Crystals

Editorial

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2 pages, 165 KiB

Open AccessEditorial

Time-Resolved Crystallography

by Connie Darmanin

Crystals 2022, 12(4), 561; https://doi.org/10.3390/cryst12040561 - 16 Apr 2022

Cited by 1 | Viewed by 1582

Abstract

This Special Issue on ‘Time-Resolved Crystallography’ is a collection of eight original articles providing interesting results that give insight into the processes involved in generating and analysing time-resolved data [...] Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

Research

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24 pages, 4622 KiB

Open AccessArticle

Heterogeneous Ice Growth in Micron-Sized Water Droplets Due to Spontaneous Freezing

by Niloofar Esmaeildoost, Olof Jönsson, Trevor A. McQueen, Marjorie Ladd-Parada, Hartawan Laksmono, Ne-Te Duane Loh and Jonas A. Sellberg

Crystals 2022, 12(1), 65; https://doi.org/10.3390/cryst12010065 - 4 Jan 2022

Cited by 7 | Viewed by 3076

Abstract

Understanding how ice nucleates and grows into larger crystals is of crucial importance for many research fields. The purpose of this study was to shed light on the phase and structure of ice once a nucleus is formed inside a metastable water droplet. [...] Read more.

Understanding how ice nucleates and grows into larger crystals is of crucial importance for many research fields. The purpose of this study was to shed light on the phase and structure of ice once a nucleus is formed inside a metastable water droplet. Wide-angle X-ray scattering (WAXS) was performed on micron-sized droplets evaporatively cooled to temperatures where homogeneous nucleation occurs. We found that for our weak hits ice grows more cubic compared to the strong hits that are completely hexagonal. Due to efficient heat removal caused by evaporation, we propose that the cubicity of ice at the vicinity of the droplet’s surface is higher than for ice formed within the bulk of the droplet. Moreover, the Bragg peaks were classified based on their geometrical shapes and positions in reciprocal space, which showed that ice grows heterogeneously with a significant population of peaks indicative of truncation rods and crystal defects. Frequent occurrences of the (100) reflection with extended in-planar structure suggested that large planar ice crystals form at the droplet surface, then fracture into smaller domains to accommodate to the curvature of the droplets. Planar faulting due to misaligned domains would explain the increased cubicity close to the droplet surface. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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11 pages, 2861 KiB

Open AccessArticle

Time-Resolved Nanobeam X-ray Diffraction of a Relaxor Ferroelectric Single Crystal under an Alternating Electric Field

by Shinobu Aoyagi, Ayumi Aoyagi, Hiroaki Takeda, Hitoshi Osawa, Kazushi Sumitani, Yasuhiko Imai and Shigeru Kimura

Crystals 2021, 11(11), 1419; https://doi.org/10.3390/cryst11111419 - 20 Nov 2021

Cited by 3 | Viewed by 2331

Abstract

Lead-containing relaxor ferroelectrics show enormous piezoelectric capabilities relating to their heterogeneous structures. Time-resolved nanobeam X-ray diffraction reveals the time and position dependences of the local lattice strain on a relaxor ferroelectric single crystal mechanically vibrating and alternately switching, as well as its polarization [...] Read more.

Lead-containing relaxor ferroelectrics show enormous piezoelectric capabilities relating to their heterogeneous structures. Time-resolved nanobeam X-ray diffraction reveals the time and position dependences of the local lattice strain on a relaxor ferroelectric single crystal mechanically vibrating and alternately switching, as well as its polarization under an alternating electric field. The complicated time and position dependences of the Bragg intensity distributions under an alternating electric field demonstrate that nanodomains with the various lattice constants and orientations exhibiting different electric field responses exist in the measured local area, as the translation symmetry breaks to the microscale. The dynamic motion of nanodomains in the heterogeneous structure, with widely distributed local lattice strain, enables enormous piezoelectric lattice strain and fatigue-free ferroelectric polarization switching. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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13 pages, 3144 KiB

Open AccessArticle

The Natural Breakup Length of a Steady Capillary Jet: Application to Serial Femtosecond Crystallography

by Alfonso M. Gañán-Calvo, Henry N. Chapman, Michael Heymann, Max O. Wiedorn, Juraj Knoska, Braulio Gañán-Riesco, José M. López-Herrera, Francisco Cruz-Mazo, Miguel A. Herrada, José M. Montanero and Saša Bajt

Crystals 2021, 11(8), 990; https://doi.org/10.3390/cryst11080990 - 20 Aug 2021

Cited by 8 | Viewed by 4073

Abstract

One of the most successful ways to introduce samples in Serial Femtosecond Crystallography has been the use of microscopic capillary liquid jets produced by gas flow focusing, whose length-to-diameter ratio and velocity are essential to fulfill the requirements of the high pulse rates [...] Read more.

