How important is molecular rigidity for the complex stability of artificial host-guest systems? a theoretical study on self-assembly of gas-phase arginine

Chemistry - A European Journal

Volumn 13, Issue 23, 2007, Pages 6644-6653

  Schlund, Sebastian ^a   Schmuck, Carsten ^a   Engels, Bernd ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

Ab initio calculations; Artificial receptors; Conformation analysis; Host guest systems; Self assembly

Indexed keywords

BINDING ENERGY; COMPUTATION THEORY; MOLECULAR STRUCTURE; MONOMERS; PERTURBATION TECHNIQUES; SELF ASSEMBLY;

AB INITIO CALCULATIONS; ARTIFICIAL RECEPTORS; CONFORMATION ANALYSIS; HOST-GUEST SYSTEMS;

DIMERS;

ARGININE; PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DIMERIZATION; METABOLISM; PROTEIN ENGINEERING; SYNTHESIS;

ARGININE; COMPUTER SIMULATION; DIMERIZATION; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEIN ENGINEERING; PROTEINS;

EID: 34547748954     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.200601741     Document Type: Article

References (63)

1. D. J. Barlow, J. M. Thornton, J. Mol. Biol. 1983, 168, 867-885.
2. J. Singh, J. M. Thornton, M. Snary, S. F. Campbell, FEBS Lett. 1987, 224, 161-171.
3. J. F. Riordan, R. D. McElvany, C. L. Borders, Science 1977, 195, 884-886.
4. D. Gandini, L. Gogioso, M. Bolognesi, D. Bordo, Protein J. 1996, 24, 439-449.
5. S. Sundaralingam, Y. C. Sekhadrudu, N. Yathindra, V. Ravichadran, Protein J. 1987, 2, 64-71.
6. P. C. Lyu, P. J. Gans, N. R. Kallenbach, J. Mol. Biol. 1992, 223, 343-350.
7. Z. B. Maksić, B. Kovačević, J. Chem. Soc. Perkin Trans. 2 1999, 2623-2629.
8. P. Skurski, M. Gutowski, R. Barrios, J. Simons, Chem. Phys. Lett. 2001, 357, 143-150.
9. J. Rak, P. Skurski, J. Simons, M. Gutowski, J. Am. Chem. Soc. 2001, 123, 11659-11707.
10. R. R. Julian, M. F. Jarrold, J. Phys. Chem. A 2004, 108, 10861-10864.
11. C. J. Chapo, J. B. Paul, R. A. Provencal, K. Roth, R. J. Saykally, J. Am. Chem. Soc. 1998, 120, 12956-12957.
12. A. Melo, M. J. Ramos, W. B. Floriano, J. A. N. F. Gomes, J. F. R. Leao, A. L. Magalhaes, B. Maigret, M. C. Nascimento, N. Reuter, J. Mol. Struct. (THEOCHEM) 1999, 463, 81-90.
13. R. R. Julian, R. Hoyss, J. L. Beauchamp, J. Am. Chem. Soc. 2001, 123, 3577-3583.
14. R. R. Julian, J. L. Beauchamp, J. Am. Soc. Mass Spectrom. 2004, 15, 616-624.
15. R. R. Julian, J. L. Beauchamp, W. A. Goddard III, J. Phys. Chem. A 2002, 106, 32-34.
16. G. R. Kinsel, Q. Zhao, J. Narayanasamy, F. Yassin, H. V. R. Dias, B. Niesner, K. Prater, C. St. Marie, L. Ly, D. S. Marynick, J. Phys. Chem. A 2004, 108, 3153-3161.
17. For recent reviews on anion binding by artificial guanidinium receptors see: a) K. A. Schug, W. Lindner, Chem. Rev. 2005, 105, 67-113;
18. b) M. D. Best, S. L. Tobey, E. V Anslyn, Coord. Chem. Rev. 2003, 240, 3-15;
19. c) P. A. Gale, Coord. Chem. Rev. 2003, 240, 191-221;
20. d) R. J. Fitzmaurice, G. M. Kyne, D. Douheret, J. D. Kilburn, J. Chem. Soc. Perkin Trans. 1 2002, 841-864;
21. e) T. S. Snowden, E. V. Anslyn, Curr. Opin. Chem. Biol. 1999, 3, 740-746;
22. f) P. D. Beer, P. Schmitt, Curr. Opin. Chem. Biol. 1997, 1, 475-482;
23. g) A. Bianchi, K. Bowman-James, E. Garcia-España, Supramolecular Chemistry of Anions, Wiley-VCH, New York, 1997;
24. h) F. P. Schmidtchen, M. Berger, Chem. Rev. 1997, 97, 1609-1646;
25. i) C. Seel, A. Galán, J. de Mendoza, Top. Curr. Chem. 1995, 175, 101-132;
26. j) Functional Synthetic Receptors (Eds.: T. Schrader, A. Hamilton), Wiley-VCH, Weinheim, 2005.
27. B. Kirchner, M. Reiher, J. Am. Chem. Soc. 2005, 127, 8748-8756.
28. C. Schmuck, Coord. Chem. Rev. 2006, 205, 3053-3067.
29. C. Schmuck, Chem. Commun. 1999, 843-844.
30. C. Schmuck, Chem. Eur. J. 2000, 6, 709-718.
31. C. Schmuck, Eur. J. Org. Chem. 1999, 2397-2403.
32. C. Schmuck, W. Wienand, J. Am. Chem. Soc. 2003, 125, 452-459.
33. C. Schmuck, Th. Rehm, K. Klein, F. Gröhn, Angew. Chem. 2007, 119, 1723-1727;
