Binding of glycine and L-cysteine on Si(111)-7 x 7

The adsorption of glycine and l-cysteine on Si(111)-7 x 7 was investigated using high-resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS). The observation of the characteristic vibrational modes and electronic structures of NH3+ and COO- groups for physisorbed glycine (l-cysteine) demonstrates the formation of zwitterionic species in multilayers. For chemisorbed molecules, the appearance of nu(Si-H), nu(Si-O), and nu(C=Omicron) and the absence of nu(O-H) clearly indicate that glycine and l-cysteine dissociate to produce monodentate carboxylate adducts on Si(111)-7 x 7. XPS results further verified the coexistence of two chemisorption states for each amino acid, corresponding to a Si-NH-CH2-COO-Si [Si-NHCH(CH2SH)COO-Si] species with new sigma-linkages of Si-N and Si-O, and a NH2-CH2-COO-Si [NH2CH(CH2SH)COO-Si] product through the cleavage of the O-H bond, respectively. Glycine/Si(111)-7 x 7 and l-cysteine/Si(111)-7 x 7 can be viewed as model systems for further modification of Si surfaces with biological molecules.     

Ultrahigh vacuum deposition of L-cysteine on Au(110) studied by high-resolution X-ray photoemission: from early stages of adsorption to molecular organization

We report on a high-resolution X-ray photoemission spectroscopy study on molecular-thick layers of L-cysteine deposited under ultrahigh vacuum conditions on Au(110). The analysis of core level shifts allowed us to distinguish unambiguously the states of the first-layer molecules from those of molecules belonging to the second layer. The first-layer molecules strongly interact with the metal through their sulfur headgroup. The multipeaked structure of the N 1s, O 1s, and C 1s core levels is interpreted in terms of different molecular moieties. The neutral acidic fraction (HSCH2CH(NH2)COOH) is abundant at low coverage likely associated with isolated molecules or dimers. The zwitterionic phase (HSCH2CH(NH3+)COO-) is largely dominant as the coverage approaches the monolayer limit and is related to the formation of ordered self-assembled molecular structures indicated by electron diffraction patterns. The occurrence of a small amount of cationic molecules (HSCH2CH(NH3+)COOH) is also discussed. The second-layer molecules mainly display zwitterionic character and are weakly adsorbed. Mild annealing up to 100 degrees C leads to the desorption of the second-layer molecules leaving electronic states of the first layer unaltered.     

Local hydration environments of amino acids and dipeptides studied by X-ray spectroscopy of liquid microjets

The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s --> sigma(NH) preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s --> pi(CN) resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the alpha amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.     

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.     

Ultrathin chromium oxide films on the W(100) surface

Ultrathin chromium oxide films were prepared on a W(100) surface under ultrahigh-vacuum conditions and investigated in situ by X-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and low-energy electron diffraction. The results show that, at Cr coverage of less than 1 monolayer, CrO2 is formed by oxidizing pre-deposited Cr at 300-320 K in approximately 10(-7) mbar oxygen. However, an increase of temperature causes formation of Cr2O3. At Cr coverage above 1 monolayer, only Cr2O3 is detected.     

Surface chemistry of CN bond formation from carbon and nitrogen atoms on Pt(111)

The mechanism of CN bond formation from CH3 and NH3 fragments adsorbed on Pt(111) was investigated with reflection absorption infrared spectroscopy (RAIRS), temperature-programmed desorption (TPD), and X-ray photoelectron spectroscopy (XPS). The surface chemistry of carbon-nitrogen coupling is of fundamental importance to catalytic processes such as the industrial-scale synthesis of HCN from CH4 and NH3 over Pt. Since neither CH4 nor NH3 thermally dissociate on Pt(111) under ultrahigh vacuum (UHV) conditions, the relevant surface intermediates were generated through the thermal decomposition of CH3I and the electron-induced dissociation of NH3. The presence of surface CN is detected with TPD through HCN desorption as well as with RAIRS through the appearance of the vibrational features characteristic of the aminocarbyne (CNH2) species, which is formed upon hydrogenation of surface CN at 300 K. The RAIRS results show that HCN desorption at approximately 500 K is kinetically limited by the formation of the CN bond at this temperature. High coverages of Cads suppress CN formation, but the results are not influenced by the coadsorbed I atoms. Cyanide formation is also observed from the reaction of adsorbed N atoms and carbon produced from the dissociation of ethylene.     

