Silica surface features and their role in the adsorption of biomolecules: computational modeling and experiments

Reaction with Water Vapor Defines Surface Reconstruction and Membranolytic Activity of Quartz Milled in Different Molecular Environments

Industrial processing of quartz (SiO2) and quartz-containing materials produces toxic dust. Fracturing quartz crystals opens the Si‒O bond and produces highly reactive surface species which mainly react with molecules like water and oxygen. This surface-reconstruction process forms silanol (Si‒OH) on the quartz surface, which can damage biological membranes under specific configurations. To comprehend the impact of the quartz surface restructuring on membranolytic activity, the formation and reactivity of quartz radicals produced in four distinct molecular environments with electron paramagnetic resonance (EPR) spectroscopy are evaluated and their membranolytic activity is measured through in vitro hemolysis test. The four molecular environments are formulated with and without molecular water vapor and oxygen (±H2O/±O2). The absence of water favored the formation of surface radical species. In water-rich environments, diamagnetic species prevailed due to radical recombination. Quartz milled in -H2O/±O2 acquired membranolytic activity when exposed to water vapor, unlike quartz milled in +H2O/±O2. After being stabilized by reaction with water vapor, the membranolytic activity of quartz is maintained over time. It is demonstrated that the type and the reactivity of radical sites on quartz are modulated by the outer molecular environment, ultimately determining the biological activity of milled quartz dust.

Amino Acid Polymerization on Silica Surfaces

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.

Evolution of myoglobin diffusion mechanisms: exploring pore and surface diffusion in a single silica particle

This study elucidates the mass transfer mechanism of myoglobin (Mb) within a single silica particle with a 50 nm pore size at various pH levels (6.0, 6.5, 6.8, and 7.0). Investigation of Mb distribution ratio (R) and distribution kinetics was conducted using absorption microspectroscopy. The highest R was observed at pH 6.8, near the isoelectric point of Mb, as the electrostatic repulsion between Mb molecules on the silica surface decreased. The time-course absorbance of Mb in the silica particle was rigorously analyzed based on a first-order reaction, yielding the intraparticle diffusion coefficient of Mb (Dp). Dp-(1 + R)-1 plots at different pH values were evaluated using the pore and surface diffusion model. Consequently, we found that at pH 6.0, Mb diffused in the silica particle exclusively through surface diffusion, whereas pore diffusion made a more substantial contribution at higher pH. Furthermore, we demonstrated that Mb diffusion was hindered by slow desorption, associated with the electrostatic charge of Mb. This comprehensive analysis provides insights into the diffusion mechanisms of Mb at acidic, neutral, and basic pH conditions.

DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman's path integral formalism of quantum mechanics. The flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.

Water Film Structure and Wettability of Different Quartz Surfaces: Hydrogen Bonding Across Various Cutting Planes

Quartz is ubiquitous in subsurface formations. The crystal faces have different atomic arrangements. Knowledge of the molecular structures on the surface of quartz is key in many processes. Molecular dynamics simulations are conducted to investigate the atomic arrangement effect on the water film structure, ion adsorption, and wettability at three different α-quartz surfaces. The interfacial structures depend on the quartz surface. Intrasurface hydrogen bonding between surface silanols differs in the α-quartz surface. At the (0001) surface, the OH density is 9.58 nm-2, consisting of Q2 units with two hydroxyl groups per silicone atom. At the (101̅0)-β surface, the OH density is 7.54 nm-2, consisting of Q3 units with one hydroxyl group per silicone atom; there is significant intrasurface hydrogen bonding. At the (101̅0)-α surface, the OH density is 7.54 nm-2, consisting of Q2 units; however, there is little intrasurface hydrogen bonding. The intrasurface hydrogen bonding results in the exposure of hydrogen-bond acceptors to the aqueous phase, causing water molecules to have an H-up (hydrogen toward surface) orientation. This orientation can be found at the (0001) and (101̅0)-β surfaces; it is related to the degree of ordering at the surface. The ordering at the (0001) and (101̅0)-β surfaces is higher than that at the (101̅0)-α surface. In aqueous systems with ions, cation adsorption is the most dominant at the (0001) surface due to the largest surface density of the intrasurface hydrogen bonding, providing interaction sites for cations to be adsorbed. We observe a pronounced decrease in water film thickness from the ions at the (0001) surface only, likely due to significant cation adsorption. In this work, we demonstrate that the hydrogen-bond network, which varies from the plane cut, affects the water film structure and ion adsorption. The contact is nearly zero despite the changes in the film thickness and molecular structure at the temperature of 318 K.

Overcoming colloidal nanoparticle aggregation in biological milieu for cancer therapeutic delivery: Perspectives of materials and particle design

Nanoparticles as cancer therapeutic carrier fail in clinical translation due to complex biological environments in vivo consisting of electrolytes and proteins which render nanoparticle aggregation and unable to reach action site. This review identifies the desirable characteristics of nanoparticles and their constituent materials that prevent aggregation from site of administration (oral, lung, injection) to target site. Oral nanoparticles should ideally be 75-100 nm whereas the size of pulmonary nanoparticles minimally affects their aggregation. Nanoparticles generally should carry excess negative surface charges particularly in fasting state and exert steric hindrance through surface decoration with citrate, anionic surfactants and large polymeric chains (polyethylene glycol and polyvinylpyrrolidone) to prevent aggregation. Anionic as well as cationic nanoparticles are both predisposed to protein corona formation as a function of biological protein isoelectric points. Their nanoparticulate surface composition as such should confer hydrophilicity or steric hindrance to evade protein corona formation or its formation should translate into steric hindrance or surface negative charges to prevent further aggregation. Unexpectedly, smaller and cationic nanoparticles are less prone to aggregation at cancer cell interface favoring endocytosis whereas aggregation is essential to enable nanoparticles retention and subsequent cancer cell uptake in tumor microenvironment. Present studies are largely conducted in vitro with simplified simulated biological media. Future aggregation assessment of nanoparticles in biological fluids that mimic that of patients is imperative to address conflicting materials and designs required as a function of body sites in order to realize the future clinical benefits.

Surface (bio)-functionalization of metallic materials: How to cope with real interfaces?

