Silk-inspired ‘molecular chimeras’: Atomistic simulation of nanoarchitectures based on thiophene–peptide copolymers

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Abstract

We present the results of an extensive molecular dynamics simulation aimed at investigating the structural organization of bioinspired copolymers consisting of thiophene and silk-forming peptide blocks. These ‘molecular chimeras’ are studied, apparently for the first time, both in adsorbed state (on the surface of graphite) and in dilute solution. It is shown that the attachment of the terminal peptide blocks to the oligothiophene fragments can lead to the formation of various stable supramolecular structures, including bilayers and fibrils, which can be promising for nanoelectronic applications.

Graphical abstract

Snapshot from MD simulation of triblock oligopeptide–oligothophene–oligopeptide ‘molecular chimeras’ adsorbed on a graphite surface.

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Introduction

During the past decade, there has been an increasing research effort in ‘organic electronics’ to improve the conducting, semiconducting, and light-emitting properties of innovative organic materials and hybrid organic–inorganic composites through novel synthesis and self-assembly techniques. These materials are considered as a promising alternative to the traditional microelectronic devices based on inorganic silicon and gallium arsenide semiconductors. The use of organic materials may enable lower cost manufacturing of electronic devices and larger area of applications. The ease of synthesis and purification is another factor that must be considered in regard to the utility of organic semiconductors. In particular, soluble materials may be purified by the standard methods, including recrystallization or chromatography. These materials can be processed at low temperatures using techniques familiar to the semiconducting and printing industries, such as solution casting, vacuum evaporation, and stamping.

A variety of conjugated polymers and oligomers have been considered as active electronic and optoelectronic organic materials. The majority of gathered research data indicates that the most promising conjugated compounds for nanoelectronic applications are those based on thiophene derivatives [1], [2]. Their electronic and optical properties originate from the π-electron system delocalized widely along a one-dimensional polymer chain.

Typically organic light-emitting diodes for display applications, organic thin-film transistors for use in plastic ‘smart chips’ and photovoltaic cells contain multiple layers. One of the possible approaches in creating functional thin-film systems is the formation of the self-organized layers by adsorption from a solution onto a solid substrate.

Of particular interest here are biologically inspired molecular hybrids (‘molecular chimeras’) consisting of synthetic and biopolymer blocks [3]. These block copolymers may inherit advantageous properties of both components, namely the conductivity and photonic properties of the synthetic block and the solubility, mutual recognition ability, high mechanical performance, or biodegradability from the biological block. It is not surprising that these hybrid compounds have become a subject of great interest over the recent years [4], [5], [6]. Perhaps the most promising molecular combinations are amphiphilic oligothiophene–oligopeptide hybrids (O2H). Owing to their unique chemical and physical properties and shape, they can possibly be used as innovative advanced materials or as precursors of novel materials. From feasibility considerations, it is favorable to use just poly- or oligopeptide blocks, for the reason that so much is already known from their natural folding patterns and motifs, and synthetic peptide chemistry is well developed and partly automatized.

Recently, Klok et al. have described the first example of an O2H conjugate composed of a head-to-tail coupled quater(3-hexylthiophene) and a short silk-inspired polypeptide sequence [7], [8]. STM investigations revealed the formation of long linear strands on graphite while FTIR experiments indicated the tendency of the peptide block to form β-sheets via multiple hydrogen bonds. However, the exact architecture of the superstructures is not yet known and the detailed scheme of the hydrogen bonds cannot yet be drawn. Therefore, more experimental and theoretical studies are necessary to deduce a structural model describing the arrangement of these oligothiophene-based hybrids.

