Formation, characterization, and chemistry of undecanoic acid-terminated silicon surfaces: patterning and immobilization of DNA

Enhancing the performance of porous silicon biosensors: the interplay of nanostructure design and microfluidic integration

This work presents the development and design of aptasensor employing porous silicon (PSi) Fabry‒Pérot thin films that are suitable for use as optical transducers for the detection of lactoferrin (LF), which is a protein biomarker secreted at elevated levels during gastrointestinal (GI) inflammatory disorders such as inflammatory bowel disease and chronic pancreatitis. To overcome the primary limitation associated with PSi biosensors-namely, their relatively poor sensitivity due to issues related to complex mass transfer phenomena and reaction kinetics-we employed two strategic approaches: First, we sought to optimize the porous nanostructure with respect to factors including layer thickness, pore diameter, and capture probe density. Second, we leveraged convection properties by integrating the resulting biosensor into a 3D-printed microfluidic system that also had one of two different micromixer architectures (i.e., staggered herringbone micromixers or microimpellers) embedded. We demonstrated that tailoring the PSi aptasensor significantly improved its performance, achieving a limit of detection (LOD) of 50 nM-which is >1 order of magnitude lower than that achieved using previously-developed biosensors of this type. Moreover, integration into microfluidic systems that incorporated passive and active micromixers further enhanced the aptasensor's sensitivity, achieving an additional reduction in the LOD by yet another order of magnitude. These advancements demonstrate the potential of combining PSi-based optical transducers with microfluidic technology to create sensitive label-free biosensing platforms for the detection of GI inflammatory biomarkers.

Recent Applications of Molecular Structures at Silicon Anode Interfaces

Silicon (Si) is a promising anode material to realize many-fold higher anode capacity in next-generation lithium-ion batteries (LIBs). Si electrochemistry has strong dependence on the property of the Si interface, and therefore, Si surface engineering has attracted considerable research interest to address the challenges of Si electrodes such as dramatic volume changes and the high reactivity of Si surface. Molecular nanostructures, including metal–organic frameworks (MOFs), covalent–organic frameworks (COFs) and monolayers, have been employed in recent years to decorate or functionalize Si anode surfaces to improve their electrochemical performance. These materials have the advantages of facile preparation, nanoscale controllability and structural diversity, and thus could be utilized as versatile platforms for Si surface modification. This review aims to summarize the recent applications of MOFs, COFs and monolayers for Si anode development. The functionalities and common design strategies of these molecular structures are demonstrated.

X-ray photoemission studies of the interaction of metals and metal ions with DNA

X-ray Photoelectron Spectroscopy (XPS) has been used to study the interactions of heavy metal ions with DNA with some success. Surface sensitivity and selectivity of XPS are advantageous for identifying and characterizing the chemical and elemental structure of the DNA to metal interaction. This review summarizes the status of what amounts to a large part of the photoemission investigations of biomolecule interactions with metals and offers insight into the mechanism for heavy metal-bio interface interactions. Specifically, it is seen that metal interaction with DNA results in conformational changes in the DNA structure.

Porous Silicon-Based Aptasensors: Toward Cancer Protein Biomarker Detection

The anterior gradient homologue-2 (AGR2) protein is an attractive biomarker for various types of cancer. In pancreatic cancer, it is secreted to the pancreatic juice by premalignant lesions, which would be an ideal stage for diagnosis. Thus, designing assays for the sensitive detection of AGR2 would be highly valuable for the potential early diagnosis of pancreatic and other types of cancer. Herein, we present a biosensor for label-free AGR2 detection and investigate approaches for enhancing the aptasensor sensitivity by accelerating the target mass transfer rate and reducing the system noise. The biosensor is based on a nanostructured porous silicon thin film that is decorated with anti-AGR2 aptamers, where real-time monitoring of the reflectance changes enables the detection and quantification of AGR2, as well as the study of the diffusion and target-aptamer binding kinetics. The aptasensor is highly selective for AGR2 and can detect the protein in simulated pancreatic juice, where its concentration is outnumbered by orders of magnitude by numerous proteins. The aptasensor's analytical performance is characterized with a linear detection range of 0.05-2 mg mL^-1, an apparent dissociation constant of 21 ± 1 μM, and a limit of detection of 9.2 μg mL^-1 (0.2 μM), which is attributed to mass transfer limitations. To improve the latter, we applied different strategies to increase the diffusion flux to and within the nanostructure, such as the application of isotachophoresis for the preconcentration of AGR2 on the aptasensor, mixing, or integration with microchannels. By combining these approaches with a new signal processing technique that employs Morlet wavelet filtering and phase analysis, we achieve a limit of detection of 15 nM without compromising the biosensor's selectivity and specificity.

