Classical hybrid Monte-Carlo simulation of the interconversion of hexabromocyclododecane stereoisomers

Molecular Simulation

Volumn 34, Issue 7, 2008, Pages 727-736

  Weber, Marcus ^a   Becker, Roland ^b   Durmaz, Vedat ^a   Köppen, Robert ^b  

^a ZUSE INSTITUTE BERLIN   (Germany)

^b BAM FEDERAL INSTITUTE FOR MATERIALS RESEARCH AND TESTING   (Germany)

Author keywords

HBCD; Isomerisation; Kinetics; Statistical thermodynamics

Indexed keywords

CONVERGENCE OF NUMERICAL METHODS; FLAME SPRAYING; FREE ENERGY; QUANTUM THEORY; STATISTICAL MECHANICS; STEREOCHEMISTRY; THERMODYNAMICS;

CANONICAL ENSEMBLES; CLASSICAL FORCE-FIELDS; CONVERGENCE PROPERTIES; ENERGY DIFFERENCES; FLAME RETARDANTS; HBCD; HEXABROMOCYCLODODECANE; INTERCONVERSION; ISOMERISATION; KINETICS; LOW TEMPERATURE; MONTE-CARLO; MONTE-CARLO SIMULATIONS; QUANTUM-MECHANICAL; SADDLE POINTS; SIMULATION RESULTS; SINK-IN; STATISTICAL THERMODYNAMICS;

MONTE CARLO METHODS;

EID: 49649126846     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020802208968     Document Type: Article

References (36)

