Direct Imaging of Hydrogen Bond Formation in Dissociative Adsorption of Glycine on Si(111)7×7 by Scanning Tunneling Microscopy

Chatterjee, Avisek; Zhang, L.; Leung, K. T.

doi:10.1021/jp300011k

Cited by 9 publications

(15 citation statements)

References 37 publications

(62 reference statements)

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“…STM data for the other proteinogenic biomolecules have also been reported. 33,51,52 Evidently, the two bright protrusions marked by an oval in the upper image of Figure 2d1 corresponds to the flat cysteine dimolecular structure within a half unit cell (Figure 2a3), while that in the lower image of Figure 2d1 corresponds to the tilted dimolecular structure across the dimer wall (Figure 2b3). Similarly, the dark depression marked by an oval in the upper image of Figure 2d2 corresponds to the flat methionine dimolecular structure across the dimer wall (Figure 2a4), while the bright protrusions of the three-point star in the lower image of Figure 2d2 shows a novel methionine trimer structure within a half unit cell.…”

Section: Biomolecules In the Gas Phasementioning

confidence: 98%

Surface-Mediated Hydrogen Bonding of Proteinogenic α-Amino Acids on Silicon

2016

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Understanding the adsorption, film growth mechanisms, and hydrogen bonding interactions of biological molecules on semiconductor surfaces has attracted much recent attention because of their applications in biosensors, biocompatible materials, and biomolecule-based electronic devices. One of the most challenging questions when studying the behavior of biomolecules on a metal or semiconductor surface is "What are the driving forces and film growth mechanisms for biomolecular adsorption on these surfaces?" Despite a large volume of work on self-assembly of amino acids on single-crystal metal surfaces, semiconductor surfaces offer more direct surface-mediated interactions and processes with biomolecules. This is due to their directional surface dangling bonds that could significantly perturb hydrogen bonding arrangements. For all the proteinogenic biomolecules studied to date, our group has observed that they generally follow a "universal" three-stage growth process on Si(111)7×7 surface. This is supported by corroborating data obtained from a three-pronged approach of combining chemical-state information provided by X-ray photoelectron spectroscopy (XPS) and the site-specific local density-of-state images obtained by scanning tunneling microscopy (STM) with large-scale quantum mechanical modeling based on the density functional theory with van der Waals corrections (DFT-D2). Indeed, this three-stage growth process on the 7×7 surface has been observed for small benchmark biomolecules, including glycine (the simplest nonchiral amino acid), alanine (the simplest chiral amino acid), cysteine (the smallest amino acid with a thiol group), and glycylglycine (the smallest (di)peptide of glycine). Its universality is further validated here for the other sulfur-containing proteinogenic amino acid, methionine. We use methionine as an example of prototypical proteinogenic amino acids to illustrate this surface-mediated process. This type of growth begins with the formation of a covalent-bond driven interfacial layer (first adlayer), followed by that of a transitional layer driven by interlayer and intralayer hydrogen bonding (second adlayer), and then finally the zwitterionic multilayers (with intralayer hydrogen bonding). The important role of surface-mediated hydrogen bonding as the key for this universal three-stage growth process is demonstrated. This finding provides new insight into biomolecule-semiconductor surface interactions often found in biosensors and biomolecular electronic devices. We also establish the trends in the H-bond length among different types of the hydrogen bonding for dimolecular structures in the gas phase and on the Si(111)7×7 surface, the latter of which could be validated by their STM images. Finally, five simple rules of thumb are developed to summarize the adsorption properties of these proteinogenic biomolecules as mediated by hydrogen bonding, and they are expected to provide a helpful guide to future studies of larger biomolecules and their potential applications.

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Section: Biomolecules In the Gas Phasementioning

confidence: 98%

Surface-Mediated Hydrogen Bonding of Proteinogenic α-Amino Acids on Silicon

2016

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“…The adsorption of hydrogen on restatom sites has also been observed for dissociative adsorption of other organic molecules, including glycine and glycylglycine, on Si(111)7×7. 14,15 To follow the self-assembly process of adsorbed cysteine molecules, we show a 30 × 30 nm 2 empty-state image for a 25 s exposure of cysteine on Si(111)7×7 in Figure 4. While both empty-state and filled-state images of adsorbed cysteine on Si(111)7×7 appear similar (Figure 3a,b), the empty-state images are more straightforward to use for identifying the distribution of adspecies over the unit cells for higher cysteine exposures than the filled-state images.…”

Section: Journal Of the American Chemical Societymentioning

confidence: 99%

Biofunctionalization of Si(111)7×7 by “Renewable” l-Cysteine Transitional Layer

et al. 2014

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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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“…We have studied the adsorption bonding configurations of glycine on Si(111)7×7 by using a three-pronged approach of combining XPS and STM data with density functional theory (DFT) calculations. , A glycine molecule is found to undergo N–H dissociative adsorption, with its amino group reacted with a Si adatom-restatom pair of the 7×7 surface through N–Si and H–Si covalent bonding. Glycine molecules in the second adlayer (transitional adlayer) could bind to those in the first adlayer by N···HO hydrogen bonding, and zwitterionic multilayer formation follows upon further deposition.…”

Section: Introductionmentioning

confidence: 99%

Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7

et al. 2021

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Molecular adsorption bonding configurations and specific interfacial chemistry of alanine on Si(111)7×7 have been determined by combining the results from scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). XPS spectra of the N 1s region show that alanine molecules bind to the 7×7 surface by N–Si covalent bonding, while STM imaging reveals that such N–H dissociative adsorption of alanine occurs on an adjacent Si adatom-restatom pair, with the dehydrogenated alanine moiety and dissociated H atom occupying the Si adatom and restatom sites, respectively. At a sample bias above +2 V, the dehydrogenated alanine appears as a bright round protrusion, slightly off-center from a Si adatom site and leaning toward the opposite Si adatom across the dimer wall. The off-center character can be attributed to an electrostatic attraction between the electron-rich carbonyl O of the dehydrogenated alanine and electron-deficient nearest Si adatom across the dimer wall. Our DFT calculation also shows that the monodentate O–Si bonding configuration resulting from O–H dissociative adsorption is more thermodynamically favorable than the experimentally observed N–Si bonding configuration, suggesting that the interfacial dissociative adsorption reaction is a kinetically controlled rather than a thermodynamically driven process. Alanine molecules in the second adlayer (transitional layer) are found to attach to those in the first adlayer (interfacial layer) by N···HO hydrogen bonding, as supported by the presence of the N 1s feature at 401.0 eV. An alanine molecule H-bonded to a dehydrogenated alanine in the first adlayer has also been observed in STM as a brighter and larger protrusion close to the expected location of the free OH group in the dehydrogenated first-adlayer alanine. No thick zwitterionic alanine film can be obtained at room temperature possibly due to steric constraint caused by the methyl group.

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Direct Imaging of Hydrogen Bond Formation in Dissociative Adsorption of Glycine on Si(111)7×7 by Scanning Tunneling Microscopy

Cited by 9 publications

References 37 publications

Surface-Mediated Hydrogen Bonding of Proteinogenic α-Amino Acids on Silicon

Surface-Mediated Hydrogen Bonding of Proteinogenic α-Amino Acids on Silicon

Biofunctionalization of Si(111)7×7 by “Renewable” l-Cysteine Transitional Layer

Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7

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