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Surface-Confined Macrocyclization via Dynamic Covalent Chemistry
Abstract
Surface-confined synthesis is a promising approach to build complex molecular nanostructures including macrocycles. However, despite the recent advances in on-surface macrocyclization under ultrahigh vacuum, selective synthesis of monodisperse and multicomponent macrocycles remains a challenge. Here, we report on an on-surface formation of [6 + 6] Schiff-base macrocycles via dynamic covalent chemistry. The macrocycles form two-dimensional crystalline domains on the micrometer scale, enabled by dynamic conversion of open-chain oligomers into well-defined ∼3.0 nm hexagonal macrocycles. We further show that by tailoring the length of the alkyl substituents, it is possible to control which of three possible products-oligomers, macrocycles, or polymers-will form at the surface. In situ scanning tunneling microscopy imaging combined with density functional theory calculations and molecular dynamics simulations unravel the synergistic effect of surface confinement and solvent in leading to preferential on-surface macrocyclization.
... However, as reported in many publications, alkyl chains have a great influence on the formation of 2D nanoarchitectures. Recent advances in 2D selfassembly include "on-surface synthesis," "in situ reactions" such as metal coordination, "correlation of the 2D and 3D structures (crystal structures)" for revealing the origins of physical properties, and "covalent functionalization" using 2D structures as templates [161][162][163][164][165][166][167][168][169][170][171]. In these systems, the molecular building blocks mostly comprise alkyl chains, and various phenomena, including the interaction of alkyl chains, continue to be revealed. ...
Nanoarchitectonics has attracted increasing attention owing to its potential applications in nanomachines, nanoelectronics, catalysis, and nanopatterning, which can contribute to overcoming global problems related to energy and environment, among others. However, the fabrication of ordered nanoarchitectures remains a challenge, even in two dimensions. Therefore, a deeper understanding of the self-assembly processes and substantial factors for building ordered structures is critical for tailoring flexible and desirable nanoarchitectures. Scanning tunneling microscopy is a powerful tool for revealing the molecular conformations, arrangements, and orientations of two-dimensional (2D) networks on surfaces. The fabrication of 2D assemblies involves non-covalent interactions that play a significant role in the molecular arrangement and orientation. Among the non-covalent interactions, dispersion interactions that derive from alkyl chain units are believed to be weak. However, alkyl chains play an important role in the adsorption onto substrates, as well as in the in-plane intermolecular interactions. In this review, we focus on the role of alkyl chains in the formation of ordered 2D assemblies at the solid/liquid interface. The alkyl chain effects on the 2D assemblies are introduced together with examples documented in the past decades.
... Research groups have been able to use this difference in adsorption energy to separate molecules from a mixture and increase the selectivity of reactions, including Schiff base reaction, olen metathesis or the synthesis of benzothiazoles. 2,[30][31][32][33][34][35] While the developed methods are very interesting from a fundamental point of view, all of them describe the separation on the nanometer scale using HOPG and characterization using STM. The importance of these concepts would increase signicantly if they could also be applied efficiently in bulk. ...
Adsorptive separation is a promising lower-energy alternative for traditional industrial separation processes. While carbon-based materials have a long history in adsorptive removal of organic contaminants from solution or gas mixtures, separation using an adsorption/desorption protocol is rarely considered. The main drawbacks are the limited control in bulk adsorption experiments, as often all organic molecules are adsorbed, and lack of desorption methods to retrieve the adsorbed molecules. Using high-resolution on-surface characterization with scanning tunneling microscopy (STM), an increased understanding of the on-surface adsorption behavior under different conditions was obtained. The insight obtained from the nanoscale experiments was used to develop a highly selective separation method using adsorption and desorption on graphite, which was tested for the separation of quinonoid zwitterions. These experiments on adsorptive separation using self-assembly on graphite show its potential and demonstrate the advantage of combining surface characterization techniques with bulk experiments to exploit different possible applications of carbon-based materials.
Two-dimensional polymers (2DPs) are molecularly thin networks consisting of monomers covalently linked in at least two directions in the molecular plane. Because of the unique structural features and emergent physicochemical properties, 2DPs promise application potentials in catalysis, chemical sensing, and organic electronic devices. On-surface synthesis is of great interest to fabricate 2DPs with atomic precision, and the properties of the 2DPs can be characterized in situ through scanning probe techniques. In this Perspective, we first introduce the recent developments of on-surface 2D polymerization, including the design principle, the synthetic reactions, and the factors affecting the synthesis of 2DPs on surface. Then, we summarize some major challenges in this field, including the fabrication of high-quality 2DPs and the study of the intrinsic electronic properties of 2DPs, and we discuss some of the available solutions to address these issues.
"Cold crystallization" is the exothermic phenomenon occurring during the heating process of a supercooled liquid. Molecules that exhibit cold crystallization can be used as heat storage materials. Schiff-base nickel(II) complexes...
The development of electrocatalysts for nitrogen reduction reaction (NRR) at ambient conditions, with both high NH3 yield and Faradaic efficiency, is currently a great challenge. To this aim, a unique metal–organic framework (MOF) crystalline matrix with disulphide trimeric unit as the building block was in situ synthesized by integration of dynamic covalent chemistry and coordination chemistry. This MOF with high porosity and excellent stability could be used as a host material to encapsulate well-dispersed Au nanoparticles (NPs) with ultrafine size of 1.9 ± 0.4 nm. After surface modification of [email protected] by using organosilicone, the hydrophobic-treated [email protected] (HT [email protected]) composite shows remarkable electrocatalytic performances for NRR, with the highest NH3 yield of 49.5 μg h–1 mgcat.–1 and the state-of-the-art Faradaic efficiency of 60.9% in water medium at ambient conditions. The favorable role of MOFs with functional sulfur groups on modulating the active Au sites and the great effect of hydrophobic coatings on suppressing the competitive hydrogen evolution reaction (HER) have been further demonstrated. This work provides a universal strategy to design composite electrocatalysts for high-efficient and long-term NH3 production.
