Molecular Self-Assembly and Adsorption Structure of 2,2'-Dipyrimidyl Disulfides on Au(111) Surfaces

The effects of solution concentration and pH on the formation and surface structure of 2-pyrimidinethiolate (2PymS) self-assembled monolayers (SAMs) on Au(111) via the adsorption of 2,2'-dipyrimidyl disulfide (DPymDS) were examined using scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). STM observations revealed that the formation and structural order of 2PymS SAMs were markedly influenced by the solution concentration and pH. 2PymS SAMs formed in a 0.01 mM ethanol solution were mainly composed of a more uniform and ordered phase compared with those formed in 0.001 mM or 1 mM solutions. SAMs formed in a 0.01 mM solution at pH 2 were composed of a fully disordered phase with many irregular and bright aggregates, whereas SAMs formed at pH 7 had small ordered domains and many bright islands. As the solution pH increased from pH 7 to pH 12, the surface morphology of 2PymS SAMs remarkably changed from small ordered domains to large ordered domains, which can be described as a (4√2 × 3)R51° packing structure. XPS measurements clearly showed that the adsorption of DPymDS on Au(111) resulted in the formation of 2PymS (thiolate) SAMs via the cleavage of the disulfide (S-S) bond in DPymDS, and most N atoms in the pyrimidine rings existed in the deprotonated form. The results herein will provide a new insight into the molecular self-assembly behaviors and adsorption structures of DPymDS molecules on Au(111) depending on solution concentration and pH.

Electrochemical atomic force microscopy of two-dimensional trinuclear ruthenium clusters molecular assembly and dynamics under redox state control

Mixed-valence ruthenium trinuclear clusters containing dichloroacetates were synthesized, and the self-assembly of a single molecular adlayer composed of these clusters on a graphite surface was investigated by atomic force microscopy (AFM). AFM clearly revealed the dynamics of two-dimensional (2D) structure formation as well as the molecular characteristics of the adlayers at different electrochemical interfaces. The results verified that the design of metal complexes is important not only for redox chemistry but also for molecular assembly and nanoarchitecture construction.

Molecular planting of a single organothiol into a "gap-site" of a 2D patterned adlayer in an electrochemical environment

The self-assembled inclusion of molecules into two-dimensional (2D) porous networks on surfaces has been extensively studied because 2D functional materials consisting of organic molecules have become an important research topic. However, the isolation of a single molecular thiol remains a challenging goal. Here, we report a method of planting and isolating organothiols onto a 2D patterned organic adlayer at an electrochemical interface. In situ scanning tunneling microscopy revealed that the phase transition of an ovalene adlayer is electrochemically induced and that the gap site created by three ovalene molecules serves as a 2D molecular template to isolate thiol molecules and to standardize the distance between them via the formation of precise selective open spaces, suggesting that electrochemical "molecular planting" opens applications for 2D patterns of isolated single organothiol molecules.

Solvent-Dependent Self-Assemblies and Pyridine Modulation of a Porphyrin Molecule at Liquid/Solid Interfaces

On the highly oriented pyrolytic graphite (HOPG) surface, a new porphyrin molecule MT-4 containing a porphine core with six alkyl chains and two carboxyl groups has been explored using scanning tunneling microscopy (STM) technology. Solvent and pyridine regulation have been proved to be two effective ways to control and tune the supramolecular structure of MT-4 at interfaces. Different high-resolution STM (HR-STM) images with highly ordered and closely packed arrangements were gained at the corresponding liquid-solid interface, including phenyl octane (PO), 1-heptanoic acid (HA), and 1-hexanol. Except for the solvent effect, introducing pyridine derivatives such as 4,4'-vinylenedipyridine (DPE) and 4,4'-((1E,1'E)-(2,5-bis(octyloxy)-1,4-phenylene) bis(ethene-2,1-diyl)) dipyridine (PEBP-C8) is also effective to modulate the self-assembly of MT-4. With careful analysis of the STM pictures and the density functional theory (DFT) computational exploration, we figured out the molecular model, interaction energies, and self-assembly mechanism of each system at the interface. This work provides a simple and effective approach for quickly building diverse nanoarchitectures by utilizing different noncovalent interactions. Meanwhile, it would give a perspective to regulate and control self-assembly arrays for devising novel molecular-based materials through more optimal strategies.

