Dipole-induced structure in aromatic-terminated self-assembled monolayers: a study by near edge x-ray absorption fine structure spectroscopy

The structure of self-assembled monolayers presenting aromatic rings at a surface is studied by near edge x-ray absorption fine structure spectroscopy (NEXAFS). Fluorine substitution at asymmetric positions in the aromatic rings is used to generate a layer of dipoles at the surface of the monolayer. We find that fluorine substituted aromatic rings are more ordered than unsubstituted aromatic rings by a factor of two based on the polarization dependence of the lowest C 1s to pi* transition, which is associated with transitions from phenyl carbons attached to hydrogens. This result is consistent with the influence of dipole-dipole interactions and quadrupolar interactions between the aromatic groups due to the substitution of fluorine atoms. The work also serves to illustrate how subtle variations in the orientation of an end group of a self-assembled monolayer can be determined by using NEXAFS.     

Orientation of pentacene molecules on SiO2: from a monolayer to the bulk

Near edge x-ray absorption fine structure (NEXAFS) spectroscopy is used to study the orientation of pentacene molecules within thin films on SiO2 for thicknesses ranging from monolayers to the bulk (150 nm). The spectra exhibit a strong polarization dependence of the pi* orbitals for all films, which indicates that the pentacene molecules are highly oriented. At all film thicknesses the orientation varies with the rate at which pentacene molecules are deposited, with faster rates favoring a thin film phase with different tilt angles and slower rates leading to a more bulklike orientation. Our NEXAFS results extend previous structural observations to the monolayer regime and to lower deposition rates. The NEXAFS results match crystallographic data if a finite distribution of the molecular orientations is included. Damage to the molecules by hot electrons from soft x-ray irradiation eliminates the splitting between nonequivalent pi* orbitals, indicating a breakup of the pentacene molecule.     

Self-assembled monolayers of peptide nucleic acids on gold surfaces: a spectroscopic study

We have characterized self-assembled monolayers (SAMs) of thiol-derivatized peptide nucleic acid (PNA) chains adsorbed on gold surfaces by using reflection absorption infrared spectroscopy (RAIRS) and X-ray photoemission spectroscopy (XPS) techniques. We have found that the molecular orientation of PNAs strongly depends on surface coverage. At low coverage, PNA chains lie flat on the surface, while at high coverage, PNA molecules realign their molecular axes with the surface normal and form SAMs without the need of co-immobilization of spacers or other adjuvant molecules. The change in the molecular orientation has been studied by infrared spectroscopy and it has been confirmed by atomic force microscopy (AFM). PNA immobilization has been followed by analyzing the N(1s) XPS core-level peak. We show that the fine line shape of the N(1s) core-level peak at optimal concentration for biosensing is due to a chemical shift. A combination of the above-mentioned techniques allow us to affirm that the structure of the SAMs is stabilized by molecule-molecule interactions through noncomplementary adjacent nucleic bases.     

Self-assembled carbon nanotubes on gold: polarization-modulated infrared reflection-absorption spectroscopy, high-resolution X-ray photoemission spectroscopy, and near-edge X-ray absorption fine structure spectroscopy study