Carbocatalysis holds a privileged position as a sustainable alternative to metal-based catalysis. While the focus in solution-based catalytic processes generally lies on how the heterogeneous catalyst affects the solution composition, more attention has recently been given to the analysis of the carbon material itself. Various outstanding surface characterisation techniques, efficient in assessing the catalyst on-surface composition, are now available. These include high-resolution imaging tools such as scanning tunneling microscopy (STM), capable of bringing new insights into the processes determining rate and selectivity effects induced by carbocatalysts. In this regard, the use of self-assembly on graphite as a strategy to direct the outcome of chemical reactions has already shown great potential. This promising approach gives the scientific community the exciting prospect of rationalising selectivity in carbocatalysis with pristine graphite by linking in-solution and on-surface composition.
The first generation of nanomedicine exhibits superior performance in the clinical treatment of various cancers compared to free conventional anticancer therapeutics. However, poor tumor penetration has been considered a major obstacle in the cancer treatment process and substantially impairs the overall therapeutic efficacy. Recently, this situation has been effectively improved through a great variety of smart size-shrinkable drug delivery nanosystems (SSDDNs), which remains stable with relatively large size in the circulation system for a prolonged plasma half-life and enhanced tumor accumulation, then specifically turn into smaller particles at the tumor site by an appropriate stimulus to promote tumor penetration for uniform drug distribution throughout the whole tumor. In this review, we systematically summarize the intelligent size-shrinkable strategies mediated by different response modes, including endogenous and external stimuli. In addition to offering enhanced penetration, the size-shrinkable strategy can companion imaging probes for specific diagnoses and image-guided therapy. The challenges and prospects are discussed, and several proposals for promoting SSDDNs clinical translation are supplied. It is anticipated that such smart SSDDNs will provide a guideline for next-generation clinical translation.
The fabrication of nanostructures in a bottom-up approach from specific molecular precursors offers the opportunity to create tailored materials for applications in nanoelec-tronics. However, the formation of defect-free two-dimensional (2D) covalent networks remains a challenge, which makes it difficult to unveil their electronic structure. Here we report on the hierarchical on-surface synthesis of nearly defect-free 2D covalent architectures with carbonyl-functionalized pores on Au(111), which is investigated by low-temperature scanning tunnelling microscopy in combination with density functional theory calculations. The carbonyl-bridged triphenylamine precursors form six-membered macrocycles and one-dimensional (1D) chains as intermediates in an Ullmann-type coupling reaction that are subsequently interlinked to 2D networks. The electronic band gap is narrowed when going from the monomer to 1D and 2D surface-confined p-conjugated organic polymers comprising the same building block. The significant drop of the electronic gap from the monomer to the polymer confirms an efficient conjugation along the triphenylamine units within the nanostructures.
At the interface with solids, the mobility of liquid molecules tends to be reduced compared with bulk, often resulting in increased local order due to interactions with the surface of the solid. At room temperature, liquids such as water and methanol can form solvation structures, but the molecules remain highly mobile, thus preventing the formation of long-lived supramolecular assemblies. Here we show that mixtures of water with methanol can form a novel type of interfaces with hydrophobic solids. Combining in situ atomic force microscopy and multiscale molecular dynamics simulations, we identify solid-like two-dimensional interfacial structures that nucleate thermally, and are held together by an extended network of hydrogen bonds. On graphite, nucleation occurs above B35 °C, resulting in robust, multilayered nanoscopic patterns. Our findings could have an impact on many fields where water-alcohol mixtures play an important role such as fuel cells, chemical synthesis, self-assembly, catalysis and surface treatments.
Here we report the synthesis of cyclic samples of poly(3-hexylthiophene) (P3HT, degrees of polymerization = 25, 40, and 75) and poly(3-heptylselenophene) (P37S, DP = 30). Cyclization was accomplished using a mild alkyne–alkyne homocoupling procedure. Alkyne-terminated poly(ethylene glycol) was then coupled to residual uncyclized polymers, which were subsequently removed by column chromatography, enabling isolation and characterization of pure cyclic polymers. Cyclization was confirmed by the disappearance of terminal alkyne protons, the decrease in hydrodynamic radius [measured by size exclusion chromatography (SEC)], and the observed identical molecular weight distribution [measured by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry]. The lower weight macrocyclic polymers have decreased self-assembly as measured by optical absorption and transmission electron microscopy. The highest weight macrocycles were imaged using scanning tunneling microscopy. Cyclic polymers adopted a tightly bent conformation, while their linear analogues assembled as fully extended chains. Our method of cyclization and purification is broadly applicable to conjugated polymers (CPs) and will enable the development of novel optoelectronic materials.
We show that the surface-supported two-dimensional covalent organic framework (COF) known as COF-1 can act as a host architecture for C60 fullerene molecules, predictably trapping the molecules under a range of conditions. The fullerenes occupy the COF-1 lattice at the solution/solid interface, and in dried films of the COF-1/fullerene network that can be synthesized through either drop-deposition of fullerene solution or by a dipstick-type synthesis in which the surface-supported COF-1 is briefly dipped into the fullerene solution.
