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1.
Struct Dyn ; 6(4): 044102, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31372369

RESUMO

Theoretical and experimental methodologies that can characterize electronic and nuclear dynamics, and the coupling between the two, are needed to understand photoinduced charge transfer in molecular building blocks used in organic photovoltaics. Ongoing developments in ultrafast pump-probe techniques such as time-resolved X-ray absorption spectroscopy, using an X-ray free electron laser in combination with an ultraviolet femtosecond laser, present desirable probes of coupled electronic and nuclear dynamics. In this work, we investigate the charge transfer dynamics of a donor-acceptor pair, which is widely used as a building block in low bandgap block copolymers for organic photovoltaics. We simulate the dynamics of the benzothiadiazole-thiophene molecule upon photoionization with a vacuum ultraviolet (VUV) pulse and study the potential of probing the subsequent charge dynamics using time-resolved X-ray absorption spectroscopy. The photoinduced dynamics are calculated using on-the-fly nonadiabatic molecular dynamics simulations based on Tully's Fewest Switches Surface Hopping approach. We calculate the X-ray absorption spectrum as a function of time after ionization at the Hartree-Fock level. The changes in the time-resolved X-ray absorption spectrum at the sulfur K-edge reveal the ultrafast charge carrier dynamics in the molecule occurring on a femtosecond time scale. These theoretical findings anticipate that ultrafast time-resolved X-ray absorption spectroscopy using an X-ray probe in combination with a VUV pump offers a new approach to investigate the detailed dynamics of organic photovoltaic materials.

2.
J Phys Chem A ; 123(34): 7351-7360, 2019 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-31364853

RESUMO

We study the temporal evolution of the CH2O···ClF halogen-bonded dimer following vertical ionization out of outer-valence molecular orbitals on a femtosecond time scale, employing mixed quantum-classical molecular dynamics simulations. The charge density pattern in the ground state that is suitable for the formation of the ground-state halogen bond can be changed upon ionization. Depending on the molecular orbital that gets ionized, the change in the charge density transiently strengthens or weakens the halogen bond through altering the electrostatic interaction. A transient increase in the halogen bond strength is observed if the ionization enhances the positive charge on the halogen atom provided that the electron donor site possesses some negative charge. The evolution of the system following ionization is driven by energetic stabilization through transferring the electronic charge from the halogen bond acceptor/electron donor (CH2O) to the halogen bond donor/electron acceptor (ClF). The charge transfer oscillations are at the same time governed by the covalent bond vibrations.

3.
J Synchrotron Radiat ; 26(Pt 4): 1017-1030, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31274423

RESUMO

The xcalib toolkit has been developed to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence-dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. Theoretical CSDs are obtained using xatom, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core-hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. The optimization procedure employing the reinforcement learning technique can automatize and organize calibration procedures which, before, had been performed manually. xcalib has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with xatom, xcalib serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.

4.
Struct Dyn ; 6(2): 024101, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30915387

RESUMO

The dynamics of N 2 2 + dications after x-ray-induced Auger decay and their probing with a delayed infrared probe pulse are theoretically investigated based on a quantum-mechanical model including all relevant electronic states for which wave-packet calculations on ab-initio potential energy curves are performed. Our results demonstrate that the N 2 2 + yield modulated by the delay of the probe pulse contains dynamical information on the wave-packet evolution in the quasi-bound final electronic states. The Fourier transform of the calculated yield can be readily compared to experimental results [Fung et al., Nature 532, 471 (2016)] and good agreement of the main frequencies is found. Moreover, assignment of these frequencies to specific vibrational energy levels in the quasi-bound potentials is reported as well.

5.
J Chem Phys ; 150(4): 044505, 2019 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-30709301

RESUMO

Highly intense, sub-picosecond terahertz (THz) pulses can be used to induce ultrafast temperature jumps (T-jumps) in liquid water. A supercritical state of gas-like water with liquid density is established, and the accompanying structural changes are expected to give rise to time-dependent chemical shifts. We investigate the possibility of using extreme ultraviolet photoelectron spectroscopy as a probe for ultrafast dynamics induced by sub-picosecond THz pulses of varying intensities and frequencies. To this end, we use ab initio methods to calculate photoionization cross sections and photoelectron energies of (H2O)20 clusters embedded in an aqueous environment represented by point charges. The cluster geometries are sampled from ab initio molecular dynamics simulations modeling the THz-water interactions. We find that the peaks in the valence photoelectron spectrum are shifted by up to 0.4 eV after the pump pulse and that they are broadened with respect to unheated water. The shifts can be connected to structural changes caused by the heating, but due to saturation effects they are not sensitive enough to serve as a thermometer for T-jumped water.

