Surface coverage and structure of mixed DNA/alkylthiol monolayers on gold: characterization by XPS, NEXAFS, and fluorescence intensity measurements

Self-assembly of thiol-terminated single-stranded DNA (HS-ssDNA) on gold has served as an important model system for DNA immobilization at surfaces. Here, we report a detailed study of the surface composition and structure of mixed self-assembled DNA monolayers containing a short alkylthiol surface diluent [11-mercapto-1-undecanol (MCU)] on gold supports. These mixed DNA monolayers were studied with X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and fluorescence intensity measurements. XPS results on sequentially adsorbed DNA/MCU monolayers on gold indicated that adsorbed MCU molecules first incorporate into the HS-ssDNA monolayer and, upon longer MCU exposures, displace adsorbed HS-ssDNA molecules from the surface. Thus, HS-ssDNA surface coverage steadily decreased with MCU exposure time. Polarization-dependent NEXAFS and fluorescence results both show changes in signals consistent with changes in DNA orientation after only 30 min of MCU exposure. NEXAFS polarization dependence (followed by monitoring the N 1s --> pi* transition) of the mixed DNA monolayers indicated that the DNA nucleotide base ring structures are oriented more parallel to the gold surface compared to DNA bases in pure HS-ssDNA monolayers. This indicates that HS-ssDNA oligomers reorient toward a more-upright position upon MCU incorporation. Fluorescence intensity results using end-labeled DNA probes on gold show little observable fluorescence on pure HS-ssDNA monolayers, likely due to substrate quenching effects between the fluorophore and the gold. MCU diluent incorporation into HS-ssDNA monolayers initially increases DNA fluorescence signal by densifying the chemisorbed monolayer, prompting an upright orientation of the DNA, and moving the terminal fluorophore away from the substrate. Immobilized DNA probe density and DNA target hybridization in these mixed DNA monolayers, as well as effects of MCU diluent on DNA hybridization in complex milieu (i.e., serum) were characterized by surface plasmon resonance (SPR) and (32)P-radiometric assays and reported in a related study (Gong, P.; Lee, C.-Y.; Gamble, L. J.; Castner, D. G.; Grainger, D. W. Anal. Chem. 2006, 78, 3326-3334.).     

XPS, TOF-SIMS, NEXAFS, and SPR characterization of nitrilotriacetic acid-terminated self-assembled monolayers for controllable immobilization of proteins

For immobilization of proteins onto surfaces in a specific and controlled manner, it is important to start with a well-defined surface that contains specific binding sites surrounded by a nonfouling background. For immobilizing histidine-tagged (his-tagged) proteins, surfaces containing nitrilotriacetic acid (NTA) headgroups and oligo(ethylene glycol) (OEG) moieties are a widely used model system. The surface composition, structure, and reactivity of mixed NTA/OEG self-assembled monolayers (SAMs) on Au substrates were characterized in detail using X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and surface plasmon resonance (SPR) biosensoring. XPS results for sequential adsorption of NTA thiols followed by OEG thiols showed that OEG molecules were incorporated into an incompletely formed NTA monolayer until a complete mixed SAM was formed. The surface concentration of NTA headgroups was estimated to be 0.9-1.3 molecule/nm2 in the mixed NTA/OEG monolayers, compared to 1.9 molecule/nm2 in pure NTA monolayers. Angle-dependent XPS indicated NTA headgroups were slightly reoriented toward an upright position after OEG incorporation, and polarization-dependent NEXAFS results indicated increased ordering of the alkane chains of the molecules. Nitrogen-containing and OEG-related secondary ion fragments from the TOF-SIMS experiments confirmed the presence of NTA headgroups and OEG moieties in the monolayers. A multivariate peak intensity ratio was developed for estimating the relative NTA concentration in the outermost (10 A) of the monolayers. SPR measurements of a his-tagged, humanized anti-lysozyme variable fragment (HuLys Fv) immobilized onto Ni(II)-treated mixed NTA/OEG and pure NTA monolayers demonstrated the reversible, site-specific immobilization of his-tagged HuLys Fv (108-205 ng/cm2) with dissociation rates (koff) between 1.0 x 10-4 and 2.1 x 10-5 s-1, both depending on the NTA surface concentration and orientation. The monolayers without Ni(II) treatment exhibited low nonspecific adsorption of his-tagged HuLys Fv (<2 ng/cm2).     

