Secondary ionization of pyrimidine nucleobases and their microhydrated derivatives in helium nanodroplets.

Radiation damage in biological systems by ionizing radiation is predominantly caused by secondary processes such as charge and energy transfer leading to the breaking of bonds in DNA. Here, we study the fragmentation of cytosine (Cyt) and thymine (Thy) molecules, clusters and microhydrated derivatives induced by direct and indirect ionization initiated by extreme-ultraviolet (XUV) irradiation. Photofragmentation mass spectra and photoelectron spectra of free Cyt and Thy molecules are compared with mass and electron spectra of Cyt/Thy clusters and microhydrated Cyt/Thy molecules formed by aggregation in superfluid helium (He) nanodroplets. Penning ionization after resonant excitation of the He droplets is generally found to cause less fragmentation compared to direct photoionization and charge-transfer ionization after photoionization of the He droplets. When Cyt/Thy molecules and oligomers are complexed with water molecules, their fragmentation is efficiently suppressed. However, a similar suppression of fragmentation is observed when homogeneous Cyt/Thy clusters are formed in He nanodroplets, indicating a general trend. Penning ionization electron spectra (PIES) of Cyt/Thy are broad and nearly featureless but PIES of their microhydrated derivatives point at a sequential ionization process ending in unfragmented microsolvated Cyt/Thy cations.

Dopant ionization and efficiency of ion and electron ejection from helium nanodroplets.

Photoionization spectroscopy and mass spectrometry of doped helium (He) nanodroplets rely on the ability to efficiently detect ions and/or electrons. Using a commercial quadrupole mass spectrometer and a photoelectron-photoion coincidence spectrometer, we systematically measure yields of ions and electrons created in pure and doped He nanodroplets in a wide size range and in two ionization regimes-direct ionization and secondary ionization after resonant photoexcitation of the droplets. For two different types of dopants (oxygen molecules, O2, and lithium atoms, Li), we infer the optimal droplet size to maximize the yield of ejected ions. When dopants are ionized by charge-transfer to photoionized He nanodroplets, the highest yield of O2 and Li ions is detected for a mean size of ∼5×104 He atoms per nanodroplet. When dopants are Penning ionized via photoexcitation of the He droplets, the highest yield of O2 and Li ions is detected for ∼103 and ∼105 He atoms per droplet, respectively. At optimum droplet sizes, the detection efficiency of dopant ions in proportion to the number of primary photoabsorption events is up to 20% for charge-transfer ionization of O2 and 2% for Li, whereas for Penning ionization it is 1% for O2 and 4% for Li. Our results are instrumental in determining optimal conditions for mass spectrometric studies and photoionization spectroscopy of molecules and complexes isolated in He nanodroplets.

Proton transfer dynamics modified by CH-stretching excitation.

Gaining insight how specific rovibrational states influence reaction kinetics and dynamics is a fundamental goal of physical chemistry. Purely statistical approaches often fail to predict the influence of a specific state on the reaction outcome, evident in a great number of both experimental and theoretical studies. Most detailed insight in atomistic reaction mechanisms is achieved using accurate collision experiments and high level dynamics calculations. For ion-molecule reactions such experiments are scarce. Here we show the influence of symmetric CH-stretching vibration on the rate and dynamics of proton transfer in the reaction of F- + CH3I. We find a pronounced shift in the reaction dynamics for excited reactions from indirect to preferred direct dynamics at higher collision energy. Moreover, excited reactions occur at larger impact parameters. Finally, we compare vibrational excitation with collision energy and find that vibration is overall more efficient in promoting reactivity, which agrees with recent theoretical calculations.

Imaging Reaction Dynamics of F-(H2O) and Cl-(H2O) with CH3I.

The dynamics of microhydrated nucleophilic substitution reactions have been studied using crossed beam velocity map imaging experiments and quasiclassical trajectory simulations at different collision energies between 0.3 and 2.6 eV. For F-(H2O) reacting with CH3I, a small fraction of hydrated product ions I-(H2O) is observed at low collision energies. This product, as well as the dominant I-, is formed predominantly through indirect reaction mechanisms. In contrast, a much smaller indirect fraction is determined for the unsolvated reaction. At the largest studied collision energies, the solvated reaction is found to also occur via a direct rebound mechanism. The measured product angular distributions exhibit an overall good agreement with the simulated angular distributions. Besides nucleophilic substitution, also ligand exchange reactions forming F-(CH3I) and, at high collision energies, proton transfer reactions are detected. The differential scattering images reveal that the Cl-(H2O) + CH3I reaction also proceeds predominantly via indirect reaction mechanisms.

Threshold photodetachment spectroscopy of the astrochemical anion CN.

