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Red fluorophores synthesized by oral bacteria are important for fluorescence-based diagnosis and treatment because they are used as markers for bacterially infected tissue, mature plaque, or calculus. A range of porphyrins have been identified as the source of this fluorescence in carious tissue. It is not clear which of these porphyrins are produced by individual oral bacteria or whether this ability depends on other factors. This study examined and compared the fluorescence spectra produced by selected cultured oral bacteria when grown on agars containing different nutrients with spectra for protoporphyrin IX, Zn-protoporphyrin IX, haematoporphyrin, and haematin. Actinomyces israelii (Deutsche Sammlung von Mikroorganismen [DSM], 43320), Actinomyces naeslundii (DSM 43013), Fusobacterium nucleatum (DSM, 20482), Lactobacillus casei (DSM, 20011), Prevotella intermedia (DSM, 20706), Streptococcus mutans (DSM, 20523), Streptococcus oralis (DSM, 20627), Streptococcus salivarius (DSM, 20560) and Streptococcus sobrinus (DSM, 20742) were rehydrated and grown anaerobically on caso, caso blood (containing 5% sheep blood), and caso chlorophyll (containing 5% spinach extract) agar for 3 days at 37°C in the dark. Colonies were harvested, transferred to ethanol, and centrifuged. Fluorescence emission spectra were recorded from the supernatant at 405 nm excitation (Fluorolog 3–22, Jobin Yvon-Spex ISA, Edison, NJ, USA). All Streptococci, L. casei, and F. nucleatum produced red fluorescence when grown on caso and caso chlorophyll agar but not on caso blood agar. A. naeslundii and P. intermedia emitted intense red fluorescence when grown on caso or caso blood agar but not on caso chlorophyll agar. Fluorescence emission spectra of A. naeslundii and P. intermedia grown on caso blood agar correlated exactly with both fluorescence peaks for protoporphyrin-IX at 632 and 701 nm. Most peaks observed could be correlated with at least one of the emission peaks of protoporphyrin IX, Zn-protoporphyrin IX, or haematoporphyrin. Oral bacteria emitted red fluorescence matching known porphyrins, but this depended on nutrients available in the agar.

Upon irradiation with a ps laser pulse, a [2 × 2] tetrairon(ii) spin crossover grid shows two types of elastic distortions: a short-range distortion in ps regime and a long-range distortion in the ns time scale.

Spin crossover complexes (SCO) are among the most studied molecular switches due to their potential use in displays, sensors, actuators and memory components. A prerequisite to using these materials is the understanding of the structural changes following the spin transition at out-of-equilibrium conditions. So far, out-of-equilibrium studies in SCO solids have been focused on mononuclear complexes, though a growing number of oligonuclear SCO complexes showing cooperative effects are being reported. Here, we use time-resolved pink Laue crystallography to study the out-of-equilibrium dynamics of a [2 × 2] tetranuclear metallogrid of the form [FeII4L

Chemistry - a European journal 27(48), 12371 - 12379 (2021). doi:10.1002/chem.202101515, We investigated the photoionization and fragmentation of isolated metal protoporphyrin IX cations (MPPIX+ with M=Fe, Co, Zn) by means of vacuum-ultraviolet (VUV) action spectroscopy in the energy range of 8.5���35 eV. Experiments were carried out in the gas phase by interfacing an electrospray ionization tandem mass spectrometer with a synchrotron beamline. The mass spectra and partial ion yields show that photoexcitation of the precursor ions predominantly leads to .CH$_2$COOH radical side-chain losses of the macrocycle with additional methyl radical (.CH$_3$) side-chain losses. Ionization, in contrast, leads to the formation of the intact ionized precursor and various doubly charged fragments which are mostly due to side-chain cleavages. Although statistical fragmentation dominates, we found evidence for non-statistical processes such as new fragments involving for example single and double H2O losses, indicating that different relaxation mechanisms are at play upon photoionization compared to photoexcitation. The measured ionization energies were 9.6��0.2 eV, 9.4��0.2 eV and 9.6��0.2 eV for FePPIX$^+$, CoPPIX$^+$ and ZnPPIX$^+$, respectively., Published by Wiley-VCH, Weinheim

Solution-processed polymeric semiconductor films are attracting wide interest for applications in flexible electronics, wherein environmental stability is still a big obstacle. In many polymeric th...

