Ab initio calculations on π-stacked thiophene dimer, trimer, and tetramer: Structure, interaction energy, cooperative effects, and intermolecular electronic parameters

3,4-Ethylenedioxythiophene (EDOT) End-Group Functionalized Poly-ε-caprolactone (PCL): Self-Assembly in Organic Solvents and Its Coincidentally Observed Peculiar Behavior in Thin Film and Protonated Media

End-group functionalization of homopolymers is a valuable way to produce high-fidelity nanostructured and functional soft materials when the structures obtained have the capacity for self-assembly (SA) encoded in their structural details. Herein, an end-functionalized PCL with a π-conjugated EDOT moiety, (EDOT-PCL), designed exclusively from hydrophobic domains, as a functional "hydrophobic amphiphile", was synthesized in the bulk ROP of ε-caprolactone. The experimental results obtained by spectroscopic methods, including NMR, UV-vis, and fluorescence, using DLS and by AFM, confirm that in solvents with extremely different polarities (chloroform and acetonitrile), EDOT-PCL presents an interaction- and structure-based bias, which is strong and selective enough to exert control over supramolecular packing, both in dispersions and in the film state. This leads to the diversity of SA structures, including spheroidal, straight, and helical rods, as well as orthorhombic single crystals, with solvent-dependent shapes and sizes, confirming that EDOT-PCL behaves as a "block-molecule". According to the results from AFM imaging, an unexpected transformation of micelle-type nanostructures into single 2D lamellar crystals, through breakout crystallization, took place by simple acetonitrile evaporation during the formation of the film on the mica support at room temperature. Moreover, EDOT-PCL's propensity for spontaneous oxidant-free oligomerization in acidic media was proposed as a presumptive answer for the unexpected appearance of blue color during its dissolution in CDCl3 at a high concentration. FT-IR, UV-vis, and fluorescence techniques were used to support this claim. Besides being intriguing and unforeseen, the experimental findings concerning EDOT-PCL have raised new and interesting questions that deserve to be addressed in future research.

Electrochromic Self-Electrostabilized Polypyrrole Films Doped with Surfactant and Azo Dye

Two azo dyes, acid red 1 (AR1) and acid red 18 (AR18), were used alone or in combination with sodium dodecyl sulfate (SDS) for the electropolymerization of a pyrrole monomer. Polypyrrole (PPy) showed higher redox capacity when SDS and AR18 were used simultaneously as dopant agents (PPy/AR18-SDS) than when the conducting polymer was produced in the presence of SDS, AR18, AR1, or an AR1/SDS mixture. Moreover, PPy/AR18-SDS is a self-stabilizing material that exhibits increasing electrochemical activity with the number of oxidation–reduction cycles. A mechanism supported by scanning electron microscopy and X-ray diffraction structural observations was proposed to explain the synergy between the SDS surfactant and the AR18 dye. On the other hand, the Bordeaux red color of PPy/AR18-SDS, which exhibits an optical band gap of 1.9 eV, rapidly changed to orange-yellow and blue colors when films were reduced and oxidized, respectively, by applying linear or step potential ramps. Overall, the results indicate that the synergistic utilization of AR18 and SDS as dopant agents in the same polymerization reaction is a very successful and advantageous strategy for the preparation of PPy films with cutting-edge electrochemical and electrochromic properties.

Theoretical and experimental studies of an oseltamivir-triazole-based thermoresponsive organogel

Low-molecular weight organic gelators have been of significant interest in recent years because of their interesting properties and potential applications in sensing technology, biomedicine and drug delivery. Herein, the synthesis, characterization and gelation properties of new oseltamivir conjugates are reported. The oseltamivir-triazole conjugate 1 was synthesized via a click-reaction in a 75% yield. The key features of this conjugate include the presence of amide, flexible ester linkages and a triazole scaffold linking a hydrophobic alkyl chain. The conjugate 1, possessing a long alkyl chain, showed gelation properties in various apolar organic solvents. This gelation behavior was not observed in the case of the deesterified conjugate 2; this indicated the necessity of the alkyl chain for gelation. The gelator 1 showed thermoreversible gelation properties in a range of linear alkane solvents (from n-pentane to n-dodecane). A scanning electron microscopic study suggests that the gelator 1 exists as cross-linked structures, which are self-aggregated in the range of submicrometers, as supported by extensive ¹H-NMR studies. The rheological parameters supported the occurrence of a soft gelation process, and the gel formed in n-decane was found to be stiffer than that formed in n-hexane. Computational studies suggested that the gelation behavior was indeed due to micelle formation and dependent on the lipophilicity of solvents.

An amphiphilic, heterografted polythiophene copolymer containing biocompatible/biodegradable side chains for use as an (electro)active surface in biomedical applications

Design of an amphiphilic heterografted block copolymer composed of a hydrophobic core backbone and both hydrophilic side chains, able to detect the redox reaction of NADH.

