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This manuscript describes a new route to prepare rapidly Ca2+-free hydrogels from unmodified sodium alginate by simply mixing with small organic molecules such as poly(carboxylic acid) compounds as cross-linker agents instead of classical divalent metal salts such as CaCl2. Dimethyl sulfoxide (DMSO) was also found to induce the rapid gelation of aqueous alginate solutions. The gelation process takes place at room temperature, and depending on the composition, gels with good thermal (90-100 °C) and mechanical properties compared to classical metal-containing analogs are obtained. DMSO-based gels showed remarkable self-supporting and thixotropic properties, which can be tuned by the biopolymer concentration. Furthermore, oxalic acid-based gels show superior elasticity than HCl, CaCl2 and DMSO-based gels. The possibility to prepare monoliths, beads, and films of these gels provide them with significant versatility. In particular, films made of alginate and oxalic acid show good potential as synergistic anticancer drug delivery carrier. Computational studies using both quantum mechanical and classical force-field methodologies reveal that hydrogen bonding networks between water and DMSO molecules located close to the alginate chains are responsible for the stability of DMSO-based gels. In contrast, the cohesion of oxalic acid-based gels is a consequence of the coexistence of multiple ionic associations involving oxalate, alginate, and Na+ counterions, which stabilize the system and keep all the interacting species grouped.

The novelty of the present study relies on the straightforward sonication of ZnO and TiO2 and incorporation to a complex formulation of latex, with other several organic-inorganic additives that influences the cross-linking reactions. The new elastomer with particles carefully sonicated exhibit improved electrical and mechanical properties. Strong interaction among the nanoparticles and the polymer amorphous phase has been proved by means of FTIR, SEM and XRD analyses. The synergistic effect of hybrid fillers with nanometric dimensions can be used to design high-performance natural rubber nanocomposites with enhanced electrical resistance and good cross-linking degree.

We have fabricated potentially generalizable sensors based on polymeric-modified electrodes for the electrochemical detection of dopamine. Sensitive and selective sensors have been successfully obtained by applying a cold-plasma treatment during 1–2 min not only to conducting polymers but also to electrochemically inert polymers, such as polyethylene, polypropylene, polyvinylpyrrolidone, polycaprolactone and polystyrene. The effects of the plasma in the electrode surface activation, which is an essential requirement for the dopamine detection when inert polymers are used, have been investigated using X-ray photoelectron spectroscopy. Results indicate that exposure of polymer-modified electrodes to cold-plasma produces the formation of a large variety of reactive species adsorbed on the electrode surface, which catalyse the dopamine oxidation. With this technology, which is based on the application of a very simple physical functionalization, we have defined a paradox-based paradigm for the fabrication of electrochemical sensors by using inert and cheap plastics.

The properties as biointerfaces of electroactive conducting polymer–peptide biocomposites formed by poly(3,4-ethylenedioxythiophene) (PEDOT) and CREKA or CR(NMe)EKA peptide sequences (where Glu has been replaced by N-methyl-Glu in the latter) have been compared. CREKA is a linear pentapeptide that recognizes clotted plasma proteins and selectively homes to tumors, while CR(NMe)EKA is an engineer to improve such properties by altering peptide–fibrin interactions. Differences between PEDOT-CREKA and PEDOT-CR(NMe)EKA reflect dissemblance in the organization of the peptides into the polymeric matrix. Both peptides affect fibrinogen thrombin-catalyzed polymerization causing the immediate formation of fibrin, whereas in the absence of thrombin this phenomenon is only observed for CR(NMe)EKA. Consistently, the fibrin-adsorption capacity is higher for PEDOT-CR(NMe)EKA than for PEDOT-CREKA, even though in both cases adsorbed fibrin exhibits round-like morphologies rather than the characteristic fibrous structure. PEDOT-peptide films coated with fibrin are selective in terms of cell adhesion, promoting the attachment of metastatic cells with respect to normal cells.

Nanoperforated poly(lactic acid) (PLA) free-standing nanomembranes (FsNMs) have been prepared using a two-step process: (1) spin-coating a mixture of immiscible polymers to provoke phase segregation and formation of appropriated nanofeatures (i.e. phase separation domains with dimensions similar to the entire film thickness); and (2) selective solvent etching to transform such nanofeatures into nanoperforations. For this purpose, PLA has been mixed with polyethylene glycol (PEG) and poly(vinyl alcohol) (PVA). Unfortunately, the characteristics of PLA:PEG mixtures were not appropriated to prepare nanoperforated FsNMs. In contrast, perforated PLA FsNMs with pores crossing the entire film thickness, which have been characterized by scanning electron microscopy and atomic force microscopy, were obtained using PLA:PVA mixtures. The diameter (¿) of such pores has been controlled through both the PLA:PVA ratio and the processing conditions of the mixtures, FsNMs with pores of ¿ ˜ 0.8 µm, 170 nm and 65 nm being achieved. Investigations on nanoperforated FsNMs (i.e. those with ¿ ˜ 170 and 65 nm), which are the more regular, reveal that pores crossing the entire membrane thickness do not affect the surface wettability of PLA but drastically enhances the cellular response of this biomaterial. Thus, cell proliferation assays indicate that cell viability in PLA with perforations of ¿ ˜ 170 nm is ~2.6 and ~2.2 higher than in non-perforated PLA and PLA with perforations of ¿ ˜ 65 nm, respectively. This excellent response has been attributed to the similarity between the nanoperforations with ¿ ˜ 170 nm and the filopodia filaments in cells (¿ ˜ 100–200 nm), which play a crucial role in cell migration processes. The favorable interaction between the perforated membrane nanofeatures and cell filopodia has been corroborated by optical and scanning electron microscopies.

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties–conformational flexibility relationships in all-Th dendrimers.

Gramicidin (GA), a very hydrophobic pentadecapeptide with important biological activities (i.e. in addition to its well-known antimicrobial and antibiotic activities, GA has been recently identified as a potent therapeutic agent against different carcinomas), has been loaded by electrospraying in poly(tetramethylene succinate) (PE44), a biodegradable and biocompatible aliphatic polyester. Microspheres (average diameter: 5.0 ± 0.7 μm) were successfully obtained from the mixture of GA and PE44 solutions in ethanol and chloroform, respectively. The loading of the peptide, which has been proved by FTIR and X-ray photoelectron spectroscopies, essentially occurred at the surface of the microspheres, as was reflected by scanning electron microscopy micrographs and atomic force microscopy phase images. In spite of this, the thermal stability of the polyester matrix remained essentially unaltered, even though the wettability decreased. The release of GA in phosphate buffer saline (PBS) was limited by the very low solubility of the peptide in aqueous solution, a fast burst effect followed by the establishment of equilibrium after 5 days of being observed in this hydrophilic environment. The release behaviour was very different when the hydrophilicity of the medium was reduced by adding ethanol. In this case, a very fast but sustained release was identified during the first few hours. On the other hand, biological tests have demonstrated that GA retains its antimicrobial activity after loading and does not alter the biocompatibility of PE44. Our results prove that, despite its hydrophobicity and relatively large number of residues, the loading of GA in a polymeric matrix represents an alternative strategy for the release of this versatile peptide in cancer therapy., Authors thank supports from MINECO and FEDER (MAT2015-69367-R, MAT2015-69547-R and CTQ2013-40855-R) and Gobierno de Aragón – Fondo Social Europeo (research group E40). Support for the research of C.A. was received through the prize “ICREA Academia” for excellence in research funded by the Generalitat de Catalunya.

