Modulating charge transfer through cyclic D,L-alpha-peptide self-assembly

Molecular Self-Assembly and Supramolecular Chemistry of Cyclic Peptides

This Review focuses on the establishment and development of self-assemblies governed by the supramolecular interactions between cyclic peptides. The Review first describes the type of cyclic peptides able to assemble into tubular structures to form supramolecular cyclic peptide nanotubes. A range of cyclic peptides have been identified to have such properties, including α-peptides, β-peptides, α,γ-peptides, and peptides based on δ- and ε-amino acids. The Review covers the design and functionalization of these cyclic peptides and expands to a recent advance in the design and application of these materials through their conjugation to polymer chains to generate cyclic peptide-polymer conjugates nanostructures. The Review, then, concentrates on the challenges in characterizing these systems and presents an overview of the various analytical and characterization techniques used to date. This overview concludes with a critical survey of the various applications of the nanomaterials obtained from supramolecular cyclic peptide nanotubes, with a focus on biological and medical applications, ranging from ion channels and membrane insertion to antibacterial materials, anticancer drug delivery, gene delivery, and antiviral applications.

Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography, NMR Spectroscopy and Molecular Dynamics

Our understanding of the factors affecting the stability of cyclic d/l peptide (CP) nanotubes remains underdeveloped. In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on CP nanotube stability through X-ray crystallography, NMR spectroscopy and molecular dynamics (MD) simulations. We characterise the distinct CP-CP alignments that can form and identify stable and unstable dimers by MD simulation. We measure H-bond half-lives of synthesised CPs by ¹ H-D exchange experiments and find good correlation with predicted CP-CP stabilities. We find that hydrophobic amino acids improve CP dimer stability but experimentally reduce solubility. Charged amino acids either increase or decrease CP dimer stability depending on the relative orientation and composition of charged groups. X-ray crystal structures are solved for two CPs, revealing non-tubular folded conformations. Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.

Naphthalene diimides: perspectives and promise

In this review, we describe the developments in the field of naphthalene diimides (NDIs) from 2016 to the presentday. NDIs are shown to be an increasingly interesting class of molecules due to their electronic properties, large electron deficient aromatic cores and tendency to self-assemble into functional structures. Almost all NDIs possess high electron affinity, good charge carrier mobility, and excellent thermal and oxidative stability, making them promising candidates for applications in organic electronics, photovoltaic devices, and flexible displays. NDIs have also been extensively studied due to their potential real-world uses across a wide variety of applications including supramolecular chemistry, sensing, host-guest complexes for molecular switching devices, such as catenanes and rotaxanes, ion-channels, catalysis, and medicine and as non-fullerene accepters in solar cells. In recent years, NDI research with respect to supramolecular assemblies and mechanoluminescent properties has also gained considerable traction. Thus, this review will assist a wide range of readers and researchers including chemists, physicists, biologists, medicinal chemists and materials scientists in understanding the scope for development and applicability of NDI dyes in their respective fields through a discussion of the main properties of NDI derivatives and of the status of emerging applications.

Electroactive peptide-based supramolecular polymers

The electroactivity as a supramolecular feature of intelligently designed self-assembled systems stimulates a wide interest in development of new stimuli-responsive biomaterials. A diverse set of nanostructures are fabricated through programmed self-assembly of molecules for functional materials. Electroactive groups are conjugated as a functional moiety for organic semiconductor applications. In this review, we present recent examples of self-assembling peptide molecules and electroactive units for supramolecular functional electronic ​and optical materials with potential biomedical and bioelectronics applications.

A Functional Hexaphenylbenzene Library Comprising of One, Three, and Six Peripheral Rylene-Diimide Substituents

Synthesis and characterization of a series of rylene-diimide substituted hexaphenylbenzenes (HPBs) is presented. The direct connection of the rylene-diimide units to the HPBs via the imide-N-position without any linkers as well as the use of naphthalene-diimides (NDIs) next to perylene-diimides (PDIs) is unprecedented. While mono-substituted products were obtained by imidization reactions with amino-HPB and the respective rylene-monoimides, key step for the formation of tri- and hexa-substituted HPBs is the Co-catalysed cyclotrimerization. Particular emphasis for physic-chemical characterization was on to the number of NDIs/PDIs per HPB and the overall substitution patterns. Lastly, Scholl oxidation conditions were applied to all HPB systems to generate the corresponding hexa-peri-hexabenzocoronenes (HBCs). Importantly, the efficiency of the transformation strongly depends on the number of NDIs/PDIs. While three rylene-diimide units already hinder the Scholl reaction, the successful synthesis of mono-substituted HBCs is possible.

