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

Native silica nanoparticles are powerful membrane disruptors

Silica nanoparticles permeabilize liposomal membranes as a function of nanoparticle size, surface chemistry and biocoating as well as membrane charge.

The ADOR mechanism for the synthesis of new zeolites

The ADOR method enables the synthesis of novel zeolitic structuresviaexploiting structural weakness present in some zeolites.

Haemolytic activity and cellular toxicity of SBA-15-type silicas: elucidating the role of the mesostructure, surface functionality and linker length

Haemolytic activity and cellular toxicity of native, amino-, mercapto-, and carboxy-terminated SBA-15-type silicates were investigated.

Strong electronic polarization of the C60 fullerene by imidazolium-based ionic liquids: accurate insights from Born–Oppenheimer molecular dynamic simulations

Fullerenes are known to be polarizable due to their strained carbon–carbon bonds and high surface curvature.

Molecular and supramolecular switches on mesoporous silica nanoparticles

This review summarizes the recent advances of molecular and supramolecular switches installed on mesoporous silica nanoparticles.

Structural stability and polarisation of ionic liquid films on silica surfaces

Using molecular dynamics simulations, we studied the structure of [BMIM][NTF2] and [BMIM][BF4] liquid films on hydroxylated silica surfaces. The results pointed out that the main features of the solid–liquid interface were present on both crystalline and amorphous silica, and how these determine their electrostatic properties.

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2 clusters of sol–gel silicate material for understanding DNA photodamage

A sol–gel silicate matrix containing entrapped guanine was prepared. The SiO₂ matrix provides UVA protection by reducing the light penetration to the entrapped guanine molecules.

Grafting of lanthanide complexes on silica surfaces dehydroxylated at 200 °C: a theoretical investigation

The grafting reaction of lanthanide silylamide complexes has been studied, in the framework of the DFT, highlighting the different grafting modes on a silica surface dehydroxylated at 200 °C.

Zwitterionic versus canonical amino acids over the various defects in zeolites: a two-layer ONIOM calculation

Defects are often considered as the active sites for chemical reactions. Here a variety of defects in zeolites are used to stabilize zwitterionic glycine that is not self-stable in gas phase; in addition, effects of acidic strengths and zeolite channels on zwitterionic stabilization are demonstrated. Glycine zwitterions can be stabilized by all these defects and energetically prefer to canonical structures over Al and Ga Lewis acidic sites rather than Ti Lewis acidic site, silanol and titanol hydroxyls. For titanol (Ti-OH), glycine interacts with framework Ti and hydroxyl sites competitively, and the former with Lewis acidity predominates. The transformations from canonical to zwitterionic glycine are obviously more facile over Al and Ga Lewis acidic sites than over Ti Lewis acidic site, titanol and silanol hydroxyls. Charge transfers that generally increase with adsorption energies are found to largely decide the zwitterionic stabilization effects. Zeolite channels play a significant role during the stabilization process. In absence of zeolite channels, canonical structures predominate for all defects; glycine zwitterions remain stable over Al and Ga Lewis acidic sites and only with synergy of H-bonding interactions can exist over Ti Lewis acidic site, while automatically transform to canonical structures over silanol and titanol hydroxyls.

Inorganic materials as supports for covalent enzyme immobilization: methods and mechanisms

Several inorganic materials are potentially suitable for enzymatic covalent immobilization, by means of several different techniques. Such materials must meet stringent criteria to be suitable as solid matrices: complete insolubility in water, reasonable mechanical strength and chemical resistance under the operational conditions, the capability to form manageable particles with high surface area, reactivity towards derivatizing/functionalizing agents. Non-specific protein adsorption should be always considered when planning covalent immobilization on inorganic solids. A huge mass of experimental work has shown that silica, silicates, borosilicates and aluminosilicates, alumina, titania, and other oxides, are the materials of choice when attempting enzyme immobilizations on inorganic supports. More recently, some forms of elemental carbon, silicon, and certain metals have been also proposed for certain applications. With regard to the derivatization/functionalization techniques, the use of organosilanes through silanization is undoubtedly the most studied and the most applied, although inorganic bridge formation and acylation with selected acyl halides have been deeply studied. In the present article, the most common inorganic supports for covalent immobilization of the enzymes are reviewed, with particular focus on their advantages and disadvantages in terms of enzyme loadings, operational stability, undesired adsorption, and costs. Mechanisms and methods for covalent immobilization are also discussed, focusing on the most widespread activating approaches (such as glutaraldehyde, cyanogen bromide, divinylsulfone, carbodiimides, carbonyldiimidazole, sulfonyl chlorides, chlorocarbonates, N-hydroxysuccinimides).

