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

A novel platform using homobifunctional hydrazide for enrichment and isolation of urinary circulating RNAs

Changes in specific circulating RNA (circRNA) expressions can serve as diagnostic noninvasive biomarkers for prostate cancer (PCa). However, there are still unmet needs, such as unclear types and roles of circRNAs, PCa detection in benign prostatic hyperplasia (BPH) by unstandardized methods, and limitations of sample volume capacity and low circRNA concentrations. This study reports a simple and rapid circRNA enrichment and isolation technique named "HAZIS-CirR" for the analysis of urinary circRNAs. The method utilizes homobifunctional hydrazides with amine-modified zeolite and polyvinylidene fluoride (PVDF) syringe filtration for combining electrostatic and covalent coupling and size-based filtration, and it offers instrument-free isolation of circRNAs in 20 min without volume limitation, thermoregulation, and lysis. HAZIS-CirR has high capture efficiency (82.03%-92.38%) and a 10-fold more sensitive detection limit (20 fM) than before enrichment (200 fM). The clinical utility of HAZIS-CirR is confirmed by analyzing circulating mRNAs and circulating miRNAs in 89 urine samples. Furthermore, three miRNA panels that differentiate PCa from BPH and control, PCa from control, and BPH from control, respectively, are established by comparing miRNA levels. HAZIS-CirR will be used as an optimal and established method for the enrichment and isolation of circRNAs as diagnostic, prognostic, and predictive biomarkers in human cancers.

Heterogeneous Rate Constant for Amorphous Silica Nanoparticle Adsorption on Phospholipid Monolayers

The interaction of amorphous silica nanoparticles with phospholipid monolayers and bilayers has received a great deal of interest in recent years and is of importance for assessing potential cellular toxicity of such species, whether natural or synthesized for the purpose of nanomedical drug delivery and other applications. This present communication studies the rate of silica nanoparticle adsorption on to phospholipid monolayers in order to extract a heterogeneous rate constant from the data. This rate constant relates to the initial rate of growth of an adsorbed layer of nanoparticles as SiO₂ on a unit area of the monolayer surface from unit concentration in dispersion. Experiments were carried out using the system of dioleoyl phosphatidylcholine (DOPC) monolayers deposited on Pt/Hg electrodes in a flow cell. Additional studies were carried out on the interaction of soluble silica with these layers. Results show that the rate constant is effectively constant with respect to silica nanoparticle size. This is interpreted as indicating that the interaction of hydrated SiO₂ molecular species with phospholipid polar groups is the molecular initiating event (MIE) defined as the initial interaction of the silica particle surface with the phospholipid layer surface promoting the adsorption of silica nanoparticles on DOPC. The conclusion is consistent with the observed significant interaction of soluble SiO₂ with the DOPC layer and the established properties of the silica-water interface.

A simple empirical model for phenanthrene adsorption on soil clay minerals

Soil clay minerals are effective substrate adsorbents of polycyclic aromatic hydrocarbons (PAHs) in natural soil. The adsorbed PAHs result in long-term contamination of soils. In this paper, a typical PAH phenanthrene (Phe) and nine high purity clay minerals are selected as representative PAH pollutants and adsorbents, respectively. A series of experiments have been conducted to disclose the relationship between the Phe adsorption effect of these clay minerals and their physical properties, including specific surface area (SSA), cation exchange capacity (CEC) and contact angle (CA). Molecular simulation methods are performed to explore the mechanism of clay mineral structure on Phe adsorption at the molecular level. Density functional theory (DFT) calculation suggests that the adsorption of Phe on clay minerals is mainly due to the van der Waals effect. The strength of the O-H-π effect is greater than that of the hydrophobic effect of Phe adsorption. Molecular dynamic (MD) simulations imply that the hydration effect of cations hinders the Phe hydrophobic adsorption by occupying the adsorption sites. Based on the mechanism explored, a simple empirical model is proposed, and the adsorption distribution coefficient K_d of clay mineral and water phases can be precisely predicted by the three physical properties of clay minerals, without rigorous quantitative analysis of soil clay minerals.

Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations

Glycine (Gly), NH₂CH₂COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.

Can Mesoporous Silica Speed Up Degradation of Benzodiazepines? Hints from Quantum Mechanical Investigations

This work reports for the first time a quantum mechanical study of the interactions of a model benzodiazepine drug, i.e., nitrazepam, with various models of amorphous silica surfaces, differing in structural and interface properties. The interest in these systems is related to the use of mesoporous silica as carrier in drug delivery. The adopted computational procedure has been chosen to investigate whether silica–drug interactions favor the drug degradation mechanism or not, hindering the beneficial pharmaceutical effect. Computed structural, energetics, and vibrational properties represent a relevant comparison for future experiments. Our simulations demonstrate that adsorption of nitrazepam on amorphous silica is a strongly exothermic process in which a partial proton transfer from the surface to the drug is observed, highlighting a possible catalytic role of silica in the degradation reaction of benzodiazepines.

