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  • Polythiophene-g-poly(ethylene glycol) graft copolymers for electroactive scaffolds

     Bendrea, Anca Dana; Fabregat Jove, Georgina; Torras Costa, Juan; Maione, Silvana; Cianga, Ioan; Del Valle Mendoza, Luis Javier; Cianga, Luminita; Aleman Llanso, Carlos Enrique
    Journal of materials chemistry B
    Date of publication: 2013
    Journal article

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    The properties, microscopic organization and behavior as the cellular matrix of an all-conjugated polythiophene backbone (PTh) and well-defined poly(ethylene glycol) (PEG) grafted chains have been investigated using different experimental techniques and molecular dynamic simulations. UV-vis spectroscopy has been used to determine the optical band gap, which has been found to vary between 2.25 and 2.9 eV depending on the length of the PEG chains and the chemical nature of the dopant anion, and to detect polaron ¿ bipolaron transitions between band gap states. The two graft copolymers have been found to be excellent cellular matrices, their behavior being remarkably better than that found for other biocompatible polythiophene derivatives [e.g. poly(3,4-ethylenedioxythiophene)]. This is fully consistent with the hydrophilicity of the copolymers, which increases with the molecular weight of the PEG chains, and the molecular organization predicted by atomistic molecular dynamics simulations. Graft copolymers tethered to the surface tend to form biphasic structures in solvated environments (i.e. extended PTh and PEG fragments are perpendicular and parallel to the surface, respectively) while they collapse onto the surface in desolvated environments. Furthermore, the electrochemical activity and the maximum of current density are remarkably higher for samples coated with cells than for uncoated samples, suggesting multiple biotechnological applications in which the transmission with cells is carried out at the electrochemical level.

  • Determination of new Cu+, Cu2+, and Zn2+ Lennard-Jones ion parameters in acetonitrile

     Torras Costa, Juan; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Date of publication: 2013-08-14
    Journal article

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    We present new Lennard-Jones (LJ) parameters for Cu+, Cu2+, and Zn2+ ion-acetonitrile interactions. The adjustment of ion parameters is made to reproduce simultaneously experimental solvation free energy and structural properties, namely ion¿N distance and coordination numbers. Initially, the methodology has been validated deriving parameters for well-studied Na+ and Cl¿ ions in acetonitrile being compared with experimental and theoretical data. The transferability of parameters is checked by the calculation of thermodynamic and structural properties with three different acetonitrile models. The results obtained for transition metal ions show an overall agreement with reference values. The solvation free energy calculated with new LJ trained parameters using a six-site acetonitrile model, and two older three- and six-site acetonitrile models presents, respectively, percent differences of 0.4, 4.8, and 7.3% when compared with experimental values.

  • Reviewing Extrapolation Procedures of the Electronic Properties on the p-Conjugated Polymer Limit

     Torras Costa, Juan; Casanovas, Jordi; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry A
    Date of publication: 2012-06-19
    Journal article

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  • Effects of ring contraction on the conformational preferences of a-substituted proline analogs

     Revilla Lopez, Guillermo; Warren, Javier G.; Torras Costa, Juan; Jiménez, Ana I.; Cativiela, Carlos; Aleman Llanso, Carlos Enrique
    Biopolymers
    Date of publication: 2012-03-01
    Journal article

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    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

  • Comment on ``A Minimal Implementation of the AMBER¿GAUSSIAN Interface for Ab Initio QM/MM-MD Simulation¿¿

     Roberts, Benjamin P.; Seabra, Gustavo M.; Roitberg, Adrian E.; Merz, Kenneth M.; Deumens, Erik; Torras Costa, Juan; Trickey, Samuel
    Journal of computational chemistry
    Date of publication: 2012-07-15
    Journal article

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    On the modeling of aggregates of an optically active regioregular polythiophene  Open access

     Torras Costa, Juan; Sanchez Navas, Cristina; Bertran Cànovas, Oscar; Aleman Llanso, Carlos Enrique
    Physical chemistry chemical physics
    Date of publication: 2012-02-14
    Journal article

