Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy

The vibrational label SCN is used to report on local structural dynamics in a protein revealing spectral diffusion on a picosecond scale. The SCN spectra are compared to the response of methylthiocyanate in solvents with different polarity and hydrogen-bonding capabilities.

Strategies for sample delivery for femtosecond crystallography

Highly efficient data-collection methods are required for successful macromolecular crystallography (MX) experiments at X-ray free-electron lasers (XFELs). XFEL beamtime is scarce, and the high peak brightness of each XFEL pulse destroys the exposed crystal volume. It is therefore necessary to combine diffraction images from a large number of crystals (hundreds to hundreds of thousands) to obtain a final data set, bringing about sample-refreshment challenges that have previously been unknown to the MX synchrotron community. In view of this experimental complexity, a number of sample delivery methods have emerged, each with specific requirements, drawbacks and advantages. To provide useful selection criteria for future experiments, this review summarizes the currently available sample delivery methods, emphasising the basic principles and the specific sample requirements. Two main approaches to sample delivery are first covered: (i) injector methods with liquid or viscous media and (ii) fixed-target methods using large crystals or using microcrystals inside multi-crystal holders or chips. Additionally, hybrid methods such as acoustic droplet ejection and crystal extraction are covered, which combine the advantages of both fixed-target and injector approaches.

Time-resolved crystallography reveals allosteric communication aligned with molecular breathing

A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework’s dynamics and entropy constitute crucial components of the catalytic machinery.

The HARE chip for efficient time-resolved serial synchrotron crystallography

Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided.

Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison

For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.

Direct observation of nuclear reorganization driven by ultrafast spin transitions

One of the most basic molecular photophysical processes is that of spin transitions and intersystem crossing between excited states surfaces. The change in spin states affects the spatial distribution of electron density through the spin orbit coupling interaction. The subsequent nuclear reorganization reports on the full extent of the spin induced change in electron distribution, which can be treated similarly to intramolecular charge transfer with effective reaction coordinates depicting the spin transition. Here, single-crystal [Fe^II(bpy)₃](PF₆)₂, a prototypical system for spin crossover (SCO) dynamics, is studied using ultrafast electron diffraction in the single-photon excitation regime. The photoinduced SCO dynamics are resolved, revealing two distinct processes with a (450 ± 20)-fs fast component and a (2.4 ± 0.4)-ps slow component. Using principal component analysis, we uncover the key structural modes, ultrafast Fe–N bond elongations coupled with ligand motions, that define the effective reaction coordinate to fully capture the relevant molecular reorganization.

Electron spin is a fundamental property of molecules, and changes in spin state affect both molecular structure and dynamics. Here, the authors resolve, by ultrafast electron diffraction, the nuclear reorganization stabilizing spin transitions in a [Fe^II(bpy)₃](PF₆)₂ crystal.

Correction: Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy

Correction for 'Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy' by Luuk J. G. W. van Wilderen et al., Phys. Chem. Chem. Phys., 2014, 16, 19643-19653.

Protein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallography

In order to utilize the high repetition rates now available at X-ray free-electron laser sources for serial crystallography, methods must be developed to softly deliver large numbers of individual microcrystals at high repetition rates and high speeds. Picosecond infrared laser (PIRL) pulses, operating under desorption by impulsive vibrational excitation (DIVE) conditions, selectively excite the OH vibrational stretch of water to directly propel the excited volume at high speed with minimized heating effects, nucleation formation or cavitation-induced shock waves, leaving the analytes intact and undamaged. The soft nature and laser-based sampling flexibility provided by the technique make the PIRL system an interesting crystal delivery approach for serial crystallography. This paper demonstrates that protein crystals extracted directly from aqueous buffer solutionviaPIRL-DIVE ablation retain their diffractive properties and can be usefully exploited for structure determination at synchrotron sources. The remaining steps to implement the technology for high-speed serial femtosecond crystallography, such as single-crystal localization, high-speed sampling and synchronization, are described. This proof-of-principle experiment demonstrates the viability of a new laser-based high-speed crystal delivery system without the need for liquid-jet injectors or fixed-target mounting solutions.

