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Genomes and Genes | Carlos AlemanSummaryCountry: Spain Publications
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Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituentsJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II N 69, 25001 Lleida, Spain
J Phys Chem B 110:5762-6. 2006..Analysis of the whole results, which are fully consistent with available experimental data, indicates that c(3)Dip tends to promote gamma-turn conformations...
Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogueCarlos Aleman
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Org Chem 74:7834-43. 2009..Their conformational propensities have been found to be strongly influenced by the specific orientation of the aromatic substituent in each stereoisomer and the conformation adopted by the cyclohexane ring, as well as by the environment...- Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acidCarlos Aleman
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Phys Chem B 110:21264-71. 2006..Molecular dynamics simulations in both chloroform and aqueous solutions were performed to demonstrate the reliability of such parameters... - Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acidsCarlos Aleman
Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
Phys Biol 3:S54-62. 2006..The major challenge facing nanobiology is to be able to exercise fine control over the performance of these target-specific molecular machines... - Acid-base and electronic structure-dependent properties of Hoechst 33342Carlos Aleman
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona E 08028, Spain
J Biomol Struct Dyn 23:29-36. 2005..Finally, the connection of some theoretical predictions with experimental evidences has been examined... - Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequencesDavid Zanuy
Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona, Spain
Biomacromolecules 8:3135-46. 2007.... - Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids databaseGuillem Revilla-López
Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
Proteins 79:1841-52. 2011.... - The energy landscape of a selective tumor-homing pentapeptideDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Phys Chem B 112:8692-700. 2008..Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems... - Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics studyDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Struct Biol 160:177-89. 2007..We conclude that if the replacement does not alter the energy balance between attractive non-covalent interactions and steric hindrance, synthetic residues are suitable candidates to nucleate beta-helix formation... - Force-field parametrization of retro-inverso modified residues: development of torsional and electrostatic parametersDavid Curcó
Departament d Enginyeria Quimica, Facultat de Quimica, Universitat de Barcelona, Marti i Franques 1, E 08028, Barcelona, Spain
J Comput Aided Mol Des 20:13-25. 2006..Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined... - Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer designFrancisco Rodríguez-Ropero
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Chem Inf Model 48:333-43. 2008..Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e., when the rigidity introduced by the strain of the ring decreases... 
Hydrogen-bonding interactions in 2-thiophen-3-ylmalonic acidJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II 69, Lleida E 25001, Spain
J Phys Chem A 112:10650-6. 2008..On the other hand, intramolecular interactions in isolated monomers are favored in the melted state, which is dominated by a thermally driven entropic process...- Comblike poly(alpha-alkyl gamma-glutamate)s: computer simulation studies of an intermediate thermal phaseDavid Curcó
Departament d Enginyeria Quimica, ETS d Enginyers Industrials de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
Biomacromolecules 4:87-95. 2003..Comparison with previously reported comblike poly(beta-peptide)s revealed significant differences in the organization of the alkyl side chains... - In silico molecular engineering for a targeted replacement in a tumor-homing peptideDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Phys Chem B 113:7879-89. 2009..These results suggest that replacement of Arg by (Pro)hArg in CREKA may be useful in providing resistance against proteolytic enzymes while retaining conformational features which are essential for tumor-homing activity... - NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acidsGuillem Revilla-López
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
J Phys Chem B 114:7413-22. 2010..Furthermore, the NCAD usefulness is demonstrated through a test-case application example... - 1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogueJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II no 69, Lleida E 25001, Spain