The EXIMIOUS project—Mapping exposure-induced immune effects: connecting the exposome and the immunome

Immune-mediated, noncommunicable diseases—such as autoimmune and inflammatory diseases—are chronic disorders, in which the interaction between environmental exposures and the immune system plays an important role. The prevalence and societal costs of these diseases are rising in the European Union. The EXIMIOUS consortium—gathering experts in immunology, toxicology, occupational health, clinical medicine, exposure science, epidemiology, bioinformatics, and sensor development—will study eleven European study populations, covering the entire lifespan, including prenatal life. Innovative ways of characterizing and quantifying the exposome will be combined with high-dimensional immunophenotyping and -profiling platforms to map the immune effects (immunome) induced by the exposome. We will use two main approaches that “meet in the middle”—one starting from the exposome, the other starting from health effects. Novel bioinformatics tools, based on systems immunology and machine learning, will be used to integrate and analyze these large datasets to identify immune fingerprints that reflect a person’s lifetime exposome or that are early predictors of disease. This will allow researchers, policymakers, and clinicians to grasp the impact of the exposome on the immune system at the level of individuals and populations.

Phase transformation of silica particles in coal and biomass combustion processes

Inhalation of respirable silica particles can cause serious lung diseases (e.g., silicosis and lung cancer), and the toxicity of respirable silica is highly dependent on its crystal form. Common combustion processes such as coal and biomass burning can provide high temperature environments that may alter the crystal forms of silica and thus affect its toxic effects. Although crystalline silica (i.e., quartz, tridymite, and cristobalite) were widely found at different temperatures during the burning processes, the sources and crystal transformation pathways of silica in the burning processes are still not well understood. Here, we investigate the crystal transformation of silica in the coal and biomass combustion processes and clarify the detailed transformation pathways of silica for the first time. Specifically, in coal burning process, amorphous silica can transform into quartz and cristobalite starting at 1100 °C, and quartz transforms into cristobalite starting at 1200 °C; in biomass burning process, amorphous silica can transform into cristobalite starting at 800 °C, and cristobalite transforms into tridymite starting at 1000 °C. These transformation temperatures are significantly lower than those predicted by the classic theory due to possibly the catalysis of coexisting metal elements (e.g., aluminum, iron, and potassium). Our results not only enable a deeper understanding on the combustion-induced crystal transformation of silica, but also contribute to the mitigation of population exposure to respirable silica.

A DFT study of the aldol condensation reaction in the processing of ethanol to 1,3-butadiene on a MgO/SiO2 surface

The ETB process on different sites of MgO/SiO2.

Molecular Dynamics Study on the Thermal Aspects of the Effect of Water Molecules at the Adhesive Interface on an Adhesive Structure

The presence of adsorbed water on hydrophilic solid surfaces should be taken into account, especially in humid environments. It significantly reduces the adhesive strength between the epoxy resin and the adherend surface. Here, the adhesion structure of interfacial water sandwiched between bisphenol A epoxy resin and a hydroxylated silica (001) surface is investigated with microsecond molecular dynamics simulations. Specifically, interfacial water layers with initial thicknesses of 7.5, 10, and 20 Å are modeled. The density curves of water and the diglycidyl ether of bisphenol A show that at room temperature, the surface of the silica with hydroxyl groups is completely covered with a thick layer of water. For water layers thinner than 10 Å, the density of epoxy resin on the silica surface increases when the system is heated and does not return to the original density when the system is cooled. Furthermore, calculation of the interaction energy revealed that the exclusion of water from the hydroxylated surface by epoxy resin during heating can contribute to the increase in the adhesive interaction between the epoxy resin and the silica surface with hydroxyl groups.

The Role of the pH in the Impregnation of Spherical Mesoporous Silica Particles with L-Arginine Aqueous Solutions

In the context of the development of carriers for amino acids delivery, Spherical Mesoporous Silica Particles (SMSP), characterized by particles size ranging from 0.15 µm to 0.80 µm and average pore diameter of 2.4 nm, were synthesised and loaded with L-arginine (ARG), a basic amino acid involved in several physiological processes. The loading was performed using water as a solvent through the wet impregnation method (with a final arginine content of 9.1% w/w). The material was characterized before and after impregnation by means of X-Ray Diffraction (XRD), nitrogen sorption analysis, Field Emission Scanning Electron Microscopy (FESEM) and Fourier Transform Infrared (FT-IR) spectroscopy. SMSP are shown to suffer degradation upon impregnation, which dramatically affects their porosity. To elucidate the role of the pH of the ARG impregnating solution (originally set at pH ≈ 11) on SMSP degradation, the loading was performed under different pH conditions (5 and 9) keeping constant the ARG concentration. The impregnation performed with acidic solution did not modify the carrier. All samples displayed ARG in amorphous form: zwitterionic species were present in SMSP impregnated at basic pH whereas positive protonated species in that impregnated at acidic pH.

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach

Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO₂ (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO₂ surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO₂ surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.

