http://hdl.handle.net/2117/3469 Wed, 22 May 2013 18:57:02 GMT 2013-05-22T18:57:02Z webmaster.bupc@upc.edu Universitat Politècnica de Catalunya. Servei de Biblioteques i Documentació no http://hdl.handle.net/2117/19027 Title: Journal of Structural Biology Authors: Zanuy Gomara, David; Kotla, Rohith; Nussinov, Ruth; Teesalu, Tambet; Sugahara, Kazuki N.; Alemán Llansó, Carlos; Haspel, Nurit Abstract: Neuropilin-1 (NRP-1) is a hub receptor that plays an essential role in angiogenesis and vascular perme- ability. It is over-expres sed in the new blood vessels grown by tumor cells and is a target for anti-tumor treatment s. Peptides that expose the consensus sequence R/K/ XX R/K at the C-terminus ( C-end rule or CendR peptides) bind to NRP-1 and are internalized into the cell. We used peptide phage display binding assays and molecular dynamics (MD) simulations to study the potential role of the central residues of CendR peptides in binding and activa tion of the NRP-1 receptor. The high stability of RPAR–receptor domain complex stems from the formation of a characteristic pattern of three hydrogen bonds between the peptide C-terminus and the residues in the NRP-1 loop III. Any changes in the peptide structure that fail to preserve this triad result in a less-stable complex. We performed a systematic study of R XX R mutants, where X = A/D/S/R/P, in order to test the effect of replacement of A or P on the binding capabil- ities. Our results, both experimental and computational, show that RRAR, RDAR, RPDR, RPRR and RPPR are capable of binding NRP-1. However, only RPPR and RPRR segments form an optimal organization around loop III with low potential energy. In other analogs, the absence of these stabilizing interactions always results in higher potential energy of the complexes. The binding of RPAR analogs does not guarantee receptor activation; only stable complexes that are properly stabilized via loop III appear able to trigger NRP-1 activati on Mon, 29 Apr 2013 08:13:25 GMT http://hdl.handle.net/2117/19027 2013-04-29T08:13:25Z Zanuy Gomara, David; Kotla, Rohith; Nussinov, Ruth; Teesalu, Tambet; Sugahara, Kazuki N.; Alemán Llansó, Carlos; Haspel, Nurit no Neuropilin-1 (NRP-1) is a hub receptor that plays an essential role in angiogenesis and vascular perme- ability. It is over-expres sed in the new blood vessels grown by tumor cells and is a target for anti-tumor treatment s. Peptides that expose the consensus sequence R/K/ XX R/K at the C-terminus ( C-end rule or CendR peptides) bind to NRP-1 and are internalized into the cell. We used peptide phage display binding assays and molecular dynamics (MD) simulations to study the potential role of the central residues of CendR peptides in binding and activa tion of the NRP-1 receptor. The high stability of RPAR–receptor domain complex stems from the formation of a characteristic pattern of three hydrogen bonds between the peptide C-terminus and the residues in the NRP-1 loop III. Any changes in the peptide structure that fail to preserve this triad result in a less-stable complex. We performed a systematic study of R XX R mutants, where X = A/D/S/R/P, in order to test the effect of replacement of A or P on the binding capabil- ities. Our results, both experimental and computational, show that RRAR, RDAR, RPDR, RPRR and RPPR are capable of binding NRP-1. However, only RPPR and RPRR segments form an optimal organization around loop III with low potential energy. In other analogs, the absence of these stabilizing interactions always results in higher potential energy of the complexes. The binding of RPAR analogs does not guarantee receptor activation; only stable complexes that are properly stabilized via loop III appear able to trigger NRP-1 activati on http://hdl.handle.net/2117/17539 Title: Thermodynamic and stereochemical aspects of the polymerizability of glycolide and lactide Authors: Alemán Llansó, Carlos; Bertran Cànovas, Òscar; Houk, K.N.; Padias, Anne Buyle; Hall, H.K. Abstract: The ring-opening polymerizations of the dilactones glycolide and the S,S- and S,R-stereoisomers of lactide were studied using quantum mechanical methods. The ring strain and the conformational distribution of these cyclic monomers and of the polymers were calculated, and the effect of the medium on the polymerization was predicted, for both bulk and solution. The polymerizability of the three monomers in the gas phase, that is, nonpolar medium, is much greater than that of d-valerolactone or 1,4-dioxan-2-one. This difference vanishes in the polar medium chloroform, which is attributed to the fact that, while all of these monomers possess polar cis-lactone bonds, the three dilactones possess small dipole moments. The data are combined to give polymerization enthalpy and free energy values. The four stereoregular lactide polymers did not differ significantly in energy. Accordingly, the ability to synthesize any one of these rests on catalyst specificity (‘‘polymer chain-end control’’). Although introduction of sterically demanding methyl groups into glycolide is expected to favor coiled conformations and decrease polymerizability, this was not found to be the case. Good agreement of calculated values with experimental data from the literature was achieved. Thu, 31 Jan 2013 11:42:00 