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  • Synergistic computational-experimental approach to improve ionene polymer-based functional hydrogels

     Bachl, Jürgen; Zanuy Gomara, David; Lopez Perez, Daniel Ernesto; Revilla Lopez, Guillermo; Cativiela, Carlos; Aleman Llanso, Carlos Enrique; Diaz Diaz, David
    Advanced functional materials
    Vol. 24, num. 31, p. 4893-4904
    DOI: 10.1002/adfm.201304230
    Date of publication: 2014-08-20
    Journal article

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    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.

    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.

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

     Caruso, M.; Gatto, Emanuela; Placidi, E.; Venanzi, Mariano; Ballano Ballano, María Gema; Formaggio, Fernando; Toniolo, Claudio; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    Soft matter
    Vol. 10, num. 15, p. 2508-2519
    DOI: 10.1039/c3sm52831f
    Date of publication: 2014-01-01
    Journal article

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

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

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    Resolving the subnanometric structure of ultrathin films of poly(3,4-ethylenedioxythiophene) on steel surfaces: A molecular modeling approach  Open access

     Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    Soft matter
    Vol. 9, num. 48, p. 11634-11644
    DOI: 10.1039/c3sm52477a
    Date of publication: 2013-12-28
    Journal article

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    Poly(3,4-ethylenedioxythiophene), abbreviated PEDOT, is one of the most outstanding electroactive polymers, whose applications cover a wide range of fields from biomedicine to electronic components. In this work the physicochemical properties of nanoconstructs obtained by growing PEDOT chains over steel surfaces are investigated. The structural features of such nanostructures, which had successfully been used to build supercapacitors, are investigated, revealing that the polymeric phase plays a key role in the charge accumulation process. The ultra-structure organization and dynamics of these constructs are explored by molecular simulations and the results are compared with the available experimental data. The outcome of this investigation has offered a detailed vision of the structural features that lead to an extraordinarily efficient charge accumulation. Atomistic models generated using stochastic methods had provided different distributions of polymer chains over a metallic surface. Molecular dynamics simulations performed on such models have demonstrated that the extraordinary capacity for charge accumulation stems from a thin balance between the electrostatic repulsion that polymer chains exercise to each other and the attraction that the counterions present in the electropolymerization exert on those oxidized PEDOT chains. This situation favors the aggregation of the PEDOT chains mediated by the perchlorate ions, which act over them as inter-chain cement and which leads to regular three dimensional organization of chains, regardless of their initial distribution over the metallic surface. At the same time, such inner proximity of the polymer chains when growing upwards forces the capture of perchlorate ions, acting as accumulated charges that could be further released if the PEDOT oxidation state is externally reversed.

    Poly(3,4-ethylenedioxythiophene), abbreviated PEDOT, is one of the most outstanding electroactive polymers, whose applications cover a wide range of fields from biomedicine to electronic components. In this work the physicochemical properties of nanoconstructs obtained by growing PEDOT chains over steel surfaces are investigated. The structural features of such nanostructures, which had successfully been used to build supercapacitors, are investigated, revealing that the polymeric phase plays a key role in the charge accumulation process. The ultra-structure organization and dynamics of these constructs are explored by molecular simulations and the results are compared with the available experimental data. The outcome of this investigation has offered a detailed vision of the structural features that lead to an extraordinarily efficient charge accumulation. Atomistic models generated using stochastic methods had provided different distributions of polymer chains over a metallic surface. Molecular dynamics simulations performed on such models have demonstrated that the extraordinary capacity for charge accumulation stems from a thin balance between the electrostatic repulsion that polymer chains exercise to each other and the attraction that the counterions present in the electropolymerization exert on those oxidized PEDOT chains. This situation favors the aggregation of the PEDOT chains mediated by the perchlorate ions, which act over them as inter-chain cement and which leads to regular three dimensional organization of chains, regardless of their initial distribution over the metallic surface. At the same time, such inner proximity of the polymer chains when growing upwards forces the capture of perchlorate ions, acting as accumulated charges that could be further released if the PEDOT oxidation state is externally reversed.

  • Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing

     Zanuy Gomara, David; Sayago García, Francisco Javier; Revilla Lopez, Guillermo; Ballano Ballano, María Gema; Agemy, Lilach; Kotamraju, Venkata Ramana; Jimenez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Sawvel, April M.; Ruoslahti, Erkki; Stucky, Galen; Aleman Llanso, Carlos Enrique
    Journal of computer-aided molecular design
    Vol. 27, num. 1, p. 31-43
    DOI: 10.1007/s10822-012-9623-5
    Date of publication: 2013-01
    Journal article

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    We present a chemical strategy to engineer analogs of the tumor-homing peptide CREKA (Cys-Arg-Glu-Lys-Ala), which binds to fibrin and fibrin-associated clotted plasma proteins in tumor vessels (Simberg et al. in Proc Natl Acad Sci USA 104:932-936, 2007) with improved ability to inhibit tumor growth. Computer modeling using a combination of simulated annealing and molecular dynamics were carried out to design targeted replacements aimed at enhancing the stability of the bioactive conformation of CREKA. Because this conformation presents a pocket-like shape with the charged groups of Arg, Glu and Lys pointing outward, non-proteinogenic amino acids alpha-methyl and N-methyl derivatives of Arg, Glu and Lys were selected, rationally designed and incorporated into CREKA analogs. The stabilization of the bioactive conformation predicted by the modeling for the different CREKA analogs matched the tumor fluorescence results, with tumor accumulation increasing with stabilization.

