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

This paper describes a simple strategy for DNA immobilization on chemically modified and patterned silicon surfaces. The photochemical modification of hydrogen-terminated Si(111) with undecylenic acid leads to the formation of an organic monolayer covalently attached to the surface through Si-C bonds without detectable reaction of the carboxylic acid group, providing indirect support of a free radical mechanism. Chemical activation of the acid function was achieved by a simple chemical route using N-hydroxysuccinimide (NHS) in the presence of N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide hydrochloride. Single strand DNA with a 5'-dodecylamine group was then coupled to the NHS-activated surface by amide bond formation. Using a previously reported chemical patterning approach, we have shown that DNA can be immobilized on silicon surfaces in spatially well-resolved domains. Methoxytetraethyleneglycolamine was used to inhibit nonspecific adsorption. The resulting DNA-modified surfaces have shown good specificity and chemical and thermal stability under hybridization conditions. The sequential reactions on the surface were monitored by ATR-FTIR, X-ray Photoelectron Spectroscopy, and fluorescence spectroscopy.     

High-resolution soft X-ray photoelectron spectroscopic studies and scanning auger microscopy studies of the air oxidation of alkylated silicon(111) surfaces

High-resolution soft X-ray photoelectron spectroscopy was used to investigate the oxidation of alkylated silicon(111) surfaces under ambient conditions. Silicon(111) surfaces were functionalized through a two-step route involving radical chlorination of the H-terminated surface followed by alkylation with alkylmagnesium halide reagents. After 24 h in air, surface species representing Si(+), Si(2+), Si(3+), and Si(4+) were detected on the Cl-terminated surface, with the highest oxidation state (Si(4+)) oxide signal appearing at +3.79 eV higher in energy than the bulk Si 2p(3/2) peak. The growth of silicon oxide was accompanied by a reduction in the surface-bound Cl signal. After 48 h of exposure to air, the Cl-terminated Si(111) surface exhibited 3.63 equivalent monoleyers (ML) of silicon oxides. In contrast, after exposure to air for 48 h, CH(3)-, C(2)H(5)-, or C(6)H(5)CH(2)-terminated Si surfaces displayed <0.4 ML of surface oxide, and in most cases only displayed approximately 0.20 ML of oxide. This oxide was principally composed of Si(+) and Si(3+) species with peaks centered at +0.8 and +3.2 eV above the bulk Si 2p(3/2) peak, respectively. The silicon 2p SXPS peaks that have previously been assigned to surface Si-C bonds did not change significantly, either in binding energy or in relative intensity, during such air exposure. Use of a high miscut-angle surface (7 degrees vs < or =0.5 degrees off of the (111) surface orientation) yielded no increase in the rate of oxidation nor change in binding energy of the resultant oxide that formed on the alkylated Si surfaces. Scanning Auger microscopy indicated that the alkylated surfaces formed oxide in isolated, inhomogeneous patches on the surface.     

Silicon surfaces as electron acceptors: dative bonding of amines with Si(001) and Si(111) surfaces.

The bonding of the trimethylamine (TMA) and dimethylamine (DMA) with crystalline silicon surfaces has been investigated using X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy, and density-functional computational methods. XPS spectra show that TMA forms stable dative-bonded adducts on both Si(001) and Si(111) surfaces that are characterized by very high N(1s) binding energies of 402.2 eV on Si(001) and 402.4 eV on Si(111). The highly ionic nature of these adducts is further evidenced by comparison with other charge-transfer complexes and through computational chemistry studies. The ability to form these highly ionic charge-transfer complexes between TMA and silicon surfaces stems from the ability to delocalize the donated electron density between different types of chemically distinct atoms within the surface unit cells. Corresponding studies of DMA on Si(001) show only dissociative adsorption via cleavage of the N-H bond. These results show that the unique geometric structures present on silicon surfaces permit silicon atoms to act as excellent electron acceptors.     

