Paul van der Schoot

Probing the solvent-assisted nucleation pathway in chemical self-assembly

Hierarchical self-assembly offers a powerful strategy for producing molecular nanostructures. Although widely used, the mechanistic details of self-assembly processes are poorly understood. We spectroscopically monitored a nucleation process in the self-assembly of p-conjugated molecules into helical supramolecular fibrillar structures. The data support a nucleation-growth pathway that gives rise to a remarkably high degree of cooperativity. Furthermore, we characterize a helical transition in the nucleating species before growth. The self-assembly process depends strongly on solvent structure, suggesting that an organized shell of solvent molecules plays an explicit role in rigidifying the aggregates and guiding them toward further assembly into bundles and/or gels.

Polymer Solar Cells : Solubility Controls Fiber Network Formation

The photoactive layer of polymer solar cells is commonly processed from a four-component solution, containing a semiconducting polymer and a fullerene derivative dissolved in a solvent-cosolvent mixture. The nanoscale dimensions of the polymer-fullerene morphology that is formed upon drying determines the solar cell performance, but the fundamental processes that govern the size of the phase-separated polymer and fullerene domains are poorly understood. Here, we investigate morphology formation of an alternating copolymer of diketopyrrolopyrrole and a thiophene-phenyl-thiophene oligomer (PDPPTPT) with relatively long 2-decyltetradecyl (DT) side chains blended with [6,6]-phenyl-C71-butyric acid methyl ester. During solvent evaporation the polymer crystallizes into a fibrous network. The typical width of these fibers is analyzed by quantification of transmission electron microscopic images, and is mainly determined by the solubility of the polymer in the cosolvent and the molecular weight of the polymer. A higher molecular weight corresponds to a lower solubility and film processing results in a smaller fiber width. Surprisingly, the fiber width is not related to the drying rate or the amount of cosolvent. We have made solar cells with fiber widths ranging from 28 to 68 nm and found an inverse relation between fiber width and photocurrent. Finally, by mixing two cosolvents, we develop a ternary solvent system to tune the fiber width. We propose a model based on nucleation-and-growth which can explain these measurements. Our results show that the width of the semicrystalline polymer fibers is not the result of a frozen dynamical state, but determined by the nucleation induced by the polymer solubility.

Design and self-assembly of simple coat proteins for artificial viruses

Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing artificial life. Moreover, they are used in biomedical and biotechnological applications, such as targeted delivery of nucleic acids for gene therapy and as scaffolds in material science. In a natural setting, survival of viruses requires that a significant fraction of the replicated genomes be completely protected by coat proteins. Complete protection of the genome is ensured by a highly cooperative supramolecular process between the coat proteins and the nucleic acids, which is based on reversible, weak and allosteric interactions only. However, incorporating this type of supramolecular cooperativity into artificial viruses remains challenging. Here, we report a rational design for a self-assembling minimal viral coat protein based on simple polypeptide domains. Our coat protein features precise control over the cooperativity of its self-assembly with single DNA molecules to finally form rod-shaped virus-like particles. We confirm the validity of our design principles by showing that the kinetics of self-assembly of our virus-like particles follows a previous model developed for tobacco mosaic virus. We show that our virus-like particles protect DNA against enzymatic degradation and transfect cells with considerable efficiency, making them promising delivery vehicles.

Supramolecular balance: using cooperativity to amplify weak interactions

Gathering precise knowledge on weak supramolecular interactions is difficult yet is of utmost importance for numerous scientific fields, including catalysis, crystal engineering, ligand binding, and protein folding. We report on a combined theoretical and experimental approach showing that it is possible to vastly improve the sensitivity of current methods to probe weak supramolecular interactions in solution. The concept consists of using a supramolecular platform involving a highly cooperative configurational transition, the perturbation of which (by the modification of the molecular building blocks) can be monitored in a temperature scanning experiment. We tested this concept with a particular bisurea platform, and our first results show that it is possible to detect the presence of interaction differences as low as 60 J/mol, which may be due to steric repulsion between vinyl and alkyl groups or may be the result of solvation effects.

Probing the cooperative nature of the conductive components in polystyrene/poly(3,4-ethylenedioxythiophene):Poly(styrene sulfonate)-single- walled carbon nanotube composites

The percolation threshold of single-walled carbon nanotubes (SWCNTs) introduced into polystyrene (PS) via a latex-based route has been reduced by using conductive surfactants. The use of the conductive polymeric latex, poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS), in conjunction with SWCNTs leads to conductive composites with loadings of both constituents below their own individual percolation thresholds. The high concentration of PEDOT:PSS in the final composites raises the concern that the composite conductivity is a result of the presence of the PEDOT:PSS alone. To elucidate the cooperative nature of the two conductive components, the contribution of the SWCNTs to the overall composite conductivity is investigated by replacing the original high-quality SWCNTs with SWCNTs of a lower quality. Percolation thresholds recorded for systems utilizing the lower quality tubes stabilized with nonconductive surfactants were over 2 wt % SWCNTs (4 times that of previously reported systems). The introduction of PEDOT:PSS was, once again, found to lower the percolation threshold (to 0.3 wt %) and to increase the ultimate conductivity up to the level of a pure PEDOT:PSS/PS blend. In the PS/PEDOT:PSS-SWCNT systems, the role of the SWCNT network is proposed to be limited to the formation of a template or scaffold on which a (more or less) continuous PEDOT:PSS layer deposits. The ultimate conductivity is therefore determined by the PEDOT:PSS alone.

