Density functional theory study of one-dimensional growth of styrene on the hydrogen-terminated Si(001)-(3 x 1) surface

Recent experimental work has shown that the addition of styrene molecules to hydrogen-terminated Si(001) surfaces leads to the formation of one-dimensional molecular structures through a radical-initiated surface chain reaction mechanism. These nanometric structures are observed to be directed parallel to the dimer rows on the H-Si(001)-(2 x 1) surface and perpendicular to the same rows on H-Si(001)-(3 x 1). Using periodic density functional theory (DFT) calculations, we have studied the initial steps of the radical chain mechanism on the H-Si(001)-(3 x 1) surface and compared them to analogous results for H-Si(001)-(2 x 1). On the H-Si(001)-(3 x 1) surface, one of the crucial steps of the surface chain reaction, namely, the abstraction of a H atom from a nearby surface hydride unit, is found to have a somewhat smaller activation energy in the direction perpendicular to the dimer rows (H abstraction from the nearest dihydride site) than along the rows (H abstraction from a neighboring dimer). Additionally, due to the steric repulsion between the styrene molecules and the SiH2 subunits, growth along the dimer rows is not thermodynamically favorable on the (3 x 1) surface. On the other hand, due to the absence of the SiH2 subunits, growth parallel to the Si dimer rows becomes favored on the H-Si(001)-(2 x 1) surface.     

Self-directed growth of contiguous perpendicular molecular lines on H-Si(100) surfaces

Future nanoscale integrated circuits will require the realization of interconnections using molecular-scale nanostructures; a practical fabrication scheme would need to be largely self-assembling and operate on a large number of like structures in parallel. The self-directed growth of organic molecules on hydrogen-terminated silicon(100) [H-Si(100)] offers a simple method of realizing one-dimensional molecular lines. In this work, we introduce the ability to change the growth direction and form more complex, contiguous shapes. Numerous styrene and trimethylene sulfide L shapes were grown on a H-Si(100)-3x1 surface in parallel with no intermediate surface lithography steps, and similar shapes were also grown using allyl mercaptan and benzaldehyde on H-Si(100)-2x1. Registered scanning tunneling microscopy (STM) images and high-resolution electron energy loss spectroscopy (HREELS) were used to investigate the growth process.     

Controlled fabrication of 1D molecular lines across the dimer rows on the Si(100)-(2 x 1)-H surface through the radical chain reaction

Current interest in the fabrication of organic nanostructures on silicon surface is focused on the self-directed growth of 1D molecular lines with predefined position, structure, composition, and the length on the H-terminated Si(100)-(2 x 1) surface. To date, no studies have succeeded in growing the molecular line across the dimer rows on Si(100)-(2 x 1)-H, which is highly desirable. Using scanning tunneling microscopy (STM), we studied a new molecular system (allyl mercaptan, CH2=CH-CH2-SH) that undergoes chain reaction across the dimer row on the Si(100)-(2 x 1)-H surface at 300 K and produces covalently bonded 1D molecular lines. In combination with the previous findings of chain reaction along the rows, the present observations of self-directed growth of 1D molecular lines across the dimer rows on the Si(100)-(2 x 1)-H surface provide a means to connect any two points (through molecular lines) on a 2D surface.     

Self-directed growth of benzonitrile line on H-terminated Si(001) surface

Using first-principles density-functional calculations we predict a self-directed growth of benzonitrile molecular line on a H-terminated Si(001) surface. The C[triple bond]N bond of benzonitrile reacts with a single Si dangling bond which can be generated by the removal of a H atom, forming one Si-N bond and one C radical. Subsequently, the produced C radical can be stabilized by abstracting a H atom from a neighboring Si dimer, creating another H-empty site. This H-abstraction process whose activation barrier is 0.65 eV sets off a chain reaction to grow one-dimensional benzonitrile line along the Si dimer row. Our calculated energy profile for formation of the benzonitrile line shows its relatively easier formation compared with previously reported styrene and vinylferrocene lines.     

