Structural transformation of two-dimensional metal-organic coordination networks driven by intrinsic in-plane compression

The coordination assembly of 1,3,5-trispyridylbenzene with Cu on a Au(111) surface has been investigated by scanning tunneling microscopy under ultrahigh vacuum conditions. An open two-dimensional (2D) metal-organic network of honeycomb structure is formed as the 2D network covers partial surface. Upon the 2D network coverage of the entire surface, further increment of molecular density on the surface results in a multistep nonreversible structural transformation in the self-assembly. The new phases consist of metal-organic networks of pentagonal, rhombic, zigzag, and eventually triangular structures. In addition to the structural change, the coordination configuration also undergoes a change from the two-fold Cu-pyridyl binding in the honeycomb, pentagonal, rhombic and zigzag structures to the three-fold Cu-pyridyl coordination in the triangular structure. As the increment of molecular packing density on the surface builds up intrinsic in-plane compression pressure in the 2D space, the transformation of the structure, as well as the coordination binding mode, is attributed to the in-plane compression pressure. The quantitative structural analysis of the various phases upon molecular density increment allows us to construct a phase diagram of network structures as a function of the in-plane compression.     

Cooperative self-assembly and molecular binding behavior of cyclodextrin-crown ether conjugates mediated by alkali metal ions

In order to quantitatively investigate their molecular binding ability, a series of cyclodextrin-crown ether conjugates containing beta-cyclodextrin (beta-CyD) and crown ether units, i.e.N-(benzoaza-15-crown-5)acylaminomethylene tethered 6-diethylenetriamino-6-deoxy-beta-CyD, N-(benzoaza-15-crown-5)acylaminomethylene tethered 6-triethylenetetraamino-6-deoxy-beta-CyD and 4',5'-dimethylene-benzo-15-crown-5 tethered 6-diethylenetriamino-6-deoxy-beta-CyD, have been prepared as ditopic molecular receptors. Their inclusion complexation behavior with four representative fluorescent dyes, i.e. ammonium 8-anilino-1-naphthalenesulfonate (ANS), sodium 6-toluidino-2-naphthalenesulfonate (TNS), acridine red (AR) and rhodamine B (RhB), has been comprehensively investigated in aqueous NaH2PO4/Na2HPO4 or KH2PO4/K2HPO4 buffer solution (pH 7.20) by means of circular dichroism, fluorescence, and 2D NMR spectra. The results indicate that the self-assembly of crown ether modified beta-CyD mediated by potassium ion exhibits a dimeric structure, which significantly enhances the original binding ability and molecular selectivity of parent beta-CyD and its derivatives towards guest molecules through the cooperative binding of two hydrophobic CyD cavities with one guest. This cooperative binding mode of K+/CyD-crown ether systems are further confirmed by Job's experiments and 2D NMR investigations. Attributed to the positive contributions from the metal-ligated crown ether cap and K+-mediated dimerization of CyDs, the binding constant (Ks) values of CyD-crown ether conjugates toward ANS are 10-83 times higher than that of beta-CyD. The increased binding ability and molecular selectivity of CyD-crown ether conjugates are discussed from the viewpoints of size/shape-fit and multiple recognition mechanism.     

Flexible eightfold interpenetrating diamondoid network generating 1D channels: selective binding with organic guests

An 8-fold interpenetrating diamondoid network, [Ni(cyclam)]2[TCM]. 2DMF x 10H2O, has been prepared by the self-assembly of a Ni-(II)cyclam macrocyclic complex and sodium tetrakis[4-(carboxyphenyl)-oxamethyl]methane in DMF/water. The network shows an unusual [4 + 4] mode of interpenetration, generating 1D channels of effective window size 6.7 A x 4.7 A. The network shows flexible behavior: it becomes nonporous on removal of the guest molecules occupying the channels, but the open structure is restored when the desolvated solid is immersed in the mixture of H2O/DMF (1:1, v/v) for 5 min. The desolvated host has different binding capacities for n-butanol, pyridine, and ethanol.     

