Self-assembling nanofibers from thiophene-peptide diblock oligomers: a combined experimental and computer simulations study

Molecular Modeling and Simulations of Peptide–Polymer Conjugates

Peptide–polymer conjugates are a class of soft materials composed of covalently linked blocks of protein/polypeptides and synthetic/natural polymers. These materials are practically useful in biological applications, such as drug delivery, DNA/gene delivery, and antimicrobial coatings, as well as nonbiological applications, such as electronics, separations, optics, and sensing. Given their broad applicability, there is motivation to understand the molecular and macroscale structure, dynamics, and thermodynamic behavior exhibited by such materials. We focus on the past and ongoing molecular simulation studies aimed at obtaining such fundamental understanding and predicting molecular design rules for the target function. We describe briefly the experimental work in this field that validates or motivates these computational studies. We also describe the various models (e.g., atomistic, coarse-grained, or hybrid) and simulation methods (e.g., stochastic versus deterministic, enhanced sampling) that have been used and the types of questions that have been answered using these computational approaches.

Supramolecular polymerization: challenges and advantages of various methods in assessing the aggregation mechanism

Oligothiophenes with branched alkyl end groups show distinct aggregation in organic solvents. The process of supramolecular polymerization is assessed by three different methods (UV-vis absorption and fluorescence emission spectroscopy and dynamic light scattering) to exclude artifacts. An apparent dependence of the degree of aggregation on the concentration of the oligomers is observed. Above the upper limit of concentration (a lower micromolar range for the present class of compounds), experimental data delivered conflicting results and the concentration should not therefore be exceeded. Scanning force microscopy and molecular dynamics simulations confirm the formation of one-dimensional aggregates with presumably helical arrangement of the achiral monomers.

Tuning Optoelectronic and Chiroptic Properties of Peptide-Based Materials by Controlling the Pathway Complexity

Supramolecular chemistry has evolved from the traditional focus on thermodynamic on-pathways to the complex study of kinetic off-pathways, which are strongly dependent on environmental conditions. Moreover, the control over pathway complexity allows nanostructures to be obtained that are inaccessible through spontaneous thermodynamic processes. Herein, we present a family of peptide-based π-extended tetrathiafulvalene (exTTF) molecules that show two self-assembly pathways leading to two distinct J-aggregates, namely metastable (M) and thermodynamic (T), with different spectroscopic, chiroptical, and electrochemical behavior. Moreover, cryo-transmission electron microscopy (cryo-TEM) reveals a different morphology for both aggregates and a direct observation of the morphological transformations from tapes to twisted ribbons.

Co-assembly of donor and acceptor towards organogels tuned by charge transfer interaction strength

Co-assembly of n-type semiconductors NDI and PDI with p-type pyrene derivatives resulted in the formation of stable organogels, which was induced by the strong charge transfer (CT) interactions between acceptors and donors in chloroform. The dimension size of the aromatic core from the acceptors was found to have a significant impact on the organogels. The width of the fibers from CT gels with NDI is about twice that from gels with PDI. It was found that the acceptor NDI preferred an alternate stacking with donors, intercalated with each other via CT interactions. In contrast, the acceptor PDI preferred to stack among themselves within the assemblies and this arose from the stronger π-π interactions because they had larger aromatic cores than the acceptor NDI. The dimension size of the aromatic core has been proved to have a significant impact on the organogels. The substituent impact of the donors was also studied.

