Grid batch-dependent tuning of glow discharge parameters.

Sample preparation on cryo-EM grids can give various results, from very thin ice and homogeneous particle distribution (ideal case) to unwanted behavior such as particles around the "holes" or complexes that do not entirely correspond to the one in solution (real life). We recently run into such a case and finally found out that variations in the 3D reconstructions were systematically correlated with the grid batches that were used. We report the use of several techniques to investigate the grids' characteristics, namely TEM, SEM, Auger spectroscopy and Infrared Interferometry. This allowed us to diagnose the origin of grid preparation problems and to adjust glow discharge parameters. The methods used for each approach are described and the results obtained on a common specific case are reported.

Post-Modification of Copolymers Obtained by ATRP for an Application in Heterogeneous Asymmetric Salen Catalysis.

Copolymers are valuable supports for obtaining heterogeneous catalysts that allow their recycling and therefore substantial savings, particularly in the field of asymmetric catalysis. This contribution reports the use of two comonomers: Azido-3-propylmethacrylate (AZMA) bearing a reactive azide function was associated with 2-methoxyethyl methacrylate (MEMA), used as a spacer, for the ATRP synthesis of copolymers, and then post-functionalized with a propargyl chromium salen complex. The controlled homopolymerization of MEMA by ATRP was firstly described and proved to be more controlled in molar mass than that of AZMA for conversions up to 63%. The ATRP copolymerization of both monomers made it possible to control the molar masses and the composition, with nevertheless a slight increase in the dispersity (from 1.05 to 1.3) when the incorporation ratio of AZMA increased from 10 to 50 mol%. These copolymers were post-functionalized with chromium salen units by click chemistry and their activity was evaluated in the asymmetric ring opening of cyclohexene oxide with trimethylsilyl azide. At an equal catalytic ratio, a significant increase in enantioselectivity was obtained by using the copolymer containing the largest part of salen units, probably allowing, in this case, the more favorable bimetallic activation of both the engaged nucleophile and electrophile. Moreover, the catalytic polymer was recovered by simple filtration and re-engaged in subsequent catalytic runs, up to seven times, without loss of activity or selectivity.

ToF-SIMS Li Depth Profiling of Pure and Methylated Amorphous Silicon Electrodes After Their Partial Lithiation.

Pure (a-Si:H) and methylated [a-Si0.95(CH3)0.05:H] amorphous silicon thin films were analyzed by time-of-flight secondary ion mass spectrometry after partial lithiation. Depth profiling gives insights into the lithiation mechanism of the material, enabling us to study the detailed biphasic process in the first lithiation process. Lithiation induces swelling and roughening of the active layer. In both a-Si:H and a-Si0.95(CH3)0.05:H, no measurable Li diffusion was observed after stopping current-induced lithiation. After applying the same lithiation charges, distinct Li profiles were observed for these two materials. Unlike a-Si:H, the Li concentration drops slowly from the heavily lithiated region to the non-lithiated region in a-Si0.95(CH3)0.05:H. This apparent progressive transition between the lithiated and lithium-free regions is attributed to the presence of nanovoids inside the material. When their concentration is high enough, these nanovoids constitute favorable quasi-percolating paths for lithium during the first lithiation. A specific model was developed to simulate the Li depth profiles, fully supporting this hypothesis.

SERS characterization of aggregated and isolated bacteria deposited on silver-based substrates.

Surface-enhanced Raman scattering (SERS), based on the enhancement of the Raman signal of molecules positioned within a few nanometres from a structured metal surface, is ideally suited to provide bacterial-specific molecular fingerprints which can be used for analytical purposes. However, for some complex structures such as bacteria, the generation of reproducible SERS spectra is still a challenging task. Among the various factors influencing the SERS variability (such as the nature of SERS-active substrate, Raman parameters and bacterial specificity), we demonstrate in this study that the environment of Gram-positive and Gram-negative bacteria deposited on ultra-thin silver films also impacts the origin of the SERS spectra. In the case of densely packed bacteria, the obtained SERS signatures were either characteristic of the secretion of adenosine triphosphate for Staphylococcus aureus (S. aureus) or the cell wall and the pili/flagella for Escherichia coli (E. coli), allowing for an easy discrimination between the various strains. In the case of isolated bacteria, SERS mapping together with principal component analysis revealed some variabilities of the spectra as a function of the bacteria environment and the bactericidal effect of the silver. However, the variability does not preclude the SERS signatures of various E. coli strains to be discriminated.