Calorimetric study of the reactions of n-alkylphosphonic acids with metal oxide surfaces

The reaction enthalpies for the solution-phase self-assembly of n-alkylphosphonic acids on the surfaces of TiO2 and ZrO2 have been determined using isothermal titration calorimetry at 298 K. The reaction enthalpies were negative (exothermic) for methyl- and n-octylphosphonic acids and positive (endothermic) for n-octadecylphosphonic acid with both metal oxides. The enthalpy/energy analysis showed that the net enthalpy of the formation of self-assembled monolayers (SAMs) at solid-liquid interface can be presented as follows: DeltaHr=-D-(DeltaHsol+DeltaHdil)-(ES-ESAM), where D is the binding energy of the SAM molecules with the solid; DeltaHsol and DeltaHdil are the enthalpies of dissolution and dilution; ES and ESAM are the surface energies of bare solid and SAM, respectively. This equation predicted an increase (and the sign change) of the reaction enthalpy as the alkyl group in n-alkylphosphonic acid increased, which explained the experimental data. Using this equation, the binding energy (D) in the SAMs of n-octyl- and n-octadecylphosphonic acids were estimated: 55+/-5 kJ/mol (for ZrO2) and 58+/-7 kJ/mol (for TiO2).     

An unusual 3D coordination polymer based on bridging interactions of the nucleobase adenine

The first 3D coordination polymer containing a nucleobase as a bridging ligand, [[Cu2(mu-ade)4(H2O)2][Cu(ox)(H2O)]2 x approximately 14H2O]n (1), has been synthesized by reaction of adenine (Hade) with a basic solution of K2[Cu(ox)2] x 2H2O (ox = oxalato dianion). Compound 1 crystallizes in the trigonal space group R3 with a = b = 31.350(1) angstroms, c = 14.285(1) angstroms, V = 12158.7(10) angstroms3, and Z = 9. X-ray analysis shows a covalent 3D network in which the copper(II) centers are bridged by tridentate mu-N3,N7,N9 adeninate ligands. The compound has relatively large, nanometer-sized tubes associated with the self-assembly process directed solely by metal-ligand interactions. The covalent 3D framework remains intact upon removal of the guest water molecules trapped in the nanotubes. Magnetic measurements indicate an overall antiferromagnetic behavior of the compound.     

Acyclic congener of cucurbituril: synthesis and recognition properties

The cucurbit[n]uril (CB[n]) family of macrocycles occupies a prominent role in molecular recognition and self-assembly studies despite the current inability to access specific cucurbit[n]uril homologues, derivatives, and analogues by straightforward tailor-made synthetic procedures. In this paper, we explore an approach that circumvents the challenges posed by the tailor-made synthesis of macrocyclic CB[n] by preparing 1, which functions as an acyclic CB[6] congener. The o-xylylene connections to the glycoluril rings preorganize 1 into the (a,a,a,a)-1 conformation required for binding and reduce its tendency to undergo self-association. We surveyed the binding properties of 1 toward 16 amines (K(a) 相似文献   

Hierarchical self-assembly of supramolecular spintronic modules into 1D- and 2D-architectures with emergence of magnetic properties

Hierarchical self-assembly of complex supramolecular architectures allows for the emergence of novel properties at each level of complexity. The reaction of the ligand components A and B with Fe(II) cations generates the [2x2] grid-type functional building modules 1 and 2, presenting spin-transition properties and preorganizing an array of coordination sites that sets the stage for a second assembly step. Indeed, binding of La(III) ions to 1 and of Ag(I) ions to 2 leads to a 1D columnar superstructure 3 and to a wall-like 2D layer 4, respectively, with concomitant modulation of the magnetic properties of 1 and 2. Thus, to each of the two levels of structural complexity generated by the two sequential self-assembly steps corresponds the emergence of novel functional features.     

