Growth induced reordering of fullerene clusters trapped in a two-dimensional supramolecular network

Patterning Porous Networks through Self-Assembly of Programmed Biomacromolecules

Two-dimensional (2D) porous networks are of great interest for the fabrication of complex organized functional materials for potential applications in nanotechnologies and nanoelectronics. This review aims at providing an overview of bottom-up approaches towards the engineering of 2D porous networks by using biomacromolecules, with a particular focus on nucleic acids and proteins. The first part illustrates how the advancements in DNA nanotechnology allowed for the attainment of complex ordered porous two-dimensional DNA nanostructures, thanks to a biomimetic approach based on DNA molecules self-assembly through specific hydrogen-bond base pairing. The second part focuses the attention on how polypeptides and proteins structural properties could be used to engineer organized networks templating the formation of multifunctional materials. The structural organization of all examples is discussed as revealed by scanning probe microscopy or transmission electron microscopy imaging techniques.

Surface-based supramolecular chemistry using hydrogen bonds

CONSPECTUS: The arrangement of molecular species into extended structures remains the focus of much current chemical science. The organization of molecules on surfaces using intermolecular interactions has been studied to a lesser degree than solution or solid-state systems, and unanticipated observations still lie in store. Intermolecular hydrogen bonds are an attractive tool that can be used to facilitate the self-assembly of an extended structure through the careful design of target building blocks. Our studies have focused on the use of 3,4,9,10-perylene tetracarboxylic acid diimides (PTCDIs), and related functionalized analogues, to prepare extended arrays on surfaces. These molecules are ideal for such studies because they are specifically designed to interact with appropriate diaminopyridine-functionalized molecules, and related species, through complementary hydrogen bonds. Additionally, PTCDI species can be functionalized in the bay region of the molecule, facilitating modification of the self-assembled structures that can be prepared. Through a combination of PTCDI derivatives, sometimes in combination with melamine, porous two-dimensional arrays can be formed that can entrap guest molecules. The factors that govern the self-assembly processes of PTCDI derivatives are discussed, and the ability to construct suitable target arrays and host-specific molecular species, including fullerenes and transition metal clusters, is demonstrated.

Self-Assembled Two-Dimensional Heteromolecular Nanoporous Molecular Arrays on Epitaxial Graphene

The development of graphene functionalization strategies that simultaneously achieve two-dimensional (2D) spatial periodicity and substrate registry is of critical importance for graphene-based nanoelectronics and related technologies. Here, we demonstrate the generation of a hydrogen-bonded molecularly thin organic heteromolecular nanoporous network on epitaxial graphene on SiC(0001) using room-temperature ultrahigh vacuum scanning tunneling microscopy. In particular, perylenetetracarboxylic diimide (PTCDI) and melamine are intermixed to form a spatially periodic 2D nanoporous network architecture with hexagonal symmetry and a lattice parameter of 3.45 ± 0.10 nm. The resulting adlayer is in registry with the underlying graphene substrate and possesses a characteristic domain size of 40-50 nm. This molecularly defined nanoporous network holds promise as a template for 2D ordered chemical modification of graphene at lengths scales relevant for graphene band structure engineering.

Bis-thioether-substituted perylene diimides: structural, electrochemical, and spectroelectrochemical properties

The synthesis and separation of the 1,6- and 1,7- isomers of N,N'-bis(alkyl)diadamantylthio-3,4,9,10-perylenetetracarboxylic acid diimide are reported. Investigations of the structural, electrochemical, spectroscopic, and spectroelectrochemical properties of the isomers reveal a sequence of electrochemically and chemically reversible reduction processes for both isomers. Three X-ray crystal structures are reported including a pair of 1,6- and 1,7-isomers demonstrating the twist of the perylene core in the solid state. Our studies thoroughly characterize the mono- and direduced states of the two isomers allowing unequivocal characterization of the reduced species by UV-vis and IR spectroscopic measurements. EPR studies also allow direct identification of the monoreduced PTCDI species and spectroscopic measurements confirm the delocalization of electronic density around the carbonyl moieties of the reduced species.