Recently we reported noncovalent functionalization of nanotubes in an aqueous medium with ionic liquid-based surfactants, 1-dodecyl-3-methylimidazolium bromide (1) and 1-(12-mercaptododecyl)-3-methylimidazolium bromide (2), resulting in positively charged single-wall carbon nanotube (SWNT)-1,2 composites. Thiolation of SWNTs with 2 provides their self-assembly on gold as well as templating gold nanoparticles on SWNT sidewalls via a covalent -S-Au bond. In this investigation, we studied the electronic structure, intermolecular interactions, and packing within noncovalently thiolated SWNTs and also nanotube alignment in the bulk of SWNT-2 dried droplets and self-assembled submonolayers (SAMs) on gold by high-resolution X-ray photoemission spectroscopy (HRXPS), C K-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS). HRXPS data confirmed the noncovalent nature of interactions within the nanocomposite of thiolated nanotubes. In PM-IRRAS spectra of SWNT SAMs on gold, the IR-active vibrational SWNT modes have been observed and identified. According to PM-IRRAS data, the hydrocarbon chains of 2 are oriented with less tilt angle to the bare gold normal in a SAM deposited from an SWNT-2 dispersion than those of 1 deposited from an SWNT-1 dispersion on the mercaptoethanesulfonic acid-primed gold. For both the dried SWNT-2 bulk and the SWNT-2 SAM on gold, the C K-edge NEXAFS spectra revealed the presence of CH-pi interactions between hydrocarbon chains of 2 and the pi electronic nanotube structure due to the highly resolved vibronic fine structure of carbon 1s --> R*/sigma*C-H series of states in the alkyl chain of 2. For the SWNT-2 bulk, the observed splitting and upshift of the SWNT pi* orbitals in the NEXAFS spectrum indicated the presence of pi-pi interactions. In the NEXAFS spectrum of the SWNT-2 SAM on gold, the upshifted values of the photon energy for R*/sigma*C-H transitions indicated close contact of 2 with nanotubes and with a gold surface. The angle-dependent NEXAFS for the SWNT-2 bulk showed that most of the molecules of 2 are aligned along the nanotubes, which are self-organized with orientation parallel to the substrate plane, whereas the NEXAFS for the SWNT-2 SAM revealed a more normal orientation of functionality 2 on gold compared with that in the SWNT-2 bulk.     

Thermal and mechanical aging of self-assembled monolayers as studied by near edge X-ray absorption fine structure

Self-assembled monolayers (SAMs) enable significant changes in the surface energy and/or specific interactions of surfaces, which are desirable for microelectromechanical systems (MEMS), superhydrophobic coatings, sensors, and other applications. However, SAMs often exhibit poor durability and rapid degradation upon mechanical, thermal, or moisture exposure. The chemical and orientational changes in SAMs due to mechanical and thermal degradation were investigated using near-edge X-ray absorption fine structure (NEXAFS) and the water contact angle. SAMs were based on unfluorinated or fluorinated linear hydrocarbons that form highly oriented and densely packed structures on silicon substrates. Complex chemical and orientational changes were observed via NEXAFS following degradation. Under heating in a dry, oxygen-rich environment, unfluorinated SAMs tended to cleave at C-C bonds on the main chain; below 250 °C, CH(3) groups were sequentially cleaved toward the surface, whereas above 250 °C, remaining hydrocarbon groups were converted to a graphitic coating dominated by C═C bonds. Under similar conditions, fluorinated SAMs began their chemical degradation at 350 °C and above, although the orientation decreased steadily from 150 to 300 °C; at and above 350 °C, the preferential removal of F occurred and the SAM was slowly converted to a graphitic layer. By contrast, under vacuum the fluorinated molecules were very thermally stable, showing good stability up to 550 °C; when degradation occurred, entire molecules were removed. Mechanical degradation followed two routes; both unfluorinated and fluorinated SAMs that were mechanically rubbed with smooth surfaces exhibited severe chemical degradation of the molecules, leading to an amorphous and poorly defined layer with C═C, C-C, C-H, and C-F bonds. Unfluorinated and fluorinated surfaces that were mechanically rubbed in the presence of free silicon particulates showed the rapid and complete destruction of both the molecular orientation and the protective SAM layer, even for short exposure periods. The resulting NEXAFS spectra were very similar to those produced by heating to 550 °C, suggesting that the friction created by granular particles may lead to extreme local heating.     

Effect of ring substitution position on the structural conformation of mercaptobenzoic acid self-assembled monolayers on Au(111)