The electrochemical properties (i.e. electroactivity, electrostability and specific capacitance) of 3-layered films made of poly(3,4-ethylenedioxythiophene) (PEDOT) and poly(N-methylpyrrole) (PNMPy) arranged alternatively have been activated by incorporating exfoliated montmorillonite (MMT) at the intermediate layer. 3-Layered films were prepared using the layer-by-layer electropolymerization technique, whereas the previously exfoliated clay was incorporated into PNMPy layer using an in situ polymerization procedure. The influence of the clay on the properties has been investigated as function of the thickness of the internal and external PEDOT layers, which has been controlled through the polymerization time. Micrometric PEDOT layers have been found to exert a template effect on the topography and morphology of the intermediate PNMPy or PNMPy-MMT layer, this effect being practically inexistent for films with nanometric PEDOT layers. The ability to exchange charge reversibly (electroactivity) and the electrochemical stability (electrostability) of films with MMT at the intermediate layer are higher than those of films without clay, these effects being more pronounced for films with micrometric PEDOT layers. The influence of the thickness is even more remarkable in the specific capacitance, which decreases rapidly with increasing thickness. The clay at the intermediate layer improves the specific capacitance of micrometric films and, most importantly, protects the capacitive behavior against electrochemical degradation in all cases. In summary, the presence of MMT in the intermediate PNMPy layer makes 3-layered films sensitive to the dielectric breakage, activating their electrochemical and capacitive properties. Such clay-induced effects are more pronounced for films made of micrometric PEDOT layers. (C) 2015 Elsevier Ltd. All rights reserved.

Sol-gel films were prepared using different ratios of two silica precursors, vinyltrimethoxysilane (VTMS) and tetraethylorthosilicate (TEOS), targeting the anticorrosion treatment of aluminum alloy 2024-T3. The electrochemical behavior of the alloy coated with such films, which was studied in a 0.05 mol L-1 NaCI solution, revealed that the VTMS/TEOS ratio drastically affects the anticorrosion performance. Electrochemical impedance spectroscopy (EIS) results provided evidences that the best anticorrosive response occurs with the films prepared from 50% (v/v) ethanol, 46% (v/v) water, 3% (v/v) VTMS and 1% (v/v) TEOS. Moreover, the effects of the addition of ethylenediamine tetra(methylene phosphonic acid) (EDTPO) to a hybrid sol-gel matrix were examined. The corrosion resistance was considerably improved when the concentration of added phosphonic acid was 3.75 x 10(-5) mol L-1. Scanning electron microscopy, energy dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy analyses revealed that EDTPO-containing films provide a more uniform coverage. Results evidenced the formation of S-O-Al linkages in the VTMS/TEOS and VTMS/TEOS/EDTPO systems and that the VTMS/TEOS/EDTPO system contained P-O-Al linkages. The P-O-Al bonds, combined with the modified silica network action, may be responsible for the good anticorrosive behavior of the VTMS/TEOS/EDTPO films. (C) 2014 Published by Elsevier B.V.

We attempt to provide direct evidence for the suggested behavior of dendronized polymers as molecular objects (i.e., single shape persistent macromolecules). For this purpose, the microscopic structure of dendronized polymers adsorbed onto mica has been investigated using atomistic molecular dynamics simulations. We find that the shape of the second to fourth generation dendronized polymers is basically kept upon adsorption due to substantial backfolding within their interior. The fluctuation strength of the polymer backbones, which is seen to decrease with increasing generation, also indicates that these individual macromolecules exhibit molecular object behavior in the nanosize range.

Fundamental characteristics of bioactive platforms based on biocomposites of poly(3,4-ethylenedioxythiophene) (PEDOT) and collagen, named P(EDOT:CLG), have been examined using an experimental–computational approach. The protein affects both the morphology and electrochemical activity of PEDOT. Specifically, P(EDOT:CLG) shows spherical-like nodules that have been attributed to the collagen rod aggregates organized in phases separated from that of PEDOT. This phase separation results in a reduction of the ability to exchange charge reversibly, even though collagen stabilizes the PEDOT matrix from electrochemical degradation. On the other hand, viability assays indicate that the bioactivity of P(EDOT:CLG) is significantly higher than that of PEDOT in terms of cellular adhesion and proliferation. Thus, the biocomposite promotes the formation of 3D biostructures formed by the superposition of cellular monolayers, mimicking the growth of biological tissues. In order to gain microscopic information about the formation of specific interactions between PEDOT and collagen molecules in the biocomposite, quantum mechanical calculations on complexes formed by their building blocks have been performed in different environments (i.e. vacuum, chloroform and aqueous solution). Results evidence the important role played by non-conventional C–HO hydrogen bonds, which is consistent with previous findings on complexes involving DNA and dopamine. The environment affects considerably the binding energy, which decreases with increasing polarity of the environment. However, in all environments the repeating units of PEDOT form stronger interactions with L-hydroxyproline than with L-proline. On the other hand, intermolecular interaction patterns predicted using implicit and explicit solvation models present a remarkable agreement and have been identified by visualizing the reduced electron density gradient.

