Protonated Clusters of Neon and Krypton.
Ontology highlight
ABSTRACT:
SUBMITTER: Gatchell M
PROVIDER: S-EPMC6914732 | biostudies-literature | 2019 Dec
REPOSITORIES: biostudies-literature
Publications
Protonated Clusters of Neon and Krypton.
Gatchell Michael M Martini Paul P Schiller Arne A Scheier Paul P
Journal of the American Society for Mass Spectrometry 20191024 12
We present a study of cationic and protonated clusters of neon and krypton. Recent studies using argon have shown that protonated rare gas clusters can have very different magic sizes than pure, cationic clusters. Here, we find that neon behaves similarly to argon, but that the cationic krypton is more similar to its protonated counterparts than the lighter rare gases are, sharing many of the same magic numbers. ...[more]
Similar Datasets
Project description:Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplification due to the electronic polarizability. Our experimental, polarization-resolved light-dark difference spectrum of the light-driven proton pump bacteriorhodopsin exhibits a pronounced dichroic continuum band. Our results suggest that the protonated water cluster responsible for the continuum band of bacteriorhodopsin is oriented perpendicularly to the membrane normal.
| S-EPMC5778031 | biostudies-literature
Project description:Protonated mixed pyrene-water clusters, (Py)m(H2O)nH+, where m = [1-3] and n = [1-10], are generated using a cryogenic molecular cluster source. Subsequently, the mass-selected mixed clusters undergo controlled collisions with rare gases, and the resulting fragmentation mass spectra are meticulously analyzed to discern distinct fragmentation channels. Notably, protonated water cluster fragments emerge for n ≥ 3, whereas they are absent for n = 1 and 2. The experimental results are complemented by theoretical calculations of structures and energetics for (Py)(H2O)nH+ with n = [1-4]. These calculations reveal a shift in proton localization, transitioning from the pyrene molecule for n = 1 and 2 to water molecules for n ≥ 3. The results support a formation scenario wherein water molecules attach to protonated pyrene PyH+ seeds, and, by extension, to (Py)2H+ and (Py)3H+ seeds. Various isomers are identified, corresponding to potential protonation sites on the pyrene molecule. Protonated polycyclic aromatic hydrocarbons are likely to be formed in cold, dense interstellar clouds and protoplanetary disks due to the high proton affinity of these species. Our findings show that the presence of protonated PAHs in these environments could lead to the formation of water clusters and mixed carbon-water nanograins, having a potential impact on the water cycle in regions of planet formation.
| S-EPMC10866126 | biostudies-literature
Project description:Structures of neutral and protonated acetonitrile in the solvent phase are important to describe proton behavior and to calculate thermodynamic quantities related to the solvation of ions or molecules in acetonitrile. In this work, we provide data related to the calculation of the solvation free energy and enthalpy of the proton in acetonitrile. We have thoroughly explored the potential energy surfaces (PESs) of neutral and protonated acetonitrile clusters from dimer to heptamer in the solvent phase at both MN15/6-31++G(d,p) and MP2/aug-cc-pVDZ levels of theory. We report the structures and relative stability of neutral and protonated acetonitrile clusters in the solvent phase at the MN15/6-31++G(d,p) level of theory. In addition, enthalpies and free energies of neutral and protonated acetonitrile are also reported at the MP2/aug-cc-pVDZ and MP2/CBS levels of theory. Furthermore, Cartesian coordinates of the clusters in the solvent phase as optimized at the MP2/aug-cc-pVDZ level of theory are provided as supplementary file. The data provided in this work will be useful for further investigations that would involve neutral and protonated acetonitrile clusters. The free energies and enthalpies of the investigated clusters in the solvent phase have been used to compute the solvation free energy and enthalpy of the proton in acetonitrile. For more insights on the solvation free energy and enthalpy of the proton in acetonitrile, see the related main research paper [1].
| S-EPMC8170116 | biostudies-literature
Project description:Under high pressure, krypton, one of the most inert elements is predicted to become sufficiently reactive to form a new class of krypton compounds; krypton oxides. Using modern ab-initio evolutionary algorithms in combination with Density Functional Theory, we predict the existence of several thermodynamically stable Kr/O species at elevated pressures. In particular, our calculations indicate that at approx. 300 GPa the monoxide, KrO, should form spontaneously and remain thermo- and dynamically stable with respect to constituent elements and higher oxides. The monoxide is predicted to form non-molecular crystals with short Kr-O contacts, typical for genuine chemical bonds.
| S-EPMC4735652 | biostudies-literature
Project description:The self-consistent charge density functional tight-binding (SCC-DFTB) method has been actively employed to study proton-transfer processes in biological systems. Recent studies in the literature employing SCC-DFTB reported that the method favors the Zundel form of the hydrated proton over the Eigen form, both in gas-phase water clusters and in bulk water, in disagreement with both higher-level calculations and experimental data. In this work, we explore the performance of SCC-DFTB for protonated gas-phase water clusters and bulk water (the latter both with and without an excess proton) with a modified O-H repulsive potential reported in our earlier work and with on-site third-order expansion of the DFT energy. Our results show that, with the proper set of published parameters, SCC-DFTB does correctly favor the Eigen form of the hydrated proton as compared to the Zundel form, both in gas-phase clusters and in the bulk; the amphiphilic character of the hydrated proton discussed in the literature has also been observed. The analyses do, however, bring forth remaining limitations in terms of the solvation structure around the hydrated proton as well as the structure of bulk water, which can guide future improvements of the method.
