Water interactions with hydrophobic groups: Assessment and recalibration of semiempirical molecular orbital methods

Journal of Chemical Physics

Volumn 141, Issue 3, 2014, Pages

  Marion, Antoine ^a,b   Monard, Gérald ^a,b   Ruiz López, Manuel F ^a,b   Ingrosso, Francesca ^a,b  

^a UNIVERSITÉ DE LORRAINE   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; HYDROGEN BONDS; HYDROPHILICITY; HYDROPHOBICITY; METHANE; ORBITAL CALCULATIONS; QUANTUM CHEMISTRY;

HYDROGEN BONDED SYSTEMS; HYDROPHILIC AND HYDROPHOBIC; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INTERMOLECULAR INTERACTIONS; NON-COVALENT INTERACTION; POTENTIAL ENERGY CURVES; SEMI-EMPIRICAL MOLECULAR ORBITAL METHOD; SEMIEMPIRICAL HAMILTONIANS;

HAMILTONIANS;

EID: 84904645115     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4886655     Document Type: Article

References (71)

1. J. Vandevondele, U. Borstnik, and J. Hutter, J. Chem. Theory Comput. 8, 3565 (2012). 10.1021/ct200897x
2. J. D. C. Maia, G. A. Urquiza Carvalho, C. P. Mangueira, S. R. Santana, L. A. F. Cabral, and G. B. Rocha, J. Chem. Theory Comput. 8, 3072 (2012). 10.1021/ct3004645
3. X. Wu, A. Koslowski, and W. Thiel, J. Chem. Theory Comput. 8, 2272 (2012). 10.1021/ct3001798
4. G. Monard, M. I. Bernal-Uruchurtu, A. Van Der Vaart, K. M. Merz, and M. F. Ruiz-López, J. Phys. Chem. A 109, 3425 (2005). 10.1021/jp0459099
5. G. Murdachaew, C. J. Mundy, G. K. Schenter, T. Laino, and J. Hutter, J. Phys. Chem. A 115, 6046 (2011). 10.1021/jp110481m
6. J. A. Pople, D. P. Santry, and G. A. Segal, J. Chem. Phys 43, S129 (1965). 10.1063/1.1701475
7. M. J. S. Dewar and W. Thiel, J. Am. Chem. Soc. 99, 4899 (1977). 10.1021/ja00457a004
8. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc. 107, 3902 (1985). 10.1021/ja00299a024
9. J. P. P. Stewart, J. Comput. Chem. 10, 209 (1989). 10.1002/jcc.540100208
10. O. N. Ventura, E. L. Coitiño, A. Lledós, and J. Berteán, J. Mol. Structure: THEOCHEM 187, 55 (1989). 10.1016/0166- 1280(89)85149-8
11. G. I. Csonka, J. Comput. Chem. 14, 895 (1993). 10.1002/jcc.540140803
12. G. I. Csonka, K. Éliás, and I. G. Csizmadia, J. Comput. Chem. 18, 330 (1997). 10.1002/(SICI)1096-987X(199702)18:3<330::AID-JCC4>3. 0.CO;2-V
13. G. I. Csonka and J. G. Ángyán, J. Mol. Struct.: THEOCHEM 393, 31 (1997). 10.1016/S0166-1280(96)04872-5
14. M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000). 10.1002/(SICI)1096- 987X(200005)21:7<572::AID-JCC6>3.0.CO;2-X
15. W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004). 10.1007/s00214-004-0576-1
16. L. Salvatella, A. Mokrane, A. Cartier, and M. F. Ruiz-López, Chem. Phys. Lett. 296, 239 (1998). 10.1016/S0009-2614(98)01033-1
17. W. Harb, Ph.D. thesis, Université Henri Poincaré, Nancy, 2003.
18. O. I. Arillo-Flores, M. F. Ruiz-López, and M. I. Bernal-Uruchurtu, Theor. Chem. Acc. 118, 425 (2007). 10.1007/s00214-007-0280-z
19. J. J. Dannenberg, J. Mol. Structure.: THEOCHEM 401, 279 (1997). 10.1016/S0166-1280(97)00029-8
