Publications
317 results found
Alaa El-Din K, Alexander O, Frasinski L, et al., 2024, Efficient prediction of attosecond two-colour pulses from an X-ray free-electron laser with machine learning, Scientific Reports, ISSN: 2045-2322
Schwickert D, Przystawik A, Diaman D, et al., 2024, Coupled electron-nuclear dynamics induced and monitored with femtosecond soft X-ray pulses in the amino acid glycine, The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory, Vol: 128, Pages: 989-995, ISSN: 1089-5639
The coupling of electronic and nuclear motion in polyatomic molecules is at the heart of attochemistry. The molecular properties, transient structures, and reaction mechanism of these many-body quantum objects are defined on the level of electrons and ions by molecular wave functions and their coherent superposition, respectively. In the present contribution, we monitor nonadiabatic quantum wave packet dynamics during molecular charge motion by reconstructing both the oscillatory charge density distribution and the characteristic time-dependent nuclear configuration coordinate from time-resolved Auger electron spectroscopic data recorded in previous studies on glycine molecules [Schwickert et al. Sci. Adv. 2022, 8, eabn6848]. The electronic and nuclear motion on the femtosecond time scale was induced and probed in kinematically complete soft X-ray experiments at the FLASH free-electron laser facility. The detailed analysis of amplitude, instantaneous phase, and instantaneous frequency of the propagating many-body wave packet during its lifecycle provides unprecedented insight into dynamical processes beyond the Born-Oppenheimer approximation. We are confident that the refined experimental data evaluation helps to develop new theoretical tools to describe time-dependent molecular wave functions in complicated but ubiquitous non-Born-Oppenheimer photochemical conditions.
Garratt D, Matthews M, Marangos J, 2024, Towards ultrafast soft X-ray spectroscopy of organic photovoltaic devices, Structural Dynamics, Vol: 11, ISSN: 2329-7778
Novel ultrafast x-ray sources based on high harmonic generation and at x-ray free electron lasers are opening up new opportunities to resolve complex ultrafast processes in condensed phase systems with exceptional temporal resolution and atomic site specificity. In this perspective, we present techniques for resolving charge localization, transfer, and separation processes in organic semiconductors and organic photovoltaic devices with time-resolved soft x-ray spectroscopy. We review recent results in ultrafast soft x-ray spectroscopy of these systems and discuss routes to overcome the technical challenges in performing time-resolved x-ray experiments on photosensitive materials with poor thermal conductivity and low pump intensity thresholds for nonlinear effects.
Alexander O, Barnard J, Larsen E, et al., 2023, Observation of recollision-based high-harmonic generation in liquid isopropanol and the role of electron scattering, Physical Review Research, ISSN: 2643-1564
Engel RY, Alexander O, Atak K, et al., 2023, Electron population dynamics in resonant non-linear x-ray absorption in nickel at a free-electron laser., Struct Dyn, Vol: 10, ISSN: 2329-7778
Free-electron lasers provide bright, ultrashort, and monochromatic x-ray pulses, enabling novel spectroscopic measurements not only with femtosecond temporal resolution: The high fluence of their x-ray pulses can also easily enter the regime of the non-linear x-ray-matter interaction. Entering this regime necessitates a rigorous analysis and reliable prediction of the relevant non-linear processes for future experiment designs. Here, we show non-linear changes in the L3-edge absorption of metallic nickel thin films, measured with fluences up to 60 J/cm2. We present a simple but predictive rate model that quantitatively describes spectral changes based on the evolution of electronic populations within the pulse duration. Despite its simplicity, the model reaches good agreement with experimental results over more than three orders of magnitude in fluence, while providing a straightforward understanding of the interplay of physical processes driving the non-linear changes. Our findings provide important insights for the design and evaluation of future high-fluence free-electron laser experiments and contribute to the understanding of non-linear electron dynamics in x-ray absorption processes in solids at the femtosecond timescale.