34. Angew. Chem. Int. Ed. 2007, 46, 1693-1697.
35. S. Schlund, C. Schmuck, B. Engels, J. Am. Chem. Soc. 2005, 127, 11115-11124.
36. I. Kolossvary, W C. Guida, J. Comput. Chem. 1999, 20, 1671-1684.
37. J. M. Goodman, W. C. Still, J. Comput. Chem. 1991, 12, 1110-1117.
38. Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, OR (USA), 97204.
39. W. L. Jorgensen, D. S. Maxwell, J. Tirado-Rives, J. Am. Chem. Soc. 1996, 118, 11225-11235.
40. T. A. Halgren, J. Comput. Chem. 1996, 17, 490-512;
41. T. A. Halgren, J. Comput. Chem. 1996, 17, 520-552;
42. T. A. Halgren, J. Comput. Chem. 1996, 17, 553-586;
43. T. A. Halgren, J. Comput. Chem. 1996, 17, 587-615;
44. T. A. Halgren, J. Comput. Chem. 1996, 17, 616-641.
45. P. S. Shenkin, D. Q. McDonald, J. Comput. Chem. 1994, 15, 899-916.
46. a) TURBOMOLE V5.6 and V5.8, R. Ahlrichs, M. Bär, H.-P. Baron, R. Bauernschmitt, S. Böcker, M. Ehrig, K. Eichkorn, S. Elliott, F. Furche, F. Haase, M. Häser, H. Horn, C. Huber, U Huniar, M. Kattannek, C. Kölmel, M. Kollwitz, K. May, C. Ochsenfeld, H. Whm, A. Schäfer, U. Schneider, O. Treutler, M. von Arnim, F. Weigend, P. Weis, H. Weiss, Universität Karlsruhe (Germany), 2003; see also http://www.turbemole.com;
47. b) R. Ahlrichs, M. Bär, M. Häser, H. Holt, C. Kölmel, Chem. Phys. Lett. 1989, 162, 165-169.
48. a) A. D. Becke, Phys. Rev. A 1988, 38, 3098-3100;
49. b) C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 1988, 37, 785-789;
50. c) A. D. Becke, J. Chem. Phys. 1997, 107, 8554-8560;
51. d) J. S. Binkley, J. A. Pople, J. Am. Chem. Soc. 1980, 102, 939-947.
52. R. Poirier, R. Kari, I. G. Csizmadia, Handbook of Gaussian Basis Sets (Physical sciences data; 24), Elsevier, Amsterdam, 1985.
53. MOLPRO, version 2006.1, A package of ab initio programs, H.-J. Werner, P. J. Knowles, R. Lindh, F. R. Manby, M. Schütz, P. Celani, T. Korona, G. Rauhut, R. D. Amos, A. Bernhardsson, A. Berning, D. L. Cooper, M. J. O. Deegan, A. J. Dobbyn, F. Eckert, C. Hampel and G. Hetzer, A. W Lloyd, S. J. McNicholas, W Meyer and M. E. Mura, A. Nicklass, P. Palmieri, R. Pitzer, U. Schumann, H. Stoll, A. J. Stone, R. Tarroni, T. Thorsteinsson, 2004.
54. a) T. H. Dunning Jr., J. Chem. Phys. 1989, 90, 1007-1023;
55. b) A. K. Wilson, T. van Mourik, T. H. Dunning Jr., J. Mol. Struct. 1996, 388, 339-349;
56. c) R. A. Kendall, T. H. Dunning Jr., R. J. Harrison, J. Chem. Phys. 1992, 96, 6796-6806.
57. S. F Boys, F. Bernardi, Mol. Phys. 1970, 19, 553-566.
58. A. P. Scott, L. Radom, J. Phys. Chem. 1996, 100, 16502-16513.
59. S. Grimme, Rev. Comput. Chem. 2004, 20, 153-218.
60. R. A. King, T. D. Crawford, J. F. Stanton, H. F. Schaefer III, J. Am. Chem. Soc. 1999, 121, 10788-10793.
61. P. E. Mason, G. W. Neilson, J. E. Enderby, M.-L. Saboungi, C. E. Dempsey, A. D. MacKerell Jr., J. W Brady, J. Am. Chem. Soc. 2004, 126, 11462-11470.
62. T. Helgekar, P. Jørgensen, J. Olsen, Molecular Electronic-Structure Theory, Wiley, Chichester, 2000.
63. The linear structure of an arginine monomer is a stationary point on the potential energy surface when performing a geometry optimization on a RI-MP2/TZVPP(aug) level of theory. For the dimer system the hydrogen atoms involved in the H-bond had to be kept fix during the geometry optimization (B3LYP/6-3-11-H-G**) since the strong charge interaction mediated through a single hydrogen bond leads to a proton transfer from the guanidinium group towards the carboxylate oxygen. The geometry optimization for the 2-(guanidiniocarbonyl)-1H-pyrrole-5-carboxylate dimer was performed on a RI-MP2/TZVPP level of theory with augmented basis functions for the carboxylate oxygens. For the optimization of the monomeric 2-(guanidiniocarbonyl)-1H- pyrrole-5-carboxylate only a standard TZVP basis could be employed since an enlargement of the basis set causes a proton transfer from the pyrrole ring to the carboxylic group (see Figure 9) in gas phase.