Self-assembly of diamondoid molecules and derivatives (MD simulations and DFT calculations)

International Journal of Molecular Sciences

Volumn 11, Issue 1, 2010, Pages 288-303

  Xue, Yong ^a   Mansoori, G Ali ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

Adamantane; Amantadine; Density functional theory; Diamantane; Diamondoids; MD simulation; Memantine; Nanotechnology; RDF, rimantadine; Self assembly; Simulation annealing; Structure factor

Indexed keywords

ADAMANTANE DERIVATIVE; AMANTADINE; CONGRESSANE; MEMANTINE; RIMANTADINE; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; GEOMETRY; HYDROGEN BOND; MOLECULAR DYNAMICS; PHASE TRANSITION; SIMULATION; SOLID STATE; TEMPERATURE;

ADAMANTANE; AMANTADINE; DENSITY FUNCTIONAL THEORY; DIAMANTANE; DIAMONDOIDS; MD SIMULATION; MEMANTINE; NANOTECHNOLOGY; RDF, RIMANTADINE; SELF-ASSEMBLY; SIMULATION ANNEALING; STRUCTURE FACTOR;

ADAMANTANE; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION;

EID: 75449089363     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms11010288     Document Type: Article

References (24)

1. Mansoori, G.A. Principles of Nanotechnology - Molecular-Based Study of Condensed Matter in Small Systems; World Scientific Pub. Co.: Hackensack, NJ, USA, 2005.
2. Mansoori, G.A. Diamondoid molecules. Adv. Chem. Phys. 2007, 136, 207-258.
3. Zhang, G.P.; George, T.F.; Assoufid, L.; Mansoori, G.A. First-principles simulation of the interaction between adamantane and an atomic-force microscope tip. Phys. Rev. B 2007, 75, 035413:1-035413:7.
4. Ramezani, H.; Mansoori, G.A.; Saberi, M.R. Diamondoids-DNA nanoarchitecture: From nanomodules design to self-assembly. J. Comput. Theory Nanosci. 2007, 4, 96-10.
5. Mansoori, G.A.; George, T.F.; Zhang, G.P.; Assoufid, L. Molecular Building Blocks for Nanotechnology: From Diamondoids to Nanoscale Materials and Applications (Topics in Applied Physics); Springer: New York, NY, USA, 2007; Volume 109, pp. 44-71.
6. Ramezani, H; Mansoori, G.A. Molecular Building Blocks for Nanotechnology: Diamondoids as Molecular Building Blocks for Nanotechnology (Topics in Applied Physics); Springer: New York, NY, USA, 2007; Volume 109, pp. 44-71.
7. Ramezani, H.; Saberi, M.R.; Mansoori, G.A. Diamondoids and DNA nanotechnologies. Int. J. Nanosci. Nanotechnol. 2007, 3, 21-35.
8. Xue, Y.; Mansoori, G.A. Quantum Conductance and Electronic Properties of Lower Diamondoids and their Derivatives. Int. J. Nanosci. 2008, 7, 63-72.
9. Marsusi, F.; Mirabbaszadeh, K.; Mansoori, G.A. Opto-electronic properties of adamantane and hydrogen-terminated sila- and germa-adamantane: A comparative study. Phys. E 2009, 41, 1151-1156.
10. Mansoori, G.A.; George, T.F.; Zhang, G.P.; Assoufid, L. Structure and opto-electronic behavior of diamondoids, with applications as mems and at the nanoscale level. In Progress Nanotechnology Research; Springer: New York, NY, USA, 2009; Chapter 1, pp. 1-19.
11. Kohn, W.; Sham, L. Self-consistent equations including exchange and correlation effects. Phys. Rev. 1965, 140, A1133-A1138.
12. Lee, C.; Yang, W.; Parr, R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1988, B37, 785-789.
13. Woon, D.E.; Dunning, T.H., Jr. Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon. J. Chem. Phys. 1993, 98, 1358-1371.
14. Curtiss, L.A.; McGrath, M.P.; Blaudeau, J.-P.; Davis, N.E.; Binning, R.C., Jr.; Radom, L. Extension of Gaussian-2 theory to molecules containing third-row atoms Ga-Kr. J. Chem. Phys. 1995, 103, 6104-6113.
15. 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, M.; Gill, P.M.W.; Johnson, B.; Chen, W.; Wong, M.W.; Gonzalez, C.; Pople, J.A. Gaussian 03, Revision D.01; Gaussian Inc.: Wallingford, CT, USA, 2004.
16. Carpenter, J.E.; Weinhold, F.J. Analysis of the geometry of the hydroxyl radical by the ldquo. Mol. Struct. (Theochem.) 1988, 169, 41-62.
17. Jorgensen, W.L.; Maxwell, D.S.; Tirado-Rives, J. Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236.
18. Damm, W.; Frontera, A.; Tirado-Rives, J.; Jorgensen, W.L. OPLS all-atom force field for carbohydrates. J. Comput. Chem. 1997, 18, 1955-1970.
19. Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 2001, 7, 306-317.
20. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G..; Mark, A.E.; Berendsen, H.J.C. GROMACS: Fast, flexible and free. J. Comp. Chem. 2005, 26, 1701-1718.
21. 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.
22. Greig, D.W.; Pawley, G.S. Molecular dynamics simulations of the order-disorder phase transition in adamantane. Mol. Phys. 1996, 89, 677-689.
23. Ciccotti, G.; Ferrario, M.; Memeo, E.; Meyer, M. Structural transition on cooling of plastic adamantane: A molecular-dynamics study. Phys. Rev. Lett. 1987, 59, 2574-2577.
24. Humphrey, W.; Dalke, A.; Schulten, K. VMD-visual molecular dynamics. J. Mol. Graph. 1996, 14, 33-38.