Effect of Structural Modifications on the Self-Assembly of Oligoprolines Conjugated with Sterically Demanding Chromophores

Conjugates between oligoprolines and sterically demanding perylene monoimides (PMIs) form hierarchical supramolecular self-assemblies. The influence of the length and stereochemistry at the attachment site between the peptide backbone and the chromophore on the self-assembly properties of the conjugates was explored. Comparison between oligoprolines bearing 4R- or 4S-configured azidoprolines (Azp) for the conjugation with the PMIs revealed that diastereoisomers with 4R configuration guide the self-assembly consistently better than conjugates with 4S configuration. Elongating the peptide chain beyond nine proline residues or introducing structural "errors", by altering the absolute configuration of one stereogenic center at the outside of the functionalizable oligoproline helix, lowered the efficacy of self-assembly significantly, both in solution phase and in the solid state. The results showed how subtle structural modifications allow for tuning the self-assembly of chromophores and provided further design principles for the development of peptide-chromophore conjugates into nanostructured materials.

Electroluminescence from Spontaneously Generated Single-Vesicle Aggregates Using Solution-Processed Small Organic Molecules

Self-assembled aggregates offer great potential for tuning the morphology of organic semiconductors, thereby controlling their size and shape. This is particularly interesting for applications in electroluminescent (EL) devices, but there has been, to date, no reports of a functional EL device in which the size and color of the emissive domains could be controlled using self-assembly. We now report a series of molecules that spontaneously self-organize into small EL domains of sub-micrometer dimensions. By tailoring the emissive chromophores in solution, spherical aggregates that have an average size of 300 nm in diameter and emit any one color, including CIE D65 white, are spontaneously formed in solution. We show that the individual aggregates can be used in EL devices built either using small patterned electrodes or using a sandwich architecture to produce devices emitting in the blue, green, red, and white. Furthermore, sequential deposition of the three primary colors yields an RGB device in which single aggregates of each color are present in close proximity.

Self-Assembly of a Functional Oligo(Aniline)-Based Amphiphile into Helical Conductive Nanowires

A tetra(aniline)-based cationic amphiphile, TANI-NHC(O)C5H10N(CH3)3(+)Br(-) (TANI-PTAB) was synthesized, and its emeraldine base (EB) state was found to self-assemble into nanowires in aqueous solution. The observed self-assembly is described by an isodesmic model, as shown by temperature-dependent UV-vis investigations. Linear dichroism (LD) studies, combined with computational modeling using time-dependent density functional theory (TD-DFT), suggests that TANI-PTAB molecules are ordered in an antiparallel arrangement within nanowires, with the long axis of TANI-PTAB arranged perpendicular to the nanowire long axis. Addition of either S- or R- camphorsulfonic acid (CSA) to TANI-PTAB converted TANI to the emeraldine salt (ES), which retained the ability to form nanowires. Acid doping of TANI-PTAB had a profound effect on the nanowire morphology, as the CSA counterions' chirality translated into helical twisting of the nanowires, as observed by circular dichroism (CD). Finally, the electrical conductivity of CSA-doped helical nanowire thin films processed from aqueous solution was 2.7 mS cm(-1). The conductivity, control over self-assembled 1D structure and water-solubility demonstrate these materials' promise as processable and addressable functional materials for molecular electronics, redox-controlled materials and sensing.

Synthesis, optical properties, and electronic structures of nucleobase-containing π-conjugated oligomers

The molecular recognition properties of the nucleobases instruct the formation of complex three-dimensional architectures in natural and synthetic systems; relatively unexplored is their use as building blocks for π-conjugated materials where they might mutually tune electronic and supramolecular structures. Toward this goal, an introductory set (1a-d and 2a-d) of six purine-terminated and two pyrimidine-terminated π-conjugated oligomers has been synthesized and used to develop experimental electronic and photophysical structure-property trends. Unlike 2,2':5',2″-terthiophene (TTT) derivatives 2a-d, intramolecular charge transfer dominates oligomers 1a-d bearing a 4,7-bisthienylbenzothiadiazole (TBT) spacer due to the strong electron-accepting ability of its benzothiadiazole (BTD) ring. The resulting donor-acceptor-donor systems feature lower HOMO-LUMO gaps than the terthiophene-linked nucleobases (ΔE(g) ∼ 1.8 eV vs 2.4 eV based on electrochemical measurements), and the lowest so far for π-conjugated molecules that include nucleobases within the π-framework. Experiments reveal a dependence of photophysical and electronic structure on the nature of the nucleobase and are in good agreement with theoretical calculations performed at the B3LYP/6-31+G** level. Overall, the results show how nucleobase heterocycles can be installed within π-systems to tune optical and electronic properties. Future work will evaluate the consequences of these information-rich components on supramolecular π-conjugated structure.