Destruction mechanisms of ozone over SARS-CoV-2

In this pandemic SARS-CoV-2 crisis, any attempt to contain and eliminate the virus will also stop its spread and consequently decrease the risk of severe illness and death. While ozone treatment has been suggested as an effective disinfection process, no precise mechanism of action has been previously reported. This study aimed to further investigate the effect of ozone treatment on SARS-CoV-2. Therefore, virus collected from nasopharyngeal and oropharyngeal swab and sputum samples from symptomatic patients was exposed to ozone for different exposure times. The virus morphology and structure were monitored and analyzed through Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), Atomic Absorption Spectroscopy (AAS), and ATR-FTIR. The obtained results showed that ozone treatment not only unsettles the virus morphology but also alters the virus proteins' structure and conformation through amino acid disturbance and Zn ion release from the virus non-structural proteins. These results could provide a clearer pathway for virus elimination and therapeutics preparation.

Chemical transformation of molecular ices containing N2O and C2D2 by low energy electrons: New chemical species of astronomical interest

We have employed electron stimulated desorption (ESD) and x-ray photoelectron spectroscopy (XPS) to study the chemical species generated from multilayer films of N₂O, C₂D₂, and mixtures thereof (i.e., N₂O/C₂D₂) by the impact of low energy electrons with energies between 30 and 70 eV. Our ESD results for pure films of N₂O show the production of numerous fragment cations and anions, and of larger molecular ions, of sufficient kinetic energy to escape into vacuum, which are likely formed by ion-molecule scattering in the film. Ion-molecule scattering is also responsible for the production of cations from C₂D₂ films that contain as many as six or seven carbon atoms. Many of the same anions and cations desorb from N₂O/C₂D₂ mixtures, as well as new species, which is the result of ion-molecule scattering in the film. Anion desorption signals further indicate the formation of C-N containing species within the irradiated films. XPS spectra of N1s, C1s, and O1s lines reveal the fragmentation of N-O bonds and gradual formation of molecules containing species containing O-C=O, C=O, and C-O functional groups. A comparison between ESD and XPS findings suggests that species observed in the ESD channel are primarily products of reactions taking place at the film-vacuum interface, while those observed in the XPS derive from reactions occurring within the solid.

Directed Assembly of Hybrid Nanomaterials and Nanocomposites

Hybrid nanomaterials are molecular or colloidal-level combinations of organic and inorganic materials, or otherwise strongly dissimilar materials. They are often, though not exclusively, anisotropic in shape. A canonical example is an inorganic nanorod or nanosheet sheathed in, or decorated by, a polymeric or other organic material, where both the inorganic and organic components are important for the properties of the system. Hybrid nanomaterials and nanocomposites have generated strong interest for a broad range of applications due to their functional properties. Generating macroscopic assemblies of hybrid nanomaterials and nanomaterials in nanocomposites with controlled orientation and placement by directed assembly is important for realizing such applications. Here, a survey of critical issues and themes in directed assembly of hybrid nanomaterials and nanocomposites is provided, highlighting recent efforts in this field with particular emphasis on scalable methods.

Vacuum Ultraviolet Treatment of Acid- and Ester-Terminated Self-Assembled Monolayers: Chemical Conversions and Friction Reduction

We have prepared COOH- and COOCH₃-terminated self-assembled monolayers (SAMs) from undec-10-enoic acid (UDA) and methyl undec-10-enoate (MUDO) molecules on hydrogen-terminated silicon (H-Si) substrates through ultraviolet (UV) irradiation. The as-prepared UDA- and MUDO-SAMs were exposed to 172 nm vacuum-UV (VUV) light in a high vacuum environment (HV, <10^-3 Pa) for different periods. The presence of COO components at the surfaces of these SAMs without prior oxidation would simplify the understanding of the origin of the chemical conversions and the changes of surface properties, as the prior oxidation would change the surface properties and generate different oxygenated groups. After the HV-VUV treatment, the abundance of COOH and COOCH₃ components of these SAMs decreased without significant dissociation of their C-C backbones. Degradation of these components occurred through dissociating their C-O bonds, resulting in different C═O components. Also, the occurrence of Norrish type pathways resulted in a slight decrease of carbon content and produced CH₃ components. We have applied the HV-VUV lithography to control the abundance of COOH and COOCH₃ components in well-defined areas and to investigate the friction differences between the irradiated and masked areas. The irradiated areas exhibited lower friction than the masked areas without observing significant height contrasts between these areas. The reduction in friction was attributed to the conversion of the COOH and COOCH₃ components to less adhesive components such as C═O and CH₃. These experiments suggest the HV-VUV treatments as an approach for low damage dry surface modifications and reductive lithographic techniques at surfaces terminated by acid and ester groups.

