Alkyl Monolayers Research Articles

Molecular Modeling of Alkyl and Alkenyl Monolayers on Hydrogen-Terminated Si(111)

On H-Si(111) surfaces monolayer formation with 1-alkenes results in alkyl monolayers with a Si-C-C linkage, while 1-alkynes yield alkenyl monolayers with a Si-C═C linkage. Recently, considerable structural differences between both types of monolayers were observed, including an increased thickness, improved packing, and higher surface coverage for the alkenyl monolayers. The precise origin thereof could experimentally not be clarified yet. Therefore, octadecyl and octadecenyl monolayers on Si(111) were studied in detail by molecular modeling via PCFF molecular mechanics calculations on periodically repeated slabs of modified surfaces. After energy minimization the packing energies, structural properties, close contacts, and deformations of the Si surfaces of monolayers structures with various substitution percentages and substitution patterns were analyzed. For the octadecyl monolayers all data pointed to a substitution percentage close to 50-55%, which is due the size of the CH(2) groups near the Si surface. This agrees with literature and the experimentally determined coverage of octadecyl monolayers. For the octadecenyl monolayers the minimum in packing energy per chain is calculated around 60% coverage, i.e., close to the experimentally observed value of 65% [Scheres et al. Langmuir 2010, 26, 4790], and this packing energy is less dependent on the substitution percentage than calculated for alkyl layers. Analysis of the chain conformations, close contacts, and Si surface deformation clarifies this, since even at coverages above 60% a relatively low number of close contacts and a negligible deformation of the Si was observed. In order to evaluate the thermodynamic feasibility of the monolayer structures, we estimated the binding energies of 1-alkenes and 1-alkynes to the hydrogen-terminated Si surface at a range of surface coverages by composite high-quality G3 calculations and determined the total energy of monolayer formation by adding the packing energies and the binding energies. It was shown that due to the significantly larger reaction exothermicity of the 1-alkynes, thermodynamically even a substitution percentage as high as 75% is possible for octadecenyl chains. However, because sterically (based on the van der Waals footprint) a coverage of 69% is the maximum for alkyl and alkenyl monolayers, the optimal substitution percentage of octadecenyl monolayers will be presumably close to this latter value, and the experimentally observed 65% is likely close to what is experimentally maximally obtainable with alkenyl monolayers.

The role of the organic layer functionalization in the formation of silicon/organic layer/metal junctions with coinage metals

The design of silicon/alkyl layer/metal junctions for the formation of optimal top metal contacts requires knowledge of the mechanistic and energetic aspects of the interactions of metal atoms with the modified surface. This involves (a) the interaction of the metal with the terminal groups of the organic layer, (b) the diffusion of metal atoms through the organic layer and (c) the reactions of metal atoms with the silicon surface atoms. The diffusion through the monolayer and the metal catalyzed breakage of Si-C bonds must be avoided to obtain high quality junctions. In this work, we performed a comprehensive density functional theory investigation to identify the reaction pathways of all these processes. In the absence of a reactive terminal group, gold atoms may penetrate through a compact alkyl monolayer on Si(111) with no energy barrier. However, the presence of thiol terminal groups introduces a high energy barrier which blocks the diffusion of metals into the monolayer. The diffusion barriers increase in the order Ag < Au < Cu and correlate with the stability of metal-thiolate complexes whereas the barriers for the formation of metal silicides increase in the order Cu < Au < Ag in correlation with the increasing metallic radii. The reactivity of gold clusters with functionalized Si(111) surfaces was also investigated. Metal silicide formation can only be avoided by a compact monolayer terminated by a reactive functional group. The mechanistic and energetic picture obtained in this work contributes to understanding of the factors that influence the quality of top metal contacts during the formation of silicon/organic layer/metal junctions.

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.

Alkyl Passivation and Amphiphilic Polymer Coating of Silicon Nanocrystals for Diagnostic Imaging

A method to produce biocompatible polymer-coated silicon nanocrystals for medical imaging is shown. Silica-embedded Si nanocrystals are formed by HSQ thermolysis. The nanocrystals are then liberated from the oxide and terminated with Si-H bonds by HF etching, followed by alkyl monolayer passivation by thermal hydrosilylation. The Si nanocrystals have an average diameter of 2.1 nm ± 0.6 nm and photoluminesce with a peak emission wavelength of 650 nm, which lies within the transmission window of 650-900 nm that is useful for biological imaging. The hydrophobic Si nanocrystals are then coated with an amphiphilic polymer for dispersion in aqueous media with the pH ranging between 7 and 10 and an ionic strength between 30 mM and 2 M, while maintaining a bright and stable photoluminescence and a hydrodynamic radius of only 20 nm. Fluorescence imaging of polymer-coated Si nanocrystals in biological tissue is demonstrated, showing the potential for in vivo imaging.