Hybrid scaffolds constituted of a mixture of conducting and biodegradable polymers are obtained by the electrospinning technique. Specifically, poly(3-thiophene methyl acetate) (P3TMA) and a copolymer derived from L-leucine, which bears ester, urea and amide groups (PEU-co-PEA), have been employed. Both polymers were selected because of their intrinsic properties and their high solubility in organic solvents. The biodegradable polymer renders continuous and homogeneous microfibers under most of the electrospinning conditions tested, appearing to be an ideal carrier for the polythiophene derivative. A spontaneous phase separation has been observed for concentrated solutions of PEU-co-PEA and P3TMA in chloroform-methanol mixtures. An enriched dense phase results on the conducting polymer and can be successfully electrospun, giving rise to scaffolds with up to 90 wt% of P3TMA. Morphological observations have indicated that continuous and regular microfibers are attained despite the high conducting polymer content. P3TMA presents a high doping level and leads to stable electrospun scaffolds by the simple addition of a low percentage of a high molecular weight carrier. The resulting scaffolds are practically amorphous and thermally stable, also presenting a pronounced electrochemical response and being electrochemically active. Thus, the formation of polarons and bipolarons at specific positions, the ability to exchange charge reversibly and the electrical stability of hybrid PEU-co-PEA/P3TMA electrospun scaffolds and P3TMA alone are practically the same. biodegradability for their use as scaffolds. Different strategies

The adsorption of orthophosphate, pyrophosphate, triphosphate and a trisphosphonate onto hydroxyapatite has been examined using experiments and quantum mechanical calculations. Adsorption studies with FTIR and X-ray photoelectron spectroscopies have been performed considering both crystalline hydroxyapatite (HAp) and amorphous calcium phosphate particles, which were specifically prepared and characterized for this purpose. Density functional theory (DFT) calculations have been carried out considering the (100) and (001) surfaces of HAp, which were represented using 1 x 2 x 2 and 3 x 3 x 1 slab models, respectively. The adsorption of phosphate onto the two crystallographic surfaces is very much favored from an energetic point of view, which is fully consistent with current interpretations of the HAp growing process. The structures calculated for the adsorption of pyrophosphate and triphosphate evidence that this process is easier for the latter than for the former. Thus, the adsorption of pyrophosphate is severely limited by the surface geometry while the flexibility of triphosphate allows transforming repulsive electrostatic interactions into molecular strain. On the other hand, calculations predict that the trisphosphonate only adsorbs onto the (001) surface of HAp. Theoretical predictions are fully consistent with experimental data. Thus, comparison of DFT results and spectroscopic data suggests that the experimental conditions used to prepare HAp particles promote the predominance of the (100) surface. Accordingly, experimental identification of the adsorption of trisphosphonate onto such crystalline particles is unclear while the adsorption of pyrophosphate and triphosphate is clearly observed.

The RPAR peptide, a prototype C-end Rule (CendR) sequence that binds to neuropilin-1 (NRP-1), has potential therapeutic uses as internalization trigger in anticancer nanodevices. Recently, the functionalization of gold nanoparticles with CendR peptides has been proved to be a successful strategy to target the NRP-1 receptor in prostate cancer cells. In this work, we investigate the influence of two gold surface facets, (100) and (111), on the conformational preferences of RPAR using molecular dynamics simulations. Both clustering and conformational analyses revealed that the peptide backbone becomes very rigid upon adsorption onto gold, which is a very fast and favored process, the only flexibility being attributed to the side chains of the two Arg residues. Thus, the different components of RPAR tend to adopt an elongated shape, which is characterized by the pseudo-extended conformation of both the backbone and the Arg side chains. This conformation is very different from the already known bioactive conformation, indicating that RPAR is drastically affected by the substrate. Interestingly, the preferred conformations of the peptide adsorbed onto gold facets are not stabilized by salt bridges and/or specific intramolecular hydrogen bonds, which represent an important difference with respect to the conformations found in other environments (e.g. the peptide in solution and interacting with NRP-1 receptor). However, the conformational changes induced by the substrate are not detrimental for the use of gold nanoparticles as appropriate vehicles for the transport and targeted delivery of the RPAR. Thus, once their high affinity for the NRP-1 receptor induces the targeted delivery of the elongated peptide molecules from the gold nanoparticles, the lack of intramolecular interactions facilitates their evolution towards the bioactive conformation, increasing the therapeutic efficacy of the peptide.

Tryptophan 7-halogenase catalyzes chlorination of free tryptophan to 7-chlorotryptophan, which is the first step in the antibiotic pyrrolnitrin biosynthesis. Many biologically and pharmaceutically active natural products contain chlorine and thus, an understanding of the mechanism of its introduction into organic molecules is important. Whilst enzyme-catalyzed chlorination is accomplished with ease, it remains a difficult task for the chemists. Therefore, utilizing enzymes in the synthesis of chlorinated organic compounds is important, and providing atomistic mechanistic insights about the reaction mechanism of tryptophan 7-halogenase is vital and timely. In this work, we examined a mechanism for the reaction of tryptophan chlorination, performed by tryptophan 7-halogenase, by calculating potential energy and free energy surfaces using two different Combined Quantum Mechanical/Molecular Mechanical (QM/MM) methods both employing Density Functional Theory (DFT) for the QM region. Both computational strategies agree on the nature of the rate-limiting step and provided close results for the reaction barriers of the two reaction steps. The calculations for both the potential energy and the free energy profiles showed very similar geometric features and hydrogen bonding interactions for the characterized stationary points.

Poly(3,4-ethylenedioxythiophene) (PEDOT) nanoparticles are loaded with curcumin and piperine by in situ emulsion polymerization using dodecyl benzene sulfonic acid both as a stabilizer and a doping agent. The loaded drugs affect the morphology, size, and colloidal stability of the nanoparticles. Furthermore, kinetics studies of nonstimulated drug release have evidenced that polymer···drug interactions are stronger for curcumin than for piperine. This observation suggests that drug delivery systems based on combination of the former drug with PEDOT are much appropriated to show an externally tailored release profile. This is demonstrated by comparing the release profiles obtained in presence and absence of electrical stimulus. Results indicate that controlled and time-programmed release of curcumin is achieved in a physiological medium by applying a negative voltage of -1.25 V to loaded PEDOT nanoparticles.

Organic polymers are widely used as coatings and adhesives to metal surfaces, but aluminum is among the most difficult substrates because of rapid oxidative passivation of its surface. Poly(1,4-disubstituted 1,2,3-triazoles) made by copper-catalyzed azide–alkyne cycloaddition form strongly bonded interfaces with several metal substrates. In this work, a variety of alkyne and azide monomers were explored as precursors to anticorrosion coatings for a standard high-strength aluminum–copper alloy. Monomers of comparatively low valency (diazide and trialkyne) were found to act as superior barriers for electrolyte transfer to the aluminum surface. These materials showed excellent resistance to corrosive pitting due to the combination of three complementary properties: good formation of highly cross-linked films, as observed by Fourier transform infrared spectroscopy and differential scanning calorimetry; good adhesion to the aluminum alloy substrate, as shown by pull-off testing; and excellent impermeability, as demonstrated by electrochemical impedance spectroscopy.

