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

Extraction and Purification of DNA from Complex Biological Sample Matrices Using Solid-Phase Microextraction Coupled with Real-Time PCR

The determination of extremely small quantities of DNA from complex biological sample matrices represents a significant bottleneck in nucleic acid analysis. In this study, polymeric ionic liquid (PIL)-based solid-phase microextraction (SPME) was applied for the extraction and purification of DNA from crude bacterial cell lysate with subsequent quantification by real-time PCR (qPCR) analysis. Using an on-fiber ultraviolet initiated polymerization technique, eight different PIL sorbent coatings were generated and their DNA extraction performance evaluated using qPCR. The PIL sorbent coating featuring halide anions and carboxylic acid groups in the cationic portion exhibited superior DNA extraction capabilities when compared to the other studied PILs and a commercial polyacrylate SPME fiber. Electrostatic interactions as well as an ion-exchange mechanism were identified as the driving forces in DNA extraction by the PIL sorbents. The selectivity of the PIL sorbent coating for DNA was demonstrated in the presence of PCR inhibitors at high concentration, where a quantifiable amount of template DNA was extracted from aqueous samples containing CaCl2 and FeCl3. Furthermore, the PIL-based SPME method was successfully applied for the extraction of DNA from crude bacterial cell lysate spiked with 1 pg mL(-1) template DNA without requiring the use of organic solvents or centrifugation steps. Following PIL-based SPME of DNA from a dilute cell lysate, the qPCR amplification efficiency was determined to be 100.3%, demonstrating the feasibility of the developed method to extract high purity DNA from complex sample matrices.

Revisiting the paradigm of silica pathogenicity with synthetic quartz crystals: the role of crystallinity and surface disorder

BACKGROUND

Exposure to some - but not all - quartz particles is associated to silicosis, lung cancer and autoimmune diseases. What imparts pathogenicity to any single quartz source is however still unclear. Crystallinity and various surface features are implied in toxicity. Quartz dusts used so far in particle toxicology have been obtained by grinding rocks containing natural quartz, a process which affects crystallinity and yields dusts with variable surface states. To clarify the role of crystallinity in quartz pathogenicity we have grown intact quartz crystals in respirable size.

METHODS

Quartz crystals were grown and compared with a fractured specimen obtained by grinding the largest synthetic crystals and a mineral quartz (positive control). The key physico-chemical features relevant to particle toxicity - particle size distribution, micromorphology, crystallinity, surface charge, cell-free oxidative potential - were evaluated. Membranolysis was assessed on biological and artificial membranes. Endpoints of cellular stress were evaluated on RAW 264.7 murine macrophages by High Content Analysis after ascertaining cellular uptake by bio-TEM imaging of quartz-exposed cells.

RESULTS

Quartz crystals were grown in the submicron (n-Qz-syn) or micron (μ-Qz-syn) range by modulating the synthetic procedure. Independently from size as-grown quartz crystals with regular intact faces did not elicit cellular toxicity and lysosomal stress on RAW 264.7 macrophages, and were non-membranolytic on liposome and red blood cells. When fractured, synthetic quartz (μ-Qz-syn-f) attained particle morphology and size close to the mineral quartz dust (Qz-f, positive control) and similarly induced cellular toxicity and membranolysis. Fracturing imparted a higher heterogeneity of silanol acidic sites and radical species at the quartz surface.

CONCLUSIONS

Our data support the hypothesis that the biological activity of quartz dust is not due to crystallinity but to crystal fragmentation, when conchoidal fractures are formed. Besides radical generation, fracturing upsets the expected long-range order of non-radical surface moieties - silanols, silanolates, siloxanes - which disrupt membranes and induce cellular toxicity, both outcomes associated to the inflammatory response to quartz.