    We present a chemical strategy to engineer analogs of the tumor-homing peptide CREKA (Cys-Arg- Glu-Lys-Ala), which binds to fibrin and fibrin-associated clotted plasma proteins in tumor vessels (Simberg et al. in Proc Natl Acad Sci USA 104:932–936, 2007) with improved ability to inhibit tumor growth. Computer mod- eling using a combination of simulated annealing and molecular dynamics were carried out to design targeted replacements aimed at enhancing the stability of the bio- active conformation of CREKA. Because this conforma- tion presents a pocket-like shape with the charged groups of Arg, Glu and Lys pointing outward, non-proteinogenic amino acids a -methyl and N -methyl derivatives of Arg, Glu and Lys were selected, rationally designed and incor- porated into CREKA analogs. The stabilization of the bioactive conformation predicted by the modeling for the different CREKA analogs matched the tumor fluorescence results, with tumor accumulation increasing with stabil- ization. Here we report the modeling, synthetic procedures, and new biological assays used to test the efficacy and utility of the analogs. Combined, our results show how studies based on multi-disciplinary collaboration can con- verge and lead to useful biomedical advances

  • Examining the formation of specific interactions between poly(3,4-ethylenedioxythiophene) and nucleotide bases

     Zanuy Gomara, David; Teixeira Dias, Fábio; Del Valle Mendoza, Luis Javier; Poater, Jordi; Solà, Miquel; Aleman Llanso, Carlos Enrique
    RSC Advances
    Vol. 3, num. 8, p. 2639-2649
    DOI: 10.1039/c2ra22640e
    Date of publication: 2013-02-28
    Journal article

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    he formation of specific interaction between poly(3,4-ethylenedioxythiophene) (PEDOT) and adenine (A), cytosine (C) and thymine (T) single stranded homonucleotides has been investigated, complementing our previous investigation on complexes formed by PEDOT and guanine (G) homonucleotide (B. Teixeira-Dias et al, Soft Matter, 2011, 7, 9922¿9932). Results derived from UV-vis and FTIR spectroscopy suggest that A and, especially, C homonucleotides form adducts dominated by non-specific electrostatic interactions, while complexes with T homonucleotides show a behavior that differ from those found for A-, C- and G-containing systems. Results provided by molecular dynamics simulations were consistent with these experimental observations. Thus, specific interactions are much less abundant in A- and C-containing complexes than in those involving G. Moreover, simulations allowed us to detect a structural re-organization in the T-containing complexes, which occurs after their initial formation. This has been attributed to the optimization of electrostatic interactions rather than to the formation of new specific interactions, as was previously found in complexes with G. From the analysis of the interaction of the different nucleotides with an EDOT molecule it is concluded that the most stabilizing specific interaction corresponds to the formation of N-HOEDOT hydrogen bonds. Stabilization comes from electrostatic interactions, although the covalent contribution is non negligible.

  • POLIMEROS CONDUCTORES Y SUS DERIVADOS HIBRIDOS CON APLICACIONES AVANZADAS

     Estrany Coda, Francisco; Armelin Diggroc, Elaine; Zanuy Gomara, David; Iribarren Laco, Jose Ignacio; Sanchez Jimenez, Margarita; Aleman Llanso, Carlos Enrique
    Competitive project

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  • Atomistic organization and characterization of tube-like assemblies comprising peptide-polymer conjugates: computer simulation studies

     Bertran Cànovas, Oscar; Curcó Cantarell, David; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    FARADAY DISCUSSIONS
    Vol. 166, p. 59-82
    DOI: 10.1039/c3fd00079f
    Date of publication: 2013
    Journal article

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    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.

  • Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor

     Zanuy Gomara, David; Kotla, Rohith; Nussinov, Ruth; Teesalu, Tambet; Sugahara, Kazuki N.; Aleman Llanso, Carlos Enrique; Haspel, Nurit
    Journal of structural biology
    Vol. 182, num. 2, p. 78-86
    DOI: 10.1016/j.jsb.2013.02.006
    Date of publication: 2013-02-24
    Journal article

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    Neuropilin-1 (NRP-1) is a hub receptor that plays an essential role in angiogenesis and vascular permeability. It is over-expressed in the new blood vessels grown by tumor cells and is a target for anti-tumor treatments. Peptides that expose the consensus sequence R/K/XXR/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 activation 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 RXXR mutants, where X = A/D/S/R/P, in order to test the effect of replacement of A or P on the binding capabilities. 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 activation.