Table of Contents
1. Introduction
2. Macrocyclic Compounds and Macrocyclization Strategies
3. Role of Preorganization in Macrocyclic Chemistry
4. Experimental Aspects in the Synthesis of Macrocycles
4.1. Kinetic Aspects
4.2. Thermodynamic Aspects
5. Synthesis of Macrocyclic Structures Assisted by the Intrinsic Favorable Preorganization of Open-Chain Precursors
5.1. Conformational Preorganization
5.1.1. Polyoxamacrocycles, Polyazamacrocycles, and Macrolactones
5.1.2. Shape Persistent Macrocycles
5.1.3. Macrocyclizations Favored by Hydrogen Bonding
5.1.4. Additional Factors for the Favorable Preorganization of Macrocyclic Precursors
5.1.5. Peptidic and Pseudopeptidic Macrocycles
5.2. Configurational Preorganization
6. Synthesis of Macrocyclic Structures by a Template-Assisted Favorable Preorganization of Open-Chain Precursors
6.1. Metal Templated Macrocyclizations
6.1.1. Crown Ethers and Polyaza Macrocycles
6.1.2. Nonclassical Metal Template Effects
6.2. Anion Templated Macrocyclizations
6.3. Arene Templated Macrocyclizations
6.4. Other Templates in Macrocyclizations
6.5. Biological and Pseudobiological Macrocyclizations
7. Outlook and Conclusions
Carbon-based nanostructures have attracted tremendous interest because of their versatile and tunable properties, which depend on the bonding type of the constituting carbon atoms. Graphene, as the most prominent representative of the π-conjugated carbon-based materials, consists entirely of sp2-hybridized carbon atoms and exhibits a zero band gap. Recently, countless efforts were made to open and tune the band gap of graphene for its applications in semiconductor devices. One promising method is periodic perforation, resulting in a graphene nanomesh (GNM), which opens the band gap while maintaining the exceptional transport properties. However, the typically employed lithographic approach for graphene perforation is difficult to control at the atomic level. The complementary bottom-up method using surface-assisted carbon–carbon (C–C) covalent coupling between organic molecules has opened up new possibilities for atomically precise fabrication of conjugated nanostructures like GNM and graphene nanoribbons (GNR), although with limited maturity. A general drawback of the bottom-up approach is that the desired structure usually does not represent the global thermodynamic minimum. It is therefore impossible to improve the long-range order by postannealing, because once the C–C bond formation becomes reversible, graphene as the thermodynamically most stable structure will be formed. This means that only carefully chosen precursors and reaction conditions can lead to the desired (non-graphene) material.
Molecular-scale electronics is mainly concerned by understanding charge transport through individual molecules. A key issue here is the charge transport capability through a single-typically linear-molecule, characterized by the current decay with increasing length. To improve the conductance of individual polymers, molecular design often either involves the use of rigid ribbon/ladder-type structures, thereby sacrificing for flexibility of the molecular wire, or a zero band gap, typically associated with chemical instability. Here we show that a conjugated polymer composed of alternating donor and acceptor repeat units, synthesized directly by an on-surface polymerization, exhibits a very high conductance while maintaining both its flexible structure and a finite band gap. Importantly, electronic delocalization along the wire does not seem to be necessary as proven by spatial mapping of the electronic states along individual molecular wires. Our approach should facilitate the realization of flexible 'soft' molecular-scale circuitry, for example, on bendable substrates.
We report on the active template synthesis of a [2]rotaxane through a Goldberg copper-catalyzed C-N bond forming reaction. A C2-symmetric cyclohexyldiamine macrocycle directs the assembly of the rotaxane, which can subsequently serve as a ligand for enantioselective nickel-catalyzed conjugate addition reactions. Rotaxanes are a previously unexplored ligand architecture for asymmetric catalysis. We find that the rotaxane gives improved enantioselectivity compared to a non-interlocked ligand, at the expense of longer reaction times.
From an interplay of UHV-STM imaging and DFT calculations, we have illustrated on-surface formation of polyphenyl chains through a hierarchical reaction pathway involving two different kinds of reactions (Ullmann coupling and cross-dehydrogenative coupling), which will provide deeper understandings of on-surface chemical reactions and an alternative and efficient strategy to fabricate desired surface molecular nanostructures.
On-surface Ullmann coupling is a versatile and appropriate approach for the bottom-up fabrication of covalent organic nanostructures. In two-dimensional networks, however, the kinetically controlled and irreversible coupling leads to high defect densities and a lack of long-range order. To derive general guidelines for optimizing reaction parameters, the structural quality of 2D porous covalent networks was evaluated for different preparation protocols. For this purpose, polymerization of an iodine and bromine functionalized monomer was studied on Au(111) by Scanning Tunneling Microscopy under ultra-high vacuum conditions. By taking advantage of the vastly different temperature thresholds for C-Br and C-I cleavage two different polymerization routes were compared - hierarchical and direct polymerization. The structural quality of the covalent networks was evaluated for different reaction parameters, such as surface temperatures, heating rates, and deposition rates by statistical analysis of STM data. Experimental results are compared to Monte Carlo simulations.
Structural and electronic properties of oligothiophene nanowires and rings synthesized on a Au(111) surface are investigated by scanning tunneling microscopy. The spectroscopic data of the linear and cyclic oligomers show remarkable differences which, to a first approximation, can be accounted by considering electronic state confinement to one-dimensional boxes having, respectively, fixed and periodic boundary conditions. A more detailed analysis shows that polythiophene must be treated as a ribbon (i.e., having an effective width) rather than a purely 1D structure. A fascinating consequence is that the molecular nanorings act as whispering gallery mode resonators for electrons, opening the way for new applications in quantum electronics.
