311
Views
3
CrossRef citations to date
0
Altmetric
Proceedings of the 3rd International Conference on Molecular Simulation

Molecular dynamics simulation of self-assembled nanocubes in methanol

, , , &
Pages 845-849 | Received 06 Feb 2014, Accepted 23 Jun 2014, Published online: 12 Aug 2014

References

  • Anfisen CB. Principles that govern the folding of protein chains. Science. 1973;181:223–230.
  • Zhang S. Fabrication of novel biomaterials through molecular self-assembly. Nat Biotechnol. 2003;21:1171–1178.
  • Seeman NC. DNA in a material world. Nature. 2003;421:427–431.
  • Ariga K, Kunitake T. Molecular recognition at air–water and related interfaces: complementary hydrogen bonding and multisite interaction. Acc Chem Res. 1998;31:371–378.
  • Meyer EE, Rosenberg KJ, Israelachvili J. Recent progress in understanding hydrophobic interactions. Proc Natl Acad Sci USA. 2006;103:15739–15746.
  • Fujita M. Metal-directed self-assembly of two- and three-dimensional synthetic receptors. Chem Soc Rev. 1998;27:417–425.
  • Jasat A, Sherman JC. Carceplexes and hemicarceplexes. Chem Rev. 1999;99:931–968.
  • MacGillivray LR, Atwood JL. Structural classification and general principles for the design of spherical molecular hosts. Angew Chem Int Ed. 1999;38:1018–1033.
  • Rebek J Jr. Simultaneous encapsulation: molecules held at close range. Angew Chem Int Ed. 2005;44:2068–2078.
  • Hiraoka S, Harano K, Shiro M, Shionoya M. A self-assembled organic capsule formed from the union of six hexagram-shaped amphiphile molecules. J Am Chem Soc. 2008;130:14368–14369.
  • Hiraoka S, Harano K, Nakamura T, Shiro M, Shionoya M. Induced-fit formation of a tetrameric organic capsule consisting of hexagram-shaped amphiphile. Angew Chem Int Ed. 2008;48:7006–7009.
  • Koseki J, Kita Y, Hiraoka S, Nagashima U, Tachikawa M. Role of CH–π interaction energy in self-assembled gear-shaped amphiphile molecules: correlated ab initio molecular orbital and density functional theory study. Theor Chem Acc. 2011;130:1055–1059.
  • Koseki J, Kita Y, Hiraoka S, Nagashima U, Tachikawa M. Temperature dependence of self-assembled molecular capsules consisting of gear-shaped amphiphile molecules with molecular dynamics simulations. Int J Quantum Chem. 2012;113:397–400.
  • Mashiko T, Yamada K, Hiraoka S, Nagashima U, Tachikawa M. Molecular dynamics and principal component analysis for a self-assembled nanocube in aqueous solution. Chem Lett. 2014;43:366–368.
  • Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA. AMBER 9. San Francisco, CA: University of California; 2006.
  • Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157–1174.
  • Bayly CI, Cieplak P, Cornell W, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem B. 1993;97:10269–10280.
  • Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr., Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ. Gaussian 09, Revision A.02. Wallingford, CT: Gaussian, Inc.; 2009.
  • Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys. 1995;103:4613–4621.
  • Darden T, York D, Pedersen L. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
  • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved. Proteins. 2006;65:712–725.
  • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.