Immobilization of dendrimers on Si-C linked carboxylic acid-terminated monolayers on silicon(111)

Poly(amidoamine) dendrimers were attached to activated undecanoic acid monolayers, covalently linked to smooth silicon surfaces via Si-C bonds. The resulting ultra-thin dendrimer films were characterized by X-ray photoelectron spectroscopy (XPS), X-ray reflectometry (XR) and atomic force microscopy (AFM). XPS results suggested amide bond formation between the dendrimer and the surface carboxylic acid groups. XR yielded thicknesses of 10 Å for the alkyl region of the undecanoic acid monolayer and 12 Å for the dendrimer layer, considerably smaller than the diameter of these spherical macromolecules in solution. This was consistent with AFM images showing collapsed dendrimers on the surface. It was concluded that the deformation arose from a large number of amine groups on the surface of each dendrimer reacting efficiently with the activated surface, whereby the dendrimers can deform to fill voids while spreading over the activated surface to form a homogeneous macromolecular layer.     

Thermodynamic and structural studies of mixed monolayers: Mutual mixing of DPPC and DPPG with DoTAP at the air–water interface

Phospholipid monomolecular films at the air–water interface are useful model membranes to understand miscibility among various components. Surface pressure (π)–area (A) isotherms of pure and mixed monolayers of dioleoyltrimethylammonium propane (DoTAP)–dipalmitoylphosphatidylcholine (DPPC) and DoTAP–dipalmitoyphosphatidylglycerol (DPPG) were constructed using a surface balance. DPPC and DPPG produced isotherms as expected and reported earlier. DoTAP, an unsaturated lipid, demonstrated a continuous π–A isotherm. Associative interactions were identified in DPPC–DoTAP mixtures compared to the pure components, while DPPG–DoTAP mixtures showed repulsive interaction up to an equimolar ratio. Compression moduli of the monolayers revealed that DPPC–DoTAP mixtures had increasing stability with increasing surface pressure, but addition of DoTAP to DPPG showed instability at low and intermediate concentrations. In both cases increased stability was returned at higher X_DoTAP values and surface pressures. Lipid monolayer film thickness values, determined on a gold coated glass substrate by surface plasmon resonance spectroscopy (SPR), indicated a systematic change in height profile for DPPC–DoTAP mixtures with increasing X_DoTAP. However, DPPG–DoTAP mixed monolayer systems demonstrated a biphasic response. The SPR data were in excellent agreement with our interpretation of the structure of solid supported lipid monolayers.     

Characterization of the dielectric properties of covalently attached organic films on silicon surfaces

Monolayers of methyl-undecanoate were constructed on silicon surfaces via a covalent Si-C bond. The molecular monolayers were characterized by high resolution electrical impedance spectroscopy (EIS), X-ray photoelectron spectroscopy (XPS) and ellipsometry and displayed a densely packed monolayer. After formation of the monolayer, the methyl ester was hydrolyzed without noticeable change in the integrity of the monolayer. The carboxyl terminated organic layer was then reacted with (1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide to form active N-hydroxy succinimide ester groups. The activation chemistry was confirmed by XPS and the substructure of the methyl-undecanoate carboxylic acid and the N-hydroxy succinimide ester terminated films were characterized using EIS. XPS and EIS spectra provided information on the chemical composition and substructure of the monolayers for each step in the chemical modification of the surface.     

