Conformational adaptation and selective adatom capturing of tetrapyridyl-porphyrin molecules on a copper (111) surface

We present a combined low-temperature scanning tunneling microscopy and near-edge X-ray adsorption fine structure study on the interaction of tetrapyridyl-porphyrin (TPyP) molecules with a Cu(111) surface. A novel approach using data from complementary experimental techniques and charge density calculations allows us to determine the adsorption geometry of TPyP on Cu(111). The molecules are centered on "bridge" sites of the substrate lattice and exhibit a strong deformation involving a saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. We propose a bonding mechanism based on the pyridyl-surface interaction, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to control the anchoring of large organic molecules on metal surfaces and tune their conformational state. Furthermore, we demonstrate that the affinity of the terminal groups for metal centers permits the selective capture of individual iron atoms at low temperature.     

Self-assembly of phospholipid molecules at a Au(111) electrode surface

We described the first scanning tunneling microscopy study of spreading unilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) at a Au(111) electrode surface. At the initial stage of the film formation, the molecular resolution images revealed that DMPC molecules are adsorbed flat with the acyl chains oriented parallel to the surface. The molecules assemble into double rows by aligning the acyl chains in the nearest neighbor direction of the reconstructed Au(111) surface and assuming a 90 +/- 10 degrees angle with respect to line of the molecular row. After approximately 30 min, this film is transformed into a hemimicellar state with long rows characteristic for the formation of hemicylindrical surface micelles. At hydrophilic surfaces such as glass, spreading of vesicles involves adsorption, rupture, and sliding of a single bilayer on a lubricating film of the solvent. We have provided the first evidence that a different mechanism is involved in spreading the vesicles at gold. The molecules released by rupture of vesicles self-assemble into an ordered film, and the assembly is controlled by the chain-substrate interaction.     

Self-assembly of alkanols on Au(111) surfaces

Self-assembled monolayers (SAMs) of alkanols (1-C(N)H(2N+1)OH) with varying carbon-chain lengths (N = 10-30) have been systematically studied by means of scanning tunneling microscopy (STM) at the interfaces between alkanol solutions (or liquids) and Au(111) surfaces. The carbon skeletons were found to lie flat on the surfaces. This orientation is consistent with SAMs of alkanols on highly oriented pyrolytic graphite (HOPG) and MoS2 surfaces, and also with alkanes on reconstructed Au(111) surfaces. This result differs from a prior report, which claimed that 1-decanol molecules (N = 10) stood on their ends with the OH polar groups facing the gold substrate. Compared to alkanes, the replacement of one terminal CH3 group with an OH group introduces new bonding features for alkanols owing to the feasibility of forming hydrogen bonds. While SAMs of long-chain alkanols (N > 18) resemble those of alkanes, in which the aliphatic chains make a greater contribution, hydrogen bonding plays a more important role in the formation of SAMs of short-chain alkanols. Thus, in addition to the titled lamellar structure, a herringbone-like structure, seldom seen in SAMs of alkanes, is dominant in alkanol SAMs for values of N < 18. The odd-even effect present in alkane SAMs is also present in alkanol SAMs. Thus, the odd N alkanols (alkanols with an odd number of carbon atoms) adopt perpendicular lamellar structures owing to the favorable interactions of the CH3 terminal groups, similar to the result observed for odd alkanes. In contrast to alkanes on Au(111) surfaces, for which no SAMs on an unreconstructed gold substrate were observed, alkanols are capable of forming SAMs on either the reconstructed or the unreconstructed gold surfaces. Structural models for the packing of alkanol molecules on Au(111) surfaces have been proposed, which successfully explain these experimental observations.     

Electron-induced isomerisation of dichlorobenzene on Cu(111) and Ag(111)

The constitutional isomerisation of single dichlorobenzene molecules adsorbed on the surfaces of Ag(111) and Cu(111) between their meta- and para-isomers is induced and investigated by means of a low temperature scanning tunneling microscope. On both substrates similar isomerisation thresholds are found indicating that the excitation mechanism of this reaction does not depend significantly on the underlying substrate. The isomerisation threshold voltage of (170 +/- 7) meV most likely corresponds to excitation of a C-C stretch mode whose gas-phase energies we calculated ab initio to lie at 174 and 172 meV for meta- and para-isomers respectively. Though the reaction is found to be localized on the submolecular scale, it depends heavily on the second substituent both in terms of excitation energy and reaction outcome.     