A key challenge in the field of nanotechnology, in particular in the design of molecular machines, novel materials or molecular electronics, is the bottom-up construction of covalently bound molecular architectures in a well-defined arrangement. To date, only rather simple structures have been obtained because of the limitation of one-step connection processes. Indeed, for the formation of sophisticated structures, step-by-step connection of molecules is required. Here, we present a strategy for the covalent connection of molecules in a hierarchical manner by the selective and sequential activation of specific sites, thereby generating species with a programmed reactivity. This approach leads to improved network quality and enables the fabrication of heterogeneous architectures with high selectivity. Furthermore, substrate-directed growth and a preferred orientation of the molecular nanostructures are achieved on an anisotropic surface. The demonstrated control over reactivity and diffusion during covalent bond formation constitutes a promising route towards the creation of sophisticated multi-component molecular nanostructures.
We herein investigated the effect of the number of alkoxy chains on the two-dimensional self-assembly of a trigonal molecular building block. To this end, a dehydrobenzo[12]annulene (DBA) derivative, DBA-OC14-OC1 having three tetradecyloxy chains and three methoxy groups in an alternating manner, was synthesized. Scanning tunneling microscopy (STM) observations at the 1,2,4-trichlorobenzene (TCB)/graphite interface revealed that DBA-OC14-OC1 forms three monolayer structures, porous honeycomb, parallelogram, and hexagonal A structures. At the 1-phenyloctane (PO)/graphite interface, DBA-OC14-OC1 also forms three structures: parallelogram, hexagonal B and dense-linear structures. In contrast to the previously reported DBA derivative DBA-OC14 having six tetradecyloxy chains, DBA-OC14-OC1 shows structural polymorphism with a variety of alkyl chain interaction modes. Since in the observed patterns DBA-OC14-OC1 adopts a low symmetric Cs or C1 geometry, the variation of the interaction modes and the resulting network patterns likely originate from the conformational flexibility on surface of this DBA by decreasing number of alkyl chains. Molecular mechanics simulations gave insight in the structural and energy aspects of this pattern formation. We also discussed the role of solvents, TCB and PO, on the polymorph formation.
Hybrid heterostructures formed by ordered molecular layers on bidimensional materials can lead to unique properties differing from those of their bulk phases. By employing principles of dynamic covalent chemistry, we have synthesized a series of conjugated polyimines that form epitaxially ordered monolayers on graphene. The interplay of the molecular physisorption and dynamic polymerization at the solid-liquid interface drives the reaction towards the generation of longer chains being formed at the surface and at higher rates than in solution. The physico-chemical properties of such assemblies at different length scales on graphene were investigated by a combination of experimental techniques ‘Covalent dynamic epitaxy’ was also found to modulate the electronic properties of both the substrate and the dynamers such as the doping and photoluminescence, respectively.
This Account describes a body of research on the design, synthesis, and application of a new class of electronic materials made from conjugated macrocycles. Our macrocyclic design takes into consideration the useful attributes of fullerenes and what properties make fullerenes efficient n-type materials. We identified four electronic and structural elements: (1) a three-dimensional shape; (2) a conjugated and delocalized π-space; (3) the presence of an interior and exterior to the π-surface; and (4) low-energy unoccupied molecular orbitals allowing them to accept electrons. The macrocyclic design incorporates some of these properties, including a three-dimensional shape, an interior/exterior to the π-surface, and low-lying LUMOs maintaining the n-type semiconducting behavior, yet we also install synthetic flexibility in our approach in order to tune the properties further. Each of the macrocycles comprises perylenediimide cores wound together with linkers. The perylenediimide building block endows each macrocycle with the ability to accept electrons, while the synthetic flexibility to install different linkers allows us to create macrocycles with different electronic properties and sizes. We have created three macrocycles that all absorb well into the visible range of the solar spectrum and possess different shapes and sizes. We then use these materials in an array of applications that take advantage of their ability to function as n-type semiconductors, absorb in the visible range of the solar spectrum, and possess intramolecular cavities. This Account will discuss our progress in incorporating these new macrocycles in organic solar cells, organic photodetectors, organic field effect transistors, and sensors. The macrocycles outperform acyclic controls in organic solar cells. We find the more rigid macrocyclic structure results in less intrinsic charges and lower dark current in organic photodetectors. Our macrocyclic-based photodetector has the highest detectivity of non-fullerene acceptors. The macrocycles also function as sensors and are able to recognize nuanced differences in analytes. Perylenediimide-based fused oligomers are efficient materials in both organic solar cells and field effect transistors. We will use the oligomers to construct macrocycles for use in solar energy conversion. In addition, we will incorporate different electron-rich linkers in our cycles in an attempt to engineer the HOMO/LUMO gap further. Looking further into the future, we envision opportunities in applying these conjugated macrocycles as electronic host/guest materials, as concatenated electronic materials by threading the macrocycles with electroactive oligomers, and as a locus for catalysis that is driven by light and electric fields.
Rationally designed halogenated hydrocarbons are widely used building blocks to fabricate covalent-bonded carbon nanostructures on surface through a reaction pathway involving generation and dissociation of organometallic intermediates and irreversible covalent bond formation. Here we provide a comprehensive picture of the on-surface-assisted homocoupling reaction of 1,3-bis(2-bromoethynyl)benzene on Au(111), aiming for the synthesis of graphdiyne nanostructures. Submolecular resolution scanning tunneling microscopy and noncontact atomic force microscopy observations identify the organometallic intermediates and their self-assemblies formed in the dehalogenation process. The demetallization of the organometallic intermediates at elevated temperatures produces butadiyne moieties that spontaneously formed two different covalent structures, i.e. graphdiyne zigzag chains and macrocycles, whose ratio was found to depend on the initial coverage of organometallic intermediates. At the optimal condition, the stepwise demetallization and cyclization led to a high yield production of graphdiyne macrocycles up to 95 %. Statistical analysis and theoretical calculations suggested that the favored formation of macrocycles was resulted from the complex interplay between thermodynamic and kinetic processes involving the organometallic bonded intermediates and the covalently bonded butadiyne moieties.