One of the most successful ways to introduce samples in Serial Femtosecond Crystallography has been the use of microscopic capillary liquid jets produced by gas flow focusing, whose length-to-diameter ratio and velocity are essential to fulfill the requirements of the high pulse rates of current XFELs. In this work, we demonstrate the validity of a classical scaling law with two universal constants to calculate that length as a function of the liquid properties and operating conditions. These constants are determined by fitting the scaling law to a large set of experimental and numerical measurements, including previously published data. Both the experimental and numerical jet lengths conform remarkably well to the proposed scaling law. We show that, while a capillary jet is a globally unstable system to linear perturbations above a critical length, its actual and shorter long-term average intact length is determined by the nonlinear perturbations coming from the jet breakup itself. Therefore, this length is determined solely by the properties of the liquid, the average velocity of the liquid and the flow rate expelled. This confirms the very early observations from Smith and Moss 1917, Proc R Soc Lond A Math Phys Eng, 93, 373, to McCarthy and Molloy 1974, Chem Eng J, 7, 1, among others, while it contrasts with the classical conception of temporal stability that attributes the natural breakup length to the jet birth conditions in the ejector or small interactions with the environment. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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13 pages, 1131 KiB

Open AccessArticle

Analysis of Multi-Hit Crystals in Serial Synchrotron Crystallography Experiments Using High-Viscosity Injectors

by Marjan Hadian-Jazi, Peter Berntsen, Hugh Marman, Brian Abbey and Connie Darmanin

Crystals 2021, 11(1), 49; https://doi.org/10.3390/cryst11010049 - 9 Jan 2021

Cited by 4 | Viewed by 3484

Abstract

Serial Synchrotron Crystallography (SSX) is rapidly emerging as a promising technique for collecting data for time-resolved structural studies or for performing room temperature micro-crystallography measurements using micro-focused beamlines. SSX is often performed using high frame rate detectors in combination with continuous sample scanning [...] Read more.

Serial Synchrotron Crystallography (SSX) is rapidly emerging as a promising technique for collecting data for time-resolved structural studies or for performing room temperature micro-crystallography measurements using micro-focused beamlines. SSX is often performed using high frame rate detectors in combination with continuous sample scanning or high-viscosity or liquid jet injectors. When performed using ultra-bright X-ray Free Electron Laser (XFEL) sources serial crystallography typically involves a process known as ’diffract-and-destroy’ where each crystal is measured just once before it is destroyed by the intense XFEL pulse. In SSX, however, particularly when using high-viscosity injectors (HVIs) such as Lipidico, the crystal can be intercepted multiple times by the X-ray beam prior to exiting the interaction region. This has a number of important consequences for SSX including whether these multiple-hits can be incorporated into the data analysis or whether they need to be excluded due to the potential impact of radiation damage. Here, we investigate the occurrence and characteristics of multiple hits on single crystals using SSX with lipidico. SSX data are collected from crystals as they tumble within a high viscous stream of silicone grease flowing through a micro-focused X-ray beam. We confirmed that, using the Eiger 16M, we are able to collect up to 42 frames of data from the same single crystal prior to it leaving the X-ray interaction region. The frequency and occurrence of multiple hits may be controlled by varying the sample flow rate and X-ray beam size. Calculations of the absorbed dose confirm that these crystals are likely to undergo radiation damage but that nonetheless incorporating multiple hits into damage-free data should lead to a significant reduction in the number of crystals required for structural analysis when compared to just looking at a single diffraction pattern from each crystal. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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19 pages, 2961 KiB

Open AccessArticle

The Sensitivity of the Pair-Angle Distribution Function to Protein Structure

by Patrick Adams, Jack Binns, Tamar L. Greaves and Andrew V. Martin

Crystals 2020, 10(9), 724; https://doi.org/10.3390/cryst10090724 - 20 Aug 2020

Cited by 4 | Viewed by 3036

Abstract

The continued development of X-ray free-electron lasers and serial crystallography techniques has opened up new experimental frontiers. Nanoscale dynamical processes such as crystal growth can now be probed at unprecedented time and spatial resolutions. Pair-angle distribution function (PADF) analysis is a correlation-based technique [...] Read more.