Adsorption of uranium composites onto saltrock oxides - experimental and theoretical study

The study encompassed experimental mass spectrometric and theoretical quantum chemical studies on adsorption of uranium species in different oxidation states of the metal ion, and oxides of UxOy(n+) type, where x = 1 or 3, y = 2 or 8, and n = 0, 1 or 2 onto nanosize-particles of saltrock oxides MO (M = Mg(II), Ca(II), Ni(II), Co(II), Sr(II) or Ba(II)), M2Oy (M = Au(III) or Ag(I), y = 3 or 1) silicates 3Al2O3.2SiO2, natural kaolinite (Al2O2·2SiO2·2H2O), illite (K0.78Ca0.02Na0.02(Mg0.34Al1.69Fe(III)0.02)[Si3.35Al0.65]O10(OH)2·nH2O), CaSiO3, 3MgO·4SiO2,H2O, and M(1)M(2)(SiO4)X2 (M(1) = M(2) = Al or M(1) = K, M(2) = Al, X = F or Cl), respectively. The UV-MALDI-Orbitrap mass spectrometry was utilized in solid-state and semi-liquid colloidal state, involving the laser ablation at λex = 337.2 nm. The theoretical modeling and experimental design was based on chemical-, physico-chemical, physical and biological processes involving uranium species under environmental conditions. Therefore, the results reported are crucial for quality control and monitoring programs for assessment of radionuclide migration. They impact significantly the methodology for evaluation of human health risk from radioactive contamination. The study has importance for understanding the coordination and red-ox chemistry of uranium compounds as well. Due to the double nature of uranium between rare element and superconductivity like materials as well as variety of oxidation states ∈ (+1)-(+6), the there remain challenging areas for theoretical and experimental research, which are of significant importance for management of nuclear fuel cycles and waste storage.

The amorphous silica-liquid water interface studied by ab initio molecular dynamics (AIMD): local organization in global disorder

The structural organization of water at a model of amorphous silica-liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface.

A fundamental understanding of catechol and water adsorption on a hydrophilic silica surface: exploring the underwater adhesion mechanism of mussels on an atomic scale

Mussels have a remarkable ability to bond to solid surfaces under water. From a microscopic perspective, the first step of this process is the adsorption of dopa molecules to the solid surface. In fact, it is the catechol part of the dopa molecule that is interacting with the surface. These molecules are able to make reversible bonds to a wide range of materials, even underwater. Previous experimental and theoretical efforts have produced only a limited understanding of the mechanism and quantitative details of the competitive adsorption of catechol and water on hydrophilic silica surfaces. In this work, we uncover the nature of this competitive absorption by atomic scale modeling of water and catechol adsorbed at the geminal (001) silica surface using density functional theory calculations. We find that catechol molecules displace preadsorbed water molecules and bond directly on the silica surface. Using molecular dynamics simulations, we observe this process in detail. We also calculate the interaction force as a function of distance, and observe a maximum of 0.5 nN of attraction. The catechol has a binding energy of 23 kcal/mol onto the silica surface with adsorbed water molecules.