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    The conformational properties of the optically active regioregular poly[(R)-3-(4-(4-ethyl-2-oxazolin-2-yl) phenyl) thiophene] (PEOPT) were explored by molecular dynamics on a single chain using several solvents of increasing polarity. Furthermore, their aggregate formation was studied over a wide range of temperatures using a replica exchange molecular dynamics simulation providing simulation data representative of the equilibrium behaviour of their aggregates. Results show a clear tendency of PEOPT to keep a syn–gauche conformation between continuous backbone thiophene rings favouring a bent chain structure in solvent. After studying their aggregation behaviour in acetonitrile, a strong tendency to pack stabilizing structures that reinforce the chirality of the polymer, in concordance with experimental data, was found. Two different aggregated structures were observed depending on oligomer length, a self-assembled helical aggregate based on stacked octamers and a bent double helix aggregate in large oligomers.

  • Key building block of photoresponsive biomimetic systems

     Revilla Lopez, Guillermo; Laurent,, Adele D.; Perpete, Eric A.; Jacquemin, Denis; Torras Costa, Juan; Assfeld, Xavier; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Date of publication: 2011-02-10
    Journal article

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

  • Influence of polarity of the medium in the saturation of the electronic properties for pi-conjugated oligothiophenes

     Aleman Llanso, Carlos Enrique; Torras Costa, Juan; Casanovas, Jordi
    Chemical physics letters
    Date of publication: 2011-08-05
    Journal article

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  • 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
    Date of publication: 2011
    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
    Defense's date: 2011-02-17
    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.

  • Structural and Electronic Properties of Poly[N-(2-cyanoalkyl)pyrrole]s Bearing Small Alkyl Groups

     Aradilla Zapata, David; Torras Costa, Juan; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Date of publication: 2011-03-31
    Journal article

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

  • 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
    Date of publication: 2011-06
    Journal article

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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
    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.

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    Field-Induced Transport in Sulfonated Poly(styrene-co-divinylbenzene) Membranes  Open access

     Bertran Cànovas, Oscar; Curcó, David; Torras Costa, Juan; Ferreira, Carlos Arthur; Aleman Llanso, Carlos Enrique
    Macromolecules
    Date of publication: 2010-12-06
    Journal article

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    Atomistic simulations have been carried to investigate electric field induced transport of hydronium ions in a sulfonated poly(styrene-co-divinylbenzene) membrane. In order to provide a good description of this cross-linked material, a methodology has been explicitly designed to construct a reliable model of the hydrated membrane. This model has been used to carry out molecular dynamics simulations in presence of electric fields, which varied from 0.001 to 3.0 V3 nm-1. Results show that the electric field affects the structure of the membrane producing both a redistribution of the unoccupied volume, which modifies the heterogeneity of the resin, and a rearrangement of the negatively charged sulfonate groups, which undergo a systematic alignment along the electric field direction. As was expected, the mobility of hydronium ions is enhanced with the strength of the electric field. Moreover, the electric field induces a significant rearrangement of the sulfonate groups, which is evidenced by the alignment of theC-S bonds along the direction of the field. The membrane has been found to behave as a spring, in which the force exerted by the electric field acts in opposite sense to the force exerted by the internal structure of the cross-linked material.

  • Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL system  Open access

     Bertran Cànovas, Oscar; Trickey, Samuel; Torras Costa, Juan
    Journal of computational chemistry
    Date of publication: 2010-11-15
    Journal article

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    The PUPIL system is a combination of software and protocols for the systematic linkage and interoperation of molecular dynamics and quantum mechanics codes to perform QM/MD (sometimes called QM/MM) calculations. The Gaussian-03 and Amber packages were added to the Pupil suite recently. However, efficient parallel QM codes are critical because calculation of the QM forces is the overwhelming majority of the computational load. Here we report details of incorporation of the deMon2k density functional suite as a new parallel QM code. An additional motivation is to add a highly optimized, purely DFT code. We illustrate with a demonstration study of the influence of perchlorate as a dopant ion of the poly(3,4-ethylenedioxythiophene) conducting polymer in explicit acetonitrile solvent using Amber and deMon2k. We discuss unanticipated requirements for use of a scheme for semi-empirical correction of Kohn-Sham eigenvalues to give physically meaningful one-electron gap energies. We provide comparison of both geometric parameters and electronic properties for non-doped and doped systems. We also present results comparing deMon2k and Gaussian03 calculation of forces for a short sequence of steps. And we discuss briefly some difficult problems of quantum zone scf convergence for the anionically doped system. The difficulties seem to be caused by well-know deficiencies in simple approximate exchange-correlation functionals.