Chiral recognition of PVBA on Pd(111) and Ag(111) surfaces

An asymmetric planar molecule, 4-trans-2-(pyrid-4-yl-vinyl) benzoic acid (PVBA), has been used to establish the organic chiral recognition on fcc(111) metal surfaces. The strong correlation between the orientation and chiral recognition of PVBA on both Ag(111) and Pd(111) guides the choice of a model potential, which determines the relative binding energy of PVBA on fcc(111). An angle-dependent calculation of relative binding energy reproduces the experimental observation of the chiral recognition of PVBA on Ag(111) but not on Pd(111).     

Self-assembly of normal alkanes on the Au (111) surfaces

The self-assembled monolayers (SAMs) of normal alkanes (n-C(n)H(2n+2)) with different carbon chain lengths (n=14-38) in the interfaces between alkane solutions (or liquids), and the reconstructed Au (111) surfaces have been systematically studied by means of scanning tunneling microscopy (STM). In contrast to previous studies, which concluded that some n-alkanes (n=18-26) can not form well-ordered structures on Au (111) surfaces, we observed SAM formations for all these n-alkanes without any exceptions. We find that gold reconstruction plays a critical role in the SAM formation. The alkane monolayers adopt a lamellar structure in which the alkane molecules are packed side-by-side, to form commensurate structures with respect to the reconstructed Au (111) surfaces. The carbon skeletons are found to lie flat on the surfaces, which is consistent with the infrared spectroscopic studies. Interestingly, we find that two-dimensional chiral lamellar structures form for alkanes with an even carbon number due to the specific packing of alkane molecules in a tilted lamella. Furthermore, we find that the orientation of alkane molecules deviates from the exact [011] direction, because of the intermolecular interactions among the terminal methyl groups of neighboring lamellae; this results in differences of molecular orientation between mirror structures of adjacent zigzag alkane lamellae. Structural models have been proposed, that shed new light on monolayer formation.     

Self-assembly of chiral molecular honeycomb networks on Au(111)

Self-assembly of the specifically designed 3-fold symmetric 1,3,5-trikis(4'-carboxylphenyl)-2,4,6-trikis(4'-tert-butylphenyl)-benzene molecule on a Au(111) surface is investigated by means of in situ ultrahigh vacuum scanning tunneling microscopy. A variety of chiral honeycomb networks with increasing interpore distance is observed. Experiments and force field calculations reveal that the formation of the two-dimensional hexagonal porous networks is driven by a balance of molecular close-packing within half-unit cells and cyclic hydrogen bonding dimerization between half-unit cells. The honeycomb networks are shown to be chiral owing to asymmetric molecular close-packing within the half-unit cells.     

Self-assembly of alkanethiol monolayers on Ag-Au(111) alloy surfaces

The self-assembly of ethanethiol (C(2)) and 1-octanethiol (C(8)) on Ag-Au(111) alloy films was studied by X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), and scanning tunneling microscopy (STM), to illuminate how the monolayer structures and chemisorption-induced substrate defect structures depend on the alloy composition. The thiolate packing density at saturation increased approximately linearly with increasing Ag ratio. The CV data for reductive desorption of thiolates evidenced predominant or major contributions of Ag atoms to the substrate-sulfur interactions for the alloy surfaces. The STM study supported the lack of elemental periodicity on Ag-Au(111) and the consequent absence of periodicity in substrate-sulfur bonding. For C(8)-covered films, we observed systematic changes of substrate defect structures from elevated monatomic islands on Ag(111) to vacancy island structure on Au(111), in good correlation with the reductive desorption characteristics. The former type of defects can be explained best in terms of breakup of atomic terraces under excess thiolate packing density for Ag(111) and Ag-rich Ag-Au(111). As for the vacancy island formation, the present results are not agreeable with the chemical etching model but compatible with the lattice relaxation model.     

Halogen-substituted thiophenol molecules on Cu(111)

Para-halosubstituted thiophenols (X-TPs, where X is Br, Cl, or F) form ordered islands and monolayers on Cu(111) at temperatures as low as 81 K. At incomplete coverages, all X-TPs adsorb with the dehydrogenated thiol group attached to the substrate and the substituted ring inclined toward the surface, as verified experimentally and theoretically. The structure of ordered islands has a pronounced dependence on the nature of the halogen substituent: while unsubstituted TP and pentafluoro-TP molecules do not self-assemble into extended ordered patterns at 81 K, X-TP molecules form a range of different structures which depend both on the size and electronegativity of the substituent, as well as on the coverage.     

