Heptagonal Molecular Tiling via Self-Assembly of Heptagonal Phenylene-Ethynylene Macrocycle at the Liquid-Solid Interface

The molecular-level scrutinization of on-surface tiling garners considerable interest among scientists. Herein, we demonstrate molecular-level heptagonal tiling using the self-assembly of a heptagonal meta-phenylene-ethynylene macrocycle featuring 14 long alkoxy substituents at the liquid-graphite interface using scanning tunneling microscopy. This heptagonal macrocycle produces an antiparallel pattern at the 1-phenyloctane-graphite interface through van der Waals interactions between the alkoxy chains. This pattern resembles the densely packed pattern of heptagonal tiles, albeit with variations in the orientations and spacing of heptagonal cores owing to intermolecular interactions between the alkoxy chains. Conversely, at the 1,2,4-trichlorobenzene-graphite interface, the heptagonal molecule forms an oblique pattern composed of four independent molecular orientations. This phenomenon arises from core distortion induced by the coadsorption of the solvent molecules within the intrinsic macrocyclic pores. This study elucidates the design strategy - specifically, the choice of heptagonal molecular building block - for heptagonal tiling and fills a crucial gap in the field of two-dimensional crystal engineering.

Breaking Radial Dipole Symmetry in Planar Macrocycles Modulates Edge-to-Edge Packing and Disrupts Cofacial Stacking

Dipolar interactions are ever-present in supramolecular architectures, though their impact is typically revealed by making dipoles stronger. While it is also possible to assess the role of dipoles by altering their orientations by using synthetic design, doing so without altering the molecular shape is not straightforward. We have now done this by flipping one triazole unit in a rigid macrocycle, tricarb. The macrocycle is composed of three carbazoles (2 Debye) and three triazoles (5 Debye) defining an array of dipoles aligned radially but organized alternately in and out. These dipoles are believed to dictate edge-to-edge tiling and face-to-face stacking. We modified our synthesis to prepare isosteric macrocycles with the orientation of one triazole dipole rotated 40°. The new dipole orientation guides edge-to-edge contacts to reorder the stability of two surface-bound 2D polymorphs. The impact on dipole-enhanced π stacking, however, was unexpected. Our stacking model identified an unchanged set of short-range (3.4 Å) anti-parallel dipole contacts. Despite this situation, the reduction in self-association was attributed to long-range (~6.4 Å) dipolar repulsions between π-stacked macrocycles. This work highlights our ability to control the build-up and symmetry of macrocyclic skeletons by synthetic design, and the work needed to further our understanding of how dipoles control self-assembly.

Triplet States of Cyanostar and Its Anion Complexes

The design of advanced optical materials based on triplet states requires knowledge of the triplet energies of the molecular building blocks. To this end, we report the triplet energy of cyanostar (CS) macrocycles, which are the key structure-directing units of small-molecule ionic isolation lattices (SMILES) that have emerged as programmable optical materials. Cyanostar is a cyclic pentamer of covalently linked cyanostilbene units that form π-stacked dimers when binding anions as 2:1 complexes. The triplet energies, E_T, of the parent cyanostar and its 2:1 complex around PF₆^- are measured to be 1.96 and 2.02 eV, respectively, using phosphorescence quenching studies at room temperature. The similarity of these triplet energies suggests that anion complexation leaves the triplet energy relatively unchanged. Similar energies (2.0 and 1.98 eV, respectively) were also obtained from phosphorescence spectra of the iodinated form, I-CS, and of complexes formed with PF₆^- and IO₄^- recorded at 85 K in an organic glass. Thus, measures of the triplet energies likely reflect geometries close to those of the ground state either directly by triplet energy transfer to the ground state or indirectly by using frozen media to inhibit relaxation. Density functional theory (DFT) and time-dependent DFT were undertaken on a cyanostar analogue, CSH, to examine the triplet state. The triplet excitation localizes on a single olefin whether in the single cyanostar or its π-stacked dimer. Restriction of the geometrical changes by forming either a dimer of macrocycles, (CSH)₂, or a complex, (CSH)₂·PF₆^-, reduces the relaxation resulting in an adiabatic energy of the triplet state of 2.0 eV. This structural constraint is also expected for solid-state SMILES materials. The obtained T₁ energy of 2.0 eV is a key guide line for the design of SMILES materials for the manipulation of triplet excitons by triplet state engineering in the future.