GMT http://hdl.handle.net/2117/17539 2013-01-31T11:42:00Z Alemán Llansó, Carlos; Bertran Cànovas, Òscar; Houk, K.N.; Padias, Anne Buyle; Hall, H.K. no The ring-opening polymerizations of the dilactones glycolide and the S,S- and S,R-stereoisomers of lactide were studied using quantum mechanical methods. The ring strain and the conformational distribution of these cyclic monomers and of the polymers were calculated, and the effect of the medium on the polymerization was predicted, for both bulk and solution. The polymerizability of the three monomers in the gas phase, that is, nonpolar medium, is much greater than that of d-valerolactone or 1,4-dioxan-2-one. This difference vanishes in the polar medium chloroform, which is attributed to the fact that, while all of these monomers possess polar cis-lactone bonds, the three dilactones possess small dipole moments. The data are combined to give polymerization enthalpy and free energy values. The four stereoregular lactide polymers did not differ significantly in energy. Accordingly, the ability to synthesize any one of these rests on catalyst specificity (‘‘polymer chain-end control’’). Although introduction of sterically demanding methyl groups into glycolide is expected to favor coiled conformations and decrease polymerizability, this was not found to be the case. Good agreement of calculated values with experimental data from the literature was achieved. http://hdl.handle.net/2117/17488 Title: Effects of ring contraction on the conformational preferences of a-substituted proline analogs Authors: Revilla López, Guillermo; Warren, Javier G.; Torras Costa, Juan; Jiménez, Ana I.; Cativiela, Carlos; Alemán Llansó, Carlos Abstract: The structural consequences derived from the incorporation of either a methyl or a phenyl group at the a 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 a-substituted proline analogs has been explored using the same computational methods. Specifically, the intrinsic conformational preferences of the N-acetyl-N 0 -methylamide derivatives of the lower proline homolog L-azetidine-2-carboxylic acid (Aze), characterized by a four- instead of a fivemembered ring, and its a-methyl (aMeAze) and aphenyl (aPhAze) 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 aMeAze derivatives, which should be attributed to the quasi-planar geometry of the fourmembered 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 aMeAze to adopt g-turns is higher than that of unsubstituted Aze and amethylproline, this feature being in full agreement with the experimental observations available Wed, 23 Jan 2013 10:40:39 GMT http://hdl.handle.net/2117/17488 2013-01-23T10:40:39Z Revilla López, Guillermo; Warren, Javier G.; Torras Costa, Juan; Jiménez, Ana I.; Cativiela, Carlos; Alemán Llansó, Carlos no The structural consequences derived from the incorporation of either a methyl or a phenyl group at the a 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 a-substituted proline analogs has been explored using the same computational methods. Specifically, the intrinsic conformational preferences of the N-acetyl-N 0 -methylamide derivatives of the lower proline homolog L-azetidine-2-carboxylic acid (Aze), characterized by a four- instead of a fivemembered ring, and its a-methyl (aMeAze) and aphenyl (aPhAze) 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 aMeAze derivatives, which should be attributed to the quasi-planar geometry of the fourmembered 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 aMeAze to adopt g-turns is higher than that of unsubstituted Aze and amethylproline, this feature being in full agreement with the experimental observations available http://hdl.handle.net/2117/17086 Title: Properties of poly(3-halidethiophene)s Authors: Casanovas, Jordi; Aradilla Zapata, David; Poater, Jordi; Solà, Miquel; Estrany Coda, Francesc; Alemán Llansó, Carlos Abstract: The influence of the halogen atom on the intrinsic properties of poly(3-halidethiophene)s has been investigated using experimental and theoretical methodologies. Specifically, the electrochemical, electrical, electronic and morphological properties of poly(3-bromothiophene) have been determined and compared with those recently reported for poly(3-chlorothiophene) [Aradilla et al., Polym. Chem., 2012, 3, 436.]. The electrochemical stability and porosity are smaller for poly(3-bromothiophene) than for poly(3-chlorothiophene) while the p–p* lowest transition energy is higher for the former than for the latter. Moreover, quantum mechanical calculations on model oligomers have evidenced that the conformational properties of poly(3-halidethiophene)s, where the halogen is fluorine, chloride or bromine, are dominated by steric interactions and, therefore, are significantly influenced by the size of the halogen atoms. Both the ionization potential and the p–p* lowest transition energy have been predicted to increase slightly when the p-p-donor character of the halogen atom decreases, in agreement with experimental observations. Mon, 10 Dec 2012 12:11:30 GMT http://hdl.handle.net/2117/17086 2012-12-10T12:11:30Z Casanovas, Jordi; Aradilla Zapata, David; Poater, Jordi; Solà, Miquel; Estrany Coda, Francesc; Alemán Llansó, Carlos no The influence of the halogen atom on the intrinsic properties of poly(3-halidethiophene)s has been investigated using experimental and theoretical methodologies. Specifically, the electrochemical, electrical, electronic and morphological properties of poly(3-bromothiophene) have been determined and compared with those recently reported for poly(3-chlorothiophene) [Aradilla et al., Polym. Chem., 2012, 3, 436.]