Controlling binding site densities on glass surfaces

The density of surface-immobilized ligands or binding sites is an important issue for the development of sensors, array- or chip-based assays, and single-molecule detection methods. The goal of this research is to control the binding site density of reactive ligands on surfaces by diluting surface amine groups in self-assembled and cross-linked monolayers on glass prepared from solutions containing very low concentrations of (3-aminopropyl)triethoxysilane (APTES) and much higher concentrations of (2-cyanoethyl)triethoxysilane. The surface amine sites are suitable for attaching labels and ligands by reaction with succinimidyl ester reagents. Labeling the amine sites with fluorescent molecules and imaging the single molecules with fluorescence microscopy provides a means of determining the density of amine sites on the surface, which were incorporated into the self-assembled monolayer with micrometer spacings in proportion to the concentration of APTES in the synthesis. Biotin ligands were also bound to these surface amine sites using a succinimidyl ester linker, and the immobilized biotin was then reacted with either streptavidin-conjugated gold colloid particles or fluorescently labeled neutravidin. Imaging of these samples yields consistent amine and biotin site coverages, indicating that quantitative control and chemical conversion of binding sites can be achieved at very low (<10(-7)) fractions of a monolayer.     

How the replacement of cholesterol by 25-hydroxycholesterol affects the interactions with sphingolipids: The Langmuir Monolayer Study complemented with theoretical calculations

In this paper, a representative of chain-oxidized sterols, 25-hydroxycholesterol (25-OH), has been studied in Langmuir monolayers mixed with the sphingolipids sphingomyelin (SM) and ganglioside (GM₁) to build lipid rafts. A classical Langmuir monolayer approach based on thermodynamic analysis of interactions was complemented with microscopic visualization of films (Brewster angle microscopy), surface-sensitive spectroscopy (polarization modulation–infrared reflection–absorption spectroscopy) and theoretical calculations (density functional theory modelling and molecular dynamics simulations). Strong interactions between 25-OH and both investigated sphingolipids enabled the formation of surface complexes. As known from previous studies, 25-OH in pure monolayers can be anchored to the water surface with a hydroxyl group at either C(3) or C(25). In this study, we investigated how the presence of additional strong interactions with sphingolipids modifies the surface arrangement of 25-OH. Results have shown that, in the 25-OH/GM₁ system, there are no preferences regarding the orientation of the 25-OH molecule in surface complexes and two types of complexes are formed. On the other hand, SM enforces one specific orientation of 25-OH: being anchored with the C(3)–OH group to the water. The strength of interactions between the studied sphingolipids and 25-OH versus cholesterol is similar, which indicates that cholesterol may well be replaced by oxysterol in the lipid raft system. In this way, the composition of lipid rafts can be modified, changing their rheological properties and, as a consequence, influencing their proper functioning.     

All-(111) surface silicon nanowires: selective functionalization for biosensing applications

We demonstrate the utilization of selective functionalization of carbon-silicon (C-Si) alkyl and alkenyl monolayers covalently linked to all-(111) surface silicon nanowire (Si-NW) biosensors. Terminal amine groups on the functional monolayer surfaces were used for conjugation of biotin n-hydroxysuccinimide ester. The selective functionalization is demonstrated by contact angle, X-ray photoelectron spectroscopy (XPS), and high-resolution scanning electron microscopy (HRSEM) of 5 nm diameter thiolated Au nanoparticles linked with streptavidin and conjugated to the biotinylated all-(111) surface Si-NWs. Electrical measurements of monolayer passivated Si-NWs show improved device behavior and performance. Furthermore, an analytical model is presented to demonstrate the improvement in detection sensitivity of the alkyl and alkenyl passivated all-(111) Si-NW biosensors compared to conventional nanowire biosensor geometries and silicon dioxide passivation layers as well as interface design and electrical biasing guidelines for depletion-mode sensors.     

Thermal stability of self-assembled octadecyltrichlorosilane monolayers on planar and curved silica surfaces

Understanding the structural and functional integrity of self-assembled monolayers (SAMs) of alkytrichlorosilane on Si/SiO₂ interface with change in temperature is critical for realizing their utility as antistiction coatings during the fabrication and functioning of microelectromechanical systems. Here we describe the thermal stability of two dimensional (2D) octadecyltrichlorosilane (OTS) monolayers on both n-type Si substrate (planar surface) and silica spheres (curved surface) using results of various surface sensitive spectroscopic techniques like the grazing angle Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. Densely packed OTS monolayer on n-type Si surface is found to be thermally stable up to 525 K, while a significant enhancement in the thermal stability is interestingly observed for the case of OTS SAM (up to 625 K) on freshly prepared spherical silica surfaces. Despite this difference in the thermal stability, the results of temperature dependent infrared spectra demonstrate monolayer decomposition in both cases through the involvement of both Si-C and C-C bonds leaving Si-O-Si bond intact.     