6.
IUCrJ ; 5(Pt 6): 699-705, 2018 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-30443354

RESUMO

X-ray free-electron lasers (XFELs) broaden horizons in X-ray crystallography. Facilitated by the unprecedented high intensity and ultrashort duration of the XFEL pulses, they enable us to investigate the structure and dynamics of macromolecules with nano-sized crystals. A limitation is the extent of radiation damage in the nanocrystal target. A large degree of ionization initiated by the incident high-intensity XFEL pulse alters the scattering properties of the atoms leading to perturbed measured patterns. In this article, the effective-form-factor approximation applied to capture this phenomenon is discussed. Additionally, the importance of temporal configurational fluctuations at high intensities, shaping these quantities besides the average electron loss, is shown. An analysis regarding the applicability of the approach to targets consisting of several atomic species is made, both theoretically and via realistic radiation-damage simulations. It is concluded that, up to intensities relevant for XFEL-based nanocrystallography, the effective-form-factor description is sufficiently accurate. This work justifies treating measured scattering patterns using conventional structure-reconstruction algorithms.

7.
Nat Commun ; 9(1): 4200, 2018 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-30305630

RESUMO

An accurate description of the interaction of intense hard X-ray pulses with heavy atoms, which is crucial for many applications of free-electron lasers, represents a hitherto unresolved challenge for theory because of the enormous number of electronic configurations and relativistic effects, which need to be taken into account. Here we report results on multiple ionization of xenon atoms by ultra-intense (about 1019 W/cm2) femtosecond X-ray pulses at photon energies from 5.5 to 8.3 keV and present a theoretical model capable of reproducing the experimental data in the entire energy range. Our analysis shows that the interplay of resonant and relativistic effects results in strongly structured charge state distributions, which reflect resonant positions of relativistically shifted electronic levels of highly charged ions created during the X-ray pulse. The theoretical approach described here provides a basis for accurate modeling of radiation damage in hard X-ray imaging experiments on targets with high-Z constituents.

8.
Phys Rev Lett ; 120(22): 223201, 2018 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-29906148

RESUMO

We show that electron and ion spectroscopy reveals the details of the oligomer formation in Ar clusters exposed to an x-ray free electron laser (XFEL) pulse, i.e., chemical dynamics triggered by x rays. With guidance from a dedicated molecular dynamics simulation tool, we find that van der Waals bonding, the oligomer formation mechanism, and charge transfer among the cluster constituents significantly affect ionization dynamics induced by an XFEL pulse of moderate fluence. Our results clearly demonstrate that XFEL pulses can be used not only to "damage and destroy" molecular assemblies but also to modify and transform their molecular structure. The accuracy of the predictions obtained makes it possible to apply the cluster spectroscopy, in connection with the respective simulations, for estimation of the XFEL pulse fluence in the fluence regime below single-atom multiple-photon absorption, which is hardly accessible with other diagnostic tools.

9.
Nat Commun ; 9(1): 2142, 2018 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-29849173

RESUMO

Reaction pathways of biochemical processes are influenced by the dissipative electrostatic interaction of the reagents with solvent water molecules. The simulation of these interactions requires a parametrization of the permanent and induced dipole moments. However, the underlying molecular polarizability of water and its dependence on ions are partially unknown. Here, we apply intense terahertz pulses to liquid water, whose oscillations match the timescale of orientational relaxation. Using a combination of terahertz pump / optical probe experiments, molecular dynamics simulations, and a Langevin dynamics model, we demonstrate a transient orientation of their dipole moments, not possible by optical excitation. The resulting birefringence reveals that the polarizability of water is lower along its dipole moment than the average value perpendicular to it. This anisotropy, also observed in heavy water and alcohols, increases with the concentration of sodium iodide dissolved in water. Our results enable a more accurate parametrization and a benchmarking of existing and future water models.