Threshold photodetachment spectroscopy has been performed on the molecular anion CN- at both 16(1) K and 295(2) K in a 22-pole ion trap and at 295(2) K from a pulsed ion beam. The spectra show a typical energy dependence of the detachment cross section yielding a determination of the electron affinity of CN to greater precision than has previously been known at 31 163(16) cm-1 [3.864(2) eV]. Allowed s-wave detachment is observed for CN-, but the dependence of the photodetachment cross section near the threshold is perturbed by the long-range interaction between the permanent dipole moment of CN and the outgoing electron. Furthermore, we observe a temperature dependence of the cross section near the threshold, which we attribute to a reduction of the effective permanent dipole due to higher rotational excitation at higher temperatures.

Unexpected Indirect Dynamics in Base-Induced Elimination.

Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) are two of the most versatile reactions that are important in preparative organic chemistry. These stereospecific reactions are often found in direct competition with each other. Elimination can proceed via two distinct transition states, referred to as anti and syn, of which anti is commonly energetically favored. To investigate the intrinsic dynamics of base-induced elimination, reactions under single-collision conditions are required. Here, we present reactive scattering results on the prototype reaction of the fluoride anion with tert-butyl halides. The observed mechanistic fingerprints are associated with the E2 reaction, because steric hindrance at the α-carbon suppresses the SN2 reaction [Carrascosa, E.; Meyer, J.; Zhang, J.; Stei, M.; Michaelsen, T.; Hase, W. L.; Yang, L.; Wester, R. Nat. Commun. 2017, 8, 25]. The reaction coordinate shows energetically submerged transition states, with anti favored over syn, and we found a very shallow prereaction well for anti. We predominantly found indirect dynamics for a range of collision energies, which can be separated into three remarkably different mechanisms. At low collision energies, the first is a large impact parameter indirect mechanism which leads to a forward-backward symmetric scattering signature. The second mechanism is attributed to low-impact parameter reactions with a near-statistical partitioning of the total available energy. The majority of events are associated with widespread isotropic scattering. Unexpectedly, the product ion kinetic energy distributions are independent of collision energy. We associate this with dynamic trapping in a prereaction well supported by a large centrifugal potential. These measured fingerprints support that atomistic reaction dynamics cannot be predicted based on stationary arguments alone.

Low frequency vibrational anharmonicity and nuclear spin effects of Cl-(H2) and Cl-(D2).

Low frequency combination bands of 35Cl-(H2) and 35Cl-(D2) have been measured in the region between 600 and 1100 cm-1 by infrared predissociation spectroscopy in a cryogenic 22-pole ion trap using a free electron laser at the FELIX Laboratory as a tunable light source. The 35Cl-(H2) (35Cl-(D2)) spectrum contains three bands at 773 cm-1 (620 cm-1), 889 cm-1 (692 cm-1), and 978 cm-1 (750 cm-1) with decreasing intensity toward higher photon energies. Comparison of the experimentally determined transition frequencies with anharmonic vibrational self-consistent field and vibrational configuration interaction calculations suggests the assignment of the combination bands v1 + v2, 2v1 + v2, and 3v1 + v2 for 35Cl-(H2) and 2v1 + v2, 3v1 + v2, and 4v1 + v2 for 35Cl-(D2), where v1 is the 35Cl-⋯H2 stretching fundamental and v2 is the Cl-(H2) bend. The observed asymmetric temperature dependent line shape of the v1 + v2 transition can be modeled by a series of ∑+-∏ ro-vibrational transitions, when substantially decreasing the rotational constant in the vibrationally excited state by 35%. The spectrum of 35Cl-(D2) shows a splitting of 7 cm-1 for the strongest band which can be attributed to the tunneling of the ortho/para states of D2.

Imaging state-to-state reactive scattering in the Ar+ + H2 charge transfer reaction.

The charge transfer reaction of Ar+ with H2 and D2 has been investigated in an experiment combining crossed beams with three-dimensional velocity map imaging. Angle-differential cross sections for two collision energies have been obtained for both neutral species. We find that the product ions are highly internally excited. In the reaction with H2, the spin-orbit excited Ar+ state's coupling to the "resonant" vibrationally excited product H2+ (υ = 2) dominates for both investigated energies, in line with previous investigations. The observed angular distributions, however, show significantly less back-scattering than was found previously. Furthermore, we discovered that the product ions are highly rotationally excited. In the case of Ar+ reacting with D2, the energetically closest lying vibrational levels are not strictly preferred and higher-lying vibrational levels are also populated. For both species, the backward-scattered products show higher internal excitation.

A lipid zipper triggers bacterial invasion.