Noncovalent bicomponent self-assemblies on a silicon surface

Two-dimensional supramolecular multicomponent networks on surfaces are of major interest for the building of highly ordered functional materials with nanometer-sized features especially designed for applications in nanoelectronics, energy storage, sensors, etc. If such molecular edifices have been previously built on noble metals or HOPG surfaces, we have successfully realized a 2D open supramolecular framework on a silicon adatom-based surface under ultrahigh vacuum with thermal stability up to 400 K by combining molecule-molecule and molecule-silicon substrate interactions. One of these robust open networks was further used to control both the growth and the periodicity of the first bicomponent arrays without forming any covalent bond with a silicon surface. Our strategy allows the formation of a well-controlled long-range periodic array of single fullerenes by site-specificity inclusion into a bicomponent supramolecular network.

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.

Complex interplay and hierarchy of interactions in two-dimensional supramolecular assemblies

In order to address the interplay of hydrogen bonding, dipolar interactions, and metal coordination, we have investigated the two-dimensional mono- and bicomponent self-assembly of three closely related diaminotriazine-based molecular building blocks and a complementary perylenetetracarboxylic diimide by means of scanning tunneling microscopy. The simplest molecular species, bis-diaminotriazine-benzene, only interacts via hydrogen bonds and forms a unique supramolecular pattern on the Au(111) surface. For the two related molecular species, which exhibit in addition to hydrogen bonding also dipolar interactions and metal coordination, the number of distinct supramolecular structures increases dramatically with the number of possible interaction channels. Deposition together with the complementary perylene species, however, always results in a single well-defined supramolecular arrangement of molecules. A detailed analysis of the observed mono- and bicomponent assemblies allows shedding light on the hierarchy of the competing interactions, with important implications for the fabrication of surface-supported supramolecular networks by design.

Supramolecular surface-confined architectures created by self-assembly of triangular phenylene-ethynylene macrocycles via van der Waals interaction

At the liquid/graphite interface triangular and rhombic phenylene-ethynylene macrocycles substituted by alkyl chains self-assemble to form porous two-dimensional (2D) molecular networks of honeycomb and Kagomé types, respectively, or close-packed non-porous structures via alkyl chain interdigitation as the directional intermolecular linkages. Factors that affect the formation of the 2D molecular networks, such as alkyl chain length, solvent, solute concentration, and co-adsorption of guest molecules, were elucidated through a systematic study. For the porous networks, various molecules and molecular clusters were adsorbed in the pores reflecting the size and shape complementarity, exploring a new field of 2D host-guest chemistry.

Surface-mediated two-dimensional growth of the pharmaceutical carbamazepine

Scanning tunneling microscopy (STM) has become a staple surface microscopy technique for a number of research fields ranging from semiconductor research to heterogeneous catalysis. Pharmaceutical compounds, however, remain largely unstudied. Here we report the first STM study of carbamazepine (CBZ), an anti-epileptic drug, on Au(111) and Cu(111) surfaces. The analysis reveals that CBZ adopts unusual chiral molecular architectures on both metals. These previously unreported structures, which are strikingly different from CBZ packing arrangements observed in 3D crystal structures, indicate that the main molecular architecture is driven by a combination of CBZ intermolecular hydrogen bonding and metal-CBZ interactions. Comparison of the 2D molecular structures reveals large differences in local geometry and packing density that are dependent on the nature of the metal surface. These results have implications for the potential role of metal surfaces as heteronuclei or templating agents for controlling polymorph formation, which continues to be a problem for many compounds in the pharmaceutical industry including CBZ.

Templating molecular adsorption using a covalent organic framework

A two-dimensional nanoporous covalent organic framework can be prepared on a Au(111) substrate with near complete surface coverage and can be used to control the organisation of a sublimed layer of C(60).

Coupling of triamines with diisocyanates on Au(111) leads to the formation of polyurea networks

The surface-confined coupling reaction between melamine (1,3,5-triazine-2,4,6-triamine) and 1,4-phenylene diisocyanate has been investigated on Au(111) by scanning tunneling microscopy. Diisocyanate species are stabilized at the edges of melamine arrays and coupling reactions to form small urea oligomers may be initiated at room temperature. These oligomers are incorporated into the two-dimensional melamine array. Annealing accelerates the formation of larger oligomers with multiple urea linkages. The oligomers can themselves form ordered 2-D structures stabilized by intermolecular H-bonding. At higher annealing temperatures, oligomers containing as many as seven or eight urea linkages were identified. These oligomers were able to form 2-D porous structures via interoligomer H-bonding interactions. We discuss the composition of all of the phases observed and identify how covalent and noncovalent interactions stabilize each phase.