J Org Chem 73:644-51. 2008..Results indicate that the conformational space of the cis stereoisomer is much more restricted than that of the trans derivative both in the gas phase and in solution... - Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)sJulien Preat
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona 08028, Spain
J Comput Chem 31:1741-51. 2010..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... - N-acetyl-N'-methylamide derivative of (2S,3S)-1-amino-2,3-diphenylcyclopropanecarboxylic acid: theoretical analysis of the conformational impact produced by the incorporation of the second phenyl group to the cyclopropane analogue of phenylalanineJordi Casanovas
Departament de Quimica, Escola Universitària Politècnica, Universitat de Lleida, c Jaume II no 69, 25001 Lleida, Spain
J Org Chem 68:7088-91. 2003..Results have been compared with those previously reported for other cyclopropane analogues of phenylalanine, and with experimental data available for c(3)diPhe-containing peptides... - Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogueGuillem Revilla-López
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Org Chem 74:2403-12. 2009..A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented... - Sensing mechanism of calix[4]arene-substituted poly(thiophene) ion receptor: effects of the selectivity on the molecular rigidityFrancisco Rodríguez-Ropero
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Phys Chem B 113:8284-7. 2009..These features are consistent with available experimental data explaining the selectivity of this material for Na+ over Li+ and K+... - Conformational profile of a proline-arginine hybridGuillermo Revilla-López
Departament d Enginyeria Química, ETS d Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Chem Inf Model 50:1781-9. 2010..Thus, both cis- and trans-((β)Pro)Arg exhibit a preference for the α(L) conformation as a consequence of the interactions established between the guanidinium moiety and the main-chain amide groups... - Effects of ring contraction on the conformational preferences of α-substituted proline analogsGuillem Revilla-López
Departament d Enginyeria Quimica, Universitat Politecnica de Catalunya, Barcelona, Spain
Biopolymers 98:98-110. 2012.... - Protonation of the side group in beta- and gamma-aminated proline analogues: effects on the conformational preferencesAlejandra Flores-Ortega
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Avda Diagonal no 647, 08028 Barcelona, Spain
J Org Chem 74:3101-8. 2009.... - Conformational preferences of alpha-substituted proline analoguesAlejandra Flores-Ortega
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain
J Org Chem 73:3418-27. 2008..The results obtained provide evidence that the distinct steric requirements of the substituent at C (alpha) may play a significant role in modulating the conformational preferences of proline... - Stochastic simulation of structural properties of natively unfolded and denatured proteinsDavid Curcó
Departament d Enginyeria Quimica, Facultat de Quimica, Universitat de Barcelona, Marí i Franques 1, Barcelona, 08028, Spain
J Mol Model 18:4503-16. 2012.... - Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptideGuillem Revilla-López
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
Phys Chem Chem Phys 13:9986-94. 2011..Moreover, the conformational profile of the mutated peptide narrows towards the most stable structures previously observed for the parent CREKA peptide... - Use of constrained synthetic amino acids in beta-helix proteins for conformational controlDavid Zanuy
Departament d Enginyeria Quimica, ETSEIB, Universitat Politecnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
J Phys Chem B 111:3236-42. 2007..Simulations of wild type and mutated segments revealed that the ability of the phenylalanine analogue to nucleate turn conformations enhances the conformational stability of the beta-helix motif in isolated peptide segments... - Unusually high pyramidal geometry of the bicyclic amide nitrogen in a complex 7-azabicyclo[2.2.1]heptane derivative: Theoretical analysis using a bottom-up strategyCarlos Aleman
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, E 08028 Barcelona, Spain
J Phys Chem B 109:11836-41. 2005..For this purpose, several derivatives were generated by removing or modifying the substituents attached to the 7-azanorbornane system. Results have been discussed in terms of intramolecular specific interactions... - Conformational preferences of beta- and gamma-aminated proline analoguesAlejandra Flores-Ortega
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona, Spain