Photoswitched Cell Adhesion on Azobenzene-Containing Self-Assembled Films

Stimuli-responsive surfaces that can regulate and control cell adhesion have attracted much attention for their great potential in diverse biomedical applications. Unlike for pH- and temperature-responsive surfaces, the process of photoswitching requires no additional input of chemicals or thermal energy. In this work, two different photoresponsive azobenzene films are synthesized by chemisorption and electrostatic layer-by-layer (LbL) assembly techniques. The LbL film exhibits a relatively loose packing of azobenzene chromophores compared with the chemisorbed film. The changes in trans/cis isomer ratio of the azobenzene moiety and the corresponding wettability of the LbL films are larger than those of the chemisorbed films under UV light irradiation. The tendency for cell adhesion on the LbL films decreases markedly after UV light irradiation, whereas adhesion on the chemisorbed films decreases only slightly, because the azobenzene chromophores stay densely packed. Interestingly, the tendency for cell adhesion can be considerably increased on rough substrates, the roughness being introduced by use of photolithography and inductively coupled plasma deep etching techniques. For the chemisorbed films on rough substrates, the amount of cells that adhere also changes slightly after UV light irradiation, whereas, the amount of cells that adhere to LbL films on rough substrates decreases significantly.

Stereochemically Distinct Cyclotetrasiloxanes Containing 3-Pyridyl Moieties and Their Functional Coordination Polymers

Synthesis of new cyclotetrasiloxane scaffolds containing peripherally functionalized 3-pyridyl moieties, [MeSiO(CH═CH(3)Py)]4 (L(1)) and [MeSiO(CH2CH2(3)Py)]4 (L(2)), and their reactivity studies with certain d(10) metal ions are reported. The ligand L(1) is obtained by the Heck-coupling reaction of tetramethyl tetravinyl tetrasiloxane (D4(vi)) and 3-bromopyridine in the presence of the Pd(0) catalysts. The as-synthesized ligand L(1) shows the presence of three stereoisomers, cis-trans-cis (L(1A)), cis-cis-trans (L(1B)), and all-trans (L(1C)), which are quantitatively separated by column chromatography. Subsequent reduction of L(1A), L(1B), and L(1C) with triethylsilane in the presence of catalytic amounts of Pd/C leads to the formation of the ligands L(2A), L(2B), and L(2C) with retention of stereochemistry due to the precursor moieties. Treatment of ZnI2 with L(1A) gives a one-dimensional coordination framework [(L(1A))4(ZnI2)2]∞, 1. These 1D-chains are further connected by π-π stacking interactions between the pyridyl groups of the adjacent chains leading to the formation of a three-dimensional network with the topology of a PtS net. The reaction of silver nitrate with ligand L(1B) gives a chain like one-dimensional cationic coordination polymer {[(L(1B))4Ag2]·2NO3·H2O·CH3OH }∞, 2, consisting of two different kinds of 32-membered macrocycles. Treatment of the all-trans ligand L(2C) with copper(I) iodide salt results in the formation of a cubane-type Cu4I4 cluster MOF [(L(2C))4Cu4I4]∞, 3, in a two-dimensional 4-connected uninodal sql/Shubnikov tetragonal plane net topology represented by the Schläfli symbol {4(4).6(2)}. This MOF displays a thermochromic luminescence behavior due to Cu4I4 clusters showing an orange emission at 298 K and a blue emission at 77 K.

Conjugation of A and B Blood Group Structures to Silica Microparticles for the Detection of Antigen-Specific B Cells

Silica microparticles were functionalized with A and B blood group carbohydrate antigens (A type I, A type II, B type I, and B type II) to enable the detection and monitoring of ABO antigen-specific B cells. Microparticles were prepared via the Stöber synthesis, labeled with an Alexafluor fluorescent dye, and characterized via TEM and fluorescence microscopy. The silica microparticles were functionalized with (3-aminopropyl)trimethoxysilane (APTMS), followed by the use of an established fluorenylmethyloxycarbonyl (Fmoc)-protected PEG-based linker. The terminal Fmoc moiety of the PEG-based linker was then deprotected, yielding free amino groups, to which the A and B antigens were coupled. The carbohydrate antigens were synthesized with a p-nitrophenol ester to enable conjugation to the functionalized silica microparticles via an amide bond. The number of free amine groups available for coupling for a given mass of PEG-functionalized silica microparticles was quantified via reaction with Fmoc-glycine. The antigen-functionalized microparticles were then evaluated for their specificity in binding to A and B antigen-reactive B-cells via flow cytometry, and for blocking of naturally occurring antibodies in human serum. Selective binding of the functionalized microparticles to blood group-reactive B cells was observed by flow cytometry and fluorescence microscopy. The modular approach outlined here is applicable to the preparation of silica microparticles containing any carbohydrate antigen and alternative fluorophores or labels. This approach therefore comprises a novel, general platform for screening B cell populations for binding to carbohydrate antigens, including, in this case, the human A and B blood group antigens.