Modifying electronic properties at the silicon–molecule interface using atomic tethers

The electronic properties at the semiconductor–molecule interface can be altered by changing the nature of covalent attachment. We examine the change in work function of the silicon surface after formation of Si–O–C, Si–C–C, and Si–S–C bonded alkyl monolayers and separate charge transfer and dipolar contributions. The chemical state, monolayer structure, and electronic properties of aliphatic monolayers with oxygen, carbon, and sulfur covalent linkages to the Si(1 1 1) surface were investigated with contact angle wetting, spectroscopic ellipsometry, infrared vibrational spectroscopy, X-ray photoemission spectroscopy, and ultraviolet photoemission spectroscopy. Vibrational spectra indicate aliphatic films tethered to Si with few gauche defects in agreement with hydrophobic contact angles and ellipsometric thickness measurements. Core level electronic spectra taken as a function of semiconductor doping reveal shifts in binding energy attributed to molecular bonding. Valence band spectra reveal the work function of the molecule–Si composite as a function of semiconductor doping and atomic tether. By combining valence band spectra with core level spectra, the electronic properties of the molecule–Si system can be understood. In particular, the relative contribution of charge transfer due to surface band bending and the polarization due to molecular dipoles were determined. The O, C, and S atomic tethers induce differing amounts of band bending and interface dipoles which can be utilized to engineer the electronic properties of molecule–semiconductor junctions.

Corrosion Resistance of Thiol- and Alkene-Passivated Germanium Nanowires

The corrosion resistance of organic monolayer-coated germanium (Ge) nanowires was tested by exposure to various harsh chemical treatments, including boiling water, concentrated sulfuric acid, and hydrogen peroxide. The Ge nanowires were grown by the supercritical fluid−liquid−solid (SFLS) process with in situ thermal hydrogermylation or thiolation, with alkyl monolayer coatings of varying chain length, from 6 to 18 C atoms. All of these nanowires exhibited almost-imperceptible surface oxidation in air or water, and degraded only when exposed to the harshest oxidative conditions. Nanowires with monolayers attached through Ge−C and Ge−S bonds exhibited similar corrosion resistance, except when exposed to peroxide, in which case the alkylated nanowires were more resistant to oxidation.

Direct Electrochemistry of Cytochrome c at Modified Si(100) Electrodes

This paper demonstrates the direct electron transfer between the heme moiety of horse hearth cytochrome c and a pyridinyl group on self-assembled-monolayer-modified Si(100) electrodes. Self-assembled monolayers (SAMs) containing the putative receptor ligand were prepared by a step-wise procedure using "click" reactions of acetylene-terminated alkyl monolayers and isonicotinic acid azide derivatives. Unoxidized Si(100) electrodes, possessing either isonicotinate or isonicotinamide receptor ligands, were characterized using X-ray photoelectron spectroscopy, contact-angle goniometry, cyclic voltammetry, and electrochemical impedance spectroscopy. The ability of isonicotinic acid terminated layers to coordinatively bind the redox center of cytochrome c was found to be restricted to pyridinyl assemblies with a para-ester linkage present. The protocol detailed here offers an experimentally simple modular approach to producing chemically well-defined SAMs on silicon surfaces for direct electrochemistry of a well-studied model redox protein.

Hg/Molecular Monolayer−Si Junctions: Electrical Interplay between Monolayer Properties and Semiconductor Doping Density

Metal−organic molecule−semiconductor junctions are controlled not only by the molecular properties, as in metal−organic molecule−metal junctions, but also by effects of the molecular dipole, the dipolar molecule−semiconductor link, and molecule−semiconductor charge transfer, and by the effects of all these on the semiconductor depletion layer (i.e., on the internal semiconductor barrier to charge transport). Here, we report on and compare the electrical properties (current−voltage, capacitance−voltage, and work function) of large area Hg/organic monolayer-Si junctions with alkyl and alkenyl monolayers on moderately and highly doped n-Si, and combine the experimental data with simulations of charge transport and electronic structure calculations. We show that, for moderately doped Si, the internal semiconductor barrier completely controls transport and the attached molecules influence the transport of such junctions only in that they drive the Si into inversion. The resulting minority carrier-controlled ju...

