Oxoanion binding by guanidiniocarbonylpyrrole cations in water: A combined DFT and MD investigation

Chemistry - A European Journal

Volumn 14, Issue 17, 2008, Pages 5207-5219

  Moiani, Davide ^a   Cavallotti, Carlo ^a   Famulari, Antonino ^a   Schmuck, Carsten ^b  

^a POLITECNICO DI MILANO   (Italy)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

Density functional calculations; Molecular dynamics; Molecular recognition; Receptors; Supramolecular chemistry

Indexed keywords

BINDING SITES; CARBOXYLATION; CHEMICAL BONDS; CHEMICALS REMOVAL (WATER TREATMENT); COMPLEXATION; DATA STRUCTURES; DISCRETE FOURIER TRANSFORMS; DYNAMICS; FLOW INTERACTIONS; HYDROGEN; HYDROGEN BONDS; METASTABLE PHASES; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULES; NUCLEIC ACIDS; OFFSHORE OIL WELL PRODUCTION; PHOTORESISTS; PROBABILITY DENSITY FUNCTION; QUANTUM CHEMISTRY; SULFUR COMPOUNDS; WATER TREATMENT;

DENSITY FUNCTIONAL CALCULATIONS; MOLECULAR RECOGNITION; RECEPTORS; SUPRAMOLECULAR CHEMISTRY;

BINDING ENERGY;

GUANIDINE DERIVATIVE; ION; OXIDE; PYRROLE DERIVATIVE; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; QUANTUM THEORY; THERMODYNAMICS;

GUANIDINES; IONS; MODELS, CHEMICAL; OXIDES; PYRROLES; QUANTUM THEORY; THERMODYNAMICS; WATER;

EID: 53849093772     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.200701745     Document Type: Article

References (57)