Anion-Selective Electrodes Based On a CH-Hydrogen Bonding Bis-macrocyclic Ionophore with a Clamshell Architecture

CH-hydrogen bonding provides access to new building blocks for making macrocyclic ionophores with high degrees of preorganization and selective anion recognition. In this study, an anion-binding ionophore in the shape of a clamshell (ClS) was employed that is composed of two cyanostar (CNstar) macrocycles with preorganized cavities linked with a 12-carbon chain. This ionophore allows for anion complexation by CH-hydrogen bonding. The potentiometric performance of membrane-based ion-selective electrodes incorporating this ionophore was evaluated. Different membrane compositions were prepared to determine the optimum concentrations of the ionophore and lipophilic additive in the membrane. The optimized electrode had a slope of -58.2 mV/decade and demonstrated an anti-Hofmeister selectivity pattern toward iodide with a nanomolar detection limit. Electrospray ionization mass spectrometry was employed to study the relative association strengths of ClS with various anions. The observed mass peaks of the ion-ionophore complexes were found to be consistent with the potentiometric selectivity pattern of the corresponding electrodes. Overall, the selectivity of the electrode could be altered by using an ionophore in which the two CNstar macrocycles are linked together with a flexible 12-carbon chain to control the molecularity of the binding event.

Nanoscale tailoring of supramolecular crystals via an oriented external electric field

The oriented external electric field of a scanning tunneling microscope (STM) has recently been adapted for controlling the chemical reaction and supramolecular phase transition at surfaces with molecular precision. However, to date, advance controls using such electric-fields for crystal engineering have not been achieved yet. Here, we present how the directional electric-field of an STM can be utilized to harness supramolecular crystallization on a solid surface. We show that a glass-like random-tiling assembly composed of p-terphenyl-3,5,3',5'-tetracarboxylic acid can transform into close-packed periodic assemblies under positive substrate bias conditions at the liquid/solid interface. Importantly, the nucleation and subsequent crystal growth for such field-induced products can be artificially tailored at the early stage in a real-time fashion. Through this method, we were able to produce a two-dimensional supramolecular single crystal. The as-prepared crystals with apparent brightness are ascribed to a spectroscopic feature linked to the electron density of states, which is thus strongly STM bias dependent.

Zero-Overlap Fluorophores for Fluorescent Studies at Any Concentration

Fluorophores are powerful tools for the study of chemistry, biology, and physics. However, fluorescence is severely impaired when concentrations climb above 5 μM as a result of effects like self-absorption and chromatic shifts in the emitted light. Herein, we report the creation of a charge-transfer (CT) fluorophore and the discovery that its emission color seen at low concentrations is unchanged even at 5 mM, some 3 orders of magnitude beyond typical limits. The fluorophore is composed of a triphenylamine-substituted cyanostar macrocycle, and it exhibits a remarkable Stokes shift of 15 000 cm^-1 to generate emission at 633 nm. Crucial to the performance of this fluorophore is the observation that its emission spectrum shows near-zero overlap with the absorption band at 325 nm. We propose that reducing the spectral overlap to zero is a key to achieving full fluorescence across all concentrations. The triphenylamine donor and five cyanostilbene acceptor units of the macrocycle generate an emissive CT state. Unlike closely related donor-acceptor control compounds showing dual emission, the cyanostar framework inhibited emission from the second state to create a zero-overlap fluorophore. We demonstrated the use of emission spectroscopy for characterization of host-guest complexation at millimolar concentrations, which are typically the exclusive domain of NMR spectroscopy. The binding of the PF₆^- anion generates a 2:1 sandwich complex with blue-shifted emission. Distinct from twisted intramolecular charge-transfer (TICT) states, experiment-supported density functional theory shows a 67° twist inside an acceptor unit in the CT state instead of displaying a twist between the donor and acceptor; it is TICT-like. Inspired by the findings, we uncovered similar concentration-independent behavior from a control compound, strongly suggesting this behavior may be latent to other large Stokes-shift fluorophores. We discuss strategies capable of generating zero-overlap fluorophores to enable accurate fluorescence characterization of processes across all practical concentrations.