Kinetic Analysis of the Mass Transfer of Zinc Myoglobin in a Single Mesoporous Silica Particle by Confocal Fluorescence Microspectroscopy

The adsorption/desorption mechanisms of biomolecules in porous materials have attracted significant attention because of their applications in many fields, including environmental, medical, and industrial sciences. Here, we employ confocal fluorescence microspectroscopy to reveal the diffusion behavior of zinc myoglobin (ZnMb, 4.4 nm × 4.4 nm × 2.5 nm) as a spherical protein in a single mesoporous silica particle (pore size of 15 nm). The measurement of the time course of the fluorescence depth profile of the particle reveals that intraparticle diffusion is the rate-limiting process of ZnMb in the particle. The diffusion coefficients of ZnMb in the particle for the distribution (D_dis) and release (D_re) processes are determined from the rate constants, e.g., D_dis = 1.65 × 10^-10 cm² s^-1 and D_re = 3.68 × 10^-10 cm² s^-1, for a 10 mM buffer solution. The obtained D values for various buffer concentrations are analyzed using the pore and surface diffusion model. Although surface diffusion is the main distribution process, the release process involves pore and surface diffusion, which have not been observed with small organic molecules; the mechanism of transfer of small molecules is pore diffusion alone. We demonstrate that the mass transfer kinetics of ZnMb in the silica particle can be explained well on the basis of pore and surface diffusion.

The role of borosilicate glass in Miller-Urey experiment

We have designed a set of experiments to test the role of borosilicate reactor on the yielding of the Miller-Urey type of experiment. Two experiments were performed in borosilicate flasks, two in a Teflon flask and the third couple in a Teflon flask with pieces of borosilicate submerged in the water. The experiments were performed in CH4, N2, and NH3 atmosphere either buffered at pH 8.7 with NH4Cl or unbuffered solutions at pH ca. 11, at room temperature. The Gas Chromatography-Mass Spectroscopy results show important differences in the yields, the number of products, and molecular weight. In particular, a dipeptide, multi-carbon dicarboxylic acids, PAHs, and a complete panel of biological nucleobases form more efficiently or exclusively in the borosilicate vessel. Our results offer a better explanation of the famous Miller's experiment showing the efficiency of borosilicate in a triphasic system including water and the reduced Miller-Urey atmosphere.

Purification of a peptide tagged protein via an affinity chromatographic process with underivatized silica

Silica is widely used for chromatography resins due to its high mechanical strength, column efficiency, easy manufacturing (i.e. controlled size and porosity), and low-cost. Despite these positive attributes to silica, it is currently used as a backbone for chromatographic resins in biotechnological downstream processing. The aim of this study is to show how the octapeptide (RH)4 can be used as peptide tag for high-purity protein purification on bare silica. The tag possesses a high affinity to deprotonated silanol groups because the tag's arginine groups interact with the surface via an ion pairing mechanism. A chromatographic workflow to purify GFP fused with (RH)4 could be implemented. Purities were determined by SDS-PAGE and RP-HPLC. The equilibrium binding capacity of the fusion protein GFP-(RH)4 on silica is 450 mg/g and the dynamic binding capacity around 3 mg/mL. One-step purification from clarified lysate achieved a purity of 93% and a recovery of 94%. Overloading the column enhances the purity to >95%. Static experiments with different buffers showed variability of the method making the system independent from buffer choice. Our designed peptide tag allows bare silica to be utilized in preparative chromatography for downstream bioprocessing; thus, providing a cost saving factor regarding expensive surface functionalization. Underivatized silica in combination with our (RH)4 peptide tag allows the purification of proteins, in all scales, without relying on complex resins.

Crystal face dependent wettability of α-quartz: Elucidation by time-of-flight secondary ion mass spectrometry techniques combined with molecular dynamics

HYPOTHESIS

Quartz is one of the most common but important minerals, and its wettability plays a significant role in affecting various natural and industrial processes. Studies have revealed that different crystal faces of quartz are with different wettabilities, but its mechanism is still vague.

EXPERIMENTS AND SIMULATIONS

For specifying the mechanism of crystal face dependent wettability, the contact angles of three different liquids on the crystal faces of α-quartz are measured; the time-of-flight secondary ion mass spectrometry (ToF-SIMS) is employed to establish the crystal surface models; molecular dynamics (MD) simulations with the surface models are performed to understand the wetting behavior at molecular scale.

FINDINGS

Based on the contact angle measurements, the wettabilities of different crystal faces of α-quartz are found different, which can be directly attributed to the concentration of hydroxyl group on crystal faces based on ToF-SIMS results. MD simulations yield consistent results with the contact angle order recognized from experiments, revealing that the surface hydroxyl group controls the wettability of α-quartz crystal faces. It is also recognized that the pristine surface atomic arrangement, especially the surface concentration of unsaturated bond (an intrinsic property of α-quartz), is the intrinsic cause of the difference in the concentration of hydroxyl group of the crystal surface.