    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

  • Conformational Exploration of Two Peptides and Their Hybrid Polymer Conjugates: Potentialities As Self-Aggregating Materials

     Haspel, Nurit; Laurent, Adele D.; Zanuy Gomara, David; Nussinov, Ruth; Aleman Llanso, Carlos Enrique; Puiggali Bellalta, Jorge; Revilla Lopez, Guillermo
    Journal of physical chemistry B
    Vol. 116, num. 48, p. 13941-13952
    DOI: 10.1021/jp3043363
    Date of publication: 2012-12-06
    Journal article

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    Response of crown ether functionalized polythiophenes to alkaline ions  Open access

     Zanuy Gomara, David; Preat, Julien; Perpete, Eric; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Vol. 116, num. 15, p. 4575-4583
    DOI: 10.1021/jp209959a
    Date of publication: 2012-04-19
    Journal article

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    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.

  • Intermolecular interactions in electron transfer through stretched helical peptides

     Lopez Perez, Daniel Ernesto; Revilla Lopez, Guillermo; Jacquemin, Denis; Zanuy Gomara, David; Palys, B.; Sek, S.; Aleman Llanso, Carlos Enrique
    Physical chemistry chemical physics
    Vol. 14, num. 29, p. 10332-10344
    DOI: 10.1039/c2cp40761b
    Date of publication: 2012-08-07
    Journal article

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  • Examining the formation of specific interactions between poly(3,4-ethylenedioxythiophene) and nucleotide bases

     Zanuy Gomara, David; da Cruz Teixeira Dias, Bruno José; Del Valle Mendoza, Luis Javier; Poater, Jordi; Solà, Miquel; Aleman Llanso, Carlos Enrique
    RSC Advances
    Vol. 3, num. 8, p. 2639-2649
    DOI: 10.1039/c2ra22640e
    Date of publication: 2012-12-17
    Journal article

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  • A theoretical approach to the engineering of bioinspired systems: Design, applications & information management  Open access  awarded activity

     Revilla Lopez, Guillermo
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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    L’enginyeria de sistemes bioinspirats ha crescut en importància i nombre d’aplicacions en el últims anys, atraient l’atenció dels científics sobre els seus usos potencials en camps com ara la bionanotecnologia, la nanomedicina i la ciència de materials. En aquesta tesis, es presenta una aproximació mitjançant mètodes computacionals a l’enginyeria de sistemes biomimètics. Em posat la nostra èmfasi en l’estudi teòric basat en principis fonamentals de sistemes peptídics, això vol dir des de mètodes mecànic quàntics d’alt nivell per als elements més bàsics fins a la simulació de tot o part del sistema en un ambient més realista a partir de diferents aproximacions computacionals. Un altre objectiu del present treball és la recopilació exhaustiva de la informació derivada dels estudis fets així com dels potencials usos en un sistema informàtic orientat a l’usuari d’emmagatzemament de dades. S’han caracteritzat anàlegs conformacionalment restringits de l’arginina, prolina i fenilalanina a través de càlculs mecànic quàntics d’alt nivell. Aquest aminoàcids no codificats (és a dir que no estan entre els 20 aminoàcids naturals) han demostrat la seva capacitat de modulació del perfil conformacional dels pèptids a on són introduïts. A més a més, indueixen resistència a l’acció de les proteases a banda d’introduir noves propietats electròniques i espectroscòpiques útils en aplicacions tals com els sistemes de diagnòstic, alliberadors de fàrmacs i del camp de l’enginyeria de materials. Els aminoàcids obtinguts són emprats per a modificar pèptids de “homing”, blocs proteics autoagregants i superfícies actives recobertes de pèptids. La remarcable quantitat d’informació sobre aminoàcids no codificats accessible en publicacions científiques expressa la necessitat urgent de sistemes que, basant-se en ordinadors recopilin, organitzin i ofereixin aquesta informació de manera intel·ligible per a l’usuari final. Una base de dades ha estat dissenyada, creada i posada en funcionament per tal d’emmagatzemar dades conformacionals teòriques sobre aminoàcids no codificats. La base de dades també conté, en cas que la informació sigui accessible, dades experimentals referents a aplicacions, caracterització estructural i propietats espectroscòpiques. En resum, aquests treball ofereix un nou enfoc a l’enginyeria assistida per ordinador i la gestió de la informació de sistemes bioinspirats des de les seves unitats més elementals fins al disseny de les aplicacions de major complexitat