J Phys Chem B 112:14045-55. 2008..e., the more favored conformers, calculated for different isomers of aminoproline and (dimethylamino)proline dipeptides showed a high degree of consistency for the two families of compounds... - On the protonation equilibrium for the benzimidazole derivative Hoechst 33258: an electronic molecular orbital studyCarlos Aleman
Departament d Enginyeria Quimica, E T S d Enginyers Industrials de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Biomol Struct Dyn 20:301-10. 2002..Comparison of these Delta(p)K(a) values with experimentally reported data have been used to highlight the advantages and limitations of this strategy... - Correlation between symmetry breaker position and the preferences of conformationally constrained homopeptides: a molecular dynamics investigationJuan Torras
Departament d Enginyeria Quimica, EUETII, Universitat Politecnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
Biopolymers 90:695-706. 2008.... - A molecular dynamics study of the stoichiometric complex formed by poly (alpha, L-glutamate) and octyltrimethylammonium ions in chloroform solutionDavid Zanuy
, E. T. S. d'Enginyers Industrials de Barcelona, , Diagonal 647, Barcelona E-08028, Spain
Biopolymers 63:151-62. 2002..It was found that the most populated arrangement was that with the surfactant cations interacting with two carboxylate groups simultaneously... - Intermolecular interactions in electron transfer through stretched helical peptidesDaniel E López-Pérez
Departament d Enginyeria Quimica, ETSEIB, Universitat Politecnica de Catalunya, Av Diagonal 647, 08028, Barcelona, Spain
Phys Chem Chem Phys 14:10332-44. 2012..Finally, quantum mechanical calculations have been used to investigate the variation of the electronic structure upon compression and stretching deformations... - Factors governing the conformational tendencies of C(α)-ethylated α-amino acids: chirality and side-chain size effectsJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, 25001 Lleida, Spain
J Phys Chem B 116:13297-307. 2012..g., C(α,α)-diphenylglycine and C(α,α)-dibenzylglycine)... - Properties of poly(3-halidethiophene)sJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II no 69, Lleida E 25001, Spain
Phys Chem Chem Phys 14:10050-62. 2012..Both the ionization potential and the π-π* lowest transition energy have been predicted to increase slightly when the π-donor character of the halogen atom decreases, in agreement with experimental observations... - Performance of SuSi: a method for generating atomistic models of amorphous polymers based on a random search of energy minimaDavid Curcó
Departament d Enginyeria Quimica, Facultat de Quimica, Universitat de Barcelona, Marti i Franques 1, Barcelona E 08028, Spain
J Comput Chem 25:790-8. 2004..Calculations have been performed on poly(L,D-lactic) acid (rho = 1.25 g/cm3) and nylon 6 (rho = 1.084 g/cm(3)), which are important commercial polymers... - Key building block of photoresponsive biomimetic systemsGuillem Revilla-López
Departament d Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
J Phys Chem B 115:1232-42. 2011..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... - 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 propertiesSergio Carrión
Departament d Enginyeria Quimica, ETSEIB, Universitat Politecnica de Catalunya, Avda Diagonal 647, Barcelona E 08028, Spain
J Phys Chem B 114:3494-9. 2010..Accordingly, the oxidized poly(3,4-phenylenedioxythiophene) shows the lowest pi-pi* electron transition energy... - Helical dendronized polymers with chiral second-generation dendrons: atomistic view and driving forces for structure formationFrancisco Rodríguez-Ropero
Departament d Enginyeria Quimica, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Phys Chem B 113:14868-76. 2009..In addition, the impact of the conformational changes produced when the protected system transforms into the deprotected one by the addition of acid has been evaluated... - Modeling an electronic conductor based on natural peptide sequencesFrancisco Rodríguez-Ropero
Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona E 08028, Spain
Biomacromolecules 10:2338-43. 2009..The overall results reflected that the system under study is a potential candidate to be used as a nanowire... - Intrinsic conformational characteristics of alpha,alpha-diphenylglycineJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, Spain
J Org Chem 72:2174-81. 2007..Molecular Dynamics simulations in aqueous solutions have been carried out to validate the parameters obtained... - Coarse-graining the self-assembly of beta-helical protein building blocksDavid Curcó
Departament d Enginyeria Quimica, Facultat de Quimica, Universitat de Barcelona, Marti i Franques 1, Barcelona E 08028, Spain
J Phys Chem B 111:14006-11. 2007..coli galactoside acteyltransferase becomes repulsive when the size of the nanotube is larger than a threshold, that is, about 45 self-assembled building blocks... - Reviewing extrapolation procedures of the electronic properties on the π-conjugated polymer limitJuan Torras