The local electronic structure of the metal-active site and the deexcitation pathways of metalloporphyrins are crucial for numerous applications but difficult to access by commonly employed techniques. Here, we applied near-edge X-ray absorption mass spectrometry and quantum-mechanical restricted active space calculations to investigate the electronic structure of the metal-active site of the isolated cobalt(iii) protoporphyrin IX cation (CoPPIX+) and its deexcitation pathways upon resonant absorption at the cobalt L-edge. The experiments were carried out in the gas phase, thus allowing for control over the chemical state and molecular environment of the metalloporphyrin. The obtained mass spectra reveal that resonant excitations of CoPPIX+ at the cobalt L3-edge lead predominantly to the formation of the intact radical dication and doubly charged fragments through losses of charged and neutral side chains from the macrocycle. The comparison between experiment and theory shows that CoPPIX+ is in a 3A2g triplet ground state and that competing excitations to metal-centred non-bonding and antibonding σ* molecular orbitals lead to distinct deexcitation pathways., Near-edge X-ray absorption mass spectrometry (NEXAMS) and restricted active space (RAS) quantum mechanical calculations at the metal L-edge reveal the electronic structure and orbital-specific deexcitation pathways of gas-phase metalloporphyrins.

Journal of the American Society for Mass Spectrometry 32(3), 670 - 684 (2021). doi:10.1021/jasms.0c00390, Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H]$^+$) and methionine enkephalin ([MetEnk+H]$^+$) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide’s amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(C═C) excitations in the aromatic amino acid side chains give evidence for a sulfur–aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H]$^+$. Furthermore, a peak associated with N 1s → π*(C═N) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H]$^+$., Published by ACS Publications, Washington, DC

Two conformational polymorphs of a donor–bridge–acceptor (D-B-A) dyad, p-(CH3)2N-C6H4-(CH2)2-(1-pyrenyl)/PyCHDMA, were studied, where the electron donor (D) moiety p-(CH3)2N-C6H4/DMA is connected through a bridging group (B), –CH2–CH2–, to the electron acceptor (A) moiety pyrene. Though molecular dyads like PyCHDMA have the potential to change solar energy into electrical current through the process of photoinduced intramolecular charge transfer (ICT), the major challenge is the real-time investigation of the photoinduced ICT process in crystals, necessary to design solid-state optoelectronic materials. The time-correlated single photon counting (TCSPC) measurements with the single crystals showed that the ICT state lifetime of the thermodynamic form, PyCHDMA1 (pyrene and DMA: axial), is ∼3 ns, whereas, for the kinetic form, PyCHDMA20 (pyrene and DMA: equatorial), it is ∼7 ns, while photoexcited with 375 nm radiation. The polymorphic crystals were photo-excited and subsequently probed with a pink Laue x-ray beam in time-resolved x-ray diffraction (TRXRD) measurements. The TRXRD results suggest that in the ICT state, due to electron transfer from the tertiary N-atom in DMA moiety to the bridging group and pyrene moiety, a decreased repulsion between the lone-pair and the bond-pair at N-atom induces planarity in the C–N–(CH3)2 moiety, in both polymorphs. The Natural Bond Orbital calculations and partial atomic charge analysis by Hirshfeld partitioning also corroborated the same. Although the interfragment charge transfer (IFCT) analysis using the TDDFT results showed that for the charge transfer excitation in both conformers, the electrons were transferred from the DMA moiety to mostly the pyrene moiety, the bridging group has little role to play in that.

The title compound, (C

Site-selective dissociation induced by core photoexcitation of biomolecules is of key importance for the understanding of radiation damage processes and dynamics and for its promising use as “chemical scissors” in various applications. However, identifying products of site-selective dissociation in large molecules is challenging at the carbon, nitrogen, and oxygen edges because of the high recurrence of these atoms and related chemical groups. In this paper, we present the observation of site-selective dissociation at the sulfur L-edge in the gas-phase peptide methionine enkephalin, which contains only a single sulfur atom. Near-edge X-ray absorption mass spectrometry has revealed that the resonant $S 2p → σ*_{C–S}$ excitation of the sulfur contained in the methionine side chain leads to site-selective dissociation, which is not the case after core ionization above the sulfur L-edge. The prospects of such results for the study of charge dynamics in biomolecular systems are discussed.