Glyco-nano-oncology: Novel therapeutic opportunities by combining small and sweet

Recent efforts toward defining the molecular features of the tumor microenvironment have revealed dramatic changes in the expression of glycan-related genes including glycosyltransferases and glycosidases. These changes affect glycosylation of proteins and lipids not only in cancer cells themselves, but also in cancer associated-stromal, endothelial and immune cells. These glycan alterations including increased frequency of β1,6-branched N-glycans and bisecting N-glycans, overexpression of tumor-associated mucins, preferred expression of T, Tn and sialyl-Tn antigen and altered surface sialylation, may contribute to tumor progression by masking or unmasking specific ligands for endogenous lectins, including members of the C-type lectin, siglec and galectin families. Differential expression of glycans or glycan-binding proteins could be capitalized for the identification of novel biomarkers and might provide novel opportunities for therapeutic intervention. This review focuses on the biological relevance of lectin-glycan interactions in the tumor microenvironment (mainly illustrated by the immunosuppressive and pro-angiogenic activities of galectin-1) and the design of functionalized nanoparticles for pharmacological delivery of multimeric glycans, lectins or selective inhibitors of lectin-glycan interactions with antitumor activity.

Silica Nanoparticle-Generated ROS as a Predictor of Cellular Toxicity: Mechanistic Insights and Safety by Design

Evaluating toxicological responses of engineered nanomaterials such as silica nanoparticles is critical in assessing health risks and exposure limits. Biological assays can be used to evaluate cytotoxicity of individual materials, but specific nano-bio interactions-which govern its physiological response-cannot currently be predicted from materials characterization and physicochemical properties. Understanding the role of free radical generation from nanomaterial surfaces facilitates understanding of a potential toxicity mechanism and provides insight into how toxic effects can be assessed. Size-matched mesoporous and nonporous silica nanoparticles in aminopropyl-functionalized and native forms were investigated to analyze the effects of porosity and surface functionalization on the observed cytotoxicity. In vitro cell viability data in a murine macrophage cell line (RAW 264.7) provides a model for what might be observed in terms of cellular toxicity upon an environmental or industrial exposure to silica nanoparticles. Electron paramagnetic resonance spectroscopy was implemented to study free radical species generated from the surface of these nanomaterials and the signal intensity was correlated with cellular toxicity. In addition, in vitro assay of intracellular reactive oxygen species (ROS) matched well with both the EPR and cell viability data. Overall, spectroscopic and in vitro studies correlate well and implicate production of ROS from a surface-catalyzed reaction as a predictor of cellular toxicity. The data demonstrate that mesoporous materials are intrinsically less toxic than nonporous materials, and that surface functionalization can mitigate toxicity in nonporous materials by reducing free radical production. The broader implications are in terms of safety by design of nanomaterials, which can only be extracted by mechanistic studies such as the ones reported here.

Influence of Protein Surface Coverage on Anomalously Strong Adsorption Sites

Serum albumin is commonly used as a blocking agent to reduce nonspecific protein adsorption in bioassays and biodevices; however, the details of this process remain poorly understood. Using single molecule techniques, we investigated the dynamics of human serum albumin (HSA) on four model surfaces as a function of protein concentration. By constructing super-resolution maps, identifying anomalously strong adsorption sites, and quantifying surface heterogeneity, we found that the concentration required for site blocking varied dramatically with surface chemistry. When expressed in terms of protein surface coverage, however, a more consistent picture emerged, where a significant fraction of strong sites were passivated at a fractional coverage of 10(-4). On fused silica (FS), "non-fouling" oligo (ethylene glycol) functionalized FS, and hydrophobically modified FS, a modest additional site blocking effect continued at higher coverage. However, on amine-functionalized surfaces, the surface heterogeneity exhibited a minimum at a coverage of ∼10(-4). Using intermolecular Förster resonance energy transfer (FRET), we determined that new anomalous strong sites were created at higher coverage on amine surfaces and that adsorption to these sites was associated with protein-protein interactions, i.e., surface-induced aggregation.

