Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7

Abstract

Molecular adsorption bonding configurations and specific interfacial chemistry of alanine on Si(111)­7×7 have been determined by combining the results from scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). XPS spectra of the N 1s region show that alanine molecules bind to the 7×7 surface by N–Si covalent bonding, while STM imaging reveals that such N–H dissociative adsorption of alanine occurs on an adjacent Si adatom-restatom pair, with the dehydrogenated alanine moiety and dissociated H atom occupying the Si adatom and restatom sites, respectively. At a sample bias above +2 V, the dehydrogenated alanine appears as a bright round protrusion, slightly off-center from a Si adatom site and leaning toward the opposite Si adatom across the dimer wall. The off-center character can be attributed to an electrostatic attraction between the electron-rich carbonyl O of the dehydrogenated alanine and electron-deficient nearest Si adatom across the dimer wall. Our DFT calculation also shows that the monodentate O–Si bonding configuration resulting from O–H dissociative adsorption is more thermodynamically favorable than the experimentally observed N–Si bonding configuration, suggesting that the interfacial dissociative adsorption reaction is a kinetically controlled rather than a thermodynamically driven process. Alanine molecules in the second adlayer (transitional layer) are found to attach to those in the first adlayer (interfacial layer) by N···HO hydrogen bonding, as supported by the presence of the N 1s feature at 401.0 eV. An alanine molecule H-bonded to a dehydrogenated alanine in the first adlayer has also been observed in STM as a brighter and larger protrusion close to the expected location of the free OH group in the dehydrogenated first-adlayer alanine. No thick zwitterionic alanine film can be obtained at room temperature possibly due to steric constraint caused by the methyl group.

Surface-Induced Keto–Enol Tautomerization of DNA Base Molecules and Consequent [4 + 2]-like Cycloaddition on Si(111)7×7

“…For the cytosine enol tautomer, the [4 + 2]-like cycloaddition with a Si–Si pair could occur through pathways involving three different sets of π bonds: (1) N1C2 and N3C4; (2) N3C4 and C5C6; and (3) C5C6 and N1C2. As both N–Si bonding and pyridinic-N N 1s features are found to have a similar binding energy near 399.1 eV, ,− the N 1s spectrum is not helpful in determining whether the pyridinic N is involved in the [4 + 2]-like cycloaddition. With smaller intrinsic widths found for individual C 1s components than those for the O 1s and N 1s features, the C 1s spectrum can be used to deduce the reaction pathway by examining the binding energy shifts of relevant C features, resulting from bond breakage and formation.…”

Odd-Even Effect on Supramolecular Co-Assemblies: Control over the Two-Dimensional Self-Assemblies of a Fluorenone Derivative with Asymmetrically Substituted Alkyl Chains

“…In recent years, surface supramolecular self-assembly has been an active research area, aimed at the realization of nanoscale functional devices, such as organic photovoltaic cells, organic light-emitting diodes, and organic field-effect transistors. − In this context, inducing and regulating diverse self-assembly structures are subjects of interest. Researchers have explored the self-assembly polymorphs of π-conjugated molecules via changing the solvent, , concentration, , temperature, , scanning tunneling microscopy (STM) bias, − molecular functional group, , the length of the alkyl chains, , and the substrate. , The used substrate contains highly oriented pyrolytic graphite (HOPG), Au (111), Ag (111), Si (111), Cu (110), and so on. − In particular, STM is the widely used visualization tool due to its atomic-level resolution. The driving forces that stabilize the self-assembled nanostructures include the weak hydrogen bonds, van der Waals interaction, dipolar interaction, halogen bonds, and π–π attractions. − …”

Solvent Co-adsorption Changing the Type of Halogen-Based Bonds Associated with the Position of Bromine Substituents Revealed by Scanning Tunneling Microscopy

“…These factors essentially change the intermolecular interaction and/or molecule–substrate interaction of self-assembly adlayers. Hence, it is necessary to deeply understand the intermolecular interaction, such as hydrogen bonding, − halogen bonding, − van der Waals (vdW) force, , π–π stacking, and metal–organic coordination, − which determines the formation of self-assembly patterns. Recently, halogen bonds have attracted many researchers due to their stronger spatial selectivity and directivity than hydrogen bonds. − The position of halogen-substituted groups in the conjugated core will affect its electrostatic distribution, thus determining the formation of hydrogen and halogen bonds.…”