Isomeric cationic ionenes as n-dopant agents of poly(3,4-ethylenedioxythiophene) for in situ gelation

Three isomeric ionene polymers containing 1,4-diazabicyclo[2.2.2]octane (DABCO) and N,N'-(x-phenylene)dibenzamide (x = ortho-/meta-/para-) linkages have been used as dopant agents to produce n-doped poly(3,4-ethylenedioxythiophene) (PEDOT) electrodes by reducing already dedoped conducting polymer (CP) films. This work focuses on the influence of the ionene topology on both the properties of n-doped PEDOT:ionene electrodes and the success of the in situ thermal gelation of the ionene inside the CP matrix. The highest doping level is reached for the para-isomeric ionene-containing electrode, even though the content of ortho- and meta-topomers in the corresponding n-doped PEDOT:ionene electrodes is greater. Thus, many of the incorporated ionene units are not directly interacting with CP chains and, therefore, they do not play an active role as n-dopant agents but they are crucial for the in situ formation of the ionene hydrogels. The effect of the ionene topology is practically non-existent on properties such as the specific capacitance and wettability of PEDOT:ionene films, and it is small but non-negligible on the electrochemical and thermal stability. In contrast, the surface morphology, topography, and distribution of dopant molecules significantly depend on the ionene topology. In situ thermal gelation was successful in PEDOT films n-doped with the ortho- and para-topomers, even though this assembly process was much faster for the former than for the latter. The gelation considerably improved the mechanical response of the electropolymerized PEDOT film, which was practically non-existent before it. Molecular dynamics simulations prove that the strength and abundance of PEDOTionene specific interactions (i.e. π-π stacking, N-HS hydrogen bonds and both N+O and N+S interactions) are higher for the meta-isomeric ionene, for which the in situ gelation was not achieved, than for the ortho- and para-ones.

Brownian orientational lath model (BOLD): A computational model relating the self-assembly in a fluid of lath like particles with its rheology and gelation

By means of a computational model, we study the relation between two complementary views of gelation, rheological tests against the characterization of a network of consecutive particles. The model we propose consists of slender, plane, colloidal sized particles, which we name laths, which self-assemble into long ordered aggregates of several particles; called whiskers in the literature. Within a whisker, the interaction potential is a minimum when: the planes of two consecutive laths are aligned, thus favoring their alignment; when the center of three consecutive laths lie in a straight line, thus favoring stacking; and when the center of two consecutive laths are located at a certain distance, which mimics excluded volume. A threshold value of the potential gives a condition for sticking free laths into whiskers, and for the breaking of whiskers. The simplicity of the model allows the simulation to reach large enough times, of the order of minutes, needed to simulate numerical rheology tests. We are able to characterize the whisker formation, as well as to simulate the gel transition, by means of an oscillatory shear numerical experiment. We conclude that according to the usual rheological definition a gel transition occurs at about 250K, even though there is no branching and less than 10% of whiskers are long enough as to percolate the system.

Modeling of canonical and C2′-O-thiophenylmethyl modified hexamers of RNA. Insights into the nature of structural changes and thermal stability

Modification of the C2′-O-position with thiophenylmethyl groups on both strands leads to thermal stabilization of the duplex. Predicting the effects that modifications will have on structure of RNA is of importance in the development of new RNA technologies.

Cationic ionene as an n-dopant agent of poly(3,4-ethylenedioxythiophene)

Poly(3,4-ethylenedioxythiophene) has been n-doped using a cationic 1,4-diazabicyclo[2.2.2]octane-based ionene bearing N,N′-(meta-phenylene)dibenzamide linkages.

Aromatic ionene topology and counterion-tuned gelation of acidic aqueous solutions

Unusual gelation of acidic solutions was achieved using polycations bearing quaternary ammonium moieties. These ionene polymers are based on a disubstituted phenylene dibenzamide core, which allows the construction of different topomers (i.e. ortho-1, meta-2 and para-3). The topology of the polymers was found to play a key role on their aggregation behaviour both in pure water and in a variety of aqueous acidic solutions leading to the formation of stable acidic gels. Specifically, ortho-1 showed superior gelation ability than the analogues meta-2 and para-3 in numerous solutions of different pH and ionic strengths. Lower critical gelation concentrations, higher gel-to-sol transition temperatures and faster gelation were usually observed for ortho-1 regardless the solvent system. Detailed computational molecular dynamic simulations revealed a major role of the counterion (Cl^-) and specific polymerpolymer interactions. In particular, hydrogen bonds, N-Hπ interactions and intramolecular π-π stacking networks are distinctive in ortho-1. In addition, counterions located at internal hydration regions also affect to such polymerpolymer interactions, acting as binders and, therefore, providing additional stability.

Conformational behavior and stacking interactions of contorted polycyclic aromatics

Computational studies of non-covalent dimers of saddle-shaped molecules unveil widely varying conformations and stacking configurations.

