PepMat 2016: The second conference on peptide-based materials for biomedicine and nanotechnology

Postprint (published version

Massive quantum regions for simulations on bio-nanomaterials: synthetic ferritin nanocages

QM/MM molecular dynamics simulations on the 4His-DC* protein cage have been performed using multiple active zones (up to 86 quantum regions). The regulation and nanocage stability exerted by the divalent transitionmetal ions in the monomer-to-cage conversion have been understood by comparing high level quantum trajectories obtained using Cu2+ and Ni2+ coordination ions.Peer ReviewedPostprint (published version

DNA - Conducting polymer complexes: A computational study of the hydrogen bond between building blocks

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.Peer ReviewedPostprint (author's final draft

Solvent effects on the properties of hyperbranched polythiophenes

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.Peer ReviewedPostprint (author's final draft

Nanophase-segregation in the dielectric layer enhances the charge storage capacity of polymeric electrochemical supercapacitors

Properties related with the charge storage capacity have been evaluated for three-layered films made with two sheets of poly(3,4-ethylenedioxythiophene) separated by a sheet of poly(N-methylpyrrole) or poly(3,4-ethylenedioxythiophene-co-N-methylpyrrole) (3l-PEDOT/PNMPy or 3l-PEDOT/P(EDOT-co-NMPy), respectively). The most distinctive trend of the copolymer, which shows electrochemical properties intermediate between those of the two homopolymers, is the formation of a biphasic structure, EDOT- and NMPy-rich blocks organizing separately. The ability to exchange charge reversibly is higher for 3l-PEDOT/P(EDOT-co-NMPy) than for 3l-PEDOT/PNMPy, the electroactivity and electrostability of such two 3-layered films being significantly better than that of single-layered PEDOT. Advantages of 3l-PEDOT/P(EDOT-co-NMPy) are mainly based on the nanophase-segregated structure of the copolymer. Thus, the intermediate layer can be considered as random disposition of ultrathin dielectrics having nanometric length and width. In terms of charge storage, the intermediate layer of 3l-PEDOT/P(EDOT-co-NMPy) can be viewed as a thin reservoir filled of heterogeneously distributed nanometric supercapacitors that are connected in series among them and in parallel to the PEDOT layers. The superiority of 3l-PEDOT/P(EDOT-co-NMPy) as organic electrochemical supercapacitor compared to other 3-layered systems, has been proved by powering a red LED bulb.Peer ReviewedPostprint (author's final draft

Soluble polythiophenes as anticorrosive additives for marine epoxy paints

This study compares the resistance against corrosion of a marine epoxy primer modified with Zn-3(PO4)(2) (10 wt%) or a small concentration (0.3 wt%) of conducting polymer (CP) as inorganic or organic anticorrosive pigment, respectively. More specifically, the behavior of three different CPs has been evaluated: polyaniline (PAni) emeraldine base, poly(3-thiophen-3-yl-acrylic acid methyl ester) and poly(2-thiophen-3-yl-malonic acid dimethyl ester), the latter two being soluble polythiophene (PTh) derivatives bearing carboxylate side groups. In a first stage, the structural, thermal, and mechanical properties of all the modified epoxy coatings were characterized using infrared spectroscopy, thermogravimetric analyses and stress-strain assays, respectively. After this, accelerated corrosion assays have evidenced that the degree of protection imparted by a small concentration of PAni is higher than that obtained using 10wt% of Zn-3(PO4)(2). Indeed, PAni has been found to be more effective as anticorrosive additive than the two PTh derivatives. This fact has been attributed to the electroactivity of the former, which is higher than that of the latter. Thus, the ability to store charge has been proposed to be also responsible of protection against corrosion imparted by organic additives, based on CPs.Peer ReviewedPostprint (author’s final draft