Molecular and Electronic Properties Transferred to Silicon via Wet-Chemistry Surface Nanofunctionalization: Ethynylferrocene on Si(100)

In the frame of our research activity on covalent anchoring of functional molecules on Si oriented surfaces, we report here on the hybrid species resulting from the reaction of ethynylferrocene with H-Si(100) either in a single, direct step, or after production of a self-assembled alpha,omega-bifunctional alkyl monolayer. In the former approach, a short Si-C covalent bond is established through visible-light activation of the unsaturated side arm of ethynylferrocene via an extra-mild approach. In the latter case, an azide-alkyne Huisgen cycloaddition reaction ("click" chemistry) is induced between the C[triple bond]C group of the molecule and the -N3 terminations of undecyl hydrocarbon chains pre-assembled onto H-Si(100). These two routes lead to electroactive monolayers wherein the ferrocene head groups are respectively located close to or far from the Si surface. This allows for a fine tuning of the properties of the resulting hybrids on Si, in terms of distinct redox potentials, electron transfer rate constants, oxidation resistance. The different reaction steps have been monitored with X-ray Photoelectron Spectroscopy (XPS), in order to evaluate the presence and the chemical nature of the anchored species, while electrochemical measurements have evidenced reversible redox responses of the resulting SAMs.

Organic Monolayers onto Oxide-Free Silicon with Improved Surface Coverage: Alkynes versus Alkenes

On H-Si(111), monolayer assembly with 1-alkenes results in alkyl monolayers with a Si-C-C linkage to the silicon substrate, while 1-alkynes yield alkenyl monolayers with a Si-C=C linkage. To investigate the influence of the different linkage groups on the final monolayer structure, organic monolayers were prepared from 1-alkenes and 1-alkynes with chain lengths from C(12) to C(18), and the final monolayer structures were studied in detail by static water contact angles measurements, ellipsometry, attenuated total reflectance infrared (ATR-IR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). The thicknesses, tilt angles, and packing densities of the alkyl monolayers are in good agreement with literature values, whereas increased thicknesses, reduced tilt angles, and improved packing densities were observed for the alkenyl monolayers. Finally, the surface coverages for alkyl monolayers were determined to be 50-55% (in line with literature values), while those for the alkenyl monolayers increased with the chain length from 55% for C(12) to as high as 65% for C(18)! The latter value is very close to the theoretical maximum of 69% obtainable on H-Si(111). Such enhanced monolayer quality and increased surface coverage of the alkenyl monolayers, in combination with the oxidation-inhibiting nature of the Si-C=C linkage, significantly increases the chance of successful implementation of organic monolayers on oxide-free silicon in molecular electronic and biosensor devices, especially in view of the importance of a defect-free monolayer structure and the corresponding stability of the monolayer-silicon interface.

Wet chemical routes to the assembly of organic monolayers on silicon surfaces via the formation of Si–C bonds: surface preparation, passivation and functionalization

Organic functionalization of non-oxidized silicon surfaces, while allowing for robust chemical passivation of the inorganic substrate, is intended and expected to broaden the chemical, physical and electronic properties of the currently most relevant technological material. Numerous protocols are now available for the preparation of Si-C, Si-O and Si-N bound layers. In particular, the covalent attachment of 1-alkenes and 1-alkynes onto hydride-terminated Si(100) and Si(111) has seen a wealth of research activity starting from the pioneering work of Linford and Chidsey (Alkyl monolayers covalently bonded to silicon surfaces, J. Am. Chem. Soc., 1993, 115(26), 12631-12632). This critical review aims to bring together the available wet-chemical routes toward the formation of silicon-organic monolayers under ambient conditions. Particular emphasis is placed on discussing the reasons behind the need for novel chemical approaches that are straightforward, modular and of wide scope so as to allow the application of silicon electrodes in aqueous electrolytes. A general introduction to biomolecular recognition events at functionalized silicon surfaces is also presented (281 references).