Stability of metallo-porphyrin networks under oxygen reduction and evolution conditions in alkaline media

Transition metal atoms stabilised by organic ligands or as oxides exhibit promising catalytic activity for the electrocatalytic reduction and evolution of oxygen. Built-up from earth-abundant elements, they offer affordable alternatives to precious-metal based catalysts for application in fuel cells and electrolysers. For the understanding of a catalyst's activity, insight into its structure on the atomic scale is of highest importance, yet commonly challenging to experimentally access. Here, the structural integrity of a bimetallic iron tetrapyridylporphyrin with co-adsorbed cobalt electrocatalyst on Au(111) is investigated using scanning tunneling microscopy and X-ray absorption spectroscopy. Topographic and spectroscopic characterization reveals structural changes of the molecular coordination network after oxygen reduction, and its decomposition and transformation into catalytically active Co/Fe (oxyhydr)oxide during oxygen evolution. The data establishes a structure-property relationship for the catalyst as a function of electrochemical potential and, in addition, highlights how the reaction direction of electrochemical interconversion between molecular oxygen and hydroxyl anions can have very different effects on the catalyst's structure.

Reversible potential-induced switching of alkyl chain aggregation in octyl-triazatriangulenium adlayers on Au(111)

In situ scanning tunneling microscopy and cyclic voltammetry studies of self-assembled octyl-triazatriangulenium monolayers on Au(111) electrode surfaces in 0.1 M HClO4 reveal a complex surface phase behavior, involving two fast, highly reversible transitions between different ordered adlayer phases: With decreasing potential, the preadsorbed (√19 × √19)R23.4° adlayer first is converted into a (7√3 × 7√3) and then into a (2√3 × 2√3)R30° phase, corresponding to a stepwise increase in the local packing density of the molecules. The (7√3 × 7√3) → (2√3 × 2√3)R30° transition is accompanied by a reorientation of the peripheral octyl chains from a more planar to a close-packed vertical arrangement. This reversible potential-induced switching between a homogeneous adlayer of small vertical extension and a Au surface partially covered by islands of a compact hydrocarbon layer is attributed to changes in the adsorbate charge state and associated changes in the intermolecular interactions.

Surface morphology and optical properties of porphyrin/Au and Au/porphyrin/Au systems

Porphyrin/Au and Au/porphyrin/Au systems were prepared by vacuum evaporation and vacuum sputtering onto glass substrate. The surface morphology of as-prepared systems and those subjected to annealing at 160°C was studied by optical microscopy, atomic force microscopy, and scanning electron microscopy techniques. Absorption and luminescence spectra of as-prepared and annealed samples were measured. Annealing leads to disintegration of the initially continuous gold layer and formation of gold nanoclusters. An amplification of Soret band magnitude was observed on the Au/meso-tetraphenyl porphyrin (TPP) system in comparison with mere TPP. Additional enhancement of luminescence was observed after the sample annealing. In the case of sandwich Au/porphyrin/Au structure, suppression of one of the two porphyrins' luminescence maxima and sufficient enhancement of the second one were observed.

Adsorption and assembly of ions and organic molecules at electrochemical interfaces: nanoscale aspects

We describe the history of electrochemical scanning tunneling microscopy (STM) and advances made in this field during the past 20 years. In situ STM allows one to monitor various electrode processes, such as the underpotential deposition of copper and silver ions; the specific adsorption of iodine and sulfate/bisulfate ions; electrochemical dissolution processes of silicon and gold single-crystal surfaces in electrolyte solutions; and the molecular assembly of metalloporphyrins, metallophthalocyanines, and fullerenes, at atomic and/or molecular resolution. Furthermore, a laser confocal microscope, combined with a differential interference contrast microscope, enables investigation of the dynamics of electrochemical processes at atomic resolution.