A diphenylalanine (FF) amphiphile blocked at the C terminus with a benzyl ester (OBzl) and stabilized at the N terminus with a trifluoroacetate (TFA) anion was synthetized and characterized. Aggregation of peptide molecules was studied by considering a peptide solution in an organic solvent and adding pure water, a KCl solution, or another organic solvent as co-solvent. The choice of the organic solvent and co-solvent and the solvent/co-solvent ratio allowed the mixture to be tuned by modulating the polarity, the ionic strength, and the peptide concentration. Differences in the properties of the media used to dissolve the peptides resulted in the formation of different self-assembled microstructures (e.g. fibers, branched-like structures, plates, and spherulites). Furthermore, crystals of TFA⋅FF-OBzl were obtained from the aqueous peptide solutions for X-ray diffraction analysis. The results revealed a hydrophilic core constituted by carboxylate (from TFA), ester, and amide groups, and the core was found to be surrounded by a hydrophobic crown with ten aromatic rings. This segregated organization explains the assemblies observed in the different solvent mixtures as a function of the environmental polarity, ionic strength, and peptide concentration., The authors are thankful for support from MINECO and FEDER (MAT2015‐69367‐R, MAT2015‐69547‐R and CTQ2013‐40855‐R) and Gobierno de Aragón—Fondo Social Europeo (research group E40). Support for the research of C.A. was received through the prize “ICREA Academia” for excellence in research funded by the Generalitat de Catalunya.

Encapsulation of DNA into hydroxyapatite (HAp) has been investigated using a rational approach that involves computer simulation and experimental techniques. The temporal evolution of the radial distribution functions derived from atomistic molecular dynamics simulations of Ca2+, PO4 3− and OH−-containing aqueous solutions in the presence and absence of B-DNA has been used to conclude that the backbone of the double helix acts as a template for HAp growth. More specifically, results reveal the formation of calcium phosphate clusters at the first stages of the simulations, which subsequently reorganize to nucleate HAp. This effect is produced in the absence and, especially, presence, of DNA indicating that the biomolecules do not inhibit but even promote mineral growth. Furthermore, computer simulations suggest that the diffusion of the OH− anions through the inorganic solution is the limiting step for the nucleation of the biomineral. Nanocapsules and crystalline nanorods of HAp containing DNA molecules inside have been prepared by mixing solutions containing Ca2+ and PO4 3− ions with fish sperm DNA at high pH. The dimensions and morphology of such nanostructures have been examined by transmission electron microscopy, while the characterization of the biomineral has been focused on the identification of DNA inside HAp using infrared, X-ray photoelectron and UV-vis spectroscopies, as well as gel electrophoresis. The biominerals reported in this work are important for biomedical applications requiring the protection of DNA from aggressive environmental conditions

Symmetric ultracapacitors have been fabricated considering nanometric 3-layered films made of alternated layers of poly(3,4-ethylenedioxythiophene) (external and internal layers) and polypyrrole (intermediate layer) deposited on steel uncoated and coated with octanethiol self-assembled monolayer. The highest electrochemical and capacitance parameters (i.e. electroactivity, doping level, stored charge, specific capacitance, Coulomb efficiency, energy density and power density) correspond to the ultracapacitor derived from the assembly of 3-layered films deposited on pre-treated steel. Thus, the interface separating the octanethiol monolayer and the most internal layer of the 3-layered film produces a very favorable interaction, which promotes important electrochemical benefits similar to those found for the interfaces in conventional multilayered films. Moreover, the pre-treatment of the steel electrode enhances the roughness and porosity of the film deposited on it, transmitting this effect layer-by-layer. Structural and morphological characteristics, which have been characterized using scanning electron microscopy and atomic force microscopy, have been related with the electrochemical and capacitance properties of the ultracapacitors.

Bioinspired free-standing nanomembranes (FSNMs) for selective ion transport have been tailored by immobilizing the Omp2a β-barrel membrane protein inside nanoperforations created in flexible poly(lactic acid) (PLA) nanomembranes. Perforated PLA FSNMs have been prepared by spin-coating a 99:1 PLA:poly(vinyl alcohol) mixture, and through a phase segregation process nanofeatures with dimensions similar to the entire nanomembrane thickness (∼110 nm) were induced. These nanofeatures have subsequently been transformed into nanoperforations (diameter: ∼51 nm) by selective solvent etching. The protein confined inside the nanopores of PLA FSNMs preserves the β-barrel structure and organizes in ovoid aggregates. The transport properties of Na+, K+, and Ca2+ across non-perforated PLA, nanoperforated PLA, and Omp2a-filled nanoperforated PLA have been monitored by measuring the nanomembrane resistance with electrochemical impedance spectroscopy (EIS). The incorporation of nanoperforations enhances the transport of ions across PLA nanomembranes, whereas the functionality of immobilized Omp2a is essential to exhibit effects similar to those observed in biological nanomembranes. Indeed, Omp2a-filled nanoperforated PLA nanomembranes exhibit stronger affinity towards Na+ and Ca2+ ions than towards K+. In summary, this work provides a novel bioinspired strategy to develop mechanically stable and flexible FSNMs with channels for ion transport, which are precisely located inside artificial nanoperforations, thus holding great potential for applications in biofiltration and biosensing.

Progress in the chemical sciences has formed the world we live in, both on a macroscopic and on a nanoscopic scale. The last decade has witnessed the development of high performance materials that store charge in many ways: from solar cells to fuel cells, and from batteries to supercapacitor devices. One could argue that inorganic hybrid materials have played a central, starring role for the assembly of various electrochemical energy conversion systems. However, energy conversion systems fabricated from biopolymers has just emerged as a new prospect. Here, we summarize the main research results on the attractive use of biohydrogels for the fabrication of either conductive electrolytes or electrodes for battery science and technology. © 2016 The Royal Society of Chemistry., This work has been supported by MICINN and FEDER funds (MAT2015-69367-R) and by DFG (DI 1748/3-1). E. A. acknowledges the Ministry of Education, Culture and Sports of Spain for a research mobility grant (PRX14/00627). Support for the research of C. A. was received through the award “ICREA Academia” for excellence in research funded by the Generalitat de Catalunya. D. D. D. thanks the DFG for the Heisenberg professorship award.

