Designed self-assembly of molecular necklaces using host-stabilized charge-transfer interactions

A novel approach to the noncovalent synthesis of molecular necklaces successfully led to the first quantitative self-assembly of a molecular necklace [6]MN, in which five small rings are threaded on a large ring, from 10 components. Our strategy involves the host-guest complex formation between the molecular host cucurbit[8]uril (CB[8]) and a guest molecule in which an electron donor and an electron acceptor unit are connected by a rigid linker with a proper angle, to form a cyclic oligomer through the host-stabilized intermolecular charge-transfer (CT) complex formation. In the structure of the molecular necklace [6]MN, five molecules of the guest form a cyclic framework by the intermolecular CT interactions, on which five CB[8] molecules are threaded with an arrangement reminiscent of a five-fold propeller. The molecular necklace measures approximately 3.7 nm in diameter and approximately 1.8 nm in thickness.     

Self organization of fluorescent molecular necklaces in aqueous solution

N-Fluoresceinyl-N-(mono-6-desoxy-6--cyclodextrinyl)-thiourea2 was synthesized from mono-6-amino-6-desoxy--CD1 and fluorescein isothiocyanate. The fluorescent CD derivative2 was threaded on a water soluble polymer, poly(N,N-dimethylammoniumhexamethylene-N,N-dimethyl-ammoniumdecamethylene dibromide)3. The existence of the molecular necklace was visualized by gel electrophoresis.     

Controlled self-assembly of triphenylene-based molecular nanostructures

Molecular nanostructures of the disc-shaped molecule hexapentyloxytriphenylene have been fabricated on length scales ranging from 30 nm to 1.5 mum following self-assembly arising from pi-pi interactions in organic solvents. The size and density of the molecular nanostructures deposited onto glass and indium tin oxide-coated glass substrates were characterized by atomic force microscopy. Dynamic light scattering and spectroscopic evidence of predeposition aggregation in solution are presented, suggesting that the nanostructures are organized in solution and then deposited onto the substrate. Correlations between the relative solvent polarity and the size of molecular nanostructures as well as between the solute concentration in dilute solutions and their density on the substrate are discussed.     

Hydrogen bonding control of molecular self-assembly

In this short review we describe approaches to the design and construction of synthetic molecules that mimic the process of self organization that is at the heart of biological complexity. Multi-subunit enzymes, viruses, and higher order DNA structures are formed by the non-covalent association of many smaller components. This self-assembly is controlled by the nature, number and orientation of interacting groups on the surface of the subunits. The central problem lies in overcoming the unfavorable entropy of multi-subunit association by significant enthalpic contribution from the binding of complementary regions on the subunits. We will place particular emphasis on the design of synthetic molecules that use hydrogen bonding interactions to control the formation of aggregates of well-defined structure.     

Indistinguishability of the models of molecular self-assembly

Numerous applications dealing with molecular aggregation at the interface of biology, physics and chemistry use either the dimer or the indefinite equilibrium constant models even though there is the well-known property of indistinguishability of the models with respect to fitting experimental data by various experimental techniques. The problem of indistinguishability is uncovered in the present work and the way in which the existing paradigm of how these models should be applied to analysis of molecular self-association is suggested.     

Construction of porphyrin-cyclodextrin self-assembly with molecular wedge

A new host porphyrin bearing four permethyl-beta-cyclodextrin moieties for multi-porphyrin assembly forms a unique 2 : 2 assembly with the tetra-anion of tetrakis(p-sulfonylphenyl)porphyrin (TPPS) in aqueous solution.     

Syntheses and molecular self-assembly of chiral phosphorami-dates

Two chiral phosphoramidates,(R)-(-)-1,1'-binaphthyl-2,2'-dihydroxy-N-[α-(S)-methylbenzyl] phosphoramidate and (-)-1,1'-biphenyl-2,2'-dihydroxy-N-[α-(S)-methylbenzyl]-phosphoramidate were synthesized.Their crystal structures were determined by X-ray single crystal diffraction analysis.The phosphoramidate molecules are self-associated by inter-molecular N-H...O = P hydrogen bonds and aromatic edge to face interactions.     