It is natural to expect that the self-assembling behavior of oligothiophene–oligopeptide block copolymers has to be determined by the delicate (competitive or synergetic) combination of intra- and intermolecular interactions that include the possibility to organize π-conjugated supramolecular assemblies from rod-like oligothiophene blocks, on one hand, and the propensity to form a reversible hydrogen bond network of secondary structures in the flexible-chain polypeptide blocks, on the other hand. Due to its weakness, hydrogen bonding allows additional freedom to control the strength of bonding, e.g., by temperature or solvent. In this respect, the processes of structure formation characteristic of these hybrid copolymers may be very different from those observed for usual synthetic block copolymers. Polypeptide self-organization occurring at surfaces and interfaces can also be different from that observed in solution. Indeed, the formation of reversible hydrogen bonding arrays and the corresponding secondary structures in this case is strongly influenced by adsorption. Therefore, tailoring polypeptide–polypeptide and polypeptide–surface interactions is of great practical importance. This field is also intriguing from a purely academic perspective since it contains several nontrivial problems and poorly understood phenomena. One such problem is connected with the irreversibility of protein adsorption via structural alteration and denaturation [9]. Up to now, research was mainly focused on questions concerning the adsorption transition and weak adsorption models [10]. However, technologically more interesting than weak adsorption is the case of strong and irreversible adsorption, i.e., when the monomer sticking energy exceeds the thermal energy. Physical processes in this case can be effectively irreversible, chains can be trapped in long lasting conformations, and partitioning of polymers on solid substrates is governed by ‘recognition’ of surface chemical patterns by adsorbing polymers. There are a lot of publications devoted to the self-organization of polypeptides in a dilute solution, but much less is known about their behavior in strongly adsorbed state. Questions need to be answered are: (i) how hydrogen bonds on a substrate are redistributed compared to that formed in a solution; (ii) how strong adsorption influences the conformational behavior of polypeptide chains and their structure formation; (iii) how adsorbed chains interact and influence each other.

Another closely related problem needed to be solved is to design optimal polypeptide sequences providing desirable materials properties. In principle, the protein folding process provides several examples of ordered polypeptide motifs that may be of interest for the engineering of thiophene-based supramolecular architectures and enhancing the control over fiber-like structure formation. In particular, these structural motifs include β-pleated sheets, which are typical for, e.g., amyloid fibrils, natural silk (spider silk and silkworm silk) [11], elastin [12], etc. The methods of sequence design as applied to the protein folding problem are well developed. However, for adsorbed heteropolypeptide chains, research in this field is sparse and needs to be developed.

The general objective of this study is to simulate the adsorption layers formed by silk-inspired oligothiophene–oligopeptide ‘molecular chimeras’ and the structures formed by these copolymers in solution. To our knowledge there has been no simulation study in this direction until now. The rest of the Letter is organized as follows: the models and computational methods are explained in Section 2; the results are given in Section 3; and the conclusions in Section 4.

Section snippets

Models and methods

The systems studied were thiophene–peptide (TP) diblock copolymers and peptide–thiophene–peptide (PTP) triblock copolymers, see Scheme 1.

The PT copolymer was built from α-tetrathiophene and short peptide block GLY–ALA–GLY–ALA–GLY, which is typical for natural silk [13], [14]. The same peptide block was considered in the experimental work [8]. This block was attached in α-position to one of the terminal thiophene rings. The PTP triblock copolymer was composed of the central α-tetrathiophene

Adsorption layers

During the course of simulations, we found that the copolymers in the bilayers on the graphite surface began rearranging within approximately 3 ns. The rearrangement process continued for another couple of nanoseconds and finally resulted in stable ribbon-like films. Fig. 1 shows typical snapshots from the simulation. It was found that these dense bilayer films composed both from diblocks and triblocks were commensurate with the graphite substrate. Commensuration is driven primarily through

Conclusion

Using atomistic molecular dynamics simulations, we have investigated the supramolecular organization of bioinspired oligothiophene–oligopeptide copolymers in the adsorbed state on the graphite surface and in dilute solution. We have found that these ‘molecular chimeras’ are capable of forming rather stable nanostructures whose behaviors are strongly determined by the propensity of the terminally attached peptide chains to organize β-sheet domains, which are characteristic of natural silk. The

Acknowledgements

The financial support from RFBR and the Deutsche Forschungsgemainschaft (SFB 569, Project A11 ‘Self-organizing bioinspired oligothiophene–oligopeptide hybrids: A joint experimental and theoretical approach’) is highly appreciated.

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