Supramolecular self-assembly codes for functional structures

Small-molecule self-assembly has proven to be a rich field for the controlled synthesis of supramolecular objects with the size scale of polymers and interesting properties. Using several recent examples from our laboratory, we discuss the development of chemical structure codes for supramolecular self-assembly objects with defined shapes. The resulting materials formed by these objects are promising for electronic functions and biological functions for regenerative medicine.     

Protein self-assembly creates a nanoscale device for biomineralization

Mammalian enamel is the unique hierarchically organized bioceramic material that owes its existence to a transient precursor, the enamel organic extracellular matrix. The organic matrix is biosynthesized by epithelial derived cells called ameloblasts and the selection of genes expressed, the timing and amount of proteins expressed serve to impose constraints on the matrix. The protein matrix components undergo self-assembly to form a microenvironment that regulates the mineral phase, serving to control crystal habit and spacing between crystallites. We have focused on amelogenin, the most abundant protein of the enamel organic matrix. Amelogenin self-assembles into nanospheres that participate in control over enamel organization. Ameloblasts also interact with the matrix and these interactions are important to the organization of hydroxyapatite crystallites into woven bundles. Changes to conserved domains within amelogenin alter protein-to-protein interactions as well as cell to matrix interactions. Changes to enamel organization observed during evolution may be accounted for, in part, by changes to critical domains within enamel proteins that form the matrix.     

Transition state annealing for defect control during colloidal self-assembly

Colloidal self-assembly is an efficient method to obtain ordered 3D nanostructures. However, it suffers from the drawback that defects are difficult to eliminate in the self-assembled nanostructures. In this report, a method to reduce the defect density is proposed. It has been observed earlier that during self-assembly, the colloidal system goes through a transition state with a higher mobility than the final rigid nanostructure. This offers an opportunity to anneal out defects like vacancies and dislocations. Using in-situ reflectance spectra measurements of a self-assembling system, we demonstrate the feasibility of this transition state annealing method.     

One-step approach for the synthesis and self-assembly of silver nanoparticles

This study demonstrates a facile approach for one-step synthesis and self-assembly of silver nanoparticles at ambient conditions. It was found that pyrogallol acid (PYA) can play multiple roles in the proposed synthesis, including a reducing agent, a stabilizer, and a linking agent for assembly. Silver ions can be readily reduced by PYA at room temperature due to its powerful reducing capability. The capability in shape and size control can be evidenced by TEM images. A third function of PYA in this case is to link the generated silver particles into chains through the action of hydrogen bonding, which leads to a new plasmon resonance emerges in the longer wavelength region centered at approximately 650 nm. These results may be useful for shape-controlled synthesis and self-assembly of other metallic nanoparticles. The self-assembly structures would be imposed more functional applications in the areas of optics, plasmonics, biomedicine labeling and ionic sensing.     

Two computational primitives for algorithmic self-assembly: copying and counting

Copying and counting are useful primitive operations for computation and construction. We have made DNA crystals that copy and crystals that count as they grow. For counting, 16 oligonucleotides assemble into four DNA Wang tiles that subsequently crystallize on a polymeric nucleating scaffold strand, arranging themselves in a binary counting pattern that could serve as a template for a molecular electronic demultiplexing circuit. Although the yield of counting crystals is low, and per-tile error rates in such crystals is roughly 10%, this work demonstrates the potential of algorithmic self-assembly to create complex nanoscale patterns of technological interest. A subset of the tiles for counting form information-bearing DNA tubes that copy bit strings from layer to layer along their length.     

Improved peptidyl linkers for self-assembly of semiconductor quantum dot bioconjugates

We demonstrate improved peptide linkers which allow both conjugation to biomolecules such as DNA and self-assembly with luminescent semiconductor quantum dots. A hexahistidine peptidyl sequence was generated by standard solid phase peptide synthesis and modified with the succinimidyl ester of iodoacetamide to yield a thiol-reactive iodoacetyl polyhistidine linker. The reactive peptide was conjugated to dye-labeled thiolated DNA which was utilized as a model target biomolecule. Agarose gel electrophoresis and fluorescence resonance energy transfer analysis confirmed that the linker allowed the DNA to self-assemble with quantum dots via metal-affinity driven coordination. In contrast to previous peptidyl linkers that were based on disulfide exchange and were thus labile to reduction, the reactive haloacetyl chemistry demonstrated here results in a more stable thioether bond linking the DNA to the peptide which can withstand strongly reducing environments such as the intracellular cytoplasm. As thiol groups occur naturally in proteins, can be engineered into cloned proteins, inserted into nascent peptides or added to DNA during synthesis, the chemistry demonstrated here can provide a simple method for self-assembling a variety of stable quantum dot bioconjugates.      

