The growth of glycine film by thermal evaporation on Si(111)7 x 7 at room temperature has been studied by X-ray photoemission. In contrast to common carboxylic acids, glycine is found to adsorb on Si(111)7 x 7 dissociatively through cleavage of a N-H bond instead of O-H bond. The intricate evolution of the observed N 1s features at 399.1, 401.4, and 402.2 eV with increasing film thickness demonstrates the existence of a transitional adlayer between the first adlayer and the zwitterionic multilayer. This transitional adlayer is estimated to be 1-2 adlayer thick and is characterized by the presence of intermolecular N...HO hydrogen bond. An intramolecular proton transfer mechanism is proposed to account for the adsorption process through the amino group.

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.

X-ray photoelectron spectroscopy (XPS) has been used to investigate the core-level electronic structures of glycine (G) and its peptides, including glycyl-glycine (GG), diglycyl-glycine (GGG), and polyglycine (poly-G), in their powder forms. Increasing the number of G units in the peptides does not change the locations of the respective C 1s, N 1s, and O 1s features corresponding to different functional groups: -COO(-), -NH(3)(+), >CH(2), and -CONH-. The electronic structures of the zwitterions of these molecules have been calculated as isolated molecules and as molecules in an aqueous environment under the periodic boundary conditions by quantum-mechanical and molecular mechanics methods. In the case of glycine zwitterion, the binding energies of the C 1s, N 1s, and O 1s XPS features are found to be in reasonable accord with the respective orbital energies obtained by Hartree-Fock self-consistent-field calculations, within the context of Koopmans' approximation. However, considerably worse agreement in the binding energies is found for the larger zwitterions (with the specific conformations considered in this work), indicating the need for higher-level calculations. The present work shows that optimizing the zwitterion in an aqueous environment under the periodic boundary conditions by molecular mechanics could be a very cost-effective approach for calculating the electronic structures of large, complex biomolecular systems.

Electron-induced reaction of physisorbed meta-diiodobenzene (mDIB) on Cu(110) at 4.6 K was studied by Scanning Tunneling Microscopy and molecular dynamics theory. Single-electron dissociation of the first C-I bond led to in-plane rotation of an iodophenyl (IPh) intermediate, whose motion could be treated as a "clock" of the reaction dynamics. Alternative reaction mechanisms, successive and concerted, were observed giving different product distributions. In the successive mechanism, two electrons successively broke single C-I bonds; the first C-I bond breaking yielded IPh that rotated directionally by three different angles, with the second C-I bond breaking giving chemisorbed I atoms (#2) at three preferred locations corresponding to the C-I bond alignments in the prior rotated IPh configurations. In the concerted mechanism a single electron broke two C-I bonds, giving two chemisorbed I atoms; significantly these were found at angles corresponding to the C-I bond direction for unrotated mDIB. Molecular dynamics accounted for the difference in reaction outcomes between the successive and the concerted mechanisms in terms of the time required for the IPh to rotate in-plane; in successive reaction the time delay between first and second C-I bond-breaking events allowed the IPh to rotate, whereas in concerted reaction the computed delay between excitation and reaction (∼1 ps) was too short for molecular rotation before the second C-I bond broke. The dependence of the extent of motion at a surface on the delay between first and second bond breaking suggested a novel means to "clock" sub-picosecond dynamics by imaging the products arising from varying time delays between impacting pairs of electrons.

Bond-selective reaction is central to heterogeneous catalysis. In heterogeneous catalysis, selectivity is found to depend on the chemical nature and morphology of the substrate. Here, however, we show a high degree of bond selectivity dependent only on adsorbate bond alignment. The system studied is the electron-induced reaction of meta-diiodobenzene physisorbed on Cu(110). Of the adsorbate’s C-I bonds, C-I aligned ‘Along’ the copper row dissociates in 99.3% of the cases giving surface reaction, whereas C-I bond aligned ‘Across’ the rows dissociates in only 0.7% of the cases. A two-electronic-state molecular dynamics model attributes reaction to an initial transition to a repulsive state of an Along C-I, followed by directed recoil of C towards a Cu atom of the same row, forming C-Cu. A similar impulse on an Across C-I gives directed C that, moving across rows, does not encounter a Cu atom and hence exhibits markedly less reaction.

Diiodomethane is used to generate C1 fragments at surfaces, en route to higher hydrocarbons. Here scanning tunneling microscopy was employed to examine the interaction of diiodomethane, CH2I2, with a Cu(110) surface, from 4.6 to 8.8 K. In this temperature range unexpectedly rapid thermal reaction resulted in the rupture of two C–I bonds, yielding pairs of I atoms recoiling in opposite directions. Approximately 65% of the carbene, CH2, product from this highly exothermic (4.1 eV) thermal reaction remained chemisorbed. Two stable physisorbed configurations of diiodomethane were found, “vertical” (75%) and “horizontal” (25%). Electron-induced reaction of these intact adsorbates led to single-electron dissociation of both the C–I bonds, with a minor path leading to single bond breaking to form CH2I. Directed recoil of chemisorbed carbene was observed in approximately half the electron-induced reactive events. Simulation of the electron-induced reaction by the impulsive two-state (I2S) model consistently predicted delayed dissociation of the second C–I bond, due to vibrational excitation of the CH2I radical product. Theory and experiment agreed in evidencing long-range recoil for the CH2 along the [11̅0] direction of the copper. This recoiling diradical was shown by the I2S model to undergo migration by a novel process of “walking” along a pair of adjacent copper rows.

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.