Cooperative self-assembly of a macrocyclic Schiff base complex

A metal template approach affords in high yield a tetra-Zn(salphen) macrocycle (3) which shows strong and cooperative self-assembly mediated by the formation of Zn(salphen) dimer units held together via μ(2)-phenoxo interactions. A cooperative binding mode for the tetranuclear Zn(4) macrocycle 3 is supported by comparison of UV-vis and fluorescence titration data recorded for 3 when compared with respective mononuclear and dinuclear Zn(salphen) model compounds. UV-vis dilution experiments carried out for Zn(4) macrocycle 3 and its Pd(4) analogue 4, as well as comparative TEM studies involving the same tetranuclear macrocycles further support the strong assembly behavior of 3. This self-assembly seems to be primarily dictated by its ability to form multiple, self-assembled dimeric [Zn(salphen)](2) units.     

Interface engineering of synthetic pores: towards hypersensitive biosensors

Hydrophilic anchoring is introduced as a promising strategy to constructively control the various interactions of synthetic pore sensors with the surrounding biphasic environment. Artificial rigid-rod beta barrels are selected as classical synthetic multifunctional pores and random-coil tetralysines are attached as hydrophilic anchors. The synthesis of this advanced pore is accomplished in 32 steps from commercially available starting materials. With regard to pore activity as such, the key impact of hydrophilic anchoring is a change from a Hill coefficient n<1 to n=4. This change confirms successful suppression of the competing self-assembly with precipitation from the aqueous phase as the origin of the accomplished increase in pore activity. The hydrophilic anchors do not interfere with the blockage of the synthetic pore sensors by anionic analytes. In the case of stoichiometric binding of blockers (K(D)=EC(50) of the pore; EC(50)=concentration needed to observe 50 % pore activity), however, the increase in pore activity achieved by hydrophilic anchoring results in improved pore blockage under high dilution conditions. Controls confirm that this increase does not occur with analytes that do not exhibit stoichiometric binding (K(D)>EC(50)). These results not only reveal stoichiometric binding as the expected origin of the sensitivity limit of synthetic pore sensors, they also provide promising solutions for this problem. The combination of hydrophilic anchoring with targeted pore formation emerges as a particularly promising strategy to further reduce effective pore concentrations. The scope and limitations of this approach are exemplified with pertinent analyte pairs that are essential for the sensing of sucrose, lactose, acetate, and glutamate with synthetic pores in samples from the supermarket.     

The self-assembly of porphine molecules on NaCl pre-covered Cu(110) surface

The self-assembly of porphine molecules on NaCl pre-covered Cu(110) surface has been investigated at a single molecular level by scanning tunneling microscopy. The pre-grown NaCl stripe pattern has been partly interrupted due to the adsorption of porphine molecules at RT. Annealing the sample at 333 K and 423 K gradually promotes the formation of self-assembly network composed of porphine molecules and Cu atoms. Annealing at 473 K helps to convert this self-assembly structure into organometallic nanoribbon through C–Cu–C connecting.     

Aromatic oligomers that form hetero duplexes in aqueous solution

The electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) and electron-rich 1,5-dialkoxynaphthalene (Dan) have been shown to complex strongly with each other in water due to the hydrophobic effect as modulated through the electrostatic complementarity of the stacked dimer. Previously, oligomers of alternating Ndi and Dan units, termed aedamers, were the first foldamers to employ intramolecular aromatic stacking to effect the formation of secondary structure of nonnatural chains in aqueous solution. Described here is the use of this aromatic-aromatic (or pi-pi) interaction, this time in an intermolecular format, to demonstrate the self-assembly of stable hetero duplexes from a set of molecular strands (1a-4a) and (1b-4b) incorporating Ndi and Dan units, respectively. A 1-to-1 binding stoichiometry was determined from NMR and isothermal titration calorimetry (ITC) investigations, and these experiments indicated that association is enthalpically favored with the tetra-Ndi (4a) and tetra-Dan (4b) strands forming hetero duplexes (4a:4b) with a stability constant of 350 000 M-1 at T = 318 K. Polyacrylamide gel electrophoresis (PAGE) also illustrated the strong interaction between 4a and 4b and support a 1-to-1 binding mode even when one component is in slight excess. Overall, this system is the first to utilize complementary aromatic units to drive discrete self-assembly in aqueous solution. This new approach for designing assemblies is encouraging for future development of duplex systems with highly programmable modes of binding in solution or on surfaces.     