Time zero determination for FEL pump-probe studies based on ultrafast melting of bismuth

A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T₀)-the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T₀ might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T₀. In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T₀ with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated). Our approach is potentially useful and applicable for fixed-target XFEL experiments, such as serial femtosecond crystallography, utilizing an optical pump pulse in the ultraviolet to near infrared spectral range and a pixelated 2D photon detector for recording crystallographic diffraction patterns in transmission geometry. In comparison to many other suitable approaches, our method is fairly independent of the pumping wavelength (UV-IR) as well as of the X-ray energy and offers a favorable signal contrast. The technique is exploitable not only for the determination of temporal characteristics of the experiment at the interaction point but also for investigating important conditions affecting experimental control such as spatial overlap and beam spot sizes.

Synthesis and characterisation of α-carboxynitrobenzyl photocaged l-aspartates for applications in time-resolved structural biology

We report a new synthetic route to a series of α-carboxynitrobenzyl photocaged l-aspartates for application in time-resolved structural biology. The resulting compounds were characterised in terms of UV/Vis absorption properties, aqueous solubility and stability, and photocleavage rates (τ = μs to ms) and quantum yields (φ = 0.05 to 0.14).

2D-IR spectroscopy of carbohydrates: Characterization of thiocyanate-labeled β -glucose in CHCl3 and H2O

Carbohydrates constitute one of the four key classes of biomacromolecules but have not been studied by 2D-IR spectroscopy so far. Similarly as for proteins, their chemical structure and the repetitive nature of native vibrational oscillators, combined with their huge structural diversity, lead to spectrally congested infrared spectra already for singlecarbohydrates. Biophysical studies are further impeded by the strong overlap between water modes and carbohydrates modes. Here, we demonstrate the application of the known vibrational reporter group thiocyanate (SCN) in glucose. In his first study, we are able to perform IR- and 2D-IR spectroscopy of β -glucose with SCN at C2 position, as proof of concept in chloroform. Upon improved synthesis and removal of all protecting groups we succeed to perform 2D-IR in H2O. All experiments are compared to results of methyl-thiocyanate as reference sample. Overall we show that theconcept of using site-specific vibrational reporter groups can be transferred to carbohydrates.

Antimicrobial Polymers of Linear and Bottlebrush Architecture: Probing the Membrane Interaction and Physicochemical Properties

Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focus on random linear copolymers, the development of APs with advanced architectures proves to be more potent. It is recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using various spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive, and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking Escheria coli membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.

Capturing ultrafast molecular motions and lattice dynamics in spin crossover film using femtosecond diffraction methods

A comprehensive insight into ultrafast dynamics of photo-switchable materials is desired for efficient control of material properties through light excitation. Here, we study a polycrystalline spin crossover thin film as a prototypical example and reveal the sequential photo-switching dynamics, from local molecular rearrangement to global lattice deformation. On the earliest femtosecond timescale, the local molecular structural rearrangement occurs within a constant unit-cell volume through a two-step process, involving initial Fe-ligand bond elongation followed by ligand rotation. The highly-oriented structure of the nanocrystalline films and the experimental geometry enables resolving the full anisotropic lattice structural dynamics in and out of the sample plane separately. While both molecular switching and lattice heating influence lattice volume, they exert varying degrees of impact at disparate time scales following photoexcitation. This study highlights the opportunities provided by Mega-electron-volt electron and X-ray free electron laser to advance the understanding of ultrafast dynamics of photo-switchable materials.

Direct observation of structural dynamics upon photo-excitation in a spin crossover crystal with femtosecond electron diffraction

Photoinduced spin transitions are studied by femtosecond electron diffraction to understand ultrafast structural dynamics associated with intersystem crossing. The results indicate the structural reorganization occurs within 2.3 ps, as the metal-ligand bond distribution narrows during intramolecular vibrational energy redistribution.