Acta crystallographica / Section E 78(8), 814 - 817 (2022). doi:10.1107/S2056989022007046, The title compound, (C$_4$H$_7$N$_2$)$_2$[Co(H$_2$O)$_6$][Co(C$_9$H$_3$O$_6$)$_2$(H$_2$O)$_4$] (1), was synthesized from cobalt(II) chloride, 1,3,5-benzene tri­carb­oxy­lic acid (Hbtc) and 2-methyl-imidazole (H-2mIm) under ambient conditions. The structure of 1 is here reported and compared with the parent complex hexa­aqua­cobalt bis­(1H-imidazol-3-ium) tetra­aqua­bis­(benzene-1,3,5-tri­carboxyl­ato)cobalt (2)., Published by National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD

Journal of physics / B 55(1), 014001 (2022). doi:10.1088/1361-6455/ac489d, The ultraviolet (UV)-induced dissociation and photofragmentation of gas-phase CH$_2$BrI molecules induced by intense femtosecond extreme ultraviolet (XUV) pulses at three different photon energies are studied by multi-mass ion imaging. Using a UV-pump���XUV-probe scheme, charge transfer between highly charged iodine ions and neutral CH$_2$Br radicals produced by C���I bond cleavage is investigated. In earlier charge-transfer studies, the center of mass of the molecules was located along the axis of the bond cleaved by the pump pulse. In the present case of CH$_2$BrI, this is not the case, thus inducing a rotation of the fragment. We discuss the influence of the rotation on the charge transfer process using a classical over-the-barrier model. Our modeling suggests that, despite the fact that the dissociation is slower due to the rotational excitation, the critical interatomic distance for charge transfer is reached faster. Furthermore, we suggest that charge transfer during molecular fragmentation may be modulated in a complex way., Published by IOP Publ., Bristol

Pyrene based molecules are inclined to form excimers through self-association upon photoexcitation. In this work, the pyrene core is functionalized with the N-methylacetamide group at the position 1 or 2 to develop pyren-1-methylacetamide (PyMA1) and pyren-2-methylacetamide (PyMA2), respectively. Upon photoexcitation with 345 nm, a portion of molecules in PyMA1 and PyMA2 solutions at ≥1.0 mM have formed static excimers. The steady state spectroscopic measurements suggest that, whether it is the dimerization of molecules in the ground state (GS) or in excimer formation, characteristic signs are more pronounced in PyMA1 than its isomeric counterpart, PyMA2. The shift of the excimer band in their respective emission spectra suggests that the extent of overlap in π-π stacking is greater for PyMA1 than for PyMA2 in the excited state. The optimized geometry of dimers in toluene shows that the overlapping area between the pyrene moieties in π-π stacking between the dimers is greater for PyMA1 than for PyMA2 in GS. The natural bond orbital analysis with the optimized GS geometries shows that the stabilization/interaction energy between the dimers in π-π stacking is higher in PyMA1 compared to PyMA2 in toluene. The transient absorption (TA) measurements in toluene over the fs-ps regime (fs-TA) showed that the formation of static excimers with pre-associated dimers in PyMA1 happens in ∼700 fs whereas the excimers for the pre-associated dimers in PyMA2 have formed in slightly slower time scale (∼1.95 ps). Contrary to what was observed in solution, the extent of overlap in π-π stacking is lower for PyMA1 dimers (∼17%) than for PyMA2 dimers (∼37%) in single crystals.

A new implementation for XAS measurements based on zone plates is presented. With a two-color scheme, several fluorescence yields can be probed simultaneously., X-ray absorption spectroscopy (XAS) is a powerful element-specific technique that allows the study of structural and chemical properties of matter. Often an indirect method is used to access the X-ray absorption (XA). This work demonstrates a new XAS implementation that is based on off-axis transmission Fresnel zone plates to obtain the XA spectrum of La0.6Sr0.4MnO3 by analysis of three emission lines simultaneously at the detector, namely the O 2p–1s, Mn 3s–2p and Mn 3d–2p transitions. This scheme allows the simultaneous measurement of an integrated total fluorescence yield and the partial fluorescence yields (PFY) of the Mn 3s–2p and Mn 3d–2p transitions when scanning the Mn L-edge. In addition to this, the reduction in O fluorescence provides another measure for absorption often referred to as the inverse partial fluorescence yield (IPFY). Among these different methods to measure XA, the Mn 3s PFY and IPFY deviate the least from the true XA spectra due to the negligible influence of selection rules on the decay channel. Other advantages of this new scheme are the potential to strongly increase the efficiency and throughput compared with similar measurements using conventional gratings and to increase the signal-to-noise of the XA spectra as compared with a photodiode. The ability to record undistorted bulk XA spectra at high flux is crucial for future in situ spectroscopy experiments on complex materials.

