Tyrosine derivatives assembled on gold

Two different tyrosine derivatives, one with the OH group free and one with the OH group phosphorylated, linked to 3-mercaptopropionic acid through an amide bond are adsorbed to gold surfaces. The adsorbates are studied by means of X-ray photoelectron spectroscopy (XPS) and infrared reflection-absorption spectroscopy (IRAS). The techniques are used to investigate the coordination to the surface and the molecular orientation of adsorbates relative to the surface. Molecular surface interactions, causing chemical shifts in the core level XPS spectra of the adsorbates on gold, are investigated using multilayer films as references. Angle-dependent XPS, XPS(theta), and IRAS are used to estimate molecular orientation relative to the surface. The tyrosine derivatives adsorb chemically to the surface through the sulfur atoms and highly organized monolayers are formed with the OH and the PO(2-)(3) exposed to the air/vacuum interface.     

Arg–Cys and Arg–cysteamine adsorbed on gold and the G-protein–adsorbate interaction

The dipeptide, Arg–Cys, and the related molecule, Arg–cysteamine, are adsorbed to gold surfaces and the monolayers are characterized. Chemical binding and electronic structure of the monolayers are obtained by X-ray photoelectron spectroscopy (XPS). Strong molecular binding of the adsorbates to gold surface through the sulfur atom is attained. Orientation of the adsorbates on gold is studied using infrared reflection absorption spectroscopy (IRAS). Arg–Cys is interpreted to be adsorbed on gold in a compact configuration. The Arg–cysteamine molecule is adsorbed on gold with the main molecular axis perpendicular to the surface. Interaction of G-protein with the adsorbates was studied using the surface plasmon resonance (SPR) technique. It is believed that arginine has a major role in G-protein recognition since the G-protein-coupled receptor (GPCR) ₂A has an arginine-rich region in the G-protein-binding part of the third intracellular loop.     

UPS, XPS, and NEXAFS study of self-assembly of standing 1,4-benzenedimethanethiol SAMs on gold

We report a study of the self-assembly of 1,4-benzenedimethanethiol monolayers on gold formed in n-hexane solution held at 60 °C for 30 min and in dark conditions. The valence band characteristics, the thickness of the layer, and the orientation of the molecules were analyzed at a synchrotron using high resolution photoelectron spectroscopy and near edge X-ray adsorption spectroscopy. These measurements unambiguously attest the formation of a single layer with molecules arranged in the upright position and presenting a free -SH group at the outer interface. Near edge X-ray absorption fine structure (NEXAFS) measurements suggest that the molecular axis is oriented at 24° with respect to the surface normal. In addition, valence band features could be successfully associated to specific molecular orbital contributions thanks to the comparison with theoretically calculated density of states projected on the different molecular units.     

Ionic hydrogen bonds controlling two-dimensional supramolecular systems at a metal surface

Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250-300 K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420 K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization.     

The electronic structure and adsorption geometry of L-histidine on Cu(110)

The adsorption of L-histidine on clean and oxygen-covered Cu(110) surfaces has been studied by soft X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The valence band spectra, carbon, nitrogen and oxygen 1 s XPS and N K edge absorption spectra were measured for submonolayer, monolayer, and multilayer films. The spectra provide a detailed picture of the electronic structure and adsorption geometry at each coverage. In the monolayer, the histidine molecules are randomly oriented, in contrast to the submonolayer regime, where the molecules are coordinated to the copper surface with the imidazole functional group nearly parallel to, and strongly interacting with, the surface. The pi*/sigma* intensity ratio in NEXAFS spectra at the nitrogen edge varies strongly with angle, showing the imidazole ring is oriented. Adsorption models are proposed.     

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.     

Molecular orientation of terephthalic acid assembly on epitaxial graphene: NEXAFS and XPS study

The adsorption of terephthalic acid molecules [C(6)H(4)(COOH)(2)), TPA] on a single layer of graphene grown epitaxially on Ni(111) has been investigated by means of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoelectron spectroscopy (XPS) at room temperature. The assignment of the NEXAFS resonances was aided by ab initio calculations for the free TPA molecule. For coverages up to a monolayer the molecular plane of TPA adopts a parallel orientation with regard to the epitaxial graphene (EG) layer. Deprotonation of TPA molecules at one monolayer coverage can be excluded. For TPA multilayers, the molecular plane is tilted on average by approximately 45° with respect to the sample surface.     

Metal ion interaction with phosphorylated tyrosine analogue monolayers on gold

Phosphorylated tyrosine analogue molecules (pTyr-PT) were assembled onto gold substrates, and the resulting monolayers were used for metal ion interaction studies. The monolayers were characterized by X-ray photoelectron spectroscopy (XPS), infrared reflection-absorption spectroscopy (IRAS), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS), both prior to and after exposure to metal ions. XPS verified the elemental composition of the molecular adsorbate and the presence of metal ions coordinated to the phosphate groups. Both the angle-dependent XPS and IRAS results were consistent with the change in the structural orientation of the pTyr-PT monolayer upon exposure to metal ions. The differential capacitance of the monolayers upon coordination of the metal ions was evaluated using EIS. These metal ions were found to significantly change the capacitance of the pTyr-PT monolayers in contrast to the nonphosphorylated tyrosine analogue (TPT). CV results showed reduced electrochemical blocking capabilities of the phosphorylated analogue monolayer when exposed to metal ions, supporting the change in the structure of the monolayer observed by XPS and IRAS. The largest change in the structure and interfacial capacitance was observed for aluminum ions, compared to calcium, magnesium, and chromium ions. This type of monolayer shows an excellent capability to coordinate metal ions and has a high potential for use as sensing layers in biochip applications to monitor the presence of metal ions.     

