Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β- and γ-glycine

Journal of Chemical Physics

Volumn 135, Issue 13, 2011, Pages

  Duff, Nathan ^a   Peters, Baron ^a,b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BULK CRYSTALS; CRYSTAL NUCLEATION; LOCAL ENVIRONMENTS; LOCAL ORDER; MATERIAL SYNTHESIS; MELTED LAYERS; ORDER PARAMETER; ROOT MEAN SQUARED DEVIATIONS; STRUCTURAL CHANGE; SUPERSATURATED AQUEOUS SOLUTIONS; SURFACE MELTING; TEMPLATE-BASED;

BIOMINERALIZATION; CRYSTAL STRUCTURE; CRYSTALLITES; CRYSTALLIZATION; MOLECULAR CRYSTALS; NUCLEATION; PHASE INTERFACES; SOLUTIONS; SURFACES;

AMINO ACIDS;

EID: 80054687260     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3638268     Document Type: Article

References (62)

1. P. R. ten Wolde, M. J. Ruiz-Montero, and D. Frenkel, J. Chem. Phys. 104, 9932 (1996). 10.1063/1.471721
2. Y. Chushak and L. S. Bartell, J. Phys. Chem. A 104, 9328 (2000). 10.1021/jp002107e
3. B. Coasne, S. K. Jain, and K. E. Gubbins, Phys. Rev. Lett. 97, 105702 (2006). 10.1103/PhysRevLett.97.105702 (Pubitemid 44373676)
4. C. Desgranges and J. Delhommelle, J. Phys. Chem. B 111, 1465 (2007). 10.1021/jp067310+
5. J. R. Errington, P. G. Debenedetti, and S. Torquato, J. Chem. Phys. 118, 2256 (2003). 10.1063/1.1532344
6. W. Lechner and C. Dellago, J. Chem. Phys. 129, 114707 (2008). 10.1063/1.2977970
7. D. Moroni, P. R. ten Wolde, and P. G. Bolhuis, Phys. Rev. Lett. 94, 235703 (2005). 10.1103/PhysRevLett.94.235703 (Pubitemid 41636560)
8. F. Trudu, D. Donadio, and M. Parrinello, Phys. Rev. Lett. 97, 105701 (2006). 10.1103/PhysRevLett.97.105701 (Pubitemid 44359794)
9. G. T. Beckham and B. Peters, J. Phys. Chem. Lett. 2, 1133 (2011). 10.1021/jz2002887
10. S. Auer and D. Frenkel, J. Chem. Phys. 120, 3015 (2004). 10.1063/1.1638740
11. A. R. Browning, M. F. Doherty, and G. H. Fredrickson, Phys. Rev. E 77, 041604 (2008). 10.1103/PhysRevE.77.041604 (Pubitemid 351561382)
12. W. Lechner, C. Dellago, and P. G. Bolhuis, Phys. Rev. Lett. 106, 085701 (2011). 10.1103/PhysRevLett.106.085701
13. S. Punnathanam and P. A. Monson, J. Chem. Phys. 125, 024508 (2006). 10.1063/1.2208998 (Pubitemid 44079143)
14. B. Peters, J. Chem. Phys. 131, 244103 (2009). 10.1063/1.3271024
15. P. R. ten Wolde and D. Frenkel, Science 277, 1975 (1997). 10.1126/science.277.5334.1975 (Pubitemid 27449135)
16. R. Radhakrishnan and B. L. Trout, J. Am. Chem. Soc. 125, 7743 (2003). 10.1021/ja0211252 (Pubitemid 36750296)
17. R. Radhakrishnan and B. L. Trout, Phys. Rev. Lett. 90, 158301 (2003). 10.1103/PhysRevLett.90.158301
18. D. Quigley and P. M. Rodger, J. Chem. Phys. 128, 154518 (2008). 10.1063/1.2888999 (Pubitemid 351574664)
19. E. B. Moore, E. de la Llave, K. Welke, D. A. Scherlis, and V. Molinero, Phys. Chem. Chem. Phys. 12, 4124 (2010). 10.1039/b919724a
20. L. C. Jacobson, W. Hujo, and V. Molinero, J. Phys. Chem. B 113, 10298 (2009). 10.1021/jp903439a
21. R. Radhakrishnan and B. L. Trout, J. Chem. Phys. 117, 1786 (2002). 10.1063/1.1485962 (Pubitemid 34923927)
22. M. R. Walsh, C. A. Koh, E. D. Sloan, A. K. Sum, and D. T. Wu, Science 326, 1095 (2009). 10.1126/science.1174010
23. R. W. Hawtin, D. Quigley, and P. M. Rodger, Phys. Chem. Chem. Phys. 10, 4853 (2008). 10.1039/b807455k
24. L. C. Jacobson, W. Hujo, and V. Molinero, J. Phys. Chem. B 114, 13796 (2010). 10.1021/jp107269q
25. D. Quigley, P. M. Rodger, C. L. Freeman, J. H. Harding, and D. M. Duffy, J. Chem. Phys. 131, 09470 (2009). 10.1063/1.3212092
26. D. Quigley, C. L. Freeman, J. H. Harding, and P. M. Rodger, J. Chem. Phys. 134, 044703 (2011). 10.1063/1.3530288
27. P. J. Steinhardt, D. R. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). 10.1103/PhysRevB.28.784
28. J. S. Vanduijneveldt and D. Frenkel, J. Chem. Phys. 96, 4655 (1992). 10.1063/1.462802
