Two-dimensional Supramolecular Assemblies Research Articles

Structural elucidation and interpretation of 2D‒3D supramolecular assemblies featuring lone-pair···π interaction in two Cu(II)‒PDA complexes: Experimental and computational assessment

The structural study of two synthesized Cu-PDA (Cu = Copper(II), PDA = deprotonated Pyridine-2,6-dicarboxylic acid) complexes has been carried out using single-crystal X-ray diffraction where complex (1) [Cu(PDA)(H2O)2] exhibits one-dimensional (1D) and two-dimensional (2D) supramolecular assemblies and complex (2) [Cu(PDA)(H2PDA)]·H2O exhibits 1D, 2D, and 3D (three-dimensional) supramolecular networks in their solid-state structure with the aid of intermolecular noncovalent interactions. Lone pair···π/π···lone pair networks are exclusively found in both complex (1) and (2). The intermolecular interactions are characterized through Hirshfeld surface analysis and quantified by 2D fingerprint plot. The noncovalent interactions are further characterized by Bader's theory of ‘Atoms in Molecules’ (AIM) and ‘noncovalent interaction’ (NCI) plot and the topological parameters at bond critical points (BCPs) have been evaluated. Therefore, the energetic factors to the stabilization of the crystal structure observed experimentally have been obtained by the computational calculations.

Nearly-freestanding supramolecular assembly with tunable structural properties

The synthesis and design of two-dimensional supramolecular assemblies with specific functionalities is one of the principal goals of the emerging field of molecule-based electronics, which is relevant for many technological applications. Although a large number of molecular assemblies have been already investigated, engineering uniform and highly ordered two-dimensional molecular assemblies is still a challenge. Here we report on a novel approach to prepare wide highly crystalline molecular assemblies with tunable structural properties. We make use of the high-reactivity of the carboxylic acid functional moiety and of the predictable structural features of non-polar alkane chains to synthesize 2D supramolecular assemblies of 4-(decyloxy)benzoic acid (4DBA;C_{17}H_{26}O_{3}) on a Au(111) surface. By means of scanning tunneling microscopy, density functional theory calculations and photoemission spectroscopy, we demonstrate that these molecules form a self-limited highly ordered and defect-free two-dimensional single-layer film of micrometer-size, which exhibits a nearly-freestanding character. We prove that by changing the length of the alkoxy chain it is possible to modify in a controlled way the molecular density of the “floating” overlayer without affecting the molecular assembly. This system is especially suitable for engineering molecular assemblies because it represents one of the few 2D molecular arrays with specific functionality where the structural properties can be tuned in a controlled way, while preserving the molecular pattern.

Successive Deprotonation Steering the Structural Evolution of Supramolecular Assemblies on Ag(111).

In this study, we demonstrate the structural evolution of a two-dimensional (2D) supramolecular assembly system, which is steered by the thermally activated deprotonation of the primary organic building blocks on a Ag(111) surface. Scanning tunneling microscopy revealed that a variety of structures, featuring distinct structural, chiral, and intermolecular bonding characters, emerged with the gradual thermal treatments. According to our structural analysis, in combination with density function theory calculations, the structural evolution can be attributed to the successive deprotonation of the organic building blocks due to the inductive effect. Our finding offers a facile strategy towards controlling the supramolecular assembly pathways and provides a comprehensive understanding of the 2D crystal engineering on surfaces.

A comparative conformational study of (C6H5O)2P(O)(NHC(S)NHCH2C6H5) and analogous X-ray structures: energy calculations (solid-state/gas phase)

The crystal structure of diphenyl (benzylcarbamothioyl)phosphoramide, (C6H5O)2P(O)(NHC(S)NHCH2C6H5), is reported. In the P(O)NHC(S)NH moiety the conformations are −ap/+ap/−sp, based on the O = P-N-C/P-N-C-N/P-N-C = S torsion angles (ap = antiperiplanar and sp = synperiplanar), which are different from the conformations of similar moiety in analogous structures retrieved from the Cambridge Structural Database (CSD). The calculated energies of the most stable seven conformers of the title compound (gas phase) are compared with the conformer found in the crystal structure, and the latter shows a relatively high energy value. In the crystal structure, a double-layered two-dimensional supramolecular assembly, along the bc plane, is mediated through (N-H···)(N-H···)O = P and π···π interactions, with cooperation from C-H···π, C-H···O and C-H···S. Energy framework calculations show the significant role of N-H···O hydrogen bonds in the c direction and the weak interactions with mainly dispersion component in the other two directions. The hydrogen bonds and weak interactions were confirmed by the quantum theory of atoms in molecules (AIM).

