Self-assembly of N3-substituted xanthines in the solid state and at the solid-liquid interface

Langmuir

Volumn 29, Issue 24, 2013, Pages 7283-7290

  Ciesielski, Artur ^a   Haar, Sébastien ^a   Bényei, Attila ^b   Paragi, Gábor ^c   Guerra, Célia Fonseca ^d   Bickelhaupt, F Matthias ^d,e   Masiero, Stefano ^f   Szolomájer, János ^g   Samorì, Paolo ^a   Spada, Gian Piero ^f   Kovács, Lajos ^g  

^a UNIVERSITÉ LOUIS PASTEUR   (France)

^b UNIVERSITY OF DEBRECEN   (Hungary)

^c INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^d VU UNIVERSITY AMSTERDAM   (Netherlands)

^e RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^f UNIVERSITY OF BOLOGNA   (Italy)

^g UNIVERSITY OF SZEGED   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL APPLICATIONS; DISPERSION-CORRECTED DENSITY FUNCTIONAL; FUNCTIONAL STRUCTURE; NEIGHBORING MOLECULES; SELF-ASSOCIATIONS; SOLID-LIQUID INTERFACES; SUPRAMOLECULAR ARCHITECTURES; SUPRAMOLECULAR POLYMERS;

ASSOCIATION REACTIONS; DENSITY FUNCTIONAL THEORY; HYDROGEN BONDS; MEDICAL APPLICATIONS; POLYMERS; SCANNING TUNNELING MICROSCOPY; SELF ASSEMBLY; X RAY DIFFRACTION;

SUPRAMOLECULAR CHEMISTRY;

XANTHINE DERIVATIVE;

ARTICLE; CHEMISTRY; HYDROGEN BOND; THEORETICAL MODEL; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; MODELS, THEORETICAL; XANTHINES;

EID: 84879175953     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/la304540b     Document Type: Article

References (76)