1. a) L. J. Prins, D.N. Reinhoudt, P. Timmerman. Angew. Chem. 2001, 113, 2446;
2. Angew. Client. Int. Ed. 2001, 40, 2382;
3. b) G. Cooke, V. M. Rotello Chem. Soc. Rev. 2002, 31, 275;
4. c) G.V. Oshovsky, D.N. Reinhoudt, W. Verboom, Angew. Chem. 2007, 119, 2418;
5. Angew. Chem. Int. Ed. 2007, 46, 2366.
6. One concept used in this context are chemical-mutant cycles: S. L. Cockroft, C. A. Hunter, Chem. Soc. Rev. 2007, 36, 172.
7. For a fascinating experimental case study involving peptide binding by vancomycin antibiotics see: a) C. C. McComas, B. M. Crowley, D. L. Boger J. Am. Chem. Soc. 2003, 125, 9314;
8. b) B. M. Crowley, D. L. Boger, J. Am. Chem. Soc. 2006, 128, 2885.
9. C. Schmuck, W. Wienand, J. Am. Chem. Soc. 2003, 125, 452.
10. S. Schlund, C. Schmuck, B. Engels, J. Am. Chem. Soc 2005, 127, 11115.
11. a) M. D. Best, S. L. Tobey, E. V. Anslyn, Coord. Chem. Rev. 2003, 240, 3;
12. b) P. A. Gale, Coord. Chem. Rev. 2003, 240, 191;
13. c) R. J. Fitzmaurice, G. M. Kyne, D. Douheret, J. D. Kilburn, J. Chem. Soc. Perkin Trans. 1 2002, 841;
14. d) F.P. Schmidtchen, M. Berger, Chem. Rev. 1997, 97, 1609;
15. e) P. Blondeau, M. Segura, R. Perez-Fernandez, J. de Mendoza, Chem. Soc. Rev. 2007, 36, 198;
16. f) K. A. Schug, W. Lindner, Chem. Rev. 2005, 105, 67.
17. C. Schmuck, Chem. Eur. J. 2000, 6, 709.
18. a) C. Schmuck, Coord. Chem. Rev. 2006, 205, 3053;
19. b) C. Schmuck, D. Rupprecht, W. Wienand, Chem. Eur. J. 2006, 12, 9186;
20. c) C. Schmuck, P. Wich, Angew. Chem. 2006, 118, 4383;
21. Angew. Chem. Int. Ed. 2006, 45, 4277;
22. d) C. Schmuck, T. Rehm, L. Geiger, M. Schä fer, J. Org. Chem. 2007, 72, 6162;
23. e) C. Schmuck, V. Bickert, J. Org. Chem. 2007, 72, 6832.
24. R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, J. K. Perry, D. E. Shaw, P. Francis. P. S. Shenkin, J. Med. Chem. 2004, 47, 1739.
25. A. D. Becke, J. Client. Phys. 1993, 98, 5648.
26. C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 1988, 37, 785.
27. Gaussian 03, Revision C01, M.J. Frisch, G.W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Monlgomery. Jr. T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kilao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochtersk, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz. Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, A. L. G. Liu, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham. C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill. B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, J. A. Pople, Gaussian, Inc, Pittsburgh, 2003.
28. R. Ditchfield, W. J. Hehre, J. A. Pople, J. Chem. Phys. 1971, 54, 724.
29. a) E. Canees, B. Mennucci, J. Tomasi, J. Chem. Phys. 1997, 107, 3032;
30. b) B. Mennucci, J. Tomasi, J. Chem. Phys. 1997, 106, 5151;
31. c) B. Mennucci, E. Canees, J. Tomasi, J. Phys. Chem. B 1997, 101, 10506;
32. d) J. Tomasi, B. Mennucci, R. Cammi. Chem. Rev. 2005, 105, 2999.
33. D. E. Woon, T. H. Dunning, Jr., J. Chem. Phys. 1993, 98.
34. a) A. Castleman, Jr., P. Hobza, Chem. Rev. 1994, 94, 1721;
35. b) B. Brutschy, P. Hobza. Chem. Rev. 2000, 100, 3861.
36. Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. M. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. M. Wang, P. Kollman, J. Comput. Chem. 2003, 24, 1999.
37. D. A. Case, T.A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang. R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, H. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross. P. A. Kollman, Amber, 8.0 ed., University of California San Francisco, 2004.
38. W. D. Cornell, P. Cieplak, C. I. Bayly, P. A. Kollman, J. Am. Chem. Soc. 1993, 115, 9620.
39. W. L. Jorgensen, J. Chandraskhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926.
40. P. H. Hunenberger, J. A. McCammon, Biophys. Chem. 1999, 78, 69.
41. V. Tsui, D. A. Case, Biopolymers 2000, 56, 275.
42. J. Wang, P. Morin, W. Wang, P. A. Kollman, J. Am. Chem. Soc. 2001, 123, 5221.
43. B. O. Brandsdal, F. Osterberg, M. Almlof, I. Feierberg, V. B. Luzhkov, J. Aqvist, Protein Simul. 2003, 66, 123.
44. G. Schaftenaar, J. H. Noordik, J. Cold Reg. Eng. J. Compu.-Aided. Mol. Des. 2000, 14, 123.
45. W. Humphrey, A. Dalke, K. Schulten. J. Mol. Graph. 1996, 14, 33.
46. J. W. Zou, Y. J. Jiang, M. Guo, G. X. Hu, B. Zhang, H. C. Liu, Q. S. Yu, Chem. Eur. J. 2005, 11, 740.
47. D. G. Truhlar, Chem. Phys. Lett. 1998, 294, 45.
48. a) J. Sponer, P. Jurecka, P. Hobza, J. Am. Chem. Soc. 2004, 126, 10142;
49. b) Y. Zhao, D. G. Truhlar. J. Chem. Theor. Comput. 2007, 3, 289.
50. J. Carlsson, J. Aqvist, Phys. Chem. Chem. Phys. 2006, 8, 5385.
51. M. Almlof, B. O. Brandsdal, J. Aqvist. J. Comput. Chem. 2004, 25, 1242.
52. C. Schmuck, S. Graupner, Tetrahedron Lett. 2005, 46, 1295.
53. D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, R. J. Woods, J. Comput. Chem. 2005, 26, 1668.
54. S. B. Dixit, R. Bhasin, E. Rajasekaran, B. Jayaram, J. Chem. Soc. Faraday Trans. 1997, 93, 1105.
55. a) H. Gohlke, D. A. Case, J. Comput. Chem. 2004, 25, 238;
56. b) N. Spackova, T. E. Cheatam. III, F. Ryjacek, F. Lankas, L. van Meervelt, P. Hobza, J. Sponer, J. Am. Chem. Soc. 2003, 125, 1759;
57. c) C. S. Page, P. A. Bates, J. Comput. Chem. 2006, 27, 1990.