Chemical and electrical passivation of silicon (111) surfaces through functionalization with sterically hindered alkyl groups

Crystalline Si(111) surfaces have been alkylated in a two-step chlorination/alkylation process using sterically bulky alkyl groups such as (CH3)2CH- (iso-propyl), (CH3)3C- (tert-butyl), and C6H5- (phenyl) moieties. X-ray photoelectron spectroscopic (XPS) data in the C 1s region of such surfaces exhibited a low energy emission at 283.9 binding eV, consistent with carbon bonded to Si. The C 1s XPS data indicated that the alkyls were present at lower coverages than methyl groups on CH(3)-terminated Si(111) surfaces. Despite the lower alkyl group coverage, no Cl was detected after alkylation. Functionalization with the bulky alkyl groups effectively inhibited the oxidation of Si(111) surfaces in air and produced low (<100 cm s(-1)) surface recombination velocities. Transmission infrared spectroscopy indicated that the surfaces were partially H-terminated after the functionalization reaction. Application of a reducing potential, -2.5 V vs Ag+/Ag, to Cl-terminated Si(111) electrodes in tetrahydrofuran resulted in the complete elimination of Cl, as measured by XPS. The data are consistent with a mechanism in which the reaction of alkyl Grignard reagents with the Cl-terminated Si(111) surfaces involves electron transfer from the Grignard reagent to the Si, loss of chloride to solution, and subsequent reaction between the resultant silicon radical and alkyl radical to form a silicon-carbon bond. Sites sterically hindered by neighboring alkyl groups abstract a H atom to produce Si-H bonds on the surface.     

Binding mechanisms of methacrylic acid and methyl methacrylate on si(111)-7 x 7 -- effect of substitution groups

The interaction of methacrylic acid and methyl methacrylate with Si(111)-7 x 7 has been investigated using high-resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS). While methacrylic acid chemisorbs dissociatively through O-H bond cleavage, methyl methacrylate is covalently attached to the silicon surface via a [4+2] cycloaddition. The different reaction pathways of these two compounds on Si(111)-7 x 7 demonstrate that the substitution groups play an important role in determining the reaction channels for multifunctional molecules, leading to the desired flexibility in the organic modification of silicon surfaces.     

Mechanism of the hydrosilylation reaction of alkenes at porous silicon: experimental and computational deuterium labeling studies

The mechanism of the formation of Si-C bonded monolayers on silicon by reaction of 1-alkenes with hydrogen-terminated porous silicon surfaces has been studied by both experimental and computational means. We propose that monolayer formation occurs via the same radical chain process as at single-crystal surfaces: a silyl radical attacks the 1-alkene to form both the Si-C bond and a radical center on the beta-carbon atom. This carbon radical may then abstract a hydrogen atom from a neighboring Si-H bond to propagate the chain. Highly deuterated porous silicon and FTIR spectroscopy were used to provide evidence for this mechanism by identifying the IR bands associated with the C-D bond formed in the proposed propagation step. Deuterated porous silicon surfaces formed by galvanostatic etching in 48% DF/D2O:EtOD (1:1) electrolytes showed a 30% greater density of Si-D sites on the surface than Si-H sites on hydrogen-terminated porous silicon surfaces prepared in the equivalent H-electrolyte. The thermal reaction of undec-1-ene and the Lewis acid catalyzed reaction of styrene on a deuterated surface both resulted in alkylated surfaces with the same C-C and C-H vibrational features as formed in the corresponding reactions at a hydrogen-terminated surface. However, a broad band around 2100 cm(-1) was observed upon alkylating the deuterated surfaces. Ab initio and density functional theory calculations on small molecule models showed that the integrated absorbance of this band was comparable to the intensity expected for the C-D stretches predicted by the chain mechanism. The calculations also indicate that there is substantial interaction between the hydrogen atoms on the beta-carbons and the hydrogen atoms on the Si(111)-H surface. These broad 2100 cm(-1) features are therefore assigned to C-D bands arising from the involvement of surface D atoms in the hydrosilylation reactions, while the line broadening can be explained partly by interaction with neighboring surface atoms/groups.     

Bonding structure of phenylacetylene on hydrogen-terminated Si(111) and Si(100): surface photoelectron spectroscopy analysis and ab initio calculations

Interfaces between phenylacetylene (PA) monolayers and two silicon surfaces, Si(111) and Si(100), are probed by X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and the results are analyzed using ab initio molecular orbital calculations. The monolayer systems are prepared via the surface hydrosilylation reaction between PA and hydrogen-terminated silicon surfaces. The following spectral features are obtained for both of the PA-Si(111) and PA-Si(100) systems: a broad π-π* shakeup peak at 292 eV (XPS), a broad first ionization peak at 3.8 eV (UPS), and a low-energy C 1s → π* resonance peak at 284.3 eV (NEXAFS). These findings are ascribed to a styrene-like π-conjugated molecular structure at the PA-Si interface by comparing the experimental data with theoretical analysis results. A conclusion is drawn that the vinyl group can keep its π-conjugation character on the hydrogen-terminated Si(100) [H:Si(100)] surface composed of the dihydride (SiH(2)) groups as well as on hydrogen-terminated Si(111) having the monohydride (SiH) group. The formation mechanism of the PA-Si(100) interface is investigated within cluster ab initio calculations, and the possible structure of the H:Si(100) surface is discussed based on available data.     

