Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structures and Energetics of Neutral and Cationic Pyrene Clusters.

ABSTRACT: The low energy structures of neutral and cationic pyrene clusters containing up to seven molecules are searched through a global exploration scheme combining parallel tempering Monte Carlo algorithm and local quenches. The potential energies are computed at the density functional based tight binding level for neutrals and configuration interaction density functional based tight binding for cations in order to treat properly the charge resonance. New simplified versions of these schemes are also presented and used during the global exploration. Neutral clusters are shown to be made of compact assemblies of sub-blocs containing up to three units whereas cations present a charged dimer or trimer core surrounded by neutral units. The structural features of the clusters are analyzed and correlated for the cation with the charge distribution. The stability of clusters is also discussed in terms of cohesive and evaporation energies. Adiabatic and vertical ionization potentials are also discussed.

SUBMITTER: Dontot L

PROVIDER: S-EPMC6917508 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Structures and Energetics of Neutral and Cationic Pyrene Clusters.

Dontot Léo L Spiegelman Fernand F Rapacioli Mathias M

The journal of physical chemistry. A 20191029 44

The low energy structures of neutral and cationic pyrene clusters containing up to seven molecules are searched through a global exploration scheme combining parallel tempering Monte Carlo algorithm and local quenches. The potential energies are computed at the density functional based tight binding level for neutrals and configuration interaction density functional based tight binding for cations in order to treat properly the charge resonance. New simplified versions of these schemes are also ...[more]

PMID: 31589446

Similar Datasets

Photoionization, Structures, and Energetics of Na-Doped Formic Acid-Water Clusters.

Project description:The influence of formic acid on water cluster aggregation has been investigated experimentally by mass spectrometry and tunable UV laser ionization applied to Na-doped clusters formed in the supersonic expansion of water vapors seeded with formic acid (FA) as well as theoretically using high level quantum chemistry methods. The mass spectra of Na-FA(H2 O)n clusters show an enlarging of mass distribution toward heavier clusters with respect to the Na-(H2 O)n clusters, suggesting similar mass distribution in neutral clusters and an influence of formic acid in water aggregation. Density functional theory and coupled-cluster type (DLPNO-CCSD(T)) calculations have been used to calculate structures and energetics of neutral and ionized Na-FA(H2 O)n as well as neutral FA(H2 O)n . Na-doped clusters are characterized by very stable geometries. The theoretical adiabatic ionization potential values match pretty well the measured appearance energies and the calculated first six electronic excited states show Rydberg-type characters, indicating possible autoionization contributions in the mass spectra. Finally, theoretical calculations on neutral FA(H2 O)n clusters show the possibility of similarly stable structures in small clusters containing up to n=4-5 water molecules, where FA interacts significantly with waters. This suggests that FA can compete with water molecules in the starting stage of the aggregation process, by forming stable nucleation seed.

| S-EPMC9303463 | biostudies-literature

Infrared Spectroscopy of Neutral and Cationic Benzonitrile–Methanol Binary Clusters in Supersonic Jets

Project description: Not available

| S-EPMC11206090 | biostudies-literature

Thermal evaporation of pyrene clusters.

Project description:This work presents a study of the thermal evaporation and stability of pyrene (C16H10)n clusters. Thermal evaporation rates of positively charged mass-selected clusters are measured for sizes in the range n = 3-40 pyrene units. The experimental setup consists of a gas aggregation source, a thermalization chamber, and a time of flight mass spectrometer. A microcanonical Phase Space Theory (PST) simulation is used to determine the dissociation energies of pyrene clusters by fitting the experimental breakdown curves. Calculations using the Density Functional based Tight Binding combined with a Configuration Interaction (CI-DFTB) model and a hierarchical optimization scheme are also performed in the range n = 2-7 to determine the harmonic frequencies and a theoretical estimation of the dissociation energies. The frequencies are used in the calculations of the density of states needed in the PST simulations, assuming an extrapolation scheme for clusters larger than 7 units. Using the PST model with a minimal set of adjustable parameters, we obtain good fits of the experimental breakdown curves over the full studied size range. The approximations inherent to the PST simulation and the influence of the used parameters are carefully estimated. The derived dissociation energies show significant variations over the studied size range. Compared with neutral clusters, significantly higher values of the dissociation energies are obtained for the smaller sizes and attributed to charge resonance in line with CI-DFTB calculations.

| S-EPMC6908449 | biostudies-literature

The size-dependent influence of palladium doping on the structures of cationic gold clusters.