    The engineering of systems inspired by biochemical molecules has grown in importance and number of applications in the recent years, focusing the researchers’ attention in its potential uses in fields such as nanotechnology, bionanotechnology, nanomedicine and material sciencie. A computational approach to engineering of biomimetic systems is presented in this work. Our emphasis is put on theoretical studies of some peptidic systems from scratch, this means from the use high level quantum mechanics studies of their primary building blocks to the simulation using different computational approaches of their behavior as part of an entire system in a more realistic environment. The thorough compilation of the derived information and its potential uses in a proper user-friendly data-storage support is also a question dealt in the thesis. Conformationaly restricted analogues of arginine, proline and phenylalanine amino acids are designed and fully characterized using high level quantum mechanics methods. These new non-coded amino acids (non-naturally occurring amino acids in proteins) demonstrate to modulate the conformational profile of peptides where they are inserted. Furthermore, they induce resistance to proteolysis altogether with new electronic and spectroscopic features useful in diagnostics, drug delivery and material engineering. The developed non-coded amino acids are used to engineer systems such as homing peptides, self-aggregating protein building blocks and peptide-coated active surfaces. The remarkable amount of information available about non-coded amino acids in scientific publications stressed out the dire need of computer-based systems to gather, to organize and to display in a user-friendly way the information about these compounds. A data base has been designed, implemented and run to store theoretically-obtained conformational information on non-coded amino acids. The data bases also contains, if available, experimentallyacquired knowledge such us structural and spectroscopic characterizations and reported applications. To conclude, this thesis offers a successful approach to the computer-aided engineering and information management of bioinspired systems from their basics to high complexity design.

  • A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides

     Curcó, David; Zanuy Gomara, David; Nussinov, Ruth; Aleman Llanso, Carlos Enrique
    Journal of computational chemistry
    Vol. 32, num. 4, p. 607-619
    DOI: 10.1002/jcc.21647
    Date of publication: 2011-03
    Journal article

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    A computational strategy to model flexible molecules tethered to a rigid inert surface is presented. The strategy is able to provide uncorrelated relaxed microstructures at the atomistic level. It combines an algorithm to generate molecules tethered to the surface without atomic overlaps, a method to insert solvent molecules and ions in the simulation box, and a powerful relaxation procedure. The reliability of the strategy has been investigated by simulating two different systems: (i) mixed monolayers consisting of binary mixtures of long-chain alkyl thiols of different lengths adsorbed on a rigid inert surface and (ii) CREKA (Cys-Arg-Glu-Lys-Ala), a short linear pentapeptide that recognizes clotted plasma proteins and selectively homes to tumors, covalently tethered to a rigid inert surface in aqueous solution. In the first, we examined the segregation of the two species in the monolayers using different long-chain:short-chain ratios, whereas in the second, we explored the conformational space of CREKA and ions distribution considering densities of peptides per nm2 ranging from 0.03 to 1.67. Results indicate a spontaneous segregation in alkyl thiol monolayers, which enhances when the concentration of longest chains increases. However, the whole conformational profile of CREKA depends on the number of molecules tethered to the surface pointing out the large influence of molecular density on the intermolecular interactions, even though the bioactive conformation was found as the most stable in all cases.

  • Binding of a C-end rule peptide to the neuropilin-1 receptor: a molecular modeling approach

     Haspel, Nurit; Zanuy Gomara, David; Nussinov, Ruth; Teesalu, Tambet; Ruoslahti, Erkki; Aleman Llanso, Carlos Enrique
    Biochemistry
    Vol. 50, num. 10, p. 1755-1762
    DOI: 10.1021/bi101662j
    Date of publication: 2011-03-15
    Journal article

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    Neuropilin-1 (NRP-1) is a receptor that plays an essential role in angiogenesis, vascular permeability, and nervous system development. Previous studies have shown that peptides with an N-terminal Arg, especially peptides with the four-residue consensus sequence R/K/XXR/K, bind to NRP-1 cell surfaces. Peptides containing such consensus sequences promote binding and internalization into cells, while blocking the C-terminal Arg (or Lys) prevents the internalization. In this study, we use molecular dynamics simulations to model the structural properties of the NRP-1 complex with a prototypic CendR peptide, RPAR. Our simulations show that RPAR binds NRP-1 through specific interactions of the RPAR C-terminus: three hydrogen bonds and a salt bridge anchor the ligand in the receptor pocket. The modeling results were used as the starting point for a systematic computational study of new RPAR analogues based on chemical modifications of their natural amino acids. Comparison of the structural properties of the new peptide-receptor complexes with the original organization suggests that some of the analogues can increase the binding affinity while reducing the natural sensitivity of RXXR to endogenous proteases.

  • Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide

     Revilla Lopez, Guillermo; Torras Costa, Juan; Nussinov, Ruth; Aleman Llanso, Carlos Enrique; Zanuy Gomara, David
    Physical chemistry chemical physics
    Vol. 13, num. 21, p. 9986-9994
    DOI: 10.1039/c0cp02572k
    Date of publication: 2011
    Journal article

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  • Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate

     Zanuy Gomara, David; Hamley, I. W.; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Vol. 115, num. 28, p. 8937-8946
    DOI: 10.1021/jp2031187
    Date of publication: 2011-07-21
    Journal article

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    The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe)residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building-up search procedure combined with B3LYP/6- 1G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helicallike arrangements. Furthermore, calculations indicate that backbone ··· side chain interactions involving the N-H of the amide groups and the π clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand,MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.

