos
Ciclo do Carbono , Halothiobacillus/ultraestrutura , Organelas , Halothiobacillus/metabolismo , Organelas/ultraestrutura , Raios X
12.
Sci Data ; 3: 160058, 2016 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-27479514

RESUMO

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.


Assuntos
Lasers , Difração de Raios X , Células , Cristalografia por Raios X , Cianobactérias , Elétrons , Modelos Moleculares , Modelos Teóricos , Nanopartículas , Proteínas , Pulso Arterial , Fatores de Tempo , Raios X
13.
Opt Express ; 24(11): 11768-81, 2016 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-27410102

RESUMO

We built a two-mirror based X-ray split and delay (XRSD) device for soft X-rays at the Linac Coherent Light Source free electron laser facility. The instrument is based on an edge-polished mirror design covering an energy range of 250 eV-1800 eV and producing a delay between the two split pulses variable up to 400 femtoseconds with a sub-100 attosecond resolution. We present experimental and simulation results regarding molecular dissociation dynamics in CH3I and CO probed by the XRSD device. We observed ion kinetic energy and branching ratio dependence on the delay times which were reliably produced by the XRSD instrument.

14.
Struct Dyn ; 3(4): 043207, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27051675

RESUMO

Ultrafast electron transfer in dissociating iodomethane and fluoromethane molecules was studied at the Linac Coherent Light Source free-electron laser using an ultraviolet-pump, X-ray-probe scheme. The results for both molecules are discussed with respect to the nature of their UV excitation and different chemical properties. Signatures of long-distance intramolecular charge transfer are observed for both species, and a quantitative analysis of its distance dependence in iodomethane is carried out for charge states up to I(21+). The reconstructed critical distances for electron transfer are in good agreement with a classical over-the-barrier model and with an earlier experiment employing a near-infrared pump pulse.

15.
Phys Chem Chem Phys ; 18(4): 3214-22, 2016 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-26744172

RESUMO

Vibrationally resolved photoionization of the 2a1 orbital in methane has been studied both experimentally and theoretically, over a wide range of photon energies (40-475 eV). A vibrational progression associated with the symmetric stretch mode of the 2a1(-1) single-hole state was observed in the experimental photoelectron spectra. Individual vibrational sub-states of the spectra were found to be best modeled by asymmetric line-shapes with linewidths gradually increasing with the vibrational quantum number. This indicates the occurrence of a pre-dissociation process for the involved ionic state, discussed here in detail. Finally, diffraction patterns were observed in the vibrational branching ratios for the first three vibrational sub-states ("v-ratios") of the experimental photoelectron spectra. They are found to be in excellent qualitative agreement with those obtained from ab initio models. Compared with previous studies of the 1a1(-1) core-shell photoionization of methane, the period of oscillation of the v-ratios is found to be very different and the phases are of opposite signs. This suggests a strong interplay between the electron diffraction and interference effects inside the molecular potential.

16.
Nat Commun ; 6: 8199, 2015 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-26354002

RESUMO

Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a 'molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

17.
J Synchrotron Radiat ; 22(3): 492-7, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25931058

RESUMO

The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump-probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.

18.
Phys Rev Lett ; 114(9): 098102, 2015 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-25793853

RESUMO

We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.


Assuntos
Imagem Tridimensional/métodos , Mimiviridae/ultraestrutura , Difração de Raios X/métodos , Algoritmos , Elétrons , Lasers , Difração de Raios X/instrumentação
19.
Nat Commun ; 6: 5704, 2015 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-25669616

RESUMO

There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.


Assuntos
Cianobactérias/citologia , Imagem Tridimensional/métodos , Lasers , Análise de Célula Única/métodos , Aerossóis , Confiabilidade dos Dados , Elétrons , Injeções , Fenômenos Ópticos , Fótons , Difração de Raios X , Raios X
20.
MedEdPublish ; 4(1)2015.
Artigo em Inglês | MEDLINE | ID: mdl-27500163

RESUMO

BACKGROUND: The USMLE Step 1 score helps differentiate applicants for competitive residency programs. Students frequently ask medical educators how to prepare for this high-stakes exam. Multiple resources exist such as books, training programs, and question banks. The purpose of this study is to provide medical educators with data on which resources correlate with higher exam scores. METHODS: 164 medical students at West Virginia University School of Medicine were given a survey following the completion of Step 1. The survey contained questions about resources used and exam date. De-identified data was paired with class quartile rankings and Step 1 scores. Average Step 1 scores were calculated for each resource and a student's t-test was used to compare between groups. Test dates were also broken into quintiles and average Step 1 scores were compared between groups. RESULTS: Students who used the USMLE World question bank had higher Step 1 scores (M=229, SE=1.4) compared to students who did not use this resource (M=215, SE=4.2). Commercial preparation courses were not associated with improved scores. The timing of when the exam was taken was also not associated with significant differences between scores. CONCLUSIONS: Interactive study options offer the best choice to improve USMLE Step 1 scores.

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