Trapping a pentagonal molecule in a self-assembled molecular network: an alkoxylated isosceles triangular molecule does the job

We herein report a unique example of on-surface adaptive self-assembly. A pentagon-shaped macrocycle, cyclic [5]meta-phenyleneacetylene [5]CMPA, is trapped by the adaptive supramolecular network formed by an isosceles triangular molecule, alkoxy substituted dehydrobenzo[14]annulene [14]ISODBA at the liquid/graphite interface, leading to a highly ordered and large-area bicomponent self-assembled molecular network (SAMN), as revealed by scanning tunneling microscopy (STM).

Stereospecific Epitaxial Growth of Bilayered Porous Molecular Networks

Stereocontrolled multilayer growth of supramolecular porous networks at the interface between graphite and a solution was investigated. For this study, we designed a chiral dehydrobenzo[12]annulene (DBA) building block bearing alkoxy chains substituted at the 2 position with hydroxy groups, which enable van der Waals stabilization in a layer and potential hydrogen-bonding interactions between the layers. Bias voltage-dependent scanning tunneling microscopy (STM) experiments revealed the diastereospecificity of the bilayer with respect to both the intrinsic chirality of the building blocks and the supramolecular chirality of the self-assembled networks. Top and bottom layers within the same crystalline domain were composed of the same enantiomers but displayed opposite supramolecular chiralities.

Electric-field-induced supramolecular phase transitions at the liquid/solid interface: cat-assembly from solvent additives

The electrically triggered phase transformations of trimesic acid can be efficiently promoted to occur in an environment where trace levels of a highly polar solvent additive are present at the liquid/solid interface, as revealed by STM and DFT simulations.

Zagreb Polynomials and redefined Zagreb indices of Dendrimers and Polyomino Chains

Dendrimers have an incredibly strong potential because their structure allows multivalent frameworks, i.e. one dendrimer molecule has many possible destinations to couple to a functioning species. Researchers expected to utilize the hydrophobic conditions of the dendritic media to lead photochemical responses that make the things that are artificially tested. Carboxylic acid and phenol- terminated water-dissolvable dendrimers were joined to set up their utility in tranquilize conveyance and furthermore driving compound reactions in their inner parts. This may empower scientists to associate both concentrating on atoms and medication particles to the equivalent dendrimer, which could diminish negative manifestations of prescriptions on sound and health cells. Topological indices are numerical numbers associated with the graphs of dendrimers and are invariant up to graph isomorphism. These numbers compare certain physicochemical properties like boiling point, strain energy, stability, etc. of a synthetic compound. There are three main types of topological indices, i.e degree-based, distance-based and spectrum-based. In this paper, our aim is to compute some degree-based indices and polynomials for some dendrimers and polyomino chains. We computed redefined first, second and third Zagreb indices of PAMAM dendrimers PD1, PD2, and DS1 and linear Polyomino chain Ln , Zigzag Polyomino chain Zn, polyomino chain with n squares and of m segments $B_{n}^{1}$and $B_{n}^{2}$We also computed some Zagreb polynomials of understudy dendrimers and chains.