  • Integrating the intrinsic conformational preferences of noncoded alpha-amino acids modified at the peptide bond into the Noncoded Amino acids Database

     Revilla Lopez, Guillermo; Rodriguez Ropero, Francisco; Curcó, David; Torras Costa, Juan; Calaza, Maria Isabel; Zanuy Gomara, David; Jimenez Sanz, Ana Isabel; Cativiela, Carlos; Nussinov, Ruth; Aleman Llanso, Carlos Enrique
    Proteins
    Vol. 79, num. 6, p. 1841-1852
    DOI: 10.1002/prot.23009
    Date of publication: 2011-06
    Journal article

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  • Atomistic modeling of peptides bound to a chemically active surface: Conformational implications

     Curcó, David; Revilla Lopez, Guillermo; Aleman Llanso, Carlos Enrique; Zanuy Gomara, David
    Journal of peptide science
    Vol. 17, num. 2, p. 132-138
    DOI: 10.1002/psc.1321
    Date of publication: 2011-02
    Journal article

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  • Binding of cationic conjugated polymers to DNA: Atomistic simulations of adducts involving the Dickerson's dodecamer

     Preat, Julien; Zanuy Gomara, David; Perpete, Eric; Aleman Llanso, Carlos Enrique
    Biomacromolecules
    Vol. 12, num. 4, p. 1298-1304
    DOI: 10.1021/bm200022n
    Date of publication: 2011-04
    Journal article

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  • Binding of 6-mer single-stranded homo-nucleotides to poly(3,4-ethylenedioxythiophene): specific hydrogen bonds with guanine

     da Cruz Teixeira Dias, Bruno José; Zanuy Gomara, David; Poater, Jordi; Solà, Miquel; Estrany Coda, Francisco; Del Valle Mendoza, Luis Javier; Aleman Llanso, Carlos Enrique
    Soft matter
    Vol. 7, num. 21, p. 9922-9932
    DOI: 10.1039/c1sm05856h
    Date of publication: 2011
    Journal article

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  • New hybrid biomaterial based on peptide-polyester: structure, properties and potential uses

     Revilla Lopez, Guillermo; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique; Lopez Perez, Daniel Ernesto
    Hybrid Materials
    Presentation's date: 2011-03-08
    Presentation of work at congresses

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  • APLICACIONES DE LOS POLÍMEROS CONDUCTORES EN INGENIERÍA Y BIOTECNOLOGÍA

     Bertran Cànovas, Oscar; Torras Costa, Juan; Estrany Coda, Francisco; Armelin Diggroc, Elaine; Iribarren Laco, Jose Ignacio; Liesa Mestres, Francisco; Zanuy Gomara, David; Revilla Lopez, Guillermo; Canales Gabriel, Manel; Aleman Llanso, Carlos Enrique
    Competitive project

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  • Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)s

     Preat, Julien; Rodriguez Ropero, Francisco; Torras Costa, Juan; Bertran Cànovas, Oscar; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    Journal of computational chemistry
    Vol. 31, num. 8, p. 1741-1751
    DOI: 10.1002/jcc.21463
    Date of publication: 2010-06
    Journal article

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    Three different strategies have been followed to develop the torsional force-field parameters of the interring dihedral angles for calix[4]arene-substituted poly(thiophene)s, a family of highly sensitive ion receptors. These procedures, which are based on the rotational profiles calculated using quantum mechanical methods, differ in the complexity of the model compounds and the processing applied to the quantum mechanical energies before the fitting. The performance of the three sets of developed parameters, which are essentially compatible with the General Amber Force Field, has been evaluated by computing the potential of mean forces for the inter-ring rotation of 2,2'-bithiophene, and its substituted analog bearing a calix[4]arene group in different environments. Finally, the ability of the new sets of torsional parameters to describe a calix[4]arene-substituted poly(thiophene) in tetrahydrofuran solution has been checked using Molecular Dynamics simulations. Specifically, the molecular shape, the polymer conformation, and the effects of the Na+ ions trapped in the cavity of the receptor have been examined. Although the potential derived from unsubstituted 2,2'-bithiophene is able to reproduce the experimental free energies of the minima, the overall results indicate that the parameters derived from the analog bearing a calix[4]arene group provide the best description of the systems under study. This should be attributed to the strong constraints found in complex substituted poly(thiophene)s, which require parameterization strategies able to capture all the interactions and phenomena involved in their inter-ring rotations.

