Photo-regulation of 2D supramolecular self-assembly: On-surface photochemistry studied by STM

During the past few years,regulation and controlling of the two-dimension(2D)self-assembled supramolecular structure on surface have drawn increasing attention in nanoscience and technology. External stimuli have been widely used to regulate these 2D nanostructures.Among various external stimuli approaches,photo-regulation as one of the most outstanding means of regulation has been extensively studied because different wave bands can lead to molecular conformation variation and new bonds to gain new molecules.In this review,the photo-regulated self-assembled structure on solid surface as well as the photo-reactions of different molecules substituted with photo-sensitive groups are introduced to give us an insight into on-surface photochemistry,which plays an important role on the nano-devices fabrication.Notably,these photo-sensitive behaviors as well as the formed structures on surface were probed at sub-molecule level by unique scanning tunneling microscopy(STM)technique.     

Inelastic electron tunneling spectroscopy by STM of phonons at solid surfaces and interfaces

Inelastic electron tunneling spectroscopy (IETS) combined with scanning tunneling microscopy (STM) allows the acquisition of vibrational signals at surfaces. In STM-IETS, a tunneling electron may excite a vibration, and opens an inelastic channel in parallel with the elastic one, giving rise to a change in conductivity of the STM junction. Until recently, the application of STM-IETS was limited to the localized vibrations of single atoms and molecules adsorbed on surfaces. The theory of the STM-IETS spectrum in such cases has been established. For the collective lattice dynamics, i.e., phonons, however, features of STM-IETS spectrum have not been understood well, though in principle STM-IETS should also be capable of detecting phonons. In this review, we present STM-IETS investigations for surface and interface phonons and provide a theoretical analysis. We take surface phonons on Cu(1?1?0) and interfacial phonons relevant to graphene on SiC substrate as illustrative examples. In the former, we provide a theoretical formalism about the inelastic phonon excitations by tunneling electrons based on the nonequilibrium Green’s function (NEGF) technique applied to a model Hamiltonian constructed in momentum space for both electrons and phonons. In the latter case, we discuss the experimentally observed spatial dependence of the STM-IETS spectrum and link it to local excitations of interfacial phonons based on ab-initio STM-IETS simulation.     

Action spectroscopy of single molecules reactions with STM – My personal view back from 2001-

Having obtained an invitation to submit this personal view back to 2001 when I started to work with Prof. Maki Kawai for developing a theory of lateral hopping of a single CO molecule on Pd (1 1 0) with Bo Persson, I briefly describe how I got an idea for elementary processes of vibrationally mediated reactions of single molecules on metal surfaces. During the work with Prof. S.G. Thihodeev on a theory of inelastic electron tunneling spectroscopy (IETS) with scanning tunneling spectrum (STM-IETS), I found that IET current is expressed in terms of a vibrational density of states of a single molecule. This enabled me to propose a formula for a reaction rate $R(V)$ or yield per electron $Y(V)=R(V)/I$, here I is a tunneling current, i.e., action spectrum (STM-AS) of a single molecule reaction. I applied this formula to reproduce the experimental result of a CO molecule hopping on Pd (1 1 0) surface and more insights into the elementary process were revealed. Thomas Frederiksen and Magus Paulsson jointed me to develop a general formula of $Y(V)$ and successfully applied it to analyse the experimental results of H-atom relay reaction of a linear chain, H(D)₂O-OH(D)-O(D) H?→?H(D)-H(D)₂-OH(D) ?→?H(D)-H(D)-OH(D)₂ that was observed by Takashi Kumagai and Hiroshi Okuyama. Actually a hydrogen atom excited at one end of a linear chain composed of H₂O and several OH generates another one at the other end. We employed our formula of to reproduce the experimental result of $Y(V)$. It was found that excitation of the three characteristic vibrational modes (free OH/OD stretch, OH¹?=?OD¹ stretch, and H₂O scissors, where H¹?=?D¹ denotes the shared H/D¹ atom in the H bond) were involved in the relay reaction. It was remarked that the OH(D¹)?=?OD(D¹ stretch modes are significantly redshifted from free OH/OD stretch and also characterized by very large broadening. The significant mode softening with respect to the free stretch modes and spectacular enhancement of the width are known to originate in the strong anharmonic character of a single H bond. Thomas investigated the reaction pathway from total energy calculations for the H-atom transfer reaction by the nudged elastic band method. The initial step is translation of the shared H-atom to the center hydroxyl, which is almost barrierless. The subsequent H-bond cleavage between OH and the center water molecule constitutes the highest barrier in which the displacement of the center water molecule along the [0 0 1] direction is mainly involved. The OH, OH¹ stretch and H₂O scissors modes are therefore postulated to couple to the reaction coordinate for the H-bond cleavage. We have demonstrated a vibrationally induced H-atom-bond relay reaction within H-bonded chains assembled on Cu(1 1 0). In this reaction H-atom transfer results in the ‘structural’ transfer of a water molecule from one end of the chain to the other end without changing the platform of the chain, or actually transferring the molecule.I have been thinking the unresolved issue of C₂H(D)₂ rotation on Cu (1 0 0) since it was published in 1998 by the W. Ho group. This experimental methods and the results obtained as the first demonstration of a single molecule switch are widely recognized as a milestone report of a single molecule manipulation by tunneling current and applied bias voltage which excites the vibrational modes of a molecule. They observed the STM images rotated at 90 degrees before and after applying appropriate bias voltage. They further compared the IETS spectrum and the $Y(V)$ for the rotation. The observed peak beautifully agreed with the threshold bias voltage, which clearly evidenced that a rotation is induced by excitation of a particular vibrational mode of C₂H(D)₂. In particular a crossover from a single electron process to a two electron process with increase in a tunneling current are of great interest. Sergei and his PhD student Yulia E. Shchadilova at that time and Magnus helped me much to reproduce all the experimental results by employing the Keldysh Green’s function theory combined with ab initio density functional theory (DFT) calculation of the optimized adsorption geometry and sophisticated vibrational analysis done by Magus. The experimental result of $Y(V)$ was reproduced by assuming a single electron process to excite the C-H stretch mode, and two electron process (ladder climbing of the C-H vibrational levels) and a excitation of the combination band. I also describe a brief theory of STM-AS I developed with Bo, Sergei, Magnus and Thomas.     