The overlap of diffraction spots from different grains was investigated to understand the influence of experimental factors on the x-ray diffraction data quality and to optimize the experimental parameters for data collection on polycrystalline samples. Diffraction patterns for photoactive polycrystals were indexed and sorted with respect to grains using multigrain approaches. The indexing of diffraction spots and the identification of grains for tetrathiafulvalene-p-chloranil samples were performed using the ImageD11, GrainSpotter, GRAINDEX and Cell_now programs. In many cases, comparison of the results from these programs shows good agreement. For the individual grains from polycrystalline samples, the crystal structure was solved and refined using the SHELXTL program. After the structural refinement of the grains, the best and the average R1 values were 1.93% and 2.06%, respectively, which are on a comparable resolution level with that obtained from the x-ray single crystal measurements.

Abstract VUV action spectroscopy has recently gained interest for the study of peptides and proteins. However, numerous aspects of the fundamental processes involved in the photodissociation are yet to be understood. It can, for example, be expected that sulfur-containing amino-acid residues have a significant impact on the dissociation processes following photoionization because of their potential involvement in the transport of electron holes in proteins. In order to investigate the influence of the sulfur-containing methionine residue on the VUV photodissociation of a small peptide a VUV action spectroscopy study of gas-phase protonated methionine-enkephalin and leucine-enkephalin in the photon energy range of 6–35 eV was performed. The results show that upon non-ionizing photoexcitation, the fragmentation patterns of the two peptides are nearly identical, whereas significant differences were observed upon photoionization. The differences between the fragment yields and the identified specific dissociation channels for methionine-enkephalin could be explained by the high electron hole affinity of sulfur, which efficiently directs the radical to the methionine side chain. Additionally, for both peptides the presence of the intact photoionized precursor ions was confirmed by their isotopic patterns and the stability of these species could be evaluated. Graphic abstract

Resonant inelastic X ray scattering RIXS is a promising method for elucidating detailed electronic structure of materials in a broad range of chemical and physical applications. Here, we use the fine fluorescence energy resolution of a RIXS spectrometer to obtain various proxies of the Mn L edge X ray absorption spectra XAS of the perovskite La0.6Sr0.4MnO3 LSMO as a model catalyst for the oxygen evolution reaction OER and evaluate the suitability for in situ surface studies of this electrocatalyst. We conclude that the inverse partial fluorescence yield IPFY of the O 2p 1s transition and the partial fluorescence yield of the 3s 2p transition 3s PFY are most suitable for determining changes at the surface of the perovskite, because distortions at grazing incidence measurements are low. In particular, the negligible angular dependence of the 3s PFY spectra can be perfectly simulated using a fluorescence model in the thin sample limit which is justified by low reabsorption of 3s photons. Remarkably, the 3s PFY reveals an influence of water vapor on the electronic reconstruction of the LSMO surface. Thus, our work paves the road for quantitative distortion free X ray spectroscopy of transition metal oxide surfaces under in situ conditions, which is needed to understand fundamental chemical processes such as corrosion and catalysis

Nanoscale Photonic Imaging / Salditt, Tim (Editor) ; Cham : Springer International Publishing, 2020, Chapter 17 ; ISSN: 0303-4216=1437-0859 ; ISBN: 978-3-030-34412-2=978-3-030-34413-9 ; doi:10.1007/978-3-030-34413-9; Cham : Springer International Publishing, Topics in Applied Physics 134, 457 - 499 (2020). doi:10.1007/978-3-030-34413-9_17, The chapter will focus on fundamental aspects and methodological challenges of X-ray free electron laser research and recent developments in the related field of ultrafast X-ray science. Selected examples proving “molecular movie capabilities” of Free-electron laser radiation investigating gas phase chemistry, chemistry in liquids and transformations in the solid state will be introduced. They will be discussed in the context of ultrafast X-ray studies of complex biochemical research, and time-resolved X-ray characterisation of energy storage materials and energy bionics., Published by Springer International Publishing, Cham