Stabilization of zwitterionic versus canonical proline by water molecules

At physiological conditions, a majority of biomolecules (e.g., amino acids, peptides and proteins) exist predominantly in the zwitterionic form that usually decides the biological functions. However, zwitterionic amino acids are not geometrically stable in gas phase and this seriously hampers the understanding of their structures, properties and biological functions. To this end, one of the recent research focuses is to demonstrate the stabilization effects of zwitterionic amino acids. Relative stabilities of canonical conformers are dependent on water contents, while zwitterionic stability improves monotonously and pronouncedly with increase of water contents. We find that one water molecule can render zwitterionic proline geometrically stable, and stabilities of different zwitterionic amino acids increase as glycine  Collapse

Key Words

• Conformational analysis
• Density functional calculations
• H-bonds
• Zwitterionic stabilization

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MESH Headings Collapse

Grants

• National Natural Science Foundation of China

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Affiliation(s)

Gang Yang />College of Resource and Environment and Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, 400715 Chongqing, People’s Republic of China
Lijun Zhou />College of Resource and Environment and Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, 400715 Chongqing, People’s Republic of China
Yang Chen />College of Chemistry Chemical Engineering and Environmental Engineering, Liaoning Shihua University, 113001 Fushun, Liaoning People’s Republic of China

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Insight into the defect–molecule interaction through the molecular-like photoluminescence of SiO2 nanoparticles

The molecular-like luminescence of SiO₂ nanoparticles is a keystone when investigating the defect–molecule interaction.

Electron stimulated hydroxylation of a metal supported silicate film

Low-energy electron irradiation of an ice precovered silicate film enhances surface hydroxylation.

Silica-supported ultra small gold nanoparticles as nanoreactors for the etherification of silanes

Ultra-small Au–SiO₂ nanoparticles worked as nanoreactors for the etherification of silanes with high selectivity and reusability.

Hydration in silica based mesoporous materials: a DFT model

In this work, calculable and realistic DFT models of MCM-41 material that follow temperature dependence of silanol density were developed. They can be easily applied in further studies of adsorption or as a support for catalysts.

New perspectives in organolanthanide chemistry from redox to bond metathesis: insights from theory

A fifteen year contribution of computational studies carried out in close synergy with experiments is summarized.

Nanoporous chalcogenides for adsorption and gas separation

A realistic model of porous chalcogenide is used to probe the viability of such a class of materials for adsorption and phase separation applications.

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension.

Amorphous SiO2 surface models: energetics of the dehydroxylation process, strain, ab initio atomistic thermodynamics and IR spectroscopic signatures

Realistic amorphous SiO₂ models of 2.1 × 2.1 nm with silanol densities ranging 1.1–7.2 OH per nm² are obtained by means of ab initio calculations via the dehydroxylation of a fully hydroxylated silica surface.

Molecular simulation of methane adsorption in slit-like quartz pores

The GCMC and MD methods were used to investigate the structural properties and adsorption behaviors of methane in quartz nanopores.

Water Contact Angle Dependence with Hydroxyl Functional Groups on Silica Surfaces under CO2 Sequestration Conditions

Functional groups on silica surfaces under CO2 sequestration conditions are complex due to reactions among supercritical CO2, brine and silica. Molecular dynamics simulations have been performed to investigate the effects of hydroxyl functional groups on wettability. It has been found that wettability shows a strong dependence on functional groups on silica surfaces: silanol number density, space distribution, and deprotonation/protonation degree. For neutral silica surfaces with crystalline structure (Q(3), Q(3)/Q(4), Q(4)), as silanol number density decreases, contact angle increases from 33.5° to 146.7° at 10.5 MPa and 318 K. When Q(3) surface changes to an amorphous structure, water contact angle increases 20°. Water contact angle decreases about 12° when 9% of silanol groups on Q(3) surface are deprotonated. When the deprotonation degree increases to 50%, water contact angle decreases to 0. The dependence of wettability on silica surface functional groups was used to analyze contact angle measurement ambiguity in literature. The composition of silica surfaces is complicated under CO2 sequestration conditions, the results found in this study may help to better understand wettability of CO2/brine/silica system.