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, photoemission spectroscopy (PES), and contact angle measurements have been used to examine the structure and bonding of self-assembled monolayers (SAMs) prepared on Au(111) from the positional isomers of mercaptobenzoic acid (MBA). The isomer of MBA and solvent chosen in SAM preparation has considerable bearing upon film morphology. Carbon K-edge NEXAFS measurements indicate that the monomers of 2-, 3-, and 4-MBA have well-defined orientations within their respective SAMs. Monomers of 3- and 4-MBA assume an upright orientation on the Au substrates in monolayers prepared using an acetic acid in ethanol solvent. The aryl ring and carboxyl group of these molecules are tilted from the surface normal by a colatitudal angle of approximately 30 degrees . Preparation of 4-MBA SAMs using pure ethanol solvent, a more traditional means of synthesis, had no appreciable effect upon the monomer orientation. Nonetheless, S(2p) PES measurements illustrate that it results in extensive bilayer formation via carboxyl group hydrogen-bonding between 4-MBA monomers. In 2-MBA monolayers prepared using acetic acid/ethanol solvent, the monomers adopt a more prostrate orientation on the Au substrates, in which the aryl ring and carboxyl group of the molecules are tilted approximately 50 degrees from the surface normal. This configuration is consistent with an interaction between both the mercaptan sulfur and carboxyl group of 2-MBA with the underlying substrate. S(2p) and C(1s) PES experiments provide supporting evidence for a bidentate interaction between 2-MBA and Au(111).     

Near-edge X-ray absorption fine structure spectroscopy of diamondoid thiol monolayers on gold

Diamondoids, hydrocarbon molecules with cubic-diamond-cage structures, have unique properties with potential value for nanotechnology. The availability and ability to selectively functionalize this special class of nanodiamond materials opens new possibilities for surface modification, for high-efficiency field emitters in molecular electronics, as seed crystals for diamond growth, or as robust mechanical coatings. The properties of self-assembled monolayers (SAMs) of diamondoids are thus of fundamental interest for a variety of emerging applications. This paper presents the effects of thiol substitution position and polymantane order on diamondoid SAMs on gold using near-edge X-ray absorption fine structure spectroscopy (NEXAFS) and X-ray photoelectron spectroscopy (XPS). A framework to determine both molecular tilt and twist through NEXAFS is presented and reveals highly ordered diamondoid SAMs, with the molecular orientation controlled by the thiol location. C 1s and S 2p binding energies are lower in adamantane thiol than alkane thiols on gold by 0.67 +/- 0.05 and 0.16 +/- 0.04 eV, respectively. These binding energies vary with diamondoid monolayer structure and thiol substitution position, consistent with different degrees of steric strain and electronic interaction with the substrate. This work demonstrates control over the assembly, in particular the orientational and electronic structure, providing a flexible design of surface properties with this exciting new class of diamond nanoparticles.     

Imaging the binding ability of proteins immobilized on surfaces with different orientations by using liquid crystals

We report an investigation of the binding ability of a protein immobilized on surfaces with different orientations but in identical interfacial microenvironments. The surfaces present mixed self-assembled monolayers (SAMs) of 11-[19-carboxymethylhexa(ethylene glycol)]undecyl-1-thiol, 1, and 11-tetra(ethylene glycol) undecyl-1-thiol, 2. Whereas 2 is used to define an interfacial microenvironment that prevents nonspecific adsorption of proteins, 1 was activated by two different schemes to immobilize ribonuclease A (RNase A) in either a preferred orientation or random orientations. The binding of the ribonuclease inhibitor protein (RI) to RNase A on these surfaces was characterized by using ellipsometry and the orientational behavior of liquid crystals. Ellipsometric measurements indicate identical extents of immobilization of RNase A via the two schemes. Following incubation of both surfaces with RI, however, ellipsometric measurements indicate a 4-fold higher binding ability of the RNase A immobilized with a preferred orientation over RNase A immobilized with a random orientation. The higher binding ability of the oriented RNase A over the randomly oriented RNase A was also apparent in the orientational behavior of nematic liquid crystals of 4-cyano-4'-pentylcyanobiphenyl (5CB) overlayed on these surfaces. These results demonstrate that the orientations of proteins covalently immobilized in controlled interfacial microenvironments can influence the binding activities of the immobilized proteins. Results reported in this article also demonstrate that the orientational states of proteins immobilized at surfaces can be distinguished by examining the optical appearances of liquid crystals.     