Whole-cell detection of live lactobacillus acidophilus on aptamer-decorated porous silicon biosensors

This work describes the design of optical aptamer-based porous silicon (PSi) biosensors for the direct capture of Lactobacillus acidophilus. Aptamers are oligonucleotides (single-stranded DNA or RNA) that can bind their targets with high affinity and specificity, making them excellent recognition elements for biosensing applications. Herein, aptamer Hemag1P, which specifically targets the important probiotic L. acidophilus, was utilized for direct bacteria capture onto oxidized PSi Fabry-Pérot thin films. Monitoring changes in the reflectivity spectrum (using reflective interferometric Fourier transform spectroscopy) allows for bacteria detection in a label-free, simple and rapid manner. The performance of the biosensor was optimized by tuning the PSi nanostructure, its optical properties, as well as the immobilization density of the aptamer. We demonstrate the high selectivity and specificity of this simple "direct-capture" biosensing scheme and show its ability to distinguish between live and dead bacteria. The resulting biosensor presents a robust and rapid method for the specific detection of live L. acidophilus at concentrations relevant for probiotic products and as low as 10(6) cells per mL. Rapid monitoring of probiotic bacteria is crucial for quality, purity and safety control as the use of probiotics in functional foods and pharmaceuticals is becoming increasingly popular.

Fabricating Water Dispersible Superparamagnetic Iron Oxide Nanoparticles for Biomedical Applications through Ligand Exchange and Direct Conjugation

Stable superparamagnetic iron oxide nanoparticles (SPIONs), which can be easily dispersed in an aqueous medium and exhibit high magnetic relaxivities, are ideal candidates for biomedical applications including contrast agents for magnetic resonance imaging. We describe a versatile methodology to render water dispersibility to SPIONs using tetraethylene glycol (TEG)-based phosphonate ligands, which are easily introduced onto SPIONs by either a ligand exchange process of surface-anchored oleic-acid (OA) molecules or via direct conjugation. Both protocols confer good colloidal stability to SPIONs at different NaCl concentrations. A detailed characterization of functionalized SPIONs suggests that the ligand exchange method leads to nanoparticles with better magnetic properties but higher toxicity and cell death, than the direct conjugation methodology.

Dielectric relaxation properties of carboxylic acid-terminated n-alkyl monolayers tethered to Si(1 1 1): dynamics of dipoles and gauche defects

Molecular-level insights into the organization and dynamics of n-alkyl monolayers covalently bonded to Si(1 1 1) were gained from admittance measurements of dipolar relaxation in rectifying Hg|| HOOC-C10H(25-n) Si junctions performed as a function of applied voltage and temperature. A collective behavior of dipole dynamics is inferred from the non-Debye asymmetric relaxation peak shape and strong coupling of the dipole relaxation path with some bending vibrations of the n-alkyl OML (multi-excitation entropy model). A variety of relaxation mechanisms is observed in the frequency range (0.1 Hz-10 MHz) with different dependence of relaxation frequency and dipolar strength on measurement temperature and applied voltage. Their microscopic origin is discussed by comparing the activation energy of relaxation frequency with previous molecular mechanics calculations of saddle point energy barriers for structural defects such as gauche conformations or chain kinks in n-alkanes assemblies. Gauche conformations organized in pairs (kinks) have vanishing relaxation strength below an order-disorder transition temperature T(D) =  175 K and their probability strongly increases with applied reverse voltage, above T(D). The presence of hydrogen bonds between terminal carboxylic acid functionalities is inferred from a comparison with a similar junction bearing a low density of carboxylic acid end groups. This temperature-dependent hydrogen-bond network provides some additional stiffness against external electrostatic stress, as deduced from the rather weak sensitivity of relaxation frequencies to applied bias voltage.

Active Acetylcholinesterase Immobilization on a Functionalized Silicon Surface

In this work, we studied the attachment of active acetylcholinesterase (AChE) enzyme on a silicon substrate as a potential biomarker for the detection of organophosphorous (OP) pesticides. A multistep functionalization strategy was developed on a crystalline silicon surface: a carboxylic acid-terminated monolayer was grafted onto a hydrogen-terminated silicon surface by photochemical hydrosilylation, and then AChE was covalently attached through amide bonds using an activation EDC/NHS process. Each step of the modification was quantitatively characterized by ex-situ Fourier transform infrared spectroscopy in attenuated-total-reflection geometry (ATR-FTIR) and atomic force microscopy (AFM). The kinetics of enzyme immobilization was investigated using in situ real-time infrared spectroscopy. The enzymatic activity of immobilized acetylcholinesterase enzymes was determined with a colorimetric test. The surface concentration of active AChE was estimated to be Γ = 1.72 × 10(10) cm(-2).