Insights into the Ochratoxin A/Aptamer Interactions on a Functionalized Silicon Surface by Fourier Transform Infrared and UV-Vis Studies.

The association of a mycotoxin-ochratoxin A (OTA)-with a high-affinity DNA aptamer (anti-OTA) immobilized on a functionalized surface has been investigated at the molecular level. Anti-OTA aptamers are coupled by aminolysis in several steps on an acid-terminated alkyl monolayer grafted on a silicon substrate, and Fourier transform infrared spectroscopy in attenuated total reflection geometry is used to assess the immobilization of anti-OTA (in its unfolded single-strand form) and determine its areal density (ca. 1.4/nm2). IR spectra further demonstrate that the OTA/anti-OTA association is efficient and selective and that several association/dissociation cycles may be conducted on the same surface. The areal density of OTA measured after association on the surface (IR spectroscopy) and after dissociation from the surface (UV-vis spectroscopy) falls in the range 0.16-0.3/nm2 which is close to the areal density of a closed-packed monolayer of anti-OTA aptamers folded to form their G-quadruplex structure. The interactions between OTA and its aptamer at the surface are discussed with the help of density functional theory calculations-to identify the complex IR vibrational modes of OTA in solution-and UV-vis spectroscopy-to determine the protonation state of the adsorbing species (i.e., OTA dissolved in the buffer solution).

Rapid and sensitive identification of uropathogenic Escherichia coli using a surface-enhanced-Raman-scattering-based biochip.

Rapid, selective and sensitive sensing of bacteria remains challenging. We report on a highly sensitive and reproducible surface-enhanced Raman spectroscopy (SERS)-based sensing approach for the detection of uropathogenic Escherichia coli (E. coli) bacteria in urine. The assay is based on the specific capture of the bacteria followed by interaction with cetyltrimethylammonium bromide (CTAB)-stabilised gold nanorods (Au NRS) as SERS markers. High sensitivity up to 10 CFU mL-1 is achieved by optimizing the capture interface based on hydrogenated amorphous silicon a-Si:H thin films. The integration of CH3O-PEG750 onto a-Si:H gives the sensing interface an efficient anti-fouling character, while covalent linkage of antibodies directed against the major type-1 fimbrial pilin FimA of the human pathogen E. coli results in the specific trapping of fimbriated E. coli onto the SERS substrate and their spectral fingerprint identification.

Bio-inspired hydrophobicity promotes CO2 reduction on a Cu surface.

The aqueous electrocatalytic reduction of CO2 into alcohol and hydrocarbon fuels presents a sustainable route towards energy-rich chemical feedstocks. Cu is the only material able to catalyse the substantial formation of multicarbon products (C2/C3), but competing proton reduction to hydrogen is an ever-present drain on selectivity. Here, a superhydrophobic surface was generated by 1-octadecanethiol treatment of hierarchically structured Cu dendrites, inspired by the structure of gas-trapping cuticles on subaquatic spiders. The hydrophobic electrode attained a 56% Faradaic efficiency for ethylene and 17% for ethanol production at neutral pH, compared to 9% and 4% on a hydrophilic, wettable equivalent. These observations are assigned to trapped gases at the hydrophobic Cu surface, which increase the concentration of CO2 at the electrode-solution interface and consequently increase CO2 reduction selectivity. Hydrophobicity is thus proposed as a governing factor in CO2 reduction selectivity and can help explain trends seen on previously reported electrocatalysts.

Structure of Mixed Acid/Decyl Monolayers Grafted on Oxide-Free Si(111) Surfaces.

The structure of mixed acid/decyl monolayers (MLs) grafted on oxide-free Si(111) surfaces by photochemical hydrosilylation in a mixture of neat undecylenic acid and 1-decene is studied in detail. After appropriate surface cleaning of the as-grafted surfaces, atomic force microscopy (AFM) (topography and phase imaging) and calibrated FTIR analysis demonstrate that a mixed monolayer is formed, free of residue. When the acid-molecule fraction (ΓSOL) is >0.1, mixed MLs are homogeneous on the scale of observations and they are only slightly enriched in acid chains with respect to the solution. Conversely, when ΓSOL < 0.1, the acid chain fraction within the ML becomes quasi-independent of the solution composition and may become much larger than ΓSOL. In addition, dark domains are observed in AFM phase images. Correlations between the characteristic parameters of νCO IR bands and AFM phase images suggest a strong phase separation of acid and alkyl chains at various length scales. A model involving a structuration of the grafting solution is proposed to explain observations.