The continued development of X-ray free-electron lasers and serial crystallography techniques has opened up new experimental frontiers. Nanoscale dynamical processes such as crystal growth can now be probed at unprecedented time and spatial resolutions. Pair-angle distribution function (PADF) analysis is a correlation-based technique that has the potential to extend the limits of current serial crystallography experiments, by relaxing the requirements for crystal order, size and number density per exposure. However, unlike traditional crystallographic methods, the PADF technique does not recover the electron density directly. Instead it encodes substantial information about local three-dimensional structure in the form of three- and four-body correlations. It is not yet known how protein structure maps into the many-body PADF correlations. In this paper, we explore the relationship between the PADF and protein conformation. We calculate correlations in reciprocal and real space for model systems exhibiting increasing degrees of order and secondary structural complexity, from disordered polypeptides, single alpha helices, helix bundles and finally a folded 100 kilodalton protein. These models systems inform us about the distinctive angular correlations generated by bonding, polypeptide chains, secondary structure and tertiary structure. They further indicate the potential to use angular correlations as a sensitive measure of conformation change that is complementary to existing structural analysis techniques. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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10 pages, 414 KiB

Open AccessArticle

Hybrid Plasma/Molecular-Dynamics Approach for Efficient XFEL Radiation Damage Simulations

by Alexander Kozlov, Andrew V. Martin and Harry M. Quiney

Crystals 2020, 10(6), 478; https://doi.org/10.3390/cryst10060478 - 4 Jun 2020

Cited by 8 | Viewed by 3464

Abstract

X-ray free-electron laser pulses initiate a complex series of changes to the electronic and nuclear structure of matter on femtosecond timescales. These damage processes include widespread ionization, the formation of a quasi-plasma state and the ultimate explosion of the sample due to Coulomb [...] Read more.

X-ray free-electron laser pulses initiate a complex series of changes to the electronic and nuclear structure of matter on femtosecond timescales. These damage processes include widespread ionization, the formation of a quasi-plasma state and the ultimate explosion of the sample due to Coulomb forces. The accurate simulation of these dynamical effects is critical in designing feasible XFEL experiments and interpreting the results. Current molecular dynamics simulations are, however, computationally intensive, particularly when they treat unbound electrons as classical point particles. On the other hand, plasma simulations are computationally efficient but do not model atomic motion. Here we present a hybrid approach to XFEL damage simulation that combines molecular dynamics for the nuclear motion and plasma models to describe the evolution of the low-energy electron continuum. The plasma properties of the unbound electron gas are used to define modified inter-ionic potentials for the molecular dynamics, including Debye screening and drag forces. The hybrid approach is significantly faster than damage simulations that treat unbound electrons as classical particles, enabling simulations to be performed on large sample volumes. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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Review

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16 pages, 20190 KiB

Open AccessReview

Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers

by Suraj Pandey, Ishwor Poudyal and Tek Narsingh Malla

Crystals 2020, 10(7), 628; https://doi.org/10.3390/cryst10070628 - 21 Jul 2020

Cited by 16 | Viewed by 6547

Abstract

With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review [...] Read more.

With time-resolved crystallography (TRX), it is possible to follow the reaction dynamics in biological macromolecules by investigating the structure of transient states along the reaction coordinate. X-ray free electron lasers (XFELs) have enabled TRX experiments on previously uncharted femtosecond timescales. Here, we review the recent developments, opportunities, and challenges of pump-probe TRX at XFELs. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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Other

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16 pages, 3058 KiB

Open AccessPerspective

A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography

by Carl Caleman, Francisco Jares Junior, Oscar Grånäs and Andrew V. Martin

Crystals 2020, 10(7), 585; https://doi.org/10.3390/cryst10070585 - 6 Jul 2020

Cited by 8 | Viewed by 4036

Abstract

X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL [...] Read more.

X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals. Full article

(This article belongs to the Special Issue Time Resolved Crystallography)

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