Photocontrolled On‐Surface Pseudorotaxane Formation with Well‐Ordered Macrocycle Multilayers

The photoinduced pseudorotaxane formation between a photoresponsive axle and a tetralactam macrocycle was investigated in solution and on glass surfaces with immobilized multilayers of macrocycles. In the course of this reaction, a novel photoswitchable binding station with azobenzene as the photoswitchable unit and diketopiperazine as the binding station was synthesized and studied by NMR and UV/Vis spectroscopy. Glass surfaces have been functionalized with pyridine‐terminated SAMs and subsequently with multilayers of macrocycles through layer‐by‐layer self assembly. A preferred orientation of the macrocycles could be confirmed by NEXAFS spectroscopy. The photocontrolled deposition of the axle into the surface‐bound macrocycle‐multilayers was monitored by UV/Vis spectroscopy and led to an increase of the molecular order, as indicated by more substantial linear dichroism effects in angle‐resolved NEXAFS spectra.     

Self-assembly of alkanols on Au(111) surfaces

Self-assembled monolayers (SAMs) of alkanols (1-C(N)H(2N+1)OH) with varying carbon-chain lengths (N = 10-30) have been systematically studied by means of scanning tunneling microscopy (STM) at the interfaces between alkanol solutions (or liquids) and Au(111) surfaces. The carbon skeletons were found to lie flat on the surfaces. This orientation is consistent with SAMs of alkanols on highly oriented pyrolytic graphite (HOPG) and MoS2 surfaces, and also with alkanes on reconstructed Au(111) surfaces. This result differs from a prior report, which claimed that 1-decanol molecules (N = 10) stood on their ends with the OH polar groups facing the gold substrate. Compared to alkanes, the replacement of one terminal CH3 group with an OH group introduces new bonding features for alkanols owing to the feasibility of forming hydrogen bonds. While SAMs of long-chain alkanols (N > 18) resemble those of alkanes, in which the aliphatic chains make a greater contribution, hydrogen bonding plays a more important role in the formation of SAMs of short-chain alkanols. Thus, in addition to the titled lamellar structure, a herringbone-like structure, seldom seen in SAMs of alkanes, is dominant in alkanol SAMs for values of N < 18. The odd-even effect present in alkane SAMs is also present in alkanol SAMs. Thus, the odd N alkanols (alkanols with an odd number of carbon atoms) adopt perpendicular lamellar structures owing to the favorable interactions of the CH3 terminal groups, similar to the result observed for odd alkanes. In contrast to alkanes on Au(111) surfaces, for which no SAMs on an unreconstructed gold substrate were observed, alkanols are capable of forming SAMs on either the reconstructed or the unreconstructed gold surfaces. Structural models for the packing of alkanol molecules on Au(111) surfaces have been proposed, which successfully explain these experimental observations.     

Tailoring the Cu(100) work function by substituted benzenethiolate self-assembled monolayers

The structure and electronic interface properties of five differently substituted benzenethiol based self-assembled monolayers (SAMs) on Cu(100) have been studied by means of low energy electron diffraction, thermal desorption spectroscopy, X-ray absorption spectroscopy (NEXAFS), and UV photoelectron spectroscopy. Because highly ordered SAMs are formed of which lateral density had been precisely determined, effective molecular dipole moments were derived from the measured work function shifts. These values are compared with gas phase dipole moments computed by quantum chemical calculations for the individual thiol molecules considering the molecular orientation determined from NEXAFS data. Furthermore, this comparison yields clear evidence for a coverage dependent depolarization effect of the adsorbed molecules within the SAMs.     

DNA-modified electrodes; part 4: optimization of covalent immobilization of DNA on self-assembled monolayers

The covalent immobilization of DNA onto self-assembled monolayer (SAM) modified gold electrodes (SAM/Au) was studied by X-ray photoelectron spectrometry and electrochemical method so as to optimize its covalent immobilization on SAMs. Three types of SAMs with hydroxyl, amino, and carboxyl terminal groups, respectively, were examined. Results obtained by both X-ray photoelectron spectrometry and cyclic voltammetry show that the largest covalent immobilization amount of dsDNA could be gained on hydroxyl-terminated SAM/Au. The ratio of amount of dsDNA immobilized on hydroxyl-terminated SAMs to that on carboxyl-terminated SAMs and to that on amino-terminated SAMs is (3-3.5): (1-1.5): 1. The dsDNA immobilized covalently on hydroxyl-terminated SAMs accounts for 82.8-87.6% of its total surface amount (including small amount of dsDNA adsorbed). So the hydroxyl-terminated SAM is a good substrate for the covalent immobilization of dsDNA on gold surfaces.     