The role of outer surface/inner bulk Brønsted acidic sites in the adsorption of a large basic molecule (simazine) on H-Y zeolite

The simple means adopted for investigating H-Y zeolite acidity in water is the pH-dependence of the amount of a basic molecule adsorbed under isochoric conditions, a technique capable of yielding, under equilibrium conditions, an estimate of the pKa value of the involved acidic centres: the behaviour with temperature of adsorbed amounts yields instead some information on thermodynamics. Simazine (Sim, 2-chloro-4,6-bis(ethylamino)-s-triazine) was chosen as an adsorbate because its transverse dimension (7.5 Å) is close to the opening of the supercage in the faujasite structure of H-Y (7.4 Å). In short term measurements, Sim adsorption at 25 °C occurs only at the outer surface of H-Y particles. Two types of mildly acidic centres are present (with pKaca. 7 and ca. 8, respectively) and no strong one is observed. Previous adsorption of ammonia from the gas phase discriminates between the two. The former survives, and shows features common with the silanols of amorphous silica. The latter is suppressed: because of this and other features distinguishing this site from silanol species (e.g. the formation of dimeric Sim2H(+) species, favoured by coverage and unfavoured by temperatures of adsorption higher than ambient temperature) a candidate is an Al based site. We propose a Lewis centre coordinating a water molecule, exhibiting acidic properties. This acidic water molecule can be replaced by the stronger base ammonia, also depleting inner strong Brønsted sites. A mechanism for the generation of the two sites from surface Brønsted species is proposed. Long term adsorption measurements at 25 °C already show the onset of the interaction with inner strongly acidic Brønsted sites: because of its size, activation is required for Sim to pass the supercage openings and reach inner acidic sites. When adsorption is run at 40-50 °C, uptake is much larger and increases with temperature. Isochoric measurements suggest a pKa value of ca. 3 compatible with its marked acidic nature, although attainment of equilibrium conditions is questionable. Measurements at 60 °C (both isochors and DRIFT) show the onset of changes at the outer surface brought about by the presence of hot water. Control experiments run with USY (Ultra Stabilized zeolite Y), featuring wormholes and cavities rendering accessible internal sites, show the extensive involvement of internal Brønsted sites already at 25 °C.

When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces

Fluorescent labels are often attached to proteins to monitor binding and adsorption processes. Docking simulations for native hen egg white lysozyme (HEWL) and HEWL labeled with fluorescein isothiocyanate show that these adsorb differently on charged surfaces. Attachment of even a small label can significantly change the interaction properties of a protein. Thus, the results of experiments with fluorescently labeled proteins should be interpreted by modeling the structures and computing the interaction properties of both labeled and unlabeled species.

A Giant Reconstruction of α-quartz (0001) Interpreted as Three Domains of Nano Dauphine Twins

Silica (SiO₂) is one of the most common materials on Earth. The crystalline form α-quartz is the stable silica polymorph at ambient conditions although metastable forms exist. α-quartz is a piezoelectric material, it can be produced artificially and is widely used for example in electronics and the biosciences. Despite the many application areas, the atomic surface structures of silica polymorphs are neither well understood nor well characterized. Here we present measurements of α-quartz (0001). Helium Atom Scattering combined with Atomic Force Microscopy reveals a giant reconstruction consisting of 5.55 ± 0.07 nm wide ribbons, oriented 10.4° ± 0.8° relative to the bulk unit cell. The ribbons, with the aid of atomistic modelling, can be explained as a self-organised pattern of nano Dauphine twins (nano electrical twins).

Promoting the Adsorption of Metal Ions on Kaolinite by Defect Sites: A Molecular Dynamics Study

Defect sites exist abundantly in minerals and play a crucial role for a variety of important processes. Here molecular dynamics simulations are used to comprehensively investigate the adsorption behaviors, stabilities and mechanisms of metal ions on defective minerals, considering different ionic concentrations, defect sizes and contents. Outer-sphere adsorbed Pb²⁺ ions predominate for all models (regular and defective), while inner-sphere Na⁺ ions, which exist sporadically only at concentrated solutions for regular models, govern the adsorption for all defective models. Adsorption quantities and stabilities of metal ions on kaolinite are fundamentally promoted by defect sites, thus explaining the experimental observations. Defect sites improve the stabilities of both inner- and outer-sphere adsorption, and (quasi) inner-sphere Pb²⁺ ions emerge only at defect sites that reinforce the interactions. Adsorption configurations are greatly altered by defect sites but respond weakly by changing defect sizes or contents. Both adsorption quantities and stabilities are enhanced by increasing defect sizes or contents, while ionic concentrations mainly affect adsorption quantities. We also find that adsorption of metal ions and anions can be promoted by each other and proceeds in a collaborative mechanism. Results thus obtained are beneficial to comprehend related processes for all types of minerals.

