Nanometer-thick glycine and glycylglycine film growth on Si(111)7×7 at room temperature in ultrahigh vacuum condition and their thermal evolution are investigated by X-ray photoelectron spectroscopy (XPS). In order to understand the XPS result of initial exposure, we also calculate equilibrium geometries and the adsorption energies of plausible glycine and glycylglycine adspecies on model 7×7 surfaces using density functional theory. N 1s spectra reveal three growth stages for both glycine and glycylglycine nanofilms. The first stage involves N–H dissociative adsorption of glycine and N–H and O–H dissociative adsorption of glycylglycine, forming N–Si and O–Si bonds at the interface, respectively. The experimental results are consistent with the most stable glycylglycine adsorption structure involving both the amino and amide N atoms bonded to a Si adatom-restatom pair or an amino N and a carboxyl O atoms bridging two Si adatoms across a dimer wall, in a bidentate configuration. In the second stage, a transitional adlayer grows in the neutral forms of glycine and glycylglycine, binding to their respective interfacial adlayer through hydrogen bonding. For glycine, the presence of head-to-tail N···H–O hydrogen bonding is indicated by a new N 1s feature at 401.4 eV binding energy, between those for neutral amino N at 400.6 eV and zwitterionic N at 402.1 eV. For glycylglycine, the existence of hydrogen bonding can be inferred from the considerable thermal stability of the transitional adlayer (at least to 200 °C). In the final stage, both glycine and glycylglycine grow continuously in the zwitterionic form into thick films. Thermal evolution studies of these as-grown glycine and glycylglycine zwitterionic films on Si(111)7×7 reveal the reverse trend, with the zwitterionic multilayer and transitional adlayer desorbing sequentially and the interfacial adlayer less affected below 250 °C. The glycylglycine film clearly exhibits a higher thermal resistance than the glycine film. The present work demonstrates the vital role of hydrogen bonding in the formation of the transitional adlayer in these important biomolecules. The intermediate bond strength of a hydrogen bond (between those of a covalent bond and the long-range van der Waals interaction) promises new bonding flexibilities for building multifunctional biomolecular structures for biosensor and bioelectronic applications.
Adsorption and desorption of several small prototypical biomolecules: glycine, glycylglycine, alanine, adenine, and thymine on a glycine-functionalized Si(111)7×7 surface have been investigated by X-ray photoelectron spectroscopy. Glycine has been found to adsorb on Si(111)7×7 through N−H dissociation, which makes the unreacted carboxyl group of the interfacial glycine adlayer an effective means to capture these biomolecules (except for thymine) through [O−H···N] hydrogen bonding. Furthermore, the captured molecules can be released simply by annealing to 120 °C for 10 s. This hydrogen-bond-mediated catch-and-release mechanism is supported by the appearance and disappearance of the characteristic hydrogen-bond N 1s features at 401.4 eV and is found to be reversible. The glycine-functionalized Si(111) surface therefore provides a flexible platform for potential applications as selective molecular traps, chemical sensors, and biomolecular electronic components.
Adsorption of glycine on a Si(111)7×7 surface at
room temperature
has been studied by scanning tunneling microscopy (STM). The observed
STM images provide strong evidence for dissociative adsorption of
glycine through N–H bond cleavage (and N–Si bond formation)
as reported in our recent X-ray photoemission study. In particular,
the dissociated H atom is found to anchor on a restatom while the
N–H dissociated glycine molecule adsorbs on an adatom in a
tilted, unidentate geometry. STM study for higher exposures further
reveals that the second adlayer is mediated by vertical hydrogen bonding,
in excellent accord with our recent X-ray photoemission results. In
addition to this vertical hydrogen bonding between a glycine molecule
and the N–H dissociated glycine adsorbate, we also observe
horizontal hydrogen bonding, not seen before, between two N–H
dissociated glycine adsorbates at two neighboring adatom sites. These
hydrogen-bonded adstructures, as implicated in the STM images, have
been corroborated with our computational DFT/B3LYP/6-31++(d,p) results
by using the two largest model surfaces: a Si16H18 cluster to simulate an adatom–restatom
pair and a Si26H24 cluster to model a double
adatom–adatom pair across the dimer wall of the 7×7 surface.
Furthermore, statistical analysis of the STM images for different
exposures shows that the center adatom is more reactive than the corner
adatom and that the faulted half is more reactive than the unfaulted
half. The horizontal hydrogen bonding appears to be favored at a lower
exposure than the vertical hydrogen bonding, which becomes dominant
at a higher exposure as formation of the second adlayer proceeds.
The present work illustrates the importance of hydrogen bonding in
the early growth and site-specific chemistry of glycine on Si(111)7×7
surfaces.
An experimental study was performed using Ottawa sand and a produced sand. A 3-D semi-analytical flow model was developed to analyze the experimental data. The results show that the ratio of sand grain size and outlet hole size, grain size distribution, and angularity are the most important factors affecting the sand arch stability. Pressure increase mode and pressure magnitude also affect arch stability.
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