Well-ordered self-assembled monolayers created via vapor-phase reactions on a monolayer template

The reaction of vapor-phase alkyl isocyanates (O=C=N-(CH2)n-1CH3) with OH-terminated alkanethiol template monolayers on Au produces well-organized self-assembled monolayers, containing intrachain carbamate linkages (Au/S(CH2)16O(C=O)NH(CH2)n-1CH3, where n = 1-8, 11, and 12). X-ray photoelectron spectroscopy, contact angle goniometry, and reflection absorption infrared spectroscopy suggest that the template surface completely reacts with the isocyanates yielding a monolayer that contains an interchain hydrogen-bonded carbamate network. Spectroscopic data indicates that the alkyl underlayer remains well ordered following reaction with the isocyanates. The order of the overlayer and the hydrogen-bonding interactions between adjacent chains increase as a function of the alkyl isocyanate chain length, n. The overlayer appears to be well ordered for n > or = 5.     

Reactivity induced at 25 K by low-energy electron irradiation of condensed NH3-CH3COOD (1 : 1) mixture

Chemical reactivity is observed following electron irradiation of a binary mixture of ammonia (NH(3)) and acetic acid (CH(3)COOD) at 25 K, without any subsequent thermal activation, as evidenced by vibrational high resolution electron energy loss spectroscopy (HREELS). Analysis of the HREEL spectra and comparison with infrared and Raman data of different molecules are compatible with glycine formation in its zwitterionic form. The onset for electron induced reaction is found to be at about approximately 13 eV. The mechanisms may involve NH radicals interaction with CH(3)COOD molecules. Then glycine formation does not imply any displacement of reactants, so that it involves only NH(3) and CH(3)COOD neighboring molecules.     

Structural study of NO adsorbed on the reconstructed Pt(110)-(1 x 2) surface with X-ray photoelectron diffraction and near-edge X-ray absorption fine structure spectroscopy

The adsorption structure of NO on the reconstructed Pt(110)-(1 x 2) surface was studied with X-ray photoelectron spectroscopy (XPS), X-ray photoelectron diffraction (XPD), low-energy scanned-angle photoelectron diffraction (LESA-PD), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The experiments were performed at 180 K, where no surface lifting from (1 x 2) to (1 x 1) takes place after NO adsorption. XPS indicates that the (1 x 2) unit cell of the Pt(110) surface contains 1.5 NO molecules at the saturated coverage. XPD and LESA-PD analyses allow us to propose a structural model for the NO adlayer, where two-thirds of the NO molecules in the (1 x 2) unit cell are adsorbed on the atop site of the close-packed Pt rows (ridges) along the [10] direction with an inclined geometry and one-third of the NO molecules adsorb on the bridge site between the Pt ridges with an upright configuration. This model is supported by the N K-edge NEXAFS experiments and is consistent with the recently reported model based on the density functional theory (Orita, H.; Nakamura, I.; Fujitani, T. J. Phys. Chem. B 2005, 109, 10312).     

Sulfate-enhanced catalytic destruction of 1,1,1-trichlorethane over Pt(111)

The catalytic destruction of 1,1,1-trichloroethane (TCA) over model sulfated Pt(111) surfaces has been investigated by fast X-ray photoelectron spectroscopy and mass spectrometry. TCA adsorbs molecularly over SO4 precovered Pt(111) at 100 K, with a saturation coverage of 0.4 monolayer (ML) comparable to that on the bare surface. Surface crowding perturbs both TCA and SO4 species within the mixed adlayer, evidenced by strong, coverage-dependent C 1s and Cl and S 2p core-level shifts. TCA undergoes complete dechlorination above 170 K, accompanied by C-C bond cleavage to form surface CH3, CO, and Cl moieties. These in turn react between 170 and 350 K to evolve gaseous CO2, C2H6, and H2O. Subsequent CH3 dehydrogenation and combustion occurs between 350 and 450 K, again liberating CO2 and water. Combustion is accompanied by SO4 reduction, with the coincident evolution of gas phase SO2 and CO2 suggesting the formation of a CO-SOx surface complex. Reactively formed HCl desorbs in a single state at 400 K. Only trace (<0.06 ML) residual atomic carbon and chlorine remain on the surface by 500 K.     