Dimensionality effects in the electronic structure of organic semiconductors consisting of polar repeat units

In conjugated organic molecules, excitation gaps typically decrease reciprocally with increasing the number of repeat units, n. This usually holds for individual molecules as well as for the corresponding bulk materials. Here, we show using density-functional theory calculations that a qualitatively different evolution is found for layers built from molecules consisting of polar repeat units. Whereas a 1/n-dependence is still observed in the case of isolated polar molecules, the global gap decreases essentially linearly with n in the corresponding 2D-periodic systems and vanishes beyond a certain molecular length, with the frontier states being localized at opposite ends of the layer. The latter is accompanied by a saturation of the dipole moment per molecule, an effect not observed in the isolated polar molecules. Interestingly, in both cases the limit of the gap for long (but finite) molecules differs qualitatively from that of infinite length obtained in 1D-periodic and 3D-periodic calculations, the latter serving as models for polymers and the bulk. We rationalize these dimensionality effects as a consequence of the potential gradient within the finite-length layers. They arise from the collective action of intra-molecular dipoles in the 2D periodic layers and can be traced back to surface effects.

Molecular assembly of fullerene-conjugated phthalocyanine derivative on Au(111) at single molecular level

Molecular adlayers of doubly C(60)-conjugated phthalocyanine derivatives ((C(60))(2)NiPc) were examined on bare and zinc(II) octaethylporphyrin (ZnOEP)- and coronene-modified Au(111) surfaces. Electrochemical scanning tunneling microscopy (EC-STM) has revealed the structure of the (C(60))(2)NiPc adlayer at single molecular level. The (C(60))(2)NiPc adlayer is strongly influenced by the underlying organic layers, i.e., a disordered, a packed structure of (C(60))(2)NiPc was found on a clean Au(111) surface because of the strong interaction between (C(60))(2)NiPc molecule and Au(111) substrate, whereas a single (C(60))(2)NiPc molecule was clearly distinguished both on ZnOEP and coronene adlayers at a low coverage of (C(60))(2)NiPc molecules. The obtained results in the present study suggest that the underlying organic adlayers play an important role in the formation process of the (C(60))(2)NiPc molecule adlayer.

Advances in supramolecularly assembled nanostructures of fullerenes and porphyrins at surfaces

The ‘bottom-up’ strategy is an attractive and promising approach for the construction of nanoarchitectures. Supramolecular assemblies based on non-covalent interactions have been explored in an attempt to control surface properties. In this minireview, we focus on advances made in the past three years in the field of scanning tunneling microscopy (STM) on supramolecular assembly and the function of porphyrins, phthalocyanines, and fullerenes, non-covalently bound on metal single crystal surfaces. Well-defined adlayers, consisting of porphyrin and phthalocyanine for the design of supramolecular nanoarchitectures, supramolecular traps of C 60 on hydrogen bond networks, a unique approach for controlling molecular orientation by a 1:1 supramolecularly assembled film consisting of C 60 and the related derivatives and metallooctaethylporphyrins, and nanoapplications of fullerenes, either induced by tip manipulation or driven by thermal fluctuations at surfaces, were clearly visualized by STM.