Role of molecular conjugation in the surface radical reaction of aldehydes with H-Si(111): first principles study

Within the current effort to understand and develop the organic functionalization of silicon surfaces, recent experiments have identified the radical chain reaction of unsaturated organic molecules with H-terminated silicon surfaces as a particularly promising route for controlled formation of such functionalized surfaces. Using periodic density functional theory calculations, we theoretically study and characterize the basic steps of the radical chain reaction mechanism for different aldehyde molecules (formaldehyde, benzaldehyde, propanaldehyde, propenaldehyde) reacting with the H-Si(111) surface, under the assumption that a Si dangling bond is initially present on the surface. Molecular conjugation is found to play a crucial role in the viability of the reaction, by controlling the delocalization of the spin density at the reaction intermediate. Interesting differences between our present results for aldehydes and our previous study for the reactions of alkene/alkyne molecules with H-Si(111) are observed and discussed (Takeuchi et al. J. Am. Chem. Soc. 2004, 126, 15890).     

Covalently modified silicon and diamond surfaces: resistance to nonspecific protein adsorption and optimization for biosensing

We report the direct covalent functionalization of silicon and diamond surfaces with short ethylene glycol (EG) oligomers via photochemical reaction of the hydrogen-terminated surfaces with terminal vinyl groups of the oligomers, and the use of these monolayers to control protein binding at surfaces. Photochemical modification of Si(111) and polycrystalline diamond surfaces produces EG monolayers linked via Si-C bond formation (silicon) or C-C bond formation (diamond). X-ray photoelectron spectroscopy was used to characterize the monolayer composition. Measurements using fluorescently labeled proteins show that the EG-functionalized surfaces effectively resist nonspecific adsorption of proteins. Additionally, we demonstrate the use of mixed monolayers on silicon and diamond and apply these surfaces to control specific versus nonspecific binding to optimize a model protein sensing assay.     

Complex thermal chemistry of vinyltrimethylsilane on Si(100)-2x1

The surface chemistry of vinyltrimethylsilane (VTMS) on Si(100)-2x1 has been investigated using multiple internal reflection-Fourier transform infrared spectroscopy, Auger electron spectroscopy, and thermal desorption mass spectrometry. Molecular adsorption of VTMS at submonolayer coverages is dominating at cryogenic temperatures (100 K). Upon adsorption at room temperature, chemical reaction involving rehybridization of the double bond in VTMS occurs. Further annealing induces several reactions: molecular desorption from a monolayer by 400 K, formation and desorption of propylene by 500 K, decomposition leading to the release of silicon-containing products around 800 K, and, finally, surface decomposition leading to the production of silicon carbide and the release of hydrogen as H(2) at 800 K. This chemistry is markedly different from the previously reported behavior of VTMS on Si(111)-7x7 surfaces resulting in 100% conversion to silicon carbide. Thus, some information about the surface intermediates of the VTMS reaction with silicon surfaces can be deduced.     

Vibrational characterization and electronic properties of long range-ordered, ideally hydrogen-terminated Si(111)

The use of a well defined, long range ordered surface is of fundamental interest for the determination of surface-specific intrinsic physical parameters. Ideally hydrogen terminated Si(111) surfaces are prepared by wet chemical treatment in basic HF solutions. The mechanism of formation is based on preferential etching of defects, leading to an ideal hydrogen terminaison of the (111) plane, without any reconstruction and with a high degree of perfection. Infrared spectroscopy is used to probe the quality of the surfaces by quantifying the extent of the perfect domains.

High resolution photoemission spectroscopy of such highly homogeneous surfaces shows exceptional narrow features in both the valence band and the core level regions. The valence band levels and their dispersion are well described by first-principles calculations using a quasi particle self-energy approach within the Heidin's GW approximation.

Two surfaces core level states are evidenced, arising from the silicon surface atoms and the backbonds. A crystal field effect splits the surface Si 2_p3/2 component. Their position and relative intensity find a satisfactory agreement with recent calculations using first principles perturbation theory.     