Insights on Alanine and Arginine Binding to Silica with Atomic Resolution

Interactions of biomolecules with inorganic oxide surfaces such as silica in aqueous solutions are of profound interest in various research fields, including chemistry, biotechnology, and medicine. While there is a general understanding of the dominating electrostatic interactions, the binding mechanism is still not fully understood. Here, chromatographic zonal elution and flow microcalorimetry experiments were combined with molecular dynamic simulations to describe the interaction of different capped amino acids with the silica surface. We demonstrate that ion pairing is the dominant electrostatic interaction. Surprisingly, the interaction strength is more dependent on the repulsive carboxy group than on the attracting amino group. These findings are essential for conducting experimental and simulative studies on amino acids when transferring the results to biomolecule-surface interactions.

Labeling and Probing the Silica Surface Using Mechanochemistry and 17 O NMR Spectroscopy*

In recent years, there has been increasing interest in developing cost‐efficient, fast, and user‐friendly ¹⁷O enrichment protocols to help to understand the structure and reactivity of materials by using ¹⁷O NMR spectroscopy. Here, we show for the first time how ball milling (BM) can be used to selectively and efficiently enrich the surface of fumed silica, which is widely used at industrial scale. Short milling times (up to 15 min) allowed modulation of the enrichment level (up to ca. 5 %) without significantly changing the nature of the material. High‐precision ¹⁷O compositions were measured at different milling times by using large‐geometry secondary‐ion mass spectrometry (LG‐SIMS). High‐resolution ¹⁷O NMR analyses (including at 35.2 T) allowed clear identification of the signals from siloxane (Si−O−Si) and silanols (Si−OH), while DNP analyses, performed by using direct ¹⁷O polarization and indirect ¹⁷O{¹H} CP excitation, agreed with selective labeling of the surface. Information on the distribution of Si−OH environments at the surface was obtained from 2D ¹H−¹⁷O D‐HMQC correlations. Finally, the surface‐labeled silica was reacted with titania and using ¹⁷O DNP, their common interface was probed and Si−O−Ti bonds identified.

Semiquantitative Solid-State NMR Study of the Adsorption of Soybean Oils on Silica and Its Significance for Rubber Processing

Soybean oil (SBO) is a renewable material used as an alternative to conventional petroleum-derived oils in the processing of rubber composites. Upon chemical modifications, such as epoxidation, its performance in the processing of rubber can be significantly improved, as indicated by a considerable reduction of the mixing energy. Although it has been hypothesized that hydrogen bonding between functional groups (e.g., epoxy) of SBOs and silanols present on the silica surface plays a key role, there is still a lack of direct evidence supporting this hypothesis. In this work, it is demonstrated that there is an overall correlation between the epoxy concentration of SBOs and the mixing energy, consistent with the long-held hypothesis. In particular, a correlation between the SBO-silica adsorption affinity and the degree of epoxidation is revealed by a set of surface-selective solid-state nuclear magnetic resonance (ssNMR) experiments. In addition, the surface-selective ssNMR technique demonstrated in this work could also be used to evaluate the adsorption affinity of other oils and/or additives more broadly.

Tuning the Surface Chemistry of Second-Harmonic-Active Lithium Niobate Nanoprobes Using a Silanol-Alcohol Condensation Reaction

The surface functionalization of nanoparticles (NPs) is of great interest for improving the use of NPs in, for example, therapeutic and diagnostic applications. The conjugation of specific molecules with NPs through the formation of covalent linkages is often sought to provide a high degree of colloidal stability and biocompatibility, as well as to provide functional groups for further surface modification. NPs of lithium niobate (LiNbO₃) have been explored for use in second-harmonic-generation (SHG)-based bioimaging, expanding the applications of SHG-based microscopy techniques. The efficient use of SHG-active LiNbO₃ NPs as probes will, however, require the functionalization of their surfaces with molecular reagents such as polyethylene glycol and fluorescent molecules to enhance their colloidal and chemical stability and to enable a correlative imaging platform. Herein, we demonstrate the surface functionalization of LiNbO₃ NPs through the covalent attachment of alcohol-based reagents through a silanol-alcohol condensation reaction. Alcohol-based reagents are widely available and can have a range of terminal functional groups such as carboxylic acids, amines, and aldehydes. Attaching these molecules to NPs through the silanol-alcohol condensation reaction could diversify the reagents available to modify NPs, but this reaction pathway must first be established as a viable route to modifying NPs. This study focuses on the attachment of a linear alcohol functionalized with carboxylic acid and its use as a reactive group to further tune the surface chemistry of LiNbO₃ NPs. These carboxylic acid groups were reacted to covalently attach other molecules to the NPs using copper-free click chemistry. This derivatization of the NPs provided a means to covalently attach polyethylene glycols and fluorescent probes to the NPs, reducing NP aggregation and enabling multimodal tracking of SHG nanoprobes, respectively. This extension of the silanol-alcohol condensation reaction to functionalize the surfaces of LiNbO₃ NPs can be extended to other types of nanoprobes for use in bioimaging, biosensing, and photodynamic therapies.