Irregularity Indices of Dendrimer Structures Used as Molecular Disrupter in QSAR Study

Dendrimers are rising polymeric structures known for their flexibility in medication conveyance and high usefulness, whose properties are same biomolecules. These nanostructured macromolecules have shown potential capacities in capturing as well as conjugating the high subatomic weight hydrophilic/hydrophobic substances by host-visitor collaborations and covalent holding (prodrug approach) individually. In quantitative structure-property relationships (QSPR), topological indices are utilized to gather properties of dendrimers. Topological indices catch symmetry of dendrimer structures and give it a logical reasoning to predict properties, for instance, viscosity, boiling points, the radius of gyrations, etc. In this report, we intend to examine dendrimers through irregularity indices that are valuable in QSPR studies. We studied sixteen irregularity indices if diverse dendrimer structures.

Electrostatically Driven Guest Binding in Self-Assembled Molecular Network of Hexagonal Pyridine Macrocycle at the Liquid/Solid Interface: Symmetry Breaking Induced by Coadsorbed Solvent Molecules

We present here the construction of a self-assembled two-dimensional network at the liquid/solid interface using a hexagonal pyridine macrocycle which binds an organic cation in its intrinsic porous space by electrostatic interactions. For this purpose, a hexagonal pyridinylene-butadiynylene macrocycle (PyBM) having six octyloxymethyl groups, PyBM-C8, was synthesized. As guests, tropylium (Tr) tetrafluoroborate and trioxatriangulenium (TOTA) hexafluorophosphate were used. In this study, we focused on (i) the network patterns of PyBM-C8 which change in response to its concentration and (ii) the position of the guest immobilized in the porous space of the macrocycle. Scanning tunneling microscopy (STM) observations at the interface of 1,2,4-trichlorobenzene (TCB) and highly oriented pyrolytic graphite (HOPG) revealed that PyBM-C8 formed four different polymorphs, oblique, loose hexagonal, linear, and rectangular, depending on the solute concentration and annealing treatment. Solvent TCB molecules are likely coadsorbed to not only the intrinsically porous space of PyBM-C8 (internal TCB) but also the space outside of the macrocycle between its alkyl chains (external TCB) in most of the cases. Upon adding the guest cation, whereas small Tr was not visualized in the pore due to size mismatching, larger TOTA was clearly observed in each pore. In addition, based on high-resolution STM images of the rhombus packing pattern of PyBM-C8, we revealed experimentally that TOTA was placed at an off-center position of the deformed hexagonal macrocyclic core in the rhombus pattern. On the basis of the molecular mechanics calculations, we hypothesize that the off-center location of TOTA is due to deformation of the hexagonal macrocycle through interaction with two external TCB molecules located at opposite edges of the macrocyclic core. Symmetry breaking of the macrocyclic host framework induced by coadsorbed surrounding solvent molecules thus plays a significant role in host-guest complexation at the liquid/solid interface.

Macrocyclic pentamers functionalised around their periphery as potential building blocks

The elaboration of a five-fold symmetric macrocyclic aromatic pentamer bearing peripheral benzyloxy and hydroxyl groups is described. These could be used to explore further functionalisation for use as pentagonal building blocks. The internal fluorine-substituted macrocycle has been prepared via a one-pot procedure which is an improvement on the stepwise chain growth approach reported in the literature.

The elaboration of a five-fold symmetric macrocyclic aromatic pentamer bearing peripheral benzyloxy and hydroxyl groups is described. The macrocycle bearing internal fluorine substituents has been prepared via a one-pot procedure.

Some Reverse Degree-Based Topological Indices and Polynomials of Dendrimers

Topological indices collect information from the graph of molecule and help to predict properties of the underlying molecule. Zagreb indices are among the most studied topological indices due to their applications in chemistry. In this paper, we compute first and second reverse Zagreb indices, reverse hyper-Zagreb indices and their polynomials of Prophyrin, Propyl ether imine, Zinc Porphyrin and Poly (ethylene amido amine) dendrimers.

Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity

Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.