Second-order nonlinear optical properties of the Ag(111)/electrolyte interface in the presence of self-assembled monolayers containing conjugated pi systems. I. Alpha-functionalized terthiophene films on Ag(111)

The nonlinear optical properties of self-assembled monolayers obtained from bonding two different alpha-functionalized terthiophenes (alpha-T3) to (111) silver electrode surfaces have been investigated using second harmonic generation (SHG). The two (alpha-T3) compounds used were functionalized with alkane chains of different lengths (C8 and C4), and each was terminated with a thiol anchoring group. A nitrile group was attached to the terminal thiophene ring of the (alpha-T3) compound with the C4 chain. The orientation of the polarization of the incident beam was changed systematically and gradually between "p" and "s" orientation and the SH signal (isotropic and anisotropic contributions) analyzed in both directions ("P" and "S"). The symmetry of the system was reduced by the presence of the adlayers from C3v to C3. The dependence on the applied potential and the incident wavelength has also been studied. The relative magnitudes and phases of the various second-order tensor elements have been estimated and compared with the values for a bare surface. A resonance process in the (alpha-T3) pi moiety has been investigated, and from this, the effective "band-gap" energies of the organic semiconductor SAMs (i.e., the energy difference between the pi-pi bands) have been estimated.     

The reaction of tetrakis(dimethylamido)titanium with self-assembled alkyltrichlorosilane monolayers possessing -OH, -NH2, and -CH3 terminal groups

The reactions of tetrakis(dimethylamido)titanium, Ti[N(CH(3))(2)](4), with alkyltrichlorosilane self-assembled monolayers (SAMs) terminated by -OH, -NH(2), and -CH(3) groups have been investigated with X-ray photoelectron spectroscopy (XPS). For comparison, a chemically oxidized Si surface, which serves as the starting point for formation of the SAMs, has also been investigated. In this work, we examined the kinetics of adsorption, the spatial extent, and stoichiometry of the reaction. Chemically oxidized Si has been found to be the most reactive surface examined here, followed by the -OH, -NH(2), and -CH(3) terminated SAMs, in that order. On all surfaces, the reaction of Ti[N(CH(3))(2)](4) was relatively facile, as evidenced by a rather weak dependence of the initial reaction probability on substrate temperature (T(s) = -50 to 110 degrees C), and adsorption could be described by first-order Langmuirian kinetics. The use of angle-resolved XPS demonstrated clearly that the anomalous reactivity of the -CH(3) terminated SAM could be attributed to reaction of Ti[N(CH(3))(2)](4) at the SAM/SiO(2) interface. Reaction on the -NH(2) terminated SAM proved to be the "cleanest", where essentially all of the reactivity could be associated with the terminal amine group. In this case, we found that approximately one Ti[N(CH(3))(2)](4) adsorbed per two SAM molecules. On all surfaces, there was significant loss of the N(CH(3))(2) ligand, particularly at high substrate temperatures, T(s) = 110 degrees C. These results show for the first time that it is possible to attach a transition metal coordination complex from the vapor phase to a surface with an appropriately functionalized self-assembled monolayer.     

Molecular orientation of evaporated pentacene films on gold: alignment effect of self-assembled monolayer