Self-directed chain reaction by small ketones with the dangling bond site on the Si(100)-(2 x 1)-H surface: acetophenone, a unique example

Using scanning tunneling microscope (STM) at 300 K, we studied the growth of one-dimensional molecular assemblies (molecular lines) on the Si(100)-(2 x 1)-H surface through the chain reaction of small ketone (CH 3COCH 3, PhCOPh, and PhCOCH 3) molecules with dangling bond (DB) sites of the substrate. Acetone and benzophenone show the growth of molecular lines exclusively parallel to the dimer row direction. In contrast, acetophenone molecules show some molecular lines perpendicular, in addition to parallel, to the dimer row direction. Most of the molecular lines perpendicular to the dimer row direction were grown by self-turning the propagation direction of a chain reaction from parallel to perpendicular directions relative to the dimer row. A chiral center created upon adsorption of an acetophenone molecule allows the adsorbed molecules to align with identical as well as alternate enantiomeric forms along the dimer row direction, whereas such variations in molecular arrangement are not observed in the case of acetone and benzophenone molecules. The observed molecular lines growth both parallel and perpendicular to dimer row directions appears to be unique to acetophenone among all the molecules studied to date. Hence, the present study opens new possibility for fabricating one-dimensional molecular assemblies of various compositions in both high-symmetry directions on the Si(100)-(2 x 1)-H surface.     

X-ray studies of self-assembled organic monolayers grown on hydrogen-terminated Si(111)

The structure of self-assembled monolayers (SAMs) of undecylenic acid methyl ester (SAM-1) and undec-10-enoic acid 2-bromo-ethyl ester (SAM-2) grown on hydrogen-passivated Si(111) were studied by X-ray reflectivity (XRR), X-ray standing waves (XSW), X-ray fluorescence (XRF), atomic force microscopy, and X-ray photoelectron spectroscopy (XPS). The two different SAMs were grown by immersion of H-Si(111) substrates into the two different concentrated esters. UV irradiation during immersion was used to create Si dangling bond sites that act as initiators of the surface free-radical addition process that leads to film growth. The XRR structural analysis reveals that the molecules of SAM-1 and SAM-2 respectively have area densities corresponding to 50% and 57% of the density of Si(111) surface dangling bonds and produce films with less than 4 angstroms root-mean-square roughness that have layer thicknesses of 12.2 and 13.2 angstroms. Considering the molecular lengths, these thicknesses correspond to a 38 degrees and 23 degrees tilt angle for the respective molecules. For SAM-2/Si(111) samples, XRF analysis reveals a 0.58 monolayer (ML) Br total coverage. Single-crystal Bragg diffraction XSW analysis reveals (unexpectedly) that 0.48 ML of these Br atoms are at a Si(111) lattice position height that is identical to the T1 site that was previously found by XSW analysis for Br adsorbed onto Si(111) from a methanol solution and from ultrahigh vacuum. From the combined XPS, XRR, XRF, and XSW evidence, it is concluded that Br abstraction by reactive surface dangling bonds competes with olefin addition to the surface.     

Formation of uniform ferrocenyl-terminated monolayer covalently bonded to Si using reaction of hydrogen-terminated Si(111) surface with vinylferrocene/n-decane solution by visible-light excitation

Electrochemically active self-assembled monolayers (SAM) have been successfully fabricated with atomic-scale uniformity on a silicon (Si)(111) surface by immobilizing vinylferrocene (VFC) molecules through Si-C covalent bonds. The reaction of VFC with the hydrogen-terminated Si (H-Si)(111) surface was photochemically promoted by irradiation of visible light on a H-Si(111) substrate immersed in n-decane solution of VFC. We found that aggregation and polymerization of VFC was avoided when n-decane was used as a solvent. Voltammetric quantification revealed that the surface density of ferrocenyl groups was 1.4×10(-10) mol cm(-2), i.e., 11% in substitution rate of Si-H bond. VFC-SAMs were then formed by the optimized preparation method on n-type and p-type Si wafers. VFC-SAM on n-type Si showed positive photo-responsivity, while VFC-SAM on p-type Si showed negative photo-responsivity.     

