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Complex Interplay and Hierarchy of Interactions in Two-Dimensional Supramolecular Assemblies
Abstract
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.
... This can be achieved by depositing differently shaped molecular building blocks on surfaces and taking advantage of molecular self-assembly through directive and selective intermolecular interactions, such as hydrogen [5][6][7] and halogen bonds [8][9][10][11][12][13][14]. Numerous multicomponent 2D nanoarchitectures have been achieved by taking advantage of hydrogen bonds [15][16][17][18][19][20], but multicomponent 2D nanoarchitectures stabilized by halogen bonds are more scarce. ...
The ability to engineer sophisticated two-dimensional tessellation organic nanoarchitectures based on triangular molecules and on-surface-synthesized covalent multimers is investigated using scanning tunneling microscopy. 1,3,5-Tris(3,5-dibromophenyl)benzene molecules are deposited on high-temperature Au(111) surfaces to trigger Ullmann coupling. The self-assembly into a semi-regular rhombitrihexagonal tiling superstructure not only depends on the synthesis of the required covalent building blocks but also depends on their ratio. The organic tessellation nanoarchitecture is achieved when the molecules are deposited on a Au(111) surface at 145 °C. This halogen-bonded structure is composed of triangular domains of intact molecules separated by rectangular rows of covalent dimers. The nearly hexagonal vertices are composed of covalent multimers. The experimental observations reveal that the perfect semi-regular rhombitrihexagonal tiling cannot be engineered because it requires, in addition to the dimers and intact molecules, the synthesis of covalent hexagons. This building block is only observed above 165 °C and does not coexist with the other required organic buildings blocks.
... Selective and directional intermolecular binding by halogen bonds [11][12][13][14][15][16][17] as well as hydrogen bonds [5,[18][19][20][21][22][23][24][25] has been successfully exploited to govern molecular self-assembly. Even multi-component organic two-dimensional nanoarchitectures have been successfully achieved [26][27][28]. Multicomponent organic nanoarchitectures have also been engineered by the formation of guest-host structures, where foreign molecules are trapped inside the cavities of a porous 2D network [29,30]. The size and shape of the trapped molecules, as well as those of the host structure cavities, are key parameters, which drastically affect the efficiency of guest-molecule trapping by the host structure [31,32]. ...
The trapping of coronene and zinc phthalocyanine (ZnPc) molecules at low concentration by a two-dimensional self-assembled nanoarchitecture of a push–pull dye is investigated using scanning tunneling microscopy (STM) at the liquid–solid interface. The push–pull molecules adopt an L-shaped conformation and self-assemble on a graphite surface into a hydrogen-bonded Kagomé network with porous hexagonal cavities. This porous host-structure is used to trap coronene and ZnPc guest molecules. STM images reveal that only 11% of the Kagomé network cavities are filled with coronene molecules. In addition, these guest molecules are not locked in the host-network and are desorbing from the surface. In contrast, STM results reveal that the occupancy of the Kagomé cavities by ZnPc evolves linearly with time until 95% are occupied and that the host structure cavities are all occupied after few hours.
... This linear-type arrangement is consistent with the results obtained for a ditopic DAT molecule reported by Fasel and co-workers. 66 Unlike the hexameric rosette formation which results from four HB-interactions per molecule, in the linear arrangement each (DAT-T) 2 molecule participates in eight non-covalent (HB) interactions per molecule, leading to a more thermodynamically stable assembly. It seems that the hexameric assembly is a kinetically trapped arrangement, and that the introduction of thermal energy causes molecular reorganization to yield the more thermodynamically favored linear superstructure. ...
A series of simple ditopic hydrogen bonding capable molecules functionalized with 2,4-diamino-1,3,5-triazine (DAT), barbiturate (B), and phthalhydrazide (PH) on both termini of a 2,2′-bithiophene linker were designed and synthesized. The intrinsic electronic structures of the ditopic DAT, PH, and B molecules were investigated with ground-state DFT calculations. Their solution absorbance was investigated with UV-vis, where it was found that increasing size of R group substituent on the bithiophene linker resulted in a general blue-shift in solution absorbance maximum. The solid-state optical properties of ditopic DAT and B thin films were evaluated by UV-vis, and it was found that the solid-state absorbance was red-shifted with respect to solution absorbance in all cases. The three DAT molecules were vacuum thermal deposited onto Au(111) substrates and the morphologies were examined using STM. (DAT-T)2
was observed to organize into six-membered rosettes on the surface, whereas (DAT-TMe)2
formed linear assemblies before and after thermal annealing. For (DAT-Toct)2
, an irregular arrangement was observed, while (B-TMe)2
showed several co-existent assembly patterns. The work presented here provides fundamental molecular-supramolecular relationships useful for semiconductive materials design based on ditopic hydrogen bonding capable building blocks.
... The other consists of 2D molecular layers held together by intermolecular attractive forces such as hydrogen bonding or van der Waals interaction. 4−8 The 2D molecular materials are usually assembled on solid substrates to achieve a rich family of geometric patterns using either simple molecules 4,9 or complex molecules such as peptides. 10 A particular 2D molecular material that has drawn extensive attentions is known as 2D molecular frameworks, for instance, 2D metal organic frameworks (MOFs). ...
A two-dimensional van der Waals supramolecular framework is created by self-assembled co-crystallization of C60 and octanethiol molecules on the Au(111) surfaces. The framework is characterized by the two-dimensional C60 network, in which the pores are filled by RS-Au-SR (R=CH3(CH2)7S) staples. The framework is stabilized by cooperative interactions involving collective self-assembly instead of the commonly observed pairwise interactions between the nearest neighbours. The pairing of two adjacent C60 molecules and the formation of C60 dimer are visualized by low temperature scanning tunneling microscopic imaging, in conjunction with first-principles calculations, suggesting a charge transfer in each C60 dimer. Such van der Waals C60 supramolecular framework with intermolecular charge transfer, serve a rare example in artificial 2D molecular crystal for inert C60 molecules, is very promising in applications of optics and devices.
... Multiple interaction pathways within a single molecule can lead to a wide array of possible stable architectures on a surface [142]. In our recent work, we found that the multiple interaction pathways intrinsic to a partially-deprotonated TMA molecule can lead to fascinating and complex assemblies on Ag(1 1 1). ...
Molecular self-assembly and reactions at surfaces provide a versatile and appealing approach to nanomaterials synthesis, with a tremendous potential for engineering purpose-driven nanoarchitectures. However, since the outcomes of these processes depend on the chosen substrate, molecular constituents and processing conditions, the parameter space that must be mastered to control the product is enormous. Carboxylated molecules are a useful model system for illustrating the challenges and opportunities in creating on-surface nanoassemblies. These molecular building blocks can self-assemble through hydrogen bonding, or can deprotonate to enable ionic hydrogen bonds or organometallic bonding. Decarboxylation can lead to C–C bond formation and the on-surface synthesis of conjugated polymers. By focussing on key lessons from studies of carboxylated molecules, we highlight the challenges and opportunities in using these building blocks to form complex assemblies at the vanguard of materials design.
... An in-depth analysis of interplay and hierarchy of interactions in the analogous systems PTCDI-BDATB/6phenyl-DAT/6-(4′-cyanophenyl)-DAT has also been published by Fasel et al. 304 As shown in Figure 11, each of these molecules comprises one (two in the case of BDATB) guanamine D-A-D group, and in the case of CPhDAT, a cyano group that can be involved in metal−organic bonds. The comparison between the behaviors of these molecular species allowed the author to explore first in homomolecular systems and then, in binary systems with PTCDI, the interplay and competition of H-bonding, dipole− dipole, and metal coordination interactions. ...
This review aims at giving the readers the basic concepts needed to understand two-dimensional bimolecular organizations at the vacuum-solid interface. The first part describes and analyzes molecules-molecules and molecules-substrates interactions. The current limitations and needs in the understanding of these forces are also detailed. Then, a critical analysis of the past and recent advances in the field is presented by discussing most of the key papers describing bicomponents self-assembly on solid surface in an ultrahigh vacuum environment. These sections are organized by considering decreasing molecule-molecule interaction strengths (i.e. starting from strong directional multiple H bonds up to weaker nondirectional bonds taking into account the increasing fundamental role played by the surface). Finally, we conclude with some research directions (predicting self-assembly, multi-components systems, and nonmetallic surfaces) and potential applications (porous networks and organic surfaces).
... Perylene derivatives sublimated under vacuum have the ability to self-assemble on flat metal surfaces and to form two-dimensional hydrogen-bonded nanoarchitectures [76][77][78][79][80]. These molecules can also form multi-component organic structures when mixed with complementary building blocks [81][82][83]. Perylene derivatives are thus very attractive to fabricate new devices as new organic flat-heterojunction solar cells for example. Annealing is often used to reduce disorder in organic films and to improve the performance of devices based on organic building blocks [84,85]. ...