Tailoring of interfacial mechanical shear strength by surface chemical modification of silicon microwires embedded in Nafion membranes

The interfacial shear strength between Si microwires and a Nafion membrane has been tailored through surface functionalization of the Si. Acidic (-COOH-terminated) or basic (-NH2-terminated) surface-bound functionality was introduced by hydrosilylation reactions to probe the interactions between the functionalized Si microwires and hydrophilic ionically charged sites in the Nafion polymeric side chains. Surfaces functionalized with SiOx, Si-H, or Si-CH3 were also synthesized and investigated. The interfacial shear strength between the functionalized Si microwire surfaces and the Nafion matrix was quantified by uniaxial wire pull-out experiments in an in situ nanomechanical instrument that allowed simultaneous collection of mechanical data and visualization of the deformation process. In this process, an axial load was applied to the custom-shaped top portions of individual wires until debonding occurred from the Nafion matrix. The shear strength obtained from the nanomechanical measurements correlated with the chemical bond strength and the functionalization density of the molecular layer, with values ranging from 7 MPa for Si-CH3 surfaces to ∼16-20 MPa for oxygen-containing surface functionalities. Hence surface chemical control can be used to influence the mechanical adhesion forces at a Si-Nafion interface.

Controlling the reproducibility of Coulomb blockade phenomena for gold nanoparticles on an organic monolayer/silicon system

Two types of highly ordered organic layers were prepared on silicon modified with an amine termination for binding gold nanoparticles (AuNPs). These two grafted organic monolayers (GOMs), consisting of alkyl chains with seven or 11 carbon atoms, were grafted on oxide-free Si(111) surfaces as tunnel barriers between the silicon electrode and the AuNPs. Three kinds of colloidal AuNPs were prepared by reducing HAuCl4 with three different reactants: citrate (Turkevich synthesis, diameter ∼16 nm), ascorbic acid (diameter ∼9 nm), or NaBH4 (Natan synthesis, diameter ∼7 nm). Scanning tunnel spectroscopy (STS) was performed in a UHV STM at 40 K, and Coulomb blockade behaviour was observed. The reproducibility of the Coulomb behavior was analysed as a function of several chemical and physical parameters: size, crystallinity of the AuNPs, influence of surrounding surfactant molecules, and quality of the GOM/Si interface (degree of oxidation after the full processing). Samples were characterized with scanning tunneling microscope, STS, atomic force microscope, Fourier transform infrared spectroscopy, x-ray photoelectron spectroscopy (XPS), and high resolution transmission electronic microscope. We show that the reproducibility in observing Coulomb behavior can be as high as ∼80% with the Natan synthesis of AuNPs and GOMs with short alkyl chains.

Star-shaped poly(2-methyl-2-oxazoline)-based films: rapid preparation and effects of polymer architecture on antifouling properties

Star-shaped poly(2-methyl-2-oxazoline)-based films prepared through polydopamine-assistance provided enhanced antifouling properties than the linear ones, and showed superior stability than PEG films.

Mild two-step method to construct DNA-conjugated silicon nanoparticles: scaffolds for the detection of microRNA-21

We describe a novel two-step method, starting from bulk silicon wafers, to construct DNA conjugated silicon nanoparticles (SiNPs). This method first utilizes reactive high-energy ball milling (RHEBM) to obtain alkene grafted SiNPs. The alkene moieties are subsequently reacted with commercially available thiol-functionalized DNA via thiol-ene click chemistry to produce SiNP DNA conjugates wherein the DNA is attached through a covalent thioether bond. Further, to show the utility of this synthetic strategy, we illustrate how these SiNP ODN conjugates can detect cancer-associated miR-21 via a fluorescence ON strategy. Given that an array of biological molecules can be prepared with thiol termini and that SiNPs are biocompatible and biodegradable, we envision that this synthetic protocol will find utility in salient SiNP systems for potential therapeutic and diagnostic applications.

Biointerfaces on indium-tin oxide prepared from organophosphonic acid self-assembled monolayers

Herein we show the development of biointerfaces on indium-tin oxide (ITO) surfaces prepared from organophosphonate self-assembled monolayers. The interfaces were prepared in a stepwise fabrication procedure containing a base monolayer modified with oligo(ethylene oxide) species to which biological recognition ligands were attached. The density of ligands was controlled by varying the ratio of two oligo(ethylene oxide) species such that only one is compatible with further coupling. The final biointerface on ITO was assessed using cell adhesion studies, which showed that the biointerfaces prepared on ITO performed similarly to equivalent monolayers on gold or silicon.

