Carlos Aleman

Summary

Country: Spain

Publications

  1. ncbi request reprint Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents
    Jordi 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
  2. ncbi request reprint Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids
    Carlos 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
  3. ncbi request reprint Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid
    Carlos 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
  4. pmc Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue
    Carlos 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
  5. ncbi request reprint Acid-base and electronic structure-dependent properties of Hoechst 33342
    Carlos 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
  6. ncbi request reprint Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences
    David Zanuy
    Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona, Spain
    Biomacromolecules 8:3135-46. 2007
  7. ncbi request reprint A molecular dynamics study of the stoichiometric complex formed by poly (alpha, L-glutamate) and octyltrimethylammonium ions in chloroform solution
    David Zanuy
    Department d Enginyeria Quimica, E T S d Enginyers Industrials de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E 08028, Spain
    Biopolymers 63:151-62. 2002
  8. pmc Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database
    Guillem 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
  9. pmc The energy landscape of a selective tumor-homing pentapeptide
    David 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
  10. ncbi request reprint Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics study
    David 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

Collaborators

Detail Information

Publications74

  1. ncbi request reprint Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents
    Jordi 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...
  2. ncbi request reprint Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids
    Carlos 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...
  3. ncbi request reprint Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid
    Carlos 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...
  4. pmc Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue
    Carlos 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...
  5. ncbi request reprint Acid-base and electronic structure-dependent properties of Hoechst 33342
    Carlos 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...
  6. ncbi request reprint Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences
    David Zanuy
    Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona, Spain
    Biomacromolecules 8:3135-46. 2007
    ....
  7. ncbi request reprint A molecular dynamics study of the stoichiometric complex formed by poly (alpha, L-glutamate) and octyltrimethylammonium ions in chloroform solution
    David Zanuy
    Department d Enginyeria Quimica, E T S d Enginyers Industrials de Barcelona, Universitat Politecnica de Catalunya, 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...
  8. pmc Integrating the intrinsic conformational preferences of noncoded α-amino acids modified at the peptide bond into the noncoded amino acids database
    Guillem 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
    ....
  9. pmc The energy landscape of a selective tumor-homing pentapeptide
    David 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...
  10. ncbi request reprint Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: a molecular dynamics study
    David 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...
  11. doi request reprint Hydrogen-bonding interactions in 2-thiophen-3-ylmalonic acid
    Jordi 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...
  12. pmc Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design
    Francisco 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...
  13. ncbi request reprint Thermally induced phase transition in helical comblike poly(beta-peptide)s: an atomistic simulation
    David Zanuy
    Departament d Enginyeria Quimica, E T S d Enginyers Industrials de Barcelona, Universitat Politecnica de Catalunya, 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...
  14. pmc NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids
    Guillem 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...
  15. ncbi request reprint 1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue
    Jordi 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...
  16. pmc Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue
    Guillem 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...
  17. pmc In silico molecular engineering for a targeted replacement in a tumor-homing peptide
    David 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...
  18. doi request reprint Sensing mechanism of calix[4]arene-substituted poly(thiophene) ion receptor: effects of the selectivity on the molecular rigidity
    Francisco 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+...
  19. doi request reprint Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)s
    Julien 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...
  20. ncbi request reprint 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 phenylalanine
    Jordi 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...
  21. ncbi request reprint The conformation of dehydroalanine in short homopeptides: molecular dynamics simulations of a 6-residue chain
    David Zanuy
    Departament d Enginyeria Quimica, ETSEIB, Universitat Politecnica de Catalunya, 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...
  22. ncbi request reprint From peptide-based material science to protein fibrils: discipline convergence in nanobiology
    David Zanuy
    Departament d Enginyeria Quimica, ETS d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, 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...
  23. ncbi request reprint Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing
    David 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...
  24. pmc Conformational profile of a proline-arginine hybrid
    Guillermo 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...
  25. doi request reprint Effects of ring contraction on the conformational preferences of α-substituted proline analogs
    Guillem Revilla-López
    Departament d Enginyeria Quimica, Universitat Politecnica de Catalunya, Barcelona, Spain
    Biopolymers 98:98-110. 2012
    ....
  26. doi request reprint Protonation of the side group in beta- and gamma-aminated proline analogues: effects on the conformational preferences
    Alejandra 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
    ....
  27. pmc Conformational preferences of alpha-substituted proline analogues
    Alejandra 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...
  28. ncbi request reprint Force-field parametrization of retro-inverso modified residues: development of torsional and electrostatic parameters
    David 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...
  29. ncbi request reprint Comblike poly(alpha-alkyl gamma-glutamate)s: computer simulation studies of an intermediate thermal phase
    David 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...
  30. ncbi request reprint Stochastic simulation of structural properties of natively unfolded and denatured proteins
    David 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
    ....
  31. doi request reprint Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide
    Guillem 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...
  32. pmc Conformational preferences of beta- and gamma-aminated proline analogues
    Alejandra 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...
  33. ncbi request reprint Use of constrained synthetic amino acids in beta-helix proteins for conformational control
    David 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...
  34. doi request reprint Correlation between symmetry breaker position and the preferences of conformationally constrained homopeptides: a molecular dynamics investigation
    Juan Torras
    Departament d Enginyeria Quimica, EUETII, Universitat Politecnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
    Biopolymers 90:695-706. 2008
    ....