Porphyrin-rylene-diimide-hexabenzocoronene triads

Hexa-peri-hexabenzocoronenes (HBCs), substituted by two different chromophores in an ortho arrangement, were synthesized for the first time and investigated towards their photophysical properties. Rylene-diimide dyes, in particular naphthalene-diimides (NDIs) and perylene-diimides (PDIs), were attached to the HBC as the first, and porphyrins as the second chromophore. Therefore, porphyrin-NDI-HPB as well as porphyrin-PDI-HPB precursors were accessed and converted into the respective HBC derivatives applying oxidative Scholl conditions. UV-vis absorption and fluorescence emission spectroscopy showed interesting photophysical behavior such as energy transfer processes. Particularly, the porphyrin-PDI-HBC displays pronounced absorption features between 330–650 nm, which cover a wide range of the visible spectrum.

Controlled Construction of Cyclic d / l Peptide Nanorods

Cyclic d / l peptides (CPs) assemble spontaneously via backbone H-bonding to form extended nanostructures. These modular materials have great potential as versatile bionanomaterials. However, the useful development of CP nanomaterials requires practical methods to direct and control their assembly. In this work, we present novel, heterogeneous, covalently linked CP tetramers that achieve local control over the CP subunit order and composition through coupling of amino acid side-chains using copper-activated azide-alkyne cycloaddition and disulfide bond formation. Cryo-transmission electron microscopy revealed the formation of highly ordered, fibrous nanostructures, while NMR studies showed that these systems have strong intramolecular H-bonding in solution. The introduction of inter-CP tethers is expected to enable the development of complex nanomaterials with controllable chemical properties, facilitating the development of precisely functionalized or "decorated" peptide nanostructures.

New self-assembling peptide nanotubes of large diameter using δ-amino acids

Here we show that 4-aminocyclohexanecarboxylic acid is a rigid stretcher building block for the preparation of cyclic peptides that self-assemble to form peptide nanotubes with large diameter and hydrophobic pores. The hydrophobic properties of the resulting nanotubes provided by the two methylene groups per δ-residue allow the encapsulation of C60 moieties forming a new type of bionanopeapod structure.

High-performance nanomaterials formed by rigid yet extensible cyclic β-peptide polymers

Organisms have evolved biomaterials with an extraordinary convergence of high mechanical strength, toughness, and elasticity. In contrast, synthetic materials excel in stiffness or extensibility, and a combination of the two is necessary to exceed the performance of natural biomaterials. We bridge this materials property gap through the side-chain-to-side-chain polymerization of cyclic β-peptide rings. Due to their strong dipole moments, the rings self-assemble into rigid nanorods, stabilized by hydrogen bonds. Displayed amines serve as functionalization sites, or, if protonated, force the polymer to adopt an unfolded conformation. This molecular design enhances the processability and extensibility of the biopolymer. Molecular dynamics simulations predict stick-slip deformations dissipate energy at large strains, thereby, yielding toughness values greater than natural silks. Moreover, the synthesis route can be adapted to alter the dimensions and displayed chemistries of nanomaterials with mechanical properties that rival nature.

Synthetic materials tend to excel in either stiffness or extensibility, whereas a combination of the two is necessary to exceed the performance of natural biomaterials. Here the authors present a bioinspired polymer consisting of cyclic β-peptide rings that is capable of transitioning between rigid and unfolded conformations on demand.