DNA Binding to the Silica: Cooperative Adsorption in Action

The adsorption and desorption of nucleic acid to a solid surface is ubiquitous in various research areas like pharmaceutics, nanotechnology, molecular biology, and molecular electronics. In spite of this widespread importance, it is still not well understood how the negatively charged deoxyribonucleic acid (DNA) binds to the negatively charged silica surface in an aqueous solution. In this article, we study the adsorption of DNA to the silica surface using both modeling and experiments and shed light on the complicated binding (DNA to silica) process. The binding agent mediated DNA adsorption was elegantly captured by cooperative Langmuir model. Bulk-depletion experiments were performed to conclude the necessity of a positively charged binding agent for efficient DNA binding, which complements the findings from the model. A profound understanding of DNA binding will help to tune various processes for efficient nucleic acid extraction and purification. However, this work goes beyond the DNA binding and can shed light on other binding agent mediated surface-surface, surface-molecule, molecule-molecule interaction.

Strain in Silica-Supported Ga(III) Sites: Neither Too Much nor Too Little for Propane Dehydrogenation Catalytic Activity

Well-defined Ga(III) sites on SiO₂ are highly active, selective, and stable catalysts in the propane dehydrogenation (PDH) reaction. In this contribution, we evaluate the catalytic activity toward PDH of tricoordinated and tetracoordinated Ga(III) sites on SiO₂ by means of first-principles calculations using realistic amorphous periodic SiO₂ models. We evaluated the three reaction steps in PDH, namely, the C-H activation of propane to form propyl, the β-hydride (β-H) transfer to form propene and a gallium hydride, and the H-H coupling to release H₂, regenerating the initial Ga-O bond and closing the catalytic cycle. Our work shows how Brønsted-Evans-Polanyi relationships are followed to a certain extent for these three reaction steps on Ga(III) sites on SiO₂ and highlights the role of the strain of the reactive Ga-O pairs on such sites of realistic amorphous SiO₂ models. It also shows how transition-state scaling holds very well for the β-H transfer step. While highly strained sites are very reactive sites for the initial C-H activation, they are more difficult to regenerate. The corresponding less strained sites are not reactive enough, pointing to the need for the right balance in strain to be an effective site for PDH. Overall, our work provides an understanding of the intrinsic activity of acidic Ga single sites toward the PDH reaction and paves the way toward the design and prediction of better single-site catalysts on SiO₂ for the PDH reaction.

Green Production of Cladribine by Using Immobilized 2'-Deoxyribosyltransferase from Lactobacillus delbrueckii Stabilized through a Double Covalent/Entrapment Technology

Nowadays, enzyme-mediated processes offer an eco-friendly and efficient alternative to the traditional multistep and environmentally harmful chemical processes. Herein we report the enzymatic synthesis of cladribine by a novel 2'-deoxyribosyltransferase (NDT)-based combined biocatalyst. To this end, Lactobacillus delbrueckii NDT (LdNDT) was successfully immobilized through a two-step immobilization methodology, including a covalent immobilization onto glutaraldehyde-activated biomimetic silica nanoparticles followed by biocatalyst entrapment in calcium alginate. The resulting immobilized derivative, SiG_{PEI 25000}-LdNDT-Alg, displayed 98% retained activity and was shown to be active and stable in a broad range of pH (5-9) and temperature (30-60 °C), but also displayed an extremely high reusability (up to 2100 reuses without negligible loss of activity) in the enzymatic production of cladribine. Finally, as a proof of concept, SiG_{PEI 25000}-LdNDT-Alg was successfully employed in the green production of cladribine at mg scale.

Piroxicam Loading onto Mesoporous Silicas by Supercritical CO2 Impregnation

Piroxicam (PRX) is a commonly prescribed nonsteroidal anti-inflammatory drug. Its efficacy, however, is partially limited by its low water solubility. In recent years, different studies have tackled this problem and have suggested delivering PRX through solid dispersions. All these strategies, however, involve the use of potentially harmful solvents for the loading procedure. Since piroxicam is soluble in supercritical CO₂ (scCO₂), the present study aims, for the first time, to adsorb PRX onto mesoporous silica using scCO₂, which is known to be a safer and greener technique compared to the organic solvent-based ones. For comparison, PRX is also loaded by adsorption from solution and incipient wetness impregnation using ethanol as solvent. Two different commercial mesoporous silicas are used (SBA-15 and Grace Syloid^® XDP), which differ in porosity order and surface silanol population. Physico-chemical analyses show that the most promising results are obtained through scCO₂, which yields the amorphization of PRX, whereas some crystallization occurs in the case of adsorption from solution and IWI. The highest loading of PRX by scCO₂ is obtained in SBA-15 (15 wt.%), where molecule distribution appears homogeneous, with very limited pore blocking.

High performance biocatalyst based on β-d-galactosidase immobilized on mesoporous silica/titania/chitosan material

A new support for the immobilization of β-d-galactosidase from Kluyveromyces lactis was developed, consisting of mesoporous silica/titania with a chitosan coating. This support presents a high available surface area and adequate pore size for optimizing the immobilization efficiency of the enzyme and, furthermore, maintaining its activity. The obtained supported biocatalyst was applied in enzyme hydrolytic activity tests with o-NPG, showing high activity 1223 Ug^-1, excellent efficiency (74%), and activity recovery (54%). Tests of lactose hydrolysis in a continuous flow reactor showed that during 14 days operation, the biocatalyst maintained full enzymatic activity. In a batch system, after 15 cycles, it retained approximately 90% of its initial catalytic activity and attained full conversion of the lactose 100% (±12%). Additionally, with the use of the mesoporous silica/titania support, the biocatalyst presented no deformation and fragmentation, in both systems, demonstrating high operational stability and appropriate properties for applications in food manufacturing.