1. Lehn, J. M. Toward self-organization and complex matter Science 2002, 295, 2400-2403
2. Davis, J. T. G-quartets 40 years later: from 5′-GMP to molecular biology and supramolecular chemistry Angew. Chem., Int. Ed. 2004, 43, 668-698
3. Greef, T. F. A.; Meijer, E. W. Materials science-supramolecular polymers Nature 2008, 453, 171-173
4. Ciesielski, A.; Palma, C.-A.; Bonini, M.; Samorì, P. Towards supramolecular engineering of functional nanomaterials: pre-programming multi-component 2D self-assembly at solid-liquid interfaces Adv. Mater. 2010, 22, 3506-3520
5. Rivera, J. M. Functional assemblies made from supramolecular G-quadruplexes. In Guanine Quartets: Structure and Application; The Royal Society of Chemistry: London, 2013; pp 15-27.
6. Theobald, J. A.; Oxtoby, N. S.; Phillips, M. A.; Champness, N. R.; Beton, P. H. Controlling molecular deposition and layer structure with supramolecular surface assemblies Nature 2003, 424, 1029-1031
7. De Feyter, S.; De Schryver, F. C. Two-dimensional supramolecular self-assembly probed by scanning tunneling microscopy Chem. Soc. Rev. 2003, 32, 139-150
8. Barth, J. V.; Costantini, G.; Kern, K. Engineering atomic and molecular nanostructures at surfaces Nature 2005, 437, 671-679
9. Nath, K. G.; Ivasenko, O.; Miwa, J. A.; Dang, H.; Wuest, J. D.; Nanci, A.; Perepichka, D. F.; Rosei, F. Rational modulation of the periodicity in linear hydrogen-bonded assemblies of trimesic acid on surfaces J. Am. Chem. Soc. 2006, 128, 4212-4213
10. MacLeod, J. M.; Ivasenko, O.; Perepichka, D. F.; Rosei, F. Stabilization of exotic minority phases in a multicomponent self-assembled molecular network Nanotechnology 2007, 18, 424031-424040
11. Slater, A. G.; Beton, P. H.; Champness, N. R. Two-dimensional supramolecular chemistry on surfaces Chem. Sci. 2011, 2, 1440-1448
12. Surin, M.; Samorì, P. Multicomponent monolayer architectures at the solid-liquid interface: towards controlled space-confined properties and reactivity of functional building blocks Small 2007, 3, 190-194
13. Ciesielski, A.; Piot, L.; Samorì, P.; Jouaiti, A.; Hosseini, M. W. Molecular tectonics at the solid/liquid interface: controlling the nanoscale geometry, directionality, and packing of 1d coordination networks on graphite surfaces Adv. Mater. 2009, 21, 1131-1136
14. Schenning, A. P. H. J.; Meijer, E. W. Supramolecular electronics; nanowires from self-assembled pi-conjugated systems Chem. Commun. 2005, 3245-3258
15. Desiraju, G. R. Hydrogen bridges in crystal engineering: Interactions without borders Acc. Chem. Res. 2002, 35, 565-573
16. Djurdjevic, S.; Leigh, D. A.; McNab, H.; Parsons, S.; Teobaldi, G.; Zerbetto, F. Extremely strong and readily accessible AAA-DDD triple hydrogen bond complexes J. Am. Chem. Soc. 2007, 129, 476-477
17. Llanes-Pallas, A.; Palma, C. A.; Piot, L.; Belbakra, A.; Listorti, A.; Prato, M.; Samorì, P.; Armaroli, N.; Bonifazi, D. Engineering of supramolecular H-bonded nanopolygons via self-assembly of programmed molecular modules J. Am. Chem. Soc. 2009, 131, 509-520
18. Seto, C. T.; Whitesides, G. M. Self-assembly based on the cyanuric acid-melamine lattice J. Am. Chem. Soc. 1990, 112, 6409-6411
19. Madueno, R.; Raisanen, M. T.; Silien, C.; Buck, M. Functionalizing hydrogen-bonded surface networks with self-assembled monolayers Nature 2008, 454, 618-621
20. Hurst, D. T. An Introduction to the Chemistry and Biochemistry of Pyrimidines, Purines, And Pteridines; John Wiley & Sons: New York, 1980.
21. Kulikowska, E.; Kierdaszuk, B.; Shugar, D. Xanthine, xanthosine and its nucleotides: solution structures of neutral and ionic forms, and relevance to substrate properties in various enzyme systems and metabolic pathways Acta Biochim. Pol. 2004, 51, 493-531