. The electrochemical stability and porosity are smaller for poly(3-bromothiophene) than for poly(3-chlorothiophene) while the p–p* lowest transition energy is higher for the former than for the latter. Moreover, quantum mechanical calculations on model oligomers have evidenced that the conformational properties of poly(3-halidethiophene)s, where the halogen is fluorine, chloride or bromine, are dominated by steric interactions and, therefore, are significantly influenced by the size of the halogen atoms. Both the ionization potential and the p–p* lowest transition energy have been predicted to increase slightly when the p-p-donor character of the halogen atom decreases, in agreement with experimental observations. http://hdl.handle.net/2117/16732 Title: Stochastic simulation of structural properties of natively unfolded and denatured proteins Authors: Curcó Cantarell, David; Michaux, Catherine; Roussel, Guillaume; Tinti, Emmanuel; Perpete, Eric A.; Alemán Llansó, Carlos Abstract: A new simulation strategy based on a stochastic process has been developed and tested to study the structural properties of the unfolded state of proteins at the atomistic level. The procedure combines a generation algorithm to produce representative uncorrelated atomistic microstructures and an original relaxation method to minimize repulsive non-bonded interactions. Using this methodology, a set of 14 unfolded proteins, including seven natively unfolded proteins as well as seven “classical” proteins experimentally described in denaturation conditions, has been investigated. Comparisons between the calculated and available experimental values of several properties, at hydrodynamic and atomic level, used to describe the unfolded state, such as the radius of gyration, the maximum length, the hydrodynamic radius, the diffusion coefficient, the sedimentation coefficient, and the NMR chemical shifts, reflect a very good agreement. Furthermore, our results indicate that the relationship between the radius of gyration and the hydrodynamic radius deviates from the Zimm’s theory of polymer dynamics for random coils, as was recently observed using single-molecule fluorescent methods. Simulations reveal that the interactions between atoms separated by three chemical bonds (1–4 interactions) play a crucial role in the generation process, suggesting that the unfolded state is essentially governed Tue, 16 Oct 2012 11:20:14 GMT http://hdl.handle.net/2117/16732 2012-10-16T11:20:14Z Curcó Cantarell, David; Michaux, Catherine; Roussel, Guillaume; Tinti, Emmanuel; Perpete, Eric A.; Alemán Llansó, Carlos no Denatured state, Hydrodynamic properties, NMR chemical shifts, Stochastic simulation, Uncorrelated atomistic microstructures, Unstructured proteins A new simulation strategy based on a stochastic process has been developed and tested to study the structural properties of the unfolded state of proteins at the atomistic level. The procedure combines a generation algorithm to produce representative uncorrelated atomistic microstructures and an original relaxation method to minimize repulsive non-bonded interactions. Using this methodology, a set of 14 unfolded proteins, including seven natively unfolded proteins as well as seven “classical” proteins experimentally described in denaturation conditions, has been investigated. Comparisons between the calculated and available experimental values of several properties, at hydrodynamic and atomic level, used to describe the unfolded state, such as the radius of gyration, the maximum length, the hydrodynamic radius, the diffusion coefficient, the sedimentation coefficient, and the NMR chemical shifts, reflect a very good agreement. Furthermore, our results indicate that the relationship between the radius of gyration and the hydrodynamic radius deviates from the Zimm’s theory of polymer dynamics for random coils, as was recently observed using single-molecule fluorescent methods. Simulations reveal that the interactions between atoms separated by three chemical bonds (1–4 interactions) play a crucial role in the generation process, suggesting that the unfolded state is essentially governed http://hdl.handle.net/2117/16707 Title: Water absorbed by polyaniline emeraldine tends to organize, forming nanodrops Authors: Casanovas, Jordi; Canales Gabriel, Manel; Fabregat Jové, Georgina; Meneguzzi, Álvaro; Alemán Llansó, Carlos Abstract: Interactions, in terms of both binding energies and microscopic organization, of water molecules absorbed by hydrophilic polyaniline emeraldine base have been investigated using quantum mechanical calculations, molecular dynamics simulation, FTIR spectroscopy, and 1H NMR. From an enthalpic point of view, water molecules interact more favorably with imine nitrogen atoms than with amine ones, even though the latter are entropically favored with respect to the former because of their two binding sites. Quantum mechanical