Direct Stabilization of a Phospholipid Monolayer on H-Terminated Silicon

This Article describes a strategy to stabilize a phospholipid monolayer directly on the surface of a H-terminated silicon substrate in order to provide a useful platform for silicon based biosensors. The stabilization of an acrylated phospholipid monolayer is obtained by two-dimensional chain polymerization. As the formation of the lipid monolayer in aqueous solution competes with the oxidation of the silicon surface, several cycles of oxide removal and lipid exposure are necessary to densify the lipid layer. Lipid monolayer formation is followed by Fourier transform infrared spectroscopy. The resulting monolayer is denser than corresponding alkyl monolayers formed on H-terminated silicon via photochemical or thermally initiated reactions.

Copper−Metal Deposition on Self Assembled Monolayer for Making Top Contacts in Molecular Electronic Devices

Molecular electronics is an attractive option for low-cost devices because it involves highly uniform self-assembly of molecules with a variety of possible functional groups. However, the potential of molecular electronics can only be turned into practical applications if reliable contacts can be established without damaging the organic layer or contaminating its interfaces. Here, a method is described to prepare tightly packed carboxyl-terminated alkyl self-assembled monolayers (SAMs) that are covalently attached to silicon surfaces and to deposit thin metallic copper top contact electrodes without damage to this layer. This method is based on a two-step procedure for SAM preparation and the implementation of atomic layer deposition (ALD) using copper di-sec-butylacetamidinate [Cu(sBu-amd)](2). In situ and ex situ infrared spectroscopy (IRS), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and electrical measurements are used to characterize the chemical modification of the Si/SAM interface, the perturbation of the SAM layer itself, and the metal homogeneity and interaction with the SAM headgroups. This work shows that (i) carboxyl-terminated alkyl monolayers can be prepared with the same high density and quality as those achieved for less versatile methyl-terminated alkyl monolayers, as evidenced by electrical properties that are not dominated by interface defects; (ii) Cu is deposited with ALD, forming a bidentate complexation between the Cu and the COOH groups during the first half cycle of the ALD reaction; and (iii) the Si/SAM interface remains chemically intact after metal deposition. The nondamaging thin Cu film deposited by ALD protects the SAM layer, making it possible to deposit a thicker metal top contact leading ultimately to a controlled preparation of molecular electronic devices.

Adsorption and Thermal Reaction of Short-Chain Iodoalkanes on Ge(100)

The adsorption and thermal decomposition of iodoalkanes CH3I, C2H5I, and C4H9I on Ge(100) were studied with temperature-programmed desorption (TPD) and X-ray photoelectron spectra (XPS) using synchrotron radiation. At 105 K, the iodoalkanes adsorb both molecularly and dissociatively on Ge(100); the shorter-chain iodoalkane dissociates to form a surface alkyl and an I adatom to a greater extent. The chemisorbed iodoalkane gradually dissociates to form a surface alkyl and an I adatom in a temperature range 200−370 K. At 720 K, most surface CH3 desorbs directly from the surface, and other surface CH3 radicals undergo disproportionation to desorb as CH4. Surface C2H5 and C4H9 mostly undergo β-hydride elimination to desorb as C2H4 and C4H8 at ∼550 K, respectively. The temperature for C4H9 to react is slightly lower than that for C2H5 because the C4H9 chain exhibits a stronger interaction with the surface than C2H5. The I adatom can react with a H atom liberated during decomposition of a surface alkyl and subsequently desorbs as molecular HI in two temperature regimes, ∼650 and ∼720 K. Some I adatoms are removed from the surface via direct desorption in atomic form at 720 K. On annealing to 770 K, the Ge surface becomes free of I adatom but retains a deposit of residual C as adatoms. According to our data, the temperature of fabrication and operation of a Ge-based device with the alkyl monolayer is suggested to be not higher than 530 K.

Controlled Oxidation, Biofunctionalization, and Patterning of Alkyl Monolayers on Silicon and Silicon Nitride Surfaces using Plasma Treatment

A new method is presented for the fast and reproducible functionalization of silicon and silicon nitride surfaces coated with covalently attached alkyl monolayers. After formation of a methyl-terminated 1-hexadecyl monolayer on H-terminated Si(100) and Si(111) surfaces, short plasma treatments (1-3 s) are sufficient to create oxidized functionalities without damaging the underlying oxide-free silicon. The new functional groups can, e.g., be derivatized using the reaction of surface aldehyde groups with primary amines to form imine bonds. In this way, plasma-treated monolayers on silicon or silicon nitride surfaces were successfully coated with nanoparticles, or proteins such as avidin. In addition, we demonstrate the possibility of micropatterning, using a soft contact mask during the plasma treatment. Using water contact angle measurements, ellipsometry, XPS, IRRAS, AFM, and reflectometry, proof of principle is demonstrated of a yet unexplored way to form patterned alkyl monolayers on oxide-free silicon surfaces.