Selective chain reaction of acetone leading to the successive growth of mutually perpendicular molecular lines on the si(100)-(2 x 1)-H surface

The successive growth of mutually perpendicular molecular lines from one dangling-bond (DB) site on the Si(100)-(2 x 1)-H surface has been realized through a substrate-mediated chain reaction at 300 K. Among various molecules, acetone molecules undergo the most facile chain reaction with a DB site, which proceeds selectively on the Si(100)-(2 x 1)-H surface, resulting in only single molecular lines in the parallel-row (parallel to the dimer row) direction. The smaller size and higher reactivity of acetone molecules enable us to successively grow a parallel-row acetone line from the end of a cross-row (perpendicular to the dimer row) allylmercaptan line simply by changing the feed of gas molecules into the reaction chamber. Since the length of a molecular line is controlled by the number of gas molecules impinged, it is possible to turn a chain reaction from the cross-row direction to the parallel-row direction at any desired point on the surface. The reaction path of the adsorbing molecules is discussed. The present study provides a new means of fabricating mutually perpendicular molecular lines through a chain reaction initiating at a preselected DB site on the Si(100)-(2 x 1) surface.     

In-situ FTIR studies on self-assembled monolayers of surfactant molecules adsorbed on H-terminated Si(111) surfaces in aqueous solutions

The adsorption of a surfactant, sodium di-2-ethylhexyl sulfosuccinate (SDES), [C4H9CH(C2H5)CH2OCO][C4H9CH(C2H5)CH2OCOCH2]CHSO3- Na+, in an aqueous solution on an atomically flat H-terminated Si(111) [abbreviated as H-Si(111)] surface with a hydrophobic property was investigated by in-situ FTIR measurements. Immersion of the H-Si(111) surface in a solution of 1.0 x 10(-2) M SDES for more than 2 h led to formation of a self-assembled monolayer (SAM) with the alkyl chains having a tendency to be assembled perpendicular to the Si surface. The in-situ FTIR observation revealed that the adsorption was nearly complete about 60 min after the start of the immersion, and after that the adsorbed molecules changed their arrangement into an ordered mode. The Si-H peak in the FTIR spectrum remained unchanged with time in aqueous surfactant solution, in contrast to the case of immersion in pure water, indicating that the adsorbed surfactant protects the H-Si(111) surface from oxidation. No structural change in the SAM was observed when a negative potential of -700 mV vs Ag/AgCl was applied to the Si, whereas the adsorbed molecules changed their arrangement, accompanied by their substantial desorption and oxidation of the Si surface, when a positive potential of +700 mV was applied.     

Two bonding configurations of acetylene on Si(001)-(2 x 1): a combined high-resolution electron energy loss spectroscopy and density functional theory study

Two coexisting adsorption states of molecularly adsorbed acetylene on the Si(001)-(2 x 1) surface have been identified by a combined study based on the high-resolution electron energy loss spectroscopy and density functional computations. Seven possible adsorbate-substrate structures are considered theoretically including their full vibrational analysis. Based on a significantly enhanced experimental resolution, the assignment of 15 C2H2- and C2D2-derived vibrational modes identifies a dominant di-sigma bonded molecule adsorbed on top of a single Si-Si dimer. Additionally there is clear evidence for a second minority species which is di-sigma bonded between two Si-Si dimers within the same dimer row (end-bridge geometry). The possible symmetries of the adsorbate complexes are discussed based on the specular and off-specular vibrational measurements. They suggest lower than ideal C(2v) and C(s) symmetries for on-top and end-bridge species, respectively. At low coverages the symmetry reductions might be lifted.     