On the HSAB based estimate of charge transfer between adsorbates and metal surfaces

The applicability of the HSAB based electron charge transfer parameter, ΔN, is analyzed for molecular and atomic adsorbates on metal surfaces by means of explicit DFT calculations. For molecular adsorbates ΔN gives reasonable trends of charge transfer if work function is used for electronegativity of metal surface. For this reason, calculated work functions of low Miller index surfaces for 11 different metals are reported. As for reactive atomic adsorbates, e.g., N, O, and Cl, the charge transfer is proportional to the adatom valence times the electronegativity difference between the metal surface and the adatom, where the electronegativity of metal is represented by a linear combination of atomic Mulliken electronegativity and the work function of metal surface. It is further shown that the adatom-metal bond strength is linearly proportional to the metal-to-adatom charge transfer thus making the ΔN parameter a useful indicator to anticipate the corresponding adsorption energy trends.     

Imaging fibrinogen adsorbed on noble metal surfaces with scanning tunneling microscopy: correlation of images with electron spectroscopy for chemical analysis, secondary ion mass spectrometry, and radiolabeling studies

Fibrinogen adsorption on gold and platinum surfaces has been studied with electron spectroscopy for chemical analysis (ESCA), secondary ion mass spectrometry (SIMS), ¹²⁵I labeling, and scanning tunneling microscopy (STM). Stable images of single molecules have been obtained, but are rare. ESCA, SIMS, and labeling studies confirm that absorbed fibrinogen is present on samples at monolayer and submonolayer coverages even when STM images show only a bare substrate. Imaging is more reproducible at high coverages at which single molecules cannot be resolved. Possible explanations for the failure of STM to observe adsorbed fibrinogen molecules are discussed.     

Quantum-chemical,spectroscopic and X-ray diffraction studies on nickel complex of 2-hydroxyacetophenone thiosemicarbazone with triphenylphospine

Reaction of 2-hydroxyacetophenone thiosemicarbazone with [Ni(PPh₃)₂Cl₂] in optimized conditions afforded a mixed ligand complex with an isolated triphenylphosphine molecule. The structure was characterized by elemental analysis, IR, NMR and UV–Vis. spectroscopies and single crystal X-ray diffraction technique. In addition, the molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO) ¹H and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated using the density functional theory (DFT/B3LYP) method with the 6-31G(d,p) basis set for the C, N, O, S, P, H atoms and LANL2DZ pseudo-potential for the Ni atom, and compared with the experimental data. Besides, atomic charge distributions, molecular electrostatic potential and frontier molecular orbitals (FMO) analysis of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained. Atomic charge distributions indicate that during forming the title compound, the free ligand of thiosemicarbazone ion transfers their negative charges to central Ni(II) ion. The effect of different solvents (chloroform, methanol and water) on the geometry, vibrational frequencies, total energies and dipole moments was studied using the density functional theory (DFT/B3LYP) method by applying the Onsager and the Polarizable Continuum Model (PCM).     

Crystallographic study of interaction between adspecies on metal surfaces

The interaction among adsorbed atoms and molecules (adspecies) on metal surfaces plays a decisive role in catalytic reactions. Such interaction may cause structural changes of the local adsorption geometry which, together with spectroscopic and energetic data, may afford useful physical and chemical insights into the basic mechanisms of surface processes. When the adsorption geometry of a single adspecies is considered as a function of coverage, a deeper understanding of the nature of the adsorbate-substrate bonding can be obtained. Depending on the adsorbate coverage, the magnitude of adsorbate-induced relaxations and reconstructions vary widely. Occasionally, chemisorption systems transform gradually into adsorbate-substrate compounds, such as oxides, nitrides, hydrides, and sulfides. For the case of adsorption of different adspecies, coadsorption, structural data can make a vital contribution to our understanding of reaction intermediates, the promotion effect in heterogeneously catalyzed reactions, and the formation of ultra-thin compound films.