Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nucleation mechanisms and speciation of metal oxide clusters.

ABSTRACT: The self-assembly mechanisms of polyoxometalates (POMs) are still a matter of discussion owing to the difficult task of identifying all the chemical species and reactions involved. We present a new computational methodology that identifies the reaction mechanism for the formation of metal-oxide clusters and provides a speciation model from first-principles and in an automated manner. As a first example, we apply our method to the formation of octamolybdate. In our model, we include variables such as pH, temperature and ionic force because they have a determining effect on driving the reaction to a specific product. Making use of graphs, we set up and solved 2.8 × 10⁵ multi-species chemical equilibrium (MSCE) non-linear equations and found which set of reactions fitted best with the experimental data available. The agreement between computed and experimental speciation diagrams is excellent. Furthermore, we discovered a strong linear dependence between DFT and empirical formation constants, which opens the door for a systematic rescaling.

SUBMITTER: Petrus E

PROVIDER: S-EPMC8163382 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters.

Project description:Here we show how a simple inorganic salt can spontaneously form autocatalytic sets of replicating inorganic molecules that work via molecular recognition based on the {PMo12} ? [PMo12O40]3- Keggin ion, and {Mo36} ? [H3Mo57M6(NO)6O183(H2O)18]22- cluster. These small clusters are able to catalyze their own formation via an autocatalytic network, which subsequently template the assembly of gigantic molybdenum-blue wheel {Mo154} ? [Mo154O462H14(H2O)70]14-, {Mo132} ? [MoVI 72MoV 60O372(CH3COO)30(H2O)72]42- ball-shaped species containing 154 and 132 molybdenum atoms, and a {PMo12}?{Mo124Ce4} ? [H16MoVI 100MoV 24Ce4O376(H2O)56 (PMoVI 10MoV 2O40)(C6H12N2O4S2)4]5- nanostructure. Kinetic investigations revealed key traits of autocatalytic systems including molecular recognition and kinetic saturation. A stochastic model confirms the presence of an autocatalytic network involving molecular recognition and assembly processes, where the larger clusters are the only products stabilized by the cycle, isolated due to a critical transition in the network.

| S-EPMC7245103 | biostudies-literature

Tuning the Magnetic Moment of Small Late 3d-Transition-Metal Oxide Clusters by Selectively Mixing the Transition-Metal Constituents.

Project description:Transition-metal oxide nanoparticles are relevant for many applications in different areas where their superparamagnetic behavior and low blocking temperature are required. However, they have low magnetic moments, which does not favor their being turned into active actuators. Here, we report a systematical study, within the framework of the density functional theory, of the possibility of promoting a high-spin state in small late-transition-metal oxide nanoparticles through alloying. We investigated all possible nanoalloys An-xBxOm (A, B = Fe, Co, Ni; n = 2, 3, 4; 0?x?n) with different oxidation rates, m, up to saturation. We found that the higher the concentration of Fe, the higher the absolute stability of the oxidized nanoalloy, while the higher the Ni content, the less prone to oxidation. We demonstrate that combining the stronger tendency of Co and Ni toward parallel couplings with the larger spin polarization of Fe is particularly beneficial for certain nanoalloys in order to achieve a high total magnetic moment, and its robustness against oxidation. In particular, at high oxidation rates we found that certain FeCo oxidized nanoalloys outperform both their pure counterparts, and that alloying even promotes the reentrance of magnetism in certain cases at a critical oxygen rate, close to saturation, at which the pure oxidized counterparts exhibit quenched magnetic moments.

| S-EPMC7559123 | biostudies-literature

Effect of Metal Oxide Nanoparticles on the Chemical Speciation of Heavy Metals and Micronutrient Bioavailability in Paddy Soil.