Metallic materials are an important class of biomaterials used in various medical devices, owing to a suitable combination of their mechanical properties. The (bio)-functionalization of their surfaces is frequently performed for biocompatibility requirements, as it offers a powerful way to control their interaction with biological systems. This is particularly important when physicochemical processes and biological events, mainly involving proteins and cells, are initiated at the host-material interface. This review addresses the state of "real interfaces" in the context of (bio)-functionalization of metallic materials, and the necessity to cope with it to avoid frequent improper evaluation of the procedure used. This issue is, indeed, well-recognized but often neglected and emerges from three main issues: (i) ubiquity of surface contamination with organic compounds, (ii) reactivity of metallic surfaces in biological medium, and (iii) discrepancy in (bio)-functionalization procedures between expectations and reality. These disturb the assessment of the strategies adopted for surface modifications and limit the possibilities to provide guidelines for their improvements. For this purpose, X-ray photoelectrons spectroscopy (XPS) comes to the rescue. Based on significant progresses made in methodological developments, and through a large amount of data compiled to generate statistically meaningful information, and to insure selectivity, precision and accuracy, the state of "real interfaces" is explored in depth, while looking after the two main constituents: (i) the bio-organic adlayer, in which the discrimination between the compounds of interest (anchoring molecules, coupling agents, proteins, etc) and organic contaminants can be made, and (ii) the metallic surface, which undergoes dynamic processes due to their reactivity. Moreover, through one of the widespread (bio)-functionalization strategy, given as a case study, a particular attention is devoted to describe the state of the interface at different stages (composition, depth distribution of contaminants and (bio)compounds of interest) and the mode of protein retention. It is highlighted, in particular, that the occurrence or improvement of bioactivity does not demonstrate that the chemical schemes worked in reality. These aspects are particularly essential to make progress on the way to choose the suitable (bio)-functionalization strategy and to provide guidelines to improve its efficiency.

Biotrapping Ureolytic Bacteria on Sand to Improve the Efficiency of Biocementation

Microbially induced calcium carbonate precipitation (MICP) has emerged as a novel technology with the potential to produce building materials through lower-temperature processes. The formation of calcium carbonate bridges in MICP allows the biocementation of aggregate particles to produce biobricks. Current approaches require several pulses of microbes and mineralization media to increase the quantity of calcium carbonate minerals and improve the strength of the material, thus leading to a reduction in sustainability. One potential technique to improve the efficiency of strength development involves trapping the bacteria on the aggregate surfaces using silane coupling agents such as positively charged 3-aminopropyl-methyl-diethoxysilane (APMDES). This treatment traps bacteria on sand through electrostatic interactions that attract negatively charged walls of bacteria to positively charged amine groups. The APMDES treatment promoted an abundant and immediate association of bacteria with sand, increasing the spatial density of ureolytic microbes on sand and promoting efficient initial calcium carbonate precipitation. Though microbial viability was compromised by treatment, urea hydrolysis was minimally affected. Strength was gained much more rapidly for the APMDES-treated sand than for the untreated sand. Three injections of bacteria and biomineralization media using APMDES-treated sand led to the same strength gain as seven injections using untreated sand. The higher strength with APMDES treatment was not explained by increased calcium carbonate accrual in the structure and may be influenced by additional factors such as differences in the microstructure of calcium carbonate bridges between sand particles. Overall, incorporating pretreatment methods, such as amine silane coupling agents, opens a new avenue in biomineralization research by producing materials with an improved efficiency and sustainability.

Reactive Simulations of Silica Functionalization with Aromatic Hydrocarbons

Reactive molecular dynamics simulations are used to model the covalent functionalization of amorphous silica with aromatic hydrocarbons. Simulations show that the surface density of silanol-terminated phenyl, naphthyl, and anthracenyl molecules is lower than the maximum value calculated based on molecule geometry, and the simulation densities decrease faster with the number of aromatic rings than the geometric densities. The trends are analyzed in terms of the surface-silanol bonding configurations, tilt angles, local conformational ordering, and aggregation of surface-bound molecules under steady-state conditions. Results show that the surface density is affected by both the size and symmetry of the aromatic hydrocarbons. The correlations among bonding, orientation, and surface density identified here may guide the selection or design of molecules for functionalized surfaces.

Facile band gap tuning in graphene-brucite heterojunctions

The zero band gap of pure graphene is a well-known issue that limits some specific applications of graphene in opto- and microelectronics. This led to several research studies in the so-called van der Waals composites (known as heterostructures, or heterojunctions), where two monolayers of different materials are stacked and held together by dispersive interactions. In this paper, we introduced and considered a single layer of brucite Mg(OH)2, an overlooked 2D material that can be easily produced by exfoliation (like graphene from graphite), for the creation of the heterojunction. First principles simulations showed that brucite/graphene composites can modify the electronic properties (position of the Dirac cone with respect to the Fermi level and band gap) according to the crystallographic stacking and the presence of point defects. The present work represents then an important step forward in understanding and finding new ways to design two-dimensional materials with tailored electronic and physical properties.

The Role of Surface Complexes in Ketene Formation from Fatty Acids via Pyrolysis over Silica: from Platform Molecules to Waste Biomass

Fatty acids (FA) are the main constituents of lipids and oil crop waste, considered to be a promising 2G biomass that can be converted into ketenes via catalytic pyrolysis. Ketenes are appraised as promising synthons for the pharmaceutical, polymer, and chemical industries. Progress in the thermal conversion of short- and long-chain fatty acids into ketenes requires a deep understanding of their interaction mechanisms with the nanoscale oxide catalysts. In this work, the interactions of fatty acids with silica are investigated using a wide range of experimental and computational techniques (TPD MS, DFT, FTIR, in situ IR, equilibrium adsorption, and thermogravimetry). The adsorption isotherms of linear and branched fatty acids C1-C6 on the silica surface from aqueous solution have been obtained. The relative quantities of different types of surface complexes, as well as kinetic parameters of their decomposition, were calculated. The formation of surface complexes with a coordination bond between the carbonyl oxygens and silicon atoms in the surface-active center, which becomes pentacoordinate, was confirmed by DFT calculations, in good agreement with the IR feature at ∼1680 cm 1. Interestingly, ketenes release relate to these complexes' decomposition as confirmed by the thermal evolution of the absorption band (1680 cm-1) synchronously with the TPD peak of the ketene molecular ion. The established regularities of the ketenezation are also observed for the silica-induced pyrolysis of glyceryl trimyristate and real waste, rapeseed meals.

Controlling Macroscopic Friction through Interfacial Siloxane Bonding

Controlling macroscopic friction is crucial for numerous natural and industrial applications, ranging from forecasting earthquakes to miniaturizing semiconductor devices, but predicting and manipulating friction phenomena remains a challenge due to the unknown relationship between nanoscale and macroscopic friction. Here, we show experimentally that dry friction at multiasperity Si-on-Si interfaces is dominated by the formation of interfacial siloxane (Si─O─Si) bonds, the density of which can be precisely regulated by exposing plasma-cleaned silicon surfaces to dry nitrogen. Our results show how the bond density can be used to quantitatively understand and control the macroscopic friction. Our findings establish a unique connection between the molecular scale at which adhesion occurs, and the friction coefficient that is the key macroscopic parameter for industrial and natural tribology challenges.

Adsorption of 4-(N,N-Dimethylamino)-4'-nitrostilbene on an Amorphous Silica Glass Surface

Stilbenes are a compelling class of organic photoswitches with a high degree of tunability that sensitively depend on their environment. In this study, we investigate the adsorption properties of 4-(N,N-dimethylamino)-4'-nitrostilbene (DANS), a push-pull stilbene, on amorphous silica glass. Plane-wave density functional theory (DFT) calculations are used to understand how the trans and cis isomers of DANS interact with the amorphous surface and which are the most preferred modes of adsorption. Our calculations revealed that the O-H···O hydrogen bonds between the nitro group and hydroxyl groups of the silica surface dominate the intramolecular interaction. In addition to hydrogen bonding, O-H···π interactions with the aromatic ring and double bond play a critical role in adsorption, whereas C-H···O interactions are present, but contribute little. Therefore, both isomers of DANS favor parallel orientations such that not only the functional groups but also the aromatic parts can strongly interact with the glass surface.