Hydration layers are ubiquitous in life and technology. Hence, interfacial aqueous layers have a central role in a wide range of phenomena from materials science to molecular and cell biology. A complete understanding of those processes requires, among other things, the development of very-sensitive and high-resolution instruments. Three-dimensional atomic force microscopy (3D-AFM) represents the latest and most successful attempt to generate atomically resolved three-dimensional images of solid-liquid interfaces. This review provides an overview of the 3D-AFM operating principles and its underlying physics. We illustrate and explain the capability of the instrument to resolve atomic defects on crystalline surfaces immersed in liquid. We also illustrate some of its applications to imaging the hydration structures on DNA or proteins. In the last section, we discuss some perspectives on emerging applications in materials science and molecular biology.
Understanding the energy it takes to build or break chemical bonds is essential for scientists and engineers in a wide range of innovative fields, including catalysis, nanomaterials, bioengineering, environmental chemistry, and space science. Reflecting the frequent additions and updates of bond dissociation energy (BDE) data throughout the literature, the Comprehensive Handbook of Chemical Bond Energies compiles the most recent experimental BDE data for more than 19,600 bonds of 102 elements. The author organizes the data by bond type, functional group, bond order, bond degree, molecular size, and structure for ease of use. Data can also be located using the Periodic table. The book presents data for organic molecules, biochemicals, and radicals as well as clusters, ions, hydrogen- and surface-bonded species, van der Waals complexes, isotopic species, and halogen-clusters/complexes. It also introduces entirely new data for inorganics and organometallics. The final chapter summarizes the heats of formation for atoms, inorganic/organic radicals, and monoatomic ions in the gas phase. The Comprehensive Handbook of Chemical Bond Energies offers quick access to experimental BDE data in the most inclusive, well-organized, and up-to-date collection available today.
In this work we demonstrate that the surface adsorption and pH play a determining role in controlling the final product of Schiff base reaction. Either 1D linear polymer or discrete...
Macrocycles based on directional bonding and dynamic covalent bond exchange can be designed with specific pore shapes, sizes, and functionality. These systems retain many of the design criteria and desirable aspects of two-dimensional (2D) covalent organic frameworks (COFs) but are more easily processed. Here we access discrete hexagonal imine-linked macrocycles by condensing truncated analogues of 1,3,5-tris(4-aminophenyl)benzene (TAPB) with terephthaldehyde (PDA). The monomers first condense into polymers but eventually convert into hexagonal macrocycles in high yield. The high selectivity for hexagonal macrocycles is enforced by their aggregation and crystallization into layered structures with more sluggish imine exchange. Their formation and exchange processes provide new insight into how imine-linked 2D COF simultaneously polymerize and crystallize Solutions of these assembled macrocycles were cast into oriented, crystalline films, expanding the potential routes to 2D materials.
We have studied, using atomistic molecular dynamics simulations, the alignment of the nematic liquid crystal 5CB on self assembled monolayers (SAMs) formed from octadecyl- and/or hexyl-trichlorosilanes (OTS and HTS) attached to glassy silica. We find a planar alignment on OTS at full coverage, and an intermediate situation at partial OTS coverage, due to a penetration of 5CB molecules in the monolayer, which also removes the tilt of the OTS SAM. Binary mixtures of HTS and OTS SAMs do instead induce homeotropic alignment. Comparison with the existing experimental literature is provided.
We report the on-surface formation and characterization of [30]-honeycombene, a cyclotriacontaphenylene, which consists of 30 phenyl rings (C180H120) and has a diameter of 4.0 nm. This shape-persistent, conjugated, and unsubstituted hexagonal hydrocarbon macrocycle was obtained by solvent-free synthesis on a silver (111) single-crystal surface, making solubility-enhancing alkyl side groups unnecessary. Side products include strained macrocycles with square, pentagonal, and heptagonal shape. The molecules were characterized by scanning tunneling microscopy and density functional theory (DFT) calculations. On the Ag(111) surface, the macrocycles act as molecular quantum corrals and lead to the confinement of surface-state electrons inside the central cavity. The energy of the confined surface state correlates with the size of the macrocycle and is well described by a particle-in-the-box model. Tunneling spectroscopy suggests conjugation within the planar rings and reveals influences of self-assembly on the electronic structure. While the adsorbed molecules appear to be approximately planar, the free molecules have nonplanar conformation, according to DFT.
Surface-confined polymerization via Ullmann coupling is a promising route to create one- and two-dimensional covalent π-conjugated structures, including the bottom-up growth of graphene nanoribbons. Understanding the mechanism of the Ullmann reaction is needed to provide a platform for rationally controlling the formation of these materials. We use fast X-ray photoelectron spectroscopy (XPS) in kinetic measurements of epitaxial surface polymerization of 1,4-dibromobenzene on a Cu(110) surface and devise a kinetic model based on mean field rate equations, involving a transient state. This state is observed in the energy landscapes calculated by nudged elastic band (NEB) within density functional theory (DFT), which assumes as initial and final geometries of the organometallic structure and the polymeric product those observed by scanning tunneling microscopy (STM). The kinetic model accounts for all the salient features observed in the experimental curves extracted from the fast-XPS measurements and enables an enhanced understanding of the polymerization process, which is found to follow a nucleation-and-growth behavior preceded by the formation of a transient state.