Project description:The effects of engineered nanoparticles (ENPs) on heavy metal fate and biotoxicity in farmland soil are mostly unknown. A flooding-drying simulation experiment was conducted to study the effects of three typical metal oxide nanoparticles (TiO2-NPs, ZnO-NPs and CuO-NPs) on the chemical speciation of heavy metals and micronutrient bioavailability in paddy soil. The results showed that the addition of ZnO-NPs and CuO-NPs caused significant increases in soil pH, Eh and EC after a 90-d flooding-drying process. ZnO-NPs and CuO-NPs addition caused clearly increase in the Zn and Cu concentrations in the acid-soluble fraction, Fe/Mn oxides-bound fraction and organic-bound fraction, leading to higher bioavailability in the soil. DTPA-extractable Zn and Cu increased to 184.6 mg kg-1 and 145.3 mg kg-1 in the maximum ZnO-NPs and CuO-NPs concentration treatments (500 mg kg-1). TiO2-NPs promoted the transformation of Mn from a Fe/Mn oxides-bound fraction to an acid-soluble fraction. Soil Cd bioavailability obviously decreased in the TiO2-NPs treatment but increased in the ZnO-NPs and CuO-NPs treatments.

| S-EPMC7177736 | biostudies-literature

Promoting CO<sub>2</sub> methanation via ligand-stabilized metal oxide clusters as hydrogen-donating motifs.

Project description:Electroreduction uses renewable energy to upgrade carbon dioxide to value-added chemicals and fuels. Renewable methane synthesized using such a route stands to be readily deployed using existing infrastructure for the distribution and utilization of natural gas. Here we design a suite of ligand-stabilized metal oxide clusters and find that these modulate carbon dioxide reduction pathways on a copper catalyst, enabling thereby a record activity for methane electroproduction. Density functional theory calculations show adsorbed hydrogen donation from clusters to copper active sites for the *CO hydrogenation pathway towards *CHO. We promote this effect via control over cluster size and composition and demonstrate the effect on metal oxides including cobalt(II), molybdenum(VI), tungsten(VI), nickel(II) and palladium(II) oxides. We report a carbon dioxide-to-methane faradaic efficiency of 60% at a partial current density to methane of 135 milliampere per square centimetre. We showcase operation over 18 h that retains a faradaic efficiency exceeding 55%.

| S-EPMC7713075 | biostudies-literature

Poly(ethylene glycol) nanocomposites of sub-nanometer metal oxide clusters for dynamic semi-solid proton conductive electrolytes.

Project description:Sub-nm-scale metal oxide clusters (PW12O40 3-) show high solubility in the melt of poly(ethylene glycol) (PEG) and the obtained semi-solid nanocomposites show promising proton conductivities under ambient conditions. Suggested from scattering studies, the clusters are homogeneously dispersed in the PEG melt at the molecular scale with high loading amounts (70 wt%) and the formed real solutions can be stable for months with no aggregation or phase separation. The conductivities of the nanocomposites which are governed by the concentrations of H3PW12O40 can reach as high as 1.01 × 10-2 S cm-1 at the highest concentration. Due to the dynamic cross-linking hydrogen bonding between clusters and PEG, the nanocomposites behave like solids with negligible flow at high concentrations of clusters. Upon the application of high-speed shear forces (>32 s-1), the composites can flow with continuously decreasing viscosities. The shear thinning properties of the nanocomposites enable their convenient processing into required morphologies and the wettability of electrolytes to electrodes under typical high shear rate processing conditions and the safety of the produced devices can be ensured by their solid-like properties in the static state.

| S-EPMC6836960 | biostudies-literature

Three-step nucleation of metal-organic framework nanocrystals.