Self-assembled monolayers of benzylmercaptan and p-cyanobenzylmercaptan on Au(111) surfaces: structural and spectroscopic characterization

The formation of self-assembled monolayers of benzylmercaptan (BM) and p-cyanobenzylmercaptan (pCBM) on Au(111) surfaces is investigated by a combination of X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and scanning tunneling microscopy (STM). The NEXAFS results of pCBM are supported by ab initio calculations. It is found that BM as well as pCBM form well-ordered monolayers with the molecules oriented almost perpendicular to the surface. BM forms a ( radical 3 x radical 3)R30 degrees structure whereas pCBM forms a slightly different c(7 x 7) hexagonal structure. No phase separation is detected for the adsorption of a 1:1 mixture of the two molecules. The implications of the results for the covalent attachment of transition-metal complexes to thiol-functionalized surfaces are discussed.     

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.     

Surface structure and chemical switching of thioctic acid adsorbed on Au(111) as observed using near-edge X-ray absorption fine structure

Thioctic acid (alpha-lipoic acid) is a molecule with a large disulfide-containing base, a short alkyl chain with four CH2 units, and a carboxyl termination. Self-assembled monolayer (SAM) films ofthioctic acid adsorbed on Au(111) have been investigated with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoelectron spectroscopy (XPS) to determine film quality, bonding, and morphology. Using standard preparation protocols for SAMs, that is, dissolving thioctic acid in ethanol and exposing gold to the solution, results in poor films. These films are highly disordered, contain a mixture of carboxyl and carboxylate terminations, have more than monolayer coverage, and exhibit unbound disulfide. Conversely, forming films by dissolving 1 mmol thioctic acid into 5% acetic acid in ethanol (as previously reported with carboxyl-terminated alkanethiols) forms ordered monolayers with small amounts of unbound sulfur. NEXAFS indicates tilted over endgroups with the carboxyl group normal on average 38 degrees from the surface normal. Slight angle-dependent intensity modulations in other features indicate alkyl chains statistically more upright than prostrate on the surface. Reflection-absorption Fourier transform infrared (RA-FTIR) spectra indicate hydrogen bonding between neighboring molecules. In such well-formed monolayers, a stark reorientation occurs upon deprotonation of the endgroup by rinsing in a KOH solution. The carboxylate plane normal is now about 66 degrees from sample normal, a much more upright orientation. Data indicate this reorientation may also cause a more upright orientation to the alkyl portion of the molecules.     

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.     

Surface sensitive study to determine the reactivity of soot with the focus on the European emission standards IV and VI

Diesel soot (Euro IV and Euro VI) was investigated with spectroscopic methods such as near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoemission spectroscopy (XPS). C and O K-edge NEXAFS show that structural disorder on the surface is accompanied by a higher amount of oxygen functional groups. O K-edge NEXAFS and O1s XPS results are discussed with the aim to elucidate the nature of the oxygen surface species. The analysis of the data presented here allows the postulation of a hypothetical structure for soot samples emitted by diesel engines.     

Oriented growth of crystalline pentacene films with preferred a-b in-plane alignment on a rubbed crystalline polymethylene surface

We have achieved a growth of highly oriented crystalline pentacene thin films, with preferred a-b in-plane orientation with respect to the rubbing direction of a rubbed polymethylene surface. The polymethylene thin film, generated on a gold surface by gold-catalyzed decomposition of diazomethane, was annealed and gently rubbed in a fixed direction by a flannelette cloth to serve as an alignment layer during the deposition of pentacene molecules. Various surface analysis techniques, including reflection absorption IR spectroscopy (RAIRS), near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, grazing incidence X-ray diffraction (GIXD), and atomic force microscopy were used to elucidate the structural details of the polymethylene and the pentacene thin films deposited on it. Two crystalline morphologies of pentacene thin film were observed: the minor one of rod-like molecular crystals having their long axes of the crystals perpendicular to the rubbing direction, and the dominant one of platelet-like and layered crystals having the molecular axes stand near vertical to the surface. Moreover, GIXD revealed that the rubbing on polymethylene indeed induced a preferential azimuthal alignment of pentacene crystallites. The deposition of pentacene at 25 degrees C led to a twin growth of crystallites with the [110] direction predominately aligned perpendicular to the rubbing direction. In contrast, the pentacene deposition at 50 degrees C produced twinned crystallites of lower twin angle and the [120] direction aligned parallel to the rubbing direction.     