22. Miyakawa, S.; Cleaves, H. J.; Miller, S. L. The cold origin of life: B. Implications based on pyrimidines and purines produced from frozen ammonium cyanide solutions Origins Life Evol. Biosphere 2002, 32, 209-218
23. Stoks, P. G.; Schwartz, A. W. Basic nitrogen-heterocyclic compounds in the murchison meteorite Geochim. Cosmochim. Acta 1982, 46, 309-315
24. Biaggioni, I.; Paul, S.; Puckett, A.; Arzubiaga, C. Caffeine and theophylline as adenosine receptor antagonists in humans J. Pharmacol. Exp. Ther. 1991, 258, 588-593
25. Thorn, C. F.; Klein, T. E.; Altman, R. B. The pharmacogenetics and pharmacogenomics knowledge base Methods Mol. Biol. 2005, 311, 179-191
26. Song, J.; Park, K. U.; Park, H. D.; Yoon, Y.; Kim, J. Q. High-throughput liquid chromatography-tandem mass spectrometry assay for plasma theophylline and its metabolites Clin. Chem. 2004, 50, 2176-2179
27. Soukup, G. A.; Emilsson, G. A. M.; Breaker, R. R. Altering molecular recognition of RNA aptamers by allosteric selection J. Mol. Biol. 2000, 298, 623-632
28. Lee, S. W.; Zhao, L.; Pardi, A.; Xia, T. B. Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands Biochemistry 2010, 49, 2943-2951
29. Szolomájer, J.; Paragi, G.; Batta, G.; Fonseca Guerra, C.; Bickelhaupt, F. M.; Kele, Z.; Pádár, P.; Kupihár, Z.; Kovács, L. 3-Substituted xanthines as promising candidates for quadruplex formation: computational, synthetic and analytical studies New J. Chem. 2011, 35, 476-482
30. Heckl, W. M.; Smith, D. P. E.; Binnig, G.; Klagges, H.; Hansch, T. W.; Maddocks, J. 2-Dimensional ordering of the DNA-base guanine observed by scanning tunneling microscopy Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 8003-8005
31. Furukawa, M.; Tanaka, H.; Kawai, T. The role of dimer formation in the self-assemblies of DNA base molecules on Cu(111) surfaces: a scanning tunneling microscope study J. Chem. Phys. 2001, 115, 3419-3423
32. Giorgi, T.; Lena, S.; Mariani, P.; Cremonini, M. A.; Masiero, S.; Pieraccini, S.; Rabe, J. P.; Samorì, P.; Spada, G. P.; Gottarelli, G. Supramolecular helices via self-assembly of 8-oxoguanosines J. Am. Chem. Soc. 2003, 125, 14741-14749
33. Xu, W.; Kelly, R. E. A.; Otero, R.; Schock, M.; Laegsgaard, E.; Stensgaard, I.; Kantorovich, L. N.; Besenbacher, F. Probing the hierarchy of thymine-thymine interactions in self-assembled structures by manipulation with scanning tunneling microscopy Small 2007, 3, 2011-2014
34. Kelly, R. E. A.; Lukas, M.; Kantorovich, L. N.; Otero, R.; Xu, W.; Mura, M.; Laegsgaard, E.; Stensgaard, I.; Besenbacher, F. Understanding the disorder of the DNA base cytosine on the Au(111) surface J. Chem. Phys. 2008, 129, 184707-184713
35. Kelly, R. E. A.; Xu, W.; Lukas, M.; Otero, R.; Mura, M.; Lee, Y. J.; Laegsgaard, E.; Stensgaard, I.; Kantorovich, L. N.; Besenbacher, F. An investigation into the interactions between self-assembled adenine molecules and a Au(111) surface Small 2008, 4, 1494-1500
36. Otero, R.; Lukas, M.; Kelly, R. E. A.; Xu, W.; Laegsgaard, E.; Stensgaard, I.; Kantorovich, L. N.; Besenbacher, F. Elementary structural motifs in a random network of cytosine adsorbed on a gold(111) surface Science 2008, 319, 312-315
37. Spada, G. P.; Lena, S.; Masiero, S.; Pieraccini, S.; Surin, M.; Samorì, P. Guanosine-based hydrogen-bonded scaffolds: controlling the assembly of oligothiophenes Adv. Mater. 2008, 20, 2433-2439
38. Surin, M.; Janssen, P. G. A.; Lazzaroni, R.; Leclere, P.; Meijer, E. W.; Schenning, A. P. H. J. Supramolecular organization of ssDNA-templated pi-conjugated oligomers via hydrogen bonding Adv. Mater. 2009, 21, 1126-1130