10.
J Phys Chem A ; 122(23): 5211-5222, 2018 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-29776312

RESUMO

Ultrashort, high-intensity terahertz (THz) pulses, e.g., generated at free-electron laser facilities, allow for direct investigation as well as the driving of intermolecular modes in liquids like water and thus will deepen our understanding of the hydrogen bonding network. In this work, the temperature-jump (T-jump) of water induced by THz radiation is simulated for ten different THz frequencies in the range from 3 to 30 THz and five different pulse intensities in the range from 1 × 1011 to 5 × 1012 W/cm2 employing both ab initio molecular dynamics (AIMD) and force field molecular dynamics (FFMD) approaches. The most efficient T-jump can be achieved with 16 THz pulses. Three distinct T-jump mechanisms can be uncovered. For all cases, the T-jump mechanism proceeds within tens of femtoseconds (fs). For frequencies between 10 and 25 THz, most of the energy is initially transferred to the rotational degrees of freedom. Subsequently, the energy is redistributed to the translational and intramolecular vibrational degrees of freedom within a maximum of 500 fs. For the lowest frequencies considered (7 THz and below), translational and rotational degrees of freedom are heated within tens of fs as the THz pulse also couples to the intermolecular vibrations. Subsequently, the intramolecular vibrational modes are heated within a few hundred fs. At the highest frequencies considered (25 THz and above), vibrational and rotational degrees of freedom are heated within tens of fs, and energy redistribution to the translational degrees of freedom happens within several hundred fs. Both AIMD and FFMD simulations show a similar dependence of the T-jump on the frequency employed. However, the FFMD simulations overestimate the total energy transfer around the main peak and drop off too fast toward frequencies higher and lower than the main peak. These differences can be rationalized by missing elements, such as the polarizability, in the TIP4P/2005f force field employed. The feasibility of performing experiments at the studied frequencies and intensities as well as important issues such as energy efficiency, penetration depth, and focusing are discussed.

11.
Phys Rev Lett ; 120(12): 123001, 2018 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-29694080

RESUMO

The effect of nuclear dynamics and conical intersections on electronic coherences is investigated employing a two-state, two-mode linear vibronic coupling model. Exact quantum dynamical calculations are performed using the multiconfiguration time-dependent Hartree method. It is found that the presence of a nonadiabatic coupling close to the Franck-Condon point can preserve electronic coherence to some extent. Additionally, the possibility of steering the nuclear wave packets by imprinting a relative phase between the electronic states during the photoionization process is discussed. It is found that the steering of nuclear wave packets is possible given that a coherent electronic wave packet embodying the phase difference passes through a conical intersection. A conical intersection close to the Franck-Condon point is thus a necessary prerequisite for control, providing a clear path towards attochemistry.

12.
J Phys Chem Lett ; 9(5): 1156-1163, 2018 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-29444399

RESUMO

In many cases fragmentation of molecules upon inner-shell ionization is very unspecific with respect to the initially localized ionization site. Often this finding is interpreted in terms of an equilibration of internal energy into vibrational degrees of freedom after Auger decay. We investigate the X-ray photofragmentation of ethyl trifluoroacetate upon core electron ionization at environmentally distinct carbon sites using photoelectron-photoion-photoion coincidence measurements and ab initio electronic structure calculations. For all four carbon ionization sites, the Auger decay weakens the same bonds and transfers the two charges to opposite ends of the molecule, which leads to a rapid dissociation into three fragments, followed by further fragmentation steps. The lack of site specificity is attributed to the character of the dicationic electronic states after Auger decay instead of a fast equilibration of internal energy.

13.
J Phys Chem A ; 122(4): 1004-1010, 2018 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-29298485

RESUMO

The challenges of simulating extreme ultraviolet (XUV)-induced dissociation dynamics of organic molecules on a multitude of coupled potential energy surfaces are discussed for the prototypical photoionization of benzene. The prospects of Koopmans' theorem-based electronic structure calculations in combination with classical trajectories and Tully's fewest switches surface hopping are explored. It is found that a Koopmans' theorem-based approach overestimates the CH dissociation barrier and thus underestimates the fragmentation yield. However, the nonadiabatic population dynamics are in good agreement with previous approaches, indicating that the Koopmans' theorem based potentials are well described around the Franck-Condon point. This is explicitly tested for the ground state potential of the benzene cation employing CASPT2 calculations, for which very good agreement is found. This work highlights the need for efficient electronic structure approaches that can treat medium-sized organic molecules with a multitude of coupled excited states and several dissociation channels.