20. T. Clark and J. J. P. Stewart, Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology, edited by J. J. Reimers (Wiley, Chichester, 2011).
21. W. Thiel, " Semiempirical quantum-chemical methods," Wiley Interdisc. Rev.: Comput. Mol. Sci. 4, 145 (2013). 10.1002/wcms.1161
22. J. Hostaš, J. Aezáč, and P. Hobza, Chem. Phys. Lett. 568-569, 161 (2013). 10.1016/j.cplett.2013.02.069
23. J. J. P. Stewart, J. Mol. Model. 13, 1173 (2007). 10.1007/s00894-007- 0233-4
24. J. J. P. Stewart, J. Mol. Model. 19, 1 (2013). 10.1007/s00894-012-1667-x
25. X. Wu, W. Thiel, S. Pezeshki, and H. Lin, J. Chem. Theory Comput. 9, 2672 (2013). 10.1021/ct400224n
26. B. Martin and T. Clark, Int. J. Quant. Chem. 106, 1208 (2006). 10.1002/qua.20856
27. R. Ahlrichs, R. Penco, and G. Scoles, Chem. Phys. 19, 119 (1977). 10.1016/0301-0104(77)85124-0
28. E. Clementi and G. Corongiu, J. Phys. Chem. A 105, 10379 (2001). 10.1021/jp011509z
29. S. Grimme, J. Comput. Chem. 25, 1463 (2004). 10.1002/jcc.20078
30. S. Grimme, J. Comput. Chem. 27, 1787 (2006). 10.1002/jcc.20495
31. J. P. McNamara and I. H. Hillier, Phys. Chem. Chem. Phys. 9, 2362 (2007). 10.1039/b701890h
32. P. Jurečka, J. Aern, P. Hobza, and D. R. Salahub, J. Comput. Chem. 28, 555 (2007). 10.1002/jcc.20570
33. T. Tuttle and W. Thiel, Phys. Chem. Chem. Phys. 10, 2159 (2008). 10.1039/b718795e
34. D. T. Chang, G. K. Schenter, and B. C. Garrett, J. Chem. Phys. 128, 164111 (2008). 10.1063/1.2905230
35. G. B. Rocha, R. O. Freire, A. M. Simas, and J. J. P. Stewart, J. Comput. Chem. 27, 1101 (2006). 10.1002/jcc.20425
36. K. E. Riley, M. Pitoňák, P. Jurečka, and P. Hobza, Chem. Rev. 110, 5023 (2010). 10.1021/cr1000173
37. J. Fanfrlík, A. K. Bronowska, J. Aezáč, O. Přenosil, J. Konvalinka, and P. Hobza, J. Phys. Chem. B 114, 12666 (2010). 10.1021/jp1032965
38. J. J. P. Stewart, J. Mol. Model. 15, 765 (2009). 10.1007/s00894-008-0420- y
39. M. Korth, M. Pitoňák, J. Aezáč, and P. Hobza, J. Chem. Theory Comput. 6, 344 (2010). 10.1021/ct900541n
40. M. Korth, J. Chem. Theory Comput. 6, 3808 (2010). 10.1021/ct100408b
41. J. Aezáč and P. Hobza, J. Chem. Theory Comput. 8, 141 (2012). 10.1021/ct200751e
42. J. Aezáč and P. Hobza, Chem. Phys. Lett. 506, 286 (2011). 10.1016/j.cplett.2011.03.009
43. M. I. Bernal-Uruchurtu and M. F. Ruiz-López, Chem. Phys. Lett. 330, 118 (2000). 10.1016/S0009-2614(00)01062-9
44. E. Thiriot and G. Monard, J. Mol. Structure: THEOCHEM 898, 31 (2009). 10.1016/j.theochem.2008.12.041
45. M. I. Bernal-Uruchurtu and M. F. Ruiz-López, Beyond Standard Quantum Chemistry: Applications from Gas to Condensed Phases, edited by R. Hernández-Lamoneda (Transworld Research Network, 2007), Chap. 4.
46. O. I. Arillo Flores and M. I. Bernal-Uruchurtu, J. Phys. Chem. A 114, 8975 (2010). 10.1021/jp101803r
47. F. Ingrosso, G. Monard, M. Hamdi Farag, A. Bastida, and M. F. Ruiz-López, J. Chem. Theory Comput. 7, 1840 (2011). 10.1021/ct2000588