Pentacene films deposited on self-assembled monolayers (SAMs) bearing different terminal functional groups have been studied by reflection-absorption IR, grazing angle XRD, NEXAFS, AFM, and SEM analyses. A film with pentacene molecules nearly perpendicularly oriented was observed on Au surfaces covered with an SAM of alkanethiol derivative of X-(CH2)(n)-SH, with X = -CH(3), -COOH, -OH, -CN, -NH(2), C(60), or an aromatic thiol p-terphenylmethanethiol. On the other hand, a film with the pentacene molecular plane nearly parallel to the substrate surface was found on bare Au surface. A similar molecular orientation was found in thinner ( approximately 5 nm) and thicker (100 nm) deposited films. Films deposited on different surfaces exhibit distinct morphologies: with apparently smaller and rod-shaped grains on clean bare Au surface but larger and islandlike crystals on SAM-modified surfaces. X-ray photoemission electron microscopy (X-PEEM) was used to analyze the orientation of pentacene molecules deposited on a SAM-patterned Au surface. With the micro-NEXAFS spectra and PEEM image analysis, the microarea-selective orientation control on Au was characterized. The ability to control the packing orientation in organic molecular crystals is of great interest in fabricating organic field effect transistors because of the anisotropic nature of charge transport in organic semiconducting materials.     

Side-chain liquid crystalline polysiloxanes containing a cyanohydrin chiral centre

A number of new ferroelectric side chain liquid crystal homopolymers derived from poly(hydromethylsiloxane), their copolymers with different mesogens and with poly(dimethylsiloxane) backbones have been prepared. The transition temperatures of the monomers, homo and copolymers have been determined. The homopolymers exhibit S*_C and N* phases, while copolymers show only a S*_C phase. A measured spontaneous polarization value of monomer, 9b, is larger than 500 nC cm^-2.     

Intermixed terpyridine-functionalized monolayers on gold: nonlinear relationship between terpyridyl density and metal ion coordination properties

Aiming at the functionalization of surfaces with terpyridine anchors for the coordinative deposition of additional layers, mixed self-assembled monolayers (SAMs) were prepared from binary solutions of 12-(2,2':6',2″-terpyridine-4'-yl)dodecane-1-thiol (TDT) and 1-decanethiol (DT). The SAMs and the order of the constituting molecules were analyzed by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and time-of-flight-secondary ion mass spectrometry (ToF-SIMS). The composition of the (TDT/DT)-SAMs and with it the surface density of terpyridyl groups correlates linearly with the relative concentrations of the two compounds in the solution used for depositing them. In marked contrast, the amount of terpyridine-coordinated Pd(II) ions significantly deviates from this trend with an optimum at a 1:3 ratio of TDT/DT. This indicates a major fraction of the terpyridines in TDT-rich SAMs not to be accessible for Pd(II) ion coordination. In agreement, NEXAFS spectroscopy reveals the alkyl backbones in TDT-rich SAMs not to be ordered, while they are preferentially upright oriented in the optimal 1:3-(TDT/DT)-SAMs. We interpret this in terms of terpyridine backfolding in TDT-rich SAMs, while they are located in accessible positions on top of the SAM in the 1:3-(TDT/DT)-SAM. While the alkyl backbones in the 1:3-(TDT/DT)-SAM are ordered, NEXAFS spectroscopy shows the terpyridyl groups not to have a preferential orientation in this SAM and thus retain enough flexibility to adjust to molecules that are deposited on top of the mixed SAM. In conclusion, the novel SAM does not undergo phase separation and consists predominantly of intermixed phases with adjustable surface density of quite flexible terpyridine anchor groups. The terpyridine-Pd(II) anchors are not only available for a future deposition of the next layer, but the metal ions also represent a sensitive probe for the accessibility of the terpyridyl groups.     

Commensurate solid-solid phase transitions in self-assembled monolayers of alkylthiolates lying on metal surfaces

A temperature-induced commensurate solid-solid phase transition in self-assembled monolayers (SAMs) of alkylthiolates lying on Pt(111) is predicted from molecular dynamics simulations based on ab initio potential energy surfaces. As the system cools down from room temperature to low enough temperature, SAMs of alkylthiolates with more than ～12 carbon atoms undergo an abrupt change of orientation from a nearly upright to a tilted configuration. As the initial hexagonal arrangement of the sulfur headgroups is kept fixed during the simulations, the phase transition is entirely governed by chain-chain interactions. Similar commensurate phase transitions are predicted for hexagonally arranged SAMs with lattice spacings of the order of 4.7-4.9 ?, which, among others, excludes the well-known cases of densely packed SAMs of alkylthiolates on Au(111) and Ag(111). These findings could be relevant for the design of novel electronic or optical devices controllable by temperature.