Accelerating NMR Shielding Calculations Through Machine Learning Methods: Application to Magnesium Sodium Silicate Glasses.

In this work, we have applied the Kernel Ridge Regression (KRR) method using a Least Square Support Vector Regression (LSSVR) approach for the prediction of the NMR isotropic magnetic shielding (σ) of active nuclei (O, Na, Mg, and Si) in a series of (Mg, Na)-silicate glasses. The Machine Learning (ML) algorithm has been trained by mapping the local environment of each atom described by the Smooth Overlap of Atomic Position (SOAP) descriptor with isotropic chemical shielding values computed with DFT using the Gauge-Included-Projector-Augmented-Wave (GIPAW) approach. The influence of different training datasets generated through molecular dynamics simulations at various temperatures and with different inter-atomic potentials has been tested and we demonstrate the importance of a wide exploration of the configurational space to enhance the transferability of the ML-regressor.

Blueshift of the CN stretching vibration of acetonitrile in solution: computational and experimental study.

Acetonitrile, a polar molecule that cannot form hydrogen bonds on its own, interacts with solvent molecules mainly through the lone pair of its nitrogen atom and the π electrons of its CN triple bond [Correction added on 17 July 2024, after first online publication: Acetole has been changed to Acetonitrile in the preceeding sentence.]. Interestingly, acetonitrile exhibits an unexpected strengthening of the triple bond's force constant in an aqueous environment, leading to an upshift (blueshift) in the corresponding stretching vibration: this effect contrasts with the usual consequence of hydrogen bonding on the vibrational frequencies of the acceptor groups, that is, frequency redshift.

Quantum-Chemistry Study of the Hydrolysis Reaction Profile in Borate Networks: A Benchmark.

This investigation involved an ab initio and Density Functional Theory (DFT) analysis of the hydrolysis mechanism and energetics in a borate network. The focus was on understanding how water molecules interact with and disrupt the borate network, an area where the experimental data are scarce and unreliable. The modeled system consisted of two boron atoms, bridging oxygen atoms, and varying numbers of water molecules.

Iron nuclearity in mineral fibres: Unravelling the catalytic activity for predictive modelling of toxicity.

Chronic inflammation induced in vivo by mineral fibres, such as asbestos, is sustained by the cyclic formation of cytotoxic/genotoxic oxidant species that are catalysed by iron. High catalytic activity is observed when iron atoms are isolated in the crystal lattice (nuclearity=1), whereas the catalytic activity is expected to be reduced or null when iron forms clusters of higher nuclearity. This study presents a novel approach for systematically measuring iron nuclearity across a large range of iron-containing standards and mineral fibres of social and economic importance, and for quantitatively assessing the relation between nuclearity and toxicity.

Impact of Atomic Defects on Ceria Surfaces on Chemical Mechanical Polishing of Silica Glass Surfaces.

This study investigates the impact of atomic defects, such as oxygen vacancies and Ce ions, on cerium oxide (ceria) surfaces during chemical mechanical polishing (CMP) for silica glass finishing. Using density functional theory (DFT) and reactive molecular dynamics simulations, the interaction of orthosilicic molecules and silica glass with dry and wet ceria surfaces is explored. Defects alter the surface reactivity, leading to the dissociation of orthosilicic acid on oxygen vacancies, forming a strong Si-O-Ce bond.

Accurate and Transferable Machine Learning Potential for Molecular Dynamics Simulation of Sodium Silicate Glasses.

An accurate and transferable machine learning (ML) potential for the simulation of binary sodium silicate glasses over a wide range of compositions (from 0 to 50% NaO) was developed. The potential energy surface is approximated by the sum of atomic energy contributions mapped by a neural network algorithm from the local geometry comprising information on atomic distances and angles with neighboring atoms using the DeePMD code [Wang, H. 2018, 228, 178-184].

New Atomistic Insights on the Chemical Mechanical Polishing of Silica Glass with Ceria Nanoparticles.

Reactive molecular dynamics simulations have been used to simulate the chemical mechanical polishing (CMP) process of silica glass surfaces with the ceria (111) and (100) surfaces, which are predominantly found in ceria nanoparticles. Since it is known that an alteration layer is formed at the glass surface as a consequence of the chemical interactions with the slurry solutions used for polishing, we have created several glass surface models with different degrees of hydroxylation and porosity for investigating their morphology and chemistry after the interaction with acidic, neutral, and basic water solutions and the ceria surfaces. Both the chemical and mechanical effects under different pressure and temperature conditions have been studied and clarified.

Evidence of Multiple Crystallization Pathways in Lithium Disilicate: A Metadynamics Investigation.

