Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot ...correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
Controlling the size and surface functionalization of nanoparticles (NPs) can lead to improved properties and applicability. Herein, we demonstrate the efficiency of the metal‐carbene template ...approach (MCTA) to synthesize highly robust and soluble three‐dimensional polyimidazolium cages (PICs) of different sizes, each bearing numerous imidazolium groups, and use these as templates to synthesize and stabilize catalytically active, cavity‐hosted, dispersed poly‐N‐heterocyclic carbene (NHC)‐anchored gold NPs. Owing to the stabilization of the NHC ligands and the effective confinement of the cage cavities, the as‐prepared poly‐NHC‐shell‐encapsulated AuNPs displayed promising stability towards heat, pH, and chemical regents. Most notably, all the Au@PCCs (PCC=polycarbene cage) exhibited excellent catalytic activities in various chemical reactions, together with high stability and durability.
Take your PIC: Polyimidazolium cages (PICs) are used as templates to synthesize and stabilize catalytically active, cavity‐hosted, dispersed poly‐N‐heterocyclic carbene (NHC)‐anchored gold nanoparticles NPs. The resulting Au NPs display impressive thermal and chemical stability and high catalytic activities.
A procedure for the synthesis of three‐dimensional hexakisimidazolium cage compounds has been developed. The reaction of the trigonal trisimidazolium salts H3L(PF6)3, decorated with three N‐olefinic ...pendants, and silver oxide yielded trinuclear trisilver(I) hexacarbene molecular cylinders of the type Ag3L23+ with the olefinic pendants from the two different tricarbene ligands arranged in three pairs. Subsequent UV irradiation gave three cyclobutane links between the two tris‐NHC ligands in three 2+2 cycloaddition reactions, thereby generating a three‐dimensional hexakis‐NHC ligand. Removal of the metal ions resulted in the formation of three‐dimensional hexakisimidazolium cages with a large internal cavity.
All good things come in threes: An efficient template synthesis has been developed for the preparation of three‐dimensional hexakisimidazolium cage compounds starting from trigonal trisimidazolium salts decorated with three N‐olefinic pendants and silver ions as metal templates.
Conspectus Over the last two decades, researchers have focused on the design and synthesis of supramolecular coordination complexes, which contain discrete functional structures with particular ...shapes and sizes, and are similar to classic metal–organic frameworks. Chemists can regulate many of these systems by judiciously choosing the metal centers and their adjoining ligands. These resulting complexes have unusual properties and therefore many applications, including molecular recognition, supramolecular catalysis, and some applications as nanomaterials. In addition, researchers have extensively developed synthetic methodologies for the construction of discrete self-assemblies. One of the most important challenges for scientists in this area is to be able to synthesize target structures that can be controlled in both length and width. For this reason, it is important that we understand the factors leading to special shapes and sizes of such architectures, especially how starting building blocks and functional ligands affect the final conformations and cavity sizes of the resulting assemblies. Towards this goal, we have developed a wide range of different organometallic architectures by rationally designing metal-containing precursors and organic ligands. In this Account, we present our recent work, focusing on half-sandwich iridium- and rhodium-based organometallic assemblies that we obtained through rational design. We discuss their synthesis, structures, and applications for the encapsulation of guests and enzyme-mimicking catalysis. We first describe a series of self-assembled organometallic metallarectangles and metallacages, which we constructed from preorganized dinuclear half-sandwich molecular clips and suitable pyridyl ligands. We extended this strategy to tune the size of the obtained rectangles, creating large cavities by introduction of larger molecular clips. The cavity was found to exhibit selective and reversible CH2Cl2 adsorption properties while retaining single crystallinity. By using suitable molecular clips, we found we could use a number of metallacycles as organometallic templates to direct photochemical 2 + 2 cycloaddition reactions, even in the solid state. Due to their chemical stability and potential applications in catalytic reactions, researchers are giving significant attention to complexes with cyclometalated backbones. We also highlight our efforts to develop efficient approaches to utilize cyclometalated building blocks for the formation of organometallic assemblies. By incorporation of imine ligands or benzoic acids, bipyridine linking subunits, and half-sandwich iridium or rhodium fragments, we built up a series of cationic and neutral metallacycles through cyclometalation-driven self-assembly. In addition, we have developed an efficient route to carborane-based metallacycles, involving the exploitation of metal-induced B–H activation. The method can provide prism-like metallacages, which are efficient hosts for the recognition of planar aromatic guests. This effort provides an incentive to generate new building blocks for the construction of organometallic assemblies. Taken together, our results may lead to a promising future for the design of complicated enzyme-mimetic-catalyzed systems.