48. M. Head-Gordon, J. A. Pople, and M. J. Frisch, Chem. Phys. Lett. 153, 503 (1988). 10.1016/0009-2614(88)85250-3
49. R. A. Kendall, T. H. Dunning Jr., and R. J. Harrison, J. Chem. Phys. 96, 6796 (1992). 10.1063/1.462569
50. J. A. Pople, M. Head-Gordon, and K. Raghavachari, J. Chem. Phys. 87, 5968 (1987). 10.1063/1.453520
51. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., Gaussian 09, Revision D.01, Gaussian, Inc., Wallingford, CT, 2009.
52. D. A. Case, T. A. Darden, T. E. Cheatham III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Goetz, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M. J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P. A. Kollman, " Amber 12," University of California, San Francisco, 2012.
53. J. J. P. Stewart, MOPAC2012, Stewart Computational Chemistry, Colorado Springs, CO, 2012, see http://OpenMOPAC.net.
54. W. Thiel and A. A. Voityuk, Theor. Chim. Acta 81, 391 (1992). 10.1007/BF01134863
55. W. Thiel and A. A. Voityuk, Theor. Chim. Acta 93, 315 (1996). 10.1007/BF01127509
56. W. Thiel and A. A. Voityuk, J. Phys. Chem. 100, 616 (1996). 10.1021/jp952148o
57. K. Nam, Q. Cui, J. Gao, and D. M. York, J. Chem. Theory Comput. 3, 486 (2007) 10.1021/ct6002466
58. J. P. McNamara, A.-M. Muslim, H. Abdel-Aal, H. Wang, M. Mohr, I. H. Hillier, and R. A. Bryce, Chem. Phys. Lett. 394, 429 (2004). 10.1016/j.cplett.2004.07.037
59. M. P. Repasky, J. Chandrasekhar, and W. L. Jorgensen, J. Comput. Chem. 23, 1601 (2002). 10.1002/jcc.10162
60. F. Luque, N. Reuter, A. Cartier, and M. Ruiz-López, J. Phys. Chem. A 104, 10923 (2000). 10.1021/jp001974g
61. V. V. Struzhkin, B. Militzer, W. L. Mao, H.-K. Mao, and R. J. Hemley, Chem. Rev. 107, 4133 (2007). 10.1021/cr050183d
62. C. A. Koh, Chem. Soc. Rev. 31, 157 (2002). 10.1039/b008672j
63. E. Dartois and D. Deboffle, Astron. Astrophys. 490, L19 (2008). 10.1051/0004-6361:200810926
64. J. Tennyson, P. F. Bernath, L. R. Brown, A. Campargue, A. G. Csszr, L. Daumont, R. R. Gamache, J. T. Hodges, O. V. Naumenko, O. L. Polyansky, L. S. Rothman, A. C. Vandaele, and N. F. Zobov, Pure Appl. Chem. 86, 71 (2014). 10.1515/pac-2014-5012
65. J.-J. Max and C. Chapados, J. Chem. Phys. 131, 184505 (2009). 10.1063/1.3258646
66. S. Grimme, J. Antony, T. Schwabe, and C. Mück-Lichtenfeld, Org. Biomol. Chem. 5, 741 (2007). 10.1039/b615319b
67. A. Khan, J. Chem. Phys. 110, 11884 (1999). 10.1063/1.479128
68. A. Schfer, C. Huber, and R. Ahlrichs, J. Chem. Phys. 100, 5829 (1994). 10.1063/1.467146
69. P. R. Rablen, J. W. Lockman, and W. L. Jorgensen, J. Phys. Chem. A 102, 3782 (1998). 10.1021/jp980708o
70. R. Krishnan, J. S. Binkley, R. Seeger, and J. A. Pople, J. Chem. Phys. 72, 650 (1980). 10.1063/1.438955
71. See supplementary material at http://dx.doi.org/10.1063/1.4886655 E-JCPSA6-141-061426 for computational details, for the integrality of the potential energy surfaces calculated with different semiempirical Hamiltonians and at the ab initio level and for the geometries of the 1:1 complexes.