Bidentate Surface Structures of Glycylglycine on Si(111)7×7 by High- Resolution Scanning Tunneling Microscopy: Site-Specific Adsorption via N-H and O-H or Double N-H Dissociation A. Chatterjee, L. Zhang, and K. T. Leung* WATLab and Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada ABSTRACT: The early adsorption stage of glycylglycine on Si(111)7×7 surface has been studied by scanning tunneling microscopy (STM). Filled-state imaging shows that glycylglycine adsorbs dissociatively in a bidentate fashion on two adjacent Si adatoms across a dimer wall or an adatom-restatom pair, with the dissociated H atoms on neighboring restatoms. The present STM result validates our hypothesis that both bidentate configurations involving N- H and O-H dissociation and double N-H dissociation are equally probable. Our STM results further show that the relative surface concentrations of the five bidentate configurations follow a specific ordering. This suggests that N-H dissociation at a center adatom site would likely be followed by N-H dissociation at an adjacent restatom, while N-H dissociation at a corner adatom site would be succeeded by O-H dissociation at an adatom across the dimer wall. Evidently, the strong bidentate interactions also inhibit surface diffusion of the adsorbed glycylglycine fragment, and the adsorption apparently follows random sequential adsorption statistics. The random nature of adsorption is also supported by the similar relative occupancies of the center adatom and corner adatom sites, indicating that the relative reactivities of these adatom sites do not play a significant role. Our DFT computational study shows that all three bidentate (Si-)NHCH 2 CONHCH 2 COO(-Si) adatom-adatom configurations (center-center, corner- corner, center-corner) have similar adsorption energies for a double adatom-adatom pair across the dimer wall, while the (Si-)NHCH 2 CON(-Si)CH 2 COOH bidentate adatom-restatom configuration is energetically favorable. The free -CONH- and -COOH groups remaining on the respective bidentate adstructures could facilitate adsorption of the second adlayer through the formation of hydrogen bonding. 1. INTRODUCTION Organic functionalization of semiconductor surfaces has provided the impetus of incorporating biological molecules into existing electronic components for novel bioelectronic devices, biosensors, and nanotechnology applications. 1-5 Among the semiconductor materials, silicon continues to attract the most attention because Si single-crystal surfaces provide the singularly most important platform for fabricating microelectronic devices, often under ultrahigh vacuum conditions. Silicon single-crystal surfaces therefore offer the natural starting point for functional integration of biomolecules to improve performance and/or to add new functions, for example, in molecular electronics and biosensing applica- tions. 6,7 This type of biodevice development requires a better understanding of Si surface chemistry, particularly the surface reactions with prototypical biomolecules under ultrahigh vacuum conditions. Si(111)7×7 and Si(100)2×1 represent two of the most fundamental (and most studied) semiconductor surfaces, and they offer unique bonding sites, each with one and two directional dangling bonds (unsaturated valencies), respec- tively, for interactions with the approaching adsorbates. In the asymmetric buckled dimer model for the Si(100)2×1 surface, one of the dangling bonds from each of two neighboring atoms forms a strong σ bond with each other, while the remaining dangling bond combines with that of a neighboring atom to form a weak π bond, creating a Si-Si dimer. 8,9 Charge transfer from the down-atom to the up-atom of the buckled dimer leads to the formation of an electrophilic-nucleophilic pair. 9,10 This structure of nucleophilic top layer (of the up-atoms) followed by an electrophilic second layer (of the down-atoms) is in marked contrast to the case of Si(111)7×7 surface. In the dimer-adatom-stacking-fault model proposed by Takayanagi et al., 11 the 7×7 unit cell consists of 12 adatoms (in the topmost layer), 6 restatoms (in the next layer) and 1 corner-hole-atom (in the third layer), each with a dangling bond, thereby reducing the total number of dangling bonds from 49 in the unreconstructed surface to 19 in the reconstructed surface. The adatom-restatom pair (with the adatom-to-restatom separation of 4.57 Å) provides the most important reaction site for the Received: May 31, 2012 Revised: July 17, 2012 Published: August 17, 2012 Article pubs.acs.org/Langmuir © 2012 American Chemical Society 12502 dx.doi.org/10.1021/la302225z | Langmuir 2012, 28, 12502-12508