Dynamical and structural insights into the smectic phase of rod-like particles

Self-diffusion in a model system of rod-like particles is studied in the smectic (or lamellar) phase. The experimental system is formed by a colloidal suspension of filamentous fd virus particles, which allows the direct visualization at the scale of the single particle of mass transport between the smectic layers. Self-diffusion takes place preferentially in the direction normal to the smectic layers and occurs in steps of one rod length, reminiscent of a hopping-type of transport. The probability density function is obtained experimentally at different times and is found to be in qualitative agreement with theoretical predictions based on a dynamical density functional theory.

Nematic droplets in aqueous dispersions of carbon nanotubes

Aqueous dispersions of exfoliated, bile-salt stabilized single-wall carbon nanotubes exhibit a first order transition to a nematic liquid-crystalline phase. The nematic phase presents itself in the form of micron-sized nematic droplets also known as tactoids, freely floating in the isotropic host dispersion. The nematic droplets are spindle shaped and have an aspect ratio of about four, irrespective of their size. We attribute this to a director field that is uniform rather than bipolar, which is confirmed by polarization microscopy. It follows that the ratio of the anchoring strength and the surface tension must be about four, which is quite larger than predicted theoretically but in line with earlier observations of bipolar tactoids. From the scatter in the data we deduce that the surface tension of the coexisting isotropic and nematic phases must be extremely low, that is, of the order of nN/m.

Quasiuniversal Connectedness Percolation of Polydisperse Rod Systems

The connectedness percolation threshold (η(c)) and critical coordination number (Z(c)) of systems of penetrable spherocylinders characterized by a length polydispersity are studied by way of Monte Carlo simulations for several aspect ratio distributions. We find that (i) η(c) is a nearly universal function of the weight-averaged aspect ratio, with an approximate inverse dependence that extends to aspect ratios that are well below the slender rod limit and (ii) that percolation of impenetrable spherocylinders displays a similar quasiuniversal behavior. For systems with a sufficiently high degree of polydispersity, we find that Z(c) can become smaller than unity, in analogy with observations reported for generalized and complex networks.

Multishell structures of virus coat proteins

Under conditions of low ionic strength and a pH ranging between about 3.7 and 5.0, solutions of purified coat proteins of cowpea chlorotic mottle virus (CCMV) form spherical multishell structures in the absence of viral RNA. The outer surfaces of the shells in these structures are negatively charged, whereas the inner surfaces are positively charged due to a disordered cationic N-terminal domain of the capsid protein, the arginine-rich RNA-binding motif that protrudes into the interior. We show that the main forces stabilizing these multishells are counterion release combined with a lower charge density in the RNA-binding motif region of the outer shells due to their larger radii of curvature, arguing that these compensate for the outer shells not being able to adopt the smaller, optimal, radius of curvature of the inner shell. This explains why the structures are only stable at low ionic strengths at pHs for which the outer surface is negatively charged and why the larger outer shells are not observed separately in solution. We show how to calculate the free energy of shells of nonoptimal radius of curvature from the elastic properties of the native shell. The spacing between shells is determined mainly by the entropic elasticity of the RNA-binding motifs. Although we focus on CCMV multishells, we also predict the solution conditions under which multishells formed by CCMV coat protein mutants with a lower RNA-binding motif charge are stable, and we examine other viruses as well. We conclude that at a given surface charge density, the boundaries separating regions of stable multishells with different numbers of shells shift to lower ionic strengths upon either increasing the length of the RNA-binding motif, increasing the stiffness of the shells, or decreasing the charge per RNA-binding motif.

RNA topology remolds electrostatic stabilization of viruses

Simple RNA viruses efficiently encapsulate their genome into a nano-sized protein shell: the capsid. Spontaneous coassembly of the genome and the capsid proteins is driven predominantly by electrostatic interactions between the negatively charged RNA and the positively charged inner capsid wall. Using field theoretic formulation we show that the inherently branched RNA secondary structure allows viruses to maximize the amount of encapsulated genome and make assembly more efficient, allowing viral RNAs to out-compete cellular RNAs during replication in infected host cells.