Gold nanoparticles on oxide-free silicon-molecule interface for single electron transport

Two different organic monolayers were prepared on silicon Si(111) and modified for attaching gold nanoparticles. The molecules are covalently bound to silicon and form very ordered monolayers sometimes improperly called self-assembled monolayers (SAM). They are designed to be electrically insulating and to have very few electrical interface states. By positioning the tip of an STM above a nanoparticle, a double barrier tunnel junction (DBTJ) is created, and Coulomb blockade is demonstrated at 40 K. This is the first time Coulomb blockade is observed with an organic monolayer on oxide-free silicon. This work focuses on the fabrication and initial electrical characterization of this double barrier tunnel junction. The organic layers were prepared by thermal hydrosilylation of two different alkene molecules with either a long carbon chain (C11) or a shorter one (C7), and both were modified to be amine-terminated. FTIR and XPS measurements confirm that the Si(111) substrate remains unoxidized during the whole chemical process. Colloidal gold nanoparticles were prepared using two methods: either with citrate molecules (Turkevich method) or with ascorbic acid as the surfactant. In both cases AFM and STM images show a well-controlled deposition on the grafted organic monolayer. I-V curves obtained by scanning tunneling spectroscopy (STS) are presented on 8 nm diameter nanoparticles and exhibit the well-known Coulomb staircases at low temperature. The curves are discussed as a function of the organic layer thickness and silicon substrate doping.

Direct characterization of native chemical ligation of peptides on silicon nanowires

We describe the site-specific and chemoselective immobilization of peptides on hydrogen-terminated silicon nanowires (SiNWs) using native chemical ligation (NCL) (i.e., the reaction of a thioester group with a cysteine moiety to give a stable amide bond). The SiNWs investigated in this work were grown via a vapor-liquid-solid mechanism and functionalized with a thioester moiety. The immobilization of the peptides on the SiNWs was demonstrated by synthesizing peptides with an N-terminal cysteine residue and labeled with tetramethylrhodamine or trifluoromethyl groups that were detected by fluorescence and X-ray photoelectron spectroscopy, respectively. The peptides labeled with tetramethylrhodamine or trifluoromethyl groups for fluorescence or X-ray photoelectron spectroscopy (XPS) detection studies were synthesized with an N-terminal cysteine residue. N-Terminal seryl peptides and carboxy-terminated SiNWs were used as controls to demonstrate the chemoselectivity of the peptide immobilization.

Mesoporous systems for poorly soluble drugs

Utilization of inorganic mesoporous materials in formulations of poorly water-soluble drugs to enhance their dissolution and permeation behavior is a rapidly growing area in pharmaceutical materials research. The benefits of mesoporous materials in drug delivery applications stem from their large surface area and pore volume. These properties enable the materials to accommodate large amounts of payload molecules, protect them from premature degradation, and promote controlled and fast release. As carriers with various morphologies and chemical surface properties can be produced, these materials may even promote adsorption from the gastrointestinal tract to the systemic circulation. The main concern regarding their clinical applications is still the safety aspect even though most of them have been reported to be safely excreted, and a rather extensive toxicity screening has already been conducted with the most frequently studied mesoporous materials. In addition, the production of the materials on a large scale and at a reasonable cost may be a challenge when considering the utilization of the materials in industrial processes. However, if mesoporous materials could be employed in the industrial crystallization processes to produce hybrid materials with poorly soluble compounds, and hence to enhance their oral bioavailability, this might open new avenues for the pharmaceutical industry to employ nanotechnology in their processes.

Towards modelling the vibrational signatures of functionalized surfaces: carboxylic acids on H-Si(111) surfaces

In this work, we investigate the adsorption process of two carboxylic acids (stearic and undecylenic) on a H-Si(111) surface via the calculation of structural and energy changes as well as the simulation of their IR and Raman spectra. The two molecules adsorb differently at the surface since the stearic acid simply physisorbs while the undecylenic acid undergoes a chemical reaction with the hydrogen atoms of the surface. This difference is observed in the change of geometry during the adsorption. Indeed, the chemisorption of the undecylenic acid has a bigger impact on the structure than the physisorption of the stearic acid. Consistently, the former is also characterized by a larger value of adsorption energy and a smaller value of the tilting angle with respect to the normal plane. For both the IR and Raman signatures, the spectra of both molecules adsorbed at the surface are in a first approximation the superposition of the spectra of the Si cluster and of the carboxylic acid considered individually. The main deviation from this simple observation is the peak of the stretching Si-H (ν(Si-H)) mode, which is split into two peaks upon adsorption. As expected, the splitting is bigger for the chemisorption than the physisorption. The modes corresponding to atomic displacements close to the adsorption site display a frequency upshift by a dozen wavenumbers. One can also see the disappearance of the peaks associated with the C=C double bond when the undecylenic acid chemisorbs at the surface. The Raman and IR spectra are complementary and one can observe here that the most active Raman modes are generally IR inactive. Two exceptions to this are the two ν(Si-H) modes which are active in both spectroscopies. Finally, we compare our simulated spectra with some experimental measurements and we find an overall good agreement.