The Significance of Nonlinear Screening and the pH Interference Mechanism in Field-Effect Transistor Molecular Sensors

Electrolyte screening is well known for its detrimental impact on the sensitivity of liquid-gated field-effect transistor (FET) molecular sensors and is mostly described by the linearized Debye-Hückel model. However, charged and pH-sensitive FET sensing surfaces can limit the FET molecular sensitivity beyond the Debye-Hückel screening formalism. Pre-existing surface charges can lead to the breakdown of Debye-Hückel screening and induce enhanced nonlinear Poisson-Boltzmann screening. Moreover, the charging of the pH-sensitive surface groups interferes with biomolecule sensing resulting in a pH interference mechanism. With analytical equations and TCAD simulations, we highlight that the Debye-Hückel approximation can underestimate screening and overestimate FET molecular sensitivity by more than an order of magnitude. Screening strengthens significantly beyond Debye-Hückel in the proximity of even moderately charged surfaces and biomolecule charge densities (≥1 × 10¹² q/cm²). We experimentally show the strong impact of both nonlinear screening and the pH interference effect on charge-based biomolecular sensing using a model system based on the covalent binding of single-stranded DNA on silicon FET sensors. The DNA signal increases from 24 mV at pH 7 to 96 mV at pH 3 in 1.5 mM PBS for a DNA density of 7 × 10¹² DNA/cm². Our model quantitatively explains the signal's pH dependence with roughly equal nonlinear screening and pH interference contributions. This work shows the importance of reducing the net charge and the pH sensitivity of the sensing surface to improve molecular sensing. Therefore, tailoring the gate dielectric and functional layer of FET sensors is a promising route to strong silicon FET molecular sensitivity boosts.

Structure and sum-frequency generation spectra of water on neutral hydroxylated silica surfaces

Structural organization and vibrational sum-frequency generation (VSFG) spectra of water on crystalline and amorphous neutral silica surfaces were investigated by classical molecular dynamics simulations. The liquid phase represented with neat water and 1 M NaCl solution was analysed in terms of bonded interfacial layer (BIL), diffuse layer (DL) and bulk region. The simulations show that the structure of BIL depends on the surface morphology and density of surface OH groups. The water-silanol H-bond network and BIL structure are mainly insensitive to the presence of ions in the liquid phase. Molecules in DL of SiO₂/neat water interfaces preferentially orient their OH bonds towards the surfaces. This effect is directly related to an effective negative charge of formally neutral surfaces. Ions of the electrolyte solution affect the intermolecular structure in DL by screening the surface electric field and by the chaotropic effect. Calculated phase-sensitive VSFG (Im[χ⁽²⁾]) spectrum of BIL features low-frequency negative and high-frequency positive bands. Characteristics of the positive band reflect the strength of water-surface interactions and surface crystallinity, while the position and shape of the negative band are common to all interfaces. The Im[χ⁽²⁾] spectrum of DL is dominated by a contribution from the third-order χ⁽³⁾ susceptibility with the sign of the contribution directly related to the sign of electrostatic potential in the interfacial region. The DL spectrum is strongly affected by the presence of solvated ions. The computed intensity and Im[χ⁽²⁾] spectra of the amorphous silica/NaCl solution interface are in a good agreement with the conventional and phase-sensitive experimental VSFG spectra of fused SiO₂/water system at low pH, in contrast to the spectra of the amorphous silica/neat water interface. Origins of the discrepancy are discussed.

Loading and Release of Charged and Neutral Fluorescent Dyes into and from Mesoporous Materials: A Key Role for Sensing Applications

The aim of this study is to determine the efficiency of loading and release of several zwitterionic, neutral, anionic and cationic dyes into/from mesoporous nanoparticles to find the optimum loading and release conditions for their application in detection protocols. The loading is carried out for MCM-41 type silica supports suspended in phosphate-buffered saline (PBS) buffer (pH 7.4) or in acetonitrile, involving the dyes (rhodamine B chloride, rhodamine 101 chloride, rhodamine 101 perchlorate, rhodamine 101 inner salt, meso-(4-hydroxyphenyl)-boron–dipyrromethene (BODIPY), sulforhodamine B sodium salt and fluorescein 27). As a general trend, rhodamine-based dyes are loaded with higher efficiency, when compared with BODIPY and fluorescein dyes. Between the rhodamine-based dyes, their charge and the solvent in which the loading process is carried out play important roles for the amount of cargo that can be loaded into the materials. The delivery experiments carried out in PBS buffer at pH 7.4 reveal for all the materials that anionic dyes are more efficiently released compared to their neutral or cationic counterparts. The overall best performance is achieved with the negatively charged sulforhodamine B dye in acetonitrile. This material also shows a high delivery degree in PBS buffer.