Graphene has unique physical and chemical properties making it appealing for a number of applications in opto-electronics, sensing, photonics, composites, smart coatings, just to cite a few. These require the development of production processes that are inexpensive and up-scalable. These criteria are met in liquid-phase exfoliation (LPE), a process that can be enhanced when specific organic molecules are used. Here we report the exfoliation of graphite in N-methyl-2-pyrrolidinone, in the presence of heneicosane linear alkanes terminated with different head groups. These molecules act as stabilizing agents during exfoliation. The efficiency of the exfoliation in terms of concentration of exfoliated single- and few-layer graphene flakes depends on the functional head group determining the strength of the molecular dimerization through dipole-dipole interactions. A thermodynamic analysis is carried out to interpret the impact of the termination group of the alkyl chain on the exfoliation yield. This combines molecular dynamics and molecular mechanics to rationalize the role of functionalized alkanes in the dispersion and stabilization process, which is ultimately attributed to a synergistic effect of the interactions between the molecules, graphene, and the solvent.
The combination of 2,6-diformylpyridine and trans-1,2-diaminocyclopentane fragments results in 2+2, 3+3, 4+4, 6+6 and 8+8 macrocyclic imine condensation products. These imines can be reduced to the corresponding 2+2, 3+3, 4+4, 6+6 and 8+8 macrocyclic amines. The X-ray crystal structures of their protonated derivatives show a rich variety of macrocycle conformations ranging from a stepped 2+2 macrocycle to a multiply folded 8+8 macrocycle of globular shape. These compounds bind anions via hydrogen bonds: two chloride anions are bound above and below the macrocyclic ring of the 2+2 amine, one chloride anion is bound approximately in the center of the 3+3 macrocycle, two chloride anions are deeply buried inside a folded container-shaped 4+4 macrocycle, while in the case of the previously reported 6+6 amine four chloride anions and two solvent molecules are buried inside a container-shaped macrocycle. Yet another situation was observed for a multiply folded protonated 8+8 macrocycle which binds six sulfate anions; two of them are deeply buried inside the container structure while four anions interact with the clefts at the surface of the container.
Mimicking the ingenuity of nature and exploiting the billions of years over which natural selection has developed numerous effective biochemical conversions is one of the most successful strategies in a chemist's toolbox. However, an inability to replicate the elegance and efficiency of the oxygen-evolving complex of photosystem II (OEC-PSII) in its oxidation of water into O2 is a significant bottleneck in the development of a closed-loop sustainable energy cycle. Here, we present an artificial metallosupramolecular macrocycle that gathers three Ru(bda) centres (bda = 2,2'-bipyridine-6,6'-dicarboxylic acid) that catalyses water oxidation. The macrocyclic architecture accelerates the rate of water oxidation via a water nucleophilic attack mechanism, similar to the mechanism exhibited by OEC-PSII, and reaches remarkable catalytic turnover frequencies >100 s(-1). Photo-driven water oxidation yields outstanding activity, even in the nM concentration regime, with a turnover number of >1,255 and turnover frequency of >13.1 s(-1).
Surface-supported coupling reactions between 1,3,5-tris(4-formylphenyl)-benzene (TFPB) and aromatic amines has been investigated on Au(111) using scanning tunneling microscopy (STM) under ultrahigh vacuum (UHV) conditions. Upon annealing to moderate temperatures, various of products, involving the discrete oligomers and the surface covalent organic frameworks (SCOF) are obtained through the thermal triggered on-surface chemical reactions. We conclude from the systematic experiments that the stoichiometric composition of the reactants is vital to the surface reaction products, which is rarely reported so far. With this knowledge, we have successfully prepared two-dimensional covalent bonded networks by optimizing the stoichiometric proportions of the reaction precursors.
Supramolecular ordering of organic semiconductors is the key factor defining their electrical characteristics. Yet, it is extremely difficult to control, particularly at the interface with metal and dielectric surfaces in semiconducting devices. We have explored the growth of n-type semiconducting films based on hydrogen–bonded monoalkylnaphthalenediimide (NDI-R) from solution and through vapor deposition on both conductive and insulating surfaces. We combined scanning tunneling and atomic force microscopies with X-ray diffraction analysis to characterize, at the submolecular level, the evolution of the NDI-R molecular packing in going from monolayers to thin films. On a conducting (graphite) surface, the first monolayer of NDI-R molecules adsorbs in a flat-lying (face-on) geometry, whereas in subsequent layers the molecules pack edge-on in islands (Stranski-Krastanov-like growth). On SiO2, the NDI-R molecules form into islands comprising edge-on packed molecules (Volmer-Weber mode). Under all the explored conditions, self-complementary H bonding of the imide groups dictates the molecular assembly. The measured electron mobility of the resulting films is similar to that of dialkylated NDI molecules without H bonding. The work emphasizes the importance of H bonding interactions for controlling the ordering of organic semiconductors, and demonstrates a connection between on-surface self-assembly and the structural parameters of thin films used in electronic devices.
The potential of surface confined self-assembly to influence the chemical equilibrium of Schiff base formation and bias the yield and distribution of reaction products is explored.
The surface-mediated synthesis of ordered linear or zigzag polymers on a highly oriented pyrolytic graphite surface was investigated either at a solid/liquid interface or with moderate heating under low vacuum. Scanning tunneling microscopy (STM) reveals the submolecular details of the structure and growth dynamics of surface-confined one-dimensional polymers. We discovered that the substituent and concentration of monomers have a significant effect on the assembling structure of the in-situ-synthesized one-dimensional polymer at the octanoic acid/graphite interface.