Cysteamine-based functionalization of InAs surfaces: revealing the critical role of oxide interactions in biasing attachment

Attaching functional molecules such as thiols and proteins to semiconductor surfaces is increasingly exploited in functional devices such as sensors. Despite extensive research to understand this interface and demonstrate a robust protocol for attachment, the bonding chemistry of thiolates to III-V surfaces has been under great debate in the literature. This study provides a comprehensive chemical model for the attachment of thiols to InAs, an increasingly device-relevant III-V semiconductor, using cysteamine as a model molecule. We examine the attachment of cysteamine to InAs via the thiol group using X-ray photoelectron spectroscopy and spectroscopic ellipsometry and confirm that thiolate bonding to the substrate occurs preferentially to As sites over In sites as a limit. These experiments explore the interplay of the native oxide chemical properties, the cysteamine concentration, and the evolving InAs surface chemistry with functionalization. The thiol-InAs interaction can be framed as a general acid-base reaction, where the nucleophilic and/or electrophilic attack of the surface (i.e., binding to In sites and/or As sites) depends on the acidity of the thiol. The roles of the initial oxide composition, the solvent of the functionalizing solution, and the cysteamine as a limiting reagent in fully displacing the oxide and creating In-S and As-S bonds are highlighted.

Immobilization of oligonucleotides onto zirconia-modified filter paper and specific molecular recognition

A morphologically complex cellulosic substance (e.g., commercial filter paper) was employed as a substrate for DNA immobilization and successive recognition. A uniform ultrathin zirconia gel film was first deposited on each cellulose nanofiber in bulk filter paper by a facile sol-gel process. Relying on the large surface area of filter paper and the strong affinity of zirconia for the phosphate group, terminal-phosphate probe DNA was abundantly immobilized on the zirconia-modified filter paper so as to convert the composite to a biofunctional material for the sensitive and repetitive recognition of the corresponding complementary target DNA on the nanomolar level. By contrast, in spite of the viability of the immobilization of the probe DNA and the recognition of target DNA on the quartz plate, the amount of captured probe DNA or recognized target DNA on such a flat substrate was much less than that captured or recognized on filter paper, resulting in a relatively insensitive recognition event. Moreover, control experiments on bare filter paper (without a zirconia nanocoating) suggested that the zirconia gel film was essential to probe DNA immobilization and subsequent target DNA recognition.

Different EDC/NHS activation mechanisms between PAA and PMAA brushes and the following amidation reactions

Infrared spectroscopy was applied to investigate the well-known EDC/NHS (N-ethyl-N'-(3-(dimethylamino)propyl)carbodiimide/N-hydroxysuccinimide) activation details of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA) brushes grafted on porous silicon. Succinimidyl ester (NHS-ester) is generally believed to be the dominant intermediate product, conveniently used to immobilize biomolecules containing free primary amino groups via amide linkage. To our surprise, the infrared spectral details revealed that the EDC/NHS activation of PMAA generated anhydride (estimated at around 76% yield and 70% composition), but not NHS-ester (around 5% yield and 11% composition) under the well-documented reaction conditions, as the predominant intermediate product. In contrast, EDC/NHS activation of PAA still follows the general rule, i.e., the expected NHS-ester is the dominant intermediate product (around 45% yield and 57% composition), anhydride the side product (40% yield and 28% composition), under the optimum reaction conditions. The following amidation on PAA-based NHS-esters with a model amine-containing compound, L-leucine methyl ester, generated approximately 70% amides and 30% carboxylates. In contrast, amidation of PAA- or PMAA-based anhydrides with L-leucine methyl ester only produced less than 30% amides but more than 70% carboxylates. The above reaction yields and percentage compositions were estimated by fitting the carbonyl stretching region with 5 possible species, NHS-ester, anhydride, N-acylurea, unreacted acid, unhydrolyzed tert-butyl ester, and using the Beer-Lambert law. The different surface chemistry mechanisms will bring significant effects on the performance of surface chemistry-derived devices such as biochips, biosensors, and biomaterials.

Electrochemical impedance study of GaAs surface charge modulation through the deprotonation of carboxylic acid monolayers

Modifications to the space charge region of p+ and p-GaAs due to surface charge modulation by the pH-induced deprotonation of bound carboxylic acid terminal monolayers were studied by electrochemical impedance spectroscopy and correlated to flat-band potential measurements from Mott-Schottky plots. We infer that the negative surface dipole formed on GaAs due to monolayer deprotonation causes an enhancement of the downward interfacial band bending. The space charge layer modifications were correlated to intermolecular electrostatic interactions and semiconductor depletion characteristics.