Chemisorption of barrelene on Si(100) from first principles calculations

The chemisorption of C8H8 bicyclo[2.2.2]-2,5,7-octatriene (barrelene) on the Si(100) surface is studied from first principles calculations. We find that, in the most stable configuration, barrelene is bonded to Si(100) through four Si-C bonds, with the C-C bonds which are orthogonal to the underlying Si dimers. The chemisorption reaction responsible for this structure is driven by the biradical nature of the Si-Si dimer bond. Two others, slightly less stable configurations, exist which are also characterized by four Si-C bonds but have a different orientation or location with respect to the Si(100) surface. The properties of these and other, less stable configurations have been investigated. For the most stable structures, the effect of different surface coverages has been also studied, showing a tendency to easily form complete monolayers of barrelene on the Si surface. On the basis of energetic and kinetic considerations, we expect that chemisorption of barrelene monolayers on the Si(100) surface will be characterized however by a certain amount of disorder. Finally, several possible reaction pathways, leading from one stable structure to another of lower energy or from a molecule in the gas phase to a chemisorbed configuration, have been investigated in detail and estimates of the relative energy barriers are given.     

Competing forward and reversed chain reactions in one-dimensional molecular line growth on the Si(100)-(2 x 1)-H surface

To explore the role of competing forward and reversed chain reactions in the growth of a one-dimensional (1D) molecular line on the Si(100)-(2 x 1)-H surface, controlled experiments were performed with various alkene molecules by scanning tunneling microscopy (STM) at various temperatures. It was observed that the end dangling bond (DB) of a styrene line, fabricated by a chain reaction on the Si(100)-(2 x 1)-H surface at 300 K, initiated a reverse chain reaction at 400 K, leading to the complete disappearance of the styrene line with zero-order desorption kinetics (rate constant k = 1.17 x 10-2 s-1 at 400 K). In the case of 2,4-dimethylstyrene, the reversed chain reaction was observed even at 300 K. These results suggest that the appearance of a molecular line in an STM image is determined by the rates of competing forward and reversed chain reactions at a given temperature. As predicted, 1D lines formed by the DB-initiated chain reaction of 1-hexene and 1-heptene on Si(100)-(2 x 1)-H were observed at 180 K because of the reduced desorption rate, despite the fact that those molecules showed no line growth at 300 K. These results indicate that the scope of forming 1D molecular lines on the Si(100)-(2 x 1)-H surface with various alkenes is much wider than anticipated in previous studies.     

Molecular simulation of alkyl monolayers on the Si(lll) surface

The structure of twelve-carbon monolayers on the H-terminated Si(111) surface is investigated by molecular simulation method. The best substitution percent on Si(111) surface obtained via molecular mechanics calculation is equal to 50%, and the (8 ε 8) simulated cell can be used to depict the structure of alkyl monolayer on Si surface. After two-dimensional cell containing alkyl chains and four-layer Si(111) crystal at the substitution 50% is constructed, the densely packed and well-ordered monolayer on Si(111) surface can be shown through energy minimization in the suitable-size simulation cell. These simulation results are in good agreement with the experiments. These conclusions show that molecular simulation can provide otherwise inaccessible mesoscopic information at the molecular level, and can be considered as an adjunct to experiments.     

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.     

Indirect adsorbate-adsorbate interactions mediated through the surface electronic structure of the Si(100) surface

Indirect adsorbate-adsorbate interactions between adsorbed ammonia (NH3) molecules on the Si(100) surface are investigated using density functional theory. Two different nonlocal effects mediated through the surface electronic structure are observed: "poisoning" and hydrogen bonding. We find that adsorbed NH3 "poisons" adsorption of NH3 on neighboring Si dimers on the same side of the dimer row whereas neighboring NH2(a) groups favor this configuration. Adsorption of NH3 involves charge transfer to the surface that localizes on neighboring Si dimer atoms, preventing adsorption of NH3 at these sites. These indirect interactions are similar to Friedel-type interactions observed on metal surfaces with an estimated range of less than 7.8 A on the Si(100) surface. These interactions may be manipulated to construct local ordering of the adsorbates on the surface.     