Roughness and Scaling Properties of Oxide Glass Surfaces at the Nanoscale

Using atomistic computer simulations we determine the roughness and topographical features of melt-formed (MS) and fracture surfaces (FS) of oxide glasses. We find that the topography of the MS is described well by the frozen capillary wave theory. The FS are significant rougher than the MS and depend strongly on glass composition. The height-height correlation function for the FS shows an unexpected logarithmic dependence on distance, in contrast to the power law found in experiments. We unravel the crucial role of spatial resolution on surface measurements and conclude that on length scales less than 10 nm FS are not self-affine fractals.

Mimicking Biosintering: The Identification of Highly Condensed Surfaces in Bioinspired Silica Materials

Interfacial interactions between inorganic surfaces and organic additives are vital to develop new complex nanomaterials. Learning from biosilica materials, composite nanostructures have been developed, which exploit the strength and directionality of specific polyamine additive-silica surface interactions. Previous interpretations of these interactions are almost universally based on interfacial charge matching and/or hydrogen bonding. In this study, we analyzed the surface chemistry of bioinspired silica (BIS) materials using solid-state nuclear magnetic resonance (NMR) spectroscopy as a function of the organic additive concentration. We found significant additional association between the additives and fully condensed (Q⁴) silicon species compared to industrial silica materials, leading to more overall Q⁴ concentration and higher hydrothermal stability, despite BIS having a shorter synthesis time. We posit that the polyfunctionality and catalytic activity of additives in the BIS synthesis lead to both of these surface phenomena, contrasting previous studies on monofunctional surfactants used in most other artificial templated silica syntheses. From this, we propose that additive polyfunctionality can be used to generate tailored artificial surfaces in situ and provide insights into the process of biosintering in biosilica systems, highlighting the need for more in-depth simulations on interfacial interactions at silica surfaces.

Probing β-alkyl elimination and selectivity in polyolefin hydrogenolysis through DFT

A long chain substrate with [(SiO)3ZrH] has been investigated to elucidate selectivity rules in β-alkyl elimination. DFT studies indicate that polypropylene preferentially undergoes β-Me elimination.

Degree of N-Methylation of Nucleosides and Metabolites Controls Binding Affinity to Pristine Silica Surfaces

Biological molecules interact with silica (SiO₂) surfaces with binding affinities that greatly vary depending on their physical-chemical properties. However, the quantitative characterization of biological compounds adsorbed on silica surfaces, especially of compounds involved in fast, reversible interactions, has been challenging, and the driving forces are not well understood. Here, we show how carbon-13 NMR spin relaxation provides quantitative atomic-detail information about the transient molecular binding to pristine silica surfaces, represented by colloidally dispersed silica nanoparticles (SNPs). Based on the quantitative analysis of almost two dozen biological molecules, we find that the addition of N-methyl motifs systematically increases molecular binding affinities to silica in a nearly quantitatively predictable manner. Among the studied compounds are methylated nucleosides, which are common in epigenetic signaling in nucleic acids. The quantitative understanding of N-methylation may open up new ways to detect and separate methylated nucleic acids or even regulate their cellular functions.

Leverage Surface Chemistry for High-Performance Triboelectric Nanogenerators

Triboelectric Nanogenerators (TENGs) are a highly efficient approach for mechanical-to-electrical energy conversion based on the coupling effects of contact electrification and electrostatic induction. TENGs have been intensively applied as both sustainable power sources and self-powered active sensors with a collection of compelling features, including lightweight, low cost, flexible structures, extensive material selections, and high performances at low operating frequencies. The output performance of TENGs is largely determined by the surface triboelectric charges density. Thus, manipulating the surface chemical properties via appropriate modification methods is one of the most fundamental strategies to improve the output performances of TENGs. This article systematically reviews the recently reported chemical modification methods for building up high-performance TENGs from four aspects: functional groups modification, ion implantation and decoration, dielectric property engineering, and functional sublayers insertion. This review will highlight the contribution of surface chemistry to the field of triboelectric nanogenerators by assessing the problems that are in desperate need of solving and discussing the field's future directions.

Nearly free surface silanols are the critical molecular moieties that initiate the toxicity of silica particles

Inhalation of silica particles can induce inflammatory lung reactions that lead to silicosis and/or lung cancer when the particles are biopersistent. This toxic activity of silica dusts is extremely variable depending on their source and preparation methods. The exact molecular moiety that explains and predicts this variable toxicity of silica remains elusive. Here, we have identified a unique subfamily of silanols as the major determinant of silica particle toxicity. This population of "nearly free silanols" (NFS) appears on the surface of quartz particles upon fracture and can be modulated by thermal treatments. Density functional theory calculations indicates that NFS locate at an intersilanol distance of 4.00 to 6.00 Å and form weak mutual interactions. Thus, NFS could act as an energetically favorable moiety at the surface of silica for establishing interactions with cell membrane components to initiate toxicity. With ad hoc prepared model quartz particles enriched or depleted in NFS, we demonstrate that NFS drive toxicity, including membranolysis, in vitro proinflammatory activity, and lung inflammation. The toxic activity of NFS is confirmed with pyrogenic and vitreous amorphous silica particles, and industrial quartz samples with noncontrolled surfaces. Our results identify the missing key molecular moieties of the silica surface that initiate interactions with cell membranes, leading to pathological outcomes. NFS may explain other important interfacial processes involving silica particles.

