Topology of cyclo-octane energy landscape

Journal of Chemical Physics

Volumn 132, Issue 23, 2010, Pages

  Martin, Shawn ^a   Thompson, Aidan ^a   Coutsias, Evangelos A ^b   Watson, Jean Paul ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGEBRAIC VARIETIES; ENERGY LANDSCAPE; EUCLIDEAN SPACES; HIGH-DIMENSIONAL; LOW-DIMENSIONAL MANIFOLDS; MATHEMATICAL COMPLEXITY; MATHEMATICAL STRUCTURE;

SPHERES;

CYCLOOCTANE; CYCLOOCTANE DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; THERMODYNAMICS;

CYCLOOCTANES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; THERMODYNAMICS;

EID: 77953851412     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3445267     Document Type: Article

References (34)

1. D. Wales, Energy Landscapes: With Applications to Clusters, Biomolecules, and Glasses (Cambridge University Press, Cambridge, 2003).
2. A. Pohorille and C. Chipot, Free Energy Calculations: Theory and Applications in Chemistry and Biology (Springer-Verlag, Berlin, 2007).
3. K. A. Dill and H. S. Chan, Nat. Struct. Biol. NSBIEW 1072-8368 4, 10 (1997). 10.1038/nsb0197-10 (Pubitemid 27020916)
4. A. E. García, Phys. Rev. Lett. PRLTAO 0031-9007 68, 2696 (1992). 10.1103/PhysRevLett.68.2696
5. S. Hayward and N. Go, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 46, 223 (1995). 10.1146/annurev.pc.46.100195.001255
6. S. B. Nolde, A. S. Arseniev, V. Y. Orekhov, and M. Billeter, Proteins: Struct., Funct., Genet. PSFGEY 0087-3585 46, 250 (2002). 10.1002/prot.10030 (Pubitemid 34150745)
7. Y. Levy and A. Caflisch, J. Phys. Chem. B JPCBFK 1089-5647 107, 3068 (2003). 10.1021/jp0219956
8. M. L. Teodoro, G. N. Phillips, and L. E. Kavraki, J. Comput. Biol. JCOBEM 1066-5277 10, 617 (2003). 10.1089/10665270360688228 (Pubitemid 37372170)
9. P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 9885 (2006). 10.1073/pnas.0603553103 (Pubitemid 43993592)
10. A. Altis, M. Otten, P. H. Nguyen, R. Hegger, and G. Stock, J. Chem. Phys. JCPSA6 0021-9606 128, 245102 (2008). 10.1063/1.2945165
11. W. M. Brown, S. Martin, S. N. Pollock, E. A. Coutsias, and J. -P. Watson, J. Chem. Phys. JCPSA6 0021-9606 129, 064118 (2008). 10.1063/1.2968610
12. M. Kirby, Geometric Data Analysis: An Empirical Approach to Dimensionality Reduction and the Study of Patterns (Wiley, New York, 2001).
13. S. Roweis and L. K. Saul, Science SCIEAS 0036-8075 290, 2323 (2000). 10.1126/science.290.5500.2323 (Pubitemid 32041578)
14. J. Tenenbaum, V. de Silva, and J. Langford, Science SCIEAS 0036-8075 290, 2319 (2000). 10.1126/science.290.5500.2319 (Pubitemid 32041577)
15. J. B. Hendrickson, J. Am. Chem. Soc. JACSAT 0002-7863 89, 7036 (1967). 10.1021/ja01002a036
16. W. R. Rocha, J. R. Pilego, S. M. Resende, H. F. Dos Santos, M. A. De Oliveira, and W. B. De Almeida, J. Comput. Chem. JCCHDD 0192-8651 19, 524 (1998). 10.1002/(SICI)1096-987X(19980415)19:5<524::AID-JCC5>3.0.CO;2-O
17. R. K. Bharadwaj, Mol. Phys. MOPHAM 0026-8976 98, 211 (2000).
18. Z. Chen and F. A. Escobedo, J. Chem. Phys. JCPSA6 0021-9606 113, 11382 (2000). 10.1063/1.1328069 (Pubitemid 32087628)
19. J. Ṕrez, K. Nolsøe, M. Kessler, L. Garcia, E. Ṕrez, and J. L. Serrano, Acta Crystallogr., Sect. B: Struct. Sci. ASBSDK 0108-7681 B61, 585 (2005). 10.1107/S0108768105023931 (Pubitemid 43923845)
20. J. M. Porta, L. Ros, F. Thomas, F. Corcho, J. Cantó, and J. J. Ṕrez, J. Comput. Chem. JCCHDD 0192-8651 28, 2170 (2007). 10.1002/jcc.20733 (Pubitemid 47265255)
21. E. A. Coutsias, C. Seok, M. J. Wester, and K. A. Dill, Int. J. Quantum Chem. IJQCB2 0020-7608 106, 176 (2006). 10.1002/qua.20751 (Pubitemid 43082078)
22. A. Y. Dymarsky and K. N. Kudin, J. Chem. Phys. JCPSA6 0021-9606 122, 124103 (2005). 10.1063/1.1864872 (Pubitemid 40537448)
23. S. Martin and J. -P. Watson, " Non-manifold surface reconstruction from high-dimensional point cloud data.," Comput. Geom. CGOME6 0925-7721 (to be published).
24. D. Freedman, Comput. Geom. CGOME6 0925-7721 36, 106 (2007). 10.1016/j.comgeo.2006.05.004 (Pubitemid 44723779)
25. G. Rote and G. Vegter, in Effective Computational Geometry for Curves and Surfaces, edited by, J. -D. Boissonnat, and, M. Teillaud, (Springer-Verlag, Berlin, 2006), pp. 277-312. 10.1007/978-3-540-33259-6-7
26. See: www.comptop.stanford.edu for additional information and to download the Plex toolbox for computational topology.
27. See: www.linalg.org to download the Linbox toolbox for exact linear algebra.
28. See supplementary material at http://dx.doi.org/10.1063/1.3445267 E-JCPSA6-132-021022 for derivation of canonical conformations and topological analysis using ring puckering coordinates.
29. See: dasher.wustl.edu to obtain the TINKER package for molecular dynamics calculations.
30. Y. H. Y. N. L. Allinger and J. H. Lii, J. Am. Chem. Soc. JACSAT 0002-7863 111, 8551 (1989). 10.1021/ja00205a001 (Pubitemid 20021795)
31. K. B. Wiberg, J. Org. Chem. JOCEAH 0022-3263 68, 9322 (2003). 10.1021/jo030227n (Pubitemid 37456500)
32. R. Elber and M. Karplus, Chem. Phys. Lett. CHPLBC 0009-2614 139, 375 (1987). 10.1016/0009-2614(87)80576-6
33. D. G. Evans and J. C. A. Boeyens, Acta Crystallogr., Sect. B: Struct. Sci. ASBSDK 0108-7681 B44, 663 (1988). 10.1107/S0108768188008730
34. K. D. Gibson and H. A. Scheraga, J. Comput. Chem. JCCHDD 0192-8651 18, 403 (1997). 10.1002/(SICI)1096-987X(199702)18:3<403::AID-JCC10>3.0.CO;2-J