Direct Imaging of Hydrogen Bond Formation in Dissociative Adsorption of Glycine on Si(111)7×7 by Scanning Tunneling Microscopy
Bibliographic record
Abstract
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 Si 16 H 18 cluster to simulate an adatom–restatom pair and a Si 26 H 24 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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".