Coordination-directed self-assembly of M12L24 nanocage: Effects of kinetic trapping on the assembly process

ACS Nano

Volumn 8, Issue 2, 2014, Pages 1290-1296

  Yoneya, Makoto ^a   Tsuzuki, Seiji ^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

kinetic trapping; metal ligand coordination; molecular dynamics simulation; nanocage; self assembly

Indexed keywords

EID: 84894629927     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn404595j     Document Type: Article

References (45)

1. Lehn, J. Supramolecular Chemistry: Concepts and Perspectives; VCH: Weinheim, Germany, 1995.
2. Cook, T. R.; Zheng, Y.-R.; Stang, P. J. Metal-Organic Frameworks and Self-Assembled Supramolecular Coordination Complexes: Comparing and Contrasting the Design, Synthesis, and Functionality of Metal-Organic Materials Chem. Rev. 2012, 113, 734-777
3. McMorran, D. A.; Steel, P. J. The First Coordinatively Saturated, Quadruply Stranded Helicate and Its Encapsulation of a Hexafluorophosphate Anion Angew. Chem., Int. Ed. Engl. 1998, 37, 3295-3297
4. Liao, P.; Langloss, B. W.; Johnson, A. M.; Knudsen, E. R.; Tham, F. S.; Julian, R. R.; Hooley, R. J. Two-Component Control of Guest Binding in a Self-Assembled Cage Molecule Chem. Commun. 2010, 46, 4932-4934
5. 12 Coordination Cube Chem. Commun. 2009, 1638-1640
6. Moulton, B.; Lu, J.; Mondal, A.; Zaworotko, M. J. Nanoballs: Nanoscale Faceted Polyhedra with Large Windows and Cavities Chem. Commun. 2001, 863-864
7. 2) 4 Paddle-Wheel Building Blocks J. Am. Chem. Soc. 2001, 123, 4368-4369
8. Tominaga, M.; Suzuki, K.; Kawano, M.; Kusukawa, T.; Ozeki, T.; Sakamoto, S.; Yamaguchi, K.; Fujita, M. Finite, Spherical Coordination Networks that Self-Organize from 36 Small Components Angew. Chem., Int. Ed. 2004, 43, 5621-5625
9. 48 Polyhedra and Their Sharp Structural Switch upon Subtle Ligand Variation Science 2010, 328, 1144
10. 4 Molecular Capsules with Anthracene Shells Chem. Commun. 2011, 47, 8605-8607
11. Han, M.; Michel, R.; He, B.; Chen, Y.-S.; Stalke, D.; John, M.; Clever, G. H. Light-Triggered Guest Uptake and Release by a Photochromic Coordination Cage Angew. Chem., Int. Ed. 2013, 52, 1319-1323
12. 2 n Spherical Complexes: Structure, Functionalisation and Applications Chem. Commun. 2013, 49, 6703-6712
13. 8 J. Am. Chem. Soc. 2012, 134, 14401-14407
14. Chand, D.; Biradha, K.; Fujita, M.; Sakamoto, S.; Yamaguchi, K. A Molecular Sphere of Octahedral Symmetry Chem. Commun. 2002, 2486-2487
15. Palma, C.-A.; Cecchini, M.; Samor, P. Predicting Self-Assembly: from Empirism to Determinism Chem. Soc. Rev. 2012, 41, 3713-3730
16. Fujita, D.; Takahashi, A.; Sato, S.; Fujita, M. Self-Assembly of Pt (II) Spherical Complexes via Temporary Labilization of the Metal-Ligand Association in 2,2,2-Trifluoroethanol J. Am. Chem. Soc. 2011, 133, 13317-13319
17. Sato, S.; Iida, J.; Suzuki, K.; Kawano, M.; Ozeki, T.; Fujita, M. Fluorous Nanodroplets Structurally Confined in an Organopalladium Sphere Science 2006, 313, 1273
18. Murase, T.; Sato, S.; Fujita, M. Nanometer-Sized Shell Molecules That Confine Endohedral Polymerizing Units Angew. Chem., Int. Ed. 2007, 46, 1083-1085
19. Fujita, D.; Suzuki, K.; Sato, S.; Yagi-Utsumi, M.; Yamaguchi, Y.; Mizuno, N.; Kumasaka, T.; Takata, M.; Noda, M.; Uchiyama, S. et al. Protein Encapsulation within Synthetic Molecular Hosts Nat. Commun. 2012, 3, 1093
20. Scheraga, H. A.; Khalili, M.; Liwo, A. Protein-Folding Dynamics: Overview of Molecular Simulation Techniques Annu. Rev. Phys. Chem. 2007, 58, 57-83