  • Poly(2-thiophene-3-yl-malonic acid), a Polythiophene with Two Carboxylic Acids Per Repeating Unit

     Bertran Cànovas, Oscar; Armelin Diggroc, Elaine; Estrany Coda, Francisco; Gomes, Alex Linardi; Torras Costa, Juan; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Date of publication: 2010-04-22
    Journal article

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

  • Modeling the structural and electronic properties of an optically active regioregular polythiophene

     Bertran Cànovas, Oscar; Torras Costa, Juan; Aleman Llanso, Carlos Enrique
    The journal of physical chemistry. Part C, nanomaterials and interfaces
    Date of publication: 2010-06-03
    Journal article

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    A comprehensive theoretical study about the structural and electronic molecular properties of the optically active regioregular poly[(R)-3-(4-(4-ethyl-2-oxazolin-2-yl)phenyl)thiophene] and its model oligomers has been developed with use of quantum mechanical calculations. Results show two stable arrangements for the investigated oligomers. The first one consists of a plain structure with all the inter-ring dihedral angles arranged in a syn-gauche+ conformation rather than the anti-gauche+ typically found in substituted polythiophenes. This produces a reduction of the steric repulsions allowing the formation of a π-stacking alignment between phenyl groups of adjacent monomers. The second is a helical structure with six repeating units per turn that is constructed by alternating the syn-gauche+ and syn-gauche- conformations. The lowest π-π* transition energy predicted for an idealized polymer chain, which was derived from Density Functional Theory calculations, is in agreement with the reported experimental values obtained by UV-vis spectroscopy.

  • Conformational preferences of proline analogues with a fused benzene ring

     Warren, Javier G.; Revilla Lopez, Guillermo; Aleman Llanso, Carlos Enrique; Jimenez Sanz, Ana Isabel; Cativiela, Carlos; Torras Costa, Juan
    Journal of physical chemistry B
    Date of publication: 2010-09-16
    Journal article

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    The intrinsic conformational preferences of indoline-2-carboxylic acid (Inc) and its R-methylated derivative (RMeInc) have been investigated using quantum mechanical calculations. Specifically, the behavior of their N-acetyl-N′-methylamide derivatives, Ac-L-Inc-NHMe and Ac-L-RMeInc-NHMe, has been explored at the B3LYP/6-31+G(d,p) level. Such amino acids are analogues of proline and (R-methyl)proline, respectively, bearing a benzene ring fused to the Cγ-Cδ bond of the five-membered pyrrolidine ring. The additional aromatic group has been shown to significantly restrict the conformational space available to these residues by reducing the flexibility of both the five-membered cycle and the peptide backbone. The fused benzene ring also plays a critical role in determining the cis-trans arrangement of the amide bond involving the pyrrolidine nitrogen, which is also modulated by the presence of the R-methyl group in the RMeInc derivative. Furthermore, the influence of the environment on the conformational propensities of these compounds has been evaluated by using both a self-consistent reaction field model and a recently developed interface in a hybrid QM/MM scheme, in which the solvent molecules are treated explicitly with classical mechanics while the solute is described by quantum mechanics at the density functional theory level.

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

     Revilla Lopez, Guillermo; Torras Costa, Juan; Curcó, David; Casanovas, 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
    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.