Departament d Enginyeria Quimica, Escola d Enginyeria d Igualada, Universitat Politecnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
J Phys Chem A 116:7571-83. 2012..Finally, implications of the environmental polarity on the electronic properties, molecular geometry, charge distribution, and aromaticity are shortly discussed... - Structural and electronic properties of poly[N-(2-cyanoalkyl)pyrrole]s bearing small alkyl groupsDavid Aradilla
Departament d Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Barcelona, Spain
J Phys Chem B 115:2882-9. 2011..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... - A first principle analysis of the structure of oligoanilines doped with alkylsulfonic acidsJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II no 69, Lleida E 25001, Spain
J Phys Chem A 113:8795-800. 2009..The overall results allow the conclusion that the interaction between alkylsulfonate dopants and polyaniline is a very local phenomenon... - Atomistic modeling of peptides bound to a chemically active surface: conformational implicationsDavid Curcó
Department d Enginyeria Quimica, Facultat de Quimica, Universitat de Barcelona, Martí Franques 1, Barcelona E 08028, Spain
J Pept Sci 17:132-8. 2011..Specifically, simulations reflect that consideration of the peptide-surface interactions affect the geometrical orientation of the side chains, whereas the main chain conformation does not undergo significant modifications... - A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptidesDavid Curcó
Department d Enginyeria Quimica, Facultat de Quimica, Universitat de Barcelona, Martí Franques 1, Barcelona E 08028, Spain
J Comput Chem 32:607-19. 2011.... - DNA-conducting polymer complexes: a computational study of the hydrogen bond between building blocksDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona, Spain
J Phys Chem B 112:3222-30. 2008.... - Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptideDavid Zanuy
Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
Biopolymers 92:83-93. 2009.... - From peptide-based material science to protein fibrils: discipline convergence in nanobiologyDavid Zanuy
, ETS d'Enginyeria Industrial de Barcelona, , Diagonal 647, Barcelona E-08028, Spain
Phys Biol 3:S80-90. 2006..For material scientists, the enhanced coverage of chemical space obtained by integrating proteins and synthetic organic chemistry through the introduction of non-natural residues allows a range of new useful potential applications... - The conformation of dehydroalanine in short homopeptides: molecular dynamics simulations of a 6-residue chainDavid Zanuy
Departament d'Enginyeria Quimica, ETSEIB, , Diagonal 647, E-08028, Barcelona, Spain
Biophys Chem 98:301-12. 2002..Furthermore, ab initio calculations have been performed in order to estimate 1[H]-NMR chemical shifts. Results have been compared with experimental data... - Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugateDavid Zanuy
Departament d Enginyeria Química, E T S d Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
J Phys Chem B 115:8937-46. 2011..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... - Structural and electronic properties of poly(thiaheterohelicene)sJuan Torras
Departament d Enginyeria Quíímica, EUETII, Universitat Politecnica de Catalunya, Pça Rei 15, 08700 Igualada, Spain
J Phys Chem B 113:15196-203. 2009..Finally, the lowest pi-pi* transitions have been extrapolated for infinite polymer chains of poly(heterohelicene) and poly(methyl-sulfonium) using different theoretical approaches... - Conformations of proline analogues having double bonds in the ringAlejandra Flores Ortega
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
J Phys Chem B 111:5475-82. 2007..Interestingly, we also found that the N-acetyl-N'-methylamide derivative of pyrrole shows a high probability of having a cis peptide bond preceding the proline analogue... - Coarse-grained representation of beta-helical protein building blocksDavid Curcó
Departament d Enginyeria Quimica, Facultat de Quimica, Universitat de Barcelona, Martí i Franquees 1, Barcelona E 08028, Spain
J Phys Chem B 111:10538-49. 2007..The reliability of the proposed model has been tested by comparing the atomistic and coarse-grained energies calculated for a large number of independent configurations of the beta-helical building block... - Intrinsic conformational preferences of C(alpha,alpha)-dibenzylglycineJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II no 69, Lleida, Spain
J Org Chem 73:4205-11. 2008.... - Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homingDavid Zanuy
Department of Chemical Engineering, ETSEIB, Universitat Politecnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