Covalently attached monolayers on crystalline hydrogen-terminated silicon: extremely mild attachment by visible light

A very mild method was developed for the attachment of high-quality organic monolayers on crystalline silicon surfaces. By using visible light sources, from 447 to 658 nm, a variety of 1-alkenes and 1-alkynes were attached to hydrogen-terminated Si(100) and Si(111) surfaces at room temperature. The presence and the quality of the monolayers were evaluated by static water contact angles, X-ray photoelectron spectroscopy, and IR spectroscopy. Monolayers prepared by thermal, UV light, or visible light initiation were compared. Additionally, the ability of infrared reflection-absorption spectroscopy to study organic monolayers on silicon was explored. A reaction mechanism is discussed on the basis of investigations of the reaction behavior of 1-alkenes with silicon wafers with varying types and levels of doping. Finally, a series of mixed monolayers derived from the mixed solutions of a 1-alkene and an omega-fluoro-1-alkene were investigated to reveal that the composition of the mixed monolayers was directly proportional to the molar ratio of the two compounds in the solutions.     

Scanning tunneling microscopy and spectroscopy of wet-chemically prepared chlorinated Si111 surfaces

Chlorine-terminated Si(111) surfaces prepared through the wet-chemical treatment of H-terminated Si(111) surfaces with PCl5 (in chlorobenzene) were investigated using ultrahigh vacuum scanning tunneling microscopy (UHV cryo-STM) and tunneling spectroscopy. STM images, collected at 77 K, revealed an unreconstructed 1 x 1 structure for the chlorination layer, consistent with what has been observed for the gas phase chlorination of H-terminated Si(111). However, the wet-chemical chlorination is shown to generate etch pits in the Si(111) surface, with an increase in etch pit density correlating with increasing PCl5 exposure temperatures. These etch pits were assumed to stabilize the edge structure through the partial removal of the <112> step edges. Tunneling spectroscopy revealed a nonzero density of states at zero bias. This is in contrast to the cases of H-, methyl-, or ethyl-terminated Si(111), in which similar measurements have revealed the presence of a large conductance gap.     

Ultra-clean Si(111) and Si(001) Surfaces Prepared by Advanced Wet Chemical Cleaning

Wet chemical cleaning of silicon is a critical step, e.g., pre-gate clean, in the semiconductor manufacturing^[1]. For example, pre-gate oxide cleaning demands ultra-clean silicon surface with least surface roughness. It is well known that metallic infinities and roughness cause the lower breakdown voltage in gate dielectric^[2]. It has stringent requirements for ultra-clean and atomically flat silicon surface as the thickness of gate oxide is decreasing. In the present work, we have extended our study on Si(100) surface13] and extensively investigated wet chemical cleaning of Si(111) and Si(100) surfaces in NH₄F-based solutions by using scanning tunneling microscopy (STM), attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and total reflection X-ray fluorescence spectrometry (TXRF). Surface roughness, organic contamination, metallic impurities and surface termination on the silicon surfaces after wet chemical cleaning with various NH₄F-based solutions have been determined and compared with those treated with RCA cleans, HF solutions and other industrially used solutions. Our results indicate that ultra-clean and smooth Si(111) and Si(001) surfaces are obtained by treatment with NH4F-based solutions.     

-NH- termination of the Si(111) surface by wet chemistry

For over a quarter of a century the hydrogen-terminated Si(111) single-crystalline surface has been the gold standard as a starting point for silicon surface modification chemistry. However, creating a well-defined and stable interface based on Si-N bonds has remained elusive. Despite the fact that azides, nitro compounds, and amines do lead to the formation of surface Si-N, each of these modification schemes produces additional carbon- or oxygen-containing functional groups that in turn react with the surface itself, leaving contaminants that affect the interface properties for any further modification protocols. We describe the preparation of a Si(111) surface functionalized predominantly with Si-NH-Si species based on chlorination followed by the room temperature ammonia treatment utilizing NH(3)-saturated tetrahydrofuran (THF). The obtained surface has been characterized by infrared spectroscopy and X-ray photoelectron spectroscopy. This analysis was supplemented with DFT calculations. This newly characterized surface will join the previously established H-Si(111) and Cl-Si(111) surfaces as a general starting point for the preparation of oxygen- and carbon-free interfaces, with numerous potential applications.     