Molecular simulation of alkyl monolayers on the Si(111)surface

The structure of twelve-carbon monolayers on the H-terminated Si(111) surface is investigated by molecular simulation method. The best substitution percent on Si(111) surface obtained via molecular mechanics calculation is equal to 50%, and the (8×8) simulated cell can be used to depict the structure of alkyl monolayer on Si surface. After two-dimensional cell containing alkyl chains and four-layer Si(111) crystal at the substitution 50% is constructed, the densely packed and well-ordered monolayer on Si(111) surface can be shown through energy minimization in the suitable-size simulation cell. These simulation results are in good agreement with the experiments. These conclusions show that molecular simulation can provide otherwise inaccessible mesoscopic information at the molecular level, and can be considered as an adjunct to experiments.     

Vibrational characterization of different benzene phases on flat and vicinal Si(100) surfaces

Based on high-resolution electron energy loss spectroscopy and temperature-programmable desorption, benzene chemisorption on vicinal and nominally flat Si(100) surfaces has been studied for various adsorption, annealing, and site blocking treatments. Three different chemisorbed benzene (C6H6 and C6D6) phases with distinct thermal desorption characteristics and different vibrational spectra have been separated and characterized on both substrates. All three phases are identified as 1,4-cyclohexadiene-like structures with butterfly geometry. Whereas the dominant phase is di-sigma bonded to the two Si atoms of a single Si-Si dimer, the benzene orientation (double bond orientation) in the other phases is rotated. Di-sigma bonding to Si atoms of adjacent Si-Si dimer for the latter cases is most likely. Coverage and temperature dependent conversions between the different phases have been addressed by vibrational spectroscopy.     

Linear nanostructure formation of aldehydes by self-directed growth on hydrogen-terminated silicon(100)

The self-directed growth of organic molecules on silicon surfaces allows for the rapid, parallel production of hybrid organic-silicon nanostructures. In this work, the formation of benzaldehyde- and acetaldehyde-derived nanostructures on hydrogen-terminated H-Si(100)-2x1 surface is studied by scanning tunneling microscopy in ultrahigh vacuum and by quantum mechanical methods. The reaction is a radical-mediated process that binds the aldehydes, through a strong Si-O covalent bond, to the surface. The aldehyde nanostructures are generally composed of double lines of molecules. Two mechanisms that lead to double line growth are elucidated.     

Facet-dependent lithium intercalation into Si crystals: Si(100) vs. Si(111)

Fast Li transport in battery electrodes is essential to meeting the demanding requirements for a high-rate capability anode. We studied the intercalation of a Li atom into the surface and subsurface layers of Si(100) and Si(111) using density functional calculations with a slab representation of the surfaces. We suggest that the Li atom migrates on the Si surfaces and is subsequently inserted into the inside for both Si(100) and Si(111). The rate-determining steps are the surface incorporation and subsurface diffusion in Si(100) and Si(111), respectively. Our diffusion rate calculations reveal that, once the Li atom is incorporated into the Si surface, Li diffuses faster by at least two orders of magnitude along the <100> direction than along the <111> direction. The importance of careful treatment of the slab thickness for the study of impurity insertion into subsurface layers is also stressed.     

Molecular simulation of alkyl monolayers on the Si(111) surface YUAN

The preparation of monolayers on silicon surface is of growing interest for potential applica-tions in biosensor or semiconductor technology[1—5]. The alkyl modified Si(111) surfaces[6—10] can be obtained using the thermal, catalyzed, or photochemical reaction of hydrogen-terminated sili-con with alkenes, Grignard reagents, and so on. At the same time, the monolayer properties on Si(111) surface have been studied by a variety of experimental methods[8—10] such as X-ray photo-electron spect…