Cyclic voltammetry on Ag(111) and Ag(100) faces in sodium hydroxide solutions

The electrochemical behavior of silver (100) and (111) single crystal surfaces was examined by cyclic voltammetry in aqueous NaOH solution. In the `double layer' region (between −1.2 and 0.1 V (SCE)) adsorption of OH⁻ ions followed by phase transformation into an Ag–OH monolayer was found to take place. The difference in peak potentials recorded in 0.1 and 0.01 mol dm⁻³ NaOH solutions of about 60 mV indicates that one electron is exchanged in the overall electrochemical reaction, implying a complete charge transfer between OH⁻ ions and the silver surface. The adsorption process has been modeled to a Frumkin adsorption isotherm. Further oxidation of silver into Ag₂O takes place at more positive potentials. The formation of bulk Ag₂O results in considerable change to the original single crystal surface. This is likely to be due to roughening of the silver surface as a consequence of the formation and reduction of the oxide.     

苯乙烯在Ag(111)和Ag(110)表面环氧化反应结构敏感性的理论研究

采用密度泛函理论(DFT)对苯乙烯在Ag(110)表面和Ag(111)表面的环氧化反应进行了计算研究. 经计算, 在Ag(110)表面预吸附氧原子更易吸附在3 重穴位(3h), 吸附能为-3.59 eV; 在Ag(111)表面预吸附氧原子的最稳定吸附位是fcc 位, 吸附能为-3.69 eV. 苯乙烯的环氧化反应过程首先经过一个金属中间体, 然后再进一步反应变为产物, 其中经过直链中间体较支链中间体更加有利. Ag(110)面的反应活化能一般大于Ag(111)面的, 并且微观动力学模拟结果表明, Ag(111)表面生成环氧苯乙烷的选择性要明显高于Ag(110)表面(0.38 与 0.003), 原因是Ag(111)面环氧化反应活化能小于苯乙醛及燃烧中间体的活化能, 而在Ag(110)上正相反.     

Propagation of conformation in the surface-aligned dissociation of single CH3SSCH3 molecules on Au(111)

Single CH3SSCH3 molecules adsorb on the Au(111) surface in a trans-conformation. Subsequent electron-induced dissociation of CH3SSCH3 cleaves the S-S bond and produces a pair of CH3S fragments. The dissociation process was found to preserve the conformation of the parent molecule with a high probability of 75% and imprint it in the relative position and orientation of the product CH3S species on the surface. The high probability of the conformation-retaining scenario is likely due to surface alignment of the S-S bond-breaking reaction coordinate.     

Equilibrium properties of Ag clusters on Pt(111)

Molecular dynamics simulations (MD) and Embedded Atom Method (EAM) potentials are employed to investigate the properties of small Ag clusters deposited on the (111) surface of Pt. The computation of the dissociation energies reveals the most stable structures up to 19 atoms, while MD simulations allow to extract the dynamical diffusion barrier for adatom, dimer and trimer. We obtain dissociation energies in the range of 0.3 eV for the trimer and 0.45 eV for the heptamer and a migration energy as low as 0.05 eV for the adatom.     

Ag(111)表面Ag配位结构的分等级组装

表面辅助的金属有机纳米结构因其结构稳定性和潜在应用受到广泛关注。在金属有机纳米结构中,金属原子来源于外部沉积的金属或金属表面原子。外部沉积的金属原子种类多样,取决于目标纳米结构。然而,金属表面原子受限于表面科学常用的金、银和铜单晶金属表面。金属有机纳米结构大多包括Au配位或是Cu配位结构,而只有少量的用表面Ag原子构成。分子金属相互作用的进一步研究有助于预期纳米结构的精确控制形成。至于构建基元,有机分子通过M―C、M―N和M―O键与表面金属原子配位。末端炔反应或者乌尔曼耦合能够实现C―M―C节点的形成。Cu和Au原子能够与含有末端氰基或吡啶基官能团的分子配位形成N―M―N键。另外,表面Ag增原子能够通过Ag―N配位键与酞菁分子配位。然而,M―O配位键的相关研究较少。因此,我们计划使用末端羟基分子与Ag增原子配位形成金属有机配位纳米结构去研究O―Ag节点。我们通过扫描隧道显微镜利用4, 4’-二羟基-1, 1’: 3’, 1’’-三联苯分子(4, 4’-dihydroxy-1, 1’: 3’, 1’’-terphenyl,H3PH)和Ag增原子成功构筑了一系列二维有序纳米结构。在室温下,蒸镀的H3PH分子自组装形成由环氢键连接的密堆积结构。当退火温度提升到330 K,一种新的纳米结构出现了,该结构由O―Ag配位键和氢键共同作用形成。进一步地提升退火温度至420 K,蜂巢结构和共存的二重配位链出现,这两种结构中仅由O―Ag―O键构成。为分析金属分子反应路径和O―Ag―O键的能量势垒,我们对该体系进行密度泛函理论计算。计算结果显示,O―Ag键形成的能量势垒是1.41 eV,小于O―Ag―O节点1.85 eV的能量势垒。这也解释了分等级金属-有机纳米结构形成的原因。我们的实验结果提供了一种利用有机小分子和金属增原子来设计和构筑分等级二维纳米结构的有效方法。     

