Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers

Unraveling the ultrafast dynamics of thermal-energy chemical reactions

In this perspective, we discuss how one can initiate, image, and disentangle the ultrafast elementary steps of thermal-energy chemical dynamics, building upon advances in technology and scientific insight. We propose that combinations of ultrashort mid-infrared laser pulses, controlled molecular species in the gas phase, and forefront imaging techniques allow to unravel the elementary steps of general-chemistry reaction processes in real time. We detail, for prototypical first reaction systems, experimental methods enabling these investigations, how to sufficiently prepare and promote gas-phase samples to thermal-energy reactive states with contemporary ultrashort mid-infrared laser systems, and how to image the initiated ultrafast chemical dynamics. The results of such experiments will clearly further our understanding of general-chemistry reaction dynamics.

Time-resolving the UV-initiated photodissociation dynamics of OCS

We present a time-resolved study of the photodissociation dynamics of OCS after UV-photoexcitation at λ = 237 nm. OCS molecules (X1Σ+) were primarily excited to the 11A'' and the 21A' Renner-Teller components of the 1Σ- and 1Δ states. Dissociation into CO and S fragments was observed through time-delayed strong-field ionisation and imaging of the kinetic energy of the resulting CO+ and S+ fragments by intense 790 nm laser pulses. Surprisingly, fast oscillations with a period of ∼100 fs were observed in the S+ channel of the UV dissociation. Based on wavepacket-dynamics simulations coupled with a simple electrostatic-interaction model, these oscillations do not correspond to the known highly-excited rotational motion of the leaving CO(X1Σ+, J ≫ 0) fragments, which has a timescale of ∼140 fs. Instead, we suggest to assign the observed oscillations to the excitation of vibrational wavepackets in the 23A'' or 21A'' states of the molecule that predissociate to form S(3PJ) photoproducts.

X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules

Alignment of molecules through electric fields minimizes the averaging over orientations, e.g., in single-particle-imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor, which is usually calculated using quantum chemistry methods. These methods are not feasible for large molecules. Here, we calculate the polarizability tensor of proteins using a regression model that correlates the polarizabilities of the 20 amino acids with perfect conductors of the same shape. The dielectric constant of the molecules could be estimated from the slope of the regression line based on the Clausius-Mossotti equation. We benchmark our predictions against the quantum chemistry results for the Trp cagemini protein and the measured dielectric constants of larger proteins. Our method has applications in computing laser alignment of macromolecules, for instance, benefiting single-particle imaging, as well as for estimation of the optical and electrostatic characteristics of proteins and other macromolecules.

Accessing the molecular frame through strong-field alignment of distributions of gas phase molecules

A rationale for creating highly aligned distributions of molecules is that it enables vector properties referenced to molecule-fixed axes (the molecular frame) to be determined. In the present work, the degree of alignment that is necessary for this to be achieved in practice is explored. Alignment is commonly parametrized in experiments by a single parameter, [Formula: see text], which is insufficient to enable predictive calculations to be performed. Here, it is shown that, if the full distribution of molecular axes takes a Gaussian form, this single parameter can be used to determine the complete set of alignment moments needed to characterize the distribution. In order to demonstrate the degree of alignment that is required to approach the molecular frame, the alignment moments corresponding to a few chosen values of [Formula: see text] are used to project a model molecular frame photoelectron angular distribution into the laboratory frame. These calculations show that [Formula: see text] needs to approach 0.9 in order to avoid significant blurring to be caused by averaging.This article is part of the theme issue 'Modern theoretical chemistry'.