results show that interaction energies of water molecules reversibly absorbed but organized individually around a binding site range from 3.0 to 6.3 kcal/mol, which is in good agreement with activation energies of 3–5 kcal/mol previously determined by thermodynamic measurements. The irreversible absorption of water to produce C–OH groups in rings of diimine units has been examined considering a three steps process in which water molecules act as both acidic and nucleophilic reagent. Although calculations predict that the whole process is disfavored by 5–8 kcal/mol only, FTIR and 1H NMR detected the existence of reversibly absorbed water but not of C–OH groups. Both the binding energies and the structural information provided by molecular dynamics simulations have been used to interpret the existence of two types of physisorbed water molecules: (i) those that interact individually with polymer chains and (ii) those immersed in nanodrops that are contained within the polymeric matrix. The binding energies calculated for these two types of water molecules are fully consistent with the thermodynamic activation energies previously reported. Wed, 10 Oct 2012 13:38:30 GMT http://hdl.handle.net/2117/16707 2012-10-10T13:38:30Z Casanovas, Jordi; Canales Gabriel, Manel; Fabregat Jové, Georgina; Meneguzzi, Álvaro; Alemán Llansó, Carlos no Interactions, in terms of both binding energies and microscopic organization, of water molecules absorbed by hydrophilic polyaniline emeraldine base have been investigated using quantum mechanical calculations, molecular dynamics simulation, FTIR spectroscopy, and 1H NMR. From an enthalpic point of view, water molecules interact more favorably with imine nitrogen atoms than with amine ones, even though the latter are entropically favored with respect to the former because of their two binding sites. Quantum mechanical results show that interaction energies of water molecules reversibly absorbed but organized individually around a binding site range from 3.0 to 6.3 kcal/mol, which is in good agreement with activation energies of 3–5 kcal/mol previously determined by thermodynamic measurements. The irreversible absorption of water to produce C–OH groups in rings of diimine units has been examined considering a three steps process in which water molecules act as both acidic and nucleophilic reagent. Although calculations predict that the whole process is disfavored by 5–8 kcal/mol only, FTIR and 1H NMR detected the existence of reversibly absorbed water but not of C–OH groups. Both the binding energies and the structural information provided by molecular dynamics simulations have been used to interpret the existence of two types of physisorbed water molecules: (i) those that interact individually with polymer chains and (ii) those immersed in nanodrops that are contained within the polymeric matrix. The binding energies calculated for these two types of water molecules are fully consistent with the thermodynamic activation energies previously reported. http://hdl.handle.net/2117/16668 Title: Hybrid polythiophene-clay exfoliated nanocomposites for ultracapacitor devices Authors: Aradilla Zapata, David; Azambuja, Denise S.; Estrany Coda, Francesc; Casas Becerra, María Teresa; Ferreira, Carlos A.; Alemán Llansó, Carlos Abstract: Exfoliated nanocomposites of poly(3,4-ethylenedioxythiophene) (PEDOT) and montmorillonite (MMT) have been prepared by in situ anodic polymerization, concentrations of clay ranging from 5% w/w to 50% w/w being included in the aqueous polymerization medium. The morphology, electrical conductivity, adherence, thermal stability, charge storage, specific capacitance, electrostability, doping level and band gap have been determined for the different PEDOT–MMT nanocomposites and compared with those of pristine PEDOT. Many of these properties have been found to depend on both the concentration of clay and the thickness (micrometric or nanometric) of the generated films. Types I and II ultracapacitors have been fabricated using nanometric and micrometric films of PEDOT and PEDOT–MMT. The properties of such devices have been characterized and compared with those reported in the literature for ultracapacitors fabricated using nanocomposites of PEDOT and other inorganic materials. Both nanometric and micrometric type II ultracapacitors, which correspond to an asymmetric configuration of PEDOT and PEDOT–MMT films, have been found to present the better properties (e.g. the specific capacitance for nanometric and micrometric devices is 429 and 116 F g 1, respectively), evidencing the favorable effect of the clay. Finally, the effects of the electrochemicaldegradation on the ultracapacitors have been rationalized using electrochemical impedance spectroscopy. Mon, 08 Oct 2012 10:17:51 GMT http://hdl.handle.net/2117/16668 2012-10-08T10:17:51Z Aradilla Zapata, David; Azambuja, Denise S.; Estrany Coda, Francesc; Casas Becerra, María Teresa; Ferreira, Carlos A.; Alemán Llansó, Carlos no Exfoliated nanocomposites of poly(3,4-ethylenedioxythiophene) (PEDOT) and montmorillonite (MMT) have been prepared by in situ anodic polymerization, concentrations of clay ranging from 5% w/w to 50% w/w being included in the aqueous polymerization medium. The morphology, electrical