Self-assembled organic monolayers terminated in perfluoroalkyl pentafluoro-lambda(6)-sulfanyl (-SF5) chemistry on gold

Recently synthesized (Winter, R.; Nixon, P. G.; Gard, G. L.; Radford, D. H.; Holcomb, N. R.; Grainger, D. W. J. Fluorine Chem. 2001, 107, 23-30) SF5-terminated perfluoroalkyl thiols (SF5(CF2)nCH2CH2SH, where n = 2, 4, and 6) and a symmetric SF5-terminated dialkyl disulfide ([SF5-CH=CH-(CH2)8-S-]2) were assembled as thin films chemisorbed onto gold surfaces. The adsorbed monolayer films of these SF5-containing molecules on polycrystalline gold were compared using ellipsometry, contact angle, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and infrared spectroscopy (FTIR) surface analytical methods. The resulting SF5-dialkyl disulfide monolayer film shows moderate angle dependence in depth-dependent XPS analysis, suggesting a preferentially oriented film. The SF5-terminated perfluoroalkyl thiols exhibit angular-dependent XPS compositional variance depending on perfluoroalkyl chain length, consistent with improved film assembly (increasingly hydrophobic, fewer defects, and more vertical chain orientation increasing film thickness) with increasing chain length. Tof-SIMS measurements indicate that both full parent ions for these film-forming molecules and the unique SF5 terminal group are readily detectable from the thin films without substantial contamination from other adsorbates.     

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.     

Adlayers of dimannoside thiols on gold: surface chemical analysis

Carbohydrate films on gold based on dimannoside thiols (DMT) were prepared, and a complementary surface chemical analysis was performed in detail by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), near-edge X-ray absorption fine structure (NEXAFS), FT-IR, and contact angle measurements in order to verify formation of ω-carbohydrate-functionalized alkylthiol films. XPS (C 1s, O 1s, and S 2p) reveals information on carbohydrate specific alkoxy (C-O) and acetal moieties (O-C-O) as well as thiolate species attached to gold. Angle-resolved synchrotron XPS was used for chemical speciation at ultimate surface sensitivity. Angle-resolved XPS analysis suggests the presence of an excess top layer composed of unbound sulfur components combined with alkyl moieties. Further support for DMT attachment on Au is given by ToF-SIMS and FT-IR analysis. Carbon and oxygen K-edge NEXAFS spectra were interpreted by applying the building block model supported by comparison to data of 1-undecanethiol, poly(vinyl alcohol), and polyoxymethylene. No linear dichroism effect was observed in the angle-resolved C K-edge NEXAFS.     

Effect of chain length and substrate temperature on the growth and morphology of n-alkane thin films

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and microscopy has been used to study the orientational morphology of thin films of the linear alkanes n-C36H74 and n-C60H122, prepared by vacuum deposition onto NaCl (001) surfaces at ambient and elevated substrate temperatures. The orientational morphology, specifically, the nature of domains with lateral and normal orientation, is explored as a function of the chain length and the substrate temperature. It is found that the longer n-C60H122 molecules are laterally oriented on the substrate surface within the investigated substrate temperatures but that the morphology of these thin films varies with substrate temperature. The shorter n-C36H74 molecules are partially laterally oriented at low substrate temperature and are completely normally oriented at high substrate temperature. The relative magnitude of "side-by-side" and "end-to-end" intermolecular interactions leads to the formation of highly ordered alkane structures with a high aspect ratio. The formation of complex, nanoscale orientational morphologies are rationalized by considering kinetic and thermodynamic effects, in particular, the relative enthalpic and entropic contributions to the free energy associated with the different molecular orientations.     

Adsorption and orientation kinetics of self‐assembled films of octadecyltrimethoxysilane on aluminium oxide surfaces

X‐ray photoelectron spectroscopy (XPS) and near‐edge x‐ray absorption fine structure (NEXAFS) spectroscopy have been used to study the time‐dependent adsorption and molecular orientation behaviour of octadecyltrimethoxysilane (ODTMS) on native aluminium oxide surfaces. By measuring the adsorption isotherm using XPS, we show that ODTMS molecules exhibit oscillatory adsorption. The oscillatory adsorption behaviour for ODTMS is analogous to that observed for its simpler short‐chain ‘cousin’—propyltrimethoxysilane (PTMS)—and suggests that the length of the functional alkyl chain on an organosilane does not have a significant influence upon the oscillatory adsorption mechanism. The oscillation in the ODTMS adsorption isotherm shows a maximum and a minimum in coverage at an adsorption time of ～30 and ～65 s, respectively, for a 0.75% ODTMS solution in a 90% ethanol–10% water mixture at pH 4. The time‐dependent orientation behaviour of the ODTMS molecules during adsorption was examined using angular‐dependent carbon K‐edge NEXAFS spectroscopy. We show that the alignment of the ODTMS film changes systematically with deposition time and appears to be correlated with coverage measurements obtained using XPS. In particular, by combining the XPS and NEXAFS results we demonstrate that the minimum ODTMS coverage corresponds to a film whose alignment appears to be predominantly randomized. Copyright © 2005 John Wiley & Sons, Ltd.     

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.