Metal aminocarboxylate coordination polymers with chain and layered structures

The synthesis and structures of metal aminocarboxylates prepared in acidic, neutral, or alkaline media have been explored with the purpose of isolating coordination polymers with linear chain and two-dimensional layered structures. Metal glycinates of the formulae [CoCl2(H2O)2(CO2CH2NH3)] (I), [MnCl2(CO2CH2NH3)2] (II), and [Cd3Cl6(CO2CH2NH3)4] (III) with one-dimensional chain structures have been obtained by the reaction of the metal salts with glycine in an acidic medium under hydro/solvothermal conditions. These chain compounds contain glycine in the zwitterionic form. 4-Aminobutyric acid transforms to a cyclic amide under such reaction conditions, and the amide forms a chain compound of the formula [CdBr2(C4H7NO)2] (IV). Glycine in the zwitterionic form also forms a two-dimensional layered compound of the formula [Mn(H2O)2(CO2CH2NH3)2]Br2 (V). 6-Aminocaproic acid under alkaline conditions forms layered compounds with metals at room temperature, the metal being coordinated both by the amino nitrogen and the carboxyl oxygen atoms. Of the two layered compounds [Cd{CO2(CH2)5NH2}2]2 H2O (VI) and [Cu{CO2(CH2)5NH2}2]2 H2O (VII), the latter has voids in which water molecules reside.     

Determination of the electron affinity of the acetyloxyl radical (CH3COO) by low-temperature anion photoelectron spectroscopy and ab initio calculations

The electronic structure and electron affinity of the acetyloxyl radical (CH3COO) were investigated by low-temperature anion photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of the acetate anion (CH3COO-) were obtained at two photon energies (355 and 266 nm) and under three different temperatures (300, 70, and 20 K) with use of a new low-temperature ion-trap photoelectron spectroscopy apparatus. In contrast to a featureless spectrum at 300 K, a well-resolved vibrational progression corresponding to the OCO bending mode was observed at low temperatures in the 355 nm spectrum, yielding an accurate electron affinity for the acetyloxyl radical as 3.250 +/- 0.010 eV. This experimental result is supported by ab initio calculations, which also indicate three low-lying electronic states observed in the 266 nm spectrum. The calculations suggest a 19 degrees decrease of the OCO angle upon detaching an electron from acetate, consistent with the vibrational progression observed experimentally.     

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.     

NH3 adsorption and decomposition on Ir(110): a combined temperature programmed desorption and high resolution fast x-ray photoelectron spectroscopy study

The adsorption and decomposition of NH3 on Ir(110) has been studied in the temperature range from 80 K to 700 K. By using high-energy resolution x-ray photoelectron spectroscopy it is possible to distinguish chemically different surface species. At low temperature a NH3 multilayer, which desorbs at approximately 110 K, was observed. The second layer of NH3 molecules desorbs around 140 K, in a separate desorption peak. Chemisorbed NH3 desorbs in steps from the surface and several desorption peaks are observed between 200 and 400 K. A part of the NH3ad decomposes into NH(ad) between 225 and 300 K. NH(ad) decomposes into N(ad) between 400 K and 500 K and the hydrogen released in this process immediately desorbs. N2 desorption takes place between 500 and 700 K via N(ad) combination. The steady state decomposition reaction of NH3 starts at 500 K. The maximum reaction rate is observed between 540 K and 610 K. A model is presented to explain the occurrence of a maximum in the reaction rate. Hydrogenation of N(ad) below 400 K results in NH(ad). No NH2ad or NH3ad/NH3 were observed. The hydrogenation of NH(ad) only takes place above 400 K. On the basis of the experimental findings an energy scheme is presented to account for the observations.     

Interactions of L-alanine with alumina as studied by vibrational spectroscopy

The interactions of L-alanine with gamma- and alpha-alumina have been investigated by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). L-alanine/alumina samples were dried from aqueous suspensions, at 36.5 degrees C, with two amino acid concentrations (0.4 and 0.8 mmol g-1) and at different pH values (1, 6, and 13). The vibrational spectra proved that the nature of L-alanine interactions with both aluminas is the same (hydrogen bonding), although the groups involved depend on the L-alanine form and on alumina surface groups, both controlled by the pH. For samples prepared at pH 1, cationic L-alanine [CH3CH(NH3+)COOH] displaces physisorbed water from alumina, and strong hydrogen bonds are established between the carbonyl groups of alanine, as electron donors, and the surface Al-OH2+ groups of alumina. This occurs at the expense of alanine dimer dissociation and breaking of intramolecular bonds. When samples are prepared at pH 6, the interacting groups are Al-OH2+ and the carboxylate groups of zwitterionic L-alanine [CH3CH(NH3+)COO-]. The affinity of L-alanine toward alumina decreases, as the strong NH3+...-OOC intermolecular hydrogen bonds prevail over the interactions with alumina. Thus, for a load of 0.8 mmol g-1, phase segregation is observed. On alpha-alumina, crystal deposition is even observed for a load of 0.4 mmol g-1. At pH 13, the carboxylate groups of anionic L-alanine [CH3CH(NH2)COO-] are not affected by alumina. Instead, hydrogen bond interactions occur between NH2 and the Al-OH surface groups of the substrate. Complementary N2 adsorption-desorption isotherms showed that adsorption of L-alanine occurs onto the alumina pore network for samples prepared at pH 1 and 13, whereas at pH 6 the amino acid/alumina interactions are not strong enough to promote adsorption. The mesoporous structure and the high specific surface area of gamma-alumina make it a more efficient substrate for adsorption of L-alanine. For each alumina, however, it is the nature of the specific interactions and not the porosity of the substrate that determines the adsorption process.     