21. 24 Spherical Frameworks through the Cooperation of 48 Pd (II)-Pyridine Interactions J. Am. Chem. Soc. 2009, 131, 6064-6065
22. 48 Polyhedra Based on Empirical Prediction Angew. Chem., Int. Ed. 2012, 51, 3161-3163
23. Williams, A. F. Ligand Design for Hollow Spherical Complexes Coord. Chem. Rev. 2011, 255, 2104-2110
24. Leininger, S.; Olenyuk, B.; Stang, P. J. Self-Assembly of Discrete Cyclic Nanostructures Mediated by Transition Metals Chem. Rev. 2000, 100, 853-908
25. Sousa, S.; Fernandes, P.; Ramos, M. Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes Kinet. Dyn. 2010, 299-330
26. Peraro, M. D.; Spiegel, K.; Lamoureux, G.; Vivo, M. D.; DeGrado, W. F.; Klein, M. L. Modeling the Charge Distribution at Metal Sites in Proteins for Molecular Dynamics Simulations J. Struct. Biol. 2007, 157, 444-453
27. Sakharov, D. V.; Lim, C. Zn Protein Simulations Including Charge Transfer and Local Polarization Effects J. Am. Chem. Soc. 2005, 127, 4921-4929
28. Sakharov, D. V.; Lim, C. Force Fields Including Charge Transfer and Local Polarization Effects: Application to Proteins Containing Multi/Heavy Metal Ions J. Comput. Chem. 2009, 30, 191-202
29. Yun-yu, S.; Lu, W.; Van Gunsteren, W. On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques Mol. Simul. 1988, 1, 369-383
30. Tironi, I.; Sperb, R.; Smith, P.; van Gunsteren, W. A Generalized Reaction Field Method for Molecular Dynamics Simulations J. Chem. Phys. 1995, 102, 5451
31. Weeks, J.; Chandler, D.; Andersen, H. Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids J. Chem. Phys. 1971, 54, 5237
32. Pang, Y. Novel Zinc Protein Molecular Dynamics Simulations: Steps Toward Antiangiogenesis for Cancer Treatment J. Mol. Model. 1999, 5, 196-202
33. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field J. Comput. Chem. 2004, 25, 1157
34. Tiberio, G.; Muccioli, L.; Berardi, R.; Zannoni, C. Towards in Silico Liquid Crystals. Realistic Transition Temperatures and Physical Properties for n-Cyanobiphenyls via Molecular Dynamics Simulations ChemPhysChem 2008, 10, 125
35. Calligaris, M.; Zangrando, E.; Milani, B.; Marson, A. Stereochemical Investigation of Palladium (II) Complexes with Phenanthroline Ligands: A Molecular Mechanics Approach Eur. J. Inorg. Chem. 2005, 2005, 704-712
36. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: the RESP Model J. Chem. Phys. 1993, 97, 10269
37. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C. et al. Gaussian03, Revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
38. Hess, B.; Kutzner, C.; Van Der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
39. van Gunsteren, W.; Berendsen, H. A Leap-Frog Algorithm for Stochastic Dynamics Mol. Simul. 1988, 1, 173-185
40. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463
41. Feenstra, K. A.; Hess, B.; Berendsen, H. J. Improving Effciency of Large Timescale Molecular Dynamics Simulations of Hydrogen-Rich Systems J. Comput. Chem. 1999, 20, 786-798
42. Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis J. Mol. Model. 2001, 7, 306
43. Villa, A.; Mark, A.; Saracino, G.; Cosentino, U.; Pitea, D.; Moro, G.; Salmona, M. Conformational Polymorphism of the PrP106-126 Peptide in Different Environments: A Molecular Dynamics Study J. Phys. Chem. B 2006, 110, 1423-1428
44. da Silva, A. W. S.; Vranken, W. F. ACPYPE-AnteChamber PYthon Parser interfacE BMC Res.Notes 2012, 5, 367
45. Wang, J.; Wang, W.; Kollman, P.; Case, D. Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations J. Mol. Graphics Modell. 2006, 25, 247-260