Solid-state organic electrochemical supercapacitors (OESCs) have been fabricated using poly(3,4-ethylenedioxythiophene) (PEDOT) electrodes, a biohydrogel as electrolyte system, and polyaniline fibers as redox additive. The effectivity of sodium alginate, κ-carrageenan, chitosan and gelatin hydrogels as electrolytic media has been evaluated considering different criteria. Results indicate that κ-carrageenan-based hydrogel is the most suitable to perform as electrolyte due to the appropriate combination of properties: mechanical stability, ease of preparation, lack of water leaking, and good medium for the electrochemical response of PEDOT electrodes. Cyclic voltammetry and galvanostatic charge-discharge assays indicate that OESCs based on PEDOT electrodes and κ-carrageenan hydrogel as electrolyte exhibits a good supercapacitor response in terms of specific capacitance, cycling stability, small leakage current and low self-discharging tendency. On the basis of these good properties, four OESC devices were assembled in series and used to power a red LED, confirming that, in addition to advantageous characteristics (e.g. elimination of liquid leaking and enhancement of the device compactness), the designed biohydrogel-containing OESC exhibits potential for practical applications. On the other hand, preliminary assays have been performed loading the κ-carrageenan hydrogel with polyaniline nanofibers, which act as a redox additive. OESC devices prepared using such loaded biohydrogel have been found to be very promising and, therefore, future work is oriented towards the improvement of their design. © The Royal Society of Chemistry 2016., Authors are indebted to supports from MICINN and FEDER (MAT2012-34498), the University of Regensburg and the DFG (DI 1748/3-1). M. M. P.-M. thanks financial support through a FPI-UPC grant and a mobility DAAD Research Grant for Doctoral Candidates and Young Academics and Scientists (German Academic Exchange Service, DAAD). D. D. D. thanks the DFG for the Heisenberg Professorship Award. Support forthe research of C.A. was received through the prize ?ICREA Academia? for excellence in research funded by the Generalitat de Catalunya.

The structural consequences derived from the incorporation of either a methyl or a phenyl group at the α carbon of proline were recently investigated by quantum mechanical calculations (J Org Chem 2008, 73, 3418). In this work, the effect produced by contraction of the pyrrolidine ring on such α-substituted proline analogs has been explored using the same computational methods. Specifically, the intrinsic conformational preferences of the N-acetyl-N′-methylamide derivatives of the lower proline homolog L-azetidine-2-carboxylic acid (Aze), characterized by a four- instead of a five-membered ring, and its α-methyl (αMeAze) and α-phenyl (αPhAze) derivatives have been determined using quantum mechanical calculations and compared to those observed before for the proline counterparts. Replacement of the pyrrolidine ring by an azetidine cycle leads to a reduction of the conformational flexibility, especially for the Aze and αMeAze derivatives, which should be attributed to the quasi-planar geometry of the four-membered ring. Furthermore, the azetidine nitrogen shows pyramidalization, which depending on the peptide backbone conformation favors the formation of an attractive N–H···N interaction or alleviates a severe steric hindrance. Calculations on different environments predict that the tendency of αMeAze to adopt γ-turns is higher than that of unsubstituted Aze and α-methylproline, this feature being in full agreement with the experimental observations available., Contract grant sponsor: Ministerio de Ciencia e Innovacion; Contract grant number: CTQ2010-17436; Contract grant sponsors: Generalitat de Catalunya; Contract grant number: 2009 SGR 925; Contract grant sponsors: Gobierno de Aragon, Caja de Ahorros Inmaculada (Programa Europa); Contract grant sponsors: ‘‘ICREA Academia’’ (Generalitat de Catalunya)

A methodological study has been undertaken to assess the conformational profile of Neuromedin B (NMB) using classical molecular dynamics simulations (MD) and replica exchange molecular dynamics (REMD) simulations under generalized Born (GB) solvent conditions. Comparison of the results obtained from these simulations suggests that the peptide has a propensity to adopt both b-turns and a-helical conformations regardless of the simulation protocols used. However, the conformations adopted more helical character under REMD conditions and showed good agreement with the NMR supported structure reported in the literature.

The Bcl-2 family of proteins plays an important role in the intrinsic pathway of cell apoptosis. Overexpression of prosurvival members of this family of proteins is often associated with the development of many types of cancer and confers resistance against conventional therapeutic treatments. Accordingly, antagonism of its protective function has emerged as an encouraging anticancer strategy. In the present work, we use a pharmacophore for describing interaction between the BH3 domain of different pro-apoptotic members and the pro-survival protein Bcl-xL in order to identify new lead compounds. In the strategy followed in the present work, the harmacophore was derived from molecular dynamics studies of different Bcl-xL/BH3 complexes. This pharmacophore was later used as query for 3D database screening. Hits obtained from the search were computationally assessed, and a subset proposed for in vitro testing. Two of the 15 compounds assayed were found able to disrupt the Bcl-xL/Bak(BH3) complex with IC50 values in the lower micromolar range. Finally, docking studies were performed to explore the binding mode of these compounds to Bcl-xL for further modifications.

The electronic and structural properties of poly[N-(2-cyanoalkyl) pyrrole]s bearing short alkyl groups have been investigated using different methodologies. Specifically, the electronic properties of poly[N-(2- cyanoethyl)pyrrole], which was prepared by anodic polymerization, have been determined using both electrochemical and spectroscopic techniques. On the other hand, quantum mechanical calculations on model oligomers of poly- [N-(2-cyanomethyl)pyrrole] have been used to propose the conformation of an idealized polymer chain and to examine the influence of the conformation on the predicted electronic properties. Results indicated that the electronic properties of poly[N-(2-cyanoalkyl)pyrrole]s are not only influenced by effect of the conformation in the conjugation of the π-system but also by the existence of secondary oxidative processes on the pyrrole ring of selected repeating units. In this case, the combination of experimental information and quantum mechanical calculations proved to be essential to propose a structural model. This consists of a cross-linked structure formed by small branches of around nine repeating units in each one, with a carbonyl group at the last repeating unit of each branch.

The conformational, electrical, and optical intrinsic properties of L-phenylazophenylalanine (L-PAP), a nonproteinogenic photoresponsive amino acid used to modulate the binding affinity and activity of peptides and proteins, have been systematically investigated using quantum mechanical calculations, with special emphasis being put on the trans-to-cis isomerization of the azobenzene side group. Analyses of the conformational maps and the minimum-energy conformations, which were obtained using density functional theory calculations at the B3LYP/6-311þþG(d, p) level, indicate that the semiextended β is the most favored conformation for both the trans and cis isomers in the gas phase. However, water tends to stabilize the helical backbone arrangement, but only for the cis isomer since this is a sterically forbidden conformation for the trans one. On the other hand, time-dependent density functional theory calculations at the BMK/6-311þG(d,p) level indicate that the peptide backbone does not induce significant changes in the optical properties of the chromophore. This feature was evidenced by both the small dependence of the πfπ* and nfπ* transition wavelengths with the backbone dihedral anglesjandψand the resemblance between the transition wavelengths determined for L-PAP and free azobenzene. In contrast, the dipole moment has been identified as a key property for this photoresponsive amino acid because of its large dependence on both the peptide backbone and the isomerization state.