1. A. Covaci, A.S.C. Gerecke, R.J. Law, S. Voorspoels, M. Kohler, N.V. Heeb, H. Leslie, C.R. Allchin, and J. De Boer, Hexabromocyclododecanes (HBCDs) in the environment and humans: A review, Environ. Sci. Technol. 40 (2006), p. 3680.
2. C.A. de Wit, An overview of brominated flame retardants in the environment, Chemosphere 40 (2002), p. 583.
3. C.A. de Wit, M. Alaee, and D.C.G. Muir, Levels and trends of brominated flame retardants in the arctic, Chemosphere 64 (2006), p. 209.
4. K. Law, V.P. Palace, T. Halldorson, R. Danell, K. Wautier, B. Evans, M. Alaee, C Marvin, and G.T. Tomy, Dietary accumulation of hexabromocyclododecane diastereoisomers in juvenile rainbow trout (Oncorhynchus mykiss) I: Bioaccumulation parameters and evidence of bioisomerization, Environ. Toxicol. Chem. 25 (2006), p. 1757.
5. J.G. Vos, G. Becher, M. van den Berg, M. de Boer, and P.E.G. Leonards, Brominated flame retardants and endocrine disruption. Pure Appl. Chem. 75 (2003), p. 2039.
6. R. Koeppen, R. Becker, F. Emmerling, C Jung, and I. Nehls, Enantioselective preparative HPLC separation of the HBCD-stereoisomers from the technical product and their absolute structure elucidation using X-ray crystallography, Chirality 19 (2007), p. 214.
7. B.N. Zegers, A. Mets, R. van Bommel, C Minkenberg, T. Hamers, J.H. Kamstra, G.J. Pierce, and J.P. Boon, Levels of hexabromocyclododecane in harbor porpoises and common dolphins from western European seas, with evidence for stereoisomer-specific biotransformation by cytochrome P450, Environ. Sci. Technol. 39 (2005), p. 2095.
8. M. Peled, R. Scharia, and D. Sondack, Thermal rearrangement of hexabromocyclododecane (HBCD), in Advances in Organobromine Chemistry, J.R. Desmurs, B. Gerard, and M.J. Goldstein, eds., Elsevier, Amsterdam, 1995, p. 92.
9. K. Janak, A. Covaci, S. Voorspoels, and G. Becher, Hexabromocyclododecane in marine species from the western Scheldt Estuary: Diastereoisomer- and enantiomerspecific accumulation, Environ. Sci. Technol. 39 (2005), p. 1987.
10. R. Koppen, R. Becker, C Jung, and I. Nehls, On the thermally induced isomerisation of hexabromocyclododecane stereoisomers, Chemosphere 71 (2008), p. 656.
11. N.V. Heeb, W.B. Schweizer, P. Mattrel, R. Haag, M. Kohler, P. Schmid, M. Zennegg, and M. Wolfensberger, Regio- and stereoselective isomerization of hexabromoeyclododecanes (HBCDs): Kinetics and mechanism of β-HBCD racemization, Chemosphere 71 (2008), p. 1547.
12. C.A. Grob and S. Winstein, Mechanismus der mutarotation von 5,6-dibromcholestan, Helv. Chim. Acta. 35 (1952), p. 780.
13. J.F. King and R.G. Pews, Reaction mechanism studies: 3. Solvent effects and nature of transition state in diaxial -→ diequatorial rearrangement, Can. J. Chem. 43 (1965), p. 847.
14. P.L. Barili, G. Bellucci, G. Berti, A. Marioni, A. Marsili, and I. Morelli, Thermal equilibrium of substituted trans-1,2-dibromocyclohexanes, J. Chem. Soc. Perk. Trans. 2(1) (1972), p. 58.
15. G. Bellucci, A. Marsili, E. Mastrorilli, I. Morelli, and V. Scartoni, Kinetics of thermal racemization of some 1,2-dihalides, J. Chem. Soc. Perkin Trans. 2(2) (1974), p. 201.
16. T.A. Halgren, The representation of Van der Waals (VdW) interactions in molecular mechanics force fields: Potential form, combination rules, and vdW parameters, J. Am. Chem. Soc. 114 (1992), p. 7827.
17. _, Merck molecular force field, J. Comp. Chem. 17 (1996), p. 490.
18. S. Duane, A.D. Kennedy, B.J. Pendleton, and D. Roweth, Hybrid Monte Carlo, Phys. Lett. B 195 (1987), p. 216.
19. C Schütte, A. Fischer, W. Huisinga, and P. Deuflhard, A direct approach to conformational dynamics based on hybrid Monte Carlo, J. Comput. Phys., Special Issue on Computational Biophysics 151 (1999), p. 146.
20. D. Frenkel and B. Smit, Understanding molecular simulation -from algorithms to applications, in Computational Science Series, Vol. 1, Academic Press, London, UK, 2002.
21. A. Fischer, An uncoupling-coupling method for Markov chain Monte Carlo simulations with an application to biomolecules, Doctoral thesis, Freie Universität Berlin (DE), 2003.
22. A. Fischer, C. Schütte, P. Deuflhard, and F. Cordes, Hierarchical uncoupling-coupllng of metastable conformations, in Computational Methods for Macromolecules: Challenges and Applications, Proc. of the 3rd Intern. Workshop on Algorithms for Macromolecular Modelling, T. Schlick and H.H. Gan, eds., Springer, Berlin, Heidelberg, New York, 2002, p. 235.
23. A. Gelman and D. Rubin, Inference from iterative simulation using multiple sequences, Stat. Sci. 7 (1992), p. 457.
24. _, Markov chain Monte Carlo methods in biostatistics, Stat. Methods Med. Res. 5 (1996), p. 339.
25. Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chem. Phys. Lett. 314 (1999), p. 141.
26. Ch. Chipot and A. Pohorille, Free energy calculations, in Springer Series In Chemical Physics, Vol. 86, Springer, Berlin, Heidelberg, 2007.
27. M.R, Hestens and E. Stiefel, Methods of conjugate gradients for solving linear systems, J. Res. Nat. Bur. Stand. 49 (1952), p. 409.
28. N.V. Heeb, W.B. Schweizer, M. Kohler, and A.C. Gerecke, Structure elucidation of hexabromocyclododecanes - a class of compounds with a complex stereochemistry, Chemosphere 61 (2005), p. 65.
29. N.V. Heeb, W.B. Schweizer, P. Mattrel, R. Haag, and M. Kohler, Crystal structure analysis of enantiomerically pure (+) and (-)- hexabromocyclododecanes, Chemosphere 66 (2007), p. 1590.
30. N.V. Heeb, W.B. Schweizer, P. Mattrel, R. Haag, A.C. Gerecke, M. Kohler, P. Schmid, M. Zennegg, and M. Wolfensberger, Solid-state conformations and absolute configurations of(+) and(- ) α-, β-, and γ-hexabromocyclododecanes (HBCDs), Chemosphere 68 (2007), p. 940.
31. W. Göpel and H.-D. Wiemdörfer, Statistische thermodynamik Spectrum, Akademischer Verlag, Germany, 2000.
32. S. Kube and M. Weber, Conformation kinetics as a reduced model for transition pathways, ZIB report 05-43, Zuse Institute Berlin '(2005).
33. M. Kijima, Markov processes for stochastic modeling, in Stochastic Modelling Series, Chapman and Hall, 1997.
34. M. Weber, Conformation-based transition state theory, ZIB report 07-18, Zuse Institute Berlin (2007).
35. _, Meshless methods in conformation dynamics, Doctoral thesis, Freie Universität Berlin, 2006.
36. M. Weber, S. Kube, L. Walter, and P. Deuflhard, Stable computation of probability densities for metastable dynamical systems, SIAM J. Multisc. Mod. Sim. 6 (2007), p. 396.