Acetylacetone photodynamics at a seeded free-electron laser

The first steps in photochemical processes, such as photosynthesis or animal vision, involve changes in electronic and geometric structure on extremely short time scales. Time-resolved photoelectron spectroscopy is a natural way to measure such changes, but has been hindered hitherto by limitations of available pulsed light sources in the vacuum-ultraviolet and soft X-ray spectral region, which have insufficient resolution in time and energy simultaneously. The unique combination of intensity, energy resolution, and femtosecond pulse duration of the FERMI-seeded free-electron laser can now provide exceptionally detailed information on photoexcitation–deexcitation and fragmentation in pump-probe experiments on the 50-femtosecond time scale. For the prototypical system acetylacetone we report here electron spectra measured as a function of time delay with enough spectral and time resolution to follow several photoexcited species through well-characterized individual steps, interpreted using state-of-the-art static and dynamics calculations. These results open the way for investigations of photochemical processes in unprecedented detail.

The first steps in photochemical processes involve changes in electronic and geometric structure on extremely short timescales. Here, the authors report femtosecond dynamics in prototypical acetylacetone, by pump-probe photoexcitation-photoemission experiments and static and dynamics calculations.

Impulsive laser-induced alignment of OCS molecules at FERMI

OCS full rotational revival dynamics induced by impulsive NIR alignment monitored by Coulomb explosion correlated fragments after S 2p excitation.

CFEL-ASG Software Suite (CASS): usage for free-electron laser experiments with biological focus

CASS [Foucar et al. (2012). Comput. Phys. Commun.183, 2207-2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.

High-intracavity-power thin-disk laser for the alignment of molecules

We propose a novel approach for strong alignment of gas-phase molecules for experiments at arbitrary repetition rates. A high-intracavity-power continuous-wave laser will provide the necessary ac electric field of 10(10)-10(11) W/cm(2). We demonstrate thin-disk lasers based on Yb:YAG and Yb:Lu(2)O(3) in a linear high-finesse resonator providing intracavity power levels in excess of 100 kW at pump power levels on the order of 50 W. The multi-longitudinal-mode operation of this laser avoids spatial-hole burning even in a linear standing-wave resonator. The system will be scaled up as in-vacuum system to allow for the generation of fields of 10(11) W/cm(2). This system will be directly applicable for experiments at modern X-ray light sources, such as synchrotrons or free-electron lasers, which operate at various very high repetition rates. This would allow to record molecular movies through temporally resolved diffractive imaging of fixed-in-space molecules, as well as the spectroscopic investigation of combined X-ray-NIR strong-field effects of atomic and molecular systems.

Single-molecule imaging with longer X-ray laser pulses

During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the 'self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5-10 fs, but can succeed for pulses 50-100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage ('damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30-50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

Ab Initio Calculation of Molecular Diffraction

We discuss the application of ab initio X-ray diffraction (AIXRD) to the interpretation of time-resolved and static X-ray diffraction. In our approach, elastic X-ray scattering is calculated directly from the ab initio multiconfigurational wave function via a Fourier transform of the electron density, using the first Born approximation for elastic scattering. Significant gains in efficiency can be obtained by performing the required Fourier transforms analytically, making it possible to combine the calculation of ab initio X-ray diffraction with expensive quantum dynamics simulations. We show that time-resolved X-ray diffraction can detect not only changes in molecular geometry but also changes in the electronic state of a molecule. Calculations for cis-, trans-, and cyclo-butadiene, as well as benzene and 1,3-cyclohexadiene are included.

Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules

This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

Disruptive photon technologies for chemical dynamics

A perspective of new and emerging technologies for chemical dynamics is given, with an emphasis on the use of X-ray sources that generate sub-picosecond pulses. The two classes of experimental techniques used for time-resolved measurements of chemical processes and their effects are spectroscopy and imaging, where the latter includes microscopy, diffractive imaging, and crystallography. X-Ray free-electron lasers have brought new impetus to the field, allowing not only temporal and spatial resolution at atomic time and length scales, but also bringing a new way to overcome limitations due to perturbation of the sample by the X-ray probe by out-running radiation damage. Associated instrumentation and methods are being developed to take advantage of the new opportunities of these sources. Once these methods of observational science have been mastered it should be possible to use the new tools to directly control those chemical processes.