Glycosphingolipids are important structural constituents of cellular membranes. They are involved in the formation of nanodomains ("lipid rafts"), which serve as important signaling platforms. Invasive bacterial pathogens exploit these signaling domains to trigger actin polymerization for the bending of the plasma membrane and the engulfment of the bacterium--a key process in bacterial uptake. However, it is unknown whether glycosphingolipids directly take part in the membrane invagination process. Here, we demonstrate that a "lipid zipper," which is formed by the interaction between the bacterial surface lectin LecA and its cellular receptor, the glycosphingolipid Gb3, triggers plasma membrane bending during host cell invasion of the bacterium Pseudomonas aeruginosa. In vitro experiments with Gb3-containing giant unilamellar vesicles revealed that LecA/Gb3-mediated lipid zippering was sufficient to achieve complete membrane engulfment of the bacterium. In addition, theoretical modeling elucidated that the adhesion energy of the LecA-Gb3 interaction is adequate to drive the engulfment process. In cellulo experiments demonstrated that inhibition of the LecA/Gb3 lipid zipper by either lecA knockout, Gb3 depletion, or application of soluble sugars that interfere with LecA binding to Gb3 significantly lowered P. aeruginosa uptake by host cells. Of note, membrane engulfment of P. aeruginosa occurred independently of actin polymerization, thus corroborating that lipid zippering alone is sufficient for this crucial first step of bacterial host-cell entry. Our study sheds new light on the impact of glycosphingolipids in the cellular invasion of bacterial pathogens and provides a mechanistic explication of the initial uptake processes.

Imaging Proton Transfer and Dihalide Formation Pathways in Reactions of F(-) + CH3I.

Ion-molecule reactions of the type X(-) + CH3Y are commonly assumed to produce Y(-) through bimolecular nucleophilic substitution (SN2). Beyond this reaction, additional reaction products have been observed throughout the last decades and have been ascribed to different entrance channel geometries differing from the commonly assumed collinear approach. We have performed a crossed beam velocity map imaging experiment on the F(-) + CH3I reaction at different relative collision energies between 0.4 and 2.9 eV. We find three additional channels competing with nucleophilic substitution at high energies. Experimental branching ratios and angle- and energy differential cross sections are presented for each product channel. The proton transfer product CH2I(-) is the main reaction channel, which competes with nucleophilic substitution up to 2.9 eV relative collision energy. At this level, the second additional channel, the formation of IF(-) via halogen abstraction, becomes more efficient. In addition, we present the first evidence for an [FHI](-) product ion. This [FHI](-) product ion is present only for a narrow range of collision energies, indicating possible dissociation at high energies. All three products show a similar trend with respect to their velocity- and scattering angle distributions, with isotropic scattering and forward scattering of the product ions occurring at low and high energies, respectively. Reactions leading to all three reaction channels present a considerable amount of energy partitioning in product internal excitation. The internally excited fraction shows a collision energy dependence only for CH2I(-). A similar trend is observed for the isoelectronic OH(-) + CH3I system. The comparison of our experimental data at 1.55 eV collision energy with a recent theoretical calculation for the same system shows a slightly higher fraction of internal excitation than predicted, which is, however, compatible within the experimental accuracy.

Multidimensional Langevin Modeling of Nonoverdamped Dynamics.

Based on a given time series, data-driven Langevin modeling aims to construct a low-dimensional dynamical model of the underlying system. When dealing with physical data as provided by, e.g., all-atom molecular dynamics simulations, effects due to small damping may be important to correctly describe the statistics (e.g., the energy landscape) and the dynamics (e.g., transition times). To include these effects in a dynamical model, an algorithm that propagates a second-order Langevin scheme is derived, which facilitates the treatment of multidimensional data. Adopting extensive molecular dynamics simulations of a peptide helix, a five-dimensional model is constructed that successfully forecasts the complex structural dynamics of the system. Neglect of small damping effects, on the other hand, is shown to lead to significant errors and inconsistencies.

Electron energy loss and angular asymmetry induced by elastic scattering in superfluid helium nanodroplets.

Helium nanodroplets are ideal model systems to unravel the complex interaction of condensed matter with ionizing radiation. Here we study the effect of purely elastic electron scattering on angular and energy distributions of photoelectrons emitted from He nanodroplets of variable size (10-109 atoms per droplets). For large droplets, photoelectrons develop a pronounced anisotropy along the incident light beam due to a shadowing effect within the droplets. In contrast, the detected photoelectron spectra are only weakly perturbed. This opens up possibilities for photoelectron spectroscopy of dopants embedded in droplets provided they are smaller than the penetration depth of the light and the trapping range of emitted electrons in liquid helium.

An electron-ion coincidence spectrometer for commissioning of a synchrotron radiation beamline: Absolute photon intensity and content of higher harmonic radiation.