Immobilization of isolated dimethyltin species on crystalline silicates through surface modification of layered octosilicate

Single metal atoms supported on silica are attractive catalysts, and precise control of the local environment around the metal species is essential. Crystalline silica is useful as an efficient support for the incorporation of well-defined metal sites. Dimethyltin species were regularly grafted onto the layer surfaces of layered octosilicate, a type of two-dimensional (2D) crystalline silica. Dimethyltin dichlorides react with the surface silanol (SiOH) groups of the silicate layers. The formation of Si-O-Sn bonds was confirmed by 29Si magic-angle spinning (MAS) NMR. X-ray absorption fine structure (XAFS) analysis showed the four-coordinated Sn species. These results suggested the presence of well-defined dipodal dimethyltin species on the layer surfaces. The degree of modification of the silanol groups with the dimethyltin groups increased with increasing amounts of dimethyltin dichloride; however, the maximum degree of modification was approximately 50%. This value was interpreted as an alternate modification of the octosilicate reaction sites with dimethyltin groups. These results demonstrate the potential for developing highly active single metal catalysts with a high density of regularly arranged active sites on high surface area supports.

First-Principles Prediction of Amorphous Silica Nanoparticle Surface Charge: Effect of Size, pH, and Ionic Strength

The quantification of surface charge properties of silica nanoparticles is essential for several applications. To determine these properties, many experimental and theoretical methods have been introduced, which are time-consuming and/or challenging to use. In this study, a first-principles approach is developed to determine the surface charge properties of amorphous silica nanoparticles against the nanoparticle size, pH, and ionic strength without relying on experimental data. An amorphous silica nanoparticle of 1.34 nm diameter is simulated by using integrated molecular dynamics and Monte Carlo methods. A detailed analysis of the nanoparticle structure is provided by analyzing the types of silanol groups on the surface. Moreover, a model is developed to estimate the probability distribution of the surface silanol groups based on the nearest neighbor distances and the diameter of the nanoparticle to determine the number of surface silanols on larger nanoparticles. Thereafter, a computational chemistry approach is used to calculate the acid dissociation constants of the corresponding deprotonation reactions. The calculated constants and the point of zero charge value are in excellent agreement with experiments. The surface charge properties of the nanoparticle with various diameters are then estimated by using a mean-field model at different pH and ionic strength values. The results of the developed model are compared to the Poisson-Boltzmann equation as a reference model. The developed model predictions agree well with the reference model for low and mid-electrolyte concentrations (1 and 10 mM) and small nanoparticles (smaller than 100 nm). However, the developed model seems to qualitatively predict the surface charge properties more accurately than the Poisson-Boltzmann model for high electrolyte concentrations.

The Role of In Situ/Operando IR Spectroscopy in Unraveling Adsorbate-Induced Structural Changes in Heterogeneous Catalysis

Heterogeneous catalysts undergo thermal- and/or adsorbate-induced dynamic changes under reaction conditions, which consequently modify their catalytic behavior. Hence, it is increasingly crucial to characterize the properties of a catalyst under reaction conditions through the so-called "operando" approach. Operando IR spectroscopy is probably one of the most ubiquitous and versatile characterization methods in the field of heterogeneous catalysis, but its potential in identifying adsorbate- and thermal-induced phenomena is often overlooked in favor of other less accessible methods, such as XAS spectroscopy and high-resolution microscopy. Without detracting from these techniques, and while aware of the enormous value of a multitechnique approach, the purpose of this Review is to show that IR spectroscopy alone can provide relevant information in this field. This is done by discussing a few selected case studies from our own research experience, which belong to the categories of both "single-site"- and nanoparticle-based catalysts.

Microscopic properties of forces from ice solidification interface acting on silica surfaces based on molecular dynamics simulations

The origin of the forces acting on a silica surface from an ice solidification interface was investigated to understand the solidification phenomenon and its impact on nanometer-scale structures using molecular dynamics simulations. The microscopic forces were determined by appropriately averaging the forces acting on the silica wall from the water molecules in time and space; the time evolutions of these microscopic forces during the solidification processes were investigated for three types of silica surfaces. The results indicate that the microscopic forces fluctuate more after the solidification interface makes contact with the wall surface. To visualize the changes in the microscopic forces and hydrogen bonds due to solidification, their differences compared to the liquid state were calculated. When the solidification interface is near the wall, the changes in these microscopic forces and hydrogen bonds due to solidification are correlated. This tendency is more significant for an amorphous wall and a wall with a structure than for a crystalline wall. The changes in the microscopic force depend on the water molecules that behave as acceptors when forming the hydrogen bonds with the wall and on the configuration of the silanol groups on the silica surfaces.

Concerted Hydrosilylation Catalysis by Silica-Immobilized Cyclic Carbonates and Surface Silanols

Developing a method for creating a novel catalysis of organic molecules is essential because of the growing interest in organocatalysis. In this study, we found that cyclic carbonates immobilized on a nonporous or mesoporous silica support showed catalytic activity for hydrosilylation, which was not observed for the free cyclic carbonates, silica supports, or their physical mixture. Analysis of the effects of linker lengths and pore sizes on the catalytic activity and carbonate C=O stretching frequency revealed that the proximity of carbonates and surface silanols was crucial for synergistic hydrosilylation catalysis. A carbonate and silanol concertedly activated the silane and aldehyde for efficient hydride transfer. Density functional theory calculations on a model reaction system demonstrated that both the carbonate and silanol contributed to the stabilization of the transition state of hydride transfer, which resulted in a reasonable barrier height of 16.8 kcal mol-1. Furthermore, SiO2/carbonate(C4) enabled the hydrosilylation of an aldehyde with an amino group without catalyst poisoning, owing to the weak acidity of surface silanols, in sharp contrast to previously developed acid catalysts. This study demonstrates that immobilization on a solid support can convert inactive organic molecules into active and heterogeneous organocatalysts.

Uncertainty and Irreproducibility of Triboelectricity Based on Interface Mechanochemistry

Triboelectrification mechanism is still not understood, despite centuries of investigations. Here, we propose a model showing that mechanochemistry is key to elucidate triboelectrification fundamental properties. Studying contact between gold and silicate glasses, we observe that the experimental triboelectric output is subject to large variations and polarity inversions. First principles analysis shows that electronic transfer is activated by mechanochemistry and the tribopolarity is determined by the termination exposed to contact, depending on the material composition, which can result in different charging at the macroscale. The electron transfer mechanism is driven by the interface barrier dynamics, regulated by mechanical forces. The model provides a unified framework to explain several experimental observations, including the systematic variations in the triboelectric output and the mixed positive-negative "mosaic" charging patterns, and paves the way to the theoretical prediction of the triboelectric properties.