Simultaneous Spin-Crossover Transition and Conductivity Switching in a Dinuclear Iron(II) Coordination Compound Based on 7,7',8,8'-Tetracyano-p-quinodimethane.

The reaction of Fe(OAc)2 and Hbpypz with neutral TCNQ results in the formation of [Fe2 (bpypz)2 (TCNQ)2 ](TCNQ)2 (1), in which Hbpypz=3,5-bis(2-pyridyl)pyrazole and TCNQ=7,7',8,8'-tetracyano-p-quinodimethane. Crystal packing of 1 with uncoordinated TCNQ and π-π stacking of bpypz- ligands produces an extended two-dimensional supramolecular coordination assembly. Temperature dependence of the dc magnetic susceptibility and heat capacity measurements indicate that 1 undergoes an abrupt spin crossover (SCO) with thermal spin transition temperatures of 339 and 337 K for the heating and cooling modes, respectively, resulting in a thermal hysteresis of 2 K. Remarkably, the temperature dependence of dc electrical transport exhibits a transition that coincides with thermal SCO, demonstrating the thermally induced magnetic and electrical bistability of 1, strongly correlating magnetism with electrical conductivity. This outstanding feature leads to thermally induced simultaneous switching of magnetism and electrical conductivity and a magnetoresistance effect.

On-Surface Evolution of meso-Isomerism in Two-Dimensional Supramolecular Assemblies.

Chiral structures created through the adsorption of molecules onto achiral surfaces play pivotal roles in many fields of science and engineering. Here, we present a systematic study of a novel chiral phenomenon on a surface in terms of organizational chirality, that is, meso-isomerism, through coverage-driven hierarchical polymorphic transitions of supramolecular assemblies of highly symmetric π-conjugated molecules. Four coverage-dependent phases of dehydrobenzo[12]annulene were uniformly fabricated on Ag(111), exhibiting unique chiral characteristics from the single-molecule level to two-dimensional supramolecular assemblies. All coverage-driven phase transitions stem from adsorption-induced pseudo-diastereomerism, and our observation of a lemniscate-type (∞) supramolecular configuration clearly reveals a drastic chiral phase transition from an enantiomeric chiral domain to a meso-isomeric achiral domain. These findings provide new insights into controlling two-dimensional chiral architectures on surfaces.

On‐Surface Evolution of meso‐Isomerism in Two‐Dimensional Supramolecular Assemblies

AbstractChiral structures created through the adsorption of molecules onto achiral surfaces play pivotal roles in many fields of science and engineering. Here, we present a systematic study of a novel chiral phenomenon on a surface in terms of organizational chirality, that is, meso‐isomerism, through coverage‐driven hierarchical polymorphic transitions of supramolecular assemblies of highly symmetric π‐conjugated molecules. Four coverage‐dependent phases of dehydrobenzo[12]annulene were uniformly fabricated on Ag(111), exhibiting unique chiral characteristics from the single‐molecule level to two‐dimensional supramolecular assemblies. All coverage‐driven phase transitions stem from adsorption‐induced pseudo‐diastereomerism, and our observation of a lemniscate‐type (∞) supramolecular configuration clearly reveals a drastic chiral phase transition from an enantiomeric chiral domain to a meso‐isomeric achiral domain. These findings provide new insights into controlling two‐dimensional chiral architectures on surfaces.

Two-dimensional supramolecular assemblies based on β-cyclodextrin-grafted graphene oxide for mitochondrial dysfunction and photothermal therapy.

β-Cyclodextrin (CD)-grafted graphene oxide (GO) is an emerging drug carrier for human diseases therapy. Herein, we report two-dimensional nano-supramolecular assemblies to specifically target and disrupt tumor cell mitochondria in a photocontrollable manner. Moreover, the nanoassemblies displayed extremely high near-infrared-induced photothermal efficiency.

The Importance of CH···X (X = O, π) Interaction of a New Mixed Ligand Cu(II) Coordination Polymer: Structure, Hirshfeld Surface and Theoretical Studies

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.

