Discrete Assemblies Research Articles

Programmed Self-Assembly of Hierarchical Nanostructures through Protein-Nanoparticle Coengineering.

Hierarchical organization of macromolecules through self-assembly is a prominent feature in biological systems. Synthetic fabrication of such structures provides materials with emergent functions. Here, we report the fabrication of self-assembled superstructures through coengineering of recombinant proteins and nanoparticles. These structures feature a highly sophisticated level of multilayered hierarchical organization of the components: individual proteins and nanoparticles coassemble to form discrete assemblies that collapse to form granules, which then further self-organize to generate superstructures with sizes of hundreds of nanometers. The components within these superstructures are dynamic and spatially reorganize in response to environmental influences. The precise control over the molecular organization of building blocks imparted by this protein-nanoparticle coengineering strategy provides a method for creating hierarchical hybrid materials.

Shape-Programmed Hierarchical Self-Assembly of Designed DNA Building Blocks into Massive Three-Dimensional Finite-Size Objects

Large and discrete biological assemblies such as the flagellar motor or viral capsids form by hierarchical self-assembly of many different protein subunits where some of these subunits often occur in multiple copies. For assemblies such as capsids the shape of the subunits and their interaction patterns effectively encode the geometry of the final assembly. Creating artificial objects with similar complexity through accurate design of the shape of molecular building blocks represents an important design challenge that tests our understanding of molecular structure, molecular flexibility, and molecular interactions.

DNA-Paint Imaging of DNA-Origami Rings Mimicking Biologically Relevant Structures

Single-molecule localization microscopy methods such as DNA-PAINT (point accumulation for imaging in nanoscale topography), utilize successive localizations of single molecules over time to reveal of biological structures with photon-limited resolution1,2. However, visualization of sub-diffracted discrete bimolecular assemblies still remains a challenge. “DNA origami” has emerged as powerful nano-templating technique capable of generating stable self-assembled scaffold for positioning of molecular species of interest with nanometer precision3,4. Recent studies of DNA-PAINT have focused on imaging different molecular species, such as fluorophores and proteins, positioned on synthetic grid-like DNA nanostructures1,4. These grids are well suited for determining the resolution limit of sparsely labelled points (e.g. one fluorophore per 5x5 nm2). However, biological structures often have a much higher local density and complex structure, making imaging more challenging. In this study, as a proof-of-concept, we explored imaging of circular “ring-like” DNA-origami nanostructures of dimension mimicking small bio-molecular structures (25-50 nm inner diameter), like membrane receptors, ion channels etc. Using a TIRF-based imaging technique, we have optimized the fluorophores density and its positioning on DNA-origami rings to reconstruct “doughnut” shaped images and have been able to resolve inner diameter of ∼25 to 50 nm. We have carried out these analyses on glass surfaces and also on supported bilayers. Our study utilizing DNA rings provides challenging targets for DNA-PAINT technology and underscores the use of size-templated nanostructures, as approximates for bio-molecular complexes, to optimize imaging and analysis protocols independent of biological sample preparation.1. Dai et al. (2016) Nat. Nanotechnol. 11:798-807.2. Baddeley, D. (2015) Nat. Methods 12:1019-1020.3. Yang et al. (2016) Nat. Chem. 8:476-483.4. Schlichthaerle et al. (2016) Curr. Opin. Biotechnol. 39: 41-47.

Building new discrete supramolecular assemblies through the interaction of iso-tellurazole N-oxides with Lewis acids and bases.

The supramolecular macrocycles spontaneously assembled by iso-tellurazole N-oxides are stable towards Lewis bases as strong as N-heterocyclic carbenes (NHC) but readily react with Lewis acids such as BR3 (R= Ph, F). The electron acceptor ability of the tellurium atom is greatly enhanced in the resulting O-bonded adducts, which consequently enables binding to a variety of Lewis bases that includes acetonitrile, 4-dimethylaminopyridine, 4,4'-bipyridine, triphenyl phosphine, a N-heterocyclic carbene and a second molecule of iso-tellurazole N-oxide.

Stepwise construction of discrete parallelogram- and prism-shaped organometallic architectures based on half-sandwich rhodium fragments.