Collectively induced quantum-confined Stark effect in monolayers of molecules consisting of polar repeating units

The electronic structure of terpyrimidinethiols is investigated by means of density-functional theory calculations for isolated molecules and monolayers. In the transition from molecule to self-assembled monolayer (SAM), we observe that the band gap is substantially reduced, frontier states increasingly localize on opposite sides of the SAM, and this polarization in several instances is in the direction opposite to the polarization of the overall charge density. This behavior can be analyzed by analogy to inorganic semiconductor quantum-wells, which, as the SAMs studied here, can be regarded as semiperiodic systems. There, similar observations are made under the influence of a, typically external, electric field and are known as the quantum-confined Stark effect. Without any external perturbation, in oligopyrimidine SAMs one encounters an energy gradient that is generated by the dipole moments of the pyrimidine repeat units. It is particularly strong, reaching values of about 1.6 eV/nm, which corresponds to a substantial electric field of 1.6 × 10(7) V/cm. Close-lying σ- and π-states turn out to be a particular complication for a reliable description of the present systems, as their order is influenced not only by the docking groups and bonding to the metal, but also by the chosen computational approach. In the latter context we demonstrate that deliberately picking a hybrid functional allows avoiding pitfalls due to the infamous self-interaction error. Our results show that when aiming to build a monolayer with a specific electronic structure one can not only resort to the traditional technique of modifying the molecular structure of the constituents, but also try to exploit collective electronic effects.

2D analogues of the inverted hexagonal phase self-assembled from 4,6-dialkoxylated isophthalic acids at solid-liquid interfaces

Self-assembly of organic molecules at solid-liquid interfaces is a route for developing novel functional materials on surfaces and modeling assembly phenomena in 3D. 5-Alkoxylated isophthalic acids (ISA) are known to self-assemble into two-dimensional (2D) lamellae at the interface between a surface of Au(111) or HOPG (highly oriented pyrolytic graphite) and a solvent. Presently, the self-assembly of 4,6-dialkoxylated isophthalic acid derivatives with variable alkyl chain length is investigated at Au(111)-water, Au(111)-tetradecane and HOPG-tetradecane interfaces with a particular focus on the first one. The main aspect of this study is to evaluate the role of the molecular geometry and different interactions in the 2D assembly of amphiphilic molecules. In contrast to 5-alkoxylated ISA, 4,6-dialkoxylated ISA derivatives self-assemble preferentially into arrays of cyclic pentameric/hexameric structures, which appear as 2D analogues of the inverted hexagonal phase of lipids. As a general trend, the derivatives bearing shorter alkyl chains show a higher level of ordering at Au(111)-liquid interfaces. In particular, at the Au(111)-water interface, the 4,6-diheptyloxy ISA derivative forms exclusively pentamers, which are arranged in a quasi-hexagonal lattice. Moreover, the cyclic pentameric features are not empty but host a single isophthalic acid residue which is found to be dynamic. Finally, the packing of the diheptyloxy derivative shows a distinct potential dependence: while at more negative potentials the pentameric arrangement is converted into lamellae, at more positive potentials a loosely packed zig-zag pattern is formed. The present results show that at different solid-liquid interfaces 4,6-dialkoxylated ISA derivatives tend to form cyclic structures that are 2D analogues of an inverted hexagonal phase, akin to lipids having two hydrophobic alkyl chains and a small polar head group. Moreover, the substrate potential at the Au(111)-water interface can tune the 2D molecular arrangement.

Structural characterization of self-assembled monolayers of pyridine-terminated thiolates on gold

Self-assembled monolayers (SAMs) fabricated on Au(111) substrates from a homologous series of pyridine-terminated organothiols have been investigated using ultra high vacuum infrared reflection adsorption spectroscopy (UHV-IRRAS), X-ray photoelectron spectroscopy (XPS), scanning tunnelling microscopy (STM) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. A total of 4 different pyridine-based organothiols have been investigated, consisting of a pyridine unit, one or two phenyl units, a spacer of between one and three methylene units and, finally, a thiol unit. For all pyridine-terminated thiols the immersion of Au-substrates in the corresponding ethanolic solutions was found to result in the formation of highly ordered and densely packed SAMs. For an even number of the methylene spacers between the SH group and the aromatic moieties, the SAM unit-cell is rather large, (5sq.rt(3) x 3)rect, whereas in case of an odd number of methylene units a smaller unit cell is adopted, (2sq.rt(3) x sq.rt(3))R30 degrees. The tilt angle of the molecules amounts to 15 degrees . In contrast to expectation, the pyridine-terminated organic surfaces exposed by the corresponding SAMs showed a surprisingly strong resistance with regard to protonation.