Novel 3D coordination palladium-network complex: a recyclable catalyst for Suzuki-Miyaura reaction

A novel solid-phase 3D metal-organic coordination network catalyst was prepared via self-assembly from PdCl2(CH3CN)2 and a trisphosphine hub with three flexible alkyl-chain linkers. This insoluble network complex efficiently catalyzed the Suzuki-Miyaura reaction under atmospheric conditions in water. This catalyst was reused without loss of catalytic activity.     

Deriving the colloidal synthesis of crystalline nanosheets to create self-assembly monolayers of nanoclusters

Two-dimensional (2D) nanomaterials with the thickness at atomic level are promising candidates for a wide range of applications, and now reach the point to create diversified 2D architectures. The colloidal synthesis route is powerful to produce crystalline nanosheets, nanoribbons and nanoplatelets, and the self-assembly strategy is robust to integrate the functionalities of different nano-objects. In this review, we bridge the colloidal synthesis of nanosheets and the 2D self-assembly of nanoclusters (NCs) with the aim to further optimize the physical and chemical properties of 2D nanomaterials. Ultrasmall NCs, the intermediate for synthesizing nanosheets, are highlighted to show the similarity of 2D crystallization and 2D self-assembly. The modification of conventional 2D colloidal synthesis route greatly permits the controlled self-assembly of NCs into free-standing monolayers in colloidal solutions.     

DNA binding by a new metallointercalator that contains a proflavine group bearing a hanging chelating unit

The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D-DNA and [ZnD]-DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+...O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.     

From arm-shaped layers to a new type of polythreaded array: a two fold interpenetrated three-dimensional network with a rutile topology

The self-assembly based on 2D motifs with side arms leads to the formation of a new type of polythreaded network which exhibits a 2-fold interpenetrated 3D array if H-bonds are taken into account.     

Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015

The growing number of protein–ligand complex structures, particularly the structures of proteins co-bound with different ligands, in the Protein Data Bank helps us tackle two major challenges in molecular docking studies: the protein flexibility and the scoring function. Here, we introduced a systematic strategy by using the information embedded in the known protein–ligand complex structures to improve both binding mode and binding affinity predictions. Specifically, a ligand similarity calculation method was employed to search a receptor structure with a bound ligand sharing high similarity with the query ligand for the docking use. The strategy was applied to the two datasets (HSP90 and MAP4K4) in recent D3R Grand Challenge 2015. In addition, for the HSP90 dataset, a system-specific scoring function (ITScore2_hsp90) was generated by recalibrating our statistical potential-based scoring function (ITScore2) using the known protein–ligand complex structures and the statistical mechanics-based iterative method. For the HSP90 dataset, better performances were achieved for both binding mode and binding affinity predictions comparing with the original ITScore2 and with ensemble docking. For the MAP4K4 dataset, although there were only eight known protein–ligand complex structures, our docking strategy achieved a comparable performance with ensemble docking. Our method for receptor conformational selection and iterative method for the development of system-specific statistical potential-based scoring functions can be easily applied to other protein targets that have a number of protein–ligand complex structures available to improve predictions on binding.     