Electrostatically Driven Guest Binding in a Self-Assembled Porous Network at the Liquid/Solid Interface

We present here the construction of a self-assembled two-dimensional (2D) porous monolayer bearing a highly polar 2D space to study guest co-adsorption through electrostatic interactions at the liquid/solid interface. For this purpose, a dehydrobenzo[12]annulene (DBA) derivative, DBA-TeEG, having tetraethylene glycol (TeEG) groups at the end of the three alternating alkoxy chains connected by p-phenylene linkers was synthesized. As a reference host molecule, DBA-C10, having nonpolar C₁₀ alkyl chains at three alternating terminals, was employed. As guest molecules, hexagonal phenylene-ethynylene macrocycles (PEMs) attached by triethylene glycol (TEG) ester and hexyl ester groups, PEM-TEG and PEM-C6, respectively, at each vertex of the macrocyclic periphery were used. Scanning tunneling microscopy observations at the 1,2,4-trichlorobenzene/highly oriented pyrolytic graphite interface revealed that PEM-TEG was immobilized in the pores formed by DBA-TeEG at higher probability because of electrostatic interactions such as dipole-dipole and hydrogen bonding interactions between oligoether units of the host and guest, in comparison to PEM-C6 with nonpolar groups. These observations are discussed based on molecular mechanics simulations to investigate the role of the polar functional groups. When a nonpolar host matrix formed by DBA-C10 was used, however, only phase separation and preferential adsorption were observed; virtually no host-guest complexation was discernible. This is ascribed to the strong affinity between the guest molecules which form by themselves densely packed van der Waals networks on the surface.

Flexible imidazolium macrocycles: building blocks for anion-induced self-assembly

This feature article summarises recent contributions of the authors in the area of anion-induced supramolecular self-assembly. It is based on the chemistry of a set of tetracationic imidazolium macrocycles, specifically the so-called 'Texas-sized' molecular box, cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene) (1⁴⁺), and its congeners, cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,2-dimethylenebenzene) (2⁴⁺), cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,3-dimethylenebenzene) (3⁴⁺), and cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](2,6-dimethylenepyridine) (4⁴⁺). These systems collectively have been demonstrated as being versatile building blocks that interact with organic carboxylate or sulfonate anions, as well as substrates (e.g., neutral molecules or metal cations). Most work to date has been carried out with 1⁴⁺, a system that has been found to support the construction of a number of stimuli responsive self-assembled ensembles. This macrocycle and others of the 'Texas-sized' box family also show the potential to react as carbene precursors and to undergo post-synthetic modification (PSM) to produce new functional macrocycles, such as trans- and cis-cyclo[2]((Z)-N-(2-((6-(1H-imidazol-1-yl)pyridin-2-yl)amino)vinyl)formamide)[2](1,4-bismethylbenzene) (5²⁺ and 6²⁺, respectively). On the basis of the work reviewed in this Feature article, we propose that the imidazolium macrocycles 1⁴⁺-4⁴⁺ can be considered as useful tools for the construction of ensembles with environmentally responsive features, including control over self-assembly and an ability to undergo precursor-specific PSM.

Phosphate-phosphate oligomerization drives higher order co-assemblies with stacks of cyanostar macrocycles

The importance of phosphate in biology and chemistry has long motivated investigation of its recognition. Despite this interest, phosphate's facile oligomerization is only now being examined following the discovery of complexes of anion-anion dimers of hydroxyanions. Here we address how oligomerization dictates phosphate's recognition properties when engaged with planar cyanostar macrocycles that can also oligomerize by stacking. The crystal structure of cyanostar with phosphate shows an unprecedented tetrameric stack of cyanostar macrocycles threaded by a phosphate trimer, [H₂PO₄···H₂PO₄···H₂PO₄]^3-. The solution behaviour, studied as a function of solvent quality, highlights how dimers and trimers of phosphate drive formation of higher order stacks of cyanostar into dimer, trimer and tetramer co-assemblies. Solution behaviors differ significantly from simpler complexes of bisulfate hydroxyanion dimers. Phosphate oligomerization is: (1) preferred over ion pairing with tetrabutylammonium cations, (2) inhibits disassembly of the complexes upon dilution, and (3) resists interference from competitive anion solvation. The phosphate oligomers also appear critical for stability; complexation of just one phosphate with cyanostars is unfavored. The cyanostar's ability to self-assemble is found to create a tubular, highly electropositive cavity that complements the size and shape of the phosphate oligomers as well as their higher charge. When given the opportunity, phosphate will cooperate with the receptor to form co-assembled architectures.