Etching and Chemical Control of the Silicon Nitride Surface.

Silicon nitride is used for many technological applications, but a quantitative knowledge of its surface chemistry is still lacking. Native oxynitride at the surface is generally removed using fluorinated etchants, but the chemical composition of surfaces still needs to be determined. In this work, the thinning (etching efficiency) of the layers after treatments in HF and NH4F solutions has been followed by using spectroscopic ellipsometry. A quantitative estimation of the chemical bonds found on the surface is obtained by a combination of infrared absorption spectroscopy in ATR mode, X-ray photoelectron spectroscopy, and colorimetry. Si-F bonds are the majority species present at the surface after silicon nitride etching; some Si-OH and a few Si-NHx bonds are also present. No Si-H bonds are present, an unfavorable feature for surface functionalization in view of the interest of such mildly reactive groups for achieving stable covalent grafting. Mechanisms are described to support the experimental results, and two methods are proposed for generating surface SiH species: enriching the material in silicon, or submitting the etched surface to a H2 plasma treatment.

A quantitative method to discriminate between non-specific and specific lectin-glycan interactions on silicon-modified surfaces.

Essential to the success of any surface-based carbohydrate biochip technology is that interactions of the particular interface with the target protein be reliable and reproducible and not susceptible to unwanted nonspecific adsorption events. This condition is particularly important when the technology is intended for the evaluation of low-affinity interactions such as those typically encountered between lectins and their monomeric glycan ligands. In this paper, we describe the fabrication of glycan (mannoside and lactoside) monolayers immobilized on hydrogenated crystalline silicon (111) surfaces. An efficient conjugation protocol featuring a key "click"-based coupling step has been developed which ensures the obtention of interfaces with controlled glycan density. The adsorption behavior of these newly developed interfaces with the lectins, Lens culinaris and Peanut agglutinin, has been probed using quantitative IR-ATR and the data interpreted using various isothermal models. The analysis reveals that protein physisorption to the interface is more prevalent than specific chemisorption for the majority of washing protocols investigated. Physisorption can be greatly suppressed through application of a strong surfactinated rinse. The coexistence of chemisorption and physisorption processes is further demonstrated by quantification of the amounts of adsorbed proteins distributed on the surface, in correlation with the results obtained by atomic force microscopy (AFM). Taken together, the data demonstrates that the nonspecific adsorption of proteins to these glycan-terminated surfaces can be effectively eliminated through the proper control of the chemical structure of the surface monolayer combined with the implementation of an appropriate surface-rinse protocol.

Carbohydrate microarray for the detection of glycan-protein interactions using metal-enhanced fluorescence.

Carbohydrate arrays are potentially one of the most attractive tools to study carbohydrate-based interactions. This paper describes a new analytical platform that exploits metal-enhanced fluorescence for the sensitive and selective screening of carbohydrate-lectin interactions. The chip consists of a glass slide covered with gold nanostructures, postcoated with a thin layer of amorphous silicon-carbon alloy (a-Si0.8C0.2:H). An immobilization strategy based on the formation of a covalent bond between propargyl-terminated glycans and surface-linked azide groups was used to attach various glycans at varying surface densities onto the interface and to fabricate a carbohydrate array via efficient local "click" chemistry strategy. The specific association of the new interface with fluorescently labeled lectins was assessed by fluorescence imaging and an excellent selectivity to specific proteins was achieved. Optimization of the surface architecture and the plasmonic transducer resulted in an enhancement of the fluorescence intensity by 1 order of magnitude, when compared to the corresponding substrate devoid of gold nanostructures. The limit of detection (LOD) of such microarrays is in the picomolar range, making it a promising system for development in pharmaceutical or biomedical applications.

Macropore formation in p-type silicon: toward the modeling of morphology.

