Chirality transfer from a single chiral molecule to 2D superstructures in alaninol on the Cu(100) surface

The formation of 2D chiral monolayers obtained by self-assembly of chiral molecules on surfaces has been widely reported in the literature. Control of chirality transfer from a single molecule to surface superstructures is a challenging and important aspect for tailoring the properties of 2D nanostructures. However, despite the wealth of investigations performed in recent years, how chiral transfer takes place on a large scale still remains an open question. In this paper we report a coupling of scanning tunneling microscopy and low energy electron diffraction measurements with an original theoretical approach, combining molecular dynamics and essential dynamics with density functional theory, to investigate self-assembled chiral structures formed when alaninol adsorbs on Cu(100). The peculiarity of this system is related to the formation of tetrameric molecular structures which constitute the building blocks of the self-assembled chiral monolayer. Such characteristics make alaninol/Cu(100) a good candidate to reveal chiral expression changes. We find that the deposition of alaninol enantiomers results in the formation of isolated tetramers that are aligned along the directions of the substrate at low coverage or when geometrical confinement prevents long-range order. Conversely, a rotation of 14° with respect to the Cu(100) unit vectors is observed when small clusters of tetramers are formed. An insight to the process leading to a 2D globally chiral surface has been obtained by monitoring molecular assemblies as they grow from the early stages of adsorption, suggesting that the distinctive orientation of the self-assembled monolayer originates from a balance of cooperating forces which start acting only when tetramers pack together to form small clusters.     

DNA-templated covalent coupling of G4 PAMAM dendrimers

Generation-4 polyamidoamine (PAMAM) dendrimers were surface-functionalized with azides or alkynes and conjugated to one DNA strand. DNA-controlled self-assembly of alternating azide and alkyne dendrimers on a DNA template enabled the coupling of the dendrimers by the azide-alkyne "click" reaction to form covalently coupled dimers, trimers, and tetramers. Polymerization of the DNA-dendrimer conjugates was also demonstrated, as well as assembly in a circular structure on DNA origami and imaging by atomic force microscopy.     

Self-assembly of [Et,Et]-bacteriochlorophyll cF on highly oriented pyrolytic graphite revealed by scanning tunneling microscopy

The chlorosomal light-harvesting antennae of green phototrophic bacteria consist of large supramolecular aggregates of bacteriochlorophyll c (BChl c). The supramolecular structure of (3(1)-R/S)-BChl c on highly oriented pyrolytic graphite (HOPG) and molybdenum disulfide (MoS2) has been investigated by scanning tunneling microscopy (STM). On MoS2, we observed single BChl c molecules, dimers or tetramers, depending on the polarity of the solvent. On HOPG, we observed extensive self-assembly of the dimers and tetramers. We propose C=O...H-O...Mg bonding networks for the observed dimer chains, in agreement with former ultraviolet-visible and infrared spectroscopic work. The BChl c moieties in the tetramers are probably linked by four C=O...H-O hydrogen bonds to form a circle and further stabilized by Mg...O-H bondings to underlying BChl c layers. The tetramers form highly ordered, distinct chains and extended two-dimensional networks. We investigated semisynthetic chlorins for comparison by STM but observed that only BChl c self-assembles to well-structured large aggregates on HOPG. The results on the synthetic chlorins support our structure proposition.     

Combinatorial synthesis of oligo(phenylene ethynylene)s

The combinatorial synthesis of oligo(phenylene ethynylene) tetramers, both in solution and on solid support, is described. These products are of interest for molecular electronics applications. An iterative sequence, coupling of aryl halides to alkynes under Sonogashira conditions, was used. Five monomers functionalized with electron-donating or electron-withdrawing groups were synthesized, and used to generate a library of 25 trimers in a solution-phase based process. A library of 24 tetramers was prepared by subsequent protodesilylation and coupling with the alligator clip 4-iodo-1-thioacetylbenzene. The solution-phase based sequence was successfully adapted to a higher yielding directed split-and-pool solid-phase process, with average yields of 78–86% for each step over seven steps. A triazene linker group was used to attach the starting monomer to the polymer beads. At the completion of the solid-phase-based process, traceless cleavage of trimers from the resin was achieved by sonication of the resin in 10% HCl/THF solution. The released products were then poised for the final step in the sequence, attachment of the alligator clip.     