29. J. R. Errington and P. G. Debenedetti, Nature (London) 409, 318 (2001). 10.1038/35053024 (Pubitemid 32151231)
30. P. L. Chau and A. J. Hardwick, Mol. Phys. 93, 511 (1998). 10.1080/002689798169195
31. E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011). 10.1063/1.3548889
32. A. S. Keys, C. R. Iacovella, and S. C. Glotzer, Annu. Rev. Condens. Matter Phys. 2, 263 (2011). 10.1146/annurev-conmatphys-062910-140526
33. R. Shetty, F. A. Escobedo, D. Choudhary, and P. Clancy, J. Chem. Phys. 117, 4000 (2002). 10.1063/1.1494986 (Pubitemid 34992685)
34. W. Kabsch, Acta Crystallogr. Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. 32, 922 (1976). 10.1107/S0567739476001873
35. W. Kabsch, Acta Crystallogr. Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. 34, 827 (1978). 10.1107/S0567739478001680
36. X. Yang, J. Lu, X. J. Wang, and C. B. Ching, J. Cryst. Growth 310, 604 (2008). 10.1016/j.jcrysgro.2007.11.072
37. S. L. Price, S. Hamad, A. Torrisi, P. G. Karamertzanis, M. Leslie, and C. R. A. Catlow, Mol. Simul. 32, 985 (2006). 10.1080/08927020600880810 (Pubitemid 47355424)
38. J. M. Wang, P. Cieplak, and P. A. Kollman, J. Comput. Chem. 21, 1049 (2000). 10.1002/1096-987X(200009)21:121049::AID-JCC33.0.CO;2-F
39. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten, J. Comput. Chem. 26, 1781 (2005). 10.1002/jcc.20289 (Pubitemid 43078511)
40. G. Ciccotti, M. Ferrario, and J. P. Ryckaert, Mol. Phys. 47, 1253 (1982). 10.1080/00268978200100942
41. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993). 10.1063/1.464397
42. S. E. Feller, Y. H. Zhang, R. W. Pastor, and B. R. Brooks, J. Chem. Phys. 103, 4613 (1995). 10.1063/1.470648
43. G. J. Martyna, D. J. Tobias, and M. L. Klein, J. Chem. Phys. 101, 4177 (1994). 10.1063/1.467468
44. J. Chen and B. L. Trout, J. Phys. Chem. B 114, 13764 (2010). 10.1021/jp1039496
45. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
46. S. Miyamoto and P. A. Kollman, J. Comput. Chem. 13, 952 (1992). 10.1002/jcc.540130805
47. Y. C. Chang and A. S. Myerson, AIChE J. 32, 1567 (1986). 10.1002/aic.690320919
48. F. H. Allen, Acta Crystallogr. Sect. B: Struct. Sci. 58, 380 (2002). 10.1107/S0108768102003890 (Pubitemid 135702674)
49. P. Langan, S. A. Mason, D. Myles, and B. P. Schoenborn, Acta Crystallogr. Sect. B: Struct. Sci. 58, 728 (2002). 10.1107/S0108768102004263 (Pubitemid 135688520)
50. E. S. Ferrari, R. J. Davey, W. I. Cross, A. L. Gillon, and C. S. Towler, Cryst. Growth Des. 3, 53 (2003). 10.1021/cg025561b
51. A. Kvick, W. M. Canning, T. F. Koetzle, and G. J. B. Williams, Acta Crystallogr. Sect. B: Struct. Sci. 36, 115 (1980). 10.1107/S0567740880002555
52. See supplementary material at http://dx.doi.org/10.1063/1.3638268 E-JCPSA6-135-006136 for detailed discussions on the creation of the dummy oxygen atom, the pruning procedure for Bicalutamide, and the local density cutoff to identify solvated glycine clusters.
53. R. Persson, S. Nordholm, G. Perlovich, and L. Lindfors, J. Phys. Chem. B 115 (12), 3062 (2011). 10.1021/jp111817h
54. N. Duff and B. Peters, J. Chem. Phys. 131, 184101 (2009). 10.1063/1.3250934
55. P. R. ten Wolde and D. Frenkel, J. Chem. Phys. 109, 9901 (1998). 10.1063/1.477658 (Pubitemid 128678420)
56. H. M. Ellerby and H. Reiss, J. Chem. Phys. 97, 5766 (1992). 10.1063/1.463760
57. H. M. Ellerby, C. L. Weakliem, and H. Reiss, J. Chem. Phys. 95, 9209 (1991). 10.1063/1.461202
58. C. L. Weakliem and H. Reiss, J. Chem. Phys. 99, 5374 (1993). 10.1063/1.465981
59. K. Kim, I. S. Lee, A. Centrone, T. A. Hatton, and A. S. Myerson, J. Am. Chem. Soc. 131, 18212 (2009). 10.1021/ja908055y
60. H. Freundlich, Colloid Capillary Chemistry. (Dutton, New York, 1922).
61. W. Ostwald, Z. Phys. Chem. 34, 495 (1900).
62. A. Navrotsky, Proc. Natl. Acad. Sci. U.S.A. 101 (33), 12096 (2004). 10.1073/pnas.0404778101 (Pubitemid 39145403)