Definition and computation of intermolecular contact in liquids using additively weighted voronoi tessellation

Journal of Physical Chemistry A

Volumn 116, Issue 18, 2012, Pages 4657-4666

  Isele Holder, Rolf E ^a,b   Rabideau, Brooks D ^a   Ismail, Ahmed E ^a,b  

^a Faculty of Mechanical Engineering   (Germany)

^b RWTH AACHEN UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COSMO-RS; INTERMOLECULAR CONTACTS; MOLECULAR DYNAMICS SIMULATIONS; ORGANIC LIQUID; PURE WATER; SURFACE CONTACT; VORONOI TESSELLATIONS;

C (PROGRAMMING LANGUAGE);

MOLECULAR DYNAMICS;

EID: 84861090702     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp3021886     Document Type: Article

References (83)

1. Klamt, A. J. Phys. Chem. 1995, 99, 2224-2235
2. Klamt, A.; Jonas, V.; Bürger, T.; Lohrenz, J. C. W. J. Phys. Chem. A 1998, 102, 5074-5085
3. Klamt, A.; Eckert, F. Fluid Phase Equilib. 2000, 172, 43-72
4. Klamt, A.; Schüürmann, G. J. Chem. Soc., Perkin Trans. 2 1993, 2, 799-805
5. Klamt, A.; Eckert, F.; Wolfgang, A. Annu. Rev. Chem. Biomol. Eng. 2010, 1, 101-122
6. Klamt, A.; Reinisch, J.; Eckert, F.; Hellweg, A.; Diedenhofen, M. Phys. Chem. Chem. Phys. 2012, 14, 955-963
7. Klamt, A.; Krooshof, G. J. P.; Taylor, R. AIChE J. 2002, 2332-2349
8. Klamt, A.; Leonhard, K. Fluid Phase Equilib. 2007, 261, 162-167
9. Neiman, M.; Cheng, H.; Parekh, V.; Peterson, B.; Klier, K. Phys. Chem. Chem. Phys. 2004, 6, 3474-3483
10. Voronoi, G. J. Reine Angew. Math. 1907, 133, 97-178
11. Okabe, A.; Boots, B.; Sugihara, K.; Chiu, D. S. N.; Chiu, S. N. Spatial Tessellations: Concepts and Application of Voronoi Diagrams, 2 nd ed.; Wiley: Chichester, U.K., 2000.
12. Kim, D.-S.; Cho, Y.; Sugihara, K.; Ryu, J.; Kim, D. Comput.-Aided Des. 2010, 42, 911-929
13. Ryu, J.; Kim, D.; Cho, Y.; Park, R.; Kim, D.-S. Comput.-Aided Des. 2005, 2, 1-10
14. Bajaj, C. L.; Pascucci, V.; Shamir, A.; Holt, R. J.; Netravali, A. N. Discrete Appl. Math. 2003, 127, 23-51
15. Ruocco, G.; Sampoli, M.; Vallauri, R. J. Chem. Phys. 1992, 96, 6167-6176
16. Montore, J. C. G.; Abascal, J. L. F. J. Phys. Chem. 1993, 97, 4211-4215
17. Brostow, W. Phys. Rev. B 1998, 57, 13448-13458
18. Jediovsyky, P. J. Chem. Phys. 2000, 113, 9113-9121
19. Voloshin, V. P.; Beaufils, S.; Medvedev, N. N. J. Mol. Liq. 2002, 96-97, 101-112
20. Alinchenko, M. G.; Anikeenko, A. V.; Medvedev, N. N.; Voloshin, V. P.; Mezei, M.; Jedlovzky, P. J. Phys. Chem. B 2004, 108, 19056-19067
21. Anikeenko, A. V.; Alinchenko, M. G.; Voloshin, V. P.; Medvedev, N. N.; Gavrilova, M. L.; Jedlovszky, P. Comput.-Aided Des. 2004, 3045, 217-226
22. Corti, D. S.; Debenedetti, P. G.; Sastry, S.; Stillinger, F. H. Phys. Rev. E 1997, 55, 5522-5534