Herein we describe how to take advantage of a multifunctional ligand to conveniently control the shapes and sizes of different types of discrete organometallic assemblies. Using a versatile ligand 2-(pyridin-2-yl)-1H-imidazole-4,5-dicarboxylate (HL2-), which features three kinds of chelating sites, together with half-sandwich rhodium fragments, a series of discrete organometallic complexes with tetranuclear parallelogram and hexanuclear trigonal prism shapes were achieved. The isomerization of the hexanuclear assemblies was confirmed by single-crystal X-ray diffraction analysis. The results also reiterate that pyridyl-substituted imidazole-4,5-dicarboxylate ligands can be used as multifunctional organic scaffolds in the construction of elegant architectures.

Sugar-coated proteins: the importance of degree of polymerisation of oligo-galacturonic acid on protein binding and aggregation.

We have simplified the structural heterogeneity of protein-polysaccharide binding by investigating protein binding to oligosaccharides. The interactions between bovine beta-lactoglobulin A (βLgA) and oligo-galacturonic acids (OGAs) with various numbers of sugar residues have been investigated with a range of biophysical techniques. We show that the βLgA-OGA interaction is critically dependent on the length of the oligosaccharide. Isothermal titration calorimetry results suggest that a minimum length of 7 or 8 sugar residues is required in order to exhibit appreciable exothermic interactions with βLgA - shorter oligosaccharides show no enthalpic interactions at any concentration ratio. When titrating βLgA into OGAs with more than 7-8 sugar residues the sample solution also became turbid with increasing amounts of βLgA, indicating the formation of macroscopic assemblies. Circular dichroism, thioflavin T fluorescence and small angle X-ray/neutron scattering experiments revealed two structural regimes during the titration. When OGAs were in excess, βLgA formed discrete assemblies upon OGA binding, and no subsequent aggregation was observed. However, when βLgA was present in excess, multi-scale structures were formed and this eventually led to the separation of the solution into two liquid-phases.

Evolution of mechanics in α-helical peptide conjugated linear- and star-block PEG.

We have designed a peptide conjugated poly-ethylene glycol (PEG) bioconjugate system that allows us to examine the intra- and inter-molecular dynamics of gelation. We measure the kinetics of gelation for end-functionalized linear- and star-architectures, and we correlate the gelation behavior with the molecular structure and self-association. The 23-amino acid peptide sequence is known to form a coiled-coil structure as a function of the solution's electrolyte concentration, and the two topologies of the PEG are peptide end-functionalized to examine formation of supramolecular assemblies. Subsequently, microrheology is used to evaluate the dynamics of self-assembly and the gelation time-scales. This study shows that the dynamics of peptide folding and assembly for linear-PEG conjugated systems yield a percolated network, but the star-PEG conjugated systems yield discrete assemblies and remain viscous. The results suggest that the degree of intra- and inter-molecular folding defines the critical gel behavior of the supramolecular system.

A monodisperse transmembrane α-helical peptide barrel.

The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing.

Two-dimensional artificial light-harvesting antennae with predesigned high-order structure and robust photosensitising activity.

Highly ordered discrete assemblies of chlorophylls that are found in natural light-harvesting antennae are key to photosynthesis, which converts light energy to chemical energy and is the principal producer of organic matter on Earth. Porphyrins and phthalocyanines, which are analogues of chlorophylls, exhibit a strong absorbance of visible and near-infrared light, respectively. A highly ordered porphyrin-co-phthalocyanine antennae would harvest photons over the entire solar spectrum for chemical transformation. However, such a robust antennae has not yet been synthesised. Herein, we report a strategy that merges covalent bonds and noncovalent forces to produce highly ordered two-dimensional porphyrin-co-phthalocyanine antennae. This methodology enables control over the stoichiometry and order of the porphyrin and phthalocyanine units; more importantly, this approach is compatible with various metalloporphyrin and metallophthalocyanine derivatives and thus may lead to the generation of a broad structural diversity of two-dimensional artificial antennae. These ordered porphyrin-co-phthalocyanine two-dimensional antennae exhibit unique optical properties and catalytic functions that are not available with single-component or non-structured materials. These 2D artificial antennae exhibit exceptional light-harvesting capacity over the entire solar spectrum as a result of a synergistic light-absorption effect. In addition, they exhibit outstanding photosensitising activities in using both visible and near-infrared photons for producing singlet oxygen.

Generation of a Chiral Giant Micelle.