Orientationally ordered C60 on p-sexiphenyl nanostripes on Ag111

Long range orientational ordering within C(60) monolayers is observed on p-sexithiophene (6P) monolayer nanostripes on Ag(111) at 77 K. Low-temperature scanning tunneling microscopy studies reveal that the C(60)-6P intermolecular interaction constrains all C(60) molecules to adsorb on their hexagons atop 6P molecules. The orientation-dependent bond-to-bond Coulomb interaction between charge deficient single bonds and double bonds with excess charge in neighboring C(60) molecules results in the in-plane orientational ordering and contributes to the lowering of the total energy of the orientationally ordered C(60) islands.

Bimolecular networks and supramolecular traps on Au(111)

We demonstrate the formation of intermixed phases and self assembled molecular templates on the Au(111) surface. The templates are stabilized by hydrogen bonding between melamine molecules with trigonal symmetry and linear PTCDI (perylene tetra-carboxylic di-imide) molecules. When annealed, these molecules spontaneously form either a chiral intermixed phase or a honeycomb arrangement in which vertexes and edges correspond respectively to melamine and PTCDI molecules. We also observe minority phases with more complex intermolecular junctions. The use of these networks as templates is demonstrated by the controlled capture of fullerenes within the pores of the network to form dimers, hexamers, and heptamers. Our results confirm that bimolecular templates can be realized on a range of substrates.

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.

Supramolecular [60]fullerene chemistry on surfaces

This critical review documents the exceptional range of research avenues in [60]fullerene-based monolayers showing unique and spectacular physicochemical properties which prompted such materials to have potential applications in several directions, ranging from sensors and photovoltaic cells to nanostructured devices for advanced electronic applications, that have been pursued during the past decade. It illustrates how progress in covalent [60]fullerene functionalisation led to the development of spectacular surface-immobilised architectures, including dyads and triads for photoinduced electron and energy transfer, self-assembled on a wide variety of surfaces. All of these molecular assemblies and supramolecular arrays feature distinct properties as a consequence of the presence of different molecular units and their spatial arrangement. Since the properties of [60]fullerene-containing films are profoundly controlled by the deposition conditions, substrate of adsorption, and influenced by impurities or disordered surface structures, the progress of such new [60]fullerene-based materials strongly relies on the development of new versatile and broad preparative methodologies. Therefore, the systematic exploration of the most common approaches to prepare and characterise [60]fullerene-containing monolayers embedded into two- or three-dimensional networks will be reviewed in great detail together with their main limitations. Recent investigations hinting at potential technological applications addressing many important fundamental issues, such as a better understanding of interfacial electron transfer, ion transport in thin films, photovoltaic devices and the dynamics associated with monolayer self-assembly, are also highlighted.

Rotation–libration in a hierarchic supramolecular rotor–stator system: Arrhenius activation and retardation by local interaction

Fourfold symmetric zinc-octaethylporphyrin (OEP) has been incorporated in the holes of the hexagonal molecular network generated by thermal dehydrogenation of 4,9-diaminoperylene-quinone-3,10-diimine (DPDI) on a Cu(111) surface and displayed hindered rotation; the reorganization between the potential minima, a rotation-libration, which is characterized by an activation energy of ED=0.17+/-0.03 eV, has been monitored in the STM tunnelling currents as a bi-state "switching".

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.

Structural rearrangement of c(70) monolayers induced by octanethiol adsorption

Mixed monolayers of C70 and octanethiol are prepared on Au(111) by a sequential adsorption method. A partial C70 monolayer is first formed and characterized, followed by the vapor deposition of octanethiol. This results in a well-ordered alkanethiol film where single C70 molecules and small molecular clusters are located at domain boundaries and in disordered regions. Substrate step defects have a large influence on the spatial distribution of C70; adjacent to a substrate defect, C70 binds preferentially on the upper terrace and is depleted on the lower terrace. We explain these observations as resulting from the kinetics of alkanethiol monolayer formation, and we present a simple model for the evolution of surface structure in the C70/octanethiol system.