Sub-10-nm patterning of oligo(ethylene glycol) monolayers on silicon surfaces via localoxidation using a conductive atomic force microscope

We demonstrate that local oxidation using a conductive atomic force microscope (c-AFM)can achieve patterning of sub-10-nm spots on protein-resistant oligo(ethyleneglycol)-terminated alkyl monolayers on silicon substrates. Such a high resolution ofnanopatterning with a c-AFM on organic thin films was realized for the firsttime by applying ultrashort (50–100 ns) voltage pulses to the silicon substraterelative to the conducting AFM tip. Furthermore, the nanopatterning can becontrolled at the surface of the hydrophilic monolayer without oxidizing the siliconinterface.

Controlled Oxidation of Alkyl Monolayers Grafted onto Flat Si(111) in an Oxygen Plasma of Low Power Density

Alkyl monolayers anchored to an atomically flat hydrogenated (111)-oriented silicon surface through covalent Si−C bonding have been submitted to an oxygen plasma treatment of controlled power density. The chemical state of the surface was monitored in situ in real time in the plasma cell using multiple-internal-reflection infrared spectroscopy and ex situ by X-ray photoelectron spectroscopy. While plasma treatments of moderate power densities (∼0.1−1 W/cm3) lead to complete removal of the organic monolayer, using very-low power densities (∼10 mW cm−3) leads to selective oxidation of the organic chains with negligible etching of the monolayer and a very limited oxidation of the silicon surface. Successive formation of alcohol, ketone, and carboxyl functions is observed before reaching a quasi steady state on an hour time scale. Modelization of the plasma shows that the dominant reactive species at these low power densities is the singlet oxygen molecule (1Δg). A molecular-scale reaction mechanism is proposed, and a simple kinetic model is derived. A major conclusion is that reaching a quasi steady state is attributable to the very low amount of atomic oxygen in the plasma and to the densification of the layer upon incorporation of oxygen-bearing groups.

Electronic Properties and pH Stability of Si(111)/Alkyl Monolayers

The electronic properties of hydrogenated and alkyl-grafted silicon surfaces have been investigated by photoluminescence, surface photovoltage and electrochemical capacitance measurements, which are sensitive methods for monitoring the presence of electronic defects. On p-type silicon, the electronic quality of the interface was found to depend critically on the surface preparation and was studied with special care. The thermal grafting of one monolayer of linear organic chains on atomically flat silicon allows the formation of stable alkyl-grafted p-Si surfaces, exhibiting a very low density of recombination centers comparable to those measured on hydrogenated silicon surfaces. Photoluminescence measurements show that the high electronic quality of the grafted surfaces is preserved on a month scale in air, indicating a much more efficient long term passivation by comparison with hydrogenated Si surfaces. The stability of the silicon/organic layer interface in aqueous buffer solution has been assessed by in situ photoluminescence and surface photovoltage measurements. Some degradation of the electronic properties was evidenced during exposure in basic solution of pH > 9.

Gold Nanoparticle Arrays Fabricated on a Silicon Substrate Covered with a Covalently Bonded Alkyl Monolayer by Electroless Plating Combined with Scanning Probe Anodization Lithography

Hexagonal nanoholes, in which an array of Au nanoparticles was located, were successfully fabricated on the basis of scanning probe anodization lithography. The lithography has been conducted to draw nanopatterns on a hexadecyl self-assembled monolayer covalently bonded to a Si substrate through Si−C bonds. Using a conductive atomic force microscope (AFM) probe as a point contact electrode, current was locally injected into the monolayer-Si sample. The monolayer was decomposed on the location where current injected. Subsequently, at this point, the substrate Si was anodized resulting in the formation of an oxide nanodot. Next, the oxide nanodot was selectively etched with HF in order to make a nanohole while the surrounding monolayer remaining unetched. As a result, a nanohole was formed at the current injected point. Employing the remained monolayer as an etch mask, the nanohole was further etched with NH4F in order to prepare a well-defined hydrogen-terminated surface in the nanohole. The nanohole becam...

Electronic Properties and pH Stability of the Interface Si(111)/alkyl Monolayers.

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