Peptide nanofibrils boost retroviral gene transfer and provide a rapid means for concentrating viruses

Inefficient gene transfer and low virion concentrations are common limitations of retroviral transduction. We and others have previously shown that peptides derived from human semen form amyloid fibrils that boost retroviral gene delivery by promoting virion attachment to the target cells. However, application of these natural fibril-forming peptides is limited by moderate efficiencies, the high costs of peptide synthesis, and variability in fibril size and formation kinetics. Here, we report the development of nanofibrils that self-assemble in aqueous solution from a 12-residue peptide, termed enhancing factor C (EF-C). These artificial nanofibrils enhance retroviral gene transfer substantially more efficiently than semen-derived fibrils or other transduction enhancers. Moreover, EF-C nanofibrils allow the concentration of retroviral vectors by conventional low-speed centrifugation, and are safe and effective, as assessed in an ex vivo gene transfer study. Our results show that EF-C fibrils comprise a highly versatile, convenient and broadly applicable nanomaterial that holds the potential to significantly facilitate retroviral gene transfer in basic research and clinical applications.

A model for the controlled assembly of semiconductor peptides

The self-assembly of small molecules provides a potentially powerful method to create functional nanomaterials for many applications ranging from optoelectronics to oncology. However, the design of well-defined nanostructures via molecular assembly is a highly empirical process, which severely hampers efforts to create functional nanostructures using this method. In this review, we describe a simple strategy to control the assembly of functionalized peptides by balancing attractive hydrophobic effects that drive assembly with opposing electrostatic repulsions. Extended π-π contacts are created in the nanostructures when assembly is driven by π-stacking interactions among chromophores that are appended to the peptide. The formation of insoluble β-sheet aggregates are mitigated by incorporating charged side-chains capable of attenuating the assembly process. Although the application of this approach to the assembly of organic semiconductors is described, we expect this strategy to be effective for many other functional organic materials.

Peptide-Based Supramolecular Semiconductor Nanomaterials via Pd-Catalyzed Solid-Phase "Dimerizations"

We report a streamlined method for the synthesis of peptides embedded with complex and easily variable π-conjugated oligomeric subunits from commercially available precursors. These modified peptides self-assemble under aqueous conditions to form one-dimensional nanomaterials containing networks of π-stacked conduits, despite the inclusion of π-conjugated oligomers with quadrupoles extended over larger areas. The procedure has circumvented solubility and other synthetic issues to allow for the facile formation of a diverse library of bioelectronic nanomaterials, including a complex sexithiophene-containing peptide whose nanostructures display gate-induced conductivity within field effect transistors.

2D self-assembly of fused oligothiophenes: molecular control of morphology

We report the synthesis and properties of two π-functional heteroaromatic tetracarboxylic acids (isomeric tetrathienoanthracene derivatives 2-TTATA and 3-TTATA) and their self-assembly on highly oriented pyrolytic graphite. Using scanning tunneling microscopy at the liquid-solid interface we show how slight geometric differences between the two isomers (position of sulfur in the molecule) lead to dramatic changes in monolayer structure. While 3-TTATA self-assembles exclusively in a highly ordered porous network via dimeric R(2)(2)(8) hydrogen-bonding connection (synthon), 2-TTATA is polymorphic, forming a less ordered porous network via R(2)(2)(8) synthons as well as a close-packed network via rare tetrameric R(4)(4)(16) synthons. Density functional theory calculations show that the self-assembly direction is governed by the angle between the carboxylic groups and secondary interactions with sulfur atoms.