Cooperative self-assembly of dendrimers via pseudorotaxane formation from a homotritopic guest molecule and complementary monotopic host dendrons

Interaction of the homotritopic guest 1,3,5-tris[p-(benzylammoniomethyl)phenyl]benzene tris(hexafluorophosphate) (1a) with dibenzo-24-crown-8 (DB24C8) leads to the sequential self-assembly of [2]-, [3]-, and [4]-pseudorotaxanes 7a, 8a, and 9a, respectively. The self-assembly processes were studied using NMR spectroscopy. In CD(3)CN and CD(3)COCD(3) the individual association constants K(1), K(2), and K(3) for 1:1, 1:2, and 1:3 complexes were determined by several methods. Via Scatchard plots, the three NH(2)(+) sites of 1a were shown to behave independently in binding DB24C8. K values (4.4 x 10(2), 1.4 x 10(2), and 41 M(-)(1), respectively, in CD(3)CN) directly determined from signals for the individual complexes (7a, 8a, and 9a) were somewhat higher than those estimated from the Scatchard plot because of concentration dependence, but the ratios of association constants followed the expected statistical order (K(1):K(2):K(3) = 3:1:(1)/(3)). These are believed to be the first evaluations of association constants leading to a [4]-pseudorotaxane. In the less polar CDCl(3), association constants could not be determined because approximately 90% of the dissolved tritopic guest, which by itself is insoluble, was present as the fully loaded [4]pseudorotaxane 9a! Self-assembly of homotritopic guest 1a with benzyl ether dendrons of the first, second, and third generations functionalized at the "focal point" with DB24C8 moieties (3-5) produces pseudorotaxane dendrimers. The self-assembly processes were studied using (1)H NMR spectroscopy. In CD(3)COCD(3) for all three generations the individual association constants K(1), K(2), and K(3) for [2]-, [3]-, and [4]-pseudorotaxane complexes 7c-e, 8c-e, and 9c-e indicated that the self-assembly was cooperative; that is, the ratios of the individual association constants exceeded the expected statistical ratios. Scatchard plots confirmed this behavior. Self-assembly processes in the less polar CDCl(3) were kinetically slow, requiring ca. 1, 2, and 3 days, respectively, for the first, second, and third generation systems to reach equilibrium with 1a; the slow rate is attributed to the insolubility of the homotritopic guest 1a in this medium and the steric demands of the resulting dendrimers. However, only dendrimers of 1:3 stoichiometry, that is, the nanoscopic [4]pseudorotaxanes 9, were formed! Moreover, it is noteworthy that the extent of dissolution of 1a (reflective of the overall association constant which is too high to measure) increases with generation number, presumably because of the more effective screening of the ionic guest by the larger dendrons and perhaps favorable pi-pi and CH-pi interactions. Such cooperative effects suggest a number of applications that can take advantage of the pH-switchable nature of these self-assembly processes.     

A coordinatively saturated sulfate encapsulated in a metal-organic framework functionalized with urea hydrogen-bonding groups

A functional coordination polymer decorated with urea hydrogen-bonding donor groups has been designed for optimal binding of sulfate; self-assembly of a tripodal tris-urea linker with Ag2SO4 resulted in the formation of a 1D metal-organic framework that encapsulates SO4(2-) anions via twelve complementary hydrogen bonds, which represents the highest coordination number observed for sulfate in a natural or synthetic host.     

Spontaneous Chirality Induction in the Assembly of a Single Layer 2D Network with Switchable Pores

Although two-dimensional (2D) chiral sheet structures are attractive because of their unique chemical and physical properties, single layer 2D chiral network structures with switchable pore interior remain elusive. Here we report spontaneous chirality induction in a single layer 2D network structure formed from the self-assembly of tetrapod azobenzene molecules. The chirality induction arises from multiple sublayers slipped in a preferred direction in which the sublayer consists of unidentical molecular arrangements in the in-plane a and b directions, breaking both the plane of symmetry and inversion symmetry. The protruded azobenzene units in the pore interior can be selectively isomerized upon UV irradiation, resulting in a reversible deformation of the chiral pores while maintaining the 2D frameworks. The chiral network can thus selectively entrap one enantiomer from a racemic solution with near perfect enantioselectivity, and then release it upon UV irradiation.