J Comput Aided Mol Des 27:31-43. 2013..Combined, our results show how studies based on multi-disciplinary collaboration can converge and lead to useful biomedical advances... - DFT-GIAO study of aryltetralin lignan lactones: conformational analyses and chemical shifts calculationsJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II n o 69, Lleida E 25001, Spain
Bioorg Chem 33:484-92. 2005..4 kcal/mol were detected. Furthermore, chemical shifts for 13C nuclei have been calculated using the GIAO method, results being compared with experimental data. A good agreement was found for both polygamain and morelensin... - Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptorDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain Electronic address
J Struct Biol 182:78-86. 2013..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... - Ab initio calculations on pi-stacked thiophene dimer, trimer, and tetramer: structure, interaction energy, cooperative effects, and intermolecular electronic parametersFrancisco Rodríguez-Ropero
Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, E 08028 Barcelona, Spain
J Comput Chem 29:69-78. 2008..Finally, we found that the lowest transition energy decreases when the size of the complex increases, this feature being attributed to desestabilization of the HOMO and stabilization of the LUMO that occur simultaneously... - Thermally induced phase transition in helical comblike poly(beta-peptide)s: an atomistic simulationDavid Zanuy
, E.T.S. d'Enginyers Industrials de Barcelona, , Diagonal 647, Barcelona E-08028, Spain
J Comput Chem 24:770-8. 2003..Results were consistent with available experimental observations. The limitations of atomistic simulations to study large length-scale phenomena are discussed... - Response of crown ether functionalized polythiophenes to alkaline ionsDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona, Spain
J Phys Chem B 116:4575-83. 2012..Eur. J. 2009, 15, 4676]. Results indicate an entropycally driven binding preference... - Water absorbed by polyaniline emeraldine tends to organize, forming nanodropsJordi Casanovas
Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II N 69, Lleida E 25001, Spain
J Phys Chem B 116:7342-50. 2012..The binding energies calculated for these two types of water molecules are fully consistent with the thermodynamic activation energies previously reported... - Properties of oligothiophene dendrimers as a function of molecular architecture and generation numberEsther Córdova-Mateo
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, 08028 Barcelona Spain, Fax 34 934017150 Departament de Física Aplicada, EEI, Universitat Politecnica de Catalunya, Pça Rei 15, Igualada 08700 Spain
Chemphyschem 13:1354-62. 2012..Two mathematical models developed to predict the lowest π-π* transition energy of all-thiophene dendrimers that are inaccessible to quantum mechanical calculations are tested on a dendrimer with 90 thiophene rings... - Molecular dynamics study of complexes of poly(glutamate) and dodecyltrimethylammoniumDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyers Industrials de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
Biomacromolecules 8:663-71. 2007..The more important differences between the results obtained using the spherical cutoff and Particle Mesh Ewald methods are discussed... - Cellular adhesion, proliferation and viability on conducting polymer substratesLuis J Del Valle
Departament d Enginyeria Agroalimentària i Biotecnologia, ESAB, Universitat Politecnica de Catalunya, Castelldefels, Spain
Macromol Biosci 8:1144-51. 2008..Furthermore, the three polymeric systems are electro-compatible with the cellular monolayers... - Modeling of amorphous polyaniline emeraldine baseManel Canales
Departament de Fisica i Enginyeria Nuclear, Facultat d Informàtica, Universitat Politecnica de Catalunya, Jordi Girona 1 3, Barcelona E 08034, Spain
J Phys Chem B 114:9771-7. 2010..On the other hand, the partial radial distribution functions indicate that this material only exhibits short-range intramolecular correlation, which is in excellent agreement with experimental evidence... - On the modeling of aggregates of an optically active regioregular polythiopheneJuan Torras
Departament d Enginyeria Quimica, Escola d Enginyeria d Igualada, Universitat Politecnica de Catalunya, Pça Rei 15, 08700 Igualada, Spain
Phys Chem Chem Phys 14:1881-91. 2012..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... - Contraction process of an electroactive actuator based on a one microsecond atomistic molecular dynamics simulationDavid Zanuy
Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona 08028, Spain
Chemistry 13:2695-700. 2007..On the other hand, the rate of the contraction process is influenced by the presence of solvent molecules, which have been found to reduce it by a factor of about 1000...