EC-STM study of potential-controlled adsorption of substituted pyrimidinethiol on Au(111)

The ability of the pyrimidine derivatives to form numerous complexes and supramolecular assemblies makes them suitable for the construction of new functional surfaces. Therefore, in this paper, the adsorption behavior of 4-hydroxy-6-(trifluoromethyl)pyrimidine-2-thiol (HTPT) on a Au(111) surface has been investigated using electrochemical scanning tunneling microscopy (EC-STM). High-resolution imaging revealed that the HTPT molecules organize on a gold surface producing a highly ordered monolayer consistent with a (4 x radical3)R-30(0) superstructure. It has been observed that the arrangement of the molecules, as well as their orientation with respect to the substrate, remains stable over a relatively broad potential range from -0.40 to 0.55 V. It has been demonstrated that the presence of the functional groups attached to the aromatic ring affects the final structure of the HTPT adlayer, giving rise to the formation of the assembly with a uniform orientation of the molecules on the substrate.

Programmable hierarchical three-component 2D assembly at a liquid-solid interface: recognition, selection, and transformation

Recognition and selection are of fundamental importance for the hierarchical assembly of supramolecular systems. Coronene induces the formation of a hydrogen-bonded isophthalic acid supramolecular macrocycle, and this well-defined heterocluster forces, in its turn, DBA1 to form a van der Waals stabilized honeycomb lattice, leading to a three-component 2D crystal containing nine molecules in the unit cell. The recognition and selection events enable efficient error correction and healing in redundant mixtures.

Directing the assembly of charged organic molecules by a hydrophilic-hydrophobic nanostructured monolayer at electrified interfaces

Nanostructured monolayers of water-insoluble amphiphilic 5-alkoxy-isophthalic acids direct the reversible self-assembly of water-soluble positively and negatively charged molecules under electrochemical control. The surface potential is in control of the monolayer composition, structure, and guest dynamics.

Epitaxial supramolecular assembly of fullerenes formed by using a coronene template on a Au(111) surface in solution

Characteristic properties of the coronene layer formed on Au(111) for the epitaxial growth of various fullerenes are described. The electrochemical behavior of the coronene adlayer prepared by immersing a Au(111) substrate into a benzene solution containing coronene was investigated in 0.1 M HClO4. The as-prepared coronene adlayer on Au(111) revealed a well-defined (4 x 4) structure. Structural changes of the array of coronene molecules induced by potential manipulation were clearly observed by in situ scanning tunneling microscopy (STM). Supramolecularly assembled layers of fullerenes such as C60, C70, C60-C60 dumbbell dimer (C120), C60-C70 cross-dimer (C130), and C60 triangle trimer (C180) were formed on the well-defined coronene adlayer on the Au(111) surface by immersing the coronene-adsorbed Au(111) substrate into benzene solutions containing those molecules. The adlayers thus prepared were characterized by comparison with those which were directly attached to the Au(111) surface. The C60 molecules formed a honeycomb array with an internal structure in each C60 cage on the coronene adlayer, whereas C70 molecules were one-dimensionally arranged with the same orientations. The dimers, C120 and C130 molecules, formed an identical structure with c(11 x 4 radical3)rect symmetry. For the C130 cross-dimer molecule, C60 and C70 cages were clearly recognized at the molecular level. It was difficult to identify the adlayer of the C180 molecule directly attached to Au(111); however, individual C180 molecules could be recognized on the coronene-modified Au(111) surface. Thus, the adlayer structures of those fullerenes were strongly influenced by the underlying coronene adlayer, suggesting that the insertion of a coronene adlayer plays an important role in the formation of supramolecular assemblies of fullerenes.