A new substituted polythiophene derivative bearing malonic acid, poly(2-thiophen-3-yl-malonic acid), has been prepared and characterized using a strategy that combines both experimental and theoretical methodologies. The chemical structure of this material has been investigated using FTIR and (1)H NMR, and its molecular conformation has been determined using quantum mechanical calculations. Interestingly, the arrangement of the inter-ring dihedral angles was found to depend on the ionization degree of the material, that is, on the pH, which has been found completely soluble in aqueous base solution. Thus, the preferred anti-gauche conformation changes to syn-gauche when the negatively charged carboxylate groups transforms into neutral carboxylic acid. UV-vis experiments and quantum mechanical calculations on model systems with a head-to-tail regiochemistry showed that the lowest pi-pi* transition energy is 2.25 and 2.39 eV for the negatively charged and the neutral polymer, respectively. These values are slightly larger than those previously reported for other polythiophenes with bulky polar side groups. The polymer presents a good thermal stability with a decomposition temperature above 215 degrees C and an electrical conductivity of 10(-5) S/cm, which is characteristic of semiconductor materials. Scanning electron microscopy micrographs showed that, after doping, the surface of this material displays regular distribution pores with irregular sizes. This surface suggests that poly(2-thiophen-3-yl-malonic acid) is a candidate for potential applications such as selective membranes for electrodialysis, wastewater treatment, or ion-selective membranes for biomedical uses.

A new polythiophene derivative bearing a malonic acid dimethyl ester substituent attached to the 3-position of the repeat unit has been prepared by chemical oxidative-coupling polymerization. The chemical structure of poly(2-thiophen-3-yl-malonic acid dimethyl ester) has been analyzed by FTIR and 1H NMR spectroscopy and, additionally, the distribution of the head-to-tail and head-to-head diads arising from polymerization was found to be a 75–25%. The glass transition temperature identified for this polymer was 17.6 °C lower than that recently determined for a closely related polythiophene derivative, in which the ester substituent arose from acrylic acid rather than from malonic acid. On the other hand, the electrical conductivity of the new material, which was soluble in polar solvents but not in water, was higher than that typically found for poly(3-alkylthiophene) derivatives. Ab initio quantum mechanical calculations on simple model compounds were used to predict the regiochemistry of the polymer chain, which was in excellent agreement with the experimental observation, and the conformational preferences of both the inter-ring dihedral angle and the bulky side group. Interestingly, calculations predict that the inter-ring dihedral angles adopt a syn-gauche conformation rather than the anti-gauche arrangement typically found in substituted polythiophenes. Thus, in this case the former conformation reduces the strong repulsive interactions induced by the bulky substituent. The lowest π–π* transition energy derived from calculations on an idealized molecular model is in agreement with the experimental estimation determined using UV–vis spectroscopy. This electronic property is significantly higher for poly(2-thiophen-3-yl-malonic acid dimethyl ester) than for other substituted polythiophene derivatives, which is consequence of the geometrical distortions induced by bulky side group.

Ab initio quantum mechanical calculations at the MP2 level were used for an extensive study concerning the stability of hydrogen-bonded complexes formed by pyrrole and thiophene, which are the most common building blocks of conducting polymers, and DNA bases. Results indicated that very stable complexes were formed with pyrrole, which shows a clear tendency to form specific hydrogen-bonding interactions with nucleic acid bases. Furthermore, the strength of such interactions depends significantly on the base, growing in the following order: thymine < adenine ˜ cytosine < guanine. On the contrary, thiophene formed complexes stabilized by nonspecific interactions between the p-cloud of the ring and the N-H groups of the nucleic acid bases rather than specific hydrogen bonds. Overall, these results are fully consistent with experimental observations: polypyrrole is able not only to stabilize adducts with DNA but also to interact specifically, while the interactions of the latter with polythiophene and their derivatives are weaker and nonspecific. © 2008 American Chemical Society.

The swelling behaviour of poly(styrene-co-divinylbenzene), P(S-DVB), ion exchange resins in 1-butanol (BuOH) has been studied by means of atomistic classical molecular dynamics simulations (MD). The topological characteristics reported for the resin in the dry state, which exhibited complex internal loops (macropores), were considered for the starting models used to examine the swelling induced by BuOH contents ranging from 10% to 50% w/w. Experimental measurements using a laser diffraction particle size analyzer indicate that swelling causes a volume variation with respect to the dry resin of 21%. According to MD simulations, such a volume increment corresponds to a BuOH absorption of 31-32% w/w, which is in excellent agreement with the indirect experimental estimation (i.e. 31% w/w). Simulations reveal that, independently of the content of BuOH, the density of the swelled resin is higher than that of the dry resin, evidencing that the alcohol provokes important structural changes in the polymeric matrix. Thus, BuOH molecules cause a collapse of the resin macropores when the content of alcohol is

Among the various types of α-peptide folding motifs, δ-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the δ-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined., C.C. is grateful to Ministerio de Economía yCompetitividad (grant CTQ2013-40855-R) and Gobierno de Aragón-FSE (research group E40), and C.A. acknowledges support from MICINN-FEDER funds (MAT2012-34498) and CESCA.

Lactide and trimethylene carbonate copolymers were successfully grafted with polyethylene glycol via previous functionalization with maleic anhydride and using N,N'-diisopropylcarbodiimide as condensing agent. Maleinization led to moderate polymer degradation. Specifically, the weight average molecular weight decreased from 36,200 to 30,200 g/mol for the copolymer having 20 mol% of trimethylene carbonate units. Copolymers were characterized by differential scanning calorimetry, thermogravimetry and X-ray diffraction. Morphology of spherulites and lamellar crystals was evaluated with optical and atomic force microscopies, respectively. The studied copolymers were able to crystallize despite the randomness caused by the trimethylene carbonate units and the lateral groups. Contact angle measurements indicated that PEG grafted copolymers were more hydrophilic than parent copolymers. This feature justified that enzymatic degradation in lipase medium and proliferation of both epithelial-like and fibroblast-like cells were enhanced. Grafted copolymers were appropriate to prepare regular drug loaded microspheres by the oil-in-water emulsion method. Triclosan release from loaded microspheres was evaluated in two media. © 2014 Elsevier B.V.