L’un des défis scientifiques les plus importants pour les prochaines décennies est deconstruire des dispositifs à l’échelle nanométrique. Ces nano-dispositifs promettent d’avoir de nombreusesapplications en physique, chimie et médecine. Par exemple, ils peuvent être utilisés pouraller plus loin dans la miniaturisation des composés électroniques afin d’améliorer les performancesdes processeurs. Une manière judicieuse de créer des nano-dispositifs est de profiter des interactionsintermoléculaires afin d’obtenir des structures auto-assemblées à l’aide d’un petit nombre demolécules (approche "bottom-up"). L’objectif de cette thèse est de créer de nouvelles monocouchesauto-assemblées (SAMs), et d’examiner leurs structures et leurs propriétés électroniques. Toutd’abord, la microscopie à effet tunnel (STM) a été utilisée pour déterminer l’organisation moléculaireavec une résolution atomique. On a observé que le squelette moléculaire et les substituantsutilisés sont des paramètres clés pour contrôler l’auto-assemblage. En outre, nous avons montréqu’un post-recuit de l’échantillon peut être utilisé non seulement pour modifier la structure d’unfilm à base de pérylène comme généralement attendu, mais permet aussi de modifier ses étatsélectroniques. Par la suite, nous avons utilisé des techniques de photoémissions combinés avec desinstallations de rayonnement synchrotron pour accéder aux propriétés chimiques et électroniquesdes SAMs. Une forte modification de la forme et des positions en énergie des états électroniques desSAMs avec l’épaisseur du film moléculaire a été observée. De la même manière nous avons montréque la dynamique de transfert de charge à l’interface PTCDI/Au(111) est fortement affectée parl’épaisseur du film.
... An in-depth analysis of interplay and hierarchy of interactions in the analogous systems PTCDI-BDATB/6phenyl-DAT/6-(4′-cyanophenyl)-DAT has also been published by Fasel et al. 304 As shown in Figure 11, each of these molecules comprises one (two in the case of BDATB) guanamine D-A-D group, and in the case of CPhDAT, a cyano group that can be involved in metal−organic bonds. The comparison between the behaviors of these molecular species allowed the author to explore first in homomolecular systems and then, in binary systems with PTCDI, the interplay and competition of H-bonding, dipole− dipole, and metal coordination interactions. ...
The fabrication of large molecular devices, directly on surfaces in UHV conditions, by covalent coupling of smaller precursors has become in the past years an attractive solution for Molecular Electronics. This review presents the state-of-the-art and an analysis of the potential of this new field, from Ullmann type C-C coupling, cyclodehydrogenation, and reactions involving heteroelements to 2D polymerisation on insulating thin films. Mechanistic insights are also mentioned, giving preliminary explanations on the influence of the substrate and the 2D confinement. Potential perspectives for further developments are then evoked.
This computational study investigates the adsorption of various spiropyran and merocyanine isomers on a NaCl substrate using a combination of density functional theory (DFT) and molecular mechanics (MM) calculations. Four different charge methods were used to determine the partial atomic charges for the adsorbate molecules, including Mulliken population analysis and three electrostatic potential (ESP) methods (Merz–Kollman, ChelpG, and Hu-Lu-Yang), while three different force fields (AMBER 3, CHARMM 27, and MM+) were employed for the MM calculations. The results show that the various DFT charge methods produced similar outcomes for the molecules’ partial atomic charges, with some exceptions for individual atoms and methods. Additionally, it was found that the ESP charge methods were more sensitive to the conformer orientation than the Mulliken approach. The adsorption behavior of merocyanine conformers with the central bond in trans orientation (T-conformers) was similar for various configurations, with the molecule adsorbing mostly flat with its aromatic rings almost parallel to the substrate. However, C-conformers (with their central bond in cis orientation) and spiropyran isomers exhibited inconsistent adsorption behavior, mostly because only some of the aromatic rings contributed to the adsorption behavior. Due to additional van der Waals interactions of more aromatic rings, the adsorption energies for T-conformers are consistently 0.2–0.3 eV higher than for C-conformers and for spiropyran. The study found that the adsorption geometries and energies of stable T-conformers were independent of the partial atomic charge scheme and force field used, and C-conformers show parameter-dependent behavior upon adsorption, leading to metastable configurations. These findings indicate viable pathways during the spiropyran-merocyanine isomerization reactions. Therefore, the results provide initial insights into the possibility of switching spiropyran isomers into merocyanine isomers and vice versa after adsorption onto substrates.
The interaction between organic photoelectric molecules leads to the formation of a certain aggregation structure, which plays a pivotal role in the charge transport at the intermolecular interface. In view of this, we investigated the mechanism and law of intermolecular interaction by detecting the self-assembled behaviors between organic photoelectric molecules at the interface by scanning tunneling microscopy (STM). In this work, the structural transformations of tetraphenylethylene acids (H4ETTCs) on graphite surface induced by temperature and triazine derivatives (zcy-19, zcy-27, and zcy-38 molecules) were studied by STM technology and density functional theory (DFT) calculations. At room temperature, zcy-19 and H4ETTC molecules formed a small range of ordered co-assembled nanostructure, while for zcy-27 or zcy-38 molecules, no co-assembled nanostructures were observed and only their own self-assembled structures existed on graphite surface, individually. In the thermal annealing trials, the original co-assembled H4ETTC/zcy-19 structure disappeared, and only zcy-19 and H4ETTC self-assembled in separate domains. Nevertheless, new well-ordered H4ETTC/zcy-27 or H4ETTC/zcy-38 co-assembled structures appeared at different annealing temperatures, respectively. Combined with DFT calculations, we further analyzed the mechanism of such structural transformations by triazine derivatives and temperature. Results reveal that triazine derivatives could interact with H4ETTC by N-H…O and O-H…N hydrogen bondings, and whether temperature or zcy series compounds could achieve successful regulation of H4ETTC assembly behavior is closely associated with the conjugated skeleton length of zcy series compounds.
The self-assembly of 3,4,9,10-perylenetetracarboxylic diimide (PTCDI) with the star-shaped 1,3,5-tris(4-aminophenyl)benzene (TAPB) on Au(111) is investigated using scanning tunneling microscopy. PTCDI forms a compact canted arrangement on the gold surface. When TAPB is sublimated at a high temperature, the molecule dissociates into a 4-aminophenyl group and a boomerang-shaped compound. The boomerang molecule self-assembles with PTCDI to create a two-dimensional (2D) nanoarchitecture stabilized by N–H···O–C hydrogen bonds between the dissociated TAPB and PTCDI. The molecular ratio of this multicomponent structure is 1:1.
Research on surface chirality is motivated by the need to develop functional chiral surfaces for enantiospecific applications. While molecular chirality in 3D has been the subject of study for almost two centuries, many aspects of 2D chiral surface chemistry have yet to be addressed. In 3D, racemic mixtures of chiral molecules tend to aggregate into racemate (molecularly heterochiral) crystals much more frequently than conglomerate (molecularly homochiral) crystals. Whether chiral adsorbates on surfaces preferentially aggregate into heterochiral rather than homochiral domains (2D crystals or clusters) is not known. In this review, we have made the first attempt to answer the following question based on available data: in 2D racemic mixtures adsorbed on surfaces, is there a clear preference for homochiral or heterochiral aggregation? The current hypothesis is that homochiral packing is preferred on surfaces; in contrast to 3D where heterochiral packing is more common. In this review, we present a simple hierarchical scheme to categorize the chirality of adsorbate–surface systems. We then review the body of work using scanning tunneling microscopy predominantly to study aggregation of racemic adsorbates. Our analysis of the existing literature suggests that there is no clear evidence of any preference for either homochiral or heterochiral aggregation at the molecular level by chiral and prochiral adsorbates on surfaces.
Kinetically controlled hierarchical self-assemblies of all-trans-retinoic acid on Au(111) were investigated via low-temperature scanning tunneling microscopy in ultra-high vacuum. The dominant molecular hierarchical superstructure could be selectively controlled to dimer, tetramer, or pentamer patterns, which were stabilized by hydrogen bonds and van der Waals interactions.
We report on low-temperature scanning tunneling microscopy and spectroscopy measurements on NC-Ph3-CN molecules adsorbed at 300 K on a Cu(111) surface. Upon cooling, the molecules form chain and honeycomb structures, incorporating Cu adatoms supplied by the substrate as metal linkers. In these assemblies, the molecules align along two main directions, with a relative abundance that depends on the coordination number and on the bond length. We show spectroscopic data about the unoccupied molecular orbitals and investigate the patterns obtained by depositing different amounts of molecules. Comparison of these results with the ones obtained for NC-Ph5-CN molecules on the same substrate enables us to establish a hierarchy of the different interaction forces at work in the system.