23. Sastry, S.; Corti, D. S.; Debenedetti, P. G.; Stillinger, F. H. Phys. Rev. E 1997, 56, 5524-5532
24. Sastry, S.; Debenedetti, P. G.; Stillinger, F. H. Phys. Rev. E 1997, 56, 5533-5543
25. Debenedetti, P. G.; Truskett, T. M. Fluid Phase Equilib. 1999, 158-160, 549-556
26. Zhang, C.; Duan, Y.; Li, M. Geochim. Cosmochim. Acta 2010, 74, 4140-4149
27. Fern, F. T.; Keffer, D. J.; Steele, W. V. J. Phys. Chem. B 2007, 111, 3469-3475
28. Fern, F. T.; Keffer, D. J.; Steele, W. V. J. Phys. Chem. B 2007, 111, 13278-13286
29. David, C. W. Biopolymers 1988, 27, 339-344
30. Kim, C.-M.; Won, C.-I.; Cho, Y.; Kim, D.; Lee, S.; Bhak, D.-S.; an Kim, J. Comput.-Aided Des. 2006, 38, 1192-1204
31. Howard, P. H.; Meylan, W. Handbook of Physical Properties of Organic Chemicals; CRC Press: Boca Raton, FL, 1996.
32. Sangster, J. J. Phys. Chem. Ref. Data 1989, 18, 1111-1227
33. Pátek, J.; Hrubý, J.; Klomfar, J.; Součková, M.; Harvey, A. H. J. Phys. Chem. Ref. Data 2009, 38, 21-29
34. Nayak, J. N.; Aralaguppi, M. I.; Aminabhavi, T. M. J. Chem. Eng. Data 2003, 48, 1152-1156
35. Harris, K. R. J. Chem. Eng. Data 2000, 45, 893-897
36. Djojoputro, H.; Ismadji, S. J. Chem. Eng. Data 2005, 50, 2003-2007
37. Nath, J. J. Chem. Thermodyn. 1996, 28, 167-170
38. Toti, U. S.; Kariduraganavar, M. Y.; Aralaguppi, M. I.; Aminabhavi, T. M. J. Chem. Eng. Data 2000, 45, 920-925
39. Estrada-Baltazar, A.; León-Rodriguez, A. d.; Hall, K. R.; Ramos-Estrada, M.; Iglesias-Silva, G. A. J. Chem. Eng. Data 2003, 48, 1425-1431
40. Gardas, R. L.; Johnson, I.; Vaz, D. M. D.; Fonseca, I. M. A.; Ferreira, A. G. M. J. Chem. Eng. Data 2007, 52, 737-751
41. Naorem, H.; Suri, S. K. Can. J. Chem. 1989, 67, 1672-1675
42. Roy, M. N.; Sarkar, B. K.; Chanda, R. J. Chem. Eng. Data 2007, 51, 1630-1637
43. Domíniguez, M.; Rodriguez, S.; López, M. C.; Royo, F. M.; Urieta, J. S. J. Chem. Eng. Data 1996, 41, 37-42
44. Nayak, J. N.; Aralaguppi, M. I.; Toti, U. S.; Aminabhavi, T. M. J. Chem. Eng. Data 2003, 48, 1483-1488
45. Cases, A. M.; Marigliano, A. C. G.; Bonatti, C. M.; Sólimo, H. N. J. Chem. Eng. Data 2001, 46, 712-715
46. Garcia-Miaja, G.; Troncoso, J.; Romani, L. J. Chem. Eng. Data 2007, 52, 2261-2265
47. McCormick, D. G.; Hamilton, W. S. J. Chem. Thermodyn. 1978, 10, 275-278
48. Marongiu, B.; Marras, G.; Porcedda, S. J. Chem. Eng. Data 1993, 38, 638-643
49. Haines, W. E.; Helm, R. V.; Bailey, C. W.; Ball, J. S. J. Phys. Chem. 1954, 58, 270-278
50. Dias, A. M. A.; Gonçalves, C. M. B.; Caço, A. I.; Santos, L. M. N. B. F.; Piñeiro, M. M.; Vega, L. F.; Coutinho, J. A. P.; Marrucho, I. M. J. Chem. Eng. Data 2005, 50, 1328-1333
51. Atik, Z. J. Chem. Eng. Data 2007, 52, 1128-1130
52. Resa, J. M.; Gonzáles, C.; Landaluce, S. O., de; Lanz, J. J. Chem. Eng. Data 2000, 45, 867-871