From a Two-Dimensional Supramolecular Network to One-Dimensional Covalent Polymer at the Liquid/Solid Interface: Insight into the Role of the Stoichiometric Ratio of the Precursors

Co-condensation reaction between 2,6-diaminoanthraquinone and aromatic aldehyde at the octanoic acid/highly oriented pyrolitic graphite (HOPG) interface has been studied with scanning tunneling microscopy (STM). We found that the stoichiometric ratio of the precursors plays a vital role in the formation of the assembling structures. By controlling the molar ratio of the amine and aldehyde monomers, either an ordered, hydrogen-bond-stabilized two-dimensional supramolecular network or assembly of one-dimensional covalent polymers can be successfully constructed. The supramolecular network can also be transformed to covalent polymers by annealing the sample to 373 K.

Cooperating dipole-dipole and van der Waals interactions driven 2D self-assembly of fluorenone derivatives: ester chain length effect.

Two-dimensional supramolecular assemblies of a series of 2,7-bis(10-n-alkoxycarbonyl-decyloxy)-9-fluorenone derivatives (BAF-Cn, n = 1, 3-6) consisting of polar fluorenone moieties and ester alkoxy chains were investigated by scanning tunneling microscopy on highly oriented pyrolytic graphite surfaces. The chain-length effect was observed in the self-assembly of BAF-Cn. Self-assembly of BAF-C1 was composed of a linear I pattern, where the side chains adopted a fully interdigitated arrangement. As the length of side chains increased, the coexistence of a linear I pattern and a cyclic pattern for the self-assembly of BAF-C3 was observed. Upon increasing the length of the alkoxy chain even further (n = 4-6), another linear II structure was observed in the BAF-Cn monolayer, in which the side chains in adjacent rows were arranged in a tail-to-tail configuration. It is reasonable to conclude that not only the van der Waals forces but also the dipole-dipole interactions from both the fluorenone cores and the ester alkoxy chains play critical roles in the self-assemblies of BAF-Cn. Our work provides detailed insights into the effect of intermolecular dipole-dipole and van der Waals interactions on the monolayer morphology of fluorenone derivatives.

Hydrodynamic and Thermophoretic Effects on the Supramolecular Chirality of Pyrene-Derived Nanosheets

Chiroptical properties of two-dimensional (2D) supramolecular assemblies (nanosheets) of achiral, charged pyrene trimers (Py3 ) are rendered chiral by asymmetric physical perturbations. Chiral stimuli in a cuvette can originate either from controlled temperature gradients or by very gentle stirring. The chiroptical activity strongly depends on the degree of supramolecular order of the nanosheets, which is easily controlled by the method of preparation. The high degree of structural order ensures strong cooperative effects within the aggregates, rendering them more susceptible to external stimuli. The samples prepared by using slow thermal annealing protocols are both CD and LD active (in stagnant and stirred solutions), whereas for isothermally aged samples chiroptical activity was in all cases undetectable. In the case of temperature gradients, the optical activity of 2D assemblies could be recorded for a stagnant solution due to migration of the aggregates from the hottest to the coldest regions of the system. However, a considerably stronger exciton coupling, coinciding with the J-band of the interacting pyrenes, is developed upon subtle vortexing (0.5 Hz, 30 rpm) of the aqueous solution of the nanosheets. The sign of the exciton coupling is inverted upon switching between clockwise and counter-clockwise rotation. The supramolecular chirality is evidenced by the appearance of CD activity. To exclude artefacts from proper CD spectra, the contribution from LD to the observed CD was determined. The data suggest that the aggregates experience asymmetrical deformation and alignment effects because of the presence of chiral flows.

Substrate, Molecular Structure, and Solvent Effects in 2D Self-Assembly via Hydrogen and Halogen Bonding

Recently, halogen···halogen interactions have been demonstrated to stabilize two-dimensional supramolecular assemblies at the liquid–solid interface. Here we study the effect of changing the halogen, and report on the 2D supramolecular structures obtained by the adsorption of 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) and 2,4,6-tris(4-iodophenyl)-1,3,5-triazine (TIPT) on both highly oriented pyrolytic graphite and the (111) facet of a gold single crystal. These molecular systems were investigated by combining room-temperature scanning tunneling microscopy in ambient conditions with density functional theory, and are compared to results reported in the literature for the similar molecules 1,3,5-tri(4-bromophenyl)benzene (TBPB) and 1,3,5-tri(4-iodophenyl)benzene (TIPB). We find that the substrate exerts a much stronger effect than the nature of the halogen atoms in the molecular building blocks. Our results indicate that the triazine core, which renders TBPT and TIPT stiff and planar, leads to stronger adsorption energies and hence structures that are different from those found for TBPB and TIPB. On the reconstructed Au(111) surface we find that the TBPT network is sensitive to the fcc- and hcp-stacked regions, indicating a significant substrate effect. This makes TBPT the first molecule reported to form a continuous monolayer at room temperature in which molecular packing is altered on the differently reconstructed regions of the Au(111) surface. Solvent-dependent polymorphs with solvent coadsorption were observed for TBPT on HOPG. This is the first example of a multicomponent self-assembled molecular networks involving the rare cyclic, hydrogen-bonded hexamer of carboxylic groups, R66(24) synthon.

