Serial X-ray Crystallography

Serial crystallography (SX) is an emerging technique to determine macromolecules at room temperature. SX with a pump–probe experiment provides the time-resolved dynamics of target molecules. SX has developed rapidly over the past decade as a technique that not only provides room-temperature structures with biomolecules, but also has the ability to time-resolve their molecular dynamics. The serial femtosecond crystallography (SFX) technique using an X-ray free electron laser (XFEL) has now been extended to serial synchrotron crystallography (SSX) using synchrotron X-rays. The development of a variety of sample delivery techniques and data processing programs is currently accelerating SX research, thereby increasing the research scope. In this editorial, I briefly review some of the experimental techniques that have contributed to advances in the field of SX research and recent major research achievements. This Special Issue will contribute to the field of SX research.

Generation and characterisation of isolated attosecond pulses at 100 kHz repetition rate

The generation of coherent light pulses in the extreme ultraviolet (XUV) spectral region with attosecond pulse durations constitutes the foundation of the field of attosecond science [1]. Twenty years after the first demonstration of isolated attosecond pulses [2], they continue to be a unique tool enabling the observation and control of electron dynamics in atoms, molecules and solids [3, 4]. It has long been identified that an increase in the repetition rate of attosecond light sources is necessary for many applications in atomic and molecular physics [5, 6], surface science [7], and imaging [8]. Although high harmonic generation (HHG) at repetition rates exceeding 100 kHz, showing a continuum in the cut-off region of the XUV spectrum was already demonstrated in 2013 [9], the number of photons per pulse was insufficient to perform pulse characterisation via attosecond streaking [10], let alone to perform a pump-probe experiment. Here we report on the generation and full characterisation of XUV attosecond pulses via HHG driven by near-single-cycle pulses at a repetition rate of 100 kHz. The high number of 106 XUV photons per pulse on target enables attosecond electron streaking experiments through which the XUV pulses are determined to consist of a dominant single attosecond pulse. These results open the door for attosecond pump-probe spectroscopy studies at a repetition rate one or two orders of magnitude above current implementations.

Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids

Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.

Filming movies of attosecond charge migration with high harmonic spectroscopy

Ultrafast electron migration in molecules is the progenitor of all chemical reactions and biological functions after light-matter interaction [1–4]. Following this ultrafast dynamics, however, has been an enduring endeavor [5, 6]. Recently, it has been shown that high-harmonic spectroscopy (HHS) is able to probe dynamics with attosecond temporal and sub-angstrom spatial resolution [7–10]. Still, real-time visualization of single-molecule dynamics continues to be a great challenge because experimental harmonic spectra are due to the coherent averages of light emission from individual molecules of different alignments. Here, we show that from high harmonics generated with single-color and two-color probe lasers in a pump-probe experiment, the complex amplitude and phase of harmonics from a single fixed-in-space molecule can be reconstructed using modern machine learning (ML) algorithm. From the complex single-molecule dipoles for different harmonics, we construct a series of film clips of hole density distributions of the cation at time steps of 50 attoseconds (1 as=10^{−18} s) to make a classical “movie” of electron migration after tunnel ionization of the molecule. Moreover, the angular dependence of molecular charge migration is fully resolved. By examining these clips, we observed that holes do not just “migrate” along the laser direction, but they may “swirl” around the atom centers. The ML-based HHS proposed here establishes a general reconstruction scheme for studying ultrafast charge migration in molecules, paving a way for further advance in tracing and controlling photochemical reactions by femtosecond lasers.

Tracing orbital images on ultrafast time scales

Frontier orbitals determine fundamental molecular properties such as chemical reactivities. Although electron distributions of occupied orbitals can be imaged in momentum space by photoemission tomography, it has so far been impossible to follow the momentum-space dynamics of a molecular orbital in time, for example through an excitation or a chemical reaction. Here, we combined time-resolved photoemission using high laser harmonics and a momentum microscope to establish a tomographic, femtosecond pump-probe experiment of unoccupied molecular orbitals. We measured the full momentum-space distribution of transiently excited electrons, connecting their excited-state dynamics to real-space excitation pathways. Because in molecules this distribution is closely linked to orbital shapes, our experiment may in the future offer the possibility to observe ultrafast electron motion in time and space.

Through Bonds or Contacts? Mapping Protein Vibrational Energy Transfer Using Non-canonical Amino Acids.

Vibrational energy transfer (VET) is essential for protein function. It is responsible for the efficient dissipation of excess energy after enzymatic reactions and photochemical processes, and has been linked to pathways of allosteric signal transduction. While it is understood that VET occurs via the backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the pathways of VET. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. This is accompanied by extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis to unravel the VET pathways. The joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.

Reconstruction of few-fs XUV pulses with a perturbative approach

A precise temporal characterization of the pulses involved in pump-probe experiments is crucial for a proper investigation of the ultrafast dynamics in several physical systems. Indeed, it is required for the assessment of the dynamical properties under examination with sufficient temporal resolution. In the fewfs/attosecond domain, typical reconstruction procedures require time-consuming interative methods, which are also sensitive to the experimental noise and to the distortion of the measurement. We developed an approach, called Simplified Trace Reconstruction In the Perturbative regimE (STRIPE), which allows us for a precise characterization of the infrared (IR) and extreme ultraviolet (XUV) pulses, used in a pump-probe experiment. Our method is not based on a phase retrival algorithm, and for this it is typically much faster than the other ones currently known. Moreover, it allows for easily including in the reconstruction the experimental non-idealities that may affect the measurement, like possible distortion due to the measurement procedure itself.

Superconducting optical response of photodoped Mott insulators

Ultrafast laser pulses can redistribute charges in Mott insulators on extremely short time scales, leading to the fast generation of photocarriers. It has recently been demonstrated that these photocarriers can form a novel [Formula: see text]-paired condensate at low temperatures, featuring a staggered superconducting pairing field. In this conference paper, we discuss the origin of the [Formula: see text]-paired hidden phase and its optical response, which may be detected in a pump-probe experiment. The hidden phase may be relevant for possible light-induced superconductivity in Mott insulators.

Energy transfer within the hydrogen bonding network of water following resonant terahertz excitation

Energy dissipation in water is very fast and more efficient than in many other liquids. This behavior is commonly attributed to the intermolecular interactions associated with hydrogen bonding. Here, we investigate the dynamic energy flow in the hydrogen bond network of liquid water by a pump-probe experiment. We resonantly excite intermolecular degrees of freedom with ultrashort single-cycle terahertz pulses and monitor its Raman response. By using ultrathin sample cell windows, a background-free bipolar signal whose tail relaxes monoexponentially is obtained. The relaxation is attributed to the molecular translational motions, using complementary experiments, force field, and ab initio molecular dynamics simulations. They reveal an initial coupling of the terahertz electric field to the molecular rotational degrees of freedom whose energy is rapidly transferred, within the excitation pulse duration, to the restricted translational motion of neighboring molecules. This rapid energy transfer may be rationalized by the strong anharmonicity of the intermolecular interactions.