Pore Size Dependence of Mass Transfer of Zinc Myoglobin in a Single Mesoporous Silica Particle

This study investigated the pore size dependence of the mass transfer of zinc myoglobin (ZnMb) in a single mesoporous silica particle through confocal fluorescence microspectroscopy. The ZnMb's fluorescence depth profile in the particle was analyzed by a spherical diffusion model, and the intraparticle diffusion coefficient was obtained. The intraparticle diffusion coefficient in the silica particle with various pore sizes (10, 15, 30, and 50 nm) was furthermore analyzed based on a pore and surface diffusion model. Although the mass transfer mechanism in all silica particles followed the pore and surface diffusion model, the adsorption and desorption of ZnMb affected the mass transfer depending on the pore size. The influence of the slow desorption of ZnMb became pronounced for large pore sizes (30 and 50 nm), which was revealed by simulation using a diffusion equation combined with the adsorption-desorption kinetics. The distribution of ZnMb was suppressed in small pore sizes (10 and 15 nm) owing to the adsorption of ZnMb onto the entrance of the pore. Thus, we revealed the mass transfer mechanism of ZnMb in the silica particle with different pore sizes.

Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity

The study of molecular recognition patterns is crucial for understanding the interactions between inorganic (nano)particles and biomolecules. In this review we focus on hydroxyls (OH) exposed at the surface of oxide particles (OxPs) which can play a key role in molecular initiating events leading to OxPs toxicity. We discuss here the main analytical methods available to characterize surface OH from a quantitative and qualitative point of view, covering thermogravimetry, titration, ζ potential measurements, and spectroscopic approaches (NMR, XPS). The importance of modelling techniques (MD, DFT) for an atomistic description of the interactions between membranes/proteins and OxPs surfaces is also discussed. From this background, we distilled a new approach methodology (NAM) based on the combination of IR spectroscopy and bioanalytical assays to investigate the molecular interactions of OxPs with biomolecules and membranes. This NAM has been already successfully applied to SiO₂ particles to identify the OH patterns responsible for the OxPs' toxicity and can be conceivably extended to other surface-hydroxylated oxides.

Review: understanding the properties of amorphous materials with high-performance computing methods

Amorphous materials have no long-range order in their atomic structure. This makes much of the formalism for the study of crystalline materials irrelevant, and so elucidating their structure and properties is challenging. The use of computational methods is a powerful complement to experimental studies, and in this paper we review the use of high-performance computing methods in the simulation of amorphous materials. Five case studies are presented to showcase the wide range of materials and computational methods available to practitioners in this field. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Effect of nanoparticle loading and magnetic field application on the thermodynamic, optical, and rheological behavior of thermoresponsive polymer solutions

Although processing via external stimuli is a promising technique to tune the structure and properties of polymeric materials, the impact of magnetic fields on phase transitions in thermoresponsive polymer solutions is not well-understood. As nanoparticle (NP) addition is also known to impact these thermodynamic and optical properties, synergistic effects from combining magnetic fields with NP incorporation provide a novel route for tuning material properties. Here, the thermodynamic, optical, and rheological properties of aqueous poly(N-isopropyl acrylamide) (PNIPAM) solutions are examined in the presence of hydrophilic silica NPs and magnetic fields, individually and jointly, via Fourier-transform infrared spectroscopy (FTIR), magneto-turbidimetry, differential scanning calorimetry (DSC), and magneto-rheology. While NPs and magnetic fields both reduce the phase separation energy barrier and lower optical transition temperatures by altering hydrogen bonding (H-bonding), infrared spectra demonstrate that the mechanism by which these changes occur is distinct. Magnetic fields primarily alter solvent polarization while NPs provide PNIPAM-NP H-bonding sites. Combining NP addition with field application uniquely alters the solution environment and results in field-dependent rheological behavior that is unseen in polymer-only solutions. These investigations provide fundamental understanding on the interplay of magnetic fields and NP addition on PNIPAM thermoresponsivity which can be harnessed for increasingly complex stimuli-responsive materials.

Hybrid Ligand Polymerization for Weakly Confined Lead Halide Perovskite Quantum Dots

Rational ligand passivation is essential to achieve a higher performance of weakly confined lead halide perovskite quantum dots (PQDs) via a mechanism of surface chemistry and/or microstrain. In situ passivation with 3-mercaptopropyltrimethoxysilane (MPTMS) produces CsPbBr₃ PQDs with an enhanced photoluminescence quantum yield (PLQY, Φ_PL) of up to 99%; meanwhile, charge transport of the PQD film can be enhanced by one order of magnitude. Herein, we examine the effect of the molecular structure of MPTMS as the ligand exchange agent in comparison to octanethiol. Both thiol ligands promote crystal growth of PQDs, inhibit nonradiative recombination, and cause blue-shifted PL, while the silane moiety of MPTMS manipulates surface chemistry and outperforms owing to its unique cross-linking chemistry characterized by FTIR vibrations at 908 and 1641 cm^-1. Emergence of the diagnostic vibrations is ascribed to hybrid ligand polymerization arising from the silyl tail group that confers the advantages of narrower size dispersion, lower shell thickness, more static surface binding, and higher moisture resistance. In contrast, the superior electrical property of the thiol-passivated PQDs is mostly determined by the covalent S-Pb bonding on the interface.

Site-Averaged Ab Initio Kinetics: Importance Learning for Multistep Reactions on Amorphous Supports

Single-atom centers on amorphous supports include catalysts for polymerization, partial oxidation, metathesis, hydrogenolysis, and more. The disordered environment makes each site different, and the kinetics exponentially magnifies these differences to make ab initio site-averaged kinetics calculations extremely difficult. This work extends the importance learning algorithm for efficient and precise site-averaged kinetics estimates to ab initio calculations and multistep reaction mechanisms. Specifically, we calculate site-averaged proton transfer relaxation rates on an ensemble of cluster models representing Brønsted acid sites on silica-alumina. We include direct and water-assisted proton transfer pathways and simultaneously estimate the water adsorption and activation enthalpies for forward and backward proton transfers. We use density functional theory (DFT) to obtain a site-averaged rate, somewhat like a turnover frequency, for the proton transfer relaxation rate. Finally, we show that importance learning can provide orders-of-magnitude acceleration over standard sampling methods for site-averaged rate calculations in cases where the rate is dominated by a few highly active sites.