Formation of supramolecular nanobelt arrays consisting of cobalt(II) "picket-fence" porphyrin on Au surfaces

Adlayers of cobalt(II) 5,10,15,20-tetrakis(alpha,alpha,alpha,alpha-2-pivalamidophenyl)porphyrin (CoTpivPP) were prepared by immersing either Au(111) or Au(100) substrate in a benzene solution containing CoTpivPP molecules, and they were investigated in 0.1 M HClO4 and 0.1 M H2SO4 by cyclic voltammetry and in situ scanning tunneling microscopy (STM). The adlayer structure and electrochemical properties of CoTpivPP are compared to those of 5,10,15,20-tetraphenyl-21H,23H-porphine cobalt(II) (CoTPP). Characteristic nanobelt arrays consisting of CoTpivPP molecules were produced on both Au(111) and Au(100) surfaces. The stability of the nanobelt arrays was controlled by manipulating the electrode potential. On the other hand, the formation of nanobelt arrays consisting of O2-adducted CoTpivPP molecules depended upon the crystallographic orientation of Au. The state of O2 trapped in the cavity of CoTpivPP was distinctly observed in STM images as a bright spot in the nanobelt array formed on reconstructed Au(100)-(hex) surface, but not on Au(111) surface. This result suggests that the arrangement of underlying Au atoms plays an important role in the formation of nanobelt arrays with the sixth ligand coordination.

Electrochemical control of the structure of two-dimensional supramolecular organization consisting of phthalocyanine and porphyrin on a gold single-crystal surface

Two-component adlayers consisting of cobalt(II) phthalocyanine (CoPc) and a metalloporphyrin such as 5,10,15,20-tetraphenyl-21H,23H-porphine copper(II) (CuTPP), 2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphine copper(II) (CuOEP), or 5,10,15,20-tetraphenyl-21H,23H-porphine cobalt(II) (CoTPP) were prepared by immersing either an Au(111) or Au(100) substrate in a benzene solution containing those molecules. The mixed adlayers thus prepared were investigated in 0.1 M HClO4 by cyclic voltammetry (CV) and in situ scanning tunneling microscopy (STM). The composition of the mixed adlayer consisting of CoPc and CuTPP molecules was found to vary with immersion time. CoPc molecules displaced CuTPP molecules during the modification process with increasing immersion time, and the CuTPP molecules were completely displaced by CoPc molecules in the mixed solution after a prolonged modification time, during which the underlying Au(100) substrate underwent phase transition from the reconstructed (hex) lattice to the unreconstructed (1 x 1) lattice. The two-component adlayer of CoPc and CuTPP was found to form a supramolecular adlayer with the constituent molecules arranged alternately on Au(100)-(hex). The striped structure was stable on Au(100)-(hex) at or near the open circuit potential (OCP), whereas the mixed adlayer was disordered on Au(100)-(1 x 1) at potentials more positive than OCP, where the phase transition of the arrangement of underlying Au atoms (i.e., the lifting of reconstruction) was induced electrochemically. A similar two-component supramolecular adlayer consisting of CoPc and CuTPP was formed on Au(111). A highly ordered, compositionally disordered adlayer of CoTPP and CuTPP was formed on Au(100)-(hex), suggesting that the adlayer structure is independent of the coordinated central metal ion for the formation of supramolecular nanostructures composed of those molecules. A supramolecular organization of CoPc and CuOEP was also found on Au(111). The surface mobility and the molecular reorganization of CoPc and CuOEP on Au(111) were tuned by modulation of the electrode potential. It is concluded that molecular assemblies of the two-component structure consisting of phthalocyanine and porphyrin were controlled not only by the crystallographic orientation of Au but also by the modulation of electrochemical potential.