| S-EPMC3101025 | biostudies-literature
Project description:The structures and spectral features of protonated noble gas clusters are examined using a first principles approach. Protonated noble gas monomers (NgH+) and dimers (NgH+Ng) have a linear structure, while the protonated noble gas trimers (Ng3H+) can have a T-shaped or linear structure. Successive binding energies for these complexes are calculated at the CCSD(T)/CBS level of theory. Anharmonic simulations for the dimers and trimers unveil interesting spectral features. The symmetric NgH+Ng are charactized by a set of progression bands, which involves one quantum of the asymmetric Ng-H+ stretch with multiple quanta of the symmetric Ng-H+ stretch. Such a spectral signature is very robust and is predicted to be observed in both T-shaped and linear isomers of Ng3H+. Meanwhile, for selected asymmetric NgH+Ng', a Fermi resonance interaction involving the first overtone of the proton bend with the proton stretch is predicted to occur in ArH+Kr and XeH+Kr.
| S-EPMC9143425 | biostudies-literature
Project description:Ultrafast spectroscopy with attosecond resolution has enabled the real time observation of ultrafast electron dynamics in atoms, molecules and solids. These experiments employ attosecond pulses or pulse trains and explore dynamical processes in a pump-probe scheme that is selectively sensitive to electronic state of matter via photoelectron or XUV absorption spectroscopy or that includes changes of the ionic state detected via photo-ion mass spectrometry. Here, we demonstrate how the implementation of combined photo-ion and absorption spectroscopy with attosecond resolution enables tracking the complex multidimensional excitation and decay cascade of an Auger auto-ionization process of a few femtoseconds in highly excited krypton. In tandem with theory, our study reveals the role of intermediate electronic states in the formation of multiply charged ions. Amplitude tuning of a dressing laser field addresses different groups of decay channels and allows exerting temporal and quantitative control over the ionization dynamics in rare gas atoms.
| S-EPMC5818503 | biostudies-literature
Project description:This is the first in vivo study to investigate the neuroprotective effects of krypton on focal cerebral ischemia. The aim of the study was to analyze the effect of 2 h of inhalation of a krypton-oxygen mixture (Kr 70%/O2 30%) on the recovery of neurological functions and the degree of brain damage in rats after photoinduced ischemic stroke (PIS) and to investigate the possible mechanisms responsible for this neuroprotection. Experiments were performed on male Wistar rats weighing 250-300 g (n = 32). Animals were randomized into four groups. Two groups (n = 20) underwent photoinduced ischemic stroke, followed by 2 h of inhalation of krypton-oxygen mixture consisting of Kr 70%/O2 30% or a nitrogen-oxygen breathing mixture consisting of N2 70%/O2 30%, followed by neurological examinations on days 3 and 7. The other two groups (n = 12) received only gas mixtures of the same concentration and exposure duration as in those in the PIS groups, then Western blot analysis of the potential molecular mechanisms was performed. The results of the study show that treatment with the krypton-oxygen mixture consisting of Kr 70%/O2 30% improves the neurological status on day 7 of observation, reduces the lesion volume according to the MRI examination and the number of Iba-1- and caspase-3-positive cells in the damaged area, promotes the activation of neoangiogenesis (an increase in the von Willebrand factor), and reduces the penumbra area and the number of NeuN-positive cells in it on day 14 of observation. Inhalation of the krypton-oxygen mixture also significantly increases the levels of phosphorylated AKT kinase (protein kinase B) and glycogen synthase kinase 3b (pGSK3b) and promotes the expression of transcription factor Nrf2, which was accompanied by the lowered expression of transcription factor NFkB (p50). Thus, we showed pronounced neuroprotection induced by krypton inhalation after stroke and identified the signaling pathways that may be responsible for restoring neurological functions and reducing damage.
| S-EPMC10968517 | biostudies-literature
Project description:We have performed a series of neutron scattering experiments on supercritical krypton. Our data and analysis allow us to characterize the Frenkel line crossover in this model monatomic fluid. The data from our measurements was analyzed using Empirical Potential Structure Refinement to determine the short- and medium-range structure of the fluids. We find evidence for several shells of neighbors which form approximately concentric rings of density about each atom. The ratio of second to first shell radius is significantly larger than in any crystal structure. Modeling krypton using a Lennard-Jones potential is shown to give significant errors, notably that the liquid is overstructured. The true potential appears to be longer ranged and with a softer core than the 6-12 powerlaws permit.
| S-EPMC9465677 | biostudies-literature
Project description:The National Ecological Observatory Network (NEON) provides open-access measurements of stable isotope ratios in atmospheric water vapor (δ2H, δ18O) and carbon dioxide (δ13C) at different tower heights, as well as aggregated biweekly precipitation samples (δ2H, δ18O) across the United States. These measurements were used to create the NEON Daily Isotopic Composition of Environmental Exchanges (NEON-DICEE) dataset estimating precipitation (P; δ2H, δ18O), evapotranspiration (ET; δ2H, δ18O), and net ecosystem exchange (NEE; δ13C) isotope ratios. Statistically downscaled precipitation datasets were generated to be consistent with the estimated covariance between isotope ratios and precipitation amounts at daily time scales. Isotope ratios in ET and NEE fluxes were estimated using a mixing-model approach with calibrated NEON tower measurements. NEON-DICEE is publicly available on HydroShare and can be reproduced or modified to fit user specific applications or include additional NEON data records as they become available. The NEON-DICEE dataset can facilitate understanding of terrestrial ecosystem processes through their incorporation into environmental investigations that require daily δ2H, δ18O, and δ13C flux data.
| S-EPMC9213549 | biostudies-literature