Aggregation of magnetic nanoparticles functionalized with trans-resveratrol in aqueous solution

In the framework of a protein-ligand-fishing strategy to identify proteins that bind to trans-resveratrol, a natural phenolic compound with pharmacological benefits, we have developed magnetic nanoparticles covalently linked to trans-resveratrol through three different derivatives and examined their aggregation behavior in aqueous solution. The monodispersed magnetic core (18 nm diameter) with its mesoporous silica shell (93 nm diameter) exhibited a notable superparamagnetic behavior useful for magnetic bioseparation. The hydrodynamic diameter, deduced from dynamic light scattering analysis, of the nanoparticle increased from 100 to 800 nm when the aqueous buffer changed from pH 10.0-3.0. A size polydispersion occurred from pH 7.0-3.0. In parallel, the value of the extinction cross section increased according to a negative power law of the UV wavelength. This was mainly due to light scattering by mesoporous silica, whereas the absorbance cross section remained very low in the 230-400 nm domain. The three types of resveratrol-grafted magnetic nanoparticles exhibited similar scattering properties, but their absorbance spectrum was consistent with the presence of trans-resveratrol. Their functionalization increased their negative zeta potential when pH increased from 3.0 to 10.0. The mesoporous nanoparticles were monodispersed in alkaline conditions, where their anionic surface strongly repulsed each other but aggregated progressively under van der Waals forces and hydrogen bonding when negative zeta potential decreased. The characterized results of nanoparticle behavior in aqueous solution provide critical insight for further study of nanoparticles with proteins in biological environment.

Constructing Collective Variables Using Invariant Learned Representations

On the time scales accessible to atomistic numerical modeling, chemical reactions are considered rare events. Therefore, the atomistic simulations are commonly biased along a low-dimensional representation of a chemical reaction in an atomic structure space, i.e., along the collective variables. However, suitable collective variables are often complicated to guess a priori. We propose a novel method of collective variable discovery based on dimensionality reduction of the atomic representation vectors. These linear-scaling and invariant representations can be either fixed (untrained) or learned by supervised training of the end-to-end machine learning potential. The learned representations are expected to reflect not only the structural but also the energetic features of the system that are transferable to all of the reactive transformation covered by the machine learning potential. We demonstrate our approach on four high-barrier reactions ranging from a simple gas-phase hydrogen jump reaction to complex reactions in periodic models of industrially relevant heterogeneous catalysts. High data efficiency, automatized feature extraction, favorable scaling, and retention of inherent invariances are all properties that are expected to enable fast and largely automatic construction of suitable collective variables even in highly complex reactive scenarios such as reactive/catalytic transformations at solid-liquid interfaces.

Effects of Interfacial Hydroxylation Microstructure on Quartz Flotation by Sodium Oleate

Quartz, a common inorganic nonmetallic mineral, is usually removed or purified by beneficiation, normally flotation. Given the strong polarity of the quartz surface, it is easy to hydrate to form a hydroxylation layer, which makes it impossible to float quartz with sodium oleate (OL) used alone. An ideal flotation method for quartz is preactivation with Ca²⁺, followed by collection with OL. Herein, the effects of surface hydroxylation on the adsorption of the anionic collector OL on the quartz surface before and after Ca²⁺ activation are systematically investigated by density functional theory (DFT) calculations. The results show that the displacement adsorption of surface hydroxyl substituted by OL^- is not feasible in thermodynamics, and the OL^- can only bind to the H atoms of the hydroxylated quartz surface via hydrogen bonds, namely, hydrogen binding adsorption. Due to the electrostatic repulsion and steric hindrance effect induced by the surface hydroxylation structure, the adsorption ability of OL^- on the quartz surface mediated by hydroxyl bridges is very weak, which is insufficient to realize quartz floating. However, Ca²⁺ ions are easily adsorbed on the hydroxylated quartz surface, providing favorable active sites for subsequent adsorption of OL^-, thus becoming a credible solution for the industrial flotation of the strong hydrophilic mineral quartz. These findings shed some new insights for accurately understanding the flotation mechanism of strongly hydrophilic oxide minerals and are beneficial to promoting the development of mineral flotation fundamentals.

Unraveling the Intrinsic Biocidal Activity of the SiO2-Ag Composite against SARS-CoV-2: A Joint Experimental and Theoretical Study

The COVID-19 pandemic has emerged as an unprecedented global healthcare emergency, demanding the urgent development of effective materials to inactivate the SARS-CoV-2 virus. This research was planned to disclose the remarkable biocidal activity of SiO2-Ag composites incorporated into low-density polyethylene. For this purpose, a joint experimental and theoretical [based on first-principles calculations at the density functional theory (DFT) level] study is performed. Biological assays showed that this material eliminatesStaphylococcus aureusand SARS-CoV-2 virus in just 2 min. Here, we investigate a previously unexplored process that we postulate may occur along the O2 and H2O adsorption and activation processes of pure and defective SiO2-Ag surfaces for the generation of reactive oxygen species (ROS). The obtained results help us to predict the nature of ROS: superoxide anion radicals, •O2-, hydroxyl radicals, •OH, and hydroperoxyl radicals, •HO2, that destroy and degrade the structure of the SARS-COV-2 virus. This is consistent with the DFT studies, where the energetic, electronic, and magnetic properties of the intermediates show a feasible formation of ROS. Present findings are expected to provide new insights into the relationship among the structure, property, and biocidal activity of semiconductor/metal SiO2-Ag composites.

Difference in Structure and Electronic Properties of Oxygen Vacancies in α-Quartz and α-Cristobalite Phases of SiO2

α-cristobalite (α-C) is a polymorph of silica, mainly found in space exploration and geochemistry research. Due to similar densities, α-C is often used as a proxy for amorphous SiO2, particularly in computer simulations of SiO2 surfaces and interfaces. However, little is known about the properties of α-C and its basic oxygen defects. Using density functional theory (DFT) simulations we provide a comprehensive report on the properties of perfect structure and oxygen vacancies in α-C. The calculated properties of α-C are compared with those of the better-characterized α-quartz (α-Q). Our results demonstrated that the positively charged O vacancy in α-C is most stable in the dimer configuration, in contrast to α-Q, which favors the puckered configuration. A back-projected configuration was also predicted in both polymorphs. We calculated the optical transition energies and isotropic hyperfine constants for O vacancies in both α-Q and α-C, and compared our findings with the results of previous studies and experiments. This work, thus, offers one of the first in-depth investigations of the properties of oxygen vacancies in α-C.

Mesoporous Silica Particles Retain Their Structure and Function while Passing through the Gastrointestinal Tracts of Mice and Humans

Mesoporous silica particles (MSPs) can be used as food additives, clinically for therapeutic applications, or as oral delivery vehicles. It has also been discussed to be used for a number of novel applications including treatment for diabetes and obesity. However, a major question for their possible usage has been if these particles persist structurally and retain their effect when passing through the gastrointestinal tract (GIT). A substantial breaking down of the particles could reduce function and be clinically problematic for safety issues. Hence, we investigated the biostability of MSPs of the SBA-15 kind prepared at large scales (100 and 1000 L). The MSPs were orally administered in a murine model and clinically in humans. A joint extraction and calcination method was developed to recover the MSPs from fecal mass, and the MSPs were characterized physically, structurally, morphologically, and functionally before and after GIT passage. Analyses with N2 adsorption, X-ray diffraction, electron microscopy, and as a proxy for general function, adsorption of the enzyme α-amylase, were conducted. The adsorption capacity of α-amylase on extracted MSPs was not reduced as compared to the pristine and control MSPs, and adsorption of up to 17% (w/w) was measured. It was demonstrated that the particles did not break down to any substantial degree and retained their function after passing through the GITs of the murine model and in humans. The fact the particles were not absorbed into the body was ascribed to that they were micron-sized and ingested as agglomerates and too big to pass the intestinal barrier. The results strongly suggest that orally ingested MSPs can be used for a number of clinical applications.