conductivity, adherence, thermal stability, charge storage, specific capacitance, electrostability, doping level and band gap have been determined for the different PEDOT–MMT nanocomposites and compared with those of pristine PEDOT. Many of these properties have been found to depend on both the concentration of clay and the thickness (micrometric or nanometric) of the generated films. Types I and II ultracapacitors have been fabricated using nanometric and micrometric films of PEDOT and PEDOT–MMT. The properties of such devices have been characterized and compared with those reported in the literature for ultracapacitors fabricated using nanocomposites of PEDOT and other inorganic materials. Both nanometric and micrometric type II ultracapacitors, which correspond to an asymmetric configuration of PEDOT and PEDOT–MMT films, have been found to present the better properties (e.g. the specific capacitance for nanometric and micrometric devices is 429 and 116 F g 1, respectively), evidencing the favorable effect of the clay. Finally, the effects of the electrochemicaldegradation on the ultracapacitors have been rationalized using electrochemical impedance spectroscopy. http://hdl.handle.net/2117/16653 Title: Phosphonic acid/silica-based films: A potential treatment for corrosion protection Authors: Dalmoro, V.; dos Santos, João Henrique Zimnoch; Armelín Diggroc, Elaine Aparecida; Alemán Llansó, Carlos; Azambuja, Denise S. Abstract: Films of tetraethyl orthosilicate (TEOS) and 1,2-diaminoethanetetrakis methylenephosphonic acid (EDTPO) were evaluated as a anticorrosive treatment against corrosion for AA2024-T3 in a 0.05 mol L−1 NaCl solution. The electrochemical behavior was investigated using electrochemical impedance spectroscopy. The chemical composition of the silanization bath and films were analyzed by infrared spectroscopy. The effect of hydrolysis time on sol–gel TEOS/EDTPO was monitored, being obtained the best performance after 72 h of hydrolysis at 25 °C. The optimal concentration of EDTPO within the TEOS matrix was 3.75 × 10−4 mol L−1. Improved barrier properties of these films were achieved by the addition of silica nanoparticles. Fri, 05 Oct 2012 10:17:13 GMT http://hdl.handle.net/2117/16653 2012-10-05T10:17:13Z Dalmoro, V.; dos Santos, João Henrique Zimnoch; Armelín Diggroc, Elaine Aparecida; Alemán Llansó, Carlos; Azambuja, Denise S. no A. Aluminium alloys, B. Electrochemical impedance spectroscopy, B. Infrared spectroscopy Films of tetraethyl orthosilicate (TEOS) and 1,2-diaminoethanetetrakis methylenephosphonic acid (EDTPO) were evaluated as a anticorrosive treatment against corrosion for AA2024-T3 in a 0.05 mol L−1 NaCl solution. The electrochemical behavior was investigated using electrochemical impedance spectroscopy. The chemical composition of the silanization bath and films were analyzed by infrared spectroscopy. The effect of hydrolysis time on sol–gel TEOS/EDTPO was monitored, being obtained the best performance after 72 h of hydrolysis at 25 °C. The optimal concentration of EDTPO within the TEOS matrix was 3.75 × 10−4 mol L−1. Improved barrier properties of these films were achieved by the addition of silica nanoparticles. http://hdl.handle.net/2117/16598 Title: Controlling the morphology of poly(N -cyanoethylpyrrole) Authors: Fabregat Jové, Georgina; Alemán Llansó, Carlos; Casas Becerra, María Teresa; Armelín Diggroc, Elaine Aparecida Abstract: The morphology of poly(N-cyanoethylpyrrole) has been controlled through the polymerization process. This polymer has been prepared by anodic polymerization, chemical oxidative polymerization in emulsion medium, and layer-by-layer templating polymerization. Anodic polymerization using LiClO4 as supporting electrolyte provides compact films, in which the oxidation degree is controlled through the thickness, useful for the microdetection of dopamine. Chemical polymerization using FeCl3 as oxidant agent results in very well-defined microspheres with porous internal structure, which may be useful in molecular loading and transport processes. Finally, the layer-by-layer templating technique produces core−shell particles of controlled size and thickness. Moreover, these core−shell particles can be easily converted in hollow microspheres by removing the template Tue, 02 Oct 2012 11:08:45 GMT http://hdl.handle.net/2117/16598 2012-10-02T11:08:45Z Fabregat Jové, Georgina; Alemán Llansó, Carlos; Casas Becerra, María Teresa; Armelín Diggroc, Elaine Aparecida no Anodic polymerization, Chemical oxidative polymerization, Chemical polymerization, Controlled size, Core-shell particle, Hollow microsphere, Internal structure, Layer-by-layers, Molecular loadings, Oxidation degree, Polymerization process, Supporting electrolyte, Templating polymerization, Templating techniques, Transport process The morphology of poly(N-cyanoethylpyrrole) has been controlled through the polymerization process. This polymer has been prepared by anodic polymerization, chemical oxidative polymerization in emulsion medium, and layer-by-layer templating polymerization. Anodic polymerization using LiClO4 as supporting electrolyte provides compact films, in which the oxidation degree is controlled through the thickness, useful for the microdetection of dopamine. Chemical polymerization using FeCl3 