Thanks to the potential of aggregation‐induced emission (AIE) phenomena, improved stabilities, and the good selectivity and sensitivity of the chemical responses exhibited by the products, ...coordination‐driven self‐assembly with tetraphenylethylene (TPE) units has recently received much attention and has been widely investigated for application in chemical sensors, cell imaging agents, light‐harvesting systems, and others. Several reviews have emerged on the topics of AIE chemistry and aggregation‐induced emission luminogen (AIEgen)‐based supramolecular assembles, however, there is still a distinct lack of full overviews of emission enhancement from the viewpoint of metal‐coordination effects. Thus, this minireview offers recent advances that have been made in the design and application of TPE‐based metallacycles, metallacages, metal‐organic frameworks (MOFs) and coordination polymers (CPs).
The motions of the tetraphenylethylene (TPE) units are restricted by coordination bonds through coordination‐driven self‐assembly, thereby their non‐radiative decay is reduced to induce fluorescence emission. This minireview offers a summary of recent advances that have been made in the design and synthesis of TPE‐based metallacycles, metallacages, metal–organic frameworks (MOFs) and coordination polymers (CPs). Their potential applications as materials for chemical sensors, cell imaging agents and light‐harvesting materials, among others, are outlined.
A new class of supramolecular metallacycles capable of undergoing photochemical reactions and in situ release of cyclobutanes in solution is described. The molecular metallacycles were generated ...through coordination‐driven self‐assembly of dinuclear metal‐carbene complexes as organometallic clips with olefin‐functionalized bridging ligands. Photolysis of these molecular metallacycles in situ led to structural interconversion and release of the formed cyclobutane products with quantitative conversion. Further modifications of the obtained cyclobutanes provided a series of new species containing the cyclobutane skeleton.
Catch and release: Photolysis of the pictured molecular metallacycles in situ leads to quantitative cycloaddition and release of the stereoselectively formed cyclobutane products. The pendant groups on the products include pyridyl, imidazole, benzimidazoles, and carboxylic derivatives.
Homoleptic and heteroleptic cylinder‐shaped poly‐NHC metallosupramolecular assemblies Ag3(L)2(BF4)3 have been prepared by control of the shape, size, and electronic properties of disk‐shaped ...trisimidazolium salts of type H3‐L(BF4)3. Both imidazolium salts with an electron‐deficient triazine backbone H3‐A(BF4)3 or an electron‐rich benzene backbone H3‐D(BF4)3 have been employed. Reaction of H3‐A(BF4)3 or H3‐D(BF4)3 with Ag2O yield trinuclear homoligand complexes Ag3(L)2(BF4)3 (L=A, D). However, equimolar mixtures of H3‐A(BF4)3 and H3‐D(BF4)3 react with Ag2O under social self‐sorting to give the heteroligand assembly Ag3(A)(D)(BF4)3. The same heteroligand assembly was obtained by transmetallation from mixtures of complexes Ag3(A)2(BF4)3 and Ag3(D)2(BF4)3. The transmetallation from Ag3(A)(D)(BF4)3 to Au3(A)(D)(BF4)3 is also demonstrated. The study expands to concepts of narcissistic and social self‐sorting from classical Werner‐type ligands to organometallic NHC chemistry thereby opening new routes for the construction of poly‐NHC metal assemblies with increasing complexity.
Unprecedented social self‐sorting occurs during the reaction of Ag2O with two trisimidazolium salts featuring either an electron‐poor H3‐A1(BF4)3 or an electron‐rich H3‐D1(BF4)3 backbone to give the heteroligand assembly Ag3(A1)(D1)(BF4)3 most likely driven by π⋅⋅⋅π stacking interactions between the electron‐rich and electron‐poor ligand backbone groups.