New equation for calculating total interaction energy in one noncyclic ABC triad and new insights into cooperativity of noncovalent bonds

In this work, a new equation consist of A⋅⋅⋅B, B⋅⋅⋅C, A⋅⋅⋅BC, and AB⋅⋅⋅C interactions is proposed for calculating the total interaction energy of noncyclic ABC triads. New equations are also proposed for calculating the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions on the formation of triad from the corresponding dyads. The advantages of equations proposed here in comparison with many-body interaction energy approach are discussed. All proposed equations were tested in F₃ MLi⋅⋅⋅NCH⋅⋅⋅HLH and F₃ MLi⋅⋅⋅HLH⋅⋅⋅HCN (M = C, Si; L = Be, Mg) as well as H₃ N⋅⋅⋅XY⋅⋅⋅HF (X, Y = F, Cl, Br) noncyclic A⋅⋅⋅B⋅⋅⋅C triads. The data show that the total cooperativity of triad correlates well with the sum of the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions calculated through new equations proposed here. © 2016 Wiley Periodicals, Inc.

Dimeric binding of plant alkaloid ellipticine to human serum proteins

Induced exciton circular dichroism signals reveal the accommodation of a pair of ellipticine molecules to the subdomain IB of human serum albumin and the β-barrel of α₁-acid glycoprotein.

Internal organization of macromonomers and dendronized polymers based on thiophene dendrons

The internal organization of macromonomers (MGs) consisting of all-thiophene dendrons of generation g = 2 and 3 attached to a phenyl core, as well as of the dendronized polymers resulting from polymerization of these macromonomers (PG2 and PG3, respectively), has been investigated using theoretical methods. The conformational preferences of the MGs, determined using density functional theory calculations, are characterized by the relative orientation between dendrons and core. We find that the strain of the MGs increases with the generation number and is alleviated by small conformational re-arrangements of the peripheral thiophene rings. The conformations obtained for the MGs have subsequently been used to construct models for the dendronized polymers. Classical molecular dynamics simulations have evidenced that the interpenetration of dendrons belonging to different repeat units is very small for PG2. In contrast, the degree of interpenetration is found to be very high for PG3, which also shows a significant degree of backfolding (i.e. occurrence of peripheral methyl groups approaching the backbone). Consequently, PG2 behaves as a conventional linear flexible polymer bearing bulk pendant groups, whereas PG3 is better characterized as a semirigid homogeneous cylinder. The two polymers are stabilized by π-π stacking interactions, even though these are significantly more abundant for PG3 than for PG2; the average numbers of interactions per repeat unit are 3.0 and 8.8 for PG2 and PG3, respectively. While in these interactions the thiophene rings can adopt either parallel (sandwich) or perpendicular (T-shaped) dispositions, the former scenario turns out to be the most abundant.

A single-residue substitution inhibits fibrillization of Ala-based pentapeptides. A spectroscopic and molecular dynamics investigation

The aggregation properties of two Ala-based pentapeptides were investigated by spectroscopic techniques and molecular dynamics (MD) simulations. The two peptides, both functionalized at the N-terminus with a pyrenyl group, differ in the insertion of an α-aminoisobutyric acid residue at position 4. We showed that this single modification of the homo-peptide sequence inhibits the aggregation of the pentapeptide in aqueous solutions. Atomic force microscopy imaging revealed that the two peptides form mesoscopic aggregates of very different morphologies when deposited on mica. MD experiments showed that the two peptides have a very different propensity to form β-pleated sheet structures, as confirmed by our spectroscopic measurements. The implications of these findings for our understanding of the mechanism leading to the formation of amyloid structures, primary responsible for numerous neurodegenerative diseases, are also discussed.

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

We report herein the synthesis of a novel type of hybrid compound that consists of a poly(ethylene oxide) (PEO) functionalized β-sheet peptide sequence covalently linked to an alkylated quaterthiophene moiety. Compounds of this class are highly promising for technological applications because their self-assembly and stimuli-responsive behavior, which is mainly caused by the peptide moieties, combined with the potential semiconducting properties of oligothiophenes provides unprecedented opportunities for the design of advanced materials at the nanoscale in such areas as, for example, organic electronics and sensor design for chemical and biomedical applications. The compound presented herein is experimentally shown to form stable fibrillar aggregates that are visualized by both transmission electron and atomic force microscopy. We developed a theoretical methodology to study the possible intermolecular arrangements and their characteristic features with the help of all-atom MD simulations, while simultaneously incorporating available experimental data into the model. Large-scale atomistic simulations of several fibrillar aggregates with different molecular arrangements were performed. The results of the simulations are compared with experimental data, which leads to the proposition of a likely model for the arrangement of the individual molecules within the observed aggregates.

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.

Modeling an electronic conductor based on natural peptide sequences

In this work we used quantum mechanical calculations, molecular dynamics simulations, and QM/MM methods to examine the formation of a pi-stacking ladder and the existence of charge transfer processes in a tubular nanostructure constructed using protein building blocks. Initially, the conformational properties of beta-3-thienylalanine, a synthetic amino acid with an aromatic side group, were studied using quantum mechanical calculations. Next, this amino acid was used to substitute the natural residues at selected positions of the nanotube. Molecular dynamics simulations showed that a rational design of the targeted replacements enhances the stability of the tubular nanostructure and forms a pi-stacking ladder in the inner core of the tube. Finally, QM/MM calculations on the oxidized nanotube evidenced the delocalization of the pi-electron deficiency between the thienyl side groups of the different synthetic residues. The overall results reflected that the system under study is a potential candidate to be used as a nanowire.