Project description:Metal-organic frameworks (MOFs) are crystalline nanoporous materials with great potential for a wide range of industrial applications. Understanding the nucleation and early growth stages of these materials from a solution is critical for their design and synthesis. Despite their importance, the pathways through which MOFs nucleate are largely unknown. Using a combination of in situ liquid-phase and cryogenic transmission electron microscopy, we show that zeolitic imidazolate framework-8 MOF nanocrystals nucleate from precursor solution via three distinct steps: 1) liquid-liquid phase separation into solute-rich and solute-poor regions, followed by 2) direct condensation of the solute-rich region into an amorphous aggregate and 3) crystallization of the aggregate into a MOF. The three-step pathway for MOF nucleation shown here cannot be accounted for by conventional nucleation models and provides direct evidence for the nonclassical nucleation pathways in open-framework materials, suggesting that a solute-rich phase is a common precursor for crystallization from a solution.

| S-EPMC7958460 | biostudies-literature

Role of clusters in nonclassical nucleation and growth of protein crystals.

Project description:The development of multistep nucleation theory has spurred on experimentalists to find intermediate metastable states that are relevant to the solidification pathway of the molecule under interest. A great deal of studies focused on characterizing the so-called "precritical clusters" that may arise in the precipitation process. However, in macromolecular systems, the role that these clusters might play in the nucleation process and in the second stage of the precipitation process, i.e., growth, remains to a great extent unknown. Therefore, using biological macromolecules as a model system, we have studied the mesoscopic intermediate, the solid end state, and the relationship that exists between them. We present experimental evidence that these clusters are liquid-like and stable with respect to the parent liquid and metastable compared with the emerging crystalline phase. The presence of these clusters in the bulk liquid is associated with a nonclassical mechanism of crystal growth and can trigger a self-purifying cascade of impurity-poisoned crystal surfaces. These observations demonstrate that there exists a nontrivial connection between the growth of the macroscopic crystalline phase and the mesoscopic intermediate which should not be ignored. On the other hand, our experimental data also show that clusters existing in protein solutions can significantly increase the nucleation rate and therefore play a relevant role in the nucleation process.

| S-EPMC3918807 | biostudies-other

Term rules for simple metal clusters.

Project description:Hund's term rules are only valid for isolated atoms, but have no generalization for molecules or clusters of several atoms. We present a benchmark calculation of Al2 and Al3, for which we find the high and low-spin ground states (3)Πu and , respectively. We show that the relative stabilities of all the molecular terms of Al2 and Al3 can be described by simple rules pertaining to bonding structures and symmetries, which serve as guiding principles to determine ground state terms of arbitrary multi-atom clusters.

| S-EPMC4620565 | biostudies-other

Cellular Mechanisms Involved in the Combined Toxic Effects of Diesel Exhaust and Metal Oxide Nanoparticles.

Project description:Diesel exhaust particles (DEPs) and non-exhaust particles from abrasion are two main representative sources of air pollution to which humans are exposed daily, together with emerging nanomaterials, whose emission is increasing considerably. In the present work, we aimed to investigate whether DEPs, metal oxide nanoparticles (MeO-NPs), and their mixtures could affect alveolar cells. The research was focused on whether NPs induced different types of death in cells, and on their effects on cell motility and migration. Autophagy and cell cycles were investigated via cytofluorimetric analyses, through the quantification of the autophagic biomarker LC3B and PI staining, respectively. Cellular ultrastructures were then observed via TEM. Changes in cell motility and migration were assessed via transwell migration assay, and by the cytofluorimetric analysis of E-cadherin expression. A colony-forming efficiency (CFE) assay was performed in order to investigate the interactions between cells inside the colonies, and to see how these interactions change after exposure to the single particles or their mixtures. The results obtained suggest that NPs can either reduce the toxicity of DEPs (CuO) or enhance it (ZnO), through a mechanism that may involve autophagy as cells' response to stressors and as a consequence of particles' cellular uptake. Moreover, NPs can induce modification of E-cadherin expression and, consequentially, of colonies' phenotypes.

| S-EPMC8228517 | biostudies-literature

Physical mechanisms of amyloid nucleation on fluid membranes.

Project description:Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein-membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways-protein-rich and lipid-rich-and quantify how the membrane fluidity and protein-membrane affinity control the relative importance of those molecular pathways. We find that the membrane's susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson's disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context.

| S-EPMC7777200 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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