39. Ciesielski, A.; Perone, R.; Pieraccini, S.; Spada, G. P.; Samorì, P. Nanopatterning the surface with ordered supramolecular architectures of N-9-alkylated guanines: STM reveals Chem. Commun. 2010, 46, 4493-4495
40. Ciesielski, A.; Colella, S.; Zalewski, L.; Bruchmann, B.; Samorì, P. Nanopatterning the graphite surface with ordered macrocyclic or ribbon-like assemblies of isocytosine derivatives: an STM study CrystEngComm 2011, 13, 5535-5537
41. Guo, Z. X.; De Cat, I.; Van Averbeke, B.; Lin, J. B.; Wang, G. J.; Xu, H.; Lazzaroni, R.; Beljonne, D.; Meijer, E. W.; Schenning, A. P. H. J.; De Feyter, S. Nucleoside-assisted self-assembly of oligo(p-phenylenevinylene)s at liquid/solid interface: chirality and nanostructures J. Am. Chem. Soc. 2011, 133, 17764-17771
42. Sowerby, S. J.; Petersen, G. B. Scanning tunnelling microscopy and molecular modelling of xanthine monolayers self-assembled at the solid-liquid interface: relevance to the origin of life Origins Life Evol. Biosphere 1999, 29, 597-614
43. Jung, D.; Seo, D. K.; Ren, J.; Whangbo, M. H. Simulation of the scanning tunneling and atomic force microscopy images of a xanthine monolayer on graphite Surf. Sci. 1998, 401, 476-481
44. Ferris, J. P.; Hill, A. R.; Liu, R. H.; Orgel, L. E. Synthesis of long prebiotic oligomers on mineral surfaces Nature 1996, 381, 59-61
45. Ertem, G.; Ferris, J. P. Synthesis of RNA oligomers on heterogeneous templates Nature 1996, 379, 238-240
46. Sowerby, S. J.; Cohn, C. A.; Heckl, W. M.; Holm, N. G. Differential adsorption of nucleic acid bases: relevance to the origin of life Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 820-822
47. Hanczyc, M. M.; Fujikawa, S. M.; Szostak, J. W. Experimental models of primitive cellular compartments: encapsulation, growth, and division Science 2003, 302, 618-622
48. Yu, M.; Wang, J. G.; Mura, M.; Meng, Q. Q.; Xu, W.; Gersen, H.; Laegsgaard, E.; Stensgaard, I.; Kelly, R. E. A.; Kjems, J.; Linderoth, T. R.; Kantorovich, L. N.; Besenbacher, F. Homochiral xanthine quintet networks self-assembled on Au(111) surfaces ACS Nano 2011, 5, 6651-6660
49. Low, J. N.; Tollin, P.; Brand, E.; Wilson, C. C. Structure of 3-methylxanthine Acta Cryst. Sect. C 1986, 42, 1447-1448
50. Ciesielski, A.; Samorì, P. Supramolecular assembly/reassembly processes: molecular motors and dynamers operating at surfaces Nanoscale 2011, 3, 1397-1410
51. Piot, L.; Bonifazi, D.; Samorì, P. Organic reactivity in confined spaces under scanning tunneling microscopy control: tailoring the nanoscale world Adv. Funct. Mater. 2007, 17, 3689-3693
52. Elemans, J. A. A. W.; Lei, S. B.; De Feyter, S. Molecular and supramolecular networks on surfaces: from two-dimensional crystal engineering to reactivity Angew. Chem., Int. Ed. 2009, 48, 7298-7332
53. MacLeod, J. M.; Lipton-Duffin, J.; Fu, C. Y.; Rosei, F. Inducing nonlocal reactions with a local probe ACS Nano 2009, 3, 3347-3351
54. Bridson, P. K.; Richmond, G.; Yeh, F. Preparation of xanthine-3-acetic acid and some derivatives Synth. Commun. 1990, 20, 2459-2467
55. Altomare, A.; Cascarano, G.; Giacovazzo, C.; Guagliardi, A. Completion and refinement of crystal-structures with Sir92 J. Appl. Crystallogr. 1993, 26, 343-350
56. Sheldrick, G. M. A short history of SHELX Acta Crystallogr. 2008, 64, 112-122
57. Farrugia, L. J. WinGX suite for small-molecule single-crystal crystallography J. Appl. Crystallogr. 1999, 32, 837-838
58. Tarini, M.; Cignoni, P.; Montani, C. Ambient occlusion and edge cueing to enhance real time molecular visualization IEEE Trans. Vis. Comput. Gr. 2006, 12, 1237-1244
