Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy.

Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.

Site-dependent nuclear dynamics in core-excited butadiene.

Symmetry breaking and competition between electronic decay and nuclear dynamics are major factors determining whether the memory of the initial core-hole localisation in a molecule is retained long enough to affect fragmentation. We investigate the fate of core holes localised at different sites in the free 1,3 trans butadiene molecule by using synchrotron radiation to selectively excite core electrons from different C 1s sites to π* orbitals. Fragmentation involving bonds localised at the site of the core hole provides clear evidence for preferential bond breaking for a core hole located at the terminal carbon site, while the signature of localisation is weak for a vacancy on the central carbon site. The origin of this difference is attributed to out-of-plane vibrations, and statistical evaporation of protons for vacancies located at the central carbon sites.

Fission of charged nano-hydrated ammonia clusters - microscopic insights into the nucleation processes.

While largely studied on the macroscopic scale, the dynamics leading to nucleation and fission processes in atmospheric aerosols are still poorly understood at the molecular level. Here, we present a joint experimental-theoretical study of a model system consisting of hydrogen-bonded ammonia and water molecules. Experimentally, the clusters were produced via adiabatic co-expansion. Double ionization ionic products were prepared using synchrotron radiation and analyzed with coincidence mass- and 3D momentum spectroscopy. Calculations were carried out using ab initio molecular dynamics to understand the fragmentation within the first ∼500 fs. Further exploration of the potential energy surfaces was performed at a DFT level of theory to gain information on the energetics of the processes. Water was identified as an efficient nano-droplet stabilizer, and is found to have a significant effect even at low water content. On the molecular level, the stabilizing role of water can be related to an increase in the dissociation energy between ammonia molecules and the water enriched environment at the cluster surface. Furthermore, our results support the role of ammonium as a charge carrier in the solution, preferentially bound to surrounding ammonia molecules, which can influence the atmospheric nucleation process.

The role of charge and proton transfer in fragmentation of hydrogen-bonded nanosystems: the breakup of ammonia clusters upon single photon multi-ionization.

The charge and proton dynamics in hydrogen-bonded networks are investigated using ammonia as a model system. The fragmentation dynamics of medium-sized clusters (1-2 nm) upon single photon multi-ionization is studied, by analyzing the momenta of small ionic fragments. The observed fragmentation pattern of the doubly- and triply-charged clusters reveals a spatial anisotropy of emission between fragments (back-to-back). Protonated fragments exhibit a distinct kinematic correlation, indicating a delay between ionization and fragmentation (fission). The different kinematics observed for channels containing protonated and unprotonated species provides possible insights into the prime mechanisms of charge and proton transfer, as well as proton hopping, in such a nanoscale system.

Photofragmentation of gas-phase acetic acid and acetamide clusters in the vacuum ultraviolet region.

Photofragmentation of gas-phase acetamide and acetic acid clusters produced by a supersonic expansion source has been studied using time-of-flight mass spectrometry and the partial ion yield (PIY) technique combined with tunable vacuum-ultraviolet synchrotron radiation. Appearance energies of the clusters and their fragments were experimentally determined from the PIY measurements. The effect of clusterization conditions on the formation and fragmentation of acetic acid clusters was investigated. Ab initio quantum mechanical calculations were performed on both samples' dimers to find their neutral and ionized geometries as well as proton transfer energy barriers leading to the optimal geometries. In the case of the acetamide dimer, the reaction resulting in the production of ammoniated acetamide was probed, and the geometry of the obtained ion was calculated.

A scanning focus nuclear microscope with multi-pinhole collimation.

Microscopic nuclear imaging down to spatial resolutions of a few hundred microns can already be achieved using low-energy gamma emitters (e.g.125I, ∼30 keV) and a basic single micro-pinhole gamma camera. This has been applied toin vivomouse thyroid imaging, for example. For clinically used radionuclides such as99mTc, this approach fails due to penetration of the higher-energy gamma photons through the pinhole edges. To overcome these resolution degradation effects, we propose a new imaging approach: scanning focus nuclear microscopy (SFNM). We assess SFNM using Monte Carlo simulations for clinically used isotopes. SFNM is based on the use of a 2D scanning stage with a focused multi-pinhole collimator containing 42 pinholes with narrow pinhole aperture opening angles to reduce photon penetration. All projections of different positions are used to iteratively reconstruct a three-dimensional image from which synthetic planar images are generated. SFNM imaging was tested using a digital Derenzo resolution phantom and a mouse ankle joint phantom containing99mTc (140 keV). The planar images were compared with those obtained using a single-pinhole collimator, either with matched pinhole diameter or with matched sensitivity. The simulation results showed an achievable99mTc image resolution of 0.04 mm and detailed99mTc bone images of a mouse ankle with SFNM. SFNM has strong advantages over single-pinhole imaging in terms of spatial resolution.

Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble.

Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.

The origin of enhanced [Formula: see text] production from photoionized CO2 clusters.

CO2-rich planetary atmospheres are continuously exposed to ionising radiation driving major photochemical processes. In the Martian atmosphere, CO2 clusters are predicted to exist at high altitudes motivating a deeper understanding of their photochemistry. In this joint experimental-theoretical study, we investigate the photoreactions of CO2 clusters (≤2 nm) induced by soft X-ray ionisation. We observe dramatically enhanced production of [Formula: see text] from photoionized CO2 clusters compared to the case of the isolated molecule and identify two relevant reactions. Using quantum chemistry calculations and multi-coincidence mass spectrometry, we pinpoint the origin of this enhancement: A size-dependent structural transition of the clusters from a covalently bonded arrangement to a weakly bonded polyhedral geometry that activates an exothermic reaction producing [Formula: see text]. Our results unambiguously demonstrate that the photochemistry of small clusters/particles will likely have a strong influence on the ion balance in atmospheres.

Chemical Understanding of the Limited Site-Specificity in Molecular Inner-Shell Photofragmentation.

In many cases fragmentation of molecules upon inner-shell ionization is very unspecific with respect to the initially localized ionization site. Often this finding is interpreted in terms of an equilibration of internal energy into vibrational degrees of freedom after Auger decay. We investigate the X-ray photofragmentation of ethyl trifluoroacetate upon core electron ionization at environmentally distinct carbon sites using photoelectron-photoion-photoion coincidence measurements and ab initio electronic structure calculations. For all four carbon ionization sites, the Auger decay weakens the same bonds and transfers the two charges to opposite ends of the molecule, which leads to a rapid dissociation into three fragments, followed by further fragmentation steps. The lack of site specificity is attributed to the character of the dicationic electronic states after Auger decay instead of a fast equilibration of internal energy.