The adsorption, chemical nature, and self-assembly of diaminotriazinyl- and carboxyl-substituted triphenylamines with dimethylmethylene bridges were studied on Au(111) and Cu(111) at submonolayer coverage by low-temperature scanning tunneling microscopy and density functional theory. On Au(111), both molecules form extended porous honeycomb networks. The geometry of the networks agrees well with density functional theory optimized hydrogen-bonded gas phase structures. Therefore, the self-assemblies on Au(111) are strongly directed by intermolecular hydrogen bond interactions. In contrast, on Cu(111) both molecules aggregate in dense islands owing to the stronger molecule-surface interaction. While the carboxyl substituents partially deprotonate at room temperature on Cu(111), the diaminotriazinyl-substituted triphenylamines adsorb mainly intact. The diaminotriazinyl groups deprotonate gradually at increased adsorption temperatures.
The self-assembly of an amphiphilic 2,7-linked pyrene trimer in an
aqueous environment into two morphologically related forms is
described. Supramolecular polymerization leads to the simultaneous
formation of nanosheets and nanotubes.
We selectively engineer three two-dimensional selfassembled hybrid PTCDI-NaCl nanoarchitectures, i.e. a flower-structure, a mesh-structure and a chain-structure on Au(111). Scanning tunneling microscopy reveals that NaCl-dimers selectively interact with molecular NH group. The PTCDI···NaCl-dimer binding appears to be highly directional. Hybrid molecular-ionic selfassembly is a promising alternative to metal-coordinated and multicomponent organic nanostructures to engineer novel nanoarchitectures on surfaces.
The use of divergent, V-shaped, 4,2':6',4''-terpyridine building blocks that self-assemble into hydrogen-bonded domains and upon addition of copper atoms undergo metallation with concomitant transformation into a coordination network is described; multiple energetically similar structural motifs are observed in both hydrogen-bonded and adatom-coordinated networks.
The influence of self-assembled trimesic acid (TMA) on the electronic properties of a heavily boron-doped silicon surface was investigated using first-principles DFT calculations. Our results demonstrate that the adsorption of isolated TMA molecules, small molecular islands, or complete monolayers is characterized by significant adsorption energy and electron charge transfer to the Si− B interface, while the bonding character of TMA to the surface remains essentially noncovalent. The stability of the adsorbed species was ensured by an attractive interaction from the Si−B interface but also through the formation of hydrogen bonds between TMA units. Beyond this significant stability of the different TMA adlayers, the weak dispersion and the energy level position of states associated with the TMA moieties observed in the band gap region of the Si−B interface suggest that the adsorbed layer can be used to tune the electronic properties of the substrate.
We previously reported that a branched quaterthiophene donor chromophore functionalized with a phthalhydrazide hydrogen bonding (H-bonding) unit (MeBQPH) gives twofold more efficient bulk heterojunction organic solar cells (with C60 acceptors) compared to a nearly identical donor incapable of H-bonding (MeBQPME). Here, scanning tunneling microscopy (STM) studies confirm the formation of MeBQPH trimer rosettes on Au(1 1 1) through phthalhydrazide H-bonding interactions that are sufficiently strong to compete with adsorbate/substrate interactions. The MeBQPME comparator molecule void of hydrogen bonding functionality does not similarly assemble on the metal surface. Complementary density functional theory (DFT) calculations facilitate a structural understanding of the MeBQPH donor assemblies and their strong stabilization through formation of six hydrogen bonds. STM studies also reveal the templated growth of C60 on ordered MeBQPH monolayers with C60 molecules preferentially occupying the threefold interstitial sites of the MeBQPH monolayer. This work supports the idea that H-bonding interactions can be used to control the morphology of organic donor-acceptor blends to potentially create efficient and stable bulk heterojunction photovoltaic devices.
The precise arraying of functional entities in a reproducible and predictable way in morphologically well-defined shapes is a key challenge in materials sciences. In this work, we describe the importance of kinetic effects in the 2D self-assembly of a negatively charged pyrene trimer (Py3) in aqueous media. Under optimized experimental conditions the chain-folded oligomers assemble into exceptionally thin planar assemblies (~ 2 nm thick) with a very high aspect ratio (area/thickness ratio ~ 107 nm). The morphology of the nano-sheets was characterized by different microscopic techniques (AFM, TEM and optical microscopy), whereas UV/vis and fluorescence spectroscopy revealed details on the intramolecular folding of the oligomer stands. Temperature control was shown to be crucial for preventing the formation of kinetically trapped states thus allowing the development of extra-large 2D assemblies.
In situ scanning tunneling microscopy (STM) has been used to examine the spatial structures of mixed molecular adlayers of dithieno[2,3-b:3,2-d]thiophene diphenyl (C6H5-DTT-C6H5, 1), 2-pentafluorophenyl-6-phenyldithieno [2,3-b:3’,2’-d]thiophene (C6F5-DTT-C6H5, 2), and 2,6-bis(pentafluorophenyl) dithieno[3,2-b;2’,3’-d]thiophene (C6F5-DTT-C6F5, 3) codeposited on Au(111) from dosing solutions made of combinations of 1, 2, and 3. 1 and 3 were coadsorbed mainly in a mixed adlattice characterized as (3√13 × 3√13)R13.9° – 1 + 3, and some minor striped structures due to 1. The phenyl and perfluorophenyl groups in 1 and 3 interacted so strongly that they arranged spatially in pairs. Three pairs of 1 and 3 formed a windmill pattern with their terminals converging to a distorted hexagon, which enabled formation of intermolecular hydrogen bonds between 1 and 3. By contrast, 2 and 3 were coadsorbed in segregated domains made of individual molecules. Electrostatic repulsion between C6F5 - groups in 2 and 3 appeared to exceed attraction between C6H5 and C6F5 groups, which drove segregation of 2 and 3. The relative strength of adsorption of these molecules on Au(111) was inferred from their coverages determined from STM results, which suggests a descending sequence of 1 > 3 > 2. Electrochemical potential controlled all spatial structures, as ordered structures were observed only between 0.2 and 0.7 V (vs. reversible hydrogen electrode).
Metal coordination assemblies of the symmetric bi-functional 4,4'-di-(1,4-buta-1,3-diynyl)-benzoic acid are investigated by scanning tunnelling microscopy on metal surfaces. The formation of long-range ordered, short-range disordered and random phases depends on the competition between the convergent and divergent coordination motifs of the individual functional groups and is crucially influenced by the substrate.
Linear bisisophthalic acids 1 and 2 and analogous structures are known to be adsorbed on graphite to give nanopatterns that are programmed by the concerted effects of topology and hydrogen bonding. For comparison, we have now studied the corresponding tetraesters 3–7, which have similar topologies and affinities for graphite but cannot form strong intermolecular interactions. As a result, they fail to crystallize in 2D and 3D according to consistent patterns. The sharply contrasting behavior of the tetraacids and tetraesters provides compelling evidence for the hypothesis that molecular organization is best controlled in both 2D and 3D by using topology and strong directional interactions in tandem to control the relative orientation of neighbors. When topology and dominant intermolecular interactions are in harmony, then organization can be expected to follow reliable patterns within a related series of compounds, and structures in 2D and 3D can be designed to show high levels of homology.
A novel supramolecular system composed of diketopyrrolopyrrole electron donors and perylene derived bisimide (PDI) electron acceptors forms superstructures that undergo fast photoinduced charge separation following assembly. This bio-inspired route towards functional hierar-chical structures, whereby assembly and electronic proper-ties are closely coupled, could lead to new materials for arti-ficial photosynthesis and organic electronics.
In the framework of the Density Functional Theory (DFT-D), we investigate the phthalocyanine (H2Pc) molecule adsorption on SiC(0001)3 × 3 and Si(111)√3 × √3R30°-B (SiB) surfaces, and particularly compare the involved molecular adsorptions. In the H2Pc-SiC(0001)3 × 3 system, the molecular adsorption can be ascribed to a [10+2] cycloaddition. The H2Pc-SiB system is considered in three cases: defectless SiB surface (denoted SiB-0D) and SiB surfaces presenting one or two boron defects (denoted SiB-1D and SiB-2D respectively). The SiB-0D surface is passivated by a charge transfer from the Si adatoms to the boron atoms and therefore no chemical bond between the molecule and the substrate is observed. A similar molecular adsorption as already evidenced in the H2Pc-SiC(0001)3 × 3 system is involved in the SiB-2D case. In the case of the SiB-1D surface, two Si-N bonds (Si1-N1 and Si2-N2) are observed. One of them, Si1-N1, is nearly similar to that found in the H2Pc-SiB-2D system, but the Si2-N2 bond is unexpected. The Bader charge analysis suggests that, in the presence of the H2Pc molecule, the boron atoms behave like an electron reservoir whose availability varies following the involved molecular adsorption process. In the SiB-1D case, charges are transferred from the substrate to the molecule, allowing the Si2-N2 bond formation. Such a kind of molecular adsorption, not yet observed, could be designed by "assisted pseudo cycloaddition".