as oxidant agent results in very well-defined microspheres with porous internal structure, which may be useful in molecular loading and transport processes. Finally, the layer-by-layer templating technique produces core−shell particles of controlled size and thickness. Moreover, these core−shell particles can be easily converted in hollow microspheres by removing the template http://hdl.handle.net/2117/16530 Title: Response of crown ether functionalized polythiophenes to alkaline ions Authors: Zanuy Gomara, David; Preat, Julien; Perpete, Eric A.; Alemán Llansó, Carlos Abstract: 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. Thu, 20 Sep 2012 08:34:28 GMT http://hdl.handle.net/2117/16530 2012-09-20T08:34:28Z Zanuy Gomara, David; Preat, Julien; Perpete, Eric A.; Alemán Llansó, Carlos no Alkaline cations, Alkaline ions, Atomistic levels, Binding process, Bound state, Counterions, Electrostatic repulsion, Entropic contributions, Free state, Functionalized, Macrocycles, Molecular dynamics simulations, Poly-thiophene, Polythiophene derivatives, Quantum mechanical levels, Quantum-mechanical calculation, Relative entropy, Repeating unit, Selective sensing, Sensing response 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. http://hdl.handle.net/2117/16527 Title: Evaluation of an environmentally friendly anticorrosive pigment for alkyd primer Authors: Martí Barroso, Mireia; Fabregat Jové, Georgina; Azambuja, Denise S.; Alemán Llansó, Carlos; Armelín Diggroc, Elaine Aparecida Abstract: An alkyd formulation containing zinc phosphate (10 wt.%) was prepared and subsequently modified replacing the latter anticorrosive additive by a very low concentration of conducting polymer. Specifically, three modified paints, which contain polyaniline emeraldine base (undoped form), polyaniline emeraldine salt (doped form) and an eco-friendly polythiophene derivative (partially oxidized), were formulated. The properties and corrosion resistance of the four alkyd coatings have been characterized. Among the three modified paints, the one containing polythiophene shows the best adherence and the highest corrosion resistance. This has been attributed to the fact that the miscibility of the polythiophene derivative with the alkyd formulation is better than that of polyaniline. Furthermore, accelerated corrosion assays and electrochemical impedance spectroscopy measurements revealed that the corrosion resistance of the paint with polythiophene is several orders of magnitude higher than that with zinc phosphate. The polythiophene derivative has been found to induce the formation of a passivating and well-adhered layer between the coating and the surface, preventing the access of chloride anions and oxygen to the substrate. Thu, 20 Sep 2012 08:09:15 GMT http://hdl.handle.net/2117/16527 2012-09-20T08:09:15Z Martí Barroso, Mireia; Fabregat Jové, Georgina; Azambuja, Denise S.; Alemán Llansó, Carlos; Armelín Diggroc, Elaine Aparecida no Alkyd primer, Polythiophene, Polyaniline, Corrosion resistance, Electrochemical impedance spectroscopy An alkyd formulation containing zinc phosphate (10 wt.%) was prepared and subsequently modified replacing the latter anticorrosive additive by a very low concentration of conducting polymer. Specifically, three modified paints, which contain polyaniline emeraldine base (undoped form), polyaniline emeraldine salt (doped form) and an eco-friendly polythiophene derivative (partially oxidized), were formulated. The properties and corrosion resistance of the four alkyd coatings have been characterized. Among the three modified paints, the one containing polythiophene shows the best adherence and the highest corrosion resistance. This has been attributed to the fact that the miscibility of the polythiophene derivative with the alkyd formulation is better than that of polyaniline. Furthermore, accelerated corrosion assays and electrochemical impedance spectroscopy measurements revealed that the corrosion resistance of the paint with polythiophene is several orders of magnitude higher than that with zinc phosphate. The polythiophene derivative has been found to induce the formation of a passivating and well-adhered layer between the coating and the surface, preventing the access of chloride anions and oxygen to the substrate. http://hdl.handle.net/2117/16503 Title: Properties of oligothiophene dendrimers as a function of molecular architecture and generation number Authors: Córdova Mateo, Esther; Rodríguez Ropero, Francisco; Bertran Cànovas, Òscar; Alemán Llansó, Carlos Abstract: Density functional and time-dependent density functional calculations using the B3LYP method combined with the 6-31G(d) and 6-311++G(d,p) basis sets are performed on symmetric and unsymmetric all-thiophene dendrimers containing up to 45 thiophene rings. Calculations consider both the neutral and the oxidized states of each dendrimer. The results are used to examine the molecular geometry, the ionization potential, the lowest p–p* transition energy, and the shape of the frontier orbitals. The molecular and electronic properties of these systems depend not only on the number of thiophene rings, as typically occurs for linear oligothiophenes, but also on their symmetric/unsymmetric molecular architecture. Two mathematical