Luminescence from nearly isolated surface defects in silica nanoparticles

A structured emission/excitation pattern, proper of isolated defects, arises in a vacuum from silica nanoparticles. The luminescence, centered around 3.0-3.5 eV, is characterised by a vibronic progression due to the phonon coupling with two localised modes of frequency  ∼1370 cm(-1) and  ∼360 cm(-1), and decays in about 300 ns at 10 K. On increasing the temperature, the intensity and the lifetime decrease due to the activation of a non-radiative rate from the excited state. Concurrently, the temperature dependence of the lineshape evidences the low coupling with non-localised modes of the matrix (Huang-Rhys factor S ~ 0.2) and the poor influence of the inhomogeneous broadening. These findings outline an uncommon behaviour in the field of the optical properties of defects in amorphous solids, evidencing that the silica surface can allocate luminescent defects almost disentangled from the basal network.

Capturing Conformation-Dependent Molecule-Surface Interactions When Surface Chemistry Is Heterogeneous

Molecular building blocks, such as carbon nanotubes and DNA origami, can be fully integrated into electronic and optical devices if they can be assembled on solid surfaces using biomolecular interactions. However, the conformation and functionality of biomolecules depend strongly on the local chemical environment, which is highly heterogeneous near a surface. To help realize the potential of biomolecular self-assembly, we introduce here a technique to spatially map molecular conformations and adsorption, based on single-molecule fluorescence microscopy. On a deliberately patterned surface, with regions of varying hydrophobicity, we characterized the conformations of adsorbed helicogenic alanine-lysine copeptides using Förster resonance energy transfer. The peptides adopted helical conformations on hydrophilic regions of the surface more often than on hydrophobic regions, consistent with previous ensemble-averaged observations of α-helix surface stability. Interestingly, this dependence on surface chemistry was not due to surface-induced unfolding, as the apparent folding and unfolding dynamics were usually much slower than desorption. The most significant effect of surface chemistry was on the adsorption rate of molecules as a function of their initial conformational state. In particular, regions with higher adsorption rates attracted more molecules in compact, disordered coil states, and this difference in adsorption rates dominated the average conformation of the ensemble. The correlation between adsorption rate and average conformation was also observed on nominally uniform surfaces. Spatial variations in the functional state of adsorbed molecules would strongly affect the success rates of surface-based molecular assembly and can be fully understood using the approach developed in this work.

Specific Interactions of Neutral Side Chains of an Adsorbed Protein with the Surface of α-Quartz and Silica Gel

Many key features of the protein adsorption on the silica surfaces still remain unraveled. One of the open questions is the interaction of nonpolar side chains with siloxane cavities. Here, we use nonequilibrium molecular dynamics simulations for the detailed investigation of the binding of several hydrophobic and amphiphilic protein side chains with silica surface. These interactions were found to be a possible driving force for protein adsorption. The free energy gain was larger for the disordered surface of amorphous silica gel as compared to α-quartz, but the impact depended on the type of amino acid. The dependence was analyzed from the structural point of view. For every amino acid an enthalpy-entropy compensation behavior was observed. These results confirm a hypothesis of an essential role of hydrophobic interactions in protein unfolding and irreversible adsorption on the silica surface.

Use of Charged Nanoparticles in NMR-Based Metabolomics for Spectral Simplification and Improved Metabolite Identification

Metabolomics aims at a complete characterization of all metabolites in biological samples in terms of both their identities and concentrations. Because changes of metabolites and their concentrations are a direct reflection of cellular activity, it allows for a better understanding of cellular processes and function to be obtained. Although NMR spectroscopy is routinely applied to complex biological mixtures without purification, overlapping NMR peaks often pose a challenge for the comprehensive and accurate identification of the underlying metabolites. To address this problem, we present a novel nanoparticle-based strategy that differentiates between metabolites based on their electric charge. By adding electrically charged silica nanoparticles to the solution NMR sample, metabolites of opposite charge bind to the nanoparticles and their NMR signals are weakened or entirely suppressed due to peak broadening caused by the slow rotational tumbling of the nanometer-sized nanoparticles. Comparison of the edited with the original spectrum significantly facilitates analysis and reduces ambiguities in the identification of metabolites. This method makes NMR directly sensitive to the detection of molecular charges at constant pH, as demonstrated here both for model mixtures and human urine. The simplicity of the approach should make it useful for a wide range of metabolomics applications.