Host-guest chemistry in two-dimensional supramolecular networks

Nanoporous supramolecular networks physisorbed on solid surfaces have been extensively used to immobilize a variety of guest molecules. Host-guest chemistry in such two-dimensional (2D) porous networks is a rapidly expanding field due to potential applications in separation technology, catalysis and nanoscale patterning. Diverse structural topologies with high crystallinity have been obtained to capture molecular guests of different sizes and shapes. A range of non-covalent forces such as hydrogen bonds, van der Waals interactions, coordinate bonds have been employed to assemble the host networks. Recent years have witnessed a surge in the activity in this field with the implementation of rational design strategies for realizing controlled and selective guest capture. In this feature article, we review the development in the field of surface-supported host-guest chemistry as studied by scanning tunneling microscopy (STM). Typical host-guest architectures studied on solid surfaces, both under ambient conditions at the solution-solid interface as well as those formed at the ultrahigh vacuum (UHV)-solid interface, are described. We focus on isoreticular host networks, hosts functionalized pores and dynamic host-guest systems that respond to external stimuli.

Complex molecular surfaces and interfaces: concluding remarks

This paper is derived from our concluding remarks presentation and the ensuing conversations at the Faraday Discussions meeting on Complex Molecular Surfaces and Interfaces, Sheffield, UK, 24th-26th July 2017. This meeting was comprised of sessions on understanding the interaction of molecules with surfaces and their subsequent organisation, reactivity or properties from both experimental and theoretical perspectives. This paper attempts to put these presentations in the wider context and focuses on topics that were debated during the meeting and where we feel that opportunities lie for the future development of this interdisciplinary research area.

Physical and chemical model of ion stability and movement within the dynamic and voltage-gated STM tip–surface tunneling junction

The interaction and mobility of ions in complex systems are fundamental to processes throughout chemistry, biology, and physics. However, nanoscale characterization of ion stability and migration remains poorly understood. Here, we examine ion movements to and from physisorbed molecular receptors at solution–graphite interfaces by developing a theoretical model alongside experimental scanning tunneling microscopy (STM) results. The model includes van der Waals forces and electrostatic interactions originating from the surface, tip, and physisorbed receptors, as well as a tip–surface electric field arising from the STM bias voltage (V_b). Our model reveals how both the electric field and tip–surface distance, d_tip, can influence anion stability at the receptor binding sites on the surface or at the STM tip, as well as the size of the barrier for anion transitions between those locations. These predictions agree well with prior and new STM results from the interactions of anions with aryl-triazole receptors that order into functional monolayers on graphite. Scanning produces clear resolution at large magnitude negative surface biases (−0.8 V) while resolution degrades at small negative surface biases (−0.4 V). The loss in resolution arises from frequent tip retractions assigned to anion migration within the tip–surface tunneling region. This experimental evidence in combination with support from the model demonstrates a local voltage gating of anions with the STM tip inside physisorbed receptors. This generalized model and experimental evidence may help to provide a basis to understand the nanoscale details of related chemical transformations and their underlying thermodynamic and kinetic preferences.