The manifold applications of ionene-based materials such as hydrogels in daily life, biomedical sciences, and industrial processes are a consequence of their unique physical and chemical properties, which are governed by a judicious balance between multiple non-covalent interactions. However, one of the most critical aspects identified for a broader use of different polyelectrolytes is the need of raising their gelation efficiency. This work focuses on surfactant-free ionene polymers 1-3 containing DABCO and N,N-(x-phenylene) dibenzamide (x = ortho-/meta-/para-) linkages as model systems to develop a combined computational-experimental approach to improve the hydrogelation through a better understanding of the gelation mechanism. Molecular dynamics simulations of isomeric ionenes 1-3 with explicit water molecules point out remarkable differences in the assembly of the polymeric chains in each case. Interchain regions with high degree of hydration (i.e., polymer·· ·water interactions) and zones dominated by polymer·· ·polymer interactions are evident in the case of ortho- (1) and meta- (2) isomeric ionenes, whereas domains controlled by polymer··· polymer interactions are practically inexistent in 3. In excellent agreement, ortho-ionene 1 provides experimentally the best hydrogels with unique features such as thixotropic behavior and dispersion ability for single-walles carbon nanotubes. © 2014 WILEY-VCH Verlag GmbH & Co. KGa, Weinheim., Financial support from Universität Regensburg (Anschubfi nanzierung von Wissenschaftlichen Projekten-2011), Ministerio de Ciencia e Innovación – FEDER (projects CTQ2010–17436 and MAT2012–34498), Gobierno de Aragón – FSE (research group E40), and the DIUE of the Generalitat de Catalunya (contracts 2009SGR 925 and XRQTC) is gratefully acknowledged. Support for the research of C.A. was received through the prize “ICREA Academia” for excellence in research funded by the Generalitat de Catalunya. D.D.D. thanks DFG for the Heisenberg Professorship Award.

The interaction of molecular oxygen with the Cu(1 0 0) surface has been studied by using both Hartree–Fock and density functional methods in the framework of the cluster model approach. In this study, we have used the Cu8(6,2) cluster in order to simulate the O2 molecular adsorption on different high symmetry chemisorption sites (top–top, bridge–fourfold, bridge–top, fourfold–fourfold) on the Cu(1 0 0) surface. High level non-local density functional (NLSD) computations indicate that the more stable chemisorption site is the bridge–bridge followed by the top–top, bridge–top and bridge–fourfold ones. The calculated 1s O XPS shifts are in good agreement with the experimental indications.

The sensing response of 15-crown-5-ether functionalized polythiophene to Li+, Na+, and K+ has been investigated at the atomistic level using molecular dynamics simulations. The stability associated with all the identified binding sites has been corroborated by quantum mechanical calculations. Although the cavity of the macrocycle is not the most visited binding site, such receptor is responsible of the selective sensing response of this polythiophene derivative. PF6– counterions reduce the mobility of the alkaline cations, which do not occupy the crown ether cavity of consecutive repeating units due to electrostatic repulsions. Furthermore, the relative entropy for the “free state → bound state” has been estimated using a procedure based on the covariance matrix atom-positional fluctuations. Evaluation of the entropic contributions allow us to complete the thermodynamics scenario of binding process, which was recently initiated by calculating the enthalpies at quantum mechanical level [ Chem. Eur. J. 2009, 15, 4676]. Results indicate an entropycally driven binding preference.

The mineralization of acidic aqueous solutions of the herbicide desmetryne has been studied by electrochemical advanced oxidation processes (EAOPs) such as anodic oxidation with electrogenerated H(2)O(2) (AO-H(2)O(2)), electro-Fenton (EF) and photoelectro-Fenton (PEF) with UVA light. Electrolyses were conducted in an open and cylindrical cell with a boron-doped diamond (BDD) anode and an O(2)-diffusion cathode for H(2)O(2) generation. The main oxidizing species are ()OH radicals formed at the BDD surface in all treatments and in the bulk from Fenton's reaction between added Fe(2+) and electrogenerated H(2)O(2) in EF and PEF. A poor mineralization was attained using AO-H(2)O(2) by the slow oxidation of persistent by-products with ()OH at the BDD surface. The synergistic action of ()OH in the bulk enhanced the degradation rate in EF, although almost total mineralization was only achieved in PEF due to the additional ()OH generation and photolysis of intermediates by UVA irradiation. The effect of current, pH and herbicide concentration on the mineralization degree and mineralization current efficiency of each EAOP was examined. Desmetryne decay always followed a pseudo first-order kinetics, being more rapidly destroyed in the sequence AO-H(2)O(2)

The prediction capabilities of atomistic simulations of peptides are hampered by different difficulties, including the reliability of force fields, the treatment of the solvent or the adequate sampling of the conformational space. In this work, we have studied the conformational profile of the 10 residue miniprotein CLN025 known to exhibit a β-hairpin in its native state to understand the limitations of implicit methods to describe solvent effects and how these may be compensated by using different force fields. For this purpose, we carried out a thorough sampling of the conformational space of CLN025 in explicit solvent using the replica exchange molecular dynamics method as a sampling technique and compared the results with simulations of the system modeled using the analytical linearized Poisson-Boltzmann (ALPB) method with three different AMBER force fields: parm94, parm96, and parm99SB. The results show the peptide to exhibit a funnel-like free energy landscape with two minima in explicit solvent. In contrast, the higher minimum nearly disappears from the energy surface when the system is studied with an implicit representation of the solvent. Moreover, the different force fields used in combination with the ALPB method do not describe the system in the same manner. The results of this work suggest that the balance between intra- and intermolecular interactions is the cause of the differences between implicit and explicit solvent simulations in this system, stressing the role of the environment to define properly the conformational profile of a peptide in solution.

A sensitive nanocalorimetric technology based on microcantilever sensors is presented. The tech- nology, which combines very short response times with very small sample consumption, uses the bimetallic effect to detect thermal transitions. Specifically, abrupt variations in the Young’s modu- lus and the thermal expansion coefficient produced by temperature changes have been employed to detect thermodynamic transitions. The technology has been used to determine the glass transition of poly(3-thiophene methyl acetate), a soluble semiconducting polymer with different nanotechno- logical applications. The glass transition temperature determined using microcantilevers coated with ultra-thin films of mass = 10 − 13 gis5.2 ◦ C higher than that obtained using a conventional differential scanning calorimeter for bulk powder samples of mass = 5 × 10 − 3 g. Atomistic molecular dynamics simulations on models that represent the bulk powder and the ultra-thin films have been carried out to provide understanding and rationalization of this feature. Simulations indicate that the film-air in- terface plays a crucial role in films with very small thickness, affecting both the organization of the molecular chains and the response of the molecules against the temperature.