Computational Study of Acidic and Basic Functionalized Crystalline Silica Surfaces as a Model for Biomaterial Interfaces

In silico modeling of acidic (CH2COOH) or basic (CH2NH2) functionalized silica surfaces has been carried out by means of a density functional approach based on a gradient-corrected functional to provide insight into the characterization of experimentally functionalized surfaces via a plasma method. Hydroxylated surfaces of crystalline cristobalite (sporting 4.8 OH/nm(2)) mimic an amorphous silica interface as unsubstituted material. To functionalize the silica surface we transformed the surface Si-OH groups into Si-CH2COOH and Si-CH2NH2 moieties to represent acidic/basic chemical character for the substitution. Structures, energetics, electronic, and vibrational properties were computed and compared as a function of the increasing loading of the functional groups (from 1 to 4 per surface unit cell). Classical molecular dynamics simulations of selected cases have been performed through a Reax-FF reactive force field to assess the mobility of the surface added chains. Both DFT and force field calculations identify the CH2NH2 moderate surface loading (1 group per unit cell) as the most stable functionalization, at variance with the case of the CH2COOH group, where higher loadings are preferred (2 groups per unit cell). The vibrational fingerprints of the surface functionalities, which are the ν(C═O) stretching and δ(NH2) bending modes for acidic/basic cases, have been characterized as a function of substitution percentage in order to guide the assignment of the experimental data. The final results highlighted the different behavior of the two types of functionalization. On the one hand, the frequency associated with the ν(C═O) mode shifts to lower wavenumbers as a function of the H-bond strength between the surface functionalities (both COOH and SiOH groups), and on the other hand, the δ(NH2) frequency shift seems to be caused by a subtle balance between the H-bond donor and acceptor abilities of the NH2 moiety. Both sets of data are in general agreement with experimental measurements on the corresponding silica-functionalized materials and provide finer details for a deeper interpretation of experimental spectra.

Exploration and exploitation of water in colloidal crystals

Water on solid surfaces is ubiquitously found in nature, in most cases due to mere adsorption from ambient moisture. Because porous structures have large surfaces, water may significantly affect their characteristics. This is particularly obvious in systems formed by separate particles, whose interactions are strongly influenced by small amounts of liquid. Water/solid phenomena, like adsorption, condensation, capillary forces, or interparticle cohesion, have typically been studied at relatively large scales down to the microscale, like in wet granular media. However, much less is known about how water is confined and acts at the nanoscale, for example, in the interstices of divided systems, something of utmost importance in many areas of materials science nowadays. With novel approaches, in-depth investigations as to where and how water is placed in the nanometer-sized pores of self-assembled colloidal crystals have been made, which are employed as a well-defined, versatile model system with useful optical properties. In this Progress Report, knowledge gained in the last few years about water distribution in such nanoconfinements is gathered, along with how it can be controlled and the consequences it brings about to extract new or enhance existing material functionalities. New methods developed and new capabilities of standard techniques are described, and the water interplay with the optical, chemical, and mechanical properties of the ensemble are discussed. Some lines for applicability are also highlighted and aspects to be addressed in the near future are critically summarized.

Surface vibrational structure of colloidal silica and its direct correlation with surface charge density

We show that attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy can be used to determine the surface charge density (SCD) of colloidal silica nanoparticles (NPs) in aqueous solution. We identify the Si-O stretch vibrations of neutral surface bound silanol, ≡Si-OH, and of the deprotonated group, ≡Si-O(-). The position of the Si-(OH) stretch vibration is shown to directly correlate with the NPs SCD as determined by traditional potentiometric titrations, shifting to lower wavenumber (cm(-1)) with increasing density of ≡Si-O(-). The origin of this shift is discussed in terms of inductive effects that reduce the ionic character of the Si-(OH) bond after delocalization of the negative charge left on a terminal ≡Si-O(-) group across the atoms within ∼1 nm of the charged site. Using this new methodology, we quantitatively determine the SCD of 9, 14, and 25 nm diameter colloidal silica in varying concentrations of NaCl electrolyte at different bulk pH. This novel spectroscopic approach to investigate SCDs provides several opportunities for in situ coupling, for example, in microfluidic channels or with liquid microjets, and requires only very little sample—all potential advantages over a traditional potentiometric titration.