Preparation and characterization of poly(amide-imide) multilayer films

Multilayer films of poly(amide-imide)s were prepared as follows: (1) monolayers of long alkyl amine salts of poly(amide-amic acid) were prepared at the air- water interface; (2) these monolayers were deposited on an appropriate plate by the Langmuir-Blodgett method; (3) the multilayers of poly(amide-amic acid) salts on the solid support were treated with acetic anhydride to afford poly(amide-imide) multilayer films. The monolayer thickness of the poly(amide-imide) multilayer films were 0.43–0.55 nm.     

Resonance energy transfer-amplifying fluorescence quenching at the surface of silica nanoparticles toward ultrasensitive detection of TNT

This paper reports a resonance energy transfer-amplifying fluorescence quenching at the surface of silica nanoparticles for the ultrasensitive detection of 2,4,6-trinitrotoluene (TNT) in solution and vapor environments. Fluorescence dye and organic amine were covalently modified onto the surface of silica nanoparticles to form a hybrid monolayer of dye fluorophores and amine ligands. The fluorescent silica particles can specifically bind TNT species by the charge-transfer complexing interaction between electron-rich amine ligands and electron-deficient aromatic rings. The resultant TNT-amine complexes bound at the silica surface can strongly suppress the fluorescence emission of the chosen dye by the fluorescence resonance energy transfer (FRET) from dye donor to the irradiative TNT-amine acceptor through intermolecular polar-polar interactions at spatial proximity. The quenching efficiency of the hybrid nanoparticles with TNT is greatly amplified by at least 10-fold that of the corresponding pure dye. The nanoparticle-assembled arrays on silicon wafer can sensitively detect down to approximately 1 nM TNT with the use of only 10 microL of solution (approximately 2 pg TNT) and several ppb of TNT vapor in air. The simple FRET-based nanoparticle sensors reported here exhibit a high and stable fluorescence brightness, strong analyte affinity, and good assembly flexibility and can thus find many applications in the detection of ultratrace analytes.     

Photoisomerization of amphiphilic azobenzene derivatives in Langmuir Blodgett films prepared as polyion complexes, using ionic polymers

Polyion complexation in mixed Langmuir and Langmuir Blodgett (LB) films of photochromic amphiphilic azobenzene carboxylic acids, 11-[4-(4-hexylphenyl)azo] phenoxyundecanoic acid, 11-(4-phenylazo)phenoxyundecanoic acid, and diamine grafted poly(methylmethaacrylate) polymers has been studied. Monolayer behaviour of the pure components and mixed films was studied through pressure–area isotherms and LB films were characterized by spectroscopic, X-ray diffraction and Atomic force microscopy techniques. Aggregation (H-type), often observed in LB films of pure amphiphilic azo acids, was partly avoided in the mixed LB films as indicated by absorption spectral studies. Photoisomerization of the polyion complexed LB films was also studied. The results altogether demonstrate that amine grafted polymer enter into a polyion complexation with azo acid carboxylate group. LB films could be obtained by transfer of the composite monolayers and these LB films exhibited different levels of aggregation of the azo acids. Reversible photoisomerization was observed in LB films with unaggregated azo acid.     

On the structure and surface chemical composition of indium-tin oxide films prepared by long-throw magnetron sputtering

Structures and surface chemical composition of indium tin oxide (ITO) thin films prepared by long-throw radio-frequency magnetron sputtering technique have been investigated. The ITO films were deposited on glass substrates using a 20 cm target-to-substrate distance in a pure argon sputtering environment. X-ray diffraction results showed that an increase in substrate temperature resulted in ITO structure evolution from amorphous to polycrystalline. Field-emission scanning electron microscopy micrographs suggested that the ITO films were free of bombardment of energetic particles since the microstructures of the films exhibited a smaller grain size and no sub-grain boundary could be observed. The surface composition of the ITO films was characterized by X-ray photoelectron spectroscopy (XPS). Oxygen atoms in both amorphous and crystalline ITO structures were observed from O 1 s XPS spectra. However, the peak of the oxygen atoms in amorphous ITO phase could only be found in samples prepared at low substrate temperatures. Its relative peak area decreased drastically when substrate temperatures were larger than 200 °C. In addition, a composition analysis from the XPS results revealed that the films deposited at low substrate temperatures contained high concentration of oxygen at the film surfaces. The oxygen-rich surfaces can be attributed to hydrolysis reactions of indium oxides, especially when large amount of the amorphous ITO were developed near the film surfaces.     