The self-assembly of cyano-substituted triarylamine derivatives on Au(111) is studied with scanning tunneling microscopy and density functional theory calculations. Two different phases, each stabilized by at least two different cyano bonding motifs are observed. In the first phase, each molecule is involved in dipolar coupling and hydrogen bonding, while in the second phase, dipolar coupling, hydrogen bonding and metal-ligand interactions are present. Interestingly, the metal–ligand bond is already observed for deposition of the molecules with the sample kept at room temperature leaving the herringbone reconstruction unaffected. It is proposed that for establishing this bond, the Au atoms are slightly displaced out of the surface to bind to the cyano ligands. Despite the intact herringbone reconstruction, the Au substrate is found to considerably interact with the cyano ligands affecting the conformation and adsorption geometry, as well as leading to correlation effects on the molecular orientation.
Indolo[2,1-b]quinazoline-6,12-dione (tryptanthrin) was imaged at the
solution-graphite interface using scanning tunneling microscopy. STM
images of the molecular monolayers show clear lobe-to-lobe resolution of
the lowest unoccupied molecular orbitals of the molecules, as well as a
somewhat unusual parallel arrangement of the molecular dipoles.
Evaluation of the dipole-dipole interactions reveals that the
interactions of the closest molecule pairs are reduced due to a magic
angle-like effect. These results represent an important step toward a
more in-depth understanding of the behavior of tryptanthrins, which are
of interest due to their potential as pharmaceutical compounds.
Supramolecular self-assembly of the organic semiconductor perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) together with Ni atoms on the inert Au(111) surface has been investigated using high-resolution scanning tunneling microscopy under ultrahigh vacuum conditions. We demonstrate that it is possible by tuning the co-adsorption conditions to synthesize three distinct self-assembled Ni-PTCDI nanostructures from zero-dimensional (0-D) nanodots over one-dimensional (1-D) chains to a two-dimensional (2-D) porous network. The subtle interplay among non-covalent interactions responsible for the formation of the observed structures has been revealed from force-field structural modeling and calculations of partial charges, bond orders and binding energies in the structures. A unifying motif for the 1-D chains and the 2-D network is found to be double N-H…O hydrogen bonds between PTCDI molecules, similar to the situation found in surface structures formed from pure PTCDI. Most interestingly, we find that the role of the Ni atoms in forming the observed structures is not to participate in metal-organic coordination bonding. Rather, the Ni adatoms acquire a negative partial charge through interaction with the substrate and the Ni-PTCDI interaction is entirely electrostatic.
Application of quantum chemical calculations is vital in understanding hydrogen bonding observed in formamide clusters, a prototype model for motifs found in protein secondary structure. DFT calculations have been performed on four arrangements of formamide clusters [HCONH2]n, (n = 1 − 10) linear, circular, helical and stacked forms. These studies reveal the maximum cooperativity in the stacked arrangement followed by the circular, helical and linear arrangements and is based on interaction energy per monomer. In all these arrangements as we increase cluster size, an increasing trend in cooperativity of hydrogen bonding is observed. Atoms-in-molecule analysis establishes the nature of bonding between the formamide monomers on the basis of electron density values obtained at the bond critical point (BCP).
Graphical Abstract
Manifestation of hydrogen bond cooperativity as a function of increasing cluster size and varying arrangement of molecules is explored using formamide [HCONH2]n (n = 1 – 10) clusters based on DFT calculations.
The substituent effect on the adsorption behaviors of four halogen/pseudohalogen-terminated biphenyls (X–BP–X, with X = F, Br, I and CN) on a Au(1 1 1) surface in 0.1 M HClO4 solution has been investigated by electrochemical scanning tunneling microscopy (ECSTM) and cyclic voltammetry (CV). All the four molecules could form ordered adlayers at adsorption potentials. From F–BP–F, Br–BP–Br to I–BP–I, the molecular adsorption configuration varies from upright, alternating upright and flat-lying to totally flat-lying. In contrast, a trimer motif connected via CN–Au coordination interaction is found as the building unit for the adlayer of CN–BP–CN on Au(1 1 1) electrode. The adlayer structures and configurations are regulated by the properties of the substituted groups.
Tailoring the structure and electronic properties of perylene diimide derivatives is essential for developing the next generation of organic photovoltaic devices. Here we show that 3,4,9,10-Perylenetetracarboxylic Diimide (PTCDI) molecules self-assemble into a new structure after annealing. Scanning tunneling microscopy (STM) reveals strong localized inter-molecular electronic coupling at room temperature when molecules are arranged in a side-by-side packing.
Organization of molecules on surfaces is of utmost importance for the construction of functional materials. Non-covalent, weak and reversible supramolecular interactions provide this organization with high specificity and selectivity. The integration of different supramolecular systems is essential for the assembly of complex and functional architectures on surfaces. Self-assembly, in particular orthogonal self-assembly, is the main route to achieve these integrated architectures. This review article gives an overview of the recent developments of orthogonal supramolecular interactions on surfaces. The first part deals with the use of noncovalent interactions, including hydrogen bonding, metal coordination, electrostatics and host–guest interactions, to modify surfaces. The second part describes the combination of different orthogonal supramolecular interaction motifs for the generation of hybrid assemblies and materials.
The research described in this thesis is focused on the combination of orthogonal
supramolecular interactions for functional monolayer architectures on surfaces. The term
“orthogonal supramolecular interactions” refers to non-covalent interactions that do not
influence each other's assembly properties when applied in the same system. Orthogonal selfassembly
allows extended control over the self-assembly process and promotes new materials
properties. Individual noncovalent interactions (e.g. hydrogen bonding, metal coordination,
electrostatic or host-guest interactions) have been employed in many studies. However, the
combination of different supramolecular interactions in the same system can improve the
properties of the materials. The research described in this thesis aims to develop hybrid,
multifunctional monolayers by using orthogonal supramolecular interactions, enabling the
control over the monolayer composition and functionality. Orthogonal host-guest and
lanthanide-ligand coordination interaction motifs have been employed to create
supramolecular luminescent monolayers in the first part of the thesis (Chapters 3 to 5). The
second part of the thesis (Chapters 6 and 7) deals with the fabrication of functional
monolayers on silicon and gold substrates for applications in electronics.
We present a full density-functional-theory study taking into account the van der Waals interactions of a 2D supramolecular network adsorbed on the Si(111)√3x√3R30°-boron surface denoted SiB. We show that, contrarily to the previous calculations [B. Baris, V. Luzet, E. Duverger, Ph. Sonnet, F. Palmino, and F. Chérioux, Angew. Chem., Int. Ed. 50, 4094 (2011)] molecule-molecule interactions are attractive, thanks to van der Waals corrections which are essential to describe such systems. We confirm the importance of the substrate effect to achieve the molecular network on the boron doped silicon surface without covalent bond. Our simulated STM images, calculated in the framework of the bSKAN code, give better agreement with the experimental STM images than those obtained by the integrated LDOS calculations within the Tersoff-Hamann approximation. The tungsten tip presence is essential to retrieve three paired lobes as observed experimentally. The observed protrusions arise from the phenyl arms located above silicon adatoms.
An open-and-shut case: By using tailored molecules, the formation of open or close-packed supramolecular network can be achieved on a silicon-based surface. The role of molecule-molecule interactions and molecule-substrate interactions to control the geometry of organic network on semi-conductor surface is investigated.
A good sort: A racemate is observed to segregate in situ upon diastereoselective adsorption on an achiral surface by surface-mediated complex formation in a liquid (see picture; yellow: enantiopure resolving agents, ovals: the enantiomers of the racemate to be resolved).
Linear D2h-symmetric bisisophthalic acids 1-2 and related substances have well-defined flattened structures, high affinities for graphite, and strong abilities to engage in specific intermolecular interactions. Their adsorption produces characteristic nanopatterns that reveal how 2D molecular organization can be controlled by reliable interadsorbate interactions such as hydrogen bonds, when properly oriented by molecular geometry. In addition, the behavior of these compounds shows how large-scale organization can be obstructed by programming molecules to associate strongly according to competing motifs that have similar stability and can coexist smoothly without creating significant defects. Analogous new bisisophthalic acids 3a-4a have similar associative properties, and their unique C2h-symmetric crankshaft geometry gives them the added ability to probe the poorly understood effect of chirality on molecular organization. Their adsorption shows how nanopatterns composed predictably of a single enantiomer can be obtained by depositing molecules that can respect established rules of association only by accepting neighbors of the same configuration. In addition, analysis of the adsorption of crankshaft compounds 3a-4a and their derivatives by STM reveals directly at the molecular level how kinetics and thermodynamics compete to control the crystallization of chiral compounds. In such ways, detailed studies of the adsorption of properly designed compounds on surfaces are proving to be a powerful way to discover and test rules that broadly govern molecular organization, in both 2D and 3D.
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.
Thermally stable nanoarchitectures are realized on the Ag(100) surface by self-assembly of asymmetrically substituted arenes. The process is instigated by adsorption-induced molecule → surface charge transfer that gives rise to in-plane dipole moments. Observation and calculation indicate that cooperative interactions further enhance the stability of these polarizable systems.