Dehydrogenative silane coupling on silicon surfaces via early transition metal catalysis

Derivatization of silicon surfaces is an area of intense interest due to the centrality of silicon in the microelectronics industry and because of potential promise for a myriad of other applications. In this paper, we investigate the feasibility of Si-Si bond formation directly on the surface to contrast with the more widely studied Si-C and Si-O bond forming reactions. Functionalization of hydride-terminated silicon surfaces with silanes is carried out via early transition metal mediated dehydrogenative silane coupling reactions. Zirconocene and titanocene catalyst systems were evaluated for heterocoupling of a molecular silane, RSiH3, with a surface Si-H group on Si(s). The zirconocene catalysts proved to be much more reactive than the titanium system, and so the former was examined exclusively. The silanes, aromatic or aliphatic, are bonded to the silicon surface through direct Si-Si bonds, although the level of incorporation of the trihydroarylsilanes was substantially higher than that of the aliphatic silanes. The reaction proceeds on nanocrystalline hydride-terminated porous silicon surfaces, as well as flat Si(100)-H(x) and Si(111)-H interfaces. The reactions were studied by a variety of techniques, including FTIR, SIMS, and XPS.     

Quantum mechanics calculations of the thermodynamically controlled coverage and structure of alkyl monolayers on Si(111) surfaces

The heat of formation, Delta E, for silicon (111) surfaces terminated with increasing densities of the alkyl groups CH3- (methyl), C2H5- (ethyl), (CH3)2CH- (isopropyl), (CH3)3C- (tert-butyl), CH3(CH2)5- (hexyl), CH3(CH2)7- (octyl), and C6H5- (phenyl) was calculated using quantum mechanics (QM) methods, with unalkylated sites being H-terminated. The free energy, Delta G, for the formation of both Si-C and Si-H bonds from Si-Cl model compounds was also calculated using QM, with four separate Si-H formation mechanisms proposed, to give overall Delta G(S) values for the formation of alkylated Si(111) surfaces through a two step chlorination/alkylation method. The data are in good agreement with measurements of the packing densities for alkylated surfaces formed through this technique, for Si-H free energies of formation, Delta G(H), corresponding to a reaction mechanism including the elimination of two H atoms and the formation of a C=C double bond in either unreacted alkyl Grignard groups or tetrahydrofuran solvent.     

Toward a mechanistic understanding of exciton-mediated hydrosilylation on nanocrystalline silicon

White-light initiated hydrosilylation of nanocrystalline porous silicon was found to be far more efficient (in terms of both kinetics and yield) in the presence of electron-accepting molecules with suitably high reduction potentials, particularly halocarbons. It is known that absorption of visible light by nanocrystalline silicon results in the formation of excitons (electron/hole pairs) and that this exciton can be harnessed to drive a hydrosilylation reaction with an alkene; the Si-C bond forms as a result of attack of the π-electrons of the alkene on the positively charged holes. In order to better understand the white-light initiated mechanism through which this reaction takes place, and to compare with UV-mediated photoemission on Si(111)-H, a series of electron acceptors were screened for their effect on surface alkene hydrosilylation. A very strong correlation between reduction potentials (E(red)) of the oxidant and reaction efficiency was observed, with a minimum "turn-on" E(red) required for an increase to take place. The oxidant appears to accept, or remove, the electron from the nanocrystallite-bound exciton, favoring attack by the alkene on the positively charged Si nanocrystallite, leading to Si-C bond formation. Radical reactions were discounted for a number of reasons, including lack of effect of radical traps, no apparent Si-Cl bond formation, lack of oxidation of the surfaces, and others. Unlike with other oxidants such as nitro-aromatics, halocarbons do not cause additional surface reactions and promote very clean, fast, and selective hydrosilylation chemistry.     

A non-oxidative approach toward chemically and electrochemically functionalizing Si(111)

A general method for the non-oxidative functionalization of single-crystal silicon(111) surfaces is described. The silicon surface is fully acetylenylated using two-step chlorination/alkylation chemistry. A benzoquinone-masked primary amine is attached to this surface via Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition ("click" chemistry). The benzoquinone is electrochemically reduced, resulting in quantitative cleavage of the molecule and exposing the amine terminus. Molecules presenting a carboxylic acid have been immobilized to the exposed amine sites. X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), cyclic voltammetry (CV), and contact angle goniometry were utilized to characterize and quantitate each step in the functionalization process. This work represents a strategy for providing a general platform that can incorporate organic and biological molecules on Si(111) with minimal oxidation of the silicon surface.     

Photochemical-controlled switching based on azobenzene monolayer modified silicon (111) surface

Azobenzene-containing compounds were covalently attached onto Si(111) surfaces via Si-O linkages using a two-step procedure. The modified Si(111) surfaces were characterized by X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FT-IR) spectroscopy measurements. The monolayer surface showed preferably chemical stability. Switchable photoisomerizability of azobenzene molecules on these modified surfaces was observed in response to alternating UV and visible light exposure. The measured conductivity showed distinct difference with trans and cis forms of azobenzene compounds on as-modified Si(111) surfaces.