Nearly free silanols drive the interaction of crystalline silica polymorphs with membranes: Implications for mineral toxicity

Crystalline silica (CS) is a well-known hazardous material that causes severe diseases including silicosis, lung cancer, and autoimmune diseases. However, the hazard associated to crystalline silica is extremely variable and depends on some specific characteristics, including crystal structure and surface chemistry. The crystalline silica polymorphs share the SiO₂ stoichiometry and differentiate for crystal structure. The different crystal lattices in turn expose differently ordered hydroxyl groups at the crystal surface, i.e., the silanols. The nearly free silanols (NFS), a specific population of weakly interacting silanols, have been recently advanced as the key surface feature that governs recognition mechanisms between quartz and cell membrane, initiating toxicity. We showed here that the nearly free silanols occur on the other crystalline silica polymorphs and take part in the molecular interactions with biomembranes. A set of crystalline silica polymorphs, including quartz, cristobalite, tridymite, coesite, and stishovite, was physico-chemically characterized and the membranolytic activity was assessed using red blood cells as model membranes. Infrared spectroscopy in highly controlled conditions was used to profile the surface silanol topochemistry and the occurrence of surface nearly free silanols on crystalline silica polymorphs. All crystalline silica polymorphs, but stishovite were membranolytic. Notably, pristine stishovite did not exhibited surface nearly free silanols. The topochemistry of surface silanols was modulated by thermal treatments, and we showed that the occurrence of nearly free silanols paralleled the membranolytic activity for the crystalline silica polymorphs. These results provide a comprehensive understanding of the structure-activity relationship between nearly free silanols and membranolytic activity of crystalline silica polymorphs, offering a possible clue for interpreting the molecular mechanisms associated with silica hazard and bio-minero-chemical interfacial phenomena, including prebiotic chemistry.

Treatment of tannery wastewater by silica nanoparticles produced from rice husk ash via a green route

Rice husk, which is one of the abundant agricultural biomasses in nature, contains organic and inorganic elements, spastically silica. This waste is frequently managed via incineration, resulting in the contamination of soil, water, and air due to emission of greenhouse gasses and ash. In the present investigation, the potential of silica powder obtained from the rice husk was demonstrated by the removal of Cr(III) from the tannery wastewater. Different combinations of sulfuric, hydrochloric, and acetic acids were used as precipitation agents to produce silica through the conventional and ultrasound-assisted techniques. The mesoporous silica fabricated via the sonication indicated the larger pores, 22 nm, compared to that produced via the conventional method by the employment of sulfuric acid, 10 nm, leading to achieve an adsorption capacity ~385 mg g^-1. Although both of applied techniques could develop mesoporous structure, precipitation should be carried out under sonication in the presence of acetic acid for the green production of silica with the appropriate adsorption performance. The conversion of rice husk into silica powder with specific surface area ~62 m² g^-1 could prevent the environmental pollution due to employment of acetic acid in the precipitation stage.

Characterization of polar surface groups on siliceous materials by inverse gas chromatography and the enthalpy-entropy compensation effect

Surface-modified porous silica is a well-established composite material. To improve its embedding and application behavior, adsorption studies of various probe molecules have been performed using the technique of inverse gas chromatography (IGC). For this purpose, IGC experiments were carried out in the infinite dilution mode on macro-porous micro glass spheres before and after surface modification with (3-mercaptopropyl)trimethoxysilane. To provide information about the polar interactions between probe molecules and the silica surface, in particular, eleven polar molecules have been injected. In summary, the free surface energy for pristine silica ( γ S t o t a l = 229 mJ/m²) and for (3-mercaptopropyl)trimethoxysilane-modified silica ( γ S t o t a l = 135 mJ/m²) indicates a reduced wettability after surface modification. This is due to the reduction of the polar component of the free surface energy ( γ S S P ) from 191 mJ/m² to 105 mJ/m². Simultaneously, with the reduction of surface silanol groups caused by surface modification of silica and, therefore, the decrease in polar interactions, a substantial loss of Lewis acidity was observed by various IGC approaches. Experiments with all silica materials have been conducted at temperatures in the range from 90°C to 120°C to determine the thermodynamic parameters, such as adsorption enthalpy ( Δ H a d s ) and adsorption entropy ( Δ S a d s ), using the Arrhenius regression procedure evaluating the IGC data. With the help of the enthalpy-entropy compensation, two types of adsorption complexes are assumed between polar probe molecules and the silica surface because of different isokinetic temperatures. Identical adsorption complexes with an isokinetic temperature of 370°C have been assigned to alkanes and weakly interacting polar probes such as benzene, toluene, dichloromethane, and chloroform. Polar probe molecules with typical functional groups such as OH, CO, and CN, having the ability to form hydrogen bonds to the silica surface, exhibit a lower isokinetic temperature of 60°C. Quantum chemical calculations of the probe molecules on a non-hydroxylated and hydroxylated silica cluster supported the formation of hydrogen bonds in the case of a strong polar adsorption complex with a bonding distance of 1.7 nm-1.9 nm to the silica surface.

Tuning the thermodynamic, optical, and rheological properties of thermoresponsive polymer solutions via silica nanoparticle shape and concentration

HYPOTHESIS

The shape and quantity of hydrophilic silica nanoparticles (NPs) can be used to tune the microstructure, rheology, and stability of phase-separating polymer solutions. In thermoresponsive polymer systems, silica nanospheres are well-studied whereas anisotropic NPs have little literature precedent. Here, we hypothesize that NP shape and concentration lower the onset of rheological and turbidimetric transitions of aqueous poly(N-isopropyl acrylamide) (PNIPAM) solutions.

EXPERIMENTS

Differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy (FTIR), turbidimetry, and oscillatory rheology are utilized to examine interactions between NPs, PNIPAM, and water and to track changes in phase separation and rheological properties due to NP concentration and shape.

FINDINGS

NP addition reduces phase separation enthalpy due to PNIPAM-NP hydrogen bonding interactions, the degree to which depends on polymer content. While NP addition minorly impacts thermodynamic and optical properties, rheological transitions and associated rheological properties are dramatically altered with increasing temperature, and depend on NP quantity, shape, and polymer molecular weight. Thus NP content and shape can be used to finely tune transition temperatures and mechanical properties for applications in stimuli-responsive materials.