Phase diagram of subphtalocyanine ordering on Ag(111)

A model of subphtalocyanine molecules ordering on Ag(111) is proposed. We have demonstrated that the driving force of the ordering into honeycomb and hexagonal close packed patterns is a balance of intermolecular and subphtalocyanine-Ag interactions which can be generally expressed by a potential with infinite exclusion in a sufficiently large number of nearest coordination spheres of Ag(111) lattice and oscillatingly decaying behavior outside the sphere of exclusion. To cope with computational problems due to large size of the molecules compared to the substrate lattice period, we introduce the rescaling of Ag(111) lattice, and took into account an infinite exclusion of first, second, and third neighbors, attraction-of fourth and fifth, and repulsion-of sixth and seventh. The phase diagram is obtained by the lattice gas model using Monte Carlo simulations. Very strong first order phase transitions, causing the two-phase coexistence, were found between disordered and honeycomb as well as between disordered and hexagonal closed packed phases.     

Supramolecular engineering through temperature-induced chemical modification of 2H-tetraphenylporphyrin on Ag(111): flat phenyl conformation and possible dehydrogenation reactions

Scratching the surface: Formation of a monolayer of 2H-tetraphenylporphyrins (2H-TPP) on Ag(111), either by sublimation of a multilayer in the range 525-600?K or by annealing (at the same temperature) a monolayer deposited at room temperature, induces a chemical modification of the molecules. Rotation of the phenyl rings into a flat conformation is observed and tentatively explained, by using DFT calculations, as a peculiar reaction due to molecular dehydrogenation.     

Self-assembly of insoluble porphyrins on Au(111) under aqueous electrochemical control

Self-assembled monolayers of a water-insoluble porphyrin, tetraphenyl porphyrin (TPP), in the presence of an aqueous electrolyte were characterized in situ with electrochemical scanning tunneling microscopy (EC-STM) at working electrode potentials of between 0.5 and -0.2 V. Isolated domains of TPP monolayers with differing orientation were observed on Au(111) in 0.1 M HClO(4) over this entire potential window. Individual TPP molecules could be resolved over a range of 700 mV, from open circuit potential (OCP) to near the hydrogen evolution potential. The unit cell is square, and the distance between neighboring molecules is about 1.4 ± 0.1 nm. High-resolution images allow the internal molecular structure to be discerned. No changes in the STM contrast of individual molecules were observed as the potential was changed. In a neutral electrolyte (0.1 M KClO(4), pH ~6), the potential range of stability of ordered structures is reduced. On HOPG, TPP forms ordered hexagonal structures with a lattice constant of about 2.6 nm in the double-layer potential region in 0.1 M HClO(4).     

NO(2) dissociation on Ag(111) revisited by theory

NO(2) dissociation on Ag(111) is investigated with first-principles calculations. For single NO(2) molecules, a high adsorption potential energy is found to prohibit dissociation. This result is surprising as experiments indicate dissociation at low temperatures. Neither entropy effects nor irregularities in the potential energy surface can remedy the discrepancy. Instead it is proposed that collective Eley-Rideal type of reaction mechanisms can drive the dissociation.     

Low-temperature adsorption of H2S on Ag(111)

H(2)S forms a rich variety of structures on Ag(111) at low temperature and submonolayer coverage. The molecules decorate step edges, exist as isolated entities on terraces, and aggregate into clusters and islands, under various conditions. One type of island exhibits a (√37×√37)R25.3° unit cell. Typically, molecules in the clusters and islands are separated by about 0.4 nm, the same as the S-S separation in crystalline H(2)S. Density functional theory indicates that hydrogen-bonded clusters contain two types of molecules. One is very similar to an isolated adsorbed H(2)S molecule, with both S-H bonds nearly parallel to the surface. The other has a S-H bond pointed toward the surface. The potential energy surface for adsorption and diffusion is very smooth.