Anions Stabilize Each Other inside Macrocyclic Hosts

Contrary to the simple expectations from Coulomb's law, Weinhold proposed that anions can stabilize each other as metastable dimers, yet experimental evidence for these species and their mutual stabilization is missing. We show that two bisulfate anions can form such dimers, which stabilize each other with self-complementary hydrogen bonds, by encapsulation inside a pair of cyanostar macrocycles. The resulting 2:2 complex of the bisulfate homodimer persists across all states of matter, including in solution. The bisulfate dimer's OH⋅⋅⋅O hydrogen bonding is seen in a ¹ H NMR peak at 13.75 ppm, which is consistent with borderline-strong hydrogen bonds.

Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles

Shape-persistent macrocycles are attractive functional targets for synthesis, molecular recognition, and hierarchical self-assembly. Such macrocycles are noncollapsible and geometrically well-defined, and they are traditionally characterized by having repeat units and low conformational flexibility. Here, we find it necessary to refine these ideas in the face of highly flexible yet shape-persistent macrocycles. A molecule is shape-persistent if it has a small change in shape when perturbed by external stimuli (e.g., heat, light, and redox chemistry). In support of this idea, we provide the first examination of the relationships between a macrocycle's shape persistence, its conformational space, and the resulting functions. We do this with a star-shaped macrocycle called cyanostar that is flexible as well as being shape-persistent. We employed molecular dynamics (MD), density functional theory (DFT), and NMR experiments. Considering a thermal bath as a stimulus, we found a single macrocycle has 332 accessible conformers with olefins undergoing rapid interconversion by up-down and in-out motions on short time scales (0.2 ns). These many interconverting conformations classify single cyanostars as flexible. To determine and confirm that cyanostars are shape-persistent, we show that they have a high 87% shape similarity across these conformations. To further test the idea, we use the binding of diglyme to the single macrocycle as guest-induced stimulation. This guest has almost no effect on the conformational space. However, formation of a 2:1 sandwich complex involving two macrocycles enhances rigidity and dramatically shifts the conformer distribution toward perfect bowls. Overall, the present study expands the scope of shape-persistent macrocycles to include flexible macrocycles if, and only if, their conformers have similar shapes.

Creating molecular macrocycles for anion recognition

The creation and functionality of new classes of macrocycles that are shape persistent and can bind anions is described. The genesis of triazolophane macrocycles emerges out of activity surrounding 1,2,3-triazoles made using click chemistry; and the same triazoles are responsible for anion capture. Mistakes made and lessons learnt in anion recognition provide deeper understanding that, together with theory, now provides for computer-aided receptor design. The lessons are acted upon in the creation of two new macrocycles. First, cyanostars are larger and like to capture large anions. Second is tricarb, which also favors large anions but shows a propensity to self-assemble in an orderly and stable manner, laying a foundation for future designs of hierarchical nanostructures.

A high-yield synthesis and acid–base response of phosphate-templated [3]rotaxanes

We show a high-yielding synthesis (80%) of [3]rotaxanes using shape-persistent macrocycles, cyanostars, and anionic organo-phosphate templates catalyzed by low steric-demand click chemistry.

A unique multi-functional cationic luminescent metal–organic nanotube for highly sensitive detection of dichromate and selective high capacity adsorption of Congo red

In this work a flexible multi-dentate 1-(4-aminobenzyl)-1,2,4-triazole (abtz) ligand has been employed, a unique cationic triazole–Ag(i) metal–organic nanotube {[Ag(μ₃-abtz)]·(NO₃)·(0.125H₂O)}_n (MONT-1) has been isolated under solvo-thermal conditions.

Size-matched recognition of large anions by cyanostar macrocycles is saved when solvent-bias is avoided

A bulky cyanostar that only forms 1 : 1 complexes was created to study the poorly understood size dependent recognition of large anions by shape-persistent macrocycles.