Over the past few years, chiral supramolecular assemblies have been successfully used for recognition, sensing and enantioselective transformations. Several approaches are available to control chirality of discrete assemblies (e.g., cages and capsules), but few are efficient in assuring chirality for micellar aggregates. Optically active amino acid-derived surfactants are commonly used to generate chiral spherical micelles. To circumvent this limitation, we benefited from the uniaxial growth of spherical micelles into long cylindrical micelles usually called wormlike or giant micelles, upon the addition of cosolutes. This paper describes the unprecedented formation of chiral giant micelles in aqueous solutions of cetyltrimethylammonium bromide (CTAB) upon increasing addition of enantiopure sodium salt of 1,1'-bi-2-naphthol (Na-binaphtholate) as a cosolute. Depending on the concentrations of CTAB and Na-binaphtholate, chiral gel-like systems are obtained. The transition from spherical to giant micellar structures was probed using rheology, cryo-transmission electron microscopy, polarimetry, and electronic circular dichroism (CD). CD can be effectively used to monitor the incorporation of Na-binaphtholate into the micelle palisade as well as to determine its transition to giant micellar structures. Our approach expands the scope for chirality induction in micellar aggregates bringing the possibility to generate "smart" chiral systems and an alternative asymmetric chiral environment to perform enantioselective transformations.

ChemInform Abstract: β‐Peptide Bundles: Design. Build. Analyze. Biosynthesize

AbstractReview: 109 refs.

Coordination polymers from mild condition reactions of copper(II) carboxylates with pyrazole (Hpz). Influence of carboxylate basicity on the self-assembly of the [Cu3(μ3-OH)(μ-pz)3]2+ secondary building unit

The reaction of some saturated and unsaturated aliphatic copper(II) monocarboxylates, Cu(RCOO)2 [R=C6H5CH2 (phenylacetate, Phac), CH2CHCH2 (vinylacetate, Vnac), C6H5CHCH (3-trans-phenylacrylate, Phacr), C6H5(CH2)2 (3-phenylpropionate, Phpr), c-C6H11 (ciclo–hexylcarboxylate, c-Hexc), CH3(CH2)10 (laurate, Lau), CH3(CH2)12 (myristate, Myr), (CH3)3C (pivalate, Piv)] with pyrazole (Hpz) and water in protic solvents, yielded trinuclear triangular derivatives based on the [Cu3(μ3-OH)(μ-pz)3] fragment whose double positive charge is balanced by two coordinated carboxylate ions, actually [Cu3(μ3-OH)(μ-pz)3(Phac)2], 1, [Cu3(μ3-OH)(μ-pz)3(Vnac)2(Hpz)], 2, [Cu3(μ3-OH)(μ-pz)3(Phacr)2], 3, [{Cu3(μ3-OH)(μ-pz)3(Phpr)2(Hpz)}{Cu3(μ3-OH)(μ-pz)3(Phpr)2(Hpz)(H2O)}]·xH2O·yMeOH, 4, [Cu3(μ3-OH)(μ-pz)3(c-Hexc)2], 5, [Cu3(μ3-OH)(μ-pz)3(Lau)2], 6, [Cu3(μ3-OH)(μ-pz)3(Myr)2], 7, [Cu3(μ3-OH)(μ-pz)3(Piv)2(HPz)(HPiv)2], 8. This behavior is consistent with some previously observed features and evidences that the basicity of carboxylate ions is the key for the deprotonation of Hpz and water, leading to the formation of pz− and OH− ions, which are determinant for the self-assembly of the trinuclear triangular species. Single crystal XRD determinations evidenced that in compounds 1, 2 and 5 the trinuclear moieties further self-assemble generating monodimensional coordination polymers or, in one case (compound 4), a dodecanuclear discrete assembly.

Modular Homogeneous Chromophore-Catalyst Assemblies.