Metallobiological necklaces: mass spectrometric and molecular modeling study of metallation in concatenated domains of metallothionein

The ubiquitous protein metallothionein (MT) has proven to be a major player not only in the homeostasis of Cu(I) and Zn(II), but also binds all the Group 11 and 12 metals. Metallothioneins are characterised by the presence of numerous cys-x-cys and cys-cys motifs in the sequence and are found naturally with either one domain or two, linked, metal-binding domains. The use of chains of these metal-thiolate domains offers the possibility of creating chemically tuneable and, therefore, chemically dependent electrochemical or photochemical surface modifiers or as nanomachinery with nanomechanical properties. In this work, the metal-binding properties of the Cd(4)-containing domain of alpha-rhMT1a assembled into chains of two and three concatenated domains, that is, "necklaces", have been studied by spectrometric techniques, and the interactions within the structures modelled and interpreted by using molecular dynamics. These chains are metallated with 4, 8 or 12 Cd(II) ions to the 11, 22, and 33 cysteinyl sulfur atoms in the alpha-rhMT1a, alphaalpha-rhMT1a, and alphaalphaalpha-rhMT1a proteins, respectively. The effect of pH on the folding of each protein was studied by ESI-MS and optical spectroscopy. MM3/MD simulations were carried out over a period of up to 500 ps by using force-field parameters based on the reported structural data. These calculations provide novel information about the motion of the clustered metallated, partially demetallated, and metal-free peptide chains, with special interest in the region of the metal-binding site. The MD energy/time trajectory conformations show for the first time the flexibility of the metal-sulfur clusters and the bound amino acid chains. We report unexpected and very different sizes for the metallated and demetallated proteins from the combination of experimental data, with molecular dynamics simulations.     

Cyclization and catenation directed by molecular self-assembly

We report here that molecular self-assembly can effectively direct and enhance specific reaction pathways. Using perylene pi-pi stacking weak attractive forces, we succeeded in synthesizing perylene bisimide macrocyclic dimer and a concatenated dimer-dimer ring from dynamic self-assembly of monomeric bis-N,N'-(2-(2-(2-(2-thioacetylethoxy)ethoxy)ethoxy)ethyl)perylenetetracarboxylic diimide. The monocyclic ring closure and the dimer-dimer ring concatenation were accomplished through formation of disulfide bonds, which was readily triggered by air oxidization under basic deacetylation conditions. The perylene cyclic dimer and its concatenated tetramer were characterized using both structural methods (NMR, mass spectroscopy) and photophysical measurements (UV-vis spectroscopy). Kinetic analyses offer informative insights about reaction pathways and possible mechanisms, which lead to the formation of complex concatenated rings. Molecular dynamic behaviors of both the monocyclic dimer and the concatenated dimer-dimer ring were modeled with the NWChem molecular dynamics software module, which shows distinct stacking activities for the monocyclic dimer and the concatenated tetramer.     

Effect of head-group chemistry on surface-mediated molecular self-assembly

Surface molecular self-assembly is a fast advancing field with broad applications in sensing, patterning, device assembly, and biochemical applications. A vast number of practical systems utilize alkane thiols supported on gold surfaces. Whereas a strong Au-S bond facilitates robust self-assembly, the interaction is so strong that the surface is reconstructed, leaving etch pits that render the monolayers susceptible to degradation. By using different head group elements to adcust the molecule-surface interaction, a vast array of new systems with novel properties may be formed. In this paper we use a carefully chosen set of molecules to make a direct comparison of the self-assembly of thioether, selenoether, and phosphine species on Au(111). Using the herringbone reconstruction of gold as a sensitive readout of molecule-surface interaction strength, we correlate head-group chemistry with monolayer (ML) properties. It is demonstrated that the hard/soft rules of inorganic chemistry can be used to rationalize the observed trend of molecular interaction strengths with the soft gold surface, that is, P>Se>S. We find that the structure of the monolayers can be explained by the geometry of the molecules in terms of dipolar, quadrupolar, or van der Waals interactions between neighboring species driving the assembly of distinct ordered arrays. As this study directly compares one element with another in simple systems, it may serve as a guide for the design of self-assembled monolayers with novel structures and properties.     

Bioactive molecular sheets from self-assembly of polymerizable peptides

We have demonstrated that polymerizable peptides self-assemble into a unique sheet-like 2D structure in bulk solution that can be covalently fixed to produce 2D molecular objects which were shown to be efficient at delivering cargos into living cells and are nearly nontoxic in contrast to non-polymerized nanostructures.     

Nanorings from the self-assembly of amphiphilic molecular dumbbells

We have prepared amphiphilic dumbbell molecules consisting of hydrophobic alkyl chains and hydrophilic oligoether dendrons at each end of the rod segment. The molecular dumbbells, in aqueous solution, self-assemble into toroids as an intermediate nanostructure between spherical and long cylindrical micelles. The formation of toroidal structure is likely to originate from side by side connections of discrete bundles through the combination of strong hydrophobic interactions and anisotropic aggregation of rod segments.     

Water-soluble molecular capsules: self-assembly and binding properties

The self-assembly and characterization of water-soluble calix[4]arene-based molecular capsules (12) is reported. The assemblies are the result of ionic interactions between negatively charged calix[4]arenes 1 a and 1 b, functionalized at the upper rim with amino acid moieties, and a positively charged tetraamidiniumcalix[4]arene 2. The formation of the molecular capsules is studied by (1)H NMR spectroscopy, ESI mass spectrometry (ESI-MS), and isothermal titration calorimetry (ITC). A molecular docking protocol was used to identify potential guest molecules for the self-assembled capsule 1 a2. Experimental guest encapsulation studies indicate that capsule 1 a2 is an effective host for both charged (N-methylquinuclidinium cation) and neutral molecules (6-amino-2-methylquinoline) in water.     