Hutchison CDM, Baxter JM, Fitzpatrick A, et al., 2023, Optical control of ultrafast structural dynamics in a fluorescent protein, NATURE CHEMISTRY, ISSN: 1755-4330
Driver T, Pipkorn R, Averbukh V, et al., 2023, Identification of cofragmented combinatorial peptide isomers by two-dimensional partial covariance mass spectrometry, Journal of the American Society for Mass Spectrometry, Vol: 34, Pages: 1230-1234, ISSN: 1044-0305
Combinatorial post-translational modifications (PTMs), such as those forming the so-called “histone code”, have been linked to cell differentiation, embryonic development, cellular reprogramming, aging, cancers, neurodegenerative disorders, etc. Nevertheless, a reliable mass spectral analysis of the combinatorial isomers represents a considerable challenge. The difficulty stems from the incompleteness of information that could be generated by the standard MS to differentiate cofragmented isomeric sequences in their naturally occurring mixtures based on the fragment mass-to-charge ratio and relative abundance information only. Here we show that fragment–fragment correlations revealed by two-dimensional partial covariance mass spectrometry (2D-PC-MS) allow one to solve the combinatorial PTM puzzles that cannot be tackled by the standard MS as a matter of principle. We introduce 2D-PC-MS marker ion correlation approach and demonstrate experimentally that it can provide the missing information enabling identification of cofragmentated combinatorially modified isomers. Our in silico study shows that the marker ion correlations can be used to unambiguously identify 5 times more cofragmented combinatorially acetylated tryptic peptides and 3 times more combinatorially modified Glu-C peptides of human histones than is possible using standard MS methods.
Grell G, Guo Z, Driver T, et al., 2023, Effect of the shot-to-shot variation on charge migration induced by sub-fs x-ray free-electron laser pulses, PHYSICAL REVIEW RESEARCH, Vol: 5
Alexander OG, Marangos JP, Ruberti M, et al., 2023, Attosecond electron dynamics in molecular systems, Advances in Atomic Molecular and Optical Physics, Vol: 72, Pages: 183-251, ISSN: 1049-250X
In this paper we review the topic of attosecond electron dynamics in molecular systems. We present a digest of recent research on this topic conducted by ourselves and other researchers with the intention of providing an accessible, but rigorous, account of the current state of this intriguing field of research. A short account of the background quantum theory is given before discussing recent theoretical advances on understanding correlation driven electron dynamics and electron nuclear coupling in molecules undergoing fast photoionization. We then review experimental advances, using both high harmonic generation and XFEL based ultrafast x-ray pulses, and provide three recent case studies from our own work to illustrate this. The final sections look forward to the next steps in this field: we discuss the prospect for controlling attochemistry as well as extending attosecond measurement methods to electron dynamics in larger molecules and condensed phase systems.
Barnard J, Lee J, Alexander O, et al., 2022, Delivery of stable ultra-thin liquid sheets in vacuum for biochemical spectroscopy, Frontiers in Molecular Biosciences, Vol: 9, ISSN: 2296-889X
The development of ultra-thin flat liquid sheets capable of running in vacuum has provided an exciting new target for X-ray absorption spectroscopy in the liquid and solution phases. Several methods have become available for delivering in-vacuum sheet jets using different nozzle designs. We compare the sheets produced by two different types of nozzle; a commercially available borosillicate glass chip using microfluidic channels to deliver colliding jets, and an in-house fabricated fan spray nozzle which compresses the liquid on an axis out of a slit to achieve collision conditions. We find in our tests that both nozzles are suitable for use in X-ray absorption spectroscopy with the fan spray nozzle producing thicker but more stable jets than the commercial nozzle. We also provide practical details of how to run these nozzles in vacuum.
