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.