The formation of macropores in silicon during electrochemical etching processes has attracted much interest. Experimental evidences indicate that charge transport in silicon and in the electrolyte should realistically be taken into account in order to be able to describe the macropore morphology. However, up to now, none of the existing models has the requested degree of sophistication to reach such a goal. Therefore, we have undertaken the development of a mathematical model (phase-field model) to describe the motion and shape of the silicon/electrolyte interface during anodic dissolution. It is formulated in terms of the fundamental expression for the electrochemical potential and contains terms which describe the process of silicon dissolution during electrochemical attack in a hydrofluoric acid (HF) solution. It should allow us to explore the influence of the physical parameters on the etching process and to obtain the spatial profiles across the interface of various quantities of interest, such as the hole concentration, the current density, or the electrostatic potential. As a first step, we find that this model correctly describes the space charge region formed at the silicon side of the interface.

Quantitative assessment of the multivalent protein-carbohydrate interactions on silicon.

A key challenge in the development of glycan arrays is that the sensing interface be fabricated reliably so as to ensure the sensitive and accurate analysis of the protein-carbohydrate interaction of interest, reproducibly. These goals are complicated in the case of glycan arrays as surface sugar density can influence dramatically the strength and mode of interaction of the sugar ligand at any interface with lectin partners. In this Article, we describe the preparation of carboxydecyl-terminated crystalline silicon (111) surfaces onto which are grafted either mannosyl moieties or a mixture of mannose and spacer alcohol molecules to provide "diluted" surfaces. The fabrication of the silicon surfaces was achieved efficiently through a strategy implicating a "click" coupling step. The interactions of these newly fabricated glycan interfaces with the lectin, Lens culinaris, have been characterized using quantitative infrared (IR) spectroscopy in the attenuated total geometry (ATR). The density of mannose probes and lectin targets was precisely determined for the first time by the aid of special IR calibration experiments, thus allowing for the interpretation of the distribution of mannose and its multivalent binding with lectins. These experimental findings were accounted for by numerical simulations of lectin adsorption.

Effect of lithiation potential and cycling on chemical and morphological evolution of Si thin film electrode studied by ToF-SIMS.

Si thin films obtained by plasma enhanced chemical vapor deposition (PECVD) were used to investigate chemical and morphological modifications induced by lithiation potential and cycling. These modifications were thoughtfully analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling, which allows to distinguish the surface and bulk processes related to the formation of the solid electrolyte interphase (SEI) layer, and Li-Si alloying, respectively. The main results are a volume expansion/shrinkage and a dynamic behavior of the SEI layer during the single lithiation/delithiation process and multicycling. Trapping of lithium and other ions corresponding to products of electrolyte decomposition are the major reasons of electrode modifications. It is shown that the SEI layer contributes to 60% of the total volume variation of Si electrodes (100 nm). The apparent diffusion coefficient of lithium (DLi) calculated from the Fick's second law directly from Li-ion ToF-SIMS profiles is of the order of ∼5.9 × 10(-15) cm(2).s(-1). This quite low value can be explained by Li trapping in the bulk of electrode material, at the interfaces, continuous growth of the SEI layer and increase of SiO2 quantity. These modifications can result in limitation the ionic transport of Li.

Influence of the molecular design on the antifouling performance of poly(ethylene glycol) monolayers grafted on (111) Si.

Various poly(ethylene glycol) monomethyl ether moieties were grafted onto hydrogenated silicon surfaces in order to investigate the influence of the molecular design on the antifouling performance of such coatings. The grafted chains were either oligo(ethylene oxide) chains (EG)(n)OMe bound to silicon via Si-O-C covalent bonds, or hybrid alkyl/oligo(ethylene oxide) chains C(p)(EG)(n)OMe bound via Si-C covalent bonds (from home-synthesized precursors). Quantitative IR spectroscopy gave the molecular coverage of the grafted layers, and AFM imaging demonstrated that a proper surfactinated rinse yields C(p)(EG)(n)OMe layers free of unwanted residues. The protein-repellent character of these grafted layers (here, toward BSA) was studied by IR and AFM imaging. C(p)(EG)(n)OMe layers exhibit a lower surface concentration than (EG)(n)OMe layers, because of the presence of a solvent in the grafting solution; they however demonstrate high resistance against BSA adsorption for high values of the n/p ratio and a higher stability than (EG)(n)OMe. This behavior is consistently explained by the poor ordering capability of the alkyl part of the layer, contrary to what is observed for similar layers on Au, and the key role of an entangled arrangement of the ethylene oxide chains which forms when these chains are long enough.