Schwickert D, Ruberti M, Kolorenc P, et al., 2022, Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy, STRUCTURAL DYNAMICS-US, Vol: 9
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- Citations: 1
Ferchaud C, Jarosch S, Avni T, et al., 2022, Interaction of an intense few-cycle infrared laser pulse with an ultrathin transparent liquid sheet, Optics Express, Vol: 30, Pages: 34684-34692, ISSN: 1094-4087
We experimentally study the interaction between intense infrared few-cycle laser pulses and an ultrathin (∼2 µm) flat liquid sheet of isopropanol running in vacuum. We observe a rapid decline in transmission above a critical peak intensity of 50 TW/cm2 of the initially transparent liquid sheet, and the emission of a plume of material. We find both events are due to the creation of a surface plasma and are similar to processes observed in dielectric solids. After calculating the electron density for different laser peak intensities, we find an electron scattering rate of 0.3 fs-1 in liquid isopropanol to be consistent with our data. We study the dynamics of the plasma plume to find the expansion velocity of the plume front.
Danilov D, Tran T, Bearpark MJJ, et al., 2022, How electronic superpositions drive nuclear motion following the creation of a localized hole in the glycine radical cation, JOURNAL OF CHEMICAL PHYSICS, Vol: 156, ISSN: 0021-9606
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- Citations: 3
Garratt D, Misiekis L, Wood D, et al., 2022, Direct observation of ultrafast exciton localization in an organic semiconductor with soft X-ray transient absorption spectroscopy, Nature Communications, Vol: 13, ISSN: 2041-1723
The localization dynamics of excitons in organic semiconductors influence the efficiency of charge transfer and separation in these materials. Here we apply time-resolved X-ray absorption spectroscopy to track photoinduced dynamics of a paradigmatic crystalline conjugated polymer: poly(3-hexylthiophene) (P3HT) commonly used in solar cell devices. The π→π* transition, the first step of solar energy conversion, is pumped with a 15 fs optical pulse and the dynamics are probed by an attosecond soft X-ray pulse at the carbon K-edge. We observe X-ray spectroscopic signatures of the initially hot excitonic state, indicating that it is delocalized over multiple polymer chains. This undergoes a rapid evolution on a sub 50 fs timescale which can be directly associated with cooling and localization to form either a localized exciton or polaron pair.
Schwickert D, Ruberti M, Kolorenc P, et al., 2022, Electronic quantum coherence in glycine molecules probed with ultrashort x-ray pulses in real time, SCIENCE ADVANCES, Vol: 8, ISSN: 2375-2548
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- Citations: 10
Li S, Driver T, Rosenberger P, et al., 2022, Attosecond coherent electron motion in Auger-Meitner decay, SCIENCE, Vol: 375, Pages: 285-+, ISSN: 0036-8075
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- Citations: 17
Driver T, Bachhawat N, Pipkorn R, et al., 2021, Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry, ANALYTICAL CHEMISTRY, Vol: 93, Pages: 14946-14954, ISSN: 0003-2700
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- Citations: 3
Barillot T, Alexander O, Cooper B, et al., 2021, Correlation-driven transient hole dynamics resolved in space and time in the isopropanol molecule, Physical Review X, Vol: 11, Pages: 1-15, ISSN: 2160-3308
The possibility of suddenly ionized molecules undergoing extremely fast electron hole (or, hole)dynamics prior to significant structural change was first recognized more than 20 years ago andtermed charge migration. The accurate probing of ultrafast electron hole dynamics requires measurements that have both sufficient temporal resolution and can detect the localization of a specifichole within the molecule. We report an investigation of the dynamics of inner valence hole states inisopropanol where we use an x-ray pump/x-ray probe experiment, with site and state-specific probing of a transient hole state localized near the oxygen atom in the molecule, together with an abinitio theoretical treatment. We record the signature of transient hole dynamics and make the firsttentative observation of dynamics driven by frustrated Auger-Meitner transitions. We verify thatthe effective hole lifetime is consistent with our theoretical prediction. This state-specific measurement paves the way to widespread application for observations of transient hole dynamics localizedin space and time in molecules and thus to charge transfer phenomena that are fundamental inchemical and material physics.
