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Adsorption and film growth of deoxyribonucleic acid (DNA) base molecules (cytosine, guanine, thymine, and adenine) on Si(111)7×7 have been studied by combining X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). Multiple tautomeric forms and keto-enol tautomerization are revealed by the O 1s, N 1s, and C 1s XPS spectra of the O-containing DNA bases: cytosine, guanine, and thymine. While the carbonyl group-containing keto tautomer is more stable in a thick film and in powder, the hydroxyl group-containing enol tautomer is found at the interface. The keto-enol tautomerization, as induced by the reactive Si(111)7×7 surface, leads to the formation of a conjugated aromatic six-membered ring with a delocalized π electron system and to the consequent [4 + 2]-like cycloaddition between the enol tautomer and the 7×7 surface. The DFT calculation suggests that the enol tautomer exhibits a kinetic advantage over the keto one for the [4 + 2]-like cycloaddition. Among the several plausible pathways for the cycloaddition provided by the enol tautomer, the experimentally determined one involves a ring N and ring C atom (a polar pair), rather than two ring C atoms (a nonpolar pair), to better match the polar Si adatom-restatom pair of the 7×7 surface. Furthermore, the reacted ring C atom does not have any attached terminal functional group (e.g., -NH2 and -OH). Further deposition leads to continuous film growth in the keto tautomeric form for cytosine and guanine. For the only O-free DNA base molecule, adenine, dative bonding N → Si, rather than the [4 + 2]-like cycloaddition, is observed on the 7×7 surface. Of the four DNA base molecules, adenine is also the only one with its aromaticity maintained when adsorbed on the Si(111)7×7 surface. A reactive surface like the 7×7 surface could therefore provide a new control to trigger tautomerization that is often associated with genetic mutation.

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The interaction of cysteine molecules with the Si(111)-√3×√3-Ag surface has been investigated over the submonolayer to multilayer regime using X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations. With both upper step and lower step terraces, step edges, and antiphase boundaries, the √3×√3-Ag overlayer supported on Si(111) provides a rich two-dimensional template for studying site-specific biomolecular interactions. As an amino acid with three functional groups, cysteine is found to chemisorb through S-H bond cleavage and S-Ag bond linkage first at step edges and antiphase boundaries followed by island formation and expanded growth onto terraces. Intermolecular interactions are dominated by zwitterionic hydrogen bonding at higher coverages, producing a porous unordered interfacial layer composed of cysteine agglomerates at room temperature. Upon annealing, cysteine adsorbates induce structural transformation of the uniform √3×√3-Ag reconstructed surface lattice into metallic Ag clusters with a narrow size distribution and short-range ordering. Preferential nanoaggregate formation of cysteine at defect sites and cysteine-induced metal cluster formation promise a new approach to fabricating nanoclusters for potential applications in chemical sensing and catalysis.

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Surface functionalization of an inorganic surface with bio-organic molecules is often aimed at creating a "permanent" bio-organic surface with receptor functional groups. We show here that L-cysteine can be used to transform a highly reactive Si(111)7×7 surface to not just a permanent bio-organic surface but also a semipermanent (or renewable) and a temporary bio-organic surfaces by manipulating the exposure. In the early growth stage, the strong bonding between the first cysteine adlayer and the Si substrate through Si-N or Si-S linkages in unidentate or bidentate arrangement provides permanent biofunctionalization by this interfacial layer. This interfacial layer can be used to build a transitional layer (second adlayer) mediated by interlayer vertical hydrogen bonding between an amino group and a carboxylic acid group. Further exposure of cysteine eventually leads to a zwitterionic multilayer film involving electrostatic interactions between cation (-NH3(+)) and anion moieties (-COO(-)). The interlayer hydrogen bonding therefore provides temporary trapping of bio-organic molecules as the second transitional layer that is stable up to 175 °C. This transitional layer can be easily removed by annealing above this temperature and then regenerated with the same molecular layer or a different one by "renewing" the interlayer hydrogen bonds. We also illustrate coverage-dependent adsorption structures of cysteine, from bidentate to unidentate attachments and to self-assembled multimers, involving formation of intralayer horizontal N···H-O hydrogen bonds, by combining our X-ray photoemission data with the local density-of-state images obtained by scanning tunnelling microscopy.

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The interaction of the Li-ion battery solvent ethylene carbonate (EC) with Cu(111) was investigated by scanning tunnelling microscopy (STM) and variable temperature X-ray photoelectron spectroscopy (XPS) under ultrahigh vacuum (UHV) conditions. Between 80 and 420 K, the decomposition of EC occurs along with distinct structural and chemical changes of the adlayer.

RESUMEN

The interaction between an adsorbed 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [BMP][TFSA], ionic liquid (IL) layer and a Ag(111) substrate, under ultrahigh-vacuum conditions, was investigated in a combined experimental and theoretical approach, by high-resolution scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and dispersion-corrected density functional theory calculations (DFT-D). Most importantly, we succeeded in unambiguously identifying cations and anions in the adlayer by comparing experimental images with submolecular resolution and simulated STM images based on DFT calculations, and these findings are in perfect agreement with the 1:1 ratio of anions and cations adsorbed on the metal derived from XPS measurements. Different adlayer phases include a mobile 2D liquid phase at room temperature and two 2D solid phases at around 100 K, i.e., a 2D glass phase with short-range order and some residual, but very limited mobility and a long-range ordered 2D crystalline phase. The mobility in the different adlayer phases, including melting of the 2D crystalline phase, was evaluated by dynamic STM imaging. The DFT-D calculations show that the interaction with the substrate is composed of mainly van der Waals and weak electrostatic (dipole-induced dipole) interactions and that upon adsorption most of the charge remains at the IL, leading to attractive electrostatic interactions between the adsorbed species.