The structure and stability of the nanotube obtained by assembling peptide-polymer conjugates consisting of two poly(n-butyl acrylate) blocks coupled to the cyclic (D-alt-L)-octapeptide cyc[(L-Gln-D-Ala-L-Lys-D-Ala)(2)], have been investigated at the molecular level using atomistic molecular dynamics simulations. The effect of the wrapping polymer shells in the tube-like core, which consists of stacked beta-sheet cyclopeptides, has been examined by simulating assemblies of both unsubstituted cyclopeptides, and conjugates in chloroform and N,N-dimethylformamide solutions. Furthermore, the influence of the environment has been investigated by comparing conjugate assemblies in solution with those deposited on mica. In addition, nanotubes stabilized by beta-sheet-like hydrogen bonds between both parallel and antiparallel oriented cyclopeptides have been considered in all cases. The results, which have been analysed in terms of energy contributions, partial radial distribution functions, inter-subunit distances, shape of the cyclopeptide ring, internal van der Waals diameters, and both height and width of the nanostructures deposited on mica, have provided important microscopic insights. For example, analysis of both the energy terms and the structural dynamics obtained for the different assemblies indicate that the mica surface interacts more favourably with the parallel assembly than with the antiparallel ones, whereas the only configuration that is structurally stable in solution is the latter. Furthermore, adsorption onto the solid substrate produces a small deformation of the cylindrical molecular system

The conformational preferences of the Arg-GlE-Asp sequence, where GlE is an engineered amino acid bearing a 3,4-ethylenedioxythiophene (EDOT) ring as side group, have been determined combining density functional theory calculations with a well-established conformational search strategy. Although the Arg-GlE-Asp sequence was designed to prepare a conducting polymer–peptide conjugate with excellent electrochemical and bioadhesive properties, the behavior of such hybrid material as adhesive biointerface is improvable. Results obtained in this work prove that the bioactive characteristics of the parent Arg-Gly-Asp sequence become unstable in Arg-GlE-Asp because of both the steric hindrance caused by the EDOT side group and the repulsive interactions between the oxygen atoms belonging to the backbone amide groups and the EDOT side group. Detailed analyses of the conformational preferences identified in this work have been used to re-engineer the Arg-GlE-Asp sequence for the future development of a new electroactive conjugate with improved bioadhesive properties. The preparation of this new conjugate is in progress.

The use of modified black wattle tannin as an antifouling pigment is reported in this work. A mixture of tannin adsorbed in activated carbon (soluble fraction of tannin) and low soluble fraction of tannin was used as an antifouling pigment. The soluble rosin resin was used as a paint matrix. C-13 NMR analysis confirm the modification of black wattle tannin through the cleavage of tannin interflavonoid bonds. FTIR spectra indicate the presence of tannin in the formulated antifouling coating even after 7 months of its exposure in a marine environment. Water contact angle analysis shows the hydrophilic characteristic of the tannin antifouling coating surface. Immersion tests at Badalona Port in the Mediterranean Sea shows the high antifouling efficiency of the TAN coating, comparable to commercial paint, until 7 months. The use of a natural black wattle tannin, without its complexation with metals, can eliminate the release of metals and other toxic biocides to the marine environment. (C) 2014 Elsevier B.V. All rights reserved.

The self-assembly of a peptide based on a sequence from the amyloid peptide but incorporating the nonnatural amino acid -2-thienylalanine (2-Thi) has been investigated in aqueous and methanol solutions. The peptide AAKLVFF was used as a design motif, replacing the phenylalanine residues (F) with 2-Thi units to yield (2-Thi)(2-Thi)VLKAA. The 2-Thi residues are expected to confer interesting electronic properties due to charge delocalization and π-stacking. The peptide is shown to form -sheet-rich amyloid fibrils with a twisted morphology, in both water and methanol solutions at sufficiently high concentration. The formation of a self-assembling hydrogel is observed at high concentration. Detailed molecular modeling using molecular dynamics methods was performed using NOE constraints provided by 2D-NMR experiments. The conformational and charge properties of 2-Thi were modeled using quantum mechanical methods, and found to be similar to those previously reported for the -3-thienylalanine analogue. The molecular dynamics simulations reveal well-defined folded structures (turn-like) in dilute aqueous solution, driven by self-assembly of the hydrophobic aromatic units, with charged lysine groups exposed to water.

The molecular and electronic structure of all-thiophene dendrimers in both the neutral and oxidized states have been investigated performing quantum mechanical calculations on systems of up to 30 rings. Results evidenced that the repulsive steric interactions between the neighboring thiophene rings induce significant distortions from the planarity independently of the electronic state. On the other hand, the ionization potential per thiophene ring and the lowest π-π* transition energy decreases with the inverse of the longest a-conjugated chain of the dendrimer, i.e. when the generation increases. The lowest π-π* transition energy predicted for an infinite generation dendrimer is 2.08 eV indicating that these materials are potential candidates to be used in optoelectronics. Additionally, Quantum mechanics/molecular mechanics calculations have been performed considering both the sandwich and T-shaped supramolecular arrangements. Results showed not only the stability of these aggregates but also the significant influence of the intermolecular electronic delocalization in the electronic properties of these materials.

Structural parameters for chemisorption of atomic carbon above a Si(100) surface have been obtained through a Si 35 H 32 cluster model and a MINDO/3 hamiltonian. The most stable position has been found to be the bridge one when considering the unrelaxed surface. The stability increases about 14 kcal/mol when relaxation of the surface is allowed. Further research has been carried out using a reduced cluster model (Si 9 H 12 ) at the ab initio Hartree-Fock level of calculation. Results confirm the increase of stability of the relaxed system. At this level, the binding energy is 90 kcal/mol for the unrelaxed surface and the stabilization when the surface is relaxed is of about 20% with respect to the non-relaxed surface.

A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hydrogen bonds in structural and dynamical properties has also been performed. The continuous and interrupted methodologies to compute hydrogen bonding lifetimes have been applied. The interrupted hydrogen bond lifetimes values are consistent with the diffusion and viscosity coefficients. The activation energies of the self-diffusion, the reorientational motions, and the hydrogen bonding lifetimes are coincident.

Amorphous polyaniline emeraldine base has been investigated using atomistic classical molecular dynamics simulations. Initially, different sets of force-field parameters, which differ in the atomic charges and/or the van der Waals parameters, were tested. The experimental density of polyaniline was satisfactorily reproduced using the following combination: (i) equilibrium bond lengths, equilibrium bond angles, and electrostatic charges derived from quantum mechanical calculations and (ii) van der Waals parameters extrapolated from GROMOS for all atoms with the exception of the CH pseudoparticles of the phenyl ring, which were taken from an anisotropic united atom potential. Next, this force field was used to investigate the structure of the polymer in the amorphous state, the trajectories performed for this purpose allowing accumulation of 750 ns. Analyses of the energies evidence that the interactions between one repeating unit containing an amine nitrogen atom and another unit with an imine nitrogen are favored with respect to those between two identical repeating units. This conclusion is also supported by quantum mechanical and quantum mechanical/molecular mechanics calculations. On the other hand, the partial radial distribution functions indicate that this material only exhibits short-range intramolecular correlation, which is in excellent agreement with experimental evidence.