A novel experimental setup is presented for resonant inelastic X-ray scattering investigations of solid and liquid samples in the soft X-ray region for studying the complex electronic configuration of (bio)chemical systems. The uniqueness of the apparatus is its high flexibility combined with optimal energy resolution and energy range ratio. The apparatus enables investigation of chemical analyses, which reflects the chemical imprints. The endstation is composed of a main sample chamber, a sample holder for either solid or liquid jet delivery system, and a soft X-ray grating spectrometer for 210–1250 eV with a resolving power of ∼1000. It combines for the first time liquid jet technology with a soft X-ray spectrometer based on the variable line spacing principle. This setup was commissioned at the soft X-ray beamline P04 at PETRA III of the Deutsches Elektronen-Synchrotron in Hamburg which is currently the most brilliant storage-ring-based X-ray radiation source in the world. The first results of liquid and solid samples show that this setup allows the detection of photons across an energy range of ∼300 eV. This covers simultaneously the emission lines of life-important elements like carbon, nitrogen and oxygen in a shot-based procedure.

The photodissociation dynamics of CH

The journal of physical chemistry letters 9(12), 3538 - 3543 (2018). doi:10.1021/acs.jpclett.8b01429, Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time-resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal–ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. π-Back-donation is found to be mainly determined by the metal site occupation, whereas the ligand hole instead influences σ-donation. Our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes., Published by ACS, Washington, DC

International audience; Due to its element and site specificity, inner-shell photoelectron spectroscopy is a widely used technique to probe the chemical structure of matter. Here, we show that time-resolved inner-shell photoelectron spectroscopy can be employed to observe ultrafast chemical reactions and the electronic response to the nuclear motion with high sensitivity. The ultraviolet dissociation of iodomethane (CH3I) is investigated by ionization above the iodine 4d edge, using time-resolved inner-shell photoelectron and photoion spectroscopy. The dynamics observed in the photoelectron spectra appear earlier and are faster than those seen in the iodine fragments. The experimental results are interpreted using crystal-field and spin-orbit configuration interaction calculations, and demonstrate that time-resolved inner-shell photoelectron spectroscopy is a powerful tool to directly track ultrafast structural and electronic transformations in gas-phase molecules.

Optics letters 43(18), 4390 - 4393 (2018). doi:10.1364/OL.43.004390, X-ray spectroscopy is a method, ideally suited for investigating the electronic structure of matter, which has been enabled by the rapid developments in light sources and instruments. The x-ray fluorescence lines of life-relevant elements such as carbon, nitrogen, and oxygen are located in the soft x-ray regime and call for suitable spectrometer devices. In this Letter, we present a high-resolution spectrum of liquid water, recorded with a soft x-ray spectrometer based on a reflection zone plate (RZP) design. The RZP-based spectrometer with meridional variation of line space density from 2953 to 3757 l/mm offers extremely high detection efficiency and, at the same time, medium energy resolution. We can reproduce the well-known splitting of liquid water in the lone pair regime with 10 s acquisition time., Published by OSA, Washington, DC

Journal of the American Society for Mass Spectrometry 29(11), 2138 - 2151 (2018). doi:10.1007/s13361-018-2035-6, We have investigated the photoionization and photofragmentation yields of gas-phase multiply protonated melittin cations for photon energies at the K-shell absorption edges of carbon,nitrogen, and oxygen. Two similar experimental approaches were employed. In both experiments, mass selected [melittin+qH]$^{q+}$ (q=2–4) ions were accumulated in radiofrequency iontraps. The trap content was exposed to intense beams of monochromatic soft X-ray photons from synchrotron beamlines and photoproducts were analyzed by means of time-of-flight mass spectrometry. Mass spectra were recorded for fixed photon energies, and partial ion yield spectra were recorded as a function of photon energy. The combination of mass spectrometry and soft X-ray spectroscopy allows for a direct correlation of protein electronic structure with various photoionization channels. Non-dissociative single and double ionizationare used as a reference. The contribution of both channels to various backbone scission channels is quantified and related to activation energies and protonation sites. Soft X-ray absorption mass spectrometry combines fast energy deposition with single and double ionization and could complement established activation techniques.Keywords: Soft X-ray spectroscopy, Soft X-ray absorption, Photodissociation, Melittin, Protonated proteins, Published by Springer, New York [u.a.]