14.
IUCrJ ; 4(Pt 5): 560-568, 2017 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-28989713

RESUMO

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

15.
J Phys Chem Lett ; 8(22): 5543-5547, 2017 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-29083926

RESUMO

Strong light fields may be used to control molecular structure, thus providing a route to new, light-induced phases of matter. In this context, we present an ab initio molecular dynamics investigation of nonlinear mode coupling in C60 and show that, under suitable conditions, resonant infrared excitation induces significant structural changes in the system. Surprisingly, exciting the highest-frequency infrared mode at field strengths employed in a recent experiment [Nature 2016, 530, 461-464], we observe no significant structural change. However, when targeting the first two infrared modes using stronger fields, all Raman modes gain energy through nonlinear coupling to the infrared modes, leading to large-amplitude vibrational excitations. We find a strong response of the Hg(5) mode, which is symmetric with respect to the equilibrium structure. For sufficiently strong field, it is of the same order as the infrared modes' excitation. This encourages further investigations into the light-induced superconducting properties of alkali-doped fullerenes.

16.
Phys Rev E ; 96(2-1): 023205, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28950476

RESUMO

When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on subpicosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate nonequilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and three-dimensional spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an ab initio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above-mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven nonequilibrium dynamics in solids. To illustrate the potential of XMDYN for treating complex systems, we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species.

17.
Chaos ; 27(12): 123103, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-29289050

RESUMO

The Hartree-Fock method is an important approximation for the ground-state electronic wave function of atoms and molecules so that its usage is widespread in computational chemistry and physics. The Hartree-Fock method is an iterative procedure in which the electronic wave functions of the occupied orbitals are determined. The set of functions found in one step builds the basis for the next iteration step. In this work, we interpret the Hartree-Fock method as a dynamical system since dynamical systems are iterations where iteration steps represent the time development of the system, as encountered in the theory of fractals. The focus is put on the convergence behavior of the dynamical system as a function of a suitable control parameter. In our case, a complex parameter λ controls the strength of the electron-electron interaction. An investigation of the convergence behavior depending on the parameter λ is performed for helium, neon, and argon. We observe fractal structures in the complex λ-plane, which resemble the well-known Mandelbrot set, determine their fractal dimension, and find that with increasing nuclear charge, the fragmentation increases as well.

18.
Struct Dyn ; 3(5): 054101, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27478859

RESUMO

We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit, we employ a Monte-Carlo-molecular dynamics-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units, we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation. Radiation damage is not spatially uniform and depends on the fluence associated with each specific region inside the crystal. To investigate the effects of uniform and non-uniform fluence distribution, we have used two different spatial beam profiles, Gaussian and flattop.

19.
Sci Rep ; 6: 24791, 2016 04 25.
Artigo em Inglês | MEDLINE | ID: mdl-27109208

RESUMO

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.


Assuntos
Simulação por Computador , Cristalografia por Raios X/instrumentação , Lasers , Modelos Teóricos , Oxirredutases/química , Cristalografia por Raios X/métodos , Elétrons , Imagem Tridimensional , Fótons , Conformação Proteica , Difração de Raios X
20.
Phys Rev E ; 93(3): 032124, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27078309

RESUMO

The dynamics of ultrafast energy transfer to water clusters and to bulk water by a highly intense, subcycle THz pulse of duration ≈150 fs is investigated in the context of force-field molecular dynamics simulations. We focus our attention on the mechanisms by which rotational and translational degrees of freedom of the water monomers gain energy from these subcycle pulses with an electric field amplitude of up to about 0.6 V/Å. It has been recently shown that pulses with these characteristics can be generated in the laboratory [C. Vicario, B. Monoszlai, and C. P. Hauri, Phys. Rev. Lett. 112, 213901 (2014)]. Through their permanent dipole moment, water molecules are acted upon by the electric field and forced off their preferred hydrogen-bond network conformation. This immediately sets them in motion with respect to one another as energy quickly transfers to their relative center of mass displacements. We find that, in the bulk, the operation of these mechanisms is strongly dependent on the initial temperature and density of the system. In low density systems, the equilibration between rotational and translational modes is slow due to the lack of collisions between monomers. As the initial density of the system approaches 1 g/cm(3), equilibration between rotational and translational modes after the pulse becomes more efficient. In turn, low temperatures hinder the direct energy transfer from the pulse to rotational motion owing to the resulting stiffness of the hydrogen bond network. For small clusters of just a few water molecules we find that fragmentation due to the interaction with the pulse is faster than equilibration between rotations and translations, meaning that the latter remain colder than the former after the pulse. In contrast, clusters with more than a few tens of water molecules already display energy gain dynamics similar to water in condensed phases owing to inertial confinement of the internal water molecules by the outer shells. In these cases, a complete equilibration becomes possible.

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