Browse
Submit Data
Databases
API
Help

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Water radiolysis by low-energy carbon projectiles from first-principles molecular dynamics.

ABSTRACT: Water radiolysis by low-energy carbon projectiles is studied by first-principles molecular dynamics. Carbon projectiles of kinetic energies between 175 eV and 2.8 keV are shot across liquid water. Apart from translational, rotational and vibrational excitation, they produce water dissociation. The most abundant products are H and OH fragments. We find that the maximum spatial production of radiolysis products, not only occurs at low velocities, but also well below the maximum of energy deposition, reaching one H every 5 Å at the lowest speed studied (1 Bohr/fs), dissociative collisions being more significant at low velocity while the amount of energy required to dissociate water is constant and much smaller than the projectile's energy. A substantial fraction of the energy transferred to fragments, especially for high velocity projectiles, is in the form of kinetic energy, such fragments becoming secondary projectiles themselves. High velocity projectiles give rise to well-defined binary collisions, which should be amenable to binary approximations. This is not the case for lower velocities, where multiple collision events are observed. H secondary projectiles tend to move as radicals at high velocity, as cations when slower. We observe the generation of new species such as hydrogen peroxide and formic acid. The former occurs when an O radical created in the collision process attacks a water molecule at the O site. The latter when the C projectile is completely stopped and reacts with two water molecules.

SUBMITTER: Kohanoff J

PROVIDER: S-EPMC5340357 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Carbon and other light element contents in the Earth's core based on first-principles molecular dynamics.

Project description:Carbon (C) is one of the candidate light elements proposed to account for the density deficit of the Earth's core. In addition, C significantly affects siderophile and chalcophile element partitioning between metal and silicate and thus the distribution of these elements in the Earth's core and mantle. Derivation of the accretion and core-mantle segregation history of the Earth requires, therefore, an accurate knowledge of the C abundance in the Earth's core. Previous estimates of the C content of the core differ by a factor of ∼20 due to differences in assumptions and methods, and because the metal-silicate partition coefficient of C was previously unknown. Here we use two-phase first-principles molecular dynamics to derive this partition coefficient of C between liquid iron and silicate melt. We calculate a value of 9 ± 3 at 3,200 K and 40 GPa. Using this partition coefficient and the most recent estimates of bulk Earth or mantle C contents, we infer that the Earth's core contains 0.1-0.7 wt% of C. Carbon thus plays a moderate role in the density deficit of the core and in the distribution of siderophile and chalcophile elements during core-mantle segregation processes. The partition coefficients of nitrogen (N), hydrogen, helium, phosphorus, magnesium, oxygen, and silicon are also inferred and found to be in close agreement with experiments and other geochemical constraints. Contents of these elements in the core derived from applying these partition coefficients match those derived by using the cosmochemical volatility curve and geochemical mass balance arguments. N is an exception, indicating its retention in a mantle phase instead of in the core.

| S-EPMC3511726 | biostudies-other

Intrinsic molecular vibration and rigorous vibrational assignment of benzene by first-principles molecular dynamics.

Project description:Vibrational assignment, which establishes the correspondence between vibrational modes and spectral frequencies, is a key step in any spectroscopic study. Due to the lack of experimental technique to directly observe the thermal vibration of atoms, the assignment is usually done by empirical trial-and-error method with considerable uncertainty. Here we demonstrate a successful study of intrinsic molecular vibration property based on first-principles molecular dynamics trajectory. A unified approach for calculating and assigning vibrational frequencies is developed and applied to solve some historical issues of benzene vibration. As a major achievement, the experimental frequencies of benzene a2g and b2u vibrations are reassigned, which breaks a deadlock in contemporary spectroscopic science and removes a cloud over the application of density-functional theory in organic chemistry. This work paves the way for the comprehensive realization of the first-principles spectroscopic research, and provides crucial clues to solve the century-old problems of Kekule resonance, π-deformation, and aromaticity.

| S-EPMC7578012 | biostudies-literature

First-Principles Molecular Dynamics Insight into the Atomic Level Degradation Pathway of Phosphorene.