Tailor-Made Functional Peptide Self-Assembling Nanostructures

Noncovalent interactions are the main driving force in the folding of proteins into a 3D functional structure. Motivated by the wish to reveal the mechanisms of the associated self-assembly processes, scientists are focusing on studying self-assembly processes of short protein segments (peptides). While this research has led to major advances in the understanding of biological and pathological process, only in recent years has the applicative potential of the resulting self-assembled peptide assemblies started to be explored. Here, major advances in the development of biomimetic supramolecular peptide assemblies as coatings, gels, and as electroactive materials, are highlighted. The guiding lines for the design of helical peptides, β strand peptides, as well as surface binding monolayer-forming peptides that can be utilized for a specific function are highlighted. Examples of their applications in diverse immerging applications in, e.g., ecology, biomedicine, and electronics, are described. Taking into account that, in addition to extraordinary design flexibility, these materials are naturally biocompatible and ecologically friendly, and their production is cost effective, the emergence of devices incorporating these biomimetic materials in the market is envisioned in the near future.

Parallel and antiparallel cyclic d/l peptide nanotubes

Nanotubes made from H-bonded cyclic d/l peptide (CP) subunits have great potential for the construction of nanomaterials of wide chemical and structural diversity but, to date, difficulties in structural characterisation have restricted development of these materials. We present the first crystal structures of continuous CP nanotubes with antiparallel and parallel stacking arrangements, assembled separately from two peptides; cyclo[(Asp-d-Leu-Lys-d-Leu)₂] and cyclo[(Asp-d-Ala-Lys-d-Ala)₂].

Recent advances in controlling the internal and external properties of self-assembling cyclic peptide nanotubes and dimers

Tuning the internal and external properties of self-assembling cyclic peptide nanotubes.

Glucose derivatives substitution and cyclic peptide diameter effects on the stability of the self-assembled cyclic peptide nanotubes; a joint QM/MD study

Dynamical behavior and the stability of eighteen nanostructures composed of cyclic peptide (CP) with the general structure of the cyclo(CO(CH₂)_{n=4, 6, 10}COCyst), in the gas phase, water and chloroform were investigated during 50ns molecular dynamic (MD) simulations. CP dimers and cyclic peptide nanotubes (CPNTs) are more stable in chloroform than water and this stability is reversely correlated with the ring size of the CP units. Also the effect of glucose derivatives substitution, d-glucose (S1) and N-methyl-d-glucamine (S2), on the stability and other physicochemical properties of the CP dimers and CPNTs were evaluated. These substitutions increase the inner-subunits hydrogen bonds (H-bond) which in turn increase the stability of these structures. Moreover, the S2 substitution in comparison to the S1 makes dimers and CPNTs more stable. Gibbs free energy analysis based on the MM-PBSA and MM-GBSA calculations confirmed that substitutions affect the stability of the studied nanostructures, considerably and an increase in the length of the CPNT units reduces their stability. Quantum chemistry calculations on the dimer structures using the density functional theory (DFT) and DFT-D3 methods were performed. Based on the DFT-D3 calculations, it was revealed that the dispersion interactions play a key role in the dimerization process. The ring size increment, elevates the dispersion interaction energy which is accordance with the MD results. H-bond formation between the CO and NH groups of the CP units inside the dimers have been analyzed by using the quantum theory of atoms in molecules and natural bond orbital description. Finally, through these analyses, the electrostatic interaction between the mentioned groups have been evaluated.

Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach

In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.

Self-assembled fibrillar networks comprised of a naturally-occurring cyclic peptide—LOB3

LOB3, a naturally-occurring orbitide, is capable of self-assembling into 1D nano-fibers and ultimately 3D molecular gel networks in acetonitrile.