  • 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
    Date of publication: 2009-06
    Journal article

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  • Controlled Isomerization of a Light-Driven Molecular Motor: A Theoretical Study

     Torras Costa, Juan; Rodriguez Ropero, Francisco; Bertran Cànovas, Oscar; Aleman Llanso, Carlos Enrique
    The journal of physical chemistry. Part C, nanomaterials and interfaces
    Date of publication: 2009
    Journal article

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  • Non-Protogenic Amino Acids Database

     Torras Costa, Juan
    49th Sanibel Symposium on atomic, molecular, biophysical, and condensed matter theory
    Presentation's date: 2009-02-27
    Presentation of work at congresses

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  • Incorporating a new parallel quantum mechanical worker in the PUPIL system

     Torras Costa, Juan
    49th Sanibel Symposium on atomic, molecular, biophysical, and condensed matter theory
    Presentation's date: 2009-02-27
    Presentation of work at congresses

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  • Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue

     Revilla Lopez, Guillermo; Torras Costa, Juan; Jimenez Sanz, Ana Isabel; Cativiela, Carlos; Aleman Llanso, Carlos Enrique
    Journal of organic chemistry
    Date of publication: 2009
    Journal article

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  • A Multiscale Treatment of Angeli's Salt Decomposition

     Torras Costa, Juan; Seabra, Gustavo M.; Roitberg, Adrian E.
    Journal of chemical theory and computation
    Date of publication: 2009
    Journal article

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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
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  • Application of the Amber/PUPIL interface for hybrid QM/MM calculations

     Torras Costa, Juan
    49th Sanibel Symposium on atomic, molecular, biophysical, and condensed matter theory
    Presentation's date: 2009-02-27
    Presentation of work at congresses

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  • Structural and electronic properties of poly(thiaheterohelicene)s

     Torras Costa, Juan; Bertran Cànovas, Oscar; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry B
    Date of publication: 2009-10-26
    Journal article

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    Quantum chemical methods have been applied on model oligomers of poly(thiaheterohelicene)s to investigate the structural and electronic properties of these systems. Specifically, the properties of the helical structures found for poly(heterohelicene) and poly(methyl-sulfonium), which were calculated using density functional theory calculations, are in good agreement with available experimental data. The geometrical parameters obtained for poly(methyl-sulfonium) reflect the enlargement of the inner carbon-carbon bond lengths at the thiophene rings, which are those closer to the helical screw axes, and lead to reduce their aromaticity of such heterocycles. On this basis, a relationship between the aromaticity and the lowest π-π* transition energy has been established. Finally, the lowest π-π* transitions have been extrapolated for infinite polymer chains of poly(heterohelicene) and poly(methyl-sulfonium) using different theoretical approaches.

  • Cross-linking in polypyrrole and poly(N-methylpyrrole): comparative experimental and theoretical studies

     Aleman Llanso, Carlos Enrique; Casanovas, J; Torras Costa, Juan; Bertran Cànovas, Oscar; Armelin Diggroc, Elaine; Oliver Pujol, Ramon; Estrany Coda, Francisco
    Polymer
    Date of publication: 2008-02
    Journal article

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  • On the molecular properties of polyaniline: A comprehensive theoretical study

     Aleman Llanso, Carlos Enrique; Ferreira, Carlos Arthur; Torras Costa, Juan; Meneguzzi, Alvaro; Canales Gabriel, Manel; Rodrigues, Marco A S; Casanovas, Jordi
    Polymer
    Date of publication: 2008-10
    Journal article

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  • Structural and electronic properties of poly(3-thiophen-3-yl-acrylic acid)

     Bertran Cànovas, Oscar; Armelin Diggroc, Elaine; Torras Costa, Juan; Estrany Coda, Francisco; Mireia, Codina; Aleman Llanso, Carlos Enrique
    Polymer
    Date of publication: 2008-04
    Journal article

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  • Correlation between symmetry breaker position and the preferences of conformationally constrained homopeptides: a molecular dynamics investigation

     Torras Costa, Juan; Zanuy Gomara, David; Crisma, Marco; Toniolo, Claudio; Bertran Cànovas, Oscar; Aleman Llanso, Carlos Enrique
    Biopolymers
    Date of publication: 2008-10
    Journal article

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  • Hydrogen bonding interactions in 2-thiophen-2-ylmalonic acid

     Casanovas, Jordi; Bertran Cànovas, Oscar; Armelin Diggroc, Elaine; Torras Costa, Juan; Estrany Coda, Francisco; Aleman Llanso, Carlos Enrique
    Journal of physical chemistry A
    Date of publication: 2008-10
    Journal article