Adsorption and desorption of CO on Ni decorated stepped Rh(553)

Vicinal surfaces are important in surface science, as they show interesting electronic structures and reactivities due to the steps. In this paper the adsorption and desorption of carbon monoxide on the stepped Rh(553) surface decorated with Ni is reported. With 0.1 to 0.3 monolayer Ni on Rh(553) one and two atoms broad Ni wires along the Rh steps are formed. The adsorption and desorption of carbon monoxide on these surfaces is investigated using thermal desorption spectroscopy (TDS) and reflection absorption infra red spectroscopy (RAIRS). TDS shows a marked change from just one broad TDS peak on pure Rh(553) to 4 distinct peaks with increasing Ni decoration. RAIRS shows that already at 0.1 monolayer Ni the CO adsorption states on bridge sites on the Rh step atoms are completely quenched. In addition it is shown that with Ni films up to 3 monolayer the on top adsorption sites for CO on Ni are preferred over the bridge and hollow adsorption sites in contrast to what is known from the Ni(111) surface.     

Adsorption and desorption of CO on Ni decorated stepped Rh(553)

Vicinal surfaces are important in surface science, as they show interesting electronic structures and reactivities due to the steps. In this paper the adsorption and desorption of carbon monoxide on the stepped Rh(553) surface decorated with Ni is reported. With 0.1 to 0.3 monolayer Ni on Rh(553) one and two atoms broad Ni wires along the Rh steps are formed. The adsorption and desorption of carbon monoxide on these surfaces is investigated using thermal desorption spectroscopy (TDS) and reflection absorption infra red spectroscopy (RAIRS). TDS shows a marked change from just one broad TDS peak on pure Rh(553) to 4 distinct peaks with increasing Ni decoration. RAIRS shows that already at 0.1 monolayer Ni the CO adsorption states on bridge sites on the Rh step atoms are completely quenched. In addition it is shown that with Ni films up to 3 monolayer the on top adsorption sites for CO on Ni are preferred over the bridge and hollow adsorption sites in contrast to what is known from the Ni(111) surface.     

Effect of grafted polymer species on particle monolayer structure at the air-water interface

We have studied poly(methyl methacrylate)-grafted(PMMA) particle monolayer systems at the air-water interface. In previous papers, we reported that PMMA chains grafted from particles (silica particle and polystyrene latex) were extended on water surfaces. Through observing deposited particle monolayers on substrates using SEM, we have confirmed that PMMA of large molecular weights were either dispersed or arrayed in structure with long inter-particle distances approximately 500 nm. In contrast, low molecular weight PMMA were observed to aggregate upon deposition. We speculated that the difference in morphology in deposited particle monolayers would be attributed to the affinity between the grafted polymer and the substrate. To examine the effect of this affinity three new polymer-grafted silica particles were synthesized with a fairly high graft density of about 0.14 approximately 0.43 nm(-2). As well as PMMA-grafted silica particles (SiO2-PMMA), poly(2-hydroxyethyl methacrylate) and poly(t-butyl methacrylate)--grafted silica particles (SiO2-PHEMA and SiO2-PtBuMA) were also prepared and subjected to pi-A isotherm measurements and SEM observations. These pi-A isotherms indicated that polymer-grafted silica formed monolayer at the air-water interface, and the onset area of increasing surface pressure suggests that the polymer chains are extended on a water surface. However, the morphology of the deposited monolayer is highly dependent on polymer species: SiO2-PHEMA showed that the dispersed particle monolayer structure was independent of grafted molecular weight while SiO2-tBuMA showed an aggregated structure that was also independent of grafted moleculer weight. SiO2-PMMA showed intermediate tendencies: dispersed structure was observed with high grafted molecular weight and aggregated structure was observed with low grafted molecule weight. The morphology on glass substrate would be explaiened by hydrophilic interaction between grafted polymer and hydrophilic glass substrate.     