Project description:The physicochemical properties of small metal clusters strongly depend on their precise geometry. Determining such geometries, however, is challenging, particularly for clusters formed by multiple elements. In this work, we combine infrared multiple photon dissociation spectroscopy and density functional theory calculations to investigate the lowest-energy structures of Pd doped gold clusters, PdAu n-1 + (n ≤ 10). The high-quality experimental spectra allow for an unambiguous determination of the structures adopted by the clusters. Our results show that the Pd-Au interaction is so large that the structures of PdAu n-1 + and Au n + are very different. Pd doping induces a 2D to 3D transition at much smaller cluster sizes than for pure Au n + clusters. PdAu n-1 + clusters are three-dimensional from n = 4, whereas for Au n + this transition only takes place at n = 7. Despite the strong Au-Pd interaction, the Au n-1 + cluster geometries remain recognizable in PdAu n-1 + up to n = 7. This is particularly clear for PdAu6 +. In PdAu8 + and PdAu9 +, Pd triggers major rearrangements of the Au clusters, which adopt pyramidal shapes. For PdAu4 + we find a geometry that was not considered in previous studies, and the geometry found for PdAu8 + does not correspond to the lowest-energy structure predicted by DFT, suggesting kinetic trapping during formation. This work demonstrates that even with the continuous improvement of computational methods, unambiguous assignment of cluster geometries still requires a synergistic approach, combining experiment and computational modelling.

| S-EPMC8548875 | biostudies-literature

Size-Resolved Electron Solvation in Neutral Water Clusters.

Project description:Cluster-size-resolved ultrafast dynamics of the solvated electron in neutral water clusters with n = 3 to ∼200 molecules are studied with pump-probe time-of-flight mass spectrometry after below band gap excitation. For the smallest clusters, no longer-lived (>100-200 fs) hydrated electrons were detected, indicating a minimum size of n ∼ 14 for being able to sustain hydrated electrons. Larger clusters show a systematic increase of the number of hydrated electrons per molecule on the femtosecond to picosecond time scale. We propose that with increasing cluster size the underlying dynamics is governed by more effective electron formation processes combined with less effective electron loss processes, such as ultrafast hydrogen ejection and recombination. It appears unlikely that any size dependence of the solvent relaxation dynamics would be reflected in the observed time-resolved ion yields.

| S-EPMC8237264 | biostudies-literature

Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds.

Project description:A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X···I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.

| S-EPMC7070532 | biostudies-literature

Liquid-like cationic sub-lattice in copper selenide clusters.

Project description:Super-ionic solids, which exhibit ion mobilities as high as those in liquids or molten salts, have been employed as solid-state electrolytes in batteries, improved thermoelectrics and fast-ion conductors in super-capacitors and fuel cells. Fast-ion transport in many of these solids is supported by a disordered, 'liquid-like' sub-lattice of cations mobile within a rigid anionic sub-lattice, often achieved at high temperatures or pressures via a phase transition. Here we show that ultrasmall clusters of copper selenide exhibit a disordered cationic sub-lattice under ambient conditions unlike larger nanocrystals, where Cu+ ions and vacancies form an ordered super-structure similar to the bulk solid. The clusters exhibit an unusual cationic sub-lattice arrangement wherein octahedral sites, which serve as bridges for cation migration, are stabilized by compressive strain. The room-temperature liquid-like nature of the Cu+ sub-lattice combined with the actively tunable plasmonic properties of the Cu2Se clusters make them suitable as fast electro-optic switches.

| S-EPMC5321727 | biostudies-literature

Argon Adsorption on Cationic Gold Clusters Aun+ (n ≤ 20).