Chemical self-assembly of graphene sheets

Chemically derived and noncovalently functionalized graphene sheets (GS) were found to self-assemble onto patterned gold structures via electrostatic interactions between the functional groups and the gold surfaces. This afforded regular arrays of single graphene sheets on large substrates, which were characterized by scanning electron microscopy (SEM), Auger microscopy imaging, and Raman spectroscopy. This represents the first time that self-assembly has been used to produce on-substrate and fully-suspended graphene electrical devices. Molecular coatings on the GS were removed by high current “electrical annealing”, which restored the high electrical conductance and Dirac point of the GS. Molecular sensors for highly sensitive gas detection using the self-assembled GS devices are demonstrated. Electronic Supplementary Material  Further characterization of GS and self-assembled structures by AFM, Raman, and Auger can be found in the ESM with nine figures and one table which are available in the online version of this article at http://dx.doi.org/ and accessible free of charge.     

Regulating self-assembly of spherical oligomers

In multistep reactions, stability of intermediates is critical to the rate of product formation and a significant factor in generating kinetic traps. The capsid protein of cowpea chlorotic mottle virus (CCMV) can be induced to assemble into spherical particles of 30, 60, and 90 dimers. Based on examining assembly kinetics and reaction end points, we find that formation of uniform, ordered structures is not always a result of reactions that reach equilibrium. Equilibration or, alternatively, kinetic trapping can be identified by a straightforward analysis. Altering the assembly path of "spherical" particles is a means of controlling the distribution of products, which has broad applicability to self-assembly reactions.     

Optimal shape design for minimum Lagrangian

One of the most efficient tools for solving optimal shape design problems offers the minimization of Lagrangian with respect to selected internal parameters. It starts with the formulation of the Lagrangian variational principle with an additional assumption that the volume of domain (in 2D the area) describing the structure in the undeformed state remains constant during the deformation process. It can be shown that the boundary density of the deformation energy at each boundary point in the optimal state is constant. A new position of the boundary is calculated from simple formula using the method of steepest descent. As the difference in energy density at boundary points may be very large, new positions of the boundary points are alternatively determined in a special way. Since the problem is strongly non-linear, iterative procedure has to be proposed in an efficient way. The proposed approach incorporating boundary element method appears to be very promising for solving shape optimization of structures.     

Stokes shape factor for lactose crystals

The alpha-lactose crystal has a tomahawk shape which needs to be accounted for when designing settling equipment. A shape factor can be used to achieve this. A variety of shape factors have been used for lactose crystals in the literature. This paper sets out to experimentally determine a shape factor for lactose. Large undamaged tomahawk shaped lactose crystals were grown in a lactose agar gel and then recovered for use in settling experiments. Typical industry produced crystals were also tested for comparison. Settling experiments enabled the calculation of a Stokes settling diameter, the diameter of a sphere with the same density and settling velocity as the tomahawk shaped lactose crystal. Using crystal mass to calculate equivalent particle volume and Stokes diameter, the Stokes shape factor for lactose gel-grown crystals was calculated to be 0.99. A Stokes height factor (B_St) was formulated which, when multiplied by the height of the lactose crystal, gives the Stokes settling diameter. The lactose B_St value was determined to be 0.595 ± 0.007 and 0.643 ± 0.008 for gel-grown and plant-grown lactose crystals, respectively.     

Optimum shape for single emission elements

Optimum laws of variation in cross-sectional areas cooled by emission from solid and hollow radiation elements of various shapes are found.     

DNA-enabled self-assembly of plasmonic nanoclusters

DNA nanotechnology provides a versatile foundation for the chemical assembly of nanostructures. Plasmonic nanoparticle assemblies are of particular interest because they can be tailored to exhibit a broad range of electromagnetic phenomena. In this Letter, we report the assembly of DNA-functionalized nanoparticles into heteropentamer clusters, which consist of a smaller gold sphere surrounded by a ring of four larger spheres. Magnetic and Fano-like resonances are observed in individual clusters. The DNA plays a dual role: it selectively assembles the clusters in solution and functions as an insulating spacer between the conductive nanoparticles. These particle assemblies can be generalized to a new class of DNA-enabled plasmonic heterostructures that comprise various active and passive materials and other forms of DNA scaffolding.     

A shape grammar for non-manifold modeling

Shape grammars offer a notationally rich representation for dealing with shapes defined over an algebra of points, lines, planes, and solids. Operations in the algebra are bound in subshape recognition and replacement, making them ideal candidates for design as formal solid modeling representations, and for manufacturing as shape-based feature recognizers. As well, given the topological hierarchy of the algebra of shapes, non-manifold modeling is clearly a fundamental part of shape grammars. Thus, one can work at the level of wireframe models, boundary models, and solid models. These characteristics make the shape grammars eminently suitable as a formal representation for both manifold and non-manifold representations of discrete shape.     

The dynamics of nacre self-assembly

We show how nacre and pearl construction in bivalve and gastropod molluscs can be understood in terms of successive processes of controlled self-assembly from the molecular- to the macro-scale. This dynamics involves the physics of the formation of both solid and liquid crystals and of membranes and fluids to produce a nanostructured hierarchically constructed biological composite of polysaccharides, proteins and mineral, whose mechanical properties far surpass those of its component parts.