The bottom-up fabrication of surface hierarchical nanostructures is of great importance for the development of molecular nanostructures for chiral molecular recognition and enantioselective catalysis. Herein, we report the construction of a series of 2D chiral hierarchical structures by trinary molecular self-assembly with copper phthalocyanine (CuPc), 2,3,7,8,12,13-hexahexyloxy-truxenone (TrO23), and 1,3,5-tris(10-carboxydecyloxy) benzene (TCDB). A series of flower-like chiral hierarchical molecular architectures with increased generations are formed, and the details of these structures are investigated by high resolution scanning tunneling microscopy (STM). The flower-like hierarchical molecular architectures could be described by a unified configuration in which the lobe of each architecture is composed of a different number of triangular shape building units (TBUs). The off-axis edge-to-edge packing of TBUs confers the organizational chirality of the hierarchical assemblies. On the other hand, the TBUs can tile the surface in a vertex-sharing configuration, resulting in the expansion of chiral unit cells, which thereby further modulate the periodicity of chiral voids in the multilevel hierarchical assemblies. The formation of desired hierarchical structures could be controlled through tuning the molar ratio of each component in liquid phase. The results are significant for the design and fabrication of multicomponent chiral hierarchical molecular nanostructures.
We studied the supramolecular assembly of a multifunctional ligand, cis-bis-terpyridine tetraphenyl ethylene, on a Cu(111) surface by low-temperature scanning tunneling microscopy (STM). Three distinctive supramolecular structures, metallacycles, propeller-shaped clusters and extended linear chains, are formed under specific assembly conditions owing to different inter-molecular binding modes of Cu-coordination, van der Waals interaction and hydrogen bonding, respectively.
One of the greatest challenges in 2D self-assembly at interfaces is the ability to grow spatially controlled supramolecular motifs in the third dimension, exploiting the surface as a template. In this manuscript a concentration-dependent study by scanning tunneling microscopy at the solid-liquid interface, corroborated by Molecular Dynamics (MD) simulations, reveals the controlled generation of mono- or bilayer self-assembled Kagomé networks based on a fully planar tetracarboxylic acid derivative. By programming the backbone of the molecular building blocks, we present a strategy to gain spatial control over the adlayer structure by conferring self-templating capacity to the 2D self-assembled network.
Insights into the formation of hydrogen bonded clusters are of outstanding importance and quantum chemical calculations play a pivotal role in achieving this understanding. Structure and energetic comparison of linear, circular and standard forms of (acetamide)(n) clusters (n = 1-15) at the B3LYP/D95** level of theory including empirical dispersion correction reveals significant cooperativity of hydrogen bonding and size dependent structural preference. A substantial amount of impact of BSSE is observed in these calculations as the cluster size increases irrespective of the kind of arrangement. The interaction energy per monomer increases from dimer to 15mer by 90% in the case of the circular arrangement, by 76% in the case of the linear arrangement and by 34% in the case of the standard arrangement respectively. The cooperativity in hydrogen bonding is also manifested by a regular decrease in average OH and C-N bond distances, while average C=O and N-H bond lengths increase with increasing cluster size. Atoms-In-Molecules (AIM) analysis is used to characterize the nature of hydrogen bonding between the acetamide molecules in the cluster on the basis of electron density (ρ) values obtained at the bond critical point. An analysis of N-H bond stretching frequencies as a function of the cluster size shows a marked red shift as the cluster size increases from 1 to 15.
Pores for thought: The pore size and pore shape (including "rectangular", triangular, tetragonal, diamond, pentagonal, and hexagonal) in binary molecular porous networks formed by trimesic acid (TMA) and 4,4′-bis(4-pyridyl)biphenyl (BPBP) molecules on Au(111) is tuned simply through changing the TMA:BPBP ratio (see picture).
Adsorption structures of low-coverage CO on Pd(110) were investigated using a low-temperature (4.7 K) scanning tunneling microscope (STM). It was observed that CO molecules dosed at room temperature prefer to form a one-dimensional (1D) chain along [1 ¯ 10], in contrast to a random distribution of CO molecules dosed near liquid-He temperature. These results indicate the existence of an attractive force between CO molecules chemisorbed on Pd(110) along [1 ¯ 10]. Here, we discuss effective intermolecular interactions for the 1D chain formation with energy estimations of individual interaction elements between chemisorbed CO molecules.
The single-crystal neutron diffraction technique was used to determine the crystal structure of melamine, C3H6H6, at 14 K. The molecule is nearly planar. There are three crystallographically inequivalent amine groups with different geometries, the asymmetric unit being the complete molecule.
A new parametric quantum mechanical molecular model, AM1 (Austin Model 1), based on the NDDO approximation, is described. In it the major weaknesses of MNDO, in particular failure to reproduce hydrogen bonds, have been overcome without any increase in computing time. Results for 167 molecules are reported. Parameters are currently available for C, H, O, and N.
The bulk properties of glasses and amorphous materials have been studied widely, but the determination of their structural details at the molecular level is hindered by the lack of long-range order. Recently, two-dimensional, supramolecular random networks were assembled on surfaces, and the identification of elementary structural motifs and defects has provided insights into the intriguing nature of disordered materials. So far, however, such networks have been obtained with homomolecular hydrogen-bonded systems of limited stability. Here we explore robust, disordered coordination networks that incorporate transition-metal centres. Cobalt atoms were co-deposited on metal surfaces with a ditopic linker that is nonlinear, prochiral (deconvoluted in three stereoisomers on two-dimensional confinement) and bears terminal carbonitrile groups. In situ scanning tunnelling microscopy revealed the formation of a set of coordination nodes of similar energy that drives a divergent assembly scenario. The expressed string formation and bifurcation motifs result in a random reticulation of the entire surface.
We demonstrate the suitability of the Ag/Pt(111) strain-relief pattern as efficient template for controlling the formation of well defined heteromolecular nanostructures. Two different species of molecular building blocks with complementary end-group functionalities are combined on this surface, which results in the formation of robust bimolecular nanoribbons driven by the interplay of the site specific adsorption on the strain-relief pattern with the highly directional intermolecular hydrogen-bonding intrinsic to the free bimolecular system.
Two-dimensional supramolecular clusters and chains are observed upon submonolayer deposition of 1-nitronaphthalene (NN) onto reconstructed Au(111). The molecules become pseudochiral upon adsorption. Their handedness is determined from high-resolution scanning tunneling microscope images and local-density calculations. Modeling shows that hydrogen bonds cause the observed self-assembly. Clusters and chains mutually interact via electrostatic repulsion.
Molecular arrangement and transition in the domain boundary of a chiral two-dimensional assembly is clearly revealed by high-resolution STM images on an HOPG surface and a linear dislocation formed by molecular trimers and located at opposite chiral domains is found to directly reverse the chirality on DTCD self-assembly.
High-resolution scanning tunneling microscopy data on the reconstructed Au(111) surface are presented that give a comprehensive picture of the atomic structure, the long-range ordering, and the interaction between reconstruction and surface defects in the reconstructed surface. On the basis of the atomically resolved structure, the stacking-fault-domain model involving periodic transitions from fcc to hcp stacking of top-layer atoms is confirmed. The practically uniform contraction in the surface layer along [11\ifmmode\bar\else\textasciimacron\fi{}0] indicates that the previously proposed soliton functionalisms are not correct descriptions for the fcc$\rightarrow${}hcp stacking transition. The lateral displacement of $\sim${}0.9 \AA{} in the ${(}_{\mathrm{$-${}}1}^{22}$ $_{2}^{0}$) unit cell along [112\ifmmode\bar\else\textasciimacron\fi{}] is in good agreement with the transition between fcc and hcp stacking. The vertical displacement in the transition regions (0.20\ifmmode\pm\else\textpm\fi{}0.05 \AA{}) is largely independent of the tunneling parameters, while the atomic corrugation (0.2 \AA{} typically, up to 1 \AA{}) depends strongly on tunneling parameters and tip conditions.
Adsorption of sub-monolayer amounts of 1-nitronaphthalene (NN) onto Au(111) leads to the aggregation of NN decamers, which exhibit two-dimensional chirality and represent a racemic mixture. In analogy to Pasteur's experiment of 1848 a scanning tunneling microscope can be used to discriminate and separate the enantiomers on a molecular scale.
Reaction of Co(NCS)2 and 2-aminobenzonitrile (ABN) produces the title one-dimensional polymer, [Co(NCS)2(ABN)2]n, where ABN is 2-aminobenzonitrile (C7H6N2). Octahedrally coordinated CoII ions are bridged by the ABN molecules, which are coordinated to the central metal via the N donors of the cyano and nitrile groups.
The family of organometallic Co(III) benzonitrile derivatives of general formula [CoCp(dppe)(p-NCR)][PF6]2 (R = C6H4NMe2, C6H4NH2, C6H4OMe, C6H4C6H5, C6H5, C6H4C6H4NO2, and C6H4NO2) have been synthesized. Spectroscopic and electrochemical data were analyzed in order to evaluate the extent of electronic coupling between the organometallic fragment and the nitrile ligands. An attempt of correlation between NMR spectroscopic data and the second-order non-linear optical properties is presented, based on this work and available published data for related η5-monocyclopentadienyliron, ruthenium and nickel complexes.