Glycine-ice nanolayers: morphology and surface energetics

Ultrathin glycine-ice films (nanolayers) have been prepared in ultrahigh vacuum by condensation of H(2)O and glycine at 110 K and 150 K on single crystalline Al(2)O(3) surfaces and have been investigated by temperature programed thermal desorption, x-ray photoelectron spectroscopy, and work function measurements. Various layer architectures have been considered, including glycine-on-ice, ice-on-glycine, and mixed glycine-ice nanolayers. Low coverages of adsorbed glycine molecules on amorphous ice surfaces suppress the amorphous-to-crystalline phase transition in the temperature range 140-160 K in near-surface regions and consequently lead to a lower desorption temperature of H(2)O molecules than from pure ice layers. Thicker glycine overlayers on ice provide a kinetic restriction to H(2)O desorption from the underlying ice layers until the glycine molecules become mobile and develop pathways for water desorption at higher temperature (>170 K). Ice overlayers do not wet glycine film surfaces, but the glycine molecules on ice are sufficiently immobile at 110 K, so that continuous glycine overlayers form. In mixed glycine-ice nanolayers the glycine phase displays hydrophobic behavior and a phase separation takes place, with the accumulation of glycine near the surfaces of the films.     

The infrared spectrum of solid L-alanine: influence of pH-induced structural changes

The influence of the pH on the infrared spectrum of L-alanine has been analyzed by diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The amino acid was precipitated from aqueous solutions and dried at 36.5 degrees C, in order to stabilize cationic L-alanine or alaninium [CH3CH(NH3(+))COOH] at pH 1, the zwitterionic form [CH3CH(NH3(+))COO(-)] at pH 6, and anionic L-alanine or alaninate [CH3CH(NH2)COO(-)] at pH 13. New insight on the specific inter and intramolecular interactions in the different forms of L-alanine was reached by a novel methodological approach: an infrared technique not used before to analyze solid amino acid samples (DRIFTS), in combination with a detailed analysis based on spectral deconvolution. The frequency ranges of interest include the carbonyl/carboxyl stretching and amine deformation modes and the OH/NH stretching modes. It was shown that intermolecular hydrogen bonds between the NH3(+) and COO(-) groups are predominant in the zwitterionic form, whereas in cationic L-alanine, H bonds between the COOH groups are responsible for the formation of dimers. In anionic L-alanine, only strong electrostatic interactions between the COO(-) groups and Na(+) ions are proposed, evidencing the relevant role of the counterion.     

Structure, morphology and interface properties of ultrathin SnTTBPP(OH)2-films adsorbed on Ag(100)

The molecular interaction of dihydroxo[5,10,15,20-tetrakis(4-tert-butyl-phenyl)porphyrinato]-tin(IV) (SnTTBPP(OH)(2)), the structural order and growth of ultrathin films on Ag(100) have been studied by means of low-energy electron diffraction (LEED) and synchrotron based photoelectron spectroscopy, i.e., X-ray photoemission (XPS) and near-edge X-ray absorption fine structure (NEXAFS/XANES) spectroscopy. For the first time, monolayer adsorption of a metalloporphyrin with octahedral coordination of the metal center by two additional axial hydroxo ligands is investigated in a multi-technique study. The delicate balance of molecule-substrate interactions and intermolecular interactions leads to the formation of a densely-packed organic monolayer which is commensurate with the Ag(100) substrate. From NEXAFS linear dichroism an almost coplanar orientation of the porphyrin system is derived. XPS and NEXAFS clearly indicate that the axial hydroxo ligands are cleaved in monolayer films, i.e., upon adsorption to the Ag substrate. With increasing film thickness orientational order gets lost and leads to polycrystalline growth for thicker films as confirmed by scanning X-ray transmission microscopy (STXM).     

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.