Peptide immobilisation on porous silicon surface for metal ions detection.

In this work, a Glycyl-Histidyl-Glycyl-Histidine (GlyHisGlyHis) peptide is covalently anchored to the porous silicon PSi surface using a multi-step reaction scheme compatible with the mild conditions required for preserving the probe activity. In a first step, alkene precursors are grafted onto the hydrogenated PSi surface using the hydrosilylation route, allowing for the formation of a carboxyl-terminated monolayer which is activated by reaction with N-hydroxysuccinimide in the presence of a peptide-coupling carbodiimide N-ethyl-N'-(3-dimethylaminopropyl)-carbodiimide and subsequently reacted with the amino linker of the peptide to form a covalent amide bond. Infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy are used to investigate the different steps of functionalization.The property of peptides to form stable complexes with metal ions is exploited to achieve metal-ion recognition by the peptide-modified PSi-based biosensor. An electrochemical study of the GlyHisGlyHis-modified PSi electrode is achieved in the presence of copper ions. The recorded cyclic voltammograms show a quasi-irreversible process corresponding to the Cu(II)/Cu(I) couple. The kinetic factors (the heterogeneous rate constant and the transfer coefficient) and the stability constant of the complex formed on the porous silicon surface are determined. These results demonstrate the potential role of peptides grafted on porous silicon in developing strategies for simple and fast detection of metal ions in solution.

Development of a metal-chelated plasmonic interface for the linking of His-peptides with a droplet-based surface plasmon resonance read-off scheme.

Monolayers of metal complexes were covalently attached to the surface of lamellar SPR interfaces (Ti/Ag/a-Si(0.63)C(0.37)) for binding histidine-tagged peptides with a controlled molecular orientation. The method is based on the activation of surface acid groups with N-hydroxysuccinimide (NHS), followed by an amidation reaction with (S)-N-(5-amino-1-carboxypentyl)iminodiacetic acid (NTA). FTIR and X-ray photoelectron spectroscopy (XPS) were used to characterize each surface modification step. The NTA modified SPR interface effectively chelated Cu(2+) ions. Once loaded with metal ions, the modified SPR interface was able to bind specifically to histidine-tagged peptides. The binding process was followed by surface plasmon resonance (SPR) in a droplet based configuration. The Cu(2+)-NTA modified interface showed protein loading comparable to commercially available NTA chips based on dextran chemistry and can thus be regarded as an interesting alternative. The sensor interface can be reused several times due to the easy regeneration step using ethylenediaminetetraacetic acid (EDTA) treatment.

Plasmonic properties of silver nanostructures coated with an amorphous silicon-carbon alloy and their applications for sensitive sensing of DNA hybridization.

The use of an amorphous silicon-carbon alloy overcoating on silver nanostructures in a localized surface plasmon resonance (LSPR) sensing platform allows for decreasing the detection limit by an order of magnitude as compared to sensors based on gold nanostructures deposited on glass. In addition, silver based multilayer structures show a distinct plasmonic behaviour as compared to gold based nanostructures, which provides the sensor with an increased short-range sensitivity and a decreased long-range sensitivity.

Electrochemically Formed Porous Silica.

Controlled electrochemical formation of porous silica can be realized in dilute aqueous, neutral-pH, fluoride medium. Formation of a porous film is initiated by sweeping the potential applied to silicon to values higher than 20 V. Film formation, reaching a steady state, may be pursued in a wide range of potentials, including lower potentials. The origin of a threshold potential for porous film initiation has been explained quantitatively. All of the films appear mesoporous. Films grown at high potentials exhibit a variety of macrostructures superimposed on the mesoporosity. These macrostructures result from selective dissolution of silica induced by local pH lowering due to oxygen evolution. Films grown at potentials lower than 15 V appear uniform on the micrometer scale. However, all of the films also exhibit a stratified structure on the scale of a few tens of nanometres. This periodic structure can be traced back to the oscillatory behavior observed during the electrochemical dissolution of silicon in fluoride medium. It suggests that periodic breaking of the growing film may be responsible for this morphology.