Photosynthetic reaction center (RC) proteins convert incident solar energy to chemical energy through a network of molecular cofactors which have been evolutionarily tuned to couple efficient light-harvesting, directional electron transfer, and long-lived charge separation with secondary reaction sequences. These molecular cofactors are embedded within a complex protein environment which precisely positions each cofactor in optimal geometries along efficient electron transfer pathways with localized protein environments facilitating sequential and accumulative charge transfer. By contrast, it is difficult to approach a similar level of structural complexity in synthetic architectures for solar energy conversion. However, by using appropriate self-assembly strategies, we anticipate that molecular modules, which are independently synthesized and optimized for either light-harvesting or redox catalysis, can be organized into spatial arrangements that functionally mimic natural photosynthesis. In this Account, we describe a modular approach to new structural designs for artificial photosynthesis which is largely inspired by photosynthetic RC proteins. We focus on recent work from our lab which uses molecular modules for light-harvesting or proton reduction catalysis in different coordination geometries and different platforms, spanning from discrete supramolecular assemblies to molecule-nanoparticle hybrids to protein-based biohybrids. Molecular modules are particularly amenable to high-resolution characterization of the ground and excited state of each module using a variety of physical techniques; such spectroscopic interrogation helps our understanding of primary artificial photosynthetic mechanisms. In particular, we discuss the use of transient optical spectroscopy, EPR, and X-ray scattering techniques to elucidate dynamic structural behavior and light-induced kinetics and the impact on photocatalytic mechanism. Two different coordination geometries of supramolecular photocatalyst based on the [Ru(bpy)3](2+) (bpy = 2,2'-bipyridine) light-harvesting module with cobaloxime-based catalyst module are compared, with progress in stabilizing photoinduced charge separation identified. These same modules embedded in the small electron transfer protein ferredoxin exhibit much longer charge-separation, enabled by stepwise electron transfer through the native [2Fe-2S] cofactor. We anticipate that the use of interchangeable, molecular modules which can interact in different coordination geometries or within entirely different structural platforms will provide important fundamental insights into the effect of environment on parameters such as electron transfer and charge separation, and ultimately drive more efficient designs for artificial photosynthesis.

Meso-hydro-mechanically informed effective stresses and effective pressures for saturated and unsaturated porous media

Abstract Based on the meso-structured Voronoi cell model and the meso-macro homogenization procedure between the discrete particle assembly and the porous continuum for wet granular materials, meso-hydro-mechanically informed effective pressure and effective stress measures for saturated and unsaturated porous media are defined. The meso-hydro-mechanically informed generalized effective stress for saturated porous continua taking into account the volumetric deformation of solid grains due to pore liquid pressure is derived. The Biot coefficient associated to the meso-hydro- mechanically informed generalized effective stress for saturated porous media is formulated. The differences of the definitions for proposed generalized effective stress and Biot coefficient compared with those defined in the generalized Biot theory of saturated porous continua and in averaging theories are discussed. The wet meso-structured Voronoi cell model, consisting of three immiscible and interrelated (i.e. solid grains, interstitial liquid and gas) phases, at low bulk saturation (below about 30%) is proposed. A meso-structural pattern with the binary bond mode of pendular liquid bridges is assumed in particular to derive the meso-hydro- mechanically informed macroscopic anisotropic effective pressure and effective stress tensors for unsaturated porous media. As the isotropic case of the wet meso-structured Voronoi cell model is considered, the meso-hydro-mechanically informed effective pressure tensor degrades to the scalar variable in the same form as in the theory of macroscopic unsaturated porous continua. The proposed meso-hydro-mechanically informed Bishop's parameter is derived and obtained as a function of saturation, porosity, and meso-structural parameters, without need to introduce any macroscopic phenomenological assumptions for the description of hydro-mechanical constitutive behavior.

Construction of Smart Supramolecular Polymeric Hydrogels Cross-linked by Discrete Organoplatinum(II) Metallacycles via Post-Assembly Polymerization.

Postassembly modification strategy has been successfully employed in the construction of discrete metallosupramolecular assemblies. However, the most known reports have been limited to the simple structural conversion through the easy covalent reactions, thus hindering the development of organometallic functional materials. In this study, we first combined coordination-driven self-assembly and postassembly reversible addition-fragmentation chain-transfer (RAFT) polymerization to produce a new family of star supramolecular polymers containing well-defined metallacycles as cores, which featured typical lower critical solution temperature (LCST) behavior in water because of the existence of poly(N-isopropylacrylamide) (PNIPAAM) moieties. Moreover, the obtained star polymers could further form supramolecular hydrogels cross-linked by discrete hexagonal metallacycles at room temperature without heating-cooling process. Interestingly, the resultant polymeric hydrogels exhibited stimuli-responsive behavior toward temperature and bromide anion as well as self-healing property. We demonstrated that the dynamic nature of Pt-N bonds in the hexagonal metallacycles played an important role in determining the stimuli-responsive and self-healing property of the final soft matters. Thus, merging coordination-driven self-assembly and postassembly polymerization provided a new avenue to the preparation of functional materials containing well-defined, discrete metal-organic assemblies as main scaffolds.