The design and construction of molecular nanostructures with tunable topological structures are great challenges in molecular nanotechnology. Herein, we demonstrate the molecular engineering of Schiff-base bond connected molecular nanostructures. Building module construction has been adopted to modulate the symmetry of resulted one dimensional (1D) and two dimensional (2D) polymers. Specifically, we have designed and constructed 1D linear and zigzag polymers, 2D hexagonal and chessboard molecular nanostructures by varying the number of reactive sites and geometry and symmetry of precursors. It is demonstrated that high-quality conjugated polymers can be fabricated by using gas-solid interface reaction. The on-demanding synthesis of polymeric architectures with diverse topologies paves the way to fabricate molecular miniature devices with various desired functionalities.
In the host of numerical schemes devised to calculate free energy differences by way of geometric transformations, the adaptive biasing force algorithm has emerged as a promising route to map complex free-energy landscapes. It relies upon the simple concept that as a simulation progresses, a continuously updated biasing force is added to the equations of motion, such that in the long-time limit it yields a Hamiltonian devoid of an average force acting along the transition coordinate of interest. This means that sampling proceeds uniformly on a flat free-energy surface, thus providing reliable free-energy estimates. Much of the appeal of the algorithm to the practitioner is in its physically intuitive underlying ideas and the absence of any requirements for prior knowledge about free-energy landscapes. Since its inception in 2001, the adaptive biasing force scheme has been the subject of considerable attention, from in-depth mathematical analysis of convergence properties to novel developments and extensions. The method has also been successfully applied to many challenging problems in chemistry and biology. In this contribution, the method is presented in a comprehensive, self-contained fashion, discussing with a critical eye its properties, applicability and inherent limitations, as well as introducing novel extensions. Through free-energy calculations prototypical molecular systems, many methodological aspects are examined, from stratification strategies to overcoming the so-called hidden barriers in orthogonal space, relevant not only to the adaptive biasing force algorithm, but also to other importance-sampling schemes. On the basis of the discussions in this paper, a number of good practices for improving the efficiency and reliability of the computed free-energy differences are proposed.
Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.
Host–guest chemistry commenced to a large degree with the work of Pedersen, who in 1967 first reported the synthesis of crown ethers. The past 45 years have witnessed a substantial progress in the field, from the design of highly selective host molecules as receptors to their application in drug delivery and, particularly, analyte sensing. Much effort has been expended on designing receptors and signaling mechanism for detecting compounds of biological and environmental relevance. Traditionally, the design of a chemosensor comprises one component for molecular recognition, frequently macrocycles of the cyclodextrin, cucurbituril, cyclophane, or calixarene type. The second component, used for signaling, is typically an indicator dye which changes its photophysical properties, preferably its fluorescence, upon analyte binding. A variety of signal transduction mechanisms are available, of which displacement of the dye from the macrocyclic binding site is one of the simplest and most popular ones. This constitutes the working principle of indicator displacement assays.
Lamellar patterns resulting from the adsorption of p-dialkoxybenzene derivatives on HOPG have been investigated as molecular templates for directing the assembly of thiol-capped gold nanoparticles (AuNP). STM characterization at the liquid-solid interface reveals the periodic arrangement of AuNP on top of the self-assembled molecular network (SAMN), spanning hundreds of nanometers. The resulting superlattices are notably non-centrosymmetric and thus differ from the close-packed structures formed by spherical nanoparticles during evaporative drying. The templating effect is based on van der Waals interactions of the alkyl chains of the SAMN and AuNP, and the assembly efficiency is greatest when these chains are of similar length.
The rotational barriers for n-butane, 1-butene, and 1,3-butadiene were calculated at the G2 and CBS-Q theoretical levels. The thermodynamic functions were obtained with explicit calculation of the effect of the rotational modes. The G2 difference in energy between the syn and anti forms of butane at 298 K is 5.1 kcal/mol, which is significantly larger than the experimental estimate. However, it is shown that a reliable experimental estimate of the barrier cannot be made based on the currently available data. The structural changes on rotation are examined and are related to the changes found for C−C bond rotation in ethane. The G2 model reproduces the observed relative energies for both 1-butene and 1,3-butadiene within the experimental uncertainties, and the CBS-Q model also gives generally satisfactory results.
A hexagonal macrocycle consisting of 18 phenylene units (hyperbenzene) was synthesized on a Cu(111) surface in ultrahigh vacuum by Ullmann coupling of six 4,4''-dibromo-m-terphenyl molecules. The large diameter of 21.3 Å and the ability to assemble in arrays makes hyperbenzene an interesting candidate for a nanotrough that could enclose metallic, semiconducting, or molecular quantum dots.
A comparative analysis between a solution and a surface-mediated synthesis of heterotriangulene macrocycles is reported. The results show a preferential formation of the π-conjugated macrocycles on surface due to two-dimensional confinement. The macrocycle prepared on a several hundred milligram scale by solution chemistry was characterized by single-crystal X-ray analysis and was furthermore extended towards next generation honeycomb species. Investigation of the photophysical and electronic properties together with the good thermal stability revealed the potential of MC6 as hole-transport material for organic electronics.
On-surface polymerization represents a novel bottom-up approach for producing macromolecular structures. To date, however, most of the structures formed using this method exhibit a broad size distribution and are disorderly adsorbed on the surface. Here we demonstrate a strategy of using metal-directed template to control the on-surface polymerization process. We chose a bifunctional compound which contains pyridyl and bromine end groups as the precursor. Linear template afforded by pyridyl-Cu-pyridyl coordination effectively promoted Ullmann coupling of the monomers on a Au(111) surface. Taking advantage of efficient topochemical enhancement owing to the conformation flexibility of the Cu-pyridyl bonds, macromolecular porphyrin structures that exhibit a narrow size distribution were synthesized. We used scanning tunneling microscopy and kinetic Monte Carlo simulation to gain insights into the metal-directed polymerization at the single molecule level. The results reveal that the polymerization process profited from the rich chemistry of Cu which catalyzed the C-C bond formation, controlled the size of the macromolecular products, and organized the macromolecules in a highly ordered manner on the surface.