Self-assembly of conjugated oligomers and polymers at the interface: structure and properties

In this review, we give a brief account on the recent scanning tunneling microscopy investigation of interfacial structures and properties of π-conjugated semiconducting oligomers and polymers, either at the solid-air (including solid-vacuum) or at the solid-liquid interface. The structural aspects of the self-assembly of both oligomers and polymers are highlighted. Conjugated oligomers can form well ordered supramolecular assemblies either at the air-solid or liquid-solid interface, thanks to the relatively high mobility and structural uniformity in comparison with polymers. The backbone structure, substitution of side chains and functional groups can affect the assembling behavior significantly, which offers the opportunity to tune the supramolecular structure of these conjugated oligomers at the interface. For conjugated polymers, the large molecular weight limits the mobility on the surface and the distribution in size also prevents the formation of long range ordered supramolecular assembly. The submolecular resolution obtained on the assembling monolayers enables a detailed investigation of the chain folding at the interface, both the structural details and the effect on electronic properties. Besides the ability in studying the assembling structures at the interfaces, STM also provides a reasonable way to evaluate the distribution of the molecular weight of conjugated polymers by statistic of the contour length of the adsorbed polymer chains. Both conjugated oligomers and polymers can form composite assemblies with other materials. The ordered assembly of oligomers can act as a template to controllably disperse other molecules such as coronene or fullerene. These investigations open a new avenue to fine tune the assembling structure at the interface and in turn the properties of the composite materials. To summarize scanning tunneling microscopy has demonstrated its surprising ability in the investigation of the assembling structures and properties of conjugated oligomers and polymers. The information obtained could benefit the understanding of the elements affecting the film morphology and helps the optimization of device performance.

Altering peptide fibrillization by polymer conjugation

A strategy is presented that exploits the ability of synthetic polymers of different nature to disturb the strong self-assembly capabilities of amyloid based β-sheet forming peptides. Following a convergent approach, the peptides of interest were synthesized via solid-phase peptide synthesis (SPPS) and the polymers via reversible addition-fragmentation chain transfer (RAFT) polymerization, followed by a copper(I) catalyzed azide-alkyne cycloaddition (CuAAC) to generate the desired peptide-polymer conjugates. This study focuses on a modified version of the core sequence of the β-amyloid peptide (Aβ), Aβ(16-20) (KLVFF). The influence of attaching short poly(N-isopropylacrylamide) and poly(hydroxyethylacrylate) to the peptide sequences on the self-assembly properties of the hybrid materials were studied via infrared spectroscopy, TEM, circular dichroism and SAXS. The findings indicate that attaching these polymers disturbs the strong self-assembly properties of the biomolecules to a certain degree and permits to influence the aggregation of the peptides based on their β-sheets forming abilities. This study presents an innovative route toward targeted and controlled assembly of amyloid-like fibers to drive the formation of polymeric nanomaterials.

Self-organizing bioinspired oligothiophene-oligopeptide hybrids

In this minireview, we survey recent advances in the synthesis, characterization, and modeling of new oligothiophene-oligopeptide hybrids capable of forming nanostructured fibrillar aggregates in solution and on solid substrates. Compounds of this class are promising for applications because their self-assembly and stimuli-responsive properties, provided by the peptide moieties combined with the semiconducting properties of the thiophene blocks, can result in novel opportunities for the design of advanced smart materials. These bio-inspired molecular hybrids are experimentally shown to form stable fibrils as visualized by AFM and TEM. While the experimental evidence alone is not sufficient to reveal the exact molecular organization of the fibrils, theoretical approaches based on quantum chemistry calculations and large-scale atomistic molecular dynamics simulations are attempted in an effort to reveal the structure of the fibrils at the nanoscale. Based on the combined theoretical and experimental analysis, the most likely models of fibril formation and aggregation are suggested.