Simulation of metal-ligand self-assembly into spherical complex M 6L 8

Journal of the American Chemical Society

Volumn 134, Issue 35, 2012, Pages 14401-14407

  Yoneya, Makoto ^a   Yamaguchi, Tomohiko ^a   Sato, Sota ^b   Fujita, Makoto ^b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COARSE-GRAINED; COORDINATION BONDS; FORMATION PROCESS; LIGAND EXCHANGES; METAL-LIGAND INTERACTIONS; MOLECULAR DYNAMICS SIMULATIONS; PALLADIUM ION; SOLVENT MODEL; SPHERICAL COMPLEXES; SPONTANEOUS FORMATION; SUPRAMOLECULAR SELF-ASSEMBLIES; TARGET SYSTEMS; TIME-SCALES; TRIDENTATE LIGANDS;

METALS; MOLECULAR DYNAMICS; NANOSPHERES; PALLADIUM; SELF ASSEMBLY; SPHERES; SUPRAMOLECULAR CHEMISTRY;

LIGANDS;

LIGAND; METAL; NANOSPHERE; PALLADIUM; PYRIDINE;

ARTICLE; CONTROLLED STUDY; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR SIZE; SIMULATION;

EID: 84865706513     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja303542r     Document Type: Article

References (35)

1. Lehn, J.; Sanders, J. Supramolecular chemistry: concepts and perspectives; VCH: Weinheim, Germany, 1995; Vol. 89.
2. Chakrabarty, R.; Mukherjee, P.; Stang, P. Chem. Rev. 2011, 111, 6810-6918
3. Tominaga, M.; Suzuki, K.; Kawano, M.; Kusukawa, T.; Ozeki, T.; Sakamoto, S.; Yamaguchi, K.; Fujita, M. Angew. Chem. 2004, 116, 5739-5743
4. Sato, S.; Iida, J.; Suzuki, K.; Kawano, M.; Ozeki, T.; Fujita, M. Science 2006, 313, 1273
5. Li, D.; Zhou, W.; Landskron, K.; Sato, S.; Kiely, C.; Fujita, M.; Liu, T. Angew. Chem. 2011, 123, 5288-5293
6. Zlotnick, A.; Stray, S. Trends Biotechnol. 2003, 21, 536-542
7. Rapaport, D. Phys. Rev. E 2004, 70, 051905
8. Rapaport, D.; Johnson, J.; Skolnick, J. Comput. Phys. Commun. 1999, 121, 231-235
9. Hagan, M.; Chandler, D. Biophys J. 2006, 91, 42-54
10. Nguyen, H.; Reddy, V.; Brooks, C., III J. Am. Chem. Soc. 2009, 131, 2606-2614
11. Johnston, I.; Louis, A.; Doye, J. J. Phys.: Condens. Matter 2010, 22, 104101
12. Chand, D.; Biradha, K.; Fujita, M.; Sakamoto, S.; Yamaguchi, K. Chem. Commun. 2002, 2486-2487
13. Sousa, S.; Fernandes, P.; Ramos, M. Kinet. Dyn. 2010, 299-330
14. Pang, Y. J. Mol. Model. 1999, 5, 196-202
15. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157
16. Tiberio, G.; Muccioli, L.; Berardi, R.; Zannoni, C. ChemPhysChem 2008, 10, 125
17. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. J. Chem. Phys. 1993, 97, 10269
18. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.;; W., P. M.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
19. Smith, P.; Pettitt, B. J. Phys. Chem. 1994, 98, 9700-9711
20. Yun-yu, S.; Lu, W.; Van Gunsteren, W. Mol. Simul. 1988, 1, 369-383
21. Tironi, I.; Sperb, R.; Smith, P.; van Gunsteren, W. J. Chem. Phys. 1995, 102, 5451
22. Weeks, J.; Chandler, D.; Andersen, H. J. Chem. Phys. 1971, 54, 5237
23. Hess, B.; Holm, C.; van der Vegt, N. Phys. Rev. Lett. 2006, 96, 147801
24. Calligaris, M.; Zangrando, E.; Milani, B.; Marson, A. Eur. J. Inorg. Chem. 2005, 2005, 704-712
25. Hess, B.; Kutzner, C.; Van Der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
26. Van Gunsteren, W.; Berendsen, H. Mol. Simul. 1988, 1, 173-185
27. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463
28. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306
29. Villa, A.; Mark, A.; Saracino, G.; Cosentino, U.; Pitea, D.; Moro, G.; Salmona, M. J. Phys. Chem. B 2006, 110, 1423-1428
30. Sousa da Silva, A. W.; Vranken, W. F.; Laue, E. D. Manuscript to be submitted.
31. Wang, J.; Wang, W.; Kollman, P.; Case, D. J. Mol. Graphics Modell. 2006, 25, 247-260
32. Sato, S.; Ishido, Y.; Fujita, M. J. Am. Chem. Soc. 2009, 131, 6064-6065
33. Liu, H.; Mueller-Plathe, F.; van Gunsteren, W. J. Am. Chem. Soc. 1995, 117, 4363-4366
34. Thomas, J.; Roeselová, M.; Dang, L.; Tobias, D. J. Phys. Chem. A 2007, 111, 3091-3098
35. Rapaport, D. Phys. Rev. Lett. 2008, 101, 186101