Self-assembly yielding supramolecular systems is a relatively
new and fascinating area in polymer science. By combining a knowledge of
organic and bio-organic chemistry with synthetic polymer chemistry many
self-assembling structures can be developed in synthetic polymer systems
via exploitation of inter- and/or intramolecular interactions.
This review describes some double, triple and quadruple hydrogen bonding
systems from the recent literature which have been used in this
context.
Reaction of the copper(II) complex of BpPh,4CN with Rh2(CF3COO)4 results in coordination of the CN groups of the Bp ligand to Rh and the formation of a coordination polymer. This material has been characterized by IR and EPR spectroscopy and electrospray mass spectrometry.
We have used scanning tunneling spectroscopy to spatially resolve the electronic structure of clean Au(111) at low temperature. We find that the long-range herringbone reconstruction on Au(111) acts as a superlattice for surface-state electrons, creating a new band structure and modulated electronic density. Low energy electrons respond to the superlattice by localizing in the hexagonal-close-packed (hcp) region of the reconstruction, while higher energy electrons reverse this trend, shifting density back to the adjacent face-centered-cubic (fcc) region. These observations are quantitatively explained by an extended Kronig-Penney model, from which we estimate the well-depth of the reconstruction-induced surface superlattice.
The interaction of two suitably designed complementary ditopic molecular components (1,2) and (3,4) generates spontaneously an organized supramolecular architecture displaying molecular sorting and orientation.
The realization of molecule-based miniature devices with advanced functions requires the development of new and efficient approaches for combining molecular building blocks into desired functional structures, ideally with these structures supported on suitable substrates. Supramolecular aggregation occurs spontaneously and can lead to controlled structures if selective and directional non-covalent interactions are exploited. But such selective supramolecular assembly has yielded almost exclusively crystals or dissolved structures; the self-assembly of absorbed molecules into larger structures, in contrast, has not yet been directed by controlling selective intermolecular interactions. Here we report the formation of surface-supported supramolecular structures whose size and aggregation pattern are rationally controlled by tuning the non-covalent interactions between individual absorbed molecules. Using low-temperature scanning tunnelling microscopy, we show that substituted porphyrin molecules adsorbed on a gold surface form monomers, trimers, tetramers or extended wire-like structures. We find that each structure corresponds in a predictable fashion to the geometric and chemical nature of the porphyrin substituents that mediate the interactions between individual adsorbed molecules. Our findings suggest that careful placement of functional groups that are able to participate in directed noncovalent interactions will allow the rational design and construction of a wide range of supramolecular architectures absorbed to surfaces.
Crystals grown from a solution containing equimolar portions of barbital (3) and N,N'-bis(4-tert-butylphenyl)-melamine (4) in toluene/isopropyl alcohol (1:1 v/v) comprise a cyclic CA(3).M(3) ''rosette'' (5). The six molecules in this supramolecular motif are held together by 18 hydrogen bonds. Characterization of solutions of equimolar mixtures of 3 and 4 in chloroform by H-1 NMR spectroscopy, gel permeation chromatography, and vapor pressure osmometry demonstrates that the same cyclic CA(3).M(3) rosette (5) is also the most probable structure, when [3] = [4] > 4 mM. H-1 NMR exchange experiments confirm that the CA(3).M(3) rosette (5) is qualitatively much less stable in chloroform solution than the supramolecular aggregate hub(M)(3):3barbital (1) that is preorganized for self-assembly by a covalent tris(melamine) derivative. Complexes formed between 4 and different isocyanurates indicate that intermolecular interactions, as a consequence of the steric bulk of the substituents on these derivatives, favor the formation of the cyclic CA(3).M(3) rosette over competing linear hydrogen-bonded motifs. There is inferential evidence for formation of a complex of modest stability with composition CA.M(2) when 2[3] = [4].
This paper describes the crystal structures of a series of seven 1:1 complexes between N,N'-bis(m-X-phenyl)-melamine and 5,5-diethylbarbituric acid (X = H, F, Cl, Br, I, CH3, and CF3). This series provides small perturbations on the structures of molecules (N,N'-bis(p-X-phenyl)melamines) used ina previous study (Zerkowski, J. A.; MacDonald, J.C.; Seto, C.T.; Wierda, D.A.; Whitesides, G.M. J. Am. Chem. Soc. In press). Both the meta and para complexes crystallize as hydrogen-bonded ''tapes''. With the phenyl substituent in the meta position, however, the melamines can adopt a greater number of molecular conformations; this feature leads to a greater variety of orientations of packing. The meta series packs in both linear and crinkled tape motifs, and four of the seven complexes are solvates. By contrast, the para series, which used the same set of phenyl substituents, always yielded linear tapes and crystals without solvent in the lattice. Inclusion of solvent increases the packing coefficients of members of the meta series to values approximately equal to those of the para series. The multiplicity of molecular conformations available to the meta series is probably largely responsible for the clathration of solvent, which does not rely upon specific non-covalent interactions except in the case of the m-iodo complex with acetonitrile. The wider range of crystalline architecture in the meta series attests only to the kinetic accessibility of these packing formats; polymorphic phases of greater thermodynamic stability may occur. Polymorphism has not been investigated in the series of meta-substituted compounds.
This paper describes the single-crystal X-ray structures of 1: 1 complexes between seven N,N'-bis(4-X-phenyl)melamines (X = H, F, Cl, Br, I, CH3, and CF3) and 5,5-diethylbarbituric acid. These complexes crystallize as infinite tapes having components joined by triads of hydrogen bonds; the tapes pack with their long axes parallel. The crystalline architecture of these complexes-parallel tapes-serves as a structurally constrained framework with which to study physical-organic relationships between the structures of the crystals and the molecules of which they are composed. The complex with X = Br exists in polymorphic forms. One of the polymorphs is isomorphous to the X = Cl complex; the other is related to the X = I complex.
The question of racemate versus conglomerate stability is tremendously important for chiral resolution via crystallization methods. Scanning tunneling microscopic studies with molecular resolution on two-dimensional (2D) model systems contribute at large to solve problems on complex crystallization phenomena. The dependence of lattice polymorphism and enantiomorphism on coverage and enantiomeric excess has been investigated for monolayers of enantiopure and racemic heptahelicene on a Cu(111) surface in ultrahigh vacuum. The densest packing is achieved in a homochiral lattice structure. This should favor 2D conglomerate formation for the racemate, since a higher coverage leads to an overall lower energy. However, only heterochiral structures are observed. Small enantiomeric excess (ee) induces lattice homochirality by suppressing one enantiomorph. At larger ee, we observe crystals disordered at the molecular level. Long-range ordered homochiral structures are suppressed due to small chiral impurities. The preference of a 2D racemic compound formation, the induction of lattice homochirality at small ee, and the solid solution formation at larger ee are discussed in the light of energetic, entropic, and kinetics effects.
The cruciform shape of spirobifluorene disfavors close molecular packing, and more complex derivatives with multiple sites of hydrogen bonding are known to associate to form highly porous networks with significant space for the inclusion of guests. In principle, the porosity can be increased by introducing spacers between the spirobifluorene core and the peripheral sites of association. To test this strategy, compounds 2−3 with multiple diaminotriazine groups attached to a tetraphenylspirobifluorene core were synthesized, and their behavior was compared with that of a model (4) lacking the phenyl spacers. As expected, extended spirobifluorenes 2−3 crystallized to produce open networks held together by hydrogen bonding of diaminotriazine groups; however, the porosities of these networks were lower (53% and 44%, respectively) than that of the network built from model 4 (60%). The decreased porosity arises largely because the added phenyl spacers change the relative contributions of hydrogen bonding and aromatic interactions to the overall lattice energy of the crystals. It becomes advantageous to optimize aromatic interactions at the expense of hydrogen bonds, and crystallization therefore favors networks that permit closer molecular packing.
A series of compounds with multiple PhNH2 groups were synthesized and crystallized, and their structures were solved by X-ray diffraction to assess the ability of -NH2 groups in anilines to direct molecular crystallization. 2,2‘,7,7‘-Tetraamino-9,9‘-spirobi[9H-fluorene] (1c) forms an inclusion complex held together in part by donation of hydrogen bonds from -NH2 groups to guest molecules. Surprisingly, the -NH2 groups do not engage in hydrogen bonding with each other. Tetrakis(4-aminophenyl)methane (2c) crystallizes to form a guest-free close-packed diamondoid network in which each -NH2 group donates and accepts one N−H···N hydrogen bond. Tetrakis[(4-aminophenoxy)methyl]methane (3c), a more flexible analogue, also crystallizes as a close-packed structure maintained by an extensive network of N−H···N hydrogen bonds. Despite the structural similarity of tetraanilines 2c and 3c, their hydrogen-bonding patterns and network topologies are different. A flexible hexaaniline, 1,1‘-oxybis[3-(4-aminophenoxy)-2,2-bis[(4-aminophenoxy)methyl]]propane (4c), produces a close-packed network joined by both N−H···N and N−H···O hydrogen bonds. Tetrakis(4-aminophenyl)ethylene (5) crystallizes as a hydrate to yield a structure consisting of layered hydrogen-bonded sheets. The diverse hydrogen-bonding motifs observed show that crystal engineering using direct interactions of the -NH2 group of anilines is a challenging endeavor, and other intermolecular interactions can compete effectively with N−H···N hydrogen bonds to determine how crystallization occurs.