Click chemistry-based functionalization on non-oxidized silicon substrates

Copper-catalyzed azide-alkyne cycloaddition (CuAAC), combined with the chemical stability of the Si-C-bound organic layer, serves as an efficient tool for the modification of silicon substrates, particularly for the immobilization of complex biomolecules. This review covers recent advances in the preparation of alkynyl- or azido-terminated "clickable" platforms on non-oxidized silicon and their further derivatization by means of the CuAAC reaction. The exploitation of these "click"-functionalized organic thin films as model surfaces to study many biological events was also addressed, as they are directly relevant to the on-going effort of creating silicon-based molecular electronics and chemical/biomolecular sensors.

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.

Green fluorescent organic nanoparticles by self-assembly induced enhanced emission of a naphthalene diimide bolaamphiphile

Naphthalene diimide (NDI) bolaamphiphilic molecules (1) self-assemble in water to form organic nanoparticles, which exhibit self-assembly induced preassociated excimer formation and hence an enhanced green fluorescence.

Catalyst-free functionalization for versatile modification of nonoxidized silicon structures

Here, we report on a simple, catalyst-free route for obtaining highly versatile subsequent functionalization on Si nanowires and Si(111) substrates. The versatility of this approach allows subsequent functionalization not only for organic species but also for inorganic (nanomaterial) species. The method has the advantage of controlling the density of reactive cross-linkers without affecting the stability of the Si samples and without having metallic (or catalyst) residues on the surface. This method also allows formation of monolayers with a variety of termination groups and is expected to open up a wide range of opportunities for producing stable molecule-based (opto)electronic and (bio)sensing devices. Immobilization of inorganic nanomaterial on the Si samples offers advanced opportunities in molecular switches, (bio)sensors, molecular scale memory, and Si-based nanoelectronic devices.

Direct photochemical functionalization of Si(111) with undecenol

Direct UV photochemical functionalization of H-terminated Si(111) with bifunctional 10-undecen-1-ol was achieved with selective attachment via its vinyl end, resulting in the formation of a compact monolayer with free terminal alcohol groups. This is due to the faster radical propagation mechanism in hydrosilylation with alkene compared to the nucleophilic attack mechanism of alcohol, which is impeded by intermolecular hydrogen bonding present at room temperature. Evidence from X-ray photoelectron spectroscopy, infrared spectroscopy, and resistance to fluoride etching shows that Si-C is the interfacial bond, and atomic force microscopy shows the presence of a smooth, uniform monolayer conforming to the atomic terraces of the Si(111) surface. The application of such a hydroxyl-terminated monolayer was demonstrated by tethering a bromoinitiator through surface esterification and thereafter subjecting the surface to the surface-initiated atom-transfer radical polymerization of butyl methacrylate. The poly(butyl methacrylate) brushes formed were found to be smooth (R(a) < 0.3 nm) and uniform even for a thin film of 4.0 nm.

Molecular monolayers on silicon as substrates for biosensors

(111) silicon surfaces can be controlled down to atomic level and offer a remarkable starting point for elaborating nanostructures. Hydrogenated surfaces are obtained by oxide dissolution in hydrofluoric acid or ammonium fluoride solution. Organic species are grafted onto the hydrogenated surface by a hydrosilylation reaction, providing a robust covalent Si-C bonding. Finally, probe molecules can be anchored to the organic end group, paving the way to the elaboration of sensors. Fluorescence detection is hampered by the high refractive index of silicon. However, improved sensitivity is obtained by replacing the bulk silicon substrate by a thin layer of amorphous silicon deposited on a reflector. The development of a novel hybrid SPR interface by the deposition of an amorphous silicon-carbon alloy is also presented. Such an interface allows the subsequent linking of stable organic monolayers through Si-C bonds for a plasmonic detection. On the other hand, the semiconducting properties of silicon can be used to implement field-effect label-free detection. However, the electrostatic interaction between adsorbed species may lead to a spreading of the adsorption isotherms, which should not be overlooked in practical operating conditions of the sensor. Atomically flat silicon surfaces may allow for measuring recognition interactions with local-probe microscopy.