We describe the commissioning of a new electron-ion coincidence spectrometer used to diagnose the photon beam from a plane grating monochromator beamline at the ASTRID2 synchrotron radiation facility. The spectrometer allows determination of the absolute photon intensity by calibration to the photoabsorption cross sections of known gases, such as the rare gases Ar, Kr, and Xe presented here. The spectrometer operates at very low pressure (∼10-8-10-9 mbar) and-due to the coincidence electron-ion detection scheme-the detector efficiencies can be determined routinely; hence, the spectrometer can be recalibrated swiftly. By variation of a single potential of the spectrometer, the content of higher order radiation in the monochromatized synchrotron radiation can be analyzed. The layout and operation of the synchrotron radiation beamline at ASTRID2 and its additional photon diagnostic units are additionally described.

A new endstation for extreme-ultraviolet spectroscopy of free clusters and nanodroplets.

In this work, we present a new endstation for the AMOLine of the ASTRID2 synchrotron at Aarhus University, which combines a cluster and nanodroplet beam source with a velocity map imaging and time-of-flight spectrometer for coincidence imaging spectroscopy. Extreme-ultraviolet spectroscopy of free nanoparticles is a powerful tool for studying the photophysics and photochemistry of resonantly excited or ionized nanometer-sized condensed-phase systems. Here, we demonstrate this capability by performing photoelectron-photoion coincidence experiments with pure and doped superfluid helium nanodroplets. Different doping options and beam sources provide a versatile platform to generate various van der Waals clusters as well as He nanodroplets. We present a detailed characterization of the new setup and show examples of its use for measuring high-resolution yield spectra of charged particles, time-of-flight ion mass spectra, anion-cation coincidence spectra, multi-coincidence electron spectra, and angular distributions. A particular focus of the research with this new endstation is on intermolecular charge and energy-transfer processes in heterogeneous nanosystems induced by valence-shell excitation and ionization.

Atomistic dynamics of elimination and nucleophilic substitution disentangled for the F- + CH3CH2Cl reaction.

Chemical reaction dynamics are studied to monitor and understand the concerted motion of several atoms while they rearrange from reactants to products. When the number of atoms involved increases, the number of pathways, transition states and product channels also increases and rapidly presents a challenge to experiment and theory. Here we disentangle the dynamics of the competition between bimolecular nucleophilic substitution (SN2) and base-induced elimination (E2) in the polyatomic reaction F- + CH3CH2Cl. We find quantitative agreement for the energy- and angle-differential reactive scattering cross-sections between ion-imaging experiments and quasi-classical trajectory simulations on a 21-dimensional potential energy hypersurface. The anti-E2 pathway is most important, but the SN2 pathway becomes more relevant as the collision energy is increased. In both cases the reaction is dominated by direct dynamics. Our study presents atomic-level dynamics of a major benchmark reaction in physical organic chemistry, thereby pushing the number of atoms for detailed reaction dynamics studies to a size that allows applications in many areas of complex chemical networks and environments.

Influence of Vibrational Excitation on the Reaction of F- with CH3I: Spectator Mode Behavior, Enhancement, and Suppression.

Detailed insight into chemical reaction dynamics can be obtained by probing the effect of mode-specific vibrational excitation. Suppression or enhancement of reactivity is possible as is already known from the Polanyi rules. In the reaction F- + CH3I, we found vibrational enhancement, suppression, and spectator mode dynamics in the four different reaction channels. For this system we have probed the influence of symmetric CH-stretching vibration over a collision energy range of 0.7-2.3 eV. Proton transfer is significantly enhanced, while for the nucleophilic substitution channel the spectator mode dynamics at lower collision energies unexpectedly move toward enhancement at higher collision energies. In contrast, for two halide abstraction channels, forming FI- and FHI-, we found an overall suppression, which stems mainly from a suppression of the FHI- product. We compare these results to quasiclassical trajectory calculations and with the sudden vector projection model.

Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noise.

It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the cell's changing environment. While there are many methods to study the effect of intrinsic noise on the system dynamics, few exist to study the influence of both types of noise. Here we show how one can extend the conventional linear-noise approximation to allow for the rapid evaluation of the molecule numbers statistics of a biochemical network influenced by intrinsic noise and by slow lognormally distributed extrinsic noise. The theory is applied to simple models of gene regulatory networks and its validity confirmed by comparison with exact stochastic simulations. In particular, we consider three important biological examples. First, we investigate how extrinsic noise modifies the dependence of the variance of the molecule number fluctuations on the rate constants. Second, we show how the mutual information between input and output of a network motif is affected by extrinsic noise. And third, we study the robustness of the ubiquitously found feed-forward loop motifs when subjected to extrinsic noise.