Homo- and heteroassemblies of lactim/lactam recognition patterns on highly ordered pyrolytic graphite: An STM investigation

The 2D assembly of phthalhydrazide 1 and aminopyrimidine 2 derivatives equipped with C16 and C8 alkyl chains, respectively, on highly ordered pyrolytic graphite (HOPG) was studied by scanning tunneling microscopy. Well-defined, rather complex surface layer patterns emerge resulting from a delicate balance of (self-) complementary (strong) hydrogen bonds and van der Waals force-driven ordering of the alkyl substituents on the HOPG surface. The four different compounds and their 1:1 mixtures yield seven different 2D structures. Phthalhydrazide offers in principle three tautomeric forms, with the lactim/lactam being the most stable. Depending on the solvent, different morphologies can be obtained. In one case, the special self-assembly of achiral 1a leads to a 2D chiral packing with the left- and right-hand motifs present in different domains. We assume that pure 1a is expressed in its lactim/lactam form, whereas in a 1:1 mixture with 2a it switches to the bislactam form. These features display a process of dynamic diversity generation through tautomerism resulting in different nanostructures in response to environmental parameters.

A Homomolecular Porous Network at a Cu(111) Surface

Anthraquinone molecules self-assemble on a Cu(111) surface into a large two-dimensional honeycomb network (square root of 304 x square root of 304)R23 degrees with pore diameters of approximately 50 A. The spontaneous formation of a pattern containing pores roughly five times larger than the size of the constituent molecules is unprecedented. The network originates from a delicate balance between substrate-mediated repulsion and intermolecular attraction involving an unusual chemical motif: hydrogen bonding between a carbonyl oxygen and an aromatic hydrogen atom. Substrate-mediated long-range adsorbate-adsorbate repulsion has been observed on anisotropic surfaces and in the context of the absence of pattern formation. Its applicability for the design of tailored molecular films is explored here.

Adsorption and Dynamics of Long-Range Interacting Fullerenes in a Flexible, Two-Dimensional, Nanoporous Porphyrin Network

Herein, a detailed investigation of the adsorption and dynamics of C60 and C70 fullerenes hosted in a self-assembled, two-dimensional, nanoporous porphyrin network on a solid Ag surface is presented. Time-resolved scanning tunneling microscopy (STM) studies of these supramolecular systems at the molecular scale reveal distinct host-guest interactions giving rise to a pronounced dissimilar mobility of the two fullerenes within the porphyrin network. Furthermore, long-range coverage-dependent interactions between the all-carbon guests, which clearly affect their mobility and are likely mediated by a complex mechanism involving the Ag substrate and the flexible porphyrin host network, are observed. At increased fullerene coverage, this unprecedented interplay results in the formation of large fullerene chains and islands. By applying a lattice gas model with nearest-neighbor interactions and by evaluating the fullerene-pair distribution functions, the respective coverage-dependent guest-guest interaction energies are estimated.

Hydrogen-Bonded PTCDA−Melamine Networks and Mixed Phases

A stable hydrogen-bonding junction is formed between 3,4,9,10-perylene-3,4,9,10-tetracarboxylic-dianhydride (PTCDA) and 1,3,5-triazine-2,4,6-triamine (melamine). This bimolecular system was studied on the Ag-Si(111) square root 3 x square root R 30 degrees surface at sub-monolayer coverage, and two distinct phases are observed. A hexagonal lattice is formed that is stabilized by hydrogen bonding between PTCDA and melamine. This phase, in which melamine acts as a 3-fold vertex, is a close analogue to the 3,4,9,10-perylene-3,4,9,10-tetracarboxylic-diimide-melamine network reported recently. To our knowledge this hydrogen-bonding junction has not been previously observed and might not be expected due to lone pair repulsion. However we confirm that this combination is stable using ab initio methods. In the second intermixed phase parallel rows of PTCDA molecules coexist with an array of melamine molecules, and we propose a model for this structure.

Formation of highly ordered porphyrin adlayers induced by electrochemical potential modulation

Molecular self-assembly of porphyrin derivatives formed with intermolecular hydrogen bonding on the surface of Au(111) electrode in acidic solution can be controlled by varying the number of peripheral carboxy groups and the applied electrochemical potential.

Surface self-assembly of the cyanuric acid-melamine hydrogen bonded network

A hydrogen-bonded bimolecular network formed between cyanuric acid (CA) and melamine (M), CA x M, has been prepared by a surface-based self-assembly process; the monolayer CA x M network is prepared under ultra-high vacuum conditions either by sequential deposition of CA followed by M, or through simultaneous deposition of the component molecular species.