Orthogonal self-assembly of low molecular weight hydrogelators and surfactants

The concurrent self-assembly of new 1,3,5-trisamide-cyclohexane-based low molecular weight hydrogelators and various surfactants in water leads to the formation of self-assembled fibrillar networks with encapsulated micelles. This prototype system presents an example of orthogonal self-assembly, that is, the independent formation of two different supramolecular structures, each with their own characteristics that coexist within a single system.     

Surface-enhanced Raman scattering on molecular self-assembly in nanoparticle-hydrogel composite

Surface-enhanced Raman scattering has been applied to study weak intermolecular interactions between small organic gelling molecules involved in the silver nanoparticle-hydrogel composite formation. Assembly and disassembly of the gelator molecules in close vicinity to embedded silver nanoparticles were followed by changes in Raman intensity of the amide II and carboxyl vibrational bands, whereas the strength of the bands related to benzene modes remained constant. This implied that the gelator molecules were strongly attached to the silver particles through the benzene units, while participating in gel structure organization by intermolecular hydrogen bonding between oxalyl amide and carboxyl groups.     

The molecular basis of self-assembly of dendron-rod-coils into one-dimensional nanostructures

We describe here a comprehensive study of solution and solid-state properties of self-assembling triblock molecules composed of a hydrophilic dendron covalently linked to an aromatic rigid rod segment, which is in turn connected to a hydrophobic flexible coil. These dendron-rod-coil (DRC) molecules form well-defined supramolecular structures that possess a ribbonlike morphology as revealed by transmission-electron and atomic-force microscopy. In a large variety of aprotic solvents, the DRC ribbons create stable networks that form gels at concentrations as low as 0.2% by weight DRC. The gels are thermally irreversible and do not melt at elevated temperatures, indicating high stability as a result of strong noncovalent interactions among DRC molecules. NMR experiments show that the strong interactions leading to aggregation involve mainly the dendron and rodlike blocks, whereas oligoisoprene coil segments remain solvated after gelation. Small-angle X-ray scattering (SAXS) profiles of different DRC molecules demonstrate an excellent correlation between the degree-of-order in the solid-state and the stability of gels. Studies on two series of analogous molecules suggest that self-assembly is very sensitive to subtle structural changes and requires the presence of at least four hydroxyl groups in the dendron, two biphenyl units in the rod, and a coil segment with a size comparable to that of the rodlike block. A detailed analysis of crystal structures of model compounds revealed the formation of stable one-dimensional structures that involve two types of noncovalent interactions, aromatic pi-pi stacking and hydrogen bonding. Most importantly, the crystal structure of the rod-dendron compound shows that hydrogen bonding not only drives the formation of head-to-head cyclic structures, but also generates multiple linkages between them along the stacking direction. The cyclic structures are tetrameric in nature and stack into ribbonlike objects. We believe that DRC molecules utilize the same arrangement of hydrogen bonds and stacking of aromatic blocks observed in the crystals, explaining the exceptional stability of the nanostructures in extremely dilute solutions as well the thermal stability of the gels they form. This study provides mechanistic insights on self-assembly of triblock molecules, and unveils general strategies to create well-defined one-dimensional supramolecular objects.     

Controlled molecular self-assembly behaviors between cucurbituril and bispyridinium derivatives

Two stable supramolecular loops (1 and 2) were successfully constructed by the molecular recognition of cucurbit[8]uril (CB[8]) and the homoditopic bispyridinium derivatives (3 and 4). Interestingly, the interconversion of molecular loops and [2]pseudorotaxanes could be reversibly switched under neutral and acidic condition, exhibiting the controlled electrochemical and spectroscopic behaviors.     

Giant molecular spoked wheels in giant voids: two-dimensional molecular self-assembly goes big

We present here the formation of giant pores in surface-confined molecular networks of a triangular-shaped dehydrobenzo-[12]annulene derivative: the diameter of the pores reaches over 7 nm and the giant pores are used as templates to accommodate a giant molecular spoked wheel, which allows us to observe rotational and adsorption-desorption dynamics of single guest molecules.     

On the role of water in molecular recognition and self-assembly

The conventional concept of hydrophobic interaction is generalized to include any kind of solvent-induced effects on the binding of two or more solutes in aqueous solutions. Specifically, we focus on the role of hydrogen-bonding between the solutes and solvent molecules. A qualitative examination of the solute-solvent hydrogen-bonding effect on molecular recognition, self-assembly, and stabilization of biopolymers shows that these effects might be quite large and possible more important than direct interactions between solute particles.