Elongated honeycombs of interknitted molecular ribbons comprising cyanuric acid and triaminopyrimidine are assembled through a programmed combination of hydrogen-bond triplexes and ion-pairing interactions.
Self-aggregation and hydrogen bond-directed superstructure formation with a perylene bisimide dye were investigated for melamines bearing two or four alkyl chains. For a melamine with two n-octadecyl substituents, large micellar aggregates of several hundred nanometers were observed in methylcyclohexane solution by dynamic light scattering. By means of hydrogen bonding these micelles were loaded with various contents of perylene bisimide dyes up to an equimolar amount. Even at low dye contents, islands of strongly aggregated perylene bisimides were formed according to UV-vis absorption spectroscopy. In a series of melamines functionalized with n-octadecyl esters of chiral amino acids, no self-aggregation of the melamines was observed, and the stability of the assemblies with the perylene bisimide dyes showed strong dependence on the melamine substituents. For four melamine–perylene bisimide combinations stable assemblies formed, which exhibited exciton-coupled circular dichroism (CD) effects for the perylene bisimide absorption bands whose sign is controlled by the stereoisomerism of the respective melamine. While for (S,S)-melamines a negative Cotton effect was observed, indicating an M-helical arrangement of the chromophores within the assembly, the (R,R)-enantiomer induced P-helicity, and no CD effect was found for the achiral (R,S)-diastereomer.
Interest in supramolecular chemistry has grown significantly during the past two decades. In this context, hydrogen bonding and/or coordinative interactions have been extensively used to generate self-assembled one-, two- or three-dimensional polymeric networks. Crystal structure prediction has progressed tremendously, and the challenge for the contemporary supramolecular chemist is now to produce custom-made functional (and multifunctional) materials involving intermolecular interactions. Since the early 1990s, 1,3,5-triazine derivatives have shown their potential as building blocks for the preparation of such materials. In this microreview, a selection of outstanding examples of supramolecular networks involving the 1,3,5-triazine unit are discussed, illustrating the possibility of forming remarkable architectures by means of coordination and/or hydrogen bonds and their applications in host-guest chemistry, catalysis, anion recognition, sensoring, electronics and magnetism.
We have investigated the first stages of organic molecular-beam deposition at room temperature of perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) ultrathin films on Pt(1 0 0) by means of various techniques: Auger electron spectroscopy (AES), low energy electron diffraction (LEED), reflection electron energy loss spectroscopy (REELS) and ultrahigh vacuum (UHV) scanning tunneling microscopy (STM).We show mainly that PTCDI grows on Pt(1 0 0) in the Stranski–Krastanov mode (as it is the case for perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) on Cu(1 1 0)). After the formation of a disordered first monolayer (ML), the formation of growing 3D crystalline islands of PTCDI was observed. Contrary to PTCDA deposited on Cu(1 1 0), annealing of the sample after deposition of the first monolayer did not lead to any molecular ordering. This could be due to a strong perpendicular interaction between platinum and adsorbed PTCDI molecules compared to molecular lateral ones. The EELS surface gap continuously opens to reach a value of 1.8 ± 0.2 eV for a deposit with an equivalent thickness of 20 ML, to be compared with 2.2 eV the expected highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap of PTCDI.
Ordentlich: Die Coabscheidung zweier Molekülspezies mit komplementären Wasserstoffbrücken-Motiven auf einer natürlich gemusterten Templatoberfläche fördert nach STM-Untersuchungen die ewartete Bildung der drei Wasserstoffbrücken pro Molekülpaar, was zu heteromolekularen „Drähten“ (siehe Bild) und supramolekularen Bändern führt. Das Übergitter der Templatoberfläche steuert die supramolekulare Organisation über große Oberflächenbereiche.
Monolayers of the organic molecules perylene-3,4,9,10-tetra-carboxylic-dianhydride (PTCDA) and diimide (PTCDI) on graphite and MoS2 have been imaged with scanning tunneling microscopy. The epitaxial growth of the two molecules is determined by the intermolecular interaction but nearly independent of the substrate. On both substrates the STM image contrast in the submolecularly resolved images is dominated by the aromatic perylene system whereas the polar oxygen and nitrogen groups are invisible. The correlation of the observed inner structure of the molecules to their molecular structure allows us to compare our results with theoretical considerations.
We present the first high resolution STM images of organic molecules on the technological important hydrogen terminated silicon surface. Ordered layers of PTCDA and PTCDI were prepared on this surface by organic molecular beam epitaxy. The submolecular contrast of these molecules on Si(111)/H obtained in the high resolution images agrees with the corresponding images on HOPG and MoS2 substrates.
Two-dimensional supramolecular chemistry on surfaces is strongly governed by directional forces,
and expression of chirality in two dimensions is quite pronounced due to confinement to the plane.
In particular the absence of certain symmetry elements has astrong influence on pattern formation.
With the appearance of scanning tunneling microscopy, two-dimensional supramolecular chirality has
become apopular issue in the field of surface self-assembly during the last decade. By using
recent examples from literature, aconceptual overview on different aspects of surface chirality
will be given. The main topics are adsorption-induced chirality, chiral recognition, transfer of
chirality from single molecules into supramolecular structures, and cooperatively driven chiral amplification
phenomena.
We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al, force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et. al., but a complex set of phi and psi parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.
Occupied and unoccupied densities of states of π-conjugated molecules measured via ultraviolet photoemission spectroscopy and inverse photoemission spectroscopy, respectively, are compared with corresponding densities of states calculated using the semi-empirical Hartree–Fock intermediate neglect of differential overlap (INDO) method. Excellent agreement is obtained for both occupied and unoccupied levels for PTCDA (3,4,9,10-perylenetetracarboxylic dianhydride), α-NPD (N,N′-diphenyl-N,N′-bis(l-naphthyl)-l,l′ biphenyl-4,4″ diamine), and Alq3 (tris(8-hydroxy-quinoline)aluminum). The results provide a full description of the electronic structure of these molecules and demonstrate that semi-empirical techniques can be successfully applied to describe the unoccupied levels of these molecules.
Self-assembly represents a promising strategy for surface functionalisation as well as creating nanostructures with well-controlled, tailor-made properties and functionality. Molecular self-assembly at solid surfaces is governed by the subtle interplay between molecule–molecule and molecule–substrate interactions that can be tuned by varying molecular building blocks, surface chemistry and structure as well as substrate temperature.In this review, basic principles behind molecular self-assembly of organic molecules on metal surfaces will be discussed. Controlling these formation principles allows for creating a wide variety of different molecular surface structures ranging from well-defined clusters, quasi one-dimensional rows to ordered, two-dimensional overlayers. An impressive number of studies exist, demonstrating the ability of molecular self-assembly to create these different structural motifs in a predictable manner by tuning the molecular building blocks as well as the metallic substrate.Here, the multitude of different surface structures of the natural amino acid cysteine on two different gold surfaces observed with scanning tunnelling microscopy will be reviewed. Cysteine on Au(110)-(1×2) represents a model system illustrating the formation of all the above mentioned structural motifs without changing the molecular building blocks or the substrate surface. The only parameters in this system are substrate temperature and molecular coverage, controlling both the molecular adsorption state (physisorption versus chemisorption) and molecular surface mobility. By tuning the adsorption state and the molecular mobility, distinctly different molecular structures are formed, exemplifying the variety of structural motifs that can be achieved by molecular self-assembly.
The design of networks of organic molecules at metal surfaces, highly attractive for a variety of applications ranging from molecular electronics to gas sensors to protective coatings, has matured to a degree that patterns with multinanometre unit cells and almost any arbitrary geometry can be fabricated. This Review provides an overview of vacuum-deposited organic networks at metal surfaces, using intermolecular hydrogen bonding, metal-atom coordination and in situ polymerization. Recent progress in these areas highlights how the design of surface patterns can benefit from the wealth of information available from solution- and bulk-phase chemistry, while at the same time providing novel insights into the nature of such bonds through the applicability of direct scanning probe imaging at metal surfaces.