  • Conformational Profile of a Proline-Arginine Hybrid

     Revilla Lopez, Guillermo; Jimenez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Aleman Llanso, Carlos Enrique; Zanuy Gomara, David
    Journal of chemical information and modeling
    Vol. 50, num. 10, p. 1781-1789
    DOI: 10.1021/ci100135f
    Date of publication: 2010
    Journal article

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  • From Poly(3,4-ethylenedioxythiophene) to Poly(3,4-phenylenedioxythiophene): Impact of the Substitution of the Ethylene Bridge by the Phenyl Ring on the Molecular Properties

     Carrión Fajardo, Sergio; Rodriguez Ropero, Francisco; Aradilla Zapata, David; Zanuy Gomara, David; Casanovas Salas, Jordi; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Vol. 114, num. 10, p. 3494-3499
    DOI: 10.1021/jp9112574
    Date of publication: 2010
    Journal article

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  • Influence of the doping level on the interactions between poly(3,4-ethylenedioxythiophene) and plasmid DNA

     da Cruz Teixeira Dias, Bruno José; Zanuy Gomara, David; Del Valle Mendoza, Luis Javier; Estrany Coda, Francisco; Armelin Diggroc, Elaine; Aleman Llanso, Carlos Enrique
    Macromolecular chemistry and physics
    Vol. 211, num. 10, p. 1117-1126
    DOI: 10.1002/macp.200900599
    Date of publication: 2010-05-17
    Journal article

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    The influence of the doping level in the formation of specific interactions between plasmid DNA and PEDOT is investigated using experimental assays and theoretical calculations. Electrochemical methods are used to prepare polymer samples with oxidation degrees ranging from 0.14 to 1.05 positive charges per repeating unit. A combination of experimental and theoretical results are used to propose a mechanism for the formation of DNA/conducting polymer complexes, which consists of the initial stabilization of the adducts through non-specific interactions followed by small structural re-arrangements that allow to be established specific hydrogen bonds involving the polar groups of the conducting polymer and selected DNA bases.

  • Nanoparticle-induced vascular blockade in human prostate cancer

     Agemy, Lilach; Sugahara, Kazuki N.; Kotamraju, Venkata Ramana; Gujraty, Kunal; Girard, Olivier M.; Kono, Yuko; Mattrey, Robert F; Park,, Ji-Ho; Sailor, Michael J.; Jimenez, Ana I.; Cativiela, Carlos; Zanuy Gomara, David; Sayago García, Francisco Javier; Aleman Llanso, Carlos Enrique; Nussinov, Ruth; Ruoslahti, Erkki
    Blood
    Vol. 15, num. 116, p. 2847-2856
    DOI: 10.1182/blood-2010-03-274258
    Date of publication: 2010-09-14
    Journal article

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  • Microscopic details of the sensing ability of 15-crown-5-ether functionalized poly(bithiophene)

     Casanovas Salas, Jordi; Rodriguez Ropero, Francisco; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    Polymer
    Vol. 51, num. 18, p. 4267-4272
    DOI: 10.1016/j.polymer.2010.06.062
    Date of publication: 2010-08-19
    Journal article

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  • Access to the full text
    NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids  Open access

     Revilla Lopez, Guillermo; Torras Costa, Juan; Curcó, David; Casanovas Salas, Jordi; Calaza, Maria Isabel; Zanuy Gomara, David; Jimenez Sanz, Ana Isabel; Cativiela, Carlos; Nussinov, Ruth; Grodzinski, Piotr; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Vol. 114, num. 21, p. 7413-7422
    DOI: 10.1021/jp102092m
    Date of publication: 2010-05-10
    Journal article

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    Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, nonproteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acidssalso called non-coded, non-canonical, or non-standardsis usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, R-tetrasubstituted R-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.

  • Electronic characterization of all-thiophene conducting dendrimers: molecules and assemblies

     Rodriguez Ropero, Francisco; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    Polymer
    Vol. 51, num. 1, p. 308-315
    DOI: 10.1016/j.polymer.2009.11.007
    Date of publication: 2010-01
    Journal article

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    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.

  • On the pi-stacking of oxidized thiophene oligomers

     Rodriguez Ropero, Francisco; Casanovas Salas, Jordi; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    Chemical physics letters
    Vol. 488, num. 4-6, p. 177-181
    DOI: 10.1016/j.cplett.2010.01.074
    Date of publication: 2010-03
    Journal article

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  • Self-Assembly of a Designed Amyloid Peptide Containing the Functional Thienylalanine Unit

     Hamley, I. W.; Brown, Gordon D.A.; Castelletto, V.; Cheng, G.; Venanzi, M.; Caruso, M.; Placidi, E.; Aleman Llanso, Carlos Enrique; Revilla Lopez, Guillermo; Zanuy Gomara, David
    Journal of physical chemistry B
    Vol. 114, num. 32, p. 10674-10683
    DOI: 10.1021/jp105508g
    Date of publication: 2010-08-19
    Journal article

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    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.