A modular approach to DNA-programmed self-assembly of macromolecular nanostructures

DNA-programmed organic reactions are new and powerful tools for assembling chemical compounds into predetermined complex structures and a brief review of their use is given. This approach is particular efficient for the selection and covalent coupling of multiple components. DNA-templated synthesis is used for polymerization of PNA tetramers and for copying of the connectivity information in DNA. Direct DNA-programmed multicomponent coupling of custom designed organic modules is described. The macromolecular structures obtained are highly conjugated potentially conducting nanoscaffolds. Some future developments in this area are discussed.     

Preparation and NMR Structure of the Cyclo-β-tripeptide [β3-HGlu]3 in Aqueous Solution: A New Class of Enterobactin-Type C3-Symmetrical Ligands?, Preliminary Communication

To date, cyclo-β-tripeptides (twelve-membered-ring trilactams, C ) have resisted structural investigations because of their extreme insolubility. Modelling and comparison with the corresponding tetramers indicate that the rings stack to form tube-like hydrogen-bonded aggregates ( D ). By exploiting the solubilizing effect of LiCl on peptides in THF, we were able to prepare the water-soluble title compound and determine its structure ( E ) by NMR spectroscopy. Structural similarities and differences between the trilactam ring of [β³-HGlu]₃ and the corresponding trilactone ring, such as that of enterobactin ( A ), are discussed, and structures (`elongated'; F , G ) are proposed that should be able to serve as tridentate or trivalent ligands for metal centers.     

Efficient sequential segment coupling using N-alkylcysteine-assisted thioesterification for glycopeptide dendrimer synthesis

A highly pure MUC1-derived glycopeptide dendrimer of 22 kDa was prepared by a sequential segment coupling, achieved by an N-alkylcysteine (NAC)-assisted thioesterification. The glycopeptide having C-terminal NAC was prepared by the Fmoc method and converted to the thioester by 3-mercaptopropionic acid treatment. The thioester was condensed with a lysine trimer carrying NAC to afford tetramer, which was then converted to the thioester. Two tetramers were condensed with ethylenediamine to give the octameric glycopeptide dendrimer.     

Clustering of nucleosides in the presence of alkali metals: Biologically relevant quartets of guanosine,deoxyguanosine and uridine observed by ESI-MS/MS

Electrospray ionization (ESI) mass spectra of nucleosides, recorded in the presence of alkali metals, display alkali metal ion-bound quartets and other clusters that may have implications for understanding non-covalent interactions in DNA and RNA. The tetramers of guanosine and deoxyguanosine and also their metaclusters (clusters of clusters), cationized by alkali metals, were observed as unusually abundant magic number clusters. The observation of these species in the gas phase parallels previous condensed-phase studies, which show that guanine derivatives can form quartets and metaclusters of quartets in solution in the presence of metal cations. This parallel behavior and also internal evidence suggest that bonding in the guanosine tetramers involves the bases rather than the sugar units. The nucleobases thymine and uracil are known to form magic number pentameric adducts with K+, Cs+ and NH4+ in the gas phase. In sharp contrast, we now show that the nucleosides uridine and deoxythymidine do not form the pentameric clusters characteristic of the corresponding bases. More subtle effects of the sugars are evident in the fact that adenosine and cytidine form numerous higher order clusters with alkali metals, whereas deoxyadenosine and deoxycytidine show no clustering. It is suggested that hydrogen bonding between the bases in the tetramers of dG and rG are the dominant interactions in the clusters, hence changing the ribose group to deoxyribose (and vice versa) generally has little effect. However, the additional hydroxyl group of RNA nucleosides enhances the non-selective formation of higher-order aggregates for adenosine and cytidine and results in the lack of highly stable magic number clusters. Some clusters are the result of aggregation in the course of ionization (ESI) whereas others appear to be intrinsic to the solution being examined.     

