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

Postprint (published version

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

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

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

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

Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly

We describe the 3D supramolecular structure of Fmoc–RGDS fibrils, where Fmoc and RGDS refer to the hydrophobic N-(fluorenyl-9-methoxycarbonyl) group and the hydrophilic Arg-Gly-Asp-Ser peptide sequence, respectively. For this purpose, we performed atomistic all-atom molecular dynamics simulations of a wide variety of packing modes derived from both parallel and antiparallel ß-sheet configurations. The proposed model, which closely resembles the cross-ß core structure of amyloids, is stabilized by p–p stacking interactions between hydrophobic Fmoc groups. More specifically, in this organization, the Fmoc-groups of ß-strands belonging to the same ß-sheet form columns of p-stacked aromatic rings arranged in a parallel fashion. Eight of such columns pack laterally forming a compact and dense hydrophobic core, in which two central columns are surrounded by three adjacent columns on each side. In addition to such Fmoc¿Fmoc interactions, the hierarchical assembly of the constituent ß-strands involves a rich variety of intra- and inter-strand interactions. Accordingly, hydrogen bonding, salt bridges and p–p stacking interactions coexist in the highly ordered packing network proposed for the Fmoc–RGDS amphiphile. Quantum mechanical calculations, which have been performed to quantify the above referred interactions, confirm the decisive role played by the p–p stacking interactions between the rings of the Fmoc groups, even though both inter-strand and intra-strand hydrogen bonds and salt bridges also play a non-negligible role. Overall, these results provide a solid reference to complement the available experimental data, which are not precise enough to determine the fibril structure, and reconcile previous independent observations.Peer ReviewedPostprint (published version

Aplicación Móvil bajo la plataforma Android para informe de Calificaciones y resultados de admisión de los Estudiantes de la Universidad Nacional Agraria, primer semestre año 2014

En el presente trabajo se abordó el análisis y diseño de una Aplicación móvil, que permitirá a los estudiantes de primer ingreso de la Universidad Nacional Agraria consultar sus resultados de admisión. A su vez accederá a las calificaciones de asignaturas semestrales de los estudiantes activos. Seguidamente se muestra los objetivos planteados y la documentación necesaria para la realización de la aplicación. La recopilación de la información se desarrolló, realizando visitas, encuestas personales y telefónicas a los estudiantes y personal de UNA. Esto permitió la obtención de datos que identifican las necesidades y expectativas de los usuarios finales de la aplicación móvil. Posteriormente se muestra cada una de las fases de la evolución del proyecto, así como los requerimientos necesarios que hicieron posible la realización de dicha aplicación móvil; se realizó un estudio de factibilidad con los requerimientos mínimos de la adquisición de los equipos para su desempeño.Para finalizar se detalla las conclusiones y recomendaciones de la aplicación en su etapa final

Nanoperforations in poly(lactic acid) free-standing nanomembranes to promote interactions with cell filopodia

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.Peer ReviewedPostprint (author's final draft

Marine-friendly antifouling coating based on the use of a fatty acid derivative as a pigment

This study was devoted to examining the application of copper dodecanoate as a non-contaminant antifouling pigment due to its low copper content and fatty acid nature. For this purpose, antifouling paints with mono-component epoxy resin and rosin matrixes were formulated, and their antifouling efficiency was evaluated. Before its incorporation into the different formulations, the synthesized pigment was characterized. Immersion tests in a marine environment were carried out for 12 months to evaluate the antifouling efficiency of the developed paints; the results were compared with those from a commercial paint. The antifouling efficiency of the new epoxy formulation was found to be considerably higher than that of the rosin formulation and very similar to that of the commercial paint. Most importantly, the release of copper from the epoxy paint formulated with copper dodecanoate was 73.5% lower than that of the commercial paint, suggesting prolonged activity of the developed paint.Peer ReviewedPostprint (published version

Estrategias para la parametrización de campos de fuerzas a partir de cálculos mecanocuánticos

Tesi de Llicenciatura per a la obtenció del Grau de Química. Universitat de Barcelona. Directors: Orozco López, Modesto i Franco Fernández, Rafael. Any: 1990