  • Modeling of peptides tethered to rigid surfaces

     Curcó, David; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    European Material Research Society Meeting
    Presentation's date: 2010-06-07
    Presentation of work at congresses

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  • INNOVACIO, MODELITZACIÓ I ENGINYERIA EN BIOMATERIALES (IMEM)

     Liesa Mestres, Francisco; Torras Costa, Juan; Bertran Cànovas, Oscar; Estrany Coda, Francisco; Zanuy Gomara, David; Armelin Diggroc, Elaine; Iribarren Laco, Jose Ignacio; Revilla Lopez, Guillermo; Aleman Llanso, Carlos Enrique
    Competitive project

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  • Non-proteogenic amino acids database

     Revilla Lopez, Guillermo; Torras Costa, Juan; Curcó, David; Casanovas Salas, Jordi; Zanuy Gomara, David; Nussinov, Ruth; Aleman Llanso, Carlos Enrique
    49th Sanibel Symposium on atomic, molecular, biophysical, and condensed matter theory
    Presentation of work at congresses

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  • Integrating the intrinsic conformational preferences of non-coded amino acids in a database for application in nanobiology

     Revilla Lopez, Guillermo; Torras Costa, Juan; Curcó, David; Casanovas Salas, Jordi; Zanuy Gomara, David; Jimenez Sanz, Ana Isabel; Cativiela, Carlos; Nussinov, Ruth; Aleman Llanso, Carlos Enrique
    Theoretical Chemistry: Modeling reactivity from gas phase to biomolecules and solids
    p. 75
    Presentation of work at congresses

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  • Appication of molecular simulation techniques to the design of nanosystems  Open access  awarded activity

     Rodriguez Ropero, Francisco
    Department of Chemical Engineering, Universitat Politècnica de Catalunya
    Theses

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    Nanotechnology is a multidisciplinary branch of science and technology that involves a widerange of different fields such as chemistry, materials science, physics or chemical engineeringwhose goal is the production of new functional materials and devicesthrough the control of their organization at the atomic and molecular scale.Nanotechnology has jumped from research laboratories to our daily life and today all theprogresses made in this field have been translated into direct applications in different fields being electronics and computer science and biomedicine, where the most striking advances have beendone.What differences nanotechnology from traditional chemistry and physics can be summarized inthree points: (i) Analysis and control of the matterat the atomic and molecular level focusing in individual atoms; (ii) the appearance of novel physical properties because of the nanoscopicdimensions; (iii) the possibility of generating new complex functional systems with novelproperties.Modeling and theory are becoming vital to designing and improving nanodevices. The intrinsicnature of nano and supramolecular scale that involves tens, hundreds and thousands of atomsmakes computational chemistry the perfect ally to design new devices and predict their properties. Computational chemistry provides the perfect tools to describe the electronic structureand the dynamic behavior, as well as the properties derived from them, through quantummechanics and classical mechanics formalisms.The suitability of such techniques in the design and improvement of nanodevices as well as theprediction of their properties is clearly proven throughout the four blocks in which this thesis isdivided:· Nanotubes based on natural peptide sequencesNanotubes have gained extensive interest because of their applicability in different fieldsranging from medicine to electronics. Among nanotubes, those based on natural peptidesequences taken from some natural proteins with a tubular or fibrillar motif are gaining abroad attention because of their high biocompatibility, the possibility of adding functionalitiesby tuning them and their potentiality to self-assemble. The enhancement of the ability to retain the tubular geometry of such structures can be achieved by substituting targeted amino acids located in the more flexible parts of the nanoconstruct by synthetic amino acids withlow conformational flexibility providing a larger rigidity to the overall structure.· Dendronized polymersDendronized polymers are a specific kind of macromolecule structure that consists of a linearpolymeric backbone where dendritic units are attached regularly leading to a highly branchedthree-dimensional architecture. This fact provides dendronized polymers the peculiarity of the coexistence within the same macromolecule of three topological regions: (i) the internalbackbone; (ii) the dendron region around the backbone and (iii) the external surface. Thesemolecules have a wide range of applications in different fields such as biomedical engineering, host-guest chemistry or catalysis.· Theoretical study of ð-conjugated systemsConducting polymers are polymers bearing a characteristic polyconjugated nature which makethem electronic conductors. In particular thiophene-based conducting polymers have been widely studied because of their electric and nonlinear optical properties, excellent environmentalstability and relatively low cost of production. Due to the crucial role played by the electronicstructure of these systems in their relevant properties, a good knowledge of it is a key factor todesign and improve new conducting polymers. To achieve this goal QM calculations suitperfectly to get accurate estimates of such properties.· Molecular actuators and sensors based on conducting polymersBoth experimental and computational research in nanoactuators and nanosensors are widelyreported in the literature. Among them, those based in conducting polymers are flourishingbecause of their great transport properties, electrical conductivity or rate of energy migrationwhich provide amplified sensitivity in nanosensors and a rapid response in nanoactuators. In thissense electron-rich thiophene-based oligomers and polymers combined with versatilecalix[4]arenes units are presented in the present thesis. Calix[4]arenes are synthetic macrocyclic molecules consisting of four phenol or anisole rings connected via methylene bridges that canhost different guest molecules leading to conformational rearrangement of the whole device making it useful to be employed as a sensor or actuator.