Metadynamics simulations driven by using two X-ray diffraction peaks identified three alternative crystallization pathways of the lithium disilicate crystal from the melt. The most favorable one passes through the formation of disordered layered structures undergoing internal ordering in a second step. The second pathway involves the formation of phase-separated structures composed of nuclei of β-cristobalite crystals surrounded by lithium-rich phases in which metasilicate chains are formed.

Can DFT Calculations Provide Useful Information for SERS Applications?

Density functional theory (DFT) calculations allow us to reproduce the SERS (surface-enhanced Raman scattering) spectra of molecules adsorbed on nanostructured metal surfaces and extract the most information this spectroscopy is potentially able to provide. The latter point mainly concerns the anchoring mechanism and the bond strength between molecule and metal as well as the structural and electronic modifications of the adsorbed molecule. These findings are of fundamental importance for the application of this spectroscopic technique.

DFT and TD-DFT Study of the Chemical Effect in the SERS Spectra of Piperidine Adsorbed on Silver Colloidal Nanoparticles.

The surface-enhanced Raman scattering (SERS) spectra of piperidine adsorbed on silver/chloride colloids were studied by a combined density functional theory (DFT)/time dependent DFT (TD-DFT) approach. The mechanism of chemical enhancement on the Raman signals is due to at least two contributions: the first comes from the changes in the molecular force constants and the dynamic polarizabilities of the normal modes, when the molecule is chemisorbed. DFT calculations satisfactorily reproduce the SERS spectra of piperidine adsorbed on silver, showing that the species formed on the silver particle is a complex formed by a deprotonated piperidine linked to a silver cation.

Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters.

Metadynamics (MetaD) is a useful technique to study rare events such as crystallization. It has been only recently applied to study nucleation and crystallization in glass-forming liquids such as silicates, but the optimal set of parameters to drive crystallization and obtain converged free energy surfaces is still unexplored. In this work, we systematically investigated the effects of the simulation conditions to efficiently study the thermodynamics and mechanism of crystallization in highly viscous systems.

HOadsorption and dissociation on various CeO(111) surface models: a first-principles study.

Periodic density functional theory (DFT) calculations using the hybrid PBE0 functional and atom-centered Gaussian functions as basis sets were carried out to investigate the absorption and the first steps involved in the decomposition of hydrogen peroxide (HO) on three different models of the ceria (111) surface. One of the models is a clean surface, and the others are defective and partially hydroxylated ceria surfaces. On the clean surface, we found that the minimum energy path of hydrogen peroxide decomposition involves a three-step process, i.

Development and Application of a ReaxFF Reactive Force Field for Cerium Oxide/Water Interfaces.

Ceria (CeO) is a well-known catalytic oxide with many environmental, energy production, and industrial applications, most of them involving water as a reactant, byproduct, solvent, or simple spectator. In this work, we parameterized a Ce/O/H ReaxFF for the study of ceria and ceria/water interfaces. The parameters were fitted to an training set obtained at the DFT/PBE0 level, including the structures, cohesive energies, and elastic properties of the crystalline phases Ce, CeO, and CeO; the O-defective structures and energies of vacancy formation on CeO bulk and CeO (111) surface, as well as the absorption and reaction energies of H and HO molecules on CeO (111).

Unraveling the internal conversion process within the Q-bands of a chlorophyll-like-system through surface-hopping molecular dynamics simulations.

The non-radiative relaxation process within the Q-bands of chlorophylls represents a crucial preliminary step during the photosynthetic mechanism. Despite several experimental and theoretical efforts performed in order to clarify the complex dynamics characterizing this stage, a complete understanding of this mechanism is still far to be reached. In this study, non-adiabatic excited-state molecular dynamic simulations have been performed to model the non-radiative process within the Q-bands for a model system of chlorophylls.

Disclosing the Interaction of Gold Nanoparticles with Aβ(1-40) Monomers through Replica Exchange Molecular Dynamics Simulations.

Amyloid-β aggregation is one of the principal causes of amyloidogenic diseases that lead to the loss of neuronal cells and to cognitive impairments. The use of gold nanoparticles treating amyloidogenic diseases is a promising approach, because the chemistry of the gold surface can be tuned in order to have a specific binding, obtaining effective tools to control the aggregation. In this paper, we show, by means of Replica Exchange Solute Tempering Molecular Simulations, how electrostatic interactions drive the absorption of Amyloid-β monomers onto citrates-capped gold nanoparticles.

Disclosing crystal nucleation mechanism in lithium disilicate glass through molecular dynamics simulations and free-energy calculations.

Unraveling detailed mechanism of crystal nucleation from amorphous materials is challenging for both experimental and theoretical approaches. In this study, we have examined two methods to understand the initial stage of crystal precipitation from lithium disilicate glasses using molecular dynamics simulations. One of the methods is a modified exploring method to find structurally similar crystalline clusters in the glass models, enabling us to find three different embryos, such as LiSiO (LS), LiSiO (LS) and LiPO (LP), in the 33LiO·66SiO·1PO glass (LSP1), in which PO is added as a nucleating agent.

Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils.

Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process.

Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aβ(1-40) Monomers by Means of Molecular Dynamics.

In this study, we compared the effects of two well-known natural compounds on the early step of the fibrillation process of amyloid-β (1-40), responsible for the formation of plaques in the brains of patients affected by Alzheimer's disease (AD). The use of extensive replica exchange simulations up to the µs scale allowed us to characterize the inhibition activity of (-)-epigallocatechin-3-gallate (EGCG) and curcumin (CUR) on unfolded amyloid fibrils. A reduced number of β-strands, characteristic of amyloid fibrils, and an increased distance between the amino acids that are responsible for the intra- and interprotein aggregations are observed.

Structural origins of the Mixed Alkali Effect in Alkali Aluminosilicate Glasses: Molecular Dynamics Study and its Assessment.

The comprehension of the nonlinear effects provided by mixed alkali effect (MAE) in oxide glasses is useful to optimize glass compositions to achieve specific properties that depend on the mobility of ions, such as the chemical durability, glass transition temperature, viscosity and ionic conductivity. Although molecular dynamics (MD) simulations have already been applied to investigate the MAE on silicates, less effort has been devoted to study such phenomenon in mixed alkali aluminosilicate glasses where alkali cations can act both as modifiers, forming non-bridging oxygens and percolation channels, and as charge compensator of the AlO units present in the network. Moreover, the ionic conductivity has not been computed yet; thus, the accuracy of the atomistic simulations in reproducing the MAE on the property is still open to question.

Structure Model and Toxicity of the Product of Biodissolution of Chrysotile Asbestos in the Lungs.

Asbestos is a commercial term indicating six natural silicates with asbestiform crystal habit. Of these, five are double-chain silicates (amphibole) and one is a layer silicate (serpentine asbestos or chrysotile). Although all species are classified as human carcinogens, their degree of toxicity is still a matter of debate.

Raman and Computational Study on the Adsorption of Xanthine on Silver Nanocolloids.

Xanthine is a nucleobase, deriving from adenine and guanine by deamination and oxidation processes, which may deposit in the human body causing diseases, similar to uric acid. Here, we have investigated the adsorption of xanthine on silver colloidal nanoparticles by means of surface-enhanced Raman scattering (SERS) with an exciting radiation in the near-infrared spectral region, where interference due to fluorescence does not occur, along with density functional theory calculations of molecule/metal model systems. By adopting a combined experimental and computational approach, we have identified the "marker" SERS bands of xanthine and the tautomer that preferentially binds the silver particles, as well as the molecular group involved in the interaction with metal.

Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles.

A multiscale molecular dynamics simulation study has been carried out in order to provide in-depth information on the adsorption of hemoglobin, myoglobin, and trypsin over citrate-capped AuNPs of 15 nm diameter. In particular, determinants for single proteins adsorption and simultaneous adsorption of the three types of proteins considered have been studied by Coarse-Grained and Meso-Scale molecular simulations, respectively. The results, discussed in the light of the controversial experimental data reported in the current experimental literature, have provided a detailed description of the (i) recognition process, (ii) number of proteins involved in the early stages of corona formation, (iii) protein competition for AuNP adsorption, (iv) interaction modalities between AuNP and protein binding sites, and (v) protein structural preservation and alteration.

SERS, XPS and DFT Study of Xanthine Adsorbed on Citrate-Stabilized Gold Nanoparticles.

We have studied the adsorption of xanthine, a nucleobase present in human tissue and fluids that is involved in important metabolic processes, on citrate-reduced gold colloidal nanoparticles by means of surface-enhanced Raman scattering (SERS), absorption, and X-ray photoelectron spectroscopy (XPS) measurements, along with density functional theory (DFT) calculations. The citrate anions stabilize the colloidal suspensions by strongly binding the gold nanoparticles. However, these anions do not impair the adsorption of xanthine on positively-charged active sites present on the metal surface.

SERS active Ag-SiO nanoparticles obtained by laser ablation of silver in colloidal silica.

Highly stable Ag-SiO nanoparticle composites were first obtained by laser ablation of a silver target in an aqueous colloidal dispersion of silica and examined by UV-vis absorption spectroscopy, transmission electron microscopy and Raman spectroscopy. The surface enhanced Raman scattering (SERS) activity of these nanocomposites was tested using 2,2'-bipyridine as a molecular reporter and excitation in the visible and near-IR spectral regions. The computational DFT approach provided evidence of ligand adsorption on positively charged adatoms of the silver nanostructured surface, in a very similar way to the metal/molecule interaction occurring in the corresponding Ag(I) coordination compound.