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  • Modelling organic molecular crystals by hybrid quantum mechanical/molecular mechanical embedding

     Torras Costa, Juan; Bromley, Stefan; Bertran Cànovas, Oscar; Francesc, Illas
    Chemical physics letters
    Date of publication: 2008-05
    Journal article

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  • A versatile AMBER-Gaussian QM/MM interface through PUPIL

     Torras Costa, Juan; Gustavo, De M Seabra; Deumens, Erik; Trickey, S B; Roitberg, Adrian E
    Journal of computational chemistry
    Date of publication: 2008-07
    Journal article

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  • Mixed QM/MM Calculations in Biological Systems

     Torras Costa, Juan
    From Computational Biophysics to Systems Biology
    Presentation of work at congresses

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  • Fracture, water dissociation, and proton conduction in SiO2 nanochains

     Torras Costa, Juan
    Journal of chemical physics
    Date of publication: 2007-06
    Journal article

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  • PUPIL: A systematic approach to software integration in multi-scale simulations

     Torras Costa, Juan
    Computer physics communications
    Date of publication: 2007-08
    Journal article

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  • Energetics and mechanical properties of silica nanotubes

     Muralidharan, Krishna; Torras Costa, Juan; Trickey, Juan Torras And S B
    Journal of physics: condensed matter
    Date of publication: 2007-09
    Journal article

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  • PUPIL: A New Tool for Multi-scale Simulation

     Torras Costa, Juan
    2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations
    Presentation's date: 2007-08-24
    Presentation of work at congresses

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  • Incoporating Existing Large Applications in the PUPIL System: Amber

     Torras Costa, Juan
    2007 American Physical Society March Meeting
    Presentation's date: 2007-03-07
    Presentation of work at congresses

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  • On the structural and electronic properties of poly(3-thiophen-3-yl-acrylic acid methyl ester)

     Bertran Cànovas, Oscar; Pfeifer, Peter; Torras Costa, Juan; Armelin Diggroc, Elaine; Estrany Coda, Francisco; Aleman Llanso, Carlos Enrique
    Polymer
    Date of publication: 2007-11
    Journal article

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  • Software integration in multi-scale simulations: the PUPIL system

     Torras Costa, Juan; Deumens, Erik; Trickey, Samuel
    Journal of computer-aided materials design
    Date of publication: 2006-07-25
    Journal article

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    The state of the art for computational tools in both computational chemistry and computational materials physics includes many algorithms and functionalities which are implemented again and again. Several projects aim to reduce, eliminate, or avoid this problem. Most such efforts seem to be focused within a particular specialty, either quantum chemistry or materials physics. Multi-scale simulations, by their very nature however, cannot respect that specialization. In simulation of fracture, for example, the energy gradients that drive the molecular dynamics (MD) come from a quantum mechanical treatment that most often derives from quantum chemistry. That “QM” region is linked to a surrounding “CM” region in which potentials yield the forces. The approach therefore requires the integration or at least inter-operation of quantum chemistry and materials physics algorithms. The same problem occurs in “QM/MM” simulations in computational biology. The challenge grows if pattern recognition or other analysis codes of some kind must be used as well. The most common mode of inter-operation is user intervention: codes are modified as needed and data files are managed “by hand” by the user (interactively and via shell scripts). User intervention is however inefficient by nature, difficult to transfer to the community, and prone to error. Some progress (e.g Sethna’s work at Cornell [C.R. Myers et al., Mat. Res. Soc. Symp. Proc., 538(1999) 509, C.-S. Chen et al., Poster presented at the Material Research Society Meeting (2000)]) has been made on using Python scripts to achieve a more efficient level of interoperation. In this communication we present an alternative approach to merging current working packages without the necessity of major recoding and with only a relatively light wrapper interface. The scheme supports communication among the different components required for a given multi-scale calculation and access to the functionalities of those components for the potential user. A general main program allows the management of every package with a special communication protocol between their interfaces following the directives introduced by the user which are stored in an XML structured file. The initial prototype of the PUPIL (Program for User Packages Interfacing and Linking) system has been done using Java as a fast, easy prototyping object oriented (OO) language. In order to test it, we have applied this prototype to a previously studied problem, the fracture of a silica nanorod. We did so joining two different packages to do a QM/MD calculation. The results show the potential for this software system to do different kind of simulations and its simplicity of maintenance.