Project description:The interaction of Aun+ (n ≤ 20) clusters with Ar is investigated by combining mass spectrometric experiments and density functional theory calculations. We show that the inert Ar atom forms relatively strong bonds with Aun+. The strength of the bond strongly varies with the cluster size and is governed by a fine interplay between geometry and electronic structure. The chemical bond between Aun+ and Ar involves electron transfer from Ar to Au, and a stronger interaction is found when the Au adsorption site has a higher positive partial charge, which depends on the cluster geometry. Au15+ is a peculiar cluster size, which stands out for its much stronger interaction with Ar than its neighbors, signaled by a higher abundance in mass spectra and a larger Ar adsorption energy. This is shown to be a consequence of a low-coordinated Au adsorption site in Au15+, which possesses a large positive partial charge.

| S-EPMC8272223 | biostudies-literature

Neutral and Cationic Complexes of Silicon(IV) Halides with Phosphine Ligands.

Project description:The reaction of SiI4 and PMe3 in n-hexane produced the yellow salt, [SiI3(PMe3)2]I, confirmed from its X-ray structure, containing a trigonal bipyramidal cation with trans-phosphines. This contrasts with the six-coordination found in (the known) trans-[SiX4(PMe3)2] (X = Cl, Br) complexes. The diphosphines o-C6H4(PMe2)2 and Et2P(CH2)2PEt2 form six-coordinate cis-[SiI4(diphosphine)], which were also characterized by X-ray crystallography, multinuclear NMR, and IR spectroscopy. Reaction of trans-[SiX4(PMe3)2] (X = Cl, Br) with Na[BArF] (BArF = [B{3,5-(CF3)2C6H3}4]) produced five-coordinate [SiX3(PMe3)2][BArF], but while Me3SiO3SCF3 also abstracted chloride from trans-[SiCl4(PMe3)2], the reaction products were six-coordinate complexes [SiCl3(PMe3)2(OTf)] and [SiCl2(PMe3)2(OTf)2] with the triflate coordinated. X-ray crystal structures were obtained for [SiCl3(PMe3)2][BArF] and [SiCl2(PMe3)2(OTf)2]. The charge distribution across the silicon species was also examined by natural bond orbital (NBO) analyses of the computed density functional theory (DFT) wavefunctions. For the [SiX4(PMe3)2] and [SiX3(PMe3)2]+ complexes, the positive charge on Si decreases and the negative charge on X decreases going from X = F to X = I. Upon going from [SiX4(PMe3)2] to [SiX3(PMe3)2]+, i.e., removal of X-, there is an increase in positive charge on Si and a decrease in negative charge on the X centers (except for the case X = F). The positive charge on P shows a slight decrease.

| S-EPMC9597660 | biostudies-literature

Supramolecular Structures of Enzyme Clusters.

Project description:The structural characterization of subtilisin mesoscale clusters, which were previously shown to induce supramolecular order in biocatalytic self-assembly of Fmoc-dipeptides, was carried out by synchrotron small-angle X-ray, dynamic, and static light scattering measurements. Subtilisin molecules self-assemble to form supramolecular structures in phosphate buffer solutions. Structural arrangement of subtilisin clusters at 55 °C was found to vary systematically with increasing enzyme concentration. Static light scattering measurements showed the cluster structure to be consistent with a fractal-like arrangement, with fractal dimension varying from 1.8 to 2.6 with increasing concentration for low to moderate enzyme concentrations. This was followed by a structural transition around the enzyme concentration of 0.5 mg mL(-1) to more compact structures with significantly slower relaxation dynamics, as evidenced by dynamic light scattering measurements. These concentration-dependent supramolecular enzyme clusters provide tunable templates for biocatalytic self-assembly.

| S-EPMC3688366 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data