Water-driven stabilization of diphenylalanine nanotube structures

Theoretical Chemistry Accounts

Volumn 135, Issue 8, 2016, Pages

  Andrade Filho, T ^a   Martins, Tiago Carvalho ^a   Ferreira, Fabio Furlan ^b   Alves, Wendel Andrade ^b   Rocha, Alexandre Reily ^c  

^a UNIVERSIDADE FEDERAL DO SUL E SUDESTE DO PARÁ   (Brazil)

^b UNIVERSIDADE FEDERAL DO ABC   (Brazil)

^c SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

DFTB; Peptide nanotubes; Structural stability; Water properties

Indexed keywords

EID: 84978823926     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-016-1936-3     Document Type: Article

References (51)

1. Adler-Abramovich L, Aronov D, Beker P, Yevnin M, Stempler S, Buzhansky L, Rosenman G, Gazit E (2009) Self-assembled arrays of peptide nanotubes by vapour deposition. Nat Nanotech 4:849–854
2. Amdursky N, Beker P, Koren I, Bank-Srour B, Mishina E, Semin S, Rasing T, Rosenberg Y, Barkay Z, Gazit E, Rosenman G (2011) Structural transition in peptide nanotubes. Biomacromolecules 12:1349–1354
3. Andersen HC (1980) Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys 72:2384–2393
4. Andrade-Filho T, Ferreira FF, Alves WA, Rocha AR (2013) The effects of water molecules on the electronic and structural properties of peptide nanotubes. Phys Chem Chem Phys 15:7555–7559
5. Aradi B, Hourahine B, Frauenheim T (2007) DFTB+, a sparse matrix-based implementation of the DFTB method. J Phys Chem A 111:5678–5684
6. Bianchi RC, da Silva ER, Dall’Antonia LH, Ferreira FF, Alves WA (2014) A nonenzymatic biosensor based on gold electrodes modified with peptide self-assemblies for detecting ammonia and urea oxidation. Langmuir 30(38):11,464–11,473
7. Calero S, Gómez-Álvarez P (2014) Effect of the confinement and presence of cations on hydrogen bonding of water in LTA-type zeolite. J Phys Chem C 118:9056–9065
8. Cipriano TC, Takahashi PM, de Lima D, Oliveira VX, Souza JA, Martinho H, Alves WA (2009) Spatial organization of peptide nanotubes for electrochemical devices. J Mater Sci 45:5101–5108
9. Clark JK, Paddison SJ, Clark JK II, Paddison SJ (2014) Ab initio molecular dynamics simulations of water and an excess proton in water confined in carbon nanotubes. Phys Chem Chem Phys 16:17,756–17,769
10. Djalali R, Samson J, Matsui H (2004) Doughnut-shaped peptide nano-assemblies and their applications as nanoreactors. J Am Chem Soc 126:7935–7939
11. Do TD, Bowers MT (2015) Diphenylalanine self assembly: novel ion mobility methods showing the essential role of water. Anal Chem 87:4245–4252
12. Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys Rev B 58:7260–7268
13. Fairman R, Akerfeldt K (2005) Peptides as novel smart materials. Curr Opin Struct Biol 15:453–463
14. Gallo P, Rovere M (2003) Anomalous dynamics of confined water at low hydration. J Phys Condens Matter 15:7625–7633
15. Gaus M, Cui Q, Elstner M (2011) DFTB3: extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput 7:931–948
16. Gaus M, Goez A, Elstner M (2013) Parametrization and benchmark of DFTB3 for organic molecules. J Chem Theory Comput 9:338–354
17. Ghadiri MR, Granja JR, Milligan RA, McRee DE, Khazanovich N (1993) Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 366:324–327
18. Görbitz CH (2003) Nanotubes from hydrophobic dipeptides: pore size regulation through side chain substitution. New J Chem 27:1789–1793
19. Görbitz CH (2007) Microporous organic materials from hydrophobic dipeptides. Chem Eur J 13:1022–1031
20. Guo C, Luo Y, Zhou R, Wei G (2012) Probing the self-assembly mechanism of diphenylalanine-based peptide nanovesicles and nanotubes. ACS Nano 6:3907–3918
21. Han TH, Kim J, Park JS, Park CB, Ihee H, Kim SO (2007) Liquid crystalline peptide nanowires. Adv Mater 19:3924–3927
22. 2 nanoribbons templating diphenylalanine assembly. J Mater Chem 19:3512–3516
23. Hartgerink JD, Granja JR, Milligan RA, Ghadiri MR (1996) Self-assembling peptide nanotubes. J Am Chem Soc 118:43–50
24. Heredia A, Bdikin I, Kopyl S, Mishina E, Semin S, Sigov A, German K, Bystrov V, Gracio J, Kholkin AL (2010) Temperature-driven phase transformation in self-assembled diphenylalanine peptide nanotubes. J Phys D: Appl Phys 43:462,001–462,006
25. Im S, Jang SW, Lee S, Lee Y, Kim B (2008) Arginine zwitterion is more stable than the canonical form when solvated by a water molecule. J Phys Chem A 112:9767–9770
