Computational studies of the x-ray scattering properties of laser aligned stilbene

Debnarova, Andrea; Techert, Simone; Schmatz, Stefan

doi:10.1063/1.3523569

Cited by 14 publications

(15 citation statements)

References 29 publications

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“…A related area is scattering from aligned molecules, which aims to minimize rotational averaging and thus enable measurement of scattering factors in the molecular frame. This has been considered theoretically [37][38][39] and realized experimentally using electrons 40 and X-rays 17 .…”

Section: Introductionmentioning

confidence: 99%

Elastic X-ray scattering from state-selected molecules

Northey

Carrascosa

Schäfer

et al. 2016

The Journal of Chemical Physics

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The characterization of electronic, vibrational, and rotational states using elastic (coherent) X-ray scattering is considered. The scattering is calculated directly from complete active space self-consistent field level ab initio wavefunctions for H molecules in the ground-state XΣ and first-excited EFΣ electronic states. The calculated scattering is compared to recent experimental measurements [Y.-W. Liu et al., Phys. Rev. A 89, 014502 (2014)], and the influence of vibrational and rotational states on the observed signal is examined. The scaling of the scattering calculations with basis set is quantified, and it is found that energy convergence of the ab initio calculations is a good indicator of the quality of the scattering calculations.

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Section: Introductionmentioning

confidence: 99%

Elastic X-ray scattering from state-selected molecules

Northey

Carrascosa

Schäfer

et al. 2016

The Journal of Chemical Physics

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“…23,24 An atomic-level structural interpretation has so far been complicated by the lack of methods that validate structural models of biomolecules against anisotropic TR-WAXS patterns. A number of studies focussed on predicting anisotropic patterns from X-ray scattering 22,[25][26][27][28][29] or electron diffraction, 30 with a focus on small molecules, such as NaI or I 2 . These calculations showed that the patterns reduce to two independent components at low excitation intensity.…”

Section: Introductionmentioning

confidence: 99%

Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics

Brinkmann

Hub

2015

The Journal of Chemical Physics

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Time-resolved wide-angle X-ray scattering (TR-WAXS) is an emerging experimental technique used to track chemical reactions and conformational transitions of proteins in real time. Thanks to increased time resolution of the method, anisotropic TR-WAXS patterns were recently reported, which contain more structural information than isotropic patterns. So far, however, no method has been available to compute anisotropic WAXS patterns of biomolecules, thus limiting the structural interpretation. Here, we present a method to compute anisotropic TR-WAXS patterns from molecular dynamics simulations. The calculations accurately account for scattering of the hydration layer and for thermal fluctuations. For many photo-excitable proteins, given a low intensity of the excitation laser, the anisotropic pattern is described by two independent components: (i) an isotropic component, corresponding to common isotropic WAXS experiments and (ii) an anisotropic component depending on the orientation of the excitation dipole of the solute. We present a set of relations for the calculation of these two components from experimental scattering patterns. Notably, the isotropic component is not obtained by a uniform azimuthal average on the detector. The calculations are illustrated and validated by computing anisotropic WAXS patterns of a spheroidal protein model and of photoactive yellow protein. Effects due to saturated excitation at high intensities of the excitation laser are discussed, including opportunities to extract additional structural information by modulating the laser intensity.

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“…Theoretical models for anisotropic scattering patterns arising from an ensemble of unidirectionally oriented molecules have previously been developed [19,[37][38][39][40][41]. Here, we briefly present a theoretical description of anisotropic x-ray scattering patterns based on the derivation by Williamson et al [41].…”

Section: Theoretical Description Of Anisotropic X-ray Scattering Patternmentioning

confidence: 99%

Rotational dephasing of a gold complex probed by anisotropic femtosecond x-ray solution scattering using an x-ray free-electron laser

Kim

Oang

et al. 2015

J. Phys. B: At. Mol. Opt. Phys.

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The orientational dynamics of a gold trimer complex in a solution are investigated by using anisotropic femtosecond x-ray solution scattering measured by an x-ray free-electron laser. A linearly polarized laser pulse preferentially excites molecules with transition dipoles oriented parallel to the laser polarization, leading to the transient alignment of excited molecules. Such photoselectively aligned molecules give rise to an anisotropic scattering pattern that has different profiles in parallel and perpendicular directions with respect to laser polarization. Anisotropic x-ray scattering patterns obtained from the transiently aligned molecules contain information on the molecular orientation. By monitoring the time evolution of the anisotropic scattering pattern, we probe the rotational dephasing dynamics of [Au(CN)2−]3 in a solution. We found that rotational dephasing of [Au(CN)2−]3 occurs with a time constant of 13 ± 4 ps. By contrast, time-resolved scattering data on FeCl3 in a water solution, which does not accompany any structural change and gives only the contributions of solvent heating, lacks any anisotropy in the scattering signal.

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Computational studies of the x-ray scattering properties of laser aligned stilbene

Cited by 14 publications

References 29 publications

Elastic X-ray scattering from state-selected molecules

Elastic X-ray scattering from state-selected molecules

Anisotropic time-resolved solution X-ray scattering patterns from explicit-solvent molecular dynamics

Rotational dephasing of a gold complex probed by anisotropic femtosecond x-ray solution scattering using an x-ray free-electron laser

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