Multifunctional Tricarbazolo Triazolophane Macrocycles: One-Pot Preparation, Anion Binding, and Hierarchical Self-Organization of Multilayers

Programming the synthesis and self-assembly of molecules is a compelling strategy for the bottom-up fabrication of ordered materials. To this end, shape-persistent macrocycles were designed with alternating carbazoles and triazoles to program a one-pot synthesis and to bind large anions. The macrocycles bind anions that were once considered too weak to be coordinated, such as PF6 (-) , with surprisingly high affinities (β2 =10(11)  M(-2) in 80:20 chloroform/methanol) and positive cooperativity, α=(4 K2 /K1 )=1200. We also discovered that the macrocycles assemble into ultrathin films of hierarchically ordered tubes on graphite surfaces. The remarkable surface-templated self-assembly properties, as was observed by using scanning tunneling microscopy, are attributed to the complementary pairing of alternating triazoles and carbazoles inscribed into both the co-facial and edge-sharing seams that exist between shape-persistent macrocycles. The multilayer assembly is also consistent with the high degree of molecular self-association observed in solution, with self-association constants of K=300 000 M(-1) (chloroform/methanol 80:20). Scanning tunneling microscopy data also showed that surface assemblies readily sequester iodide anions from solution, modulating their assembly. This multifunctional macrocycle provides a foundation for materials composed of hierarchically organized and nanotubular self-assemblies.

Concentration-dependent rhombitrihexagonal tiling patterns at the liquid/solid interface

We report STM investigations on a linear oligophenyleneethylene (OPE)-based self-assembling Pd(ii) complex 1 that forms highly-ordered concentration dependent patterns on HOPG. At high concentration, 2D lamellar structures are observed whereas the dilution of the system below a critical concentration leads to the formation of visually attractive rhombitrihexagonal Archimedean tiling arrangements featuring three different kinds of polygons: triangles, hexagons and rhombi. The key participation of the Cl ligands attached to the Pd(ii) centre in multiple C-H···Cl interactions was demonstrated by comparing the patterns of 1 with those of an analogous non-metallic system 2.

Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles

Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multimolecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that biomacromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar presents difficulties seen in supramolecular crystallography including whole molecule disorder and highly flexible solvent molecules sitting in macrocyclic and intermolecule void spaces. We used the force-field assisted refinement method, molecular dynamics flexible fitting algorithm for X-ray crystallography (xMDFF), along with tools from the macromolecular structure determination suite PHENIX. We found that a standard implementation of PHENIX, namely one without xMDFF, either fails to produce a solution by molecular replacement alone or produces an inaccurate structure when using generic geometry restraints, even at a very high diffraction data resolution of 0.84 Å. The problems disappear when taking advantage of xMDFF, which applies an optimized force field to realign molecular models during phasing by providing accurate restraints. The structure determination for this model system shows excellent agreement with the small-molecule methods. Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies.

Triazole based Ag coordination clusters: synthesis, structural diversity and anion exchange properties

In this work three novel triazole based cluster-based silver(i) clusters have been isolated. 2 and 3 can effectively capturing the anion pollutants Cr₂O₇²⁻, MnO₄⁻ in water solutions and Congo Red in methanol solutions.

Selective anion-induced crystal switching and binding in surface monolayers modulated by electric fields from scanning probes

Anion-selective (Br(-) and I(-)) and voltage-driven crystal switching between two differently packed phases (α ⇆ β) was observed in 2D crystalline monolayers of aryl-triazole receptors ordered at solution-graphite interfaces. Addition of Br(-) and I(-) was found to stimulate the α → β phase transformation and to produce ion binding to the β phase assembly, while Cl(-) and BF4(-) addition retained the α phase. Unlike all other surface assemblies of either charged molecules or ion-templated 2D crystallization of metal-ligand or receptor-based adsorbates, the polarity of the electric field between the localized scanning tip and the graphite substrate was found to correlate with phase switching: β → α is driven at -1.5 V, while α → β occurs at +1.1 V. Ion-pairing between the countercations and the guest anions was also observed. These observations are supported by control studies including variation of anion species, relative anion concentration, surface temperature, tip voltage, and scanning time.