  • Desarrollo de polímeros conductores con aplicaciones en ingeniería y biotecnología mediante simulación molecular y técnicas electroquímicas

     Aleman Llanso, Carlos Enrique; Iribarren Laco, Jose Ignacio; Armelin Diggroc, Elaine; Estrany Coda, Francisco; Torras Costa, Juan; Bertran Cànovas, Oscar; Zanuy Gomara, David; Liesa Mestres, Francisco
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  • Chemisorption of molecular oxygen on Cu(1 0 0): a Hartree¿Fock and density functional study

     Torras Costa, Juan; Lacaze-Dufaure, C.; Russo, Nino; Ricart Pla, Josep Manel
    Journal of molecular catalysis A. Chemical
    Date of publication: 2001-02-20
    Journal article

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

  • Density functional study of atomic nitrogen and oxygen chemisorption on model clusters simulating the Cu and Ag ( 100) surfaces

     Torras Costa, Juan; Toscano, M; Russo, Nino; Ricart Pla, Josep Manel
    Journal of molecular catalysis A. Chemical
    Date of publication: 1997-05-23
    Journal article

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    Density functional calculations which explicitly use the density gradient type nonlocal corrections to exchange and correlation are reported for the adsorption of atomic nitrogen and oxygen on the four-fold sites of (100) copper and silver surfaces simulated by Cu, and Ag, clusters. Binding energies, equilibrium distances and harmonic vibrational frequencies are in good agreement with the available experimental and high level theoretical data. An ionic contribution is found in the bonds between N and 0 and Cu and Ag clusters. Metal d orbitals are involved in the covalent part of the bond.

  • Cluster model study of the chemisorption of atomic carbon on Si(100) surfaces

     Torras Costa, Juan; Ricart Pla, Josep Manel; Vilarrubias, Pere; Fraxedas, J.
    Journal of crystal growth
    Date of publication: 1997-02-02
    Journal article

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    Structural parameters for chemisorption of atomic carbon above a Si(100) surface have been obtained through a Si35H 32 cluster model and a MINDO/3 hamiltonian. The most stable position has been found to be the bridge one when considering the unrelaxed surface. The stability increases about 14 kcal/mol when relaxation of the surface is allowed. Further research has been carried out using a reduced cluster model (SigH i2) at the ab initio Hartree-Fock level of calculation. Results confirm the increase of stability of the relaxed system. At this level, the binding energy is 90 kcal/mol for the unrelaxed surface and the stabilization when the surface is relaxed is of about 20% with respect to the non-relaxed surface.

  • Ab initio cluster model study of geometry and bonding character of atomic nitrogen chemisorbed on the Cu(100) and Ag(100) surfaces

     Ricart Pla, Josep Manel; Torras Costa, Juan; Rubio, Jaime; Illas, Francesc
    Surface science
    Date of publication: 1997-03-10
    Journal article

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    The chemisorption of atomic nitrogen on the four-fold site Cu(100) and Ag(100) surfaces has been modeled by Cu5N, AgsN and Cu41N cluster models. For these clusters, ab initio Hartree Fock electronic wave functions have been obtained and the chemisorption bond analyzed using a variety of techniques. In particular, the interaction energy has been decomposed by means of the constrained space orbital variation (CSOV), method. To obtain a reliable description of the interaction energy, electronic correlation effects have been explicitly accounted for. It is concluded that, contrary to other adsorbates such as halides or oxygen, the bond is essentially covalent but with a large charge transfer from the substrate to the adsorbate. Use of the CSOV analysis permits us to conclude that the direct covalent participation of the metal d electrons to the bond is very important. Finally, a preliminary attempt to study the relaxation of the substrate has been performed for the larger cluster only.

  • Bonding of atomic oxygen to Cu(100) and Ag(100) surfaces: a study of the nature of the interaction

     Ricart Pla, Josep Manel; Torras Costa, Juan; Illas, Francesc; Rubio, Jaime
    Surface science
    Date of publication: 1994-04-20
    Journal article

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