Linear NiII-MnIII2-NiII tetramers: an oligomeric component of the MnIII2NiII single-chain magnets

Heterometallic linear tetramers [Mn(5-R-saltmen)Ni(pao)(bpy)(2)](2)(ClO(4))(4) (5-R-saltmen(2-) = N,N'-1,1,2,2-tetramethylethylene bis(5-R-salicylideneiminate); pao(-) = pyridine-2-aldoximate; bpy = 2,2'-bipyridine, R = H, 1; Cl, 2; Br, 3; MeO, 4) have been synthesized and structurally characterized. These compounds exhibit a [Ni(II)-NO-Mn(III)-(O)(2)-Mn(III)-ON-Ni(II)] skeleton where -ON- is an oximate bridge between Mn(III) and Ni(II) ions and -(O)(2)- is a bi-phenolate bridge between Mn(III) ions. These tetramers can be seen as oligomeric units of the heterometallic Mn(III)(2)-Ni(II) chain observed in a family of single-chain magnets (Clérac, R.; Miyasaka, H.; Yamashita, M.; Coulon, C. J. Am. Chem. Soc. 2002, 124, 12837. Miyasaka, H.; Clérac, R.; Mizushima, K.; Sugiura, K.; Yamashita, M.; Wernsdorfer, W.; Coulon, C. Inorg. Chem. 2003, 42, 8203.). Magnetic measurements on these tetramers confirm the nature of the magnetic interactions reported for the Mn(III)(2)-Ni(II) chains: a strong antiferromagnetic Mn(III)/Ni(II) coupling via the oximate bridge (J(Ni-Mn) ranges from -23.7 to -26.1 K) and a weak ferromagnetic Mn(III)/Mn(III) coupling through the bi-phenolate bridge (J(Mn-Mn) ranges from +0.4 to +0.9 K). These magnetic interactions lead to tetramers with an S = 2 ground state.     

Controlled Construction of Cyclic d / l Peptide Nanorods

Cyclic d / l peptides (CPs) assemble spontaneously via backbone H‐bonding to form extended nanostructures. These modular materials have great potential as versatile bionanomaterials. However, the useful development of CP nanomaterials requires practical methods to direct and control their assembly. In this work, we present novel, heterogeneous, covalently linked CP tetramers that achieve local control over the CP subunit order and composition through coupling of amino acid side‐chains using copper‐activated azide–alkyne cycloaddition and disulfide bond formation. Cryo‐transmission electron microscopy revealed the formation of highly ordered, fibrous nanostructures, while NMR studies showed that these systems have strong intramolecular H‐bonding in solution. The introduction of inter‐CP tethers is expected to enable the development of complex nanomaterials with controllable chemical properties, facilitating the development of precisely functionalized or “decorated” peptide nanostructures.     

A new type of calixarene: octahydroxypyridin

A new type of calixarene has been synthesised. Like resorcinol and a number of resorcinol derivatives, 2,6-dihydroxypyridine has been proven to form cyclic tetramers in moderate yields with a number of aliphatic and two aromatic aldehydes in acidic media. The problem of the formation of configurational isomers can be reduced by increasing the reaction temperature and time. With electron-rich aromatic aldehydes, 2,6-dihydroxypyridine unexpectedly yields deep-coloured acyclic quinoid systems. The octahydroxypyridine[4]arenes may have a high potential as receptors for molecular recognition and self organisation.     

Ce（SO4）2-mediated Oxidative Coupling of Primary Aromatic Amines in Water

The oxidative coupling of primary aromatic amines was investigated. Ce(SO4)2 can mediate the oxidative coupling of primary aromatic amines in water to dimers, trimers and/or tetramers, which depended on the substituents of primary aromatic amines. When 2,6-dimethylaniline or 2,6-diethylaniline was used as substrate, dimer, and tetramer were formed as major products. When 2,6-diisopropylaniline or 2,6-dihaloanilines was used as substrate, dimer, and trimer were formed. The mechanistic aspect was also investi...     

Isolation of an [SNS]Pd(II) pincer with a water ladder and its Suzuki coupling activity in water

A water-compatible Pd(ii) pincer with a hybrid [SNS]-donor set, [L(1)PdCl]Cl.2H(2)O [L(1) = bis-(2-(i-butylsulfanyl)-ethyl)-amine] has been isolated and crystallographically characterized; its solid lattice at 223 K contains a ladder-like water polymer of tetramers and extensive H-bonding exists among the cation, anion and water cluster, and this water-soluble complex is active in Suzuki-Miyaura coupling of phenylboronic acid and selected aryl bromides in water at 75 degrees C.     