models developed to predict the lowest p–p* transition energy of all-thiophene dendrimers that are inaccessible to quantum mechanical calculations are tested on a dendrimer with 90 thiophene rings. Mon, 17 Sep 2012 08:40:19 GMT http://hdl.handle.net/2117/16503 2012-09-17T08:40:19Z Córdova Mateo, Esther; Rodríguez Ropero, Francisco; Bertran Cànovas, Òscar; Alemán Llansó, Carlos no dendrimers, density functional calculations, electronic structure, oxidation, sulfur heterocycles Density functional and time-dependent density functional calculations using the B3LYP method combined with the 6-31G(d) and 6-311++G(d,p) basis sets are performed on symmetric and unsymmetric all-thiophene dendrimers containing up to 45 thiophene rings. Calculations consider both the neutral and the oxidized states of each dendrimer. The results are used to examine the molecular geometry, the ionization potential, the lowest p–p* transition energy, and the shape of the frontier orbitals. The molecular and electronic properties of these systems depend not only on the number of thiophene rings, as typically occurs for linear oligothiophenes, but also on their symmetric/unsymmetric molecular architecture. Two mathematical models developed to predict the lowest p–p* transition energy of all-thiophene dendrimers that are inaccessible to quantum mechanical calculations are tested on a dendrimer with 90 thiophene rings. http://hdl.handle.net/2117/16499 Title: Ultraporous poly(3,4-ethylenedioxythiophene) for nanometric electrochemical supercapacitor Authors: Aradilla Zapata, David; Estrany Coda, Francesc; Armelín Diggroc, Elaine Aparecida; Alemán Llansó, Carlos Abstract: Ultrathin films of poly(3,4-ethylenedioxythiophene) (PEDOT) have been prepared by electropolymerization on steel and indium-tin oxide (ITO) substrates under identical experimental conditions. Scanning electron microscopy and atomic force microscopy indicate that the substrate affects dramatically both the morphology and topography of films when the polymerization times are very short. An ultraporous three-dimensional network involving ultrathin sticks with a fiber-like morphology was formed on ITO. Asymmetric and symmetric supercapacitors have been fabricated by assembling electrodes of PEDOT deposited on ITO and steel. The specific capacitance, electrochemical stability, supercapacitor behavior and Coulombic efficiency measured for devices with an ITO/steel configuration were similar to those reported for advanced PEDOT-inorganic hybrid composites. Furthermore, the performance of the ITO/steel assembly is higher than those determined for symmetric supercapacitors derived from two identical electrodes of PEDOT deposited on steel or on ITO. The unique properties of the asymmetric supercapacitors have been attributed to the ultraporous structure of the ultrathin films deposited on ITO, which is not significantly perturbed when the device is submitted to a very high number of consecutive oxidation–reduction processes, and the different electroactivities of the two electrodes. Fri, 14 Sep 2012 11:47:07 GMT http://hdl.handle.net/2117/16499 2012-09-14T11:47:07Z Aradilla Zapata, David; Estrany Coda, Francesc; Armelín Diggroc, Elaine Aparecida; Alemán Llansó, Carlos no Conducting polymers, Electrochemical stability, Poly(3, 4-ethylenedioxythiophene), Supercapacitors, Ultrathin films Ultrathin films of poly(3,4-ethylenedioxythiophene) (PEDOT) have been prepared by electropolymerization on steel and indium-tin oxide (ITO) substrates under identical experimental conditions. Scanning electron microscopy and atomic force microscopy indicate that the substrate affects dramatically both the morphology and topography of films when the polymerization times are very short. An ultraporous three-dimensional network involving ultrathin sticks with a fiber-like morphology was formed on ITO. Asymmetric and symmetric supercapacitors have been fabricated by assembling electrodes of PEDOT deposited on ITO and steel. The specific capacitance, electrochemical stability, supercapacitor behavior and Coulombic efficiency measured for devices with an ITO/steel configuration were similar to those reported for advanced PEDOT-inorganic hybrid composites. Furthermore, the performance of the ITO/steel assembly is higher than those determined for symmetric supercapacitors derived from two identical electrodes of PEDOT deposited on steel or on ITO. The unique properties of the asymmetric supercapacitors have been attributed to the ultraporous structure of the ultrathin films deposited on ITO, which is not significantly perturbed when the device is submitted to a very high number of consecutive oxidation–reduction processes, and the different electroactivities of the two electrodes. http://hdl.handle.net/2117/16315 Title: Reviewing Extrapolation Procedures of the Electronic Properties on the p-Conjugated Polymer Limit Authors: Torras Costa, Juan; Casanovas, Jordi; Alemán Llansó, Carlos Abstract: In this article, the extrapolation procedures of π−π* electronic transition energy on π-conjugated oligomers are reexamined. Different models, including the simplest coupled oscillator, the free electron, the Hückel approach, the molecular exciton model, and some specific fitting-functions, are compared using the