Conspectus As versatile, modular, and strongly coordinating moieties in organometallic compounds, N-heterocyclic carbenes (NHCs) have led to numerous breakthroughs in transition-metal catalysis, main ...group chemistry, and organocatalysis. In contrast, the chemistry of NHC-based metallosupramolecular assemblies, in which discrete individual components are held together via metal (M)–CNHC bonds, has been underdeveloped. Integrating NHCs into supramolecular assemblies would endow them with some unforeseen functions. However, one of the most critical challenges is seeking an appropriate combination of the rigid CNHC–M–CNHC units with the resulting topologies and applications. Toward this goal, for the last decade we have focused on the development of M–NHC directed toward metallosupramolecular synthesis. This Account aims to summarize our contributions to the application of M–NHC chemistry toward supramolecular synthesis from structural design to postassembly modification (PAM) and their functional applications since integrating NHCs into supramolecular assemblies has garnered much attention among organometallic, photochemical, and supramolecular researchers. While presenting representative examples of NHC-based architectures, we try to illustrate the purposes and concepts behind the systems developed to aid the rational approach to the design and fabrication of complex assemblies and M–NHC-templated photochemical reactions. We present synthetic approaches for new architectures by the rational design of starting NHC precursors, including the poly-NHC-based mechanically interlocked metallacages and the heteroleptic architectures based on electronic complementary and self-sorting mechanisms. The structural regulation of poly-NHC-based architectures with increasing topological complexity is elaborated on by selective combinations of tetraphenylethylene (TPE) units, NHC backbones, and N-wingtip substituents in a controllable manner. Subsequently, we move to elucidating an M–NHC-templated PAM approach that leads to functional organic cages featuring polyimidazolium/triazolium groups of different shapes and sizes that are difficult to access using alternative organic approaches. These organic cages possess well-defined cavities, and their in situ-generated NHC sites are ideal platforms for stabilizing metal nanoparticles (MNPs) within their cavities for improved catalytic performance. Finally, we demonstrate how to design supramolecular M–NHC templates to synthesize cyclobutane derivatives in homogeneous solutions in a catalytic fashion. Selected examples of M–NHC template-dependent structural transformations and photoreactions are discussed. Their applications in molecular recognition, aggregation-induced emission (AIE), cell imaging, anticancer activity, radical chemistry, and stimuli-responsive materials are also described. Taken together, M–NHC-templated approaches have proven to be powerful methods for constructing diverse architectures with functional applications. The development of this methodology is still in its infancy, with tremendous growth potential and a promising future. We believe that this Account will guide researchers to design fascinating and valuable M–carbene species for diverse applications.
New hindered tetraphenylethylene (TPE) helicates with substitution at 2,6‐position of phenyl rings were designed and synthesized. Due to the increased hindrance, the TPE helicates emit strong ...deep‐blue to violet fluorescence both in the solid state and in solution, and could be resolved into enantiomers that emit strong and multicolor circularly polarized luminescence (CPL), and exhibit a high enantioselective recognition of chiral tartaric acid and its derivatives. Surprisingly, the derived helicate tetramines possess amino groups with an unpredented planar structure and sp2‐hybridized nitrogen, arousing the change between AIE effect and ACQ phenomenon through photoinduced electron transfer (PET). With advantages of short synthetic route, many modification positions, deep‐blue to violet emission, wide CPL tuning, and high chiral recognition ability, the hindered TPE helicates show broad prospects as chiral materials.
Hindered tetraphenylethylene (TPE) helicates, with a completely immobilized propeller‐like conformation through substitution at the 2,6‐positions of the phenyl rings, were prepared by a short synthetic route. These helicates, with their many modification positions, show deep‐blue to violet emission, circularly polarized luminescence (CPL) that can be tuned over a wide range, and highly enantioselective chiral recognition.
A series of supramolecular assemblies of types Ag8(L)4(PF6)8 and Ag4(L)2(PF6)4, obtained from the tetraphenylethylene (TPE) bridged tetrakis(1,2,4‐triazolium) salts H4‐L(PF6)4 and AgI ions, is ...described. The assembly type obtained dependends on the N‐wingtip substituents of H4‐L(PF6)4. Changes in the lengths of the N4‐wingtip substituents enables controlled formation of assemblies with either Ag4(L)2(PF6)4 or Ag8(L)4(PF6)8 stoichiometry. The molecular structures of selected Ag8(L)4(PF6)8 and Ag4(L)2(PF6)4 assemblies were determined by X‐ray diffraction analyses. While H4‐L(PF6)4 does not exhibit fluorescence in solution, their tetra‐NHC (NHC=N‐heterocyclic carbene) assemblies do upon NHC–metal coordination. Upon irradiation, all assemblies undergo a light‐induced, supramolecule‐to‐supramolecule structural transformation by an oxidative photocyclization involving phenyl groups of the TPE core, resulting in a significant change of the luminescence properties.
Silver links: Tetrakis(1,2,4‐triazolium) salts H4‐L(PF6)4, featuring different N4 substituents, react with Ag2O to give, depending on the length of the N4 alkyl substituent, tetranuclear metallo‐supramolecular assemblies of type Ag4(L)2(PF6)4 or octanuclear assemblies of type Ag8(L)4(PF6)8. Both types of assemblies, upon irradiation, undergo oxidative photocyclization of the central tetrakisarylethylene unit to yield the complexes with a 9,10‐phenyl‐substituted phenanthrene bridge.
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