59. Baerends, E. J.; Ziegler, T.; Autschbach, J.; Bashford, D.; Bérces, A.; Bickelhaupt, F. M.; Bo, P.; Boerrigter, P. M.; Cavallo, L.; Chong, D. P.; Deng, L.; Dickson, R. M.; Ellis, D. E.; van Faassen, M.; Fan, L.; Fischer, T. H.; Fonseca Guerra, C.; Ghysels, A.; Giammona, A.; Van Gisbergen, S. J. A.; Götz, A. W.; Groeneveld, J. A.; Gritsenko, O. V.; Grüning, M.; Gusarov, S.; Harris, F. E.; van den Hoek, P.; Jacob, R.; Jacobsen, H.; Jensen, L.; Kaminski, J. W.; van Kessel, G.; Kootstra, F.; Kovalenko, A.; Krykunov, M. V.; van Lenthe, E.; McCormack, D. A.; Michalak, A.; Mitoraj, M.; Neugebauer, J.; Nicu, V. P.; Noodleman, L.; Osinga, V. P.; Patchkovskii, S.; Philipsen, P. H. T.; Post, D.; Pye, C. C.; Ravenek, W.; Rodríguez, J. I.; Ros, P.; Schipper, P. R. T.; Schreckenbach, G.; Seldenthuis, J. S.; Seth, M.; Snijders, J. G.; Sola, M.; Swart, M.; Swerhone, D.; te Velde, G.; Vernooijs, P.; Versluis, L.; Visscher, L.; Visser, O.; Wang, F.; Wesolowski, T. A.; van Wezenbeek, E. M.; Wiesenekker, G.; Wolff, S. K.; Woo, T. K.; Yakovlev, A. L. ADF2010.01; SCM: ADF2010.01; SCM, Theoretical Chemistry; Vrije Universiteit: Amsterdam, http://www.scm.com
60. Baerends, E. J.; Ellis, D. E.; Ros, P. Self-consistent molecular Hartree-Fock-Slater calculations I. The computational procedure Chem. Phys. 1973, 2, 41
61. Snijders, J. G.; Vernooijs, P.; Baerends, E. J. Roothaan-Hartree-Fock- Slater atomic wave functions: single-zeta, double-zeta, and extended Slater-type basis sets for 87 Fr-103Lr At. Nucl. Data Tables 1981, 26, 483-509
62. te Velde, G.; Baerends, E. J. Numerical-integration for polyatomic systems J. Comput. Phys. 1992, 99, 84-98
63. Fonseca Guerra, C.; Visser, O.; Snijders, J. G.; te Velde, G.; Baerends, E. J. In Methods and Techniques in Computational Chemistry: METECC-95; Clementi, E.; Corongiu, G., Eds.; STEF: Cagliari, Italy, 1995; pp 305-395.
64. Fonseca Guerra, C.; Snijders, J. G.; te Velde, G.; Baerends, E. J. Towards an order-N DFT method Theor. Chem. Acc. 1998, 99, 391-403
65. te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; Van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. Chemistry with ADF J. Comput. Chem. 2001, 22, 931-967
66. Swart, M.; Bickelhaupt, F. M. Optimization of strong and weak coordinates Int. J. Quantum Chem. 2006, 106, 2536-2544
67. Swart, M.; Bickelhaupt, F. M. QUILD: QUantum-regions interconnected by local descriptions J. Comput. Chem. 2008, 29, 724-734
68. Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior Phys. Rev. A 1988, 38, 3098-3100
69. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 1988, 37, 785-789
70. Grimme, S. Accurate description of van der Waals complexes by density functional theory including empirical corrections J. Comput. Chem. 2004, 25, 1463-1473
71. Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction J. Comput. Chem. 2006, 27, 1787-1799
72. Fonseca Guerra, C.; van der Wijst, T.; Poater, J.; Swart, M.; Bickelhaupt, F. M. Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in pi-stacking and hydrogen-bonding behavior Theor. Chem. Acc. 2010, 125, 245-252
73. van der Wijst, T.; Fonseca Guerra, C.; Swart, M.; Bickelhaupt, F. M.; Lippert, B.; Ditopic Ion-Pair, A. Receptor based on stacked nucleobase quartets Angew. Chem., Int. Ed. 2009, 48, 3285-3287
74. Fonseca Guerra, C.; Zijlstra, H.; Paragi, G.; Bickelhaupt, F. M. Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets Chem.-Eur. J. 2011, 17, 12612-12622
75. Ciesielski, A.; Lena, S.; Masiero, S.; Spada, G. P.; Samorì, P. Dynamers at the solid-liquid interface: controlling the reversible assembly/reassembly process between two highly ordered supramolecular guanine motifs Angew. Chem., Int. Ed. 2010, 49, 1963-1966
76. Bernstein, J. Polymorphism in Molecular Crystals; Oxford University Press: New York, 2008; Vol. 14.