Properties of Cu nanoparticles-poly(N-methylpyrrole) composites

© 2014 Society of Plastics Engineers. Spherical copper nanoparticles (Cu-NPs) have been immobilized on the compact surface of potentiostatically generated poly(N-methylpyrrole) (PNMPy) films by applying a reduction potential of -0.60 V to a deionized water solution of CuCl2. Although the number density of Cu-NPs obtained using this procedure is not high (4·106 cm-2), the average diameter is relatively high (?50 nm). The surface topology and roughness of films with Cu-NPs-PNMPy are intermediate between those obtained for as prepared PNMPy and reduced PNMPy. Analysis of the electrochemical properties indicates that Cu-NPs promote the electroactivity of the PNMPy, this effect being more evident for composited made with the thinnest PNMPy films. In opposition, the electrostability and electrical conductivity are not enhanced by deposited Cu-NPs. Similar findings are obtained for bilayered PNMPy-Cu-NPs-PNMPy films. POLYM. COMPOS., 37:594-601, 2016.Peer ReviewedPreprin

Improving the fabrication of all-polythiophene supercapacitors

The influence of the preparation method in the properties of poly(3,4-ethylenedioxythiophene) (PEDOT) electrodes used to manufacture organic energy storage devices, as for example supercapacitors, have been examined by considering a reduction of both monomer and supporting electrolyte concentrations during the anodic polymerization reaction. Thus, the excellent electrochemical properties of PEDOT films prepared using quiescent solutions have been preserved by applying controlled agitation to the polymerization process, even though the concentration of monomer and supporting electrolyte were reduced 5 and 2 times, respectively. For example, the charge stored for reversible exchange in a redox process, the electrochemical stability and the current productivity of films achieved using quiescent solutions have been preserved using a dynamic reaction medium in which the concentrations of monomer and supporting electrolyte are several times lower. The excellent properties of PEDOT electrodes prepared using optimized dynamic conditions have also been proved by constructing a symmetric supercapacitor. This energy storage device, which has been used as power source for a LED bulb, is rechargeable and exhibits higher charge-discharge capacities than supercapacitors prepared with electrodes derived from quiescent solutions. In addition of bring an efficacious procedure for preparing cost-effective PEDOT films with excellent properties, the proposed dynamic conditions reduce the environmental hazards of depleted reaction media.Peer ReviewedPostprint (author's final draft

Electrodeposición de composites de poli(n-metilpirrol) con nanopartículas de Cu

Nanopartículas esféricas (NPs-Cu) se han inmovilizado en la superficie compacta de películas de poly(N-metilpirrol) (PNMPy) generadas potenciostáticamente por aplicación de un potencial de reducción de -0,60 V a una solución acuosa de CuCl2. Aunque la densidad numérica de NPs-Cu obtenidas usando este procedimiento no es alta (4•106 cm-2), el diámetro promedio es relativamente alto (~50 nm. La topología superficial y rugosidad de los films de Cu-NPs-PNMPy son intermedias entre aquellas obtenidas para el PNMPy y el PNMPy reducido. Análisis de las propiedades electroquímicas indican que las NPs-Cu promueven la electroactividad del PNMPy, este efecto es más evidente para el compuesto obtenido con los films de PNMPy más finos. Por el contrario, la electroestabilidad y conductividad eléctrica no se ha mejorado por deposición de NPs-Cu. Hallazgos similares se han obtenido para films bicapa PNMpy-Cu-NPs-PNMPy.Peer Reviewe

Study on the control of porosity in films of polythiophene derivatives

Conducting polymers typically exhibit different oxidation states, which are easily interchangeable among them by means of the application of an electrical potential. In this work, we present a theoretical and experimental study to regulate the pore size of poly(3,4-ethylenedioxythiophene) (PEDOT) films doped with ClO4- ions by controlling their oxidation state. More specifically, different bulk and surface PEDOT models have been evaluated applying 2D- and 3-D periodic boundary conditions to density functional theory calculations. In highly oxidized PEDOT films, calculations predict that the incorporation of dopant ions increases the separation between neighboring chains, causing a structural re-organization. Thus, the calculated average pore size, which has been modeled as a structural defect in 2D surface models, increases by 15.1%. This increment is consistent with experimental measures of the nanopore size in PEDOT films with enhanced porosity, which reflect a difference of 25.2% between the oxidized and reduced forms. This superficial phenomenon could easily be used to retain and release controlled drugs through the application of different electric potentialsPeer ReviewedPostprint (author's final draft