The journal of chemical physics 149(20), 204313 (2018). doi:10.1063/1.5041381, The photodissociation dynamics of CH$_3$I and CH$_2$ClI at 272 nm were investigated by time-resolved Coulomb explosion imaging, with an intense non-resonant 815 nm probe pulse. Fragment ion momenta over a wide m/z range were recorded simultaneously by coupling a velocity map imaging spectrometer with a pixel imaging mass spectrometry camera. For both molecules, delay-dependent pump-probe features were assigned to ultraviolet-induced carbon-iodine bond cleavage followed by Coulomb explosion. Multi-mass imaging also allowed the sequential cleavage of both carbon-halogen bonds in CH$_2$ClI to be investigated. Furthermore, delay-dependent relative fragment momenta of a pair of ions were directly determined using recoil-frame covariance analysis. These results are complementary to conventional velocity map imaging experiments and demonstrate the application of time-resolved Coulomb explosion imaging to photoinduced real-time molecular motion., Published by American Institute of Physics, Melville, NY

Chemistry - a European journal 24(30), 7631-7636 (2018). doi:10.1002/chem.201801440, Preservation of protein conformation upon transfer into the gas phase is key for structure determination of free single molecules, for example using X‐ray free‐electron lasers. In the gas phase, the helicity of melittin decreases strongly as the protein's protonation state increases. We demonstrate the sensitivity of soft X‐ray spectroscopy to the gas‐phase structure of melittin cations ([melittin+qH]q+, q=2–4) in a cryogenic linear radiofrequency ion trap. With increasing helicity, we observe a decrease of the dominating carbon 1 s–π* transition in the amide C=O bonds for non‐dissociative single ionization and an increase for non‐dissociative double ionization. As the underlying mechanism we identify inelastic electron scattering. Using an independent atom model, we show that the more compact nature of the helical protein conformation substantially increases the probability for off‐site intramolecular ionization by inelastic Auger electron scattering., Published by Wiley-VCH, Weinheim

Bio-catalysis is the outcome of a subtle interplay between internal motions in enzymes and chemical kinetics. Small-angle X-ray scattering (SAXS) investigation of an enzyme’s internal motions during catalysis offers an integral view of the protein’s structural plasticity, dynamics, and function, which is useful for understanding allosteric effects and developing novel medicines. Guanylate kinase (GMPK) is an essential enzyme involved in the guanine nucleotide metabolism of unicellular and multicellular organisms. It is also required for the intracellular activation of numerous antiviral and anticancer purine nucleoside analog prodrugs. Catalytically active recombinant human GMPK (hGMPK) was purified for the first time and changes in the size and shape of open/closed hGMPK were tracked by SAXS. The binding of substrates (GMP + AMPPNP or Ap5G or GMP + ADP) resulted in the compaction of size and shape of hGMPK. The structural changes between open and completely closed hGMPK conformation were confirmed by observing differences in the hGMPK secondary structures with circular dichroism spectroscopy. Graphical abstract Electronic supplementary material The online version of this article (doi:10.1007/s00249-015-1079-9) contains supplementary material, which is available to authorized users.

Three new Cu(I) complexes containing bidentate N^N donor ligands with the general formula [Cu(N^N)2][PF6] (N^N = 2,3-diphenyl-6,7-di-p-tolyl-1,4,5,8-tetraazaphenanthrene (1L), 2,3-diphenyl-6,7-di(2-thienyl)-1,4,5,8-tetraazaphenanthrene (2L), and 2,3-diphenyl-6,7-di-p-fluorophenyl-1,4,5,8-tetraazaphenanthrene (3L), were prepared by the reaction of [Cu(CH3CN)4][PF6] with two equivalents of the N^N ligand. Single-crystal X-ray diffraction analysis confirmed that in each complex the metal displays a distorted tetrahedral geometry surrounded by the four N atoms of the two sterically hindered substituted tetraazaphenanthrene (TAP) ligands. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT), calculations were used to study the ground state properties and interpret the absorption spectra for these Cu(I) complexes. The calculations show that the lowest-energy excitations of all complexes are dominated by dπ(Cu) → π∗(L), metal-to-ligand charge transfer, (MLCT) excitations. Electronic difference density maps (EDDMs) were calculated, indicating the change of electron density in the singlet excited states. The degree of filling of the coordination sphere (G parameter) by the ligands was calculated taking into account the ligand–ligand overlap, and compared to the related bis(2,9-disubstituted phenanthroline) Cu(I) complexes.