Driver T, Averbukh V, Frasiński LJ, et al., 2021, Two-dimensional partial covariance mass spectrometry for the top-down analysis of intact proteins., Analytical Chemistry, Vol: 93, Pages: 10779-10788, ISSN: 0003-2700
Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation pathway of the same parent (e.g., peptide) ion. Here, we apply 2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap mass analyzer, using the fact that the fragment-fragment correlation signals are much more specific to the biomolecular sequence than one-dimensional (1D) tandem mass spectrometry (MS/MS) signals at the same mass accuracy and resolution. We show that from the distribution of signals on a 2D-PC-MS map it is possible to extract the charge state of both parent and fragment ions without resolving the isotopic envelope. Furthermore, the 2D map of fragment-fragment correlations naturally separates the products of the primary decomposition pathways of the molecular ions from those of the secondary ones. We access this spectral information using an adapted version of the Hough transform. We demonstrate the successful identification of highly charged, intact protein molecules bypassing the need for high mass resolution. Using this technique, we also perform the in silico deconvolution of the overlapping fragment ion signals from two co-isolated and co-fragmented intact proteins, demonstrating a viable new method for the concurrent mass spectrometric identification of a mixture of intact protein ions from the same fragment ion spectrum.
Li S, Driver T, Al Haddad A, et al., 2021, Two-dimensional correlation analysis for x-ray photoelectron spectroscopy, Journal of Physics B: Atomic, Molecular and Optical Physics, Vol: 54, Pages: 1-9, ISSN: 0953-4075
X-ray photoelectron spectroscopy (XPS) measures the binding energy of core-level electrons, which are well-localised to specific atomic sites in a molecular system, providing valuable information on the local chemical environment. The technique relies on measuring the photoelectron spectrum upon x-ray photoionisation, and the resolution is often limited by the bandwidth of the ionising x-ray pulse. This is particularly problematic for time-resolved XPS, where the desired time resolution enforces a fundamental lower limit on the bandwidth of the x-ray source. In this work, we report a novel correlation analysis which exploits the correlation between the x-ray and photoelectron spectra to improve the resolution of XPS measurements. We show that with this correlation-based spectral-domain ghost imaging method we can achieve sub-bandwidth resolution in XPS measurements. This analysis method enables XPS for sources with large bandwidth or spectral jitter, previously considered unfeasible for XPS measurements.
Driver T, Bachhawat N, Frasinski L, et al., 2021, Chimera spectrum diagnostics for peptides using two-dimensional partial covariance mass spectrometry, Molecules, Vol: 26, ISSN: 1420-3049
The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.
Li S, Driver T, Alexander O, et al., 2021, Time-resolved pump-probe spectroscopy with spectral domain ghost imaging, FARADAY DISCUSSIONS, Vol: 228, Pages: 488-501, ISSN: 1359-6640
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- Citations: 14
Austin D, Johnson A, McGrath F, et al., 2021, Extracting sub-cycle electronic and nuclear dynamics from high harmonic spectra, Scientific Reports, Vol: 11, ISSN: 2045-2322
We present a new methodology for measuring few-femtosecond electronic and nuclear dynamics in both atoms and polyatomic molecules using multidimensional high harmonic generation (HHG) spectroscopy measurements, in which the spectra are recorded as a function of the laser intensity to form a two-dimensional data set. The method is applied to xenon atoms and to benzene molecules, the latter exhibiting significant fast nuclear dynamics following ionization. We uncover the signature of the sub-cycle evolution of the returning electron flux in strong-field ionized xenon atoms, implicit in the strong field approximation but not previously observed directly. We furthermore extract the nuclear autocorrelation function in strong field ionized benzene cations, which is determined to have a decay of τ0=4±1 fs, in good agreement with the τ0=3.5 fs obtained from direct dynamics variational multi-configuration Gaussian calculations. Our method requires minimal assumptions about the system, and is applicable even to un-aligned polyatomic molecules.