Project description:Despite its remarkable properties, phosphorene is not promising for device application due to its instability or gradual degradation under ambient conditions. The issue still persists, and no technological solution is available to address this degradation due to a lack of clarity about degradation dynamics at the atomic level. Here, we discuss atomic level degradation dynamics of phosphorene under ambient conditions while investigating the involvement of degrading agents like oxygen and water using density functional theory and first-principles molecular dynamics computations. The study reveals that the oxygen molecule dissociates spontaneously over pristine phosphorene in an ambient environment, resulting in an exothermic reaction, which is boosted further by increasing the partial pressure and temperature. The surface reaction is mainly due to the lone pair electrons of phosphorous atoms, making the degradation directional and spontaneous under oxygen atoms. We also found that while the pristine phosphorene is hydrophobic, it becomes hydrophilic after surface oxidation. Furthermore, water molecules play a vital role in the degradation process by changing the reaction dynamics path of the phosphorene-oxygen interaction and reducing the activation energy and reaction energy due to its catalyzing action. In addition, our study reveals the role of phosphorous vacancies in the degradation, which we found to act as an epicenter for the observed oxidation. The oxygen attacks directly over the vacant site and reacts faster compared to its pristine counterpart. As a result, phosphorene edges resembling extended vacancy are prominent reaction sites that oxidize anisotropically due to different bond angle strains. Our study clears the ambiguities in the kinetics of phosphorene degradation, which will help engineer passivation techniques to make phosphorene devices stable in the ambient environment.

| S-EPMC8756585 | biostudies-literature

Penetration of granular projectiles into a water target.

Project description:The penetration of low-speed projectiles into a water target has been studied in the last several years to understand the physics behind the formation and collapse of cavities. In such studies, the projectiles employed were solid bodies or liquid drops. Here we report similar impact experiments using granular projectiles, with the aim to investigate how the morphology of the cavities is determined by the balance between the dynamic pressure exerted by the fluid and the cohesive strength of the impactors. From the results we present and discuss in this manuscript, we speculate on the dynamics of meteorite disintegration in the atmosphere of our planet.

| S-EPMC4208039 | biostudies-literature

Porous Si Partially Filled with Water Molecules-Crystal Structure, Energy Bands and Optical Properties from First Principles.

Project description:The paper reports the results on first-principles investigation of energy band spectrum and optical properties of bulk and nanoporous silicon. We present the evolution of energy band-gap, refractive indices and extinction coefficients going from the bulk Si of cubic symmetry to porous Si with periodically ordered square-shaped pores of 7.34, 11.26 and 15.40 Å width. We consider two natural processes observed in practice, the hydroxylation of Si pores (introduction of OH groups into pores) and the penetration of water molecules into Si pores, as well as their impact on the electronic spectrum and optical properties of Si superstructures. The penetration of OH groups into the pores of the smallest 7.34 Å width causes a disintegration of hydroxyl groups and forms non-bonded protons which might be a reason for proton conductivity of porous Si. The porosity of silicon increases the extinction coefficient, k, in the visible range of the spectrum. The water structuring in pores of various diameters is analysed in detail. By using the bond valence sum approach we demonstrate that the types and geometry of most of hydrogen bonds created within the pores manifest a structural evolution from distorted hydrogen bonds inherent to small pores (?7 Å) to typical hydrogen bonds observed by us in larger pores (?15 Å) which are consistent with those observed in a wide database of inorganic crystals.

| S-EPMC7075300 | biostudies-literature

Role of Water on the Rotational Dynamics of the Organic Methylammonium Cation: A First Principles Analysis.

Project description:Understanding the degradation mechanisms of lead-halide perovskites (CH3NH3PbI3) under exposure to liquid/aerosol water is an essential problem within the photovoltaic community. Herein we investigate both the static and the dynamic properties of the methylammonuim cation (MA) as it coordinates with invading water molecules (MA.(H2O)n, n?=?1, 2, 3, 4) using both stationary state quantum mechanics and first principle molecular dynamics simulations. Various solvation structures of MA were characterized by their stabilization energies, dipoles, and Maximally-Localized Wannier Function (MLWF) centers. Calculation - and analysis - of vibrational shifts in the IR spectral region were performed for hydrated complexes; the locations of [Formula: see text] stretching vibrations allude to significant hydrogen bonding between MA and the water molecules. Through Fourier analysis of the rotational dynamics on several MA · (H2O)n complexes, we conclude that the water molecules dampen the rotational motion of the MA as the intermolecular bonds formed between the water molecules and the MA act to hinder the rotation of the cation; these findings give explanatory support to earlier computational observations of humidity effects on perovskites (i.e., CH3NH3PbI3) materials. This work is a step toward understanding the water-MA cation interaction in bulk perovskites, thus providing greater understanding of in situ instability/degradation of perovskite bulk materials.

| S-EPMC6346111 | biostudies-literature

First-Principles Molecular Dynamics Simulations on Water-Solid Interface Behavior of H<sub>2</sub>O-Based Atomic Layer Deposition of Zirconium Dioxide.