  • Helical Dendronized Polymers with Chiral Second-Generation Dendrons: Atomistic View and Driving Forces for Structure Formation

     Rodriguez Ropero, Francisco; Canales Gabriel, Manel; Zanuy Gomara, David; Zhang, Afang; Schlüter, A. Dieter; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Vol. 113, num. 45, p. 14868-14876
    DOI: 10.1021/jp903782f
    Date of publication: 2009
    Journal article

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  • A comprehensive study of the interactions between DNA and poly(3,4-ethylenedioxythiophene)

     Aleman Llanso, Carlos Enrique; da Cruz Teixeira Dias, Bruno José; Zanuy Gomara, David; Estrany Coda, Francisco; Armelin Diggroc, Elaine; Del Valle Mendoza, Luis Javier
    Polymer
    Vol. 50, num. 8, p. 1965-1974
    Date of publication: 2009-04
    Journal article

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  • Influence of the Dye Presence on the Conformational Preferences of CREKA, a Tumor Homing Linear Pentapeptide

     Zanuy Gomara, David; Curcó, David; Nussinov, R; Aleman Llanso, Carlos Enrique
    Biopolymers
    Vol. 92, num. 2, p. 83-93
    Date of publication: 2009-01
    Journal article

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  • Sensing Abilities of Crown Ether Functionalized Polythiophenes

     Casanovas, J; Preat, J; Zanuy Gomara, David; Aleman Llanso, Carlos Enrique
    Chemistry: a european journal
    Vol. 15, num. 18, p. 4676-4684
    Date of publication: 2009-03
    Journal article

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  • Sensing Mechanism of Calix[4]arene-Substituted Poly(thiophene) Ion Receptor: Effects of the Selectivity on the Molecular Rigidity

     Rodriguez-Ropero, F; Rodriguez Ropero, Francisco; Preat, J; Zanuy Gomara, David; Torras Costa, Juan; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Vol. 113, num. 24, p. 8284-8287
    Date of publication: 2009-06
    Journal article

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  • In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide

     Zanuy Gomara, David; Flores-Ortega, A; Jimenez, AI; Calaza, MI; Cativiela, Carlos; Nussinov, R; Ruoslahti, Erkki; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Vol. 113, num. 22, p. 7879-7889
    Date of publication: 2009-06
    Journal article

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  • Modeling an Electronic Conductor Based on Natural Peptide Sequences

     Rodriguez-Ropero, F; Rodriguez Ropero, Francisco; Zanuy Gomara, David; Assfeld, X; Aleman Llanso, Carlos Enrique
    Biomacromolecules
    Vol. 10, num. 8, p. 2338-2343
    Date of publication: 2009-08
    Journal article

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  • Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale

     Zanuy Gomara, David; Ballano Ballano, María Gema; Jimenez, AI; Casanovas, J; Haspel, N; Cativiela, Carlos; Curcó, David; Nussinov, R; Aleman Llanso, Carlos Enrique
    Journal of chemical information and computer sciences
    Vol. 49, num. 7, p. 1623-1629
    Date of publication: 2009-01
    Journal article

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  • Study of specific interactions in complexes formed by polythiophene derivatives and plasmid DNA

     da Cruz Teixeira Dias, Bruno José; Del Valle Mendoza, Luis Javier; Zanuy Gomara, David; Estrany Coda, Francisco; Armelin Diggroc, Elaine; Aleman Llanso, Carlos Enrique
    Reunión del Grupo Especializado de Polímeros
    p. 151
    Presentation's date: 2009-09-20
    Presentation of work at congresses

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  • Descripción microscópica de sensores basados en politiofenos funcionalizados con macrociclos complejos

     Aleman Llanso, Carlos Enrique; Casanovas Salas, Jordi; Preat, Julien; Rodriguez Ropero, Francisco; Torras Costa, Juan; Zanuy Gomara, David
    Reunión del Grupo Especializado de Polímeros
    p. 150
    Presentation's date: 2009-09-20
    Presentation of work at congresses

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  • Modeling a nanowire based on natural peptide sequences

     Rodriguez Ropero, Francisco; Zanuy Gomara, David; Assfeld, Xavier; Aleman Llanso, Carlos Enrique
    Theoretical Chemistry: Modeling Reactivity from Gas Phase to Biomolecules and Solids
    p. 77
    Presentation's date: 2009-06-29
    Presentation of work at congresses

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  • In silico improvement of a tumor homing peptide using a conformationally restricted arginine analogue

     Revilla Lopez, Guillermo; Zanuy Gomara, David; Torras Costa, Juan; Nussinov, Ruth
    Peptide Engineering Meeting
    Presentation's date: 2009-10-26
    Presentation of work at congresses

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