Part 1 From molecular to supramolecular chemistry: concepts and language of supramolecular chemistry. Part 2 Molecular recognition: recognition, information, complementarity molecular receptors - design principles spherical recognition - cryptates of metal cations tetrahedral recognition by macrotricyclic cryptands recognition of ammonium ions and related substrates binding and recognition of neutral moelcules. Part 3 Anion co-ordination chemistry and the recognition of anionic substrates. Part 4 Coreceptor molecules and multiple recognition: dinuclear and polynuclear metal ion cryptates linear recognition of molecular length by ditopic coreceptors heterotopic coreceptors - cyclophane receptors, amphiphilic receptors, large molecular cage multiple recognition in metalloreceptors supramolecular dynamics. Part 5 Supramolecular reactivity and catalysis: catalysis by reactive macrocyclic cation receptor molecules catalysis by reactive anion receptor molecules catalysis with cyclophane type receptors supramolecular metallo-catalysis cocatalysis - catalysis of synthetic reactions biomolecular and abiotic catalysis. Part 6 Transport processes and carrier design: carrier-mediated transport cation-transport processes - cation carriers anion transport processes - anion carriers coupled transport processes electron-coupled transpoort in a redox gradient proton-coupled transport in a pH gradient light-coupled transport processes transfer via transmembrane channels. Part 7 From supermolecules to polymolecular assemblies: heterogeneous molecular recognition - supramolecular solid materials from endoreceptors to exoreceptors - molecular recognition at surfaces molecular and supramolecular morphogenesis supramolecular heterogeneous catalysis. Part 8 Molecular and supramolecular devices: molecular recognition, information and signals - semiochemistry supramolecular photochemistry - molecular and supramolecular photonic devices light conversion and energy transfer devices photosensitive molecular receptors photoinduced electron transfer in photoactive devices photoinduced reactions in supramolecular species non-linear optical properties of supramolecular species supramolecular effects in photochemical hole burning molecular and supramolecular electronic devices supramolecular electrochemistry electron conducting devices - molecular wires polarized molecular wires - rectifying devices modified and switchable molecular wires molecular magnetic devices molecular and supramolecular ionic devices tubular mesophases. (Part contents).
On-surface self-condensation of 1,4-benzenediboronic acid was previously shown to yield extended surface-supported, long-range-ordered two-dimensional covalent organic frameworks (2D COFs). The most important prerequisite for obtaining high structural quality is that the polycondensation (dehydration) reaction is carried out under slightly reversible reaction conditions, i.e., in the presence of water. Only then can the subtle balance between kinetic and thermodynamic control of the polycondensation be favorably influenced, and defects that are unavoidable during growth can be corrected. In the present study we extend the previously developed straightforward preparation protocol to a variety of para-diboronic acid building blocks with the aim to tune lattice parameters and pore sizes of 2D COFs. Scanning tunneling microscopy is employed for structural characterization of the covalent networks and of noncovalently self-assembled structures that form on the surface prior to the thermally activated polycondensation reaction.
A solution processible polymer -poly(3,3‴-didodecylquaterthiophene) (PQT-12) is investigated at the liquid/solid interface using the scanning tunneling microscopy (STM). Two-dimensional ordered films made up of self-assembled domains, with dimensions of 100 nm × 50 nm adsorbed on highly oriented pyrolytic graphite (HOPG) were formed. These domains consist of parallel lamellar polymer chains, with the alkyl chains forming interdigitated structures, along with U-shaped and closed ring segments of the polymer chains. A polymer chain packing model is proposed herein, which attempts to propose a correlation between the packing of long chains and charge mobilities. These STM results could help in understanding the relationship between the extended conjugation and molecular organization of the PQT-12 chains.
(Figure Presented) New tool for surface modification: The 2D pattern formed by physisorbed dehydrobenzoannulene molecules on a graphite surface depends on their concentration in solution. The concentration dependence is directly related to the difference in stability between the linear andthe honeycomb polymorphs andtheir respective molecular densities (see picture).
Exposure to even very low levels of lead, cadmium, and mercury ions is known to cause neurological, reproductive, cardiovascular, and developmental disorders, which are more serious problems for children particularly. Accordingly, great efforts have been devoted to the development of fluorescent and colorimetric sensors, which can selectively detect lead, cadmium, and mercury ions. In this critical review, the fluorescent and colorimetric sensors are classified according to their receptors into several categories, including small molecule based sensors, calixarene based chemosensors, BODIPY based chemosensors, polymer based chemosensors, DNA functionalized sensing systems, protein based sensing systems and nanoparticle based sensing systems (197 references).
Two different straightforward synthetic approaches are presented to fabricate long-range-ordered monolayers of a covalent organic framework (COF) on an inert, catalytically inactive graphite surface. Boronic acid condensation (dehydration) is employed as the polymerization reaction. In the first approach, the monomer is prepolymerized by a mere thermal treatment into nanocrystalline precursor COFs. The precursors are then deposited by drop-casting onto a graphite substrate and characterized by scanning tunneling microscopy (STM). While in the precursors monomers are already covalently interlinked into the final COF structure, the resulting domain size is still rather small. We show that a thermal treatment under reversible reaction conditions facilitates on-surface ripening associated with a striking increase of the domain size. Although this first approach allows studying different stages of the polymerization, the direct polymerization, that is, without the necessity of preceding reaction steps, is desirable. We demonstrate that even for a comparatively small diboronic acid monomer a direct thermally activated polymerization into extended COF monolayers is achievable.