Direct characterization of protein oligomers and their quaternary structures by single-molecule FRET

Using a single-molecule method, we directly distinguish among oligomers from monomers to tetramers and determine their quaternary structures. Using this method, we found that RecR forms a stable dimer and its oligomeric form is modulated by its own concentration and the interaction with RecO.     

A reinvestigation of phenylene- and polyphenylene-mercurials

Evidence is presented to show that ortho-phenylenemercury is a trimer; no evidence was obtained for the previously reported hexameric form. Similarly, ortho-biphenylenemercury and its perfluoro-analogue exist as trimers and not tetramers, while ortho-terphenylenemercury is a dimer.     

Steric factor in ligand displacement of zirconium alkoxides dissolved in alcohols

The present study indicates EXAFS direct structural data obtained for zirconium ethoxide, iso- and n-propoxide are alike those for zirconium n-butoxide complexes. This is evident for agreement of structural units of abovementioned alkoxides complexes. Our group developed structural model of n-butoxide earlier. Six interconnected tetramers assemble a structural unit of the alkoxides under study. The tetramers build of zirconium atoms in the highly flattened pyramid corners. Four zirconium atoms are bonded in series by double bridges through oxygen atoms of alkoxide ligands. Two of the four zirconium atoms are bias bonded by single ligand bridges. The distances between pairs of zirconium atoms inside the tetramer are 3.3 and 3.5 Å. Tetramers are linked together also by a single ligand bridges. The distance between zirconium atoms of the two neighbor tetramers is 3.9 Å. Primary particles (tetramer sextet) form aggregates in a solution. Possible shapes of the anisotropically sized aggregates is a large diameter cylinder with small height (a disk), or a small diameter cylinder with large height (a rod). Primary particles composed through ligands. The distance between the neighbor zirconium atoms of different primary particles is 4.8 or 5.1 Å depending on the coordination nature and the neighboring particles number.     

Copper coupling of 1-chloro-2-iodo- and 1,2-di-iodo-perfluorocycloalkenes

Reductive coupling of 1-chloro-2-iodoperfluorocyclobutene (I), cyclopentene (III) and cyclohexene (VI) has been carried out with copper powder and a trace amount of dimethylformamide to give the corresponding 2,2′-dichloroperfluoro-(bi-1-cycloalken-1-yl) derivatives in 69%, 36% and 73% yield, respectively. A reduced by-product, 2H,2′H-dodecafluoro-(bi-1-cyclopenten-1-yl) was also obtained in the copper coupling of (III). Coupling of 1,2-di-iodoperfluorocyclobutene (IX) and cyclopentene (XII) under similar conditions gave good yields of cyclic trimers and tetramers. Mass spectra, infrared and ¹⁹F NMR data are discussed.     

Two-photon absorption of hydrogen-bonded octupolar molecule clusters

Charge-transfer octupolar molecules can form clusters in solution through intermolecular hydrogen bonds. In the present work we explore the role of such clustering on two-photon absorption (TPA) spectra assuming 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) as a model system. Using density functional quadratic response theory we examine different cluster structures of TATB dimers, trimers, and tetramers taken from snapshots of molecular dynamics simulations. In comparison with the TPA spectrum of a monomer, significant red shifts of charge-transfer states are predicted for all chosen clusters, which mainly is the result of the distortion of the structures induced by the aggregation. The TPA spectra for dimers and trimers show strong conformation dependence, whereas they turn out to be more stable for tetramers. Enhancements of TPA absorption have also been found for clusters containing less distorted molecules connected by hydrogen bonds.     

Photoresponsive supramolecular systems: self-assembly of azodibenzoic acid linear tapes and cyclic tetramers

A new strategy to effect photoinduced control over molecular self-assembly is reported. This strategy uses the reversible trans-cis photoisomerization of a novel azobenzene system, where the trans- and cis-forms self-assemble into dramatically different higher-order structures. The trans-azobenzene form of this molecule associates into infinite hydrogen-bonded linear tapes, while the cis-azobenzene form undergoes hydrogen-bonded self-assembly into cyclic tetramers. This results in a second level of association, where the cis-hydrogen-bonded supramolecular cycles ultimately form long, rod-like aggregates through stacking interactions.