A DFT study of the interaction between olefins and Cu2+ on silica and MCM-41 model surfaces

The interaction between ethylene and Cu(2+) on a silica model surface was studied by density functional theory (DFT) with nine popular functionals. It is found that B3LYP with BSSE correction is the best method by comparing the calculated results with reported experimental data. This method was also used to study the interactions of Cu(2+) with β-carotene, 1,3,5,7,9,11,13-tetradecaheptaene and ethylene on a MCM-41 model surface. The relationship between the reorganization energy of an olefin and its conjugation length was studied, and the roles of the electrostatic interaction between the olefin and the Cu(2+) were investigated. It is also found that the different environments of Cu(2+) affect the Cu(2+)-olefin interaction significantly.

Enzymes immobilized in mesoporous silica: a physical-chemical perspective

Mesoporous materials as support for immobilized enzymes have been explored extensively during the last two decades, primarily not only for biocatalysis applications, but also for biosensing, biofuels and enzyme-controlled drug delivery. The activity of the immobilized enzymes inside the pores is often different compared to that of the free enzymes, and an important challenge is to understand how the immobilization affects the enzymes in order to design immobilization conditions that lead to optimal enzyme activity. This review summarizes methods that can be used to understand how material properties can be linked to changes in enzyme activity. Real-time monitoring of the immobilization process and techniques that demonstrate that the enzymes are located inside the pores is discussed by contrasting them to the common practice of indirectly measuring the depletion of the protein concentration or enzyme activity in the surrounding bulk phase. We propose that pore filling (pore volume fraction occupied by proteins) is the best standard for comparing the amount of immobilized enzymes at the molecular level, and present equations to calculate pore filling from the more commonly reported immobilized mass. Methods to detect changes in enzyme structure upon immobilization and to study the microenvironment inside the pores are discussed in detail. Combining the knowledge generated from these methodologies should aid in rationally designing biocatalyst based on enzymes immobilized in mesoporous materials.

pH-dependent interaction and resultant structures of silica nanoparticles and lysozyme protein

Small-angle neutron scattering (SANS) and UV-visible spectroscopy studies have been carried out to examine pH-dependent interactions and resultant structures of oppositely charged silica nanoparticles and lysozyme protein in aqueous solution. The measurements were carried out at fixed concentration (1 wt %) of three differently sized silica nanoparticles (8, 16, and 26 nm) over a wide concentration range of protein (0-10 wt %) at three different pH values (5, 7, and 9). The adsorption curve as obtained by UV-visible spectroscopy shows exponential behavior of protein adsorption on nanoparticles. The electrostatic interaction enhanced by the decrease in the pH between the nanoparticle and protein (isoelectric point ∼11.4) increases the adsorption coefficient on nanoparticles but decreases the overall amount protein adsorbed whereas the opposite behavior is observed with increasing nanoparticle size. The adsorption of protein leads to the protein-mediated aggregation of nanoparticles. These aggregates are found to be surface fractals at pH 5 and change to mass fractals with increasing pH and/or decreasing nanoparticle size. Two different concentration regimes of interaction of nanoparticles with protein have been observed: (i) unaggregated nanoparticles coexisting with aggregated nanoparticles at low protein concentrations and (ii) free protein coexisting with aggregated nanoparticles at higher protein concentrations. These concentration regimes are found to be strongly dependent on both the pH and nanoparticle size.

The use of a well-defined surface organometallic complex as a probe molecule: [(SiO)TaVCl2Me2] shows different isolated silanol sites on the silica surface

Ta^VCl₂Me₃ reacts with silica₍₇₀₀₎ and produces two different surface organometallic species, the heterogeneity of the silica surface was disclosed and studied with experimental and theoretical approach.

Silica-surface reorganization during organotin grafting evidenced by 119Sn DNP SENS: a tandem reaction of gem-silanols and strained siloxane bridges

Bu₃Sn(allyl) reacts with Q₂-geminal disilanols and strained siloxane bridges of partially dehydroxylated silica to yield bipodal species through surface rearrangement.

First and second deprotonation of H2SO4on wet hydroxylated (0001) α-quartz

We present anab initiomolecular dynamics study of deprotonation of sulfuric acid on wet quartz, a topic of atmospheric interest.