Project description:As an important inorganic material, zirconium dioxide (ZrO2) has a wide range of applications in the fields of microelectronics, coating, catalysis and energy. Due to its high dielectric constant and thermodynamic stability, ZrO2 can be used as dielectric material to replace traditional silicon dioxide. Currently, ZrO2 dielectric films can be prepared by atomic layer deposition (ALD) using water and zirconium precursors, namely H2O-based ALD. Through density functional theory (DFT) calculations and first-principles molecular dynamics (FPMD) simulations, the adsorption and dissociation of water molecule on the ZrO2 surface and the water-solid interface reaction were investigated. The results showed that the ZrO2 (111) surface has four Lewis acid active sites with different coordination environments for the adsorption and dissociation of water. The Zr atom on the surface can interacted with the O atom of the water molecule via the p orbital of the O atom and the d orbital of the Zr atom. The water molecules could be dissociated via the water-solid interface reaction of the first or second layer of water molecules with the ZrO2 (111) surface. These insights into the adsorption and dissociation of water and the water-solid interface reaction on the ZrO2 surface could also provide a reference for the water-solid interface behavior of metal oxides, such as H2O-based ALD.

| S-EPMC9783483 | biostudies-literature

Influence of water contamination on the sputtering of silicon with low-energy argon ions investigated by molecular dynamics simulations.

Project description:Focused ion beams (FIB) are a common tool in nanotechnology for surface analysis, sample preparation for electron microscopy and atom probe tomography, surface patterning, nanolithography, nanomachining, and nanoprinting. For many of these applications, a precise control of ion-beam-induced processes is essential. The effect of contaminations on these processes has not been thoroughly explored but can often be substantial, especially for ultralow impact energies in the sub-keV range. In this paper we investigate by molecular dynamics (MD) simulations how one of the most commonly found residual contaminations in vacuum chambers (i.e., water adsorbed on a silicon surface) influences sputtering by 100 eV argon ions. The incidence angle was changed from normal incidence to close to grazing incidence. For the simulation conditions used in this work, the adsorption of water favours the formation of defects in silicon by mixing hydrogen and oxygen atoms into the substrate. The sputtering yield of silicon is not significantly changed by the contamination, but the fraction of hydrogen and oxygen atoms that is sputtered largely depends on the incidence angle. This fraction is the largest for incidence angles between 70 and 80° defined with respect to the sample surface. Overall, it changes from 25% to 65%.

| S-EPMC9520830 | biostudies-literature

First-principles-based reaction kinetics from reactive molecular dynamics simulations: Application to hydrogen peroxide decomposition.

Project description:This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over ∼10-nm spatial scales for ∼1 ns, which is prohibitively impractical with QM. Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the reactive molecular dynamics (RMD). We focus here on showing that it is practical to extract from such RMD the reaction mechanisms and kinetics information needed to describe the reactions analytically. This analytic description can then be used to incorporate the correct reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of ∼10 nm to micrometers to millimeters to meters using analytic approaches of computational fluid dynamics and/or continuum chemical dynamics. In the paper we lay out the strategy to extract the mechanisms and rate parameters automatically without the necessity of knowing any details of the chemistry. We consider this to be a proof of concept. We refer to the process as RMD2Kin (reactive molecular dynamics to kinetics) for the general approach and as ReaxMD2Kin (ReaxFF molecular dynamics to kinetics) for QM-ReaxFF-based reaction kinetics.

| S-EPMC6744889 | biostudies-literature

Catchment Level Water Resource Constraints on UK Policies for Low-Carbon Energy System Transitions by 2030.

Project description:The UK government has proposed different low-carbon energy system options that lead to meeting its greenhouse gas emissions target of 80% reduction on 1990 levels by 2050. While these energy system options meet emission targets at feasible economic cost, water requirement for the deployment of the proposed energy technology mix is not adequately accounted for. This may become critical, as some of the proposed energy technologies are relatively more water-intensive, and could result in significant future water resource constraints. Previous studies have analyzed the potential water resource constraints of future energy systems in the UK at national scale. However, water must be considered as a local resource with significant regional variability. This paper uses a linear spatial-downscaling model to allocate water-intensive energy system infrastructure/technologies at catchment level, and estimates water requirements for the deployment of these technologies for the Committee on Climate Change Carbon Budgets in 2030. The paper concludes that while national-scale analysis shows minimal long-term water related impacts, catchment level appraisal of water resource requirements reveals significant constraints in some locations. This has important implications for regions where the water-energy nexus must be analyzed at appropriate spatial resolution to capture the full water resource impact of national energy policy.

| S-EPMC6607168 | 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