Garratt D, Misiekis L, Wood D, et al., 2021, Ultrafast Exciton Dynamics in Poly(3-hexylthiophene) Probed with Time Resolved X-ray Absorption Spectroscopy at the Carbon K- edge, Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE
Alexander O, Barillot T, Cooper B, et al., 2021, Inner Valence Hole Migration in Isopropanol, Conference on Lasers and Electro-Optics Europe / European Quantum Electronics Conference (CLEO/Europe-EQEC), Publisher: IEEE
Driver T, Cooper B, Ayers R, et al., 2020, Two-dimensional partial covariance mass spectrometry of large molecules based on fragment correlations, Physical Review X, Vol: 10, Pages: 041004 – 1-041004 – 13, ISSN: 2160-3308
Covariance mapping [L. J. Frasinski, K. Codling, and P. A. Hatherly, Science 246, 1029 (1989)] is a well-established technique used for the study of mechanisms of laser-induced molecular ionization and decomposition. It measures statistical correlations between fluctuating signals of pairs of detected species (ions, fragments, electrons). A positive correlation identifies pairs of products originating from the same dissociation or ionization event. A major challenge for covariance-mapping spectroscopy is accessing decompositions of large polyatomic molecules, where true physical correlations are overwhelmed by spurious signals of no physical significance induced by fluctuations in experimental parameters. As a result, successful applications of covariance mapping have so far been restricted to low-mass systems, e.g., organic molecules of around 50 daltons (Da). Partial-covariance mapping was suggested to tackle the problem of spurious correlations by taking into account the independently measured fluctuations in the experimental conditions. However, its potential has never been realized for the decomposition of large molecules, because in these complex situations, determining and continuously monitoring multiple experimental parameters affecting all the measured signals simultaneously becomes unfeasible. We introduce, through deriving theoretically and confirming experimentally, a conceptually new type of partial-covariance mapping—self-correcting partial-covariance spectroscopy—based on a parameter extracted from the measured spectrum itself. We use the readily available total ion count as the self-correcting partial-covariance parameter, thus eliminating the challenge of determining experimental parameter fluctuations in covariance measurements of large complex systems. The introduced self-correcting partial covariance enables us to successfully resolve correlations of molecules as large as
O'Neal JT, Champenois EG, Oberli S, et al., 2020, Electronic Population Transfer via Impulsive Stimulated X-Ray Raman Scattering with Attosecond Soft-X-Ray Pulses, PHYSICAL REVIEW LETTERS, Vol: 125, ISSN: 0031-9007
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- Citations: 30
Weaver B, Greening D, Tisch J, et al., 2020, Generation and measurement of isolated attosecond pulses with enhanced flux using a two colour synthesized laser field, Optics Express, Vol: 28, Pages: 23329-23337, ISSN: 1094-4087
We have generated isolated attosecond pulses and performed attosecond streaking measurements using a two-colour synthesized laser field consisting of a strong near-infrared few-cycle pulse and a weaker multi-cycle pulse centred at 400 nm. An actively stabilized interferometer was used to coherently combine the two pulses. Using attosecond streaking we characterised the electric fields of the two pulses and accurately retrieved the spectrum of the multi-cycle pulse. We demonstrated a two-fold increase in the flux of isolated attosecond pulses produced and show that their duration was minimally affected by the presence of the weaker field due to spectral filtering by a multilayer mirror.
Marangos JP, 2020, Accessing the quantum spatial and temporal scales with XFELs, Nature Reviews Physics, Vol: 2, Pages: 332-334, ISSN: 2522-5820
X-ray free-electron lasers (XFELs) are unique tools that are making possible time-resolved measurements of structural and electronic dynamics at the quantum spatial and temporal scales. Jonathan Marangos discusses the transformative scientific potential of this capability but also stresses the importance of lowering barriers to access to maximize scientific reach.
Johnson AS, Austin DR, Wood DA, et al., 2020, High-flux soft x-ray harmonic generation from ionization-shaped few-cycle laser pulses (vol 4, eaar3761, 2018), SCIENCE ADVANCES, Vol: 6, ISSN: 2375-2548
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