Nicotinamide Mononucleotide Ameliorates Silica-Induced Lung Injury through the Nrf2-Regulated Glutathione Metabolism Pathway in Mice

Nicotinamide mononucleotide (NMN) is a natural antioxidant approved as a nutritional supplement and food ingredient, but its protective role in silicosis characterized by oxidative damage remains unknown. In this study, we generated a silicosis model by intratracheal instillation of silica, and then performed histopathological, biochemical, and transcriptomic analysis to evaluate the role of NMN in silicosis. We found that NMN mitigated lung damage at 7 and 28 days, manifested as a decreasing coefficient of lung weight and histological changes, and alleviated oxidative damage by reducing levels of reactive oxygen species and increasing glutathione. Meanwhile, NMN treatment also reduced the recruitment of inflammatory cells and inflammatory infiltration in lung tissue. Transcriptomic analysis showed that NMN treatment mainly regulated immune response and glutathione metabolism pathways. Additionally, NMN upregulated the expression of antioxidant genes Gstm1, Gstm2, and Mgst1 by promoting the expression and nuclear translocation of nuclear factor-erythroid 2 related factor 2 (Nrf2). Gene interaction analysis showed that Nrf2 interacted with Gstm1 and Mgst1 through Gtsm2. Promisingly, oxidative damage mediated by these genes occurred mainly in fibroblasts. In summary, NMN alleviates silica-induced oxidative stress and lung injury by regulating the endogenous glutathione metabolism pathways. This study reveals that NMN supplementation might be a promising strategy for mitigating oxidative stress and inflammation in silicosis.

Emergence of Order in Origin-of-Life Scenarios on Mineral Surfaces: Polyglycine Chains on Silica

The polymerization of amino acids (AAs) to peptides on oxide surfaces has attracted interest owing to its high importance in biotechnology, prebiotic chemistry, and origin of life theories. However, its mechanism is still poorly understood. We tried to elucidate the reactivity of glycine (Gly) from the vapor phase on the surface of amorphous silica under controlled atmosphere at 160 °C. Infrared (IR) spectroscopy reveals that Gly functionalizes the silica surface through the formation of ester species, which represent, together with the weakly interacting silanols, crucial elements for monomers activation and polymerization. Once activated, β-turns start to form as initiators for the growth of long linear polypeptides (poly-Gly) chains, which elongate into ordered structures containing both β-sheet and helical conformations. The work also points to the role of water vapor in the formation of further self-assembled β-sheet structures that are highly resistant to hydrolysis.

Top-Down Preparation of Nanoquartz for Toxicological Investigations

Occupational exposure to quartz dust is associated with fatal diseases. Quartz dusts generated by mechanical fracturing are characterized by a broad range of micrometric to nanometric particles. The contribution of this nanometric fraction to the overall toxicity of quartz is still largely unexplored, primarily because of the strong electrostatic adhesion forces that prevent isolation of the nanofraction. Furthermore, fractured silica dust exhibits special surface features, namely nearly free silanols (NFS), which impart a membranolytic activity to quartz. Nanoquartz can be synthetized via bottom-up methods, but the surface chemistry of such crystals strongly differs from that of nanoparticles resulting from fracturing. Here, we report a top-down milling procedure to obtain a nanometric quartz that shares the key surface properties relevant to toxicity with fractured quartz. The ball milling was optimized by coupling the dry and wet milling steps, using water as a dispersing agent, and varying the milling times and rotational speeds. Nanoquartz with a strong tendency to form submicrometric agglomerates was obtained. The deagglomeration with surfactants or simulated body fluids was negligible. Partial lattice amorphization and a bimodal crystallite domain size were observed. A moderate membranolytic activity, which correlated with the number of NFS, signaled coherence with the previous toxicological data. A membranolytic nanoquartz for toxicological investigations was obtained.

Building the uracil skeleton in primitive ponds at the origins of life: carbamoylation of aspartic acid

A large set of nucleobases and amino acids is found in meteorites, implying that several chemical reservoirs are present in the solar system. The "geochemical continuity" hypothesis explores how protometabolic paths developed from so-called "bricks" in an enzyme-free prebiotic world and how they affected the origins of life. In the living cell, the second step of synthesizing uridine and cytidine RNA monomers is a carbamoyl transfer from a carbamoyl donor to aspartic acid. Here we compare two enzyme-free scenarios: aqueous and mineral surface scenarios in a thermal range up to 250 °C. Both processes could have happened in ponds under open atmosphere on the primeval Earth. Carbamoylation of aspartic acid with cyanate in aqueous solutions at 25 °C gives high N-carbamoyl aspartic acid yields within 16 h. It is important to stress that, while various molecules could be efficient carbamoylating agents according to thermodynamics, kinetics plays a determining role in selecting prebiotically possible pathways.

Plasma Functionalization of Silica Bilayer Polymorphs

Ultrathin silica films are considered suitable two-dimensional model systems for the study of fundamental chemical and physical properties of all-silica zeolites and their derivatives, as well as novel supports for the stabilization of single atoms. In the present work, we report the creation of a new model catalytic support based on the surface functionalization of different silica bilayer (BL) polymorphs with well-defined atomic structures. The functionalization is carried out by means of in situ H-plasma treatments at room temperature. Low energy electron diffraction and microscopy data indicate that the atomic structure of the films remains unchanged upon treatment. Comparing the experimental results (photoemission and infrared absorption spectra) with density functional theory simulations shows that H₂ is added via the heterolytic dissociation of an interlayer Si-O-Si siloxane bond and the subsequent formation of a hydroxyl and a hydride group in the top and bottom layers of the silica film, respectively. Functionalization of the silica films constitutes the first step into the development of a new type of model system of single-atom catalysts where metal atoms with different affinities for the functional groups can be anchored in the SiO₂ matrix in well-established positions. In this way, synergistic and confinement effects between the active centers can be studied in a controlled manner.

Oriented multivalent silaffin-affinity immobilization of recombinant lipase on diatom surface: Reliable loading and high performance of biocatalyst

Microbial lipases are widely used biocatalysts; however, their functional surface immobilization should be designed for successful industrial applications. One of the unmet challenges is to develop a practical surface immobilization to achieve both high stability and activity of lipases upon the large loading. Herein, we present a silaffin-based multivalent design as a simple and oriented approach for Bacillus subtilis lipase A (LipA) immobilization on economic diatom biosilica matrix to yield highly-stable activity with reliable loading. Specifically, silaffin peptides Sil3H, Sil3K, and Sil3R, as monovalent or divalent genetic fusion tags, selectively immobilized LipA on biosilica surfaces. Sil3K peptide fusion to LipA termini most efficiently produced high catalytic activity upon immobilization. The activity was 70-fold greater than that of immobilized wild-type LipA. Compared to single fusion, the double Sil3K fusion displayed 1.7 higher enzymatic loading combined with high catalytic performances of LipA on biosilica surfaces. The multivalent immobilized LipA was distributed uniformly on biosilica surfaces. The biocatalyst was stable over a wide pH range with 98% retention activity after 10 reuses. The stabilized lipase fusion was compatible with laundry detergents, making it an attractive biocatalyst for detergent formulations. These findings demonstrate that multivalent surface immobilization is a plausible method for developing high-performance biocatalysts suitable for industrial biotechnological applications.