Dynamic Peptide Library for the Discovery of Charge Transfer Hydrogels

Coupling of peptide self-assembly to dynamic sequence exchange provides a useful approach for the discovery of self-assembling materials. In here, we demonstrate the discovery and optimization of aqueous, gel-phase nanostructures based on dynamically exchanging peptide sequences that self-select to maximize charge transfer of n-type semiconducting naphthalenediimide (NDI)-dipeptide bioconjugates with various π-electron-rich donors (dialkoxy/hydroxy/amino-naphthalene or pyrene derivatives). These gel-phase peptide libraries are characterized by spectroscopy (UV-vis and fluorescence), microscopy (TEM), HPLC, and oscillatory rheology and it is found that, of the various peptide sequences explored (tyrosine Y-NDI with tyrosine Y, phenylalanine F, leucine L, valine V, alanine A or glycine G-NH2), the optimum sequence is tyrosine-phenylalanine in each case; however, both its absolute and relative yield amplification is dictated by the properties of the donor component, indicating cooperativity of peptide sequence and donor/acceptor pairs in assembly. The methodology provides an in situ discovery tool for nanostructures that enable dynamic interfacing of supramolecular electronics with aqueous (biological) systems.

Functional architectures based on self-assembly of bio-inspired dipeptides: Structure modulation and its photoelectronic applications

Getting inspiration from nature and further developing functional architectures provides an effective way to design innovative materials and systems. Among bio-inspired materials, dipeptides and its self-assembled architectures with functionalities have recently been the subject of intensive studies. However, there is still a great challenge to explore its applications likely due to the lack of effective adaptation of their self-assembled structures as well as a lack of understanding of the self-assembly mechanisms. In this context, taking diphenylalanine (FF, a core recognition motif for molecular self-assembly of the Alzheimer's β-amyloid polypeptides) as a model of bio-inspired dipeptides, recent strategies on modulation of dipeptide-based architectures were introduced with regard to both covalent (architectures modulation by coupling functional groups) and non-covalent ways (controlled architectures by different assembly pathways). Then, applications are highlighted in some newly emerging fields of innovative photoelectronic devices and materials, such as artificial photosynthetic systems for renewable solar energy storage and renewable optical waveguiding materials for optoelectronic devices. At last, the challenges and future perspectives of these bio-inspired dipeptides are also addressed.

Introducing charge transfer functionality into prebiotically relevant β-sheet peptide fibrils

Incorporation of naphthalene diimide moieties as side chains of short amphiphilic peptide results in the formation of fibrils that exhibit substantial intermolecular π-stacking interactions. These interactions can be manipulated without affecting the structure. The new system is suggested as a first step towards functional self-synthesizing materials.

Effect of the amino acid composition of cyclic peptides on their self-assembly in lipid bilayers

The effect of amino acid composition on the formation of transmembrane channels in lipid bilayers upon self-assembly of alt-(l,d)-α-cyclic octapeptides has been investigated.

Solution scattering studies of the hierarchical assembly of porphyrin trimers based on benzene triscarboxamide

The self-assembly of achiral and chiral porphyrin trimers based on benzene triscarboxamide in solution is studied with the help of NMR, FT-IR, UV-vis, and CD spectroscopy. These studies revealed that in apolar solvents the porphyrin trimers self-assembled in columnar stacks via a combination of hydrogen bonding and π-π stacking interactions. While the critical aggregation constant is about 0.2 mM in chloroform, aggregation already occurs at micromolar concentrations in n-hexane. Small angle neutron scattering (SANS) studies in chloroform, toluene, and n-hexane confirmed aggregation of the trimers into columnar stacks. In chloroform and n-hexane, but not in toluene, the trimers gelated the solvent. In chloroform the stacks of the achiral trimer were found to contain on average about 70 molecules, while in toluene the stacks were much smaller and contained on average 7-9 molecules. In n-hexane the SANS studies revealed that the chiral trimer formed a gel with an average mesh size of the transient network of chains of approximately 90 nm, with chains being built up from effective cylindrical aggregates with an average length of 20 nm.