Formation and properties of thin films of iron silicides on Si(111) Surface: Ab initio simulation

Density functional theory in the generalized gradient approximation has been used to calculate the total energy and model the atomic and electronic structures of thin FeSi films with CsCl type lattice and γ-FeSi₂ films with CaF₂ fluorite type lattice on a Si(111) surface. It is shown that, upon the adsorption of two monolayers of iron atoms on Si(111), the most energetically favorable process is the growth of a γ-FeSi₂ film with CaF₂ type structure. The electronic structure of a silicide film formed upon the adsorption of one monolayer of iron atoms exhibits features that are characteristic of both FeSi and γ-FeSi₂. The density of states calculated for the γ-FeSi₂ well agrees with the experimental photoemission spectra reported in the literature.     

A trough with radial compression for studies of monolayers and fabrication of Langmuir-Blodgett films

A new type of Langmuir trough with radial compression is reported for studies of monolayer properties and fabrication of Langmuir-Blodgett (LB) films. The trough included twenty curved diaphragms, which form a circular shape on water and compress monolayers. Typical monolayers of arachidic acid, DL--phosphatidylcholine dipalmitoyl, cellulose tridecanoate, and poly (butyl methacrylate) showed reproducible surface pressure-area isotherms with radial compression. Flow profiles were studied of monolayers on cellulose tridecanoate and poly(butyl methacrylate) and suggested that the monolayers are radially compressed with no particular film disturbance. A Wilhelmy glass plate preserved no deflection in the subphase surface from low to high surface pressures during the film compression and decompression; no pressure excess causing the deflection, which is frequently observed in the case of the film compression with a sliding barrier, was found on both sides of the Wilhelmy plate. Application of the radial compression enabled to do a symmetrical deposition for the fabrication of LB films.     

Sequential reactions with amine-terminated monolayers and isolated molecules on H/Si(111)

A simple method for preparing monolayers with terminal amine functionality is demonstrated. A gas-phase photochemical reaction of 1,3-diaminopropane with a H-terminated Si(111) surface results in the molecules covalently attaching to the surface, primarily through the formation of a Si--N bond. These monolayers are characterized by scanning tunneling microscopy (STM) and high-resolution electron energy loss spectroscopy (HREELS). The reactivity of the terminal amine is confirmed by exposing the monolayer to benzaldehyde, resulting in the formation of an imine link and the grafting of phenyl rings onto the surface. For short irradiation times, this reaction leads to the formation of isolated amine groups on an otherwise pristine H-terminated surface. STM and HREELS studies of the benzaldehyde reaction on these low-coverage surfaces (less than 0.005 monolayers) indicate that the reaction is restricted to the reactive amine groups, leaving the remainder of the surface unaffected. This simple approach for a sequential coupling reaction is expected to facilitate attachment of more complex molecules (molecular switches, biomolecules) for single-molecule STM studies.     

Gd@C_(82) Langmuir-Blodgett纳米薄膜的表面微观结构

采用Langmuir-Blodgett(LB)技术在新解理的云母和氧化铟锡(ITO)基片上成功地制备出富勒烯金属包合物Gd@C82/SA的单层及多层Langmuir-Blodgett分子薄膜,采用原子力显微镜(AFM)和X射线光电子能谱(XPS)对所制备纳米超分子薄膜的表面形貌和表面元素组成进行了系统研究,结果表明,与纯的Gd@C82 Langmuir薄膜相比,以硬脂酸(SA)为辅助成膜材料所得到的Gd@C82/SA复合Langmuir薄膜能更好地转移到云母和ITO基片表面,其镀膜转移比接近1,当硬脂酸(SA)与Gd@C82的摩尔比达到4:1时,所对应的Gd@C82/SA LB薄膜表现出良好的均一性和理想的层状结构。