53. Nayak, J. N.; Aralaguppi, M. I.; Aminabhavi, T. M. J. Chem. Eng. Data 2003, 48, 1152-1156
54. Bhattacharjee, A.; Roy, M. N. J. Chem. Eng. Data 2010, 55, 5914-5920
55. Eckert, F. COSMOtherm Users Manual; COSMOlogic GmbH & Co. KG: Leverkusen, Germany, 2009.
56. Plimpton, S. J. Comput. Chem. 1995, 117, 1-19
57. Jorgensen, W. J.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
58. Damm, W.; Frontera, A.; Tirado-Rives, J.; Jorgensen, W. L. J. Comput. Chem. 1997, 18, 1955-1970
59. Rizzo, R. C.; Jorgensen, W. L. J. Am. Chem. Soc. 1999, 121, 4827-4836
60. Price, M. L. P.; Ostrovsky, D.; Jorgensen, W. J. J. Comput. Chem. 2001, 22, 1340-1352
61. Jorgensen, W. L.; McDonald, N. A. J. Mol. Struct. (THEOCHEM) 1998, 424, 145-155
62. McDonald, N. A.; Jorgensen, W. L. J. Phys. Chem. B 1998, 102, 8040-8059
63. Watkins, E. K.; Jorgensen, W. L. J. Phys. Chem. A 2001, 105, 4118-4125
64. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269-6271
65. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Phys. Chem. 1983, 79, 926-935
66. Durell, S. R.; Brooks, B. R.; Ben-Naim, A. J. Phys. Chem. 1994, 98, 2198-2202
67. Price, J. D.; Brooks, C. L., III. J. Chem. Phys. 2004, 121, 10096-10103
68. Horn, H. W.; Swope, J. C.; Pitera, J. W.; Madera, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. J. Chem. Phys. 2004, 120, 9665-9678
69. Ryckaert, J. P.; Berendsen, H. J. C.; Ciscotti, G. J. Comput. Phys. 1977, 23, 327-341
70. Martínez, L.; Andrade, R.; Birgin, E. G.; Martínez, J. M. J. Comput. Chem. 2009, 30, 2157-2164
71. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, U.K., 1987.
72. Hockney, R.; Eastwood, J. Computer Simulations Using Particles; McGraw-Hill Inc.: New York, 1981.
73. Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994, 101, 4177-4189
74. Shinoda, W.; Shiga, M.; Mikami, M. Phys. Rev. B 2004, 69, 134103
75. Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190
76. Tuckerman, M. E.; Alejandre, J.; López-rendón, R.; Jochim, A. L.; Martyna, G. J. J. Phys. A 2006, 39, 5629-5651
77. Gervois, A. Lect. Notes Comput. Sci. 2002, 2331, 95-104
78. Medvedev, N. N.; Voloshin, V. P.; Luchnikov, V. A.; Gavrilova, M. L. J. Comput. Chem. 2006, 27, 1676-1692
79. Kim, D.-S.; Cho, Y.; Kim, D. Comput.-Aided Des. 2005, 37, 1412-1424
80. Dong, P. Comput. Geosci. 2008, 34, 411-421
81. Rycroft, C. H. Voro++: A Three-Dimensional Voronoi Cell Library in C++; Lawrence Berkeley National Laboratory: Berkeley, CA, 2009; available at http://math.lbl.gov/voro++/.
82. Rycroft, C. H. Multiscale Modeling in Granular Flow. Ph.D. Thesis, Massachusetts Institute of Technology, Cambridge, MA, 2007.
83. Bondi, A. J. Phys. Chem. 1964, 68, 441-451