Surface chemistry for stable and smart molecular and biomolecular interfaces via photochemical grafting of alkenes

Many emerging fields such as biotechnology and renewable energy require functionalized surfaces that are "smart" and highly stable. Surface modification schemes developed previously have often been limited to simple molecules or have been based on weakly bound layers that have limited stability. In this Account, we report on recent developments enabling the preparation of molecular and biomolecular interfaces that exhibit high selectivity and unprecedented stability on a range of covalent materials including diamond, vertically aligned carbon nanofibers, silicon, and metal oxides. One particularly successful pathway to ultrastable interfaces involves the photochemical grafting of organic alkenes to the surfaces. Bifunctional alkenes with a suitable functional group at the distal end can directly impart functionality and can serve as attachment points for linking complex structures such as DNA and proteins. The successful application of photochemical grafting to a surprisingly wide range of materials has motivated researchers to better understand the underlying photochemical reaction mechanisms. The resulting studies using experimental and computational methods have provided fundamental insights into the electronic structure of the molecules and the surface control photochemical reactivity. Such investigations have revealed the important role of a previously unrecognized process, photoelectron emission, in initiating photochemical grafting of alkenes to surfaces. Molecular and biomolecular interfaces formed on diamond and other covalent materials are leading to novel types of molecular electronic interfaces. For example, electrical, optical, or electromechanical structures that convert biological information directly into analytical signals allow for direct label-free detection of DNA and proteins. Because of the preferential adherence of molecules to graphitic edge-plane sites, the grafting of redox-active species to vertically aligned carbon nanofibers leads to good electrochemical activity. Therefore researchers could graft electrocatalytic materials to carbon nanofibers to develop new types of selective electrocatalytic interfaces. Extending this chemistry to include metal oxides such as TiO(2) may lead to highly specific and efficient chemical reactions and new materials with useful applications in photovoltaic and photocatalytic energy conversion.

Micro- and nanopatterning of functional organic monolayers on oxide-free silicon by laser-induced photothermal desorption

The photothermal laser patterning of functional organic monolayers, prepared on oxide-free hydrogen-terminated silicon, and subsequent backfilling of the laser-written lines with a second organic monolayer that differs in its terminal functionality, is described. Since the thermal monolayer decomposition process is highly nonlinear in the applied laser power density, subwavelength patterning of the organic monolayers is feasible. After photothermal laser patterning of hexadecenyl monolayers, the lines freed up by the laser are backfilled with functional acid fluoride monolayers. Coupling of cysteamine to the acid fluoride groups and subsequent attachment of Au nanoparticles allows easy characterization of the functional lines by atomic force microscopy (AFM) and scanning electron microscopy (SEM). Depending on the laser power and writing speed, functional lines with widths between 1.1 μm and 250 nm can be created. In addition, trifluoroethyl-terminated (TFE) monolayers are also patterned. Subsequently, the decomposed lines are backfilled with a nonfunctional hexadecenyl monolayer, the TFE stripes are converted into thiol stripes, and then finally covered with Au nanoparticles. By reducing the lateral distance between the laser lines, Au-nanoparticle stripes with widths close to 100 nm are obtained. Finally, in view of the great potential of this type of monolayer in the field of biosensing, the ease of fabricating biofunctional patterns is demonstrated by covalent binding of fluorescently labeled oligo-DNA to acid-fluoride-backfilled laser lines, which--as shown by fluorescence microscopy--is accessible for hybridization.

Characterization of streptavidin binding to biotinylated, binary self-assembled thiol monolayers--influence of component ratio and solvent

Many biosensor applications are based on streptavidin (SA) binding to partially biotinylated self-assembled thiol monolayers (SAMs). In our study, binary SAMs on gold were prepared from solutions containing 16-mercapto-1-hexadecanol (thiol I) and N-(8-biotinyl-3,6-dioxa-octanamidyl)-16-mercaptohexadecanamide (thiol II) in varying component ratios. Either chloroform or ethanol was used as solvent. After 24 h thiol incubation, SA was immobilized on the resulting SAMs using the strong SA-biotin interaction. The SA binding process was monitored by QCM-D (quartz crystal microbalance monitoring dissipation factor). It is shown that the Sauerbrey equation is valid to calculate the mass quantities of the immobilized SA layers. Under the chosen incubation conditions, marginal fractions of the biotinylated component II in chloroform ((n(I)/n(II))(solution) approximately = 1000) lead to SAMs which ensure a maximal SA binding quantity of m(Sauerbrey SA) approximately = 400 ng x cm(-2), being equivalent to a SA single-layer arrangement on the SAM surface. In case of incubations from ethanolic solutions, a complete SA layer formation needs significantly higher amounts of the biotinylated component II during SAM preparation ((n(I)/n(II))(solution) approximately = 50). X-ray photoelectron spectroscopy data show that the fraction of biotinylated thiol II in the SAM determines the amount of surface-bound SA. The SAM thiol ratio ((n(I)/n(II))(SAM)) not only depends on the corresponding component ratio in the incubation solution, but is also strongly influenced by the solvent. Using chloroform as solvent during SAM preparation significantly increased the fraction of biotinylated thiol II in the SAMs compared to ethanol.