26. Jeon J, Mills CE, Shell MS (2013) Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization. J Phys Chem B 117:3935–3943
27. Kelly CM, Northey T, Ryan K, Brooks BR, Kholkin AL, Rodriguez BJ, Buchete NV (2015) Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field. Biophys Chem 196:16–24
28. Kim J, Han TH, Kim YI, Park JS, Choi J, Churchill DG, Kim SO, Ihee H (2010) Role of water in directing diphenylalanine assembly into nanotubes and nanowires. Adv Mater 22:583–587
29. Kim JY, Ahn DS, Park SW, Lee S (2014) Gas phase hydration of amino acids and dipeptides: effects on the relative stability of zwitterion vs. canonical conformers. RSC Adv 4:16,352–16,361
30. Kogikoski S, Sousa CP, Liberato MS, Andrade-Filho T, Prieto T, Ferreira FF, Rocha AR, Guha S, Alves WA (2016) Multifunctional biosensors based on peptide–polyelectrolyte conjugates. Phys Chem Chem Phys 18:3223–3233
31. Lee JS, Yoon I, Kim J, Ihee H, Kim B, Park CB (2011) Self-assembly of semiconducting photoluminescent peptide nanowires in the vapor phase. Angew Chem Int Ed 50:1164–1167
32. Martínez JM, Martínez L (2003) Packing optimization for automated generation of complex system’s initial configurations for molecular dynamics and docking. J Comput Chem 24:819–825
33. Martínez L, Andrade R, Birgin EG, Martínez JM (2009) Packmol: a package for building initial configurations for molecular dynamics simulations. J Comput Chem 30:2157–2164
34. Monkhorst HJ, Pack JD (1976) Special points for Brillouin-zone integrations. Phys Rev 13:5188–5192
35. Reches M, Gazit E (2003) Casting metal nanowires within discrete self-assembled peptide nanotubes. Science 300:625–627
36. Reches M, Gazit E (2006) Molecular self-assembly of peptide nanostructures: mechanism of association and potential uses. Curr Nanosci 2:105–111
37. Rovere M, Ricci MA, Vellati D, Bruni F (1998) A molecular dynamics simulation of water confined in a cylindrical SiO2 pore. J Chem Phys 108:9859–9867
38. Ryu J, Kim SW, Kang K, Park CB (2009) Synthesis of diphenylalanine/cobalt oxide hybrid nanowires and their application to energy storage. ACS Nano 4:159–164
39. Soper AK, Bruni F, Ricci MA (1998) Water confined in Vycor glass. II. Excluded volume effects on the radial distribution functions. J Chem Phys 109:1486–1494
40. Souza MI, Silva ER, Jaques YM, Ferreira FF, Fileti EE, Alves WA (2014) The role of water and structure on the generation of reactive oxygen species in peptide/hypericin complexes. J Pept Sci 20:554–562
41. Tortonda FR, Pascual-Ahuir JL, Silla E, Tuñón I, Ramírez FJ (1998) Aminoacid zwitterions in solution: geometric, energetic, and vibrational analysis using density functional theory-continuum model calculations. J Chem Phys 109(2):592–603
42. Vauthey S, Santoso S, Gong H, Watson N, Zhang S (2002) Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles. Proc Nat Acad Sci 99:5355–5360
43. Wang J, Liu K, Yan L, Wang A, Bai S, Yan X (2016) Trace solvent as a predominant factor to tune dipeptide self-assembly. ACS Nano 10:2138–2143
44. Wang L, Zhao J, Li F, Fang H, Lu JP (2009) First-principles study of water chains encapsulated in single-walled carbon nanotube. J Phys Chem C 113:5368–5375
45. Wang M, Xiong S, Wu X, Chu PK (2011) Effects of water molecules on photoluminescence from hierarchical peptide nanotubes and water probing capability. Small 7:2801–2807
46. Yan X, He Q, Wang K, Duan L, Cui Y, Li J (2007) Transition of cationic dipeptide nanotubes into vesicles and oligonucleotide delivery. Angew Chem Int Ed 46:2431–2434
47. Yang R, Hilder TA, Chung SH, Rendell A (2011) First-principles study of water confined in single-walled silicon carbide nanotubes. J Phys Chem C 115:17,255–17,264
48. Yemini M, Reches M, Gazit E, Rishpon J (2005) Peptide nanotube-modified electrodes for enzyme-biosensor applications. Anal Chem 77:5155–5159
49. Youssef M, Pellenq RJM, Yildiz B (2011) Glassy nature of water in an ultraconfining disordered material: the case of calcium–silicate–hydrate. J Am Chem Soc 133:2499–2510
50. Zhang J, Wu X, Gan Z, Zhu X, Jin Y (2014) Unidirectionally aligned diphenylalanine nanotube/microtube arrays with excellent supercapacitive performance. Nano Res 7:929–937
51. Zhang S (2003) Fabrication of novel biomaterials through molecular self-assembly. Nat Biotech 21:1171–1178