Naphthalene bisimides asymmetrically and symmetrically N-substituted with triarylamine--comparison of spectroscopic, electrochemical, electronic and self-assembly properties

Two semiconducting naphthalene bisimides were comparatively studied: NBI-(TAA)(2), symmetrically N-substituted with triaryl amine and asymmetric NBI-TAA-Oc with triaryl amine and octyl N-substituents. Both compounds show very similar spectroscopic and redox properties but differ in their supramolecular organization. As evidenced by STM, in monolayers on HOPG they form ordered 2D structures, however of different packing patterns. NBI-(TAA)(2) does not form ordered 3D structures, yielding amorphous thin films whereas films of NBI-TAA-Oc are highly crystalline. DFT calculations predict the ionization potential (IP) of 5.22 eV and 5.18 eV for NBI-TAA-Oc and NBI-(TAA)(2), respectively, as well as the electron affinity values (EA) of -3.25 eV and -3.22 eV. These results are consistent with the cyclic voltammetry data which yield similar values of IP (5.20 eV and 5.19 eV) and somehow different values of EA (-3.80 eV and -3.83 eV). As judged from these data, both semiconductors should exhibit ambipolar behavior. Indeed, NBI-TAA-Oc is ambipolar, showing hole and electron mobilities of 4.5 × 10(-5) cm(2)/(V s) and of 2.6 × 10(-4) cm(2)/(V s), respectively, in the field effect transistor configuration. NBI-(TAA)(2) is not ambipolar and yields field effect only in the p-channel configuration. This different behavior is rationalized on the basis of structural factors.

Metal chelates anchored to poly-L-peptides and linear D,L-α-peptides with promising nanotechnological applications

Regular configurationally alternating amino acid sequences generate cyclic and linear helical peptides with a local β-conformation able to self-assemble in nanowires and nanoscaffolds directed and stabilized by hydrogen bonds. The possibility of modulating the chemical profile of the various amino acid residues containing reactive side chains means that peptides could be flexible templates for creating various building blocks. A method for the design of molecules with potential spintronic properties is described. Peptides containing lysine residues, the side chains of which are bridged through the formation of metal chelates via Schiff bases, could provide stable molecular channels. When metal chelates with high electron spin states are used, their coupling could generate materials that are interesting due to their magnetic properties as well as for the patterning of nanometric lattices driven by their orientation under a magnetic field. With this aim, three alternating D- and L-lysine-containing octapeptides are synthesized and the formation of their bis(pyridoxalaldimine) copper(II) chelate derivatives is shown by absorption and circular dichroism spectroscopies.

Amino acid derivatized arylenediimides: a versatile modular approach for functional molecular materials

Nature's elegant molecular designs and their assemblies with specific structure-property correlations have inspired researchers to design and develop bio-mimics for advanced functional applications. To realize such advanced molecular materials, naturally evolved amino acids are arguably the ideal auxiliaries due to their remarkable molecular/chiral recognition and distinctive sequence specific self-assembling properties. Over the years, this modular approach of derivatizing naphthalenediimides (NDIs) and perylenediimides (PDIs) with amino acids and peptides have resulted in several hitherto unknown molecular assemblies with phenomenal impact on their performance. Derivatization with versatile arylenediimides is especially interesting due to their wide spread applications in fields ranging from biomedicine to electronics. Herein some of these seminal reports of this rapidly emerging field and the design principles embraced are discussed.

Charge transport in vertically aligned, self-assembled peptide nanotube junctions

The self-assembly propensity of peptides has been extensively utilized in recent years for the formation of supramolecular nanostructures. In particular, the self-assembly of peptides into fibrils and nanotubes makes them promising building blocks for electronic and electro-optic applications. However, the mechanisms of charge transfer in these wire-like structures, especially in ambient conditions, are not yet fully understood. We describe here a layer-by-layer deposition methodology of short self-assembled cyclic peptide nanotubes, which results in vertically oriented nanotubes on gold substrates. Using this novel deposition methodology, we have fabricated molecular junctions with a conductive atomic force microscopy tip as a second electrode. Studies of the junctions' current-voltage characteristics as a function of the nanotube length revealed an efficient charge transfer in these supramolecular structures, with a low current attenuation constant of 0.1 Å(-1), which indicate that electron transfer is dominated by hopping. Moreover, the threshold voltage to field-emission dominated transport was found to increase with peptide length in a manner that depends on the nature of the contact with the electrodes. The flexibility in the design of the peptide monomers and the ability to control their sequential order over the nanotube by means of the layer-by-layer assembly process, which is demonstrated in this work, can be used to engineer the electronic properties of self-assembled peptide nanotubes toward device applications.