The toxicity of respirable South African mine tailings dust in relation to their physicochemical properties

INTRODUCTION

Decades of mining in South Africa has given rise to hundreds of tailings storage facilities (TSFs) and several tonnes of waste. These TSFs have contributed to air pollution due to the lack of proper rehabilitation measures. Currently, it is not known whether tailings emissions could be the cause of respiratory-related ill effects. In addition, the physicochemical properties that may govern their toxicity have not yet been identified.

AIM

The aim of this research was to determine the toxicity of tailings dust and identify the physicochemical properties likely to govern toxicity.

METHODS

Dust samples were collected from five TSFs in the Gauteng and North West Provinces of South Africa and sieved to enrich the airborne particle fraction more likely to be inhaled. Thereafter, their physicochemical characteristics were assessed i.e. size distribution, specific surface area, shape, surface elemental composition, mineral composition, total elemental composition and surface activity. In addition, the toxicity and cellular internalization of the particles were assessed using the BEAS-2B epithelial and U937 monocytic-macrophage cell lines.

Results: The results showed that all tailings dusts showed toxicity, particularly in the BEAS-2B cell line. This toxicity could have been governed by either their elemental composition, e.g. high transition elements e.g. Fe, Cu, Cr and V in the dusts from TSF 4, or a combination of other physicochemical properties, e.g. higher quartz content, lower size and higher surface area in the dusts from TSF 1.

CONCLUSION

These results provide mechanistic evidence to support future epidemiological studies attempting to link tailings dust exposure to adverse health effects.

Buffer Influence on the Amino Acid Silica Interaction

Protein-surface interactions are exploited in various processes in life sciences and biotechnology. Many of such processes are performed in presence of a buffer system, which is generally believed to have an influence on the protein-surface interaction but is rarely investigated systematically. Combining experimental and theoretical methodologies, we herein demonstrate the strong influence of the buffer type on protein-surface interactions. Using state of the art chromatographic experiments, we measure the interaction between individual amino acids and silica, as a reference to understand protein-surface interactions. Among all the 20 proteinogenic amino acids studied, we found that arginine (R) and lysine (K) bind most strongly to silica, a finding validated by free energy calculations. We further measured the binding of R and K at different pH in presence of two different buffers, MOPS (3-(N-morpholino)propanesulfonic acid) and TRIS (tris(hydroxymethyl)aminomethane), and find dramatically different behavior. In presence of TRIS, the binding affinity of R/K increases with pH, whereas we observe an opposite trend for MOPS. These results can be understood using a multiscale modelling framework combining molecular dynamics simulation and Langmuir adsorption model. The modelling approach helps to optimize buffer conditions in various fields like biosensors, drug delivery or bio separation engineering prior to the experiment.

Adsorption, desorption and coadsorption behaviors of sulfamerazine, Pb(II) and benzoic acid on carbon nanotubes and nano-silica

In this study, nano-silica (Nano-SiO₂), oxidized (O-CNTs) and graphitized multi-walled carbon nanotubes (G-CNTs) were applied as model adsorbents to study the adsorption, desorption and coadsorption behaviors of sulfamerazine (SMR), Pb(II) and benzoic acid (BA). The results showed that charge assisted H-bond (CAHB) formation played an important role in adsorption of SMR and BA on O-riched nanomaterials. The adsorption capacities of Pb(II) on CNTs were 21.46- 26.77 times higher than that on Nano-SiO₂, which was mainly attributed to surface complexation and cation-π interaction. The fraction of Pb²⁺ adsorbed in the inside channel of CNTs should not be ignored. In coexisting systems, the absolute sorption inhibition of the SMR (ΔQ_e^SMR) was compared with the amount of competitor adsorbed. Competitive sorption was observed as indicated by adding Pb(II) decreased adsorption of SMR on Nano-SiO₂ (ΔQ_e^SMR > 0), but hardly affected SMR adsorption on CNTs (ΔQ_e^SMR ≈ 0) which was attributed to cation-π interaction. In addition, CAHB formed between SMR and Nano-SiO₂ (ΔpK_a ≈ 4.34) was weaker than that formed between SMR and O-CNTs (ΔpK_a ≈ 3.15), which also consequently resulted in stronger competition of Pb(II) to SMR on Nano-SiO₂ than that on O-CNTs. Moreover, coexisting BA increased adsorption of SMR on Nano-SiO₂ and G-CNTs (ΔQ_e^SMR < 0), but did not result in an apparent competition on SMR adsorption by O-CNTs (ΔQ_e^SMR ≈ 0). These results emphasize that the environmental behaviors of a certain pollutant should be assessed carefully by considering the presence of other pollutants.