Calix[2]thia[4]phyrin: An Expanded Calixphyrin with Aggregation-Induced Enhanced Emission and Anion Receptor Properties

The synthesis of calix[2]thia[4]phyrin 3, a core-modified expanded calixphyrin, by an efficient synthetic route is reported. 3 exhibits an aggregation-induced enhanced emission (AIEE) phenomenon upon addition of increasing amounts of water. This is attributed to the restricted intramolecular rotation of the meso-aryl rings present on the sp(3) bridging carbons. SEM studies revealed the formation of aggregation in an acetonitrile/water mixture with an average diameter of the aggregate in the range 0.38-2.08 μm. The photoluminescence quantum yield of 3 in 9:1 water/acetonitrile is 5-fold higher than the quantum yield in acetonitrile alone. Single-crystal X-ray analysis of 3 revealed a chairlike conformation stabilized by N-H···N and C-H···π intramolecular hydrogen-bonding interactions. Fluorine atoms on the meso-pentafluorophenyl groups are involved in C-H···F intermolecular hydrogen-bonding interactions to generate a two-dimensional supramolecular assembly in the solid state. In the diprotonated state, 3 has affinity for anions and forms 1:1 complexes with SO4(2-), NO3(-), Cl(-), and ClO4(-) in solution. The tetrahedral anions bind more strongly than the other anions. Single-crystal X-ray structure studies of the ClO4(-) anion complex with 3 revealed the formation of both 1:1 and 1:2 complexes in the solid state, with the host and the guest being held together by N-H···O hydrogen-bonding interactions.

The synthesis of networks based on the coordination of cucurbit[8]urils and alkali or alkaline earth ions in the presence of the polychloride transition-metal anions

To extend the strategy for the induced formation of cucurbit[n]uril–metal by a third species, we introduced alkali or alkaline earth metal ions (Malkali or alkaline earth metal) into cucurbit[8]uril (Q[8])–HCl systems in the presence of polychloride transition-metal anions. The polychloride transition-metal anions acted as structure inducers. A series of Q[8]–Malkali or alkaline earth metal complexes and their corresponding two-dimensional (2D) supramolecular assemblies were first synthesized and characterized by single-crystal X-ray diffraction analysis. The crystal structural analysis revealed that the Q[8]-based trigonal-planar branches in the related compounds are the key building blocks for the construction of the novel 2D Q[8]–Malkali or alkaline earth metal networks in which one or two alkali or alkaline earth metal ions link three Q[8] molecules through direct coordination. Moreover, the novel 2D Q[8]–Malkali or alkaline earth metal networks have a honeycomb shape with hexagonal “nanoholes”. The superimposition of the 2D networks could create novel nanochannels which numerous water molecules and counter anions could occupy.

Supramolecular assemblies of germanium(ii) halides with O-, S- and Se-donor macrocycles – the effects of donor atom type upon structure