The dynamics following laser-induced molecular photodissociation of gas-phase CH2BrI at 271.6 nm were investigated by time-resolved Coulomb-explosion imaging using intense near-IR femtosecond laser pulses. The observed delay-dependent photofragment momenta reveal that CH2BrI undergoes C-I cleavage, depositing 65.6% of the available energy into internal product states, and that absorption of a second UV photon breaks the C-Br bond of CH2Br. Simulations confirm that this mechanism is consistent with previous data recorded at 248 nm, demonstrating the sensitivity of Coulomb-explosion imaging as a real-time probe of chemical dynamics.

The unique properties of free-electron lasers (FELs) allow for the systematic study and precise characterization of electronic and structural chemical and biochemical reactions in space and time—from minutes to femtosecond time resolution. Rationalizing the ultra-fast behaviour in the chemical reactions of unimolecular reactions (reactions of one type of molecule), allows entirely new types of opto-electronic devices (such as solar cells or organic light emitting diodes) to be constructed. In bimolecular reactions (with two types of molecules), FELs allow for entirely new types of electronic and structural characterization schemes.

Thermally driven chemistry as well as materials' functionality are determined by the potential energy surface of a systems electronic ground state. This makes the potential energy surface a central and powerful concept in physics, chemistry and materials science. However, direct experimental access to the potential energy surface locally around atomic centers and to its long-range structure are lacking. Here we demonstrate how sub-natural linewidth resonant inelastic soft x-ray scattering at vibrational resolution is utilized to determine ground state potential energy surfaces locally and detect long-range changes of the potentials that are driven by local modifications. We show how the general concept is applicable not only to small isolated molecules such as O2 but also to strongly interacting systems such as the hydrogen bond network in liquid water. The weak perturbation to the potential energy surface through hydrogen bonding is observed as a trend towards softening of the ground state potential around the coordinating atom. The instrumental developments in high resolution resonant inelastic soft x-ray scattering are currently accelerating and will enable broad application of the presented approach. With this multidimensional potential energy surfaces that characterize collective phenomena such as (bio)molecular function or high-temperature superconductivity will become accessible in near future.

Understanding and controlling the relaxation process of optically excited charge carriers in solids with strong correlations is of great interest in the quest for new strategies to exploit solar energy. Usually, optically excited electrons in a solid thermalize rapidly on a femtosecond to picosecond timescale due to interactions with other electrons and phonons. New mechanisms to slow down thermalization will thus be of great significance for efficient light energy conversion, e.g., in photovoltaic devices. Ultrafast optical pump–probe experiments in the manganite Pr$_{0.65}$Ca$_{0.35}$MnO$_{3}$, a photovoltaic, thermoelectric, and electrocatalytic material with strong polaronic correlations, reveal an ultraslow recombination dynamics on a nanosecond-time scale. The nature of long living excitations is further elucidated by photovoltaic measurements, showing the presence of photodiffusion of excited electron–hole polaron pairs. Theoretical considerations suggest that the excited charge carriers are trapped in a hot polaron state. Escape from this state is possible via a slow dipole-forbidden recombination process or via rare thermal fluctuations toward a conical intersection followed by a radiation-less decay. The strong correlation between the excited polaron and the octahedral dynamics of its environment appears to be substantial for stabilizing the hot polaron.

We have investigated the electronic and geometric structures in the lowest excited states of six phosphorescent heteroleptic [CuI(NN)(DPEphos)]+ (DPEphos = bis[(2-diphenylphosphino)phenyl]ether) complexes with varying NN = diimine ligand structures using density functional theory. In comparison to the ground state, the results show a decrease of the dihedral angle between the N–Cu–N and P–Cu–P planes for these excited states with mixed ligand-to-ligand (DPEphos lone pair → π∗(NN)) and metal-to-ligand charge transfer (dπ(Cu) → π∗(NN)) character. Sterically less demanding ligands facilitate this process, which is accompanied by a geometric relaxation of the DPEphos ligand and contraction of the Cu–N bonds. The density functional for the excited state calculations has been selected based on ground state validation studies. We evaluated the ability of seven density functionals to reproduce the molecular ground state geometries and absorption spectra obtained by single-crystal X-ray diffraction and solution-phase UV–Vis absorption spectroscopy respectively. Standard methods (PBE and B3LYP), which do not account for dispersion, systematically overestimate internuclear distances. In contrast, approaches including dispersion (B97D3, PBE0-GD3, M06L, M06, ωB97XD) remove this systematic effect and give less expanded molecular structures. We found that only the hybrid functionals (B3LYP, PBE0-GD3, M06), incorporating a portion of exact exchange from Hartree–Fock theory, accurately predict the experimental absorption energies.