Reactivity of Group 13 Elements Tl and Element 113, Nh, and of Their Hydroxides with Respect to Various Quartz Surfaces from Periodic Relativistic DFT Calculations

Adsorption properties of group 13 element Tl and the superheavy element Nh, as well of their hydroxides on various modified quartz surfaces, are predicted on the basis of relativistic periodic DFT calculations using the BAND software. The obtained adsorption energies, E_ads, of the MOH (M = Tl and Nh) molecules are indicative of the relatively strong interaction of the hydroxides with all the considered quartz surfaces. In contrast, adsorption of the Tl and Nh atoms was found to be significantly weaker. The adsorption strength of both M and MOH (M = Tl and Nh) was shown to increase with the dehydroxylation of the quartz surface. Very good agreement is reached between the calculated E_ads(TlOH) of 133 kJ/mol on the fully hydroxylated quartz surface and of 157 kJ/mol on the partially dehydroxylated quartz surface on the one hand and experimental adsorption enthalpies, -ΔH_ads, of 134/137 ± 5 kJ/mol (at ∼300 °C) and 158 ± 3 kJ/mol (at ∼500 °C), respectively, on the other hand. Thus, we suggest that all the experimental ΔH_ads values for Tl should be assigned to the adsorption/desorption of the TlOH molecule. For NhOH, its adsorption properties on various quartz surfaces should be very similar to those of TlOH, with slightly smaller E_ads values. Adsorption of the Nh atom should, however, be much weaker than that of the Tl atom due to stronger spin-orbit effects in Nh.

Selective isolation of hyaluronan by solid phase adsorption to silica

A solid phase adsorption method for selective isolation of hyaluronan (HA) from biological samples is presented. Following enzymatic degradation of protein, HA can be separated from sulfated glycosaminoglycans, other unsulfated glycosaminoglycans, nucleic acids, and proteolytic fragments by adsorption to amorphous silica at specific salt concentrations. The adsorbed HA can be released from silica using neutral and basic aqueous solutions. HA ranging in size from ∼9 kDa to MDa polymers has been purified by this method from human serum and conditioned medium of cultured cells.

Molecular recognition between membrane epitopes and nearly free surface silanols explains silica membranolytic activity

Inhaled crystalline silica causes inflammatory lung diseases, but the mechanism for its unique activity compared to other oxides remains unclear, preventing the development of potential therapeutics. Here, the molecular recognition mechanism between membrane epitopes and "nearly free silanols" (NFS), a specific subgroup of surface silanols, is identified and proposed as a novel broad explanation for particle toxicity in general. Silica samples having different bulk and surface properties, specifically different amounts of NFS, are tested with a set of membrane systems of decreasing molecular complexity and different charge. The results demonstrate that NFS content is the primary determinant of membrane disruption causing red blood cell lysis and changes in lipid order in zwitterionic, but not in negatively charged liposomes. NFS-rich silica strongly and irreversibly adsorbs zwitterionic self-assembled phospholipid structures. This selective interaction is corroborated by density functional theory and supports the hypothesis that NFS recognize membrane epitopes that exhibit a positive quaternary amino and negative phosphate group. These new findings define a new paradigm for deciphering particle-biomembrane interactions that will support safer design of materials and what types of treatments might interrupt particle-biomembrane interactions.

Sensitivity Analysis of ReaxFF Potential: The Case of Si/O System

Sensitivity analysis of the ReaxFF potential for two Si and SiO₂ systems has been carried out using the method of Morris. The goal is to identify the most important force field parameters for selected properties. Thus, a clearer physical interpretation for some of the parameters can be obtained while the ranking of the parameters per magnitude of sensitivity for each property facilitates the development of parametrizations with improved quality. The parameters related to the σ-bond and van der Waals interactions have the greatest influence on the properties of the cubic diamond Si phase. Counterintuitively, parameters which have an impact on mechanical properties, such as the ones for ππ-bonds, do not influence pressure and vice versa. For the β-cristobalite SiO₂ phase, the Si-O cross-interaction parameters have stronger effect on all properties than the Si-Si and O-O elemental ones. This dependence is attributed to the tetrahedral structure of the SiO₂ phase. Regarding the sensitivity measures, the mean of the absolute values of the elementary effect (EE) distribution correlates with the standard deviation of the EE distribution in all cases; it quantifies the sensitivity of a property on a parameter and the cross-correlation of the parameter with the other ones. The mean of the EE distribution has a poor performance and its use should be avoided. It is also argued that performing a sensitivity analysis before force field optimization might greatly enhance the efficiency of the optimization methods by considering a two-step procedure, where the most relevant parameters are optimized first.

Leucine on Silica: A Combined Experimental and Modeling Study of a System Relevant for Origins of Life, and the Role of Water Coadsorption

Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO₂ together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.

Two-Dimensional Ultrathin Silica Films

Two-dimensional (2D) ultrathin silica films have the potential to reach technological importance in electronics and catalysis. Several well-defined 2D-silica structures have been synthesized so far. The silica bilayer represents a 2D material with SiO₂ stoichiometry. It consists of precisely two layers of tetrahedral [SiO₄] building blocks, corner connected via oxygen bridges, thus forming a self-saturated silicon dioxide sheet with a thickness of ∼0.5 nm. Inspired by recent successful preparations and characterizations of these 2D-silica model systems, scientists now can forge novel concepts for realistic systems, particularly by atomic-scale studies with the most powerful and advanced surface science techniques and density functional theory calculations. This Review provides a solid introduction to these recent developments, breakthroughs, and implications on ultrathin 2D-silica films, including their atomic/electronic structures, chemical modifications, atom/molecule adsorptions, and catalytic reactivity properties, which can help to stimulate further investigations and understandings of these fundamentally important 2D materials.

Ultrafast bandgap narrowing and cohesion loss of photoexcited fused silica

Coupling and spatial localization of energy on ultrafast timescales and particularly on the timescale of the excitation pulse in ultrashort laser irradiated dielectric materials are key elements for enabling processing precision beyond the optical limit. Transforming matter on mesoscopic scales facilitates the definition of nanoscale photonic functions in optical glasses. On these timescales, quantum interactions induced by charge non-equilibrium become the main channel for energy uptake and transfer as well as for the material structural change. We apply a first-principles model to determine dynamic distortions of energy bands following the rapid increase in the free-carrier population in an amorphous dielectric excited by an ultrashort laser pulse. Fused silica glass is reproduced using a system of (SiO₄)^4- tetrahedra, where density functional theory extended to finite-temperature fractional occupation reproduces ground and photoexcited states. Triggered by electronic charge redistribution, a bandgap narrowing of more than 2 eV is shown to occur in fused silica under geometry relaxation. Calculations reveal that the bandgap decrease results from the rearrangement of atoms altering the bonding strength. Despite an atomic movement impacting strongly the structural stability, the observed change of geometry remains limited to 7% of the interatomic distance and occurs on the femtosecond timescale. This structural relaxation is thus expected to take place quasi-instantly following the photon energy flux. Moreover, under intense laser pulse excitation, fused silica loses its stability when an electron temperature of around 2.8 eV is reached. A further increase in the excitation energy leads to the collapse of both the structure and bandgap.