Reaction of [GeCl(2)(dioxane)] with [18]aneS(6) (1,4,7,10,13,16-hexathiacyclooctadecane) gives the neutral [GeCl(2)([18]aneS(6))] which forms a supramolecular sheet network involving exocyclic coordination, with the macrocycles bridging Ge atoms which are in a pseudo-trigonal bipyramidal environment from two Cl and two S atoms (saw-horse), with one lone pair assumed to occupy the remaining equatorial void. Conversely, using the mixed S/O macrocycles [18]aneS(3)O(3) (1,4,7-trithia-10,13,16-trioxacyclooctadecane) and [15]aneS(2)O(3) (1,4-dithia-7,10,13-trioxacyclopentadecane) (L) leads to the monocationic pentagonal pyramidal [GeCl(L)](+) whose structures show endocyclic Ge coordination, and displacement of one Cl. The Ge-S and Ge-O bond lengths are surprisingly disparate in these two complexes, and in the former the coordinated Cl is axial, while in the latter it occupies the pentagonal plane (with an S atom axial). Cyclic selenoethers form one-dimensional or two-dimensional supramolecular assemblies with Ge(ii) halides, including [GeCl(2)([8]aneSe(2))] ([8]aneSe(2) = 1,5-diselenacyclooctane), [(GeCl(2))(2)([16]aneSe(4))] ([16]aneSe(4) = 1,5,9,13-tetraselenacyclohexadecane), [GeBr(2)([16]aneSe(4))] and [(GeI(2))(2)([16]aneSe(4))]·GeI(4)- these represent the first germanium species with selenoether ligation. Structural studies on each of these show exocyclic GeX(2) coordination, giving networks based upon Se(2)X(2) coordination at Ge(ii) with a distorted pseudo-trigonal bipyramidal environment in which the Ge-based lone pair is assumed to occupy the vacant equatorial vertex. Further weak GeX contacts are also evident in some cases. The weak, secondary GeS/Se and GeX interactions that pervade these systems may be regarded as a further type of supramolecular interaction allowing assembly of new network structures, and the long II contacts evident between the GeI(2) and GeI(4) units in [(GeI(2))(2)([16]aneSe(4))]·GeI(4) probably provide a small thermodynamic contribution leading to co-crystallisation of ordered GeI(4) molecules within the network.

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.

Effect of Intermolecular Dipole−Dipole Interactions on Interfacial Supramolecular Structures of C3-Symmetric Hexa-peri-hexabenzocoronene Derivatives

Two-dimensional (2D) supramolecular assemblies of a series of novel C(3)-symmetric hexa-peri-hexabenzocoronene (HBC) derivatives bearing different substituents adsorbed on highly oriented pyrolytic graphite were studied by using scanning tunneling microscopy at a solid-liquid interface. It was found that the intermolecular dipole-dipole interactions play a critical role in controlling the interfacial supramolecular assembly of these C(3)-symmetric HBC derivatives at the solid-liquid interface. The HBC molecule bearing three -CF(3) groups could form 2D honeycomb structures because of antiparallel dipole-dipole interactions, whereas HBC molecules bearing three -CN or -NO(2) groups could form hexagonal superstructures because of a special trimeric arrangement induced by dipole-dipole interactions and weak hydrogen bonding interactions ([C-H···NC-] or [C-H···O(2)N-]). Molecular mechanics and dynamics simulations were performed to reveal the physics behind the 2D structures as well as detailed functional group interactions. This work provides an example of how intermolecular dipole-dipole interactions could enable fine control over the self-assembly of disklike π-conjugated molecules.

A nimesulide derivative with potential anti-inflammatory activity: Synthesis, X-ray powder structure analysis and DFT study

A nimesulide derivative, N-[4-(2,5-dioxo-2,5-dihydropyrrol-1-yl)-2-phenoxyphenyl]methanesulfonamide ( 2), was synthesized and its crystal structure has been determined from X-ray powder diffraction data following direct-space global optimization technique and refined by the Rietveld method. The molecular geometry and electronic structure of the title compound were calculated at the DFT level using the hybrid exchange–correlation functional, BLYP. The optimized molecular geometry of 2 corresponds closely to that obtained from the X-ray structure analysis. Intermolecular N–H···O and C–H···O hydrogen bonds in 2 form one-dimensional polymeric chains of R 2 2 (8) rings propagating along the [1 0 0] direction. Further linking between parallel chains via C–H···π (arene) hydrogen bonds generates a two-dimensional supramolecular assembly in the (1 1 0) plane. The title compound exhibits potential anti-inflammatory activity and can induce 64% edema inhibition in rat paws.

Two-dimensional supramolecular assemblies involving neoglycoplipids: Self-organization and insertion properties into Langmuir monolayers

In nature, interfacial molecular recognition and chirality are of fundamental significance for the construction of biological assemblies. Lipid monolayers at liquid interface can be used as biomimetic models for studying molecular interactions in such assemblies. In this article, we will focus on the use of Langmuir monolayers for studying self-organization and insertion properties of several neoglycolipids. Two types of glycolipids have been considered, one in the context of the analysis of glycoconjugates of biological relevance, and one dealing with the ability of some glycoprobes to insert into a monolayer in relation with their efficiency for serving as membrane imaging systems.