transition energies derived from theoretical calculations on three thiophene-based oligomer series. Specifically, oligomers of up to 30 repeating units have been considered to include the saturation effects as a function of chain length. The coupled oscillator model of W. Kuhn and the fitting-function of Hirayama are the models that present the better suit on the transition energy interpolation as a function of chain length. Using only the first four oligomers of the series (n = 2 up to 8) yields an estimation of the transition energy on the polymer limit with an average error of ∼1.5%. The vertical and adiabatic ionization potential present a better fit with the Hückel model approach. Finally, implications of the environmental polarity on the electronic properties, molecular geometry, charge distribution, and aromaticity are shortly discussed. Mon, 23 Jul 2012 11:51:38 GMT http://hdl.handle.net/2117/16315 2012-07-23T11:51:38Z Torras Costa, Juan; Casanovas, Jordi; Alemán Llansó, Carlos no In this article, the extrapolation procedures of π−π* electronic transition energy on π-conjugated oligomers are reexamined. Different models, including the simplest coupled oscillator, the free electron, the Hückel approach, the molecular exciton model, and some specific fitting-functions, are compared using the transition energies derived from theoretical calculations on three thiophene-based oligomer series. Specifically, oligomers of up to 30 repeating units have been considered to include the saturation effects as a function of chain length. The coupled oscillator model of W. Kuhn and the fitting-function of Hirayama are the models that present the better suit on the transition energy interpolation as a function of chain length. Using only the first four oligomers of the series (n = 2 up to 8) yields an estimation of the transition energy on the polymer limit with an average error of ∼1.5%. The vertical and adiabatic ionization potential present a better fit with the Hückel model approach. Finally, implications of the environmental polarity on the electronic properties, molecular geometry, charge distribution, and aromaticity are shortly discussed. http://hdl.handle.net/2117/15800 Title: Electronic properties of poly(thiophene-3-methyl acetate) Authors: Gomes, Alex; Casanovas, Jordi; Bertran Cànovas, Òscar; Campos, Joao Sinezio de C.; Armelín Diggroc, Elaine Aparecida; Alemán Llansó, Carlos Abstract: The electronic structure of poly(thiophene-3- methyl acetate) has been investigated using UV–vis absorption spectroscopy and quantum mechanical calculations. Experimental measures in chloroform solution indicate that the π-conjugation length increases with the polymer concentration, which is reflected by the red shift of the absorbance peak of the π-π* transition. On the other hand, the energy required for the π-π* transition has been found to decrease with the volatility of the solvent for concentrated polymer solutions, even though the influence of the solvent is very small for dilute solutions. Quantum mechanical calculations indicate that the interactions between the π-conjugated backbone and the methyl acetate side groups are very weak. On the other hand, the lowest energy transition predicted for an infinite polymer chain that adopts the anti-gauche and all-anti conformations is 2.8 and 1.9 eV, respectively. Finally, measurements on spincasted nanofilms reflect that the π-π* transition energy increases with the thickness, which has been attributed to the distortion of the molecular conformation. In spite of this, the energy gap obtained for the thinnest film (1.52 eV) is significantly smaller than that determined for dilute and concentrated chloroform solutions (2.56 and 2.09 eV, respectively) Wed, 09 May 2012 10:57:31 GMT http://hdl.handle.net/2117/15800 2012-05-09T10:57:31Z Gomes, Alex; Casanovas, Jordi; Bertran Cànovas, Òscar; Campos, Joao Sinezio de C.; Armelín Diggroc, Elaine Aparecida; Alemán Llansó, Carlos no The electronic structure of poly(thiophene-3- methyl acetate) has been investigated using UV–vis absorption spectroscopy and quantum mechanical calculations. Experimental measures in chloroform solution indicate that the π-conjugation length increases with the polymer concentration, which is reflected by the red shift of the absorbance peak of the π-π* transition. On the other hand, the energy required for the π-π* transition has been found to decrease with the volatility of the solvent for concentrated polymer solutions, even though the influence of the solvent is very small for dilute solutions. Quantum mechanical calculations indicate that the interactions between the π-conjugated backbone and the methyl acetate side groups are very weak. On the other hand, the lowest energy transition predicted for an infinite polymer chain that adopts the anti-gauche and all-anti conformations is 2.8 and 1.9 eV, respectively. Finally, measurements on spincasted nanofilms reflect that the π-π* transition energy increases with the thickness, which has been attributed to the distortion of the molecular conformation. In spite of this, the energy gap obtained for the thinnest film (1.52 eV) is significantly smaller than that determined for dilute and concentrated chloroform solutions (2.56 and 2.09 eV, respectively)