  35. ncbi request reprint On the protonation equilibrium for the benzimidazole derivative Hoechst 33258: an electronic molecular orbital study
    Carlos 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...
  36. ncbi request reprint 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 strategy
    Carlos 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...
  37. doi request reprint Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor
    David 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 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...
  38. doi request reprint Intermolecular interactions in electron transfer through stretched helical peptides
    Daniel 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...
  39. doi request reprint Factors governing the conformational tendencies of C(α)-ethylated α-amino acids: chirality and side-chain size effects
    Jordi 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)...
  40. ncbi request reprint Performance of SuSi: a method for generating atomistic models of amorphous polymers based on a random search of energy minima
    David 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...
  41. doi request reprint Properties of poly(3-halidethiophene)s
    Jordi 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...
  42. doi request reprint Key building block of photoresponsive biomimetic systems
    Guillem 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...
  43. doi request reprint 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
    Sergio 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...
  44. ncbi request reprint Intrinsic conformational characteristics of alpha,alpha-diphenylglycine
    Jordi 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...
  45. ncbi request reprint Coarse-graining the self-assembly of beta-helical protein building blocks
    David 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...
  46. doi request reprint Helical dendronized polymers with chiral second-generation dendrons: atomistic view and driving forces for structure formation
    Francisco 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...
  47. doi request reprint Modeling an electronic conductor based on natural peptide sequences
    Francisco 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...
  48. doi request reprint Reviewing extrapolation procedures of the electronic properties on the π-conjugated polymer limit
    Juan 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...
  49. doi request reprint Structural and electronic properties of poly[N-(2-cyanoalkyl)pyrrole]s bearing small alkyl groups
    David 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...
  50. doi request reprint DNA-conducting polymer complexes: a computational study of the hydrogen bond between building blocks
    David 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
    ....
  51. doi request reprint Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptide
    David 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
    ....
  52. doi request reprint A first principle analysis of the structure of oligoanilines doped with alkylsulfonic acids
    Jordi 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...
  53. doi request reprint Atomistic modeling of peptides bound to a chemically active surface: conformational implications
    David 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...
  54. doi request reprint A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides
    David 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
    ....
  55. doi request reprint Modeling biominerals formed by apatites and DNA
    Guillermo Revilla-López
    Departament d Enginyeria Quimica, E T S d Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona, 08028, Spain
    Biointerphases 8:8. 2013
    ....
  56. doi request reprint Solvent-induced conformational flexibility of a bicyclic proline analogue: Octahydroindole-2-carboxylic acid
    Juan Torras
    Departament d Enginyeria Quimica, EEI, Universitat Politecnica de Catalunya, Pça Rei 15, Igualada, 08700, Spain
    Biopolymers 102:176-90. 2014
    ..2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 176-190, 2014. ..
  57. ncbi request reprint Conformations of proline analogues having double bonds in the ring
    Alejandra 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...
  58. doi request reprint Modeling the tetraphenylalanine-PEG hybrid amphiphile: from DFT calculations on the peptide to molecular dynamics simulations on the conjugate
    David 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...
  59. doi request reprint Structural and electronic properties of poly(thiaheterohelicene)s
    Juan 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...
  60. pmc Intrinsic conformational preferences of C(alpha,alpha)-dibenzylglycine
    Jordi Casanovas
    Departament de Quimica, Escola Politecnica Superior, Universitat de Lleida, c Jaume II no 69, Lleida, Spain
    J Org Chem 73:4205-11. 2008
    ....
  61. ncbi request reprint Coarse-grained representation of beta-helical protein building blocks
    David 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...
  62. ncbi request reprint Electro-biocompatibility of conjugates designed by chemical similarity
    Silvana Maione
    Departament d Enginyeria Quimica, E T S d Enginyers Industrials, Universitat Politecnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain Center for Research in Nano Engineering, Universitat Politecnica de Catalunya, Campus Sud, Edifici C, C Pasqual i Vila s n, Barcelona, E 08028, Spain
    J Pept Sci 20:537-46. 2014
    ..Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd. ..
  63. doi request reprint Determination of new Cu+, Cu2+, and Zn2+ Lennard-Jones ion parameters in acetonitrile
    Juan Torras
    Department of Chemical Engineering, Igualada School of Engineering, Universitat Politecnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
    J Phys Chem B 117:10513-22. 2013
    ..4, 4.8, and 7.3% when compared with experimental values. ..
  64. doi request reprint Mineralization of DNA into nanoparticles of hydroxyapatite
    Oscar Bertran
    Departament de Fisica Aplicada, EEI, Universitat Politecnica de Catalunya, Pça Rei 15, 08700 Igualada, Spain
    Dalton Trans 43:317-27. 2014
    ..The biominerals reported in this work are important for biomedical applications requiring the protection of DNA from aggressive environmental conditions. ..
  65. ncbi request reprint DFT-GIAO study of aryltetralin lignan lactones: conformational analyses and chemical shifts calculations
    Jordi 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...
  66. ncbi request reprint Ab initio calculations on pi-stacked thiophene dimer, trimer, and tetramer: structure, interaction energy, cooperative effects, and intermolecular electronic parameters
    Francisco 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...
  67. ncbi request reprint Response of crown ether functionalized polythiophenes to alkaline ions
    David 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...
  68. ncbi request reprint Water absorbed by polyaniline emeraldine tends to organize, forming nanodrops
    Jordi 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...
  69. ncbi request reprint Properties of oligothiophene dendrimers as a function of molecular architecture and generation number
    Esther 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...
  70. ncbi request reprint Cellular adhesion, proliferation and viability on conducting polymer substrates
    Luis 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...
  71. ncbi request reprint Modeling of amorphous polyaniline emeraldine base
    Manel 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...
  72. ncbi request reprint On the modeling of aggregates of an optically active regioregular polythiophene
    Juan 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...
  73. ncbi request reprint Molecular dynamics study of complexes of poly(glutamate) and dodecyltrimethylammonium
    David 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...
  74. ncbi request reprint Contraction process of an electroactive actuator based on a one microsecond atomistic molecular dynamics simulation
    David 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...