The structure of ultrathin NaCl films on Au(1 1 1) and on Au(11 12 12), as well as the one of bimolecular 3,4,9,10-perylenetetracarboxylic diimide (PTCDI) and 1,4-bis-(2,4-diamino-1,3,5,-triazine)-benzene (BDATB) islands on NaCl films on both surfaces have been studied with a low-temperature scanning tunnelling microscope. We show that intermixed bimolecular assemblies based on selective three-fold hydrogen-bonding (H-bonding), that have previously been observed on Au(1 1 1) and on Au(11 12 12), can also be stabilized on insulating NaCl films on Au, however, only if these films are grown on Au(11 12 12) and not on Au(1 1 1). The behaviour of the heterocomplex structures is found to be largely influenced by the structural properties of the underlying substrate and by the number of NaCl layers. On a partly NaCl-covered Au(1 1 1) surface, the excess of molecules after completion of the first layer on Au prefers to form a second molecular layer based on ordered heterocomplex structures rather than to adsorb on the NaCl islands. The use of a vicinal surface together with the strong cohesion characteristic of the NaCl film introduces smooth elastic deformations on the NaCl(0 0 1) plane. As a consequence, the periodically modified structure of the overlayer provides preferential binding sites and allows adsorption of two-dimensional molecular structures. In contrast to what is observed on Au(11 12 12), the molecular domains on the NaCl film do not follow the Au step directions, but the NaCl(0 0 1) high symmetry directions. Our results provide a strategy to increase the adsorption energy of flat molecules on insulating layers by choosing a vicinal metal substrate. © 2009 Elsevier B.V. All rights reserved.
The self-assembly of sexiphenyl-dicarbonitrile molecules on the Ag(111) surface is investigated using low-temperature scanning tunneling microscopy (STM) in ultrahigh vacuum. Several nanoporous networks with varying symmetry and pore size coexist on the surface after submonolayer deposition at room temperature. The different rectangular, rhombic, and kagom shaped phases are commensurate with the Ag(111) substrate and extend over micrometer-sized domains separated by step edges. All phases are chiral and have very similar formation energetics. We attribute this to common construction principles: the approximately flat-lying polyphenyl backbones following high-symmetry directions of the substrate, the epitaxial fit and the nodal motif composed of CN end groups laterally attracted by phenyl hydrogens. Close to saturation coverage, a single dense-packed phase prevails with all molecules aligned parallel within one domain. Our results demonstrate that porous networks of different complexity can evolve by the self-assembly of only one molecular species on a metal surface.
Adsorption of sub-monolayer amounts of 1-nitronaphthalene (NN) onto Au(111) leads to the aggregation of NN decamers, which exhibit two-dimensional chirality and represent a racemic mixture. In analogy to Pasteur's experiment of 1848 a scanning tunneling microscope can be used to discriminate and separate the enantiomers on a molecular scale.
Molecular networks: Chiral and metallized Salen molecules on a Cu(111) are investigated using local probe techniques (see figure). Whereas for the parent Co-Salen molecule no self-assembly is observed, in the metal–organic complexes the growth of large and regular molecular networks is achieved through a target-oriented synthetic design of the local electrostatic dipolar molecular fields.
The growth of rubrene (C(42)H(28), 5,6,11,12-tetraphenylnaphthacene) multilayer islands up to a thickness of six layers on a Au(111) surface has been investigated by scanning tunneling microscopy. The molecules self-organize in parallel twin rows, forming mirror domains of defined local structural chirality. Each layer is composed of twin-row domains of the same structural handedness rotated by 120 degrees with respect to each other. Moreover, this structural chirality is transferred to all successive layers in the island, resulting in the formation of three-dimensional objects having a defined structural chirality. The centered rectangular surface unit cell differs from the one characteristic for the single-crystal orthorhombic phase.
A surface-supported open metal-organic nanomesh featuring a 24 nm(2) cavity size and extending to mum domains was fabricated by Co-directed assembly of para-hexaphenyl-dicarbonitrile linker molecules in two dimensions. The metallosupramolecular lattice is thermally robust and resides fully commensurate on the employed Ag(111) substrate as directly verified by high-resolution scanning tunneling microscopy observations.
Self-assembly techniques allow for the fabrication of highly organized architectures with atomic-level precision. Here, we report on molecular-level scanning tunneling microscopy observations demonstrating the supramolecular engineering of complex, regular, and long-range ordered periodic networks on a surface atomic lattice using simple linear molecular bricks. The length variation of the employed de novo synthesized linear dicarbonitrile polyphenyl molecules translates to distinct changes of the bonding motifs that lead to hierarchic order phenomena and unexpected changes of the surface tessellations. The achieved 2D organic networks range from a close-packed chevron pattern via a rhombic network to a hitherto unobserved supramolecular chiral kagomé lattice.
Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally
well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies
the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent
interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural
biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological
structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the
upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would
open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography
and other techniques of microfabrication.
1-Nitronaphthalene adsorbs onto Au(111) in a planar manner leading to two-dimensional chirality. The “handedness” of individual molecules is determined by high resolution scanning tunneling microscopy (see picture). At low coverages enantiopure molecular chains are observed. With increasing coverage, molecules with opposite chirality are admixed until at monolayer coverage racemic structures prevail. The chiral phase transition observed is due to an interplay between electrostatic interactions among the molecules and their interaction with the Au(111) surface.
Chiral molecules have asymmetric arrangements of atoms, forming structures that are non-superposable mirror images of each other. Specific mirror images ('enantiomers') may be obtained either from enantiomerically pure precursor compounds, through enantioselective synthesis, or by resolution of so-called racemic mixtures of opposite enantiomers, provided that racemization (the spontaneous interconversion of enantiomers) is sufficiently slow. Non-covalent assemblies can similarly adopt chiral supramolecular structures, and if they are held together by relatively strong interactions, such as metal coordination, methods analogous to those used to obtain chiral molecules yield enantiomerically pure non-covalent products. But the resolution of assemblies formed through weak interactions, such as hydrogen-bonding, remains challenging, reflecting their lower stability and significantly higher susceptibility to racemization. Here we report the design of supramolecular structures from achiral calix[4]arene dimelamines and cyanurates, which form multiple cooperative hydrogen bonds that together provide sufficient stability to allow the isolation of enantiomerically pure assemblies. Our design strategy is based on a non-covalent 'chiral memory' concept, whereby we first use chiral barbiturates to induce the supramolecular chirality in a hydrogen-bonded assembly, and then substitute them by achiral cyanurates. The stability of the resultant chiral assemblies in benzene, a non-polar solvent not competing for hydrogen bonds, is manifested by a half-life to racemization of more than four days at room temperature.
Hydrogen bonds are like human beings in the sense that they exhibit typical grouplike behavior. As an individual they are feeble, easy to break, and sometimes hard to detect. However, when acting together they become much stronger and lean on each other. This phenomenon, which in scientific terms is called cooperativity, is based on the fact that "1+1 is more than 2". By using this principle, chemists have developed a wide variety of chemically stable structures that are based on the reversible formation of multiple hydrogen bonds. More than 20 years of fundamental studies on these phenomena have gradually developed into a new discipline within the field of organic synthesis, and is nowadays called "noncovalent synthesis". This review describes noncovalent synthesis based on the reversible formation of multiple hydrogen bonds. Starting with a thorough description of what the "hydrogen bond" really is, it guides the reader through a variety of bimolecular and higher order assemblies and exemplifies the general principles that determine their stability. Special focus is given to reversible capsules based on hydrogen-bonding interactions that exhibit interesting encapsulation phenomena. Furthermore, the role of hydrogen-bond formation in self-replicating processes is actively discussed, and finally the review briefly summarizes the development of novel materials (nanotubes, liquid crystals, polymers, etc.) and principles (dynamic libraries) that recently have emanated from this intriguing field of research.
We made theoretical calculations for a benzonitrile molecule and its clusters in the gas phase and as adsorbed on the Au(111) surface, to explain the observation by scanning tunneling microscope, that is, the trimer formation of cyanophenyl porphyrins adsorbed onto the Au(111) surface. With regard to the gas-phase species, ab initio calculations showed that (1) the benzonitrile dimer has a single stable structure that is planar and antiparallel; (2) the trimer has two isoenergetic stable structures, that is, a planar and cyclic structure and an antiparallel and nonplanar one; (3) the clusters are more stable, at low temperatures, than the monomer. For the adsorbed species, we made quantum mechanical/molecular mechanical calculations in which the interaction between the adsorbates and the surface is evaluated in a molecular-mechanical way by using analytical potential functions and an image charge model. Because the stable structures were found to be similar to those in the gas phase, the cluster formation of adsorbed cyanophenyl porphyrins was attributed to the interaction between cyanophenyl groups, which is barely affected by adsorbate-surface interaction. It was also found that the adsorbed cyclic benzonitrile trimer is more stable than the monomer and the dimer because the relative stability is dependent on enthalpy alone. We therefore concluded that the preferential formation of trimers by the adsorbed cyanophenyl porphyrins is due to the negligible contribution of entropy to the relative stability of the adsorbed species and that the adsorption hardly changes the situation found in the gas phase.