A study of the influence of REV variability in double‐scale FEM ×DEM analysis

SummaryIn this work, the consequences of using several different discrete element granular assemblies for the representation of the microscale structure, in the framework of multiscale modeling, have been investigated. The adopted modeling approach couples, through computational homogenization, a macroscale continuum with microscale discrete simulations. Several granular assemblies were used depending on the location in the macroscale finite element mesh. The different assemblies were prepared independently as being representative of the same material, but their geometrical differences imply slight differences in their response to mechanical loading. The role played by the micro‐assemblies, with weaker macroscopic mechanical properties, on the initiation of strain localization in biaxial compression tests is demonstrated and illustrated by numerical modeling of different macroscale configurations. Copyright © 2016 John Wiley & Sons, Ltd.

Mixed FEM–Crushable DEM Nested Scheme in Second-Order Computational Homogenization for Granular Materials

AbstractA mixed FEM–crushable discrete-element method (DEM) nested scheme in the frame of second-order computational homogenization for granular materials was proposed. The particle breakage followed by the discontinuity and dissipative relative movements between each of two immediate neighboring particles were modeled at the mesoscale to perform both the downscaling and upscaling between the mixed FEM at the macroscopic continuum scale and the crushable DEM at the mesoscopic discrete particle assembly scale. To develop the crushable DEM for modeling the mesostructural evolution within representative volume elements (RVEs) assigned to integrating points of the macroscopic Cosserat continuum in the homogenization, two grain breakage models consisting of crushing criteria and the fracture mode for an individual crushable particle were developed. Not only the contact forces, but also contact moments exerted on each individual grain via the contacting points on the grain surface, were taken into account to se...

On the Application of Agility Principles in Ramp-up Management: Approaching the Challenges in the High-end Powder Metallurgy Industry

In recent years, the field of ramp-up management has received wide attention in both science and industrial practice. However, current research mainly focuses on discrete manufacturing and assembly industries, whereas companies in process-oriented industries are still lacking a practicable approach to manage their highly interdependent ramp-up operations.This paper presents findings of a detailed requirements analysis at a world leading metal producing and processing company. It outlines the specific characteristics of such hybrid industries and emphasizes the need for agility considerations in ramp-up management in order to outperform competitors in increasingly volatile and uncertain business environments. Main criteria for agile ramp-ups are derived from theoretical as well as industry-specific considerations and first steps towards a practice-oriented management approach are taken. This paper shows that early and reliable information on product and process maturity is a major imperative for process-oriented industries and reveals how standardized ramp-up readiness levels shall contribute substantially to the success of future ramp-up projects.

β-Peptide bundles: Design. Build. Analyze. Biosynthesize.

Peptides containing β-amino acids are unique non-natural polymers known to assemble into protein-like tertiary and quaternary structures. When composed solely of β-amino acids, the structures formed, defined assemblies of 14-helices called β-peptide bundles, fold cooperatively in water solvent into unique and discrete quaternary assemblies that are highly thermostable, bind complex substrates and metal ion cofactors, and, in certain cases, catalyze chemical reactions. In this Perspective, we recount the design and elaboration of β-peptide bundles and provide an outlook on recent, unexpected discoveries that could influence research on β-peptides and β-peptide bundles (and β-amino acid-containing proteins) for decades to come.

Arrays of infinite and discrete non-covalent interactions in the supramolecular adduct based upon trimeric perfluoro-ortho-phenylenemercury and 9-fluorenone

As a direct consequence of the accessibility to electrophilic Hg(II) atoms on its molecular surface coupled with its heightened electron-withdrawing properties, trimeric perfluoro-ortho-phenylenemercury, (o-C6F4Hg)3, has exhibited a propensity to form supramolecular adducts with a wide array of substrates. Numerous examples of carbonyl-containing substrates as well as a number of polycyclic aromatics have been reported in the literature. However, the incorporation of these two organic functionalities within the same substrate has yet to be investigated in terms of complexation to (o-C6F4Hg)3. In this contribution, we report the synthesis, structural, and spectroscopic properties of a novel supramolecular adduct involving (o-C6F4Hg)3 and 9-fluorenone [(o-C6F4Hg)3(9-fluorenone)2] 1 wherein the various non-covalent interactions observed are discussed. In particular, we address not only the interactions found between (o-C6F4Hg)3 and 9-fluorenone, but also the interactions observed between 9-fluorenone molecules that produce either infinite or discrete assemblies perpetuated by C–H⋯O hydrogen bonds. Lastly, we will also discuss observed phenyl–phenyl and phenyl–perfluorophenyl interactions which form an extended molecular complex.