Pauling's third rule beyond the bulk: chemical bonding at quartz-type GeO2surfaces

In an age of high-performance computing, classical chemical concepts still have their place, and may be applied using new tools.

Visible-ultraviolet vibronic emission of silica nanoparticles

We report the study of the visible-ultraviolet emission properties and the structural features of silica nanoparticles prepared through a laboratory sol–gel technique.

Single-molecule studies on individual peptides and peptide assemblies on surfaces

This review is intended to reflect the recent progress in single-molecule studies of individual peptides and peptide assemblies on surfaces. The structures and the mechanism of peptide assembly are discussed in detail. The contents include the following topics: structural analysis of single peptide molecules, adsorption and assembly of peptides on surfaces, folding structures of the amyloid peptides, interaction between amyloid peptides and dye or drug molecules, and modulation of peptide assemblies by small molecules. The explorations of peptide adsorption and assembly will benefit the understanding of the mechanisms for protein-protein interactions, protein-drug interactions and the pathogenesis of amyloidoses. The investigations on peptide assembly and its modulations could also provide a potential approach towards the treatment of the amyloidoses.

In search of the chemical basis of the hemolytic potential of silicas

The membranolytic activity of silica particles toward red blood cells (RBCs) has been known for a long time and is sometimes associated with silica pathogenicity. However, the molecular mechanism and the reasons why hemolysis differs according to the silica form are still obscure. A panel of 15 crystalline (pure and commercial) and amorphous (pyrogenic, precipitated from aqueous solutions, vitreous) silica samples differing in size, origin, morphology, and surface chemical composition were selected and specifically prepared. Silica particles were grouped into six groups to compare their potential in disrupting RBC membranes so that one single property differed in each group, while other features were constant. Free radical production and crystallinity were not strict determinants of hemolytic activity. Particle curvature and morphology modulated the hemolytic effect, but silanols and siloxane bridges at the surface were the main actors. Hemolysis was unrelated to the overall concentration of silanols as fully rehydrated surfaces (such as those obtained from aqueous solution) were inert, and one pyrogenic silica also lost its membranolytic potential upon progressive dehydration. Overall results are consistent with a model whereby hemolysis is determined by a defined surface distribution of dissociated/undissociated silanols and siloxane groups strongly interacting with specific epitopes on the RBC membrane.

Does Dispersion Dominate over H-Bonds in Drug-Surface Interactions? The Case of Silica-Based Materials As Excipients and Drug-Delivery Agents

Amorphous silica is widely employed in pharmaceutical formulations both as a tableting, anticaking agent and as a drug delivery system, whereas MCM-41 mesoporous silica has been recently proposed as an efficient support for the controlled release of drugs. Notwithstanding the relevance of this topic, the atomistic details about the specific interactions between the surfaces of the above materials and drugs and the energetic of adsorption are almost unknown. In this work, we resort to a computational ab initio approach, based on periodic Density Functional Theory (DFT), to study the adsorption behavior of two popular drugs (aspirin and ibuprofen) on two models of an amorphous silica surface characterized by different hydrophilic/hydrophobic properties due to different SiOH surface groups' density. Particular effort was devoted to understand the role of dispersive (vdW) interactions in the adsorption mechanism and their interplay with H-bond interactions. On the hydrophilic silica surface, the H-bond pattern of the Si-OH groups rearranges to comply with the formation of new H-bond interactions triggered by the adsorbed drug. The interaction energy of ibuprofen with the hydrophilic model of the silica surface is computed to be very close to the sublimation energy of the ibuprofen molecular crystal, accounting for the experimental evidence of ibuprofen crystal amorphization induced by the contact with the mesoporous silica material. For both surface models, dispersion interactions play a crucial role in dictating the features of the drug/silica system, and they become dominant for the hydrophobic surface. It was proved that a competition may exist between directional H-bonds and nonspecific dispersion driven interactions, with important structural and energetic consequences for the adsorption. The results of this work emphasize the inadequacy of plain DFT methods to model adsorption processes involving inorganic surfaces and drugs of moderate size, due to the missing term accounting for London dispersion interactions.