Citation: YANG Li-Jiang, GAO Yi-Qin. Molecular Dynamic Simulations of the Effects of Trimethylamine- N-oxide/Urea Mixture on the Hydration of Single-Walled Carbon Nanotube Interiors[J]. Acta Physico-Chimica Sinica, ;2016, 32(1): 313-320. doi: 10.3866/PKU.WHXB201512161 shu

Molecular Dynamic Simulations of the Effects of Trimethylamine- N-oxide/Urea Mixture on the Hydration of Single-Walled Carbon Nanotube Interiors

YANG Li-Jiang ^1,2 ,
GAO Yi-Qin ^1,2

1.
1 Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China;
2.
2 Biodynamic Optical Imaging Center, Peking University, Beijing 100871, P. R. China

Received Date: 8 October 2015
Available Online: 15 December 2015

Urea is known for protein denaturation. The counteracting effect of trimethylamine-N-oxide (TMAO) against urea-induced protein denaturation is also well established. However, what is largely unknown is the mechanism TMAO counteracts urea. In this article, the hydration of the interior of a simple single-walled carbon nanotube in a urea/TMAO mixture is studied as a model system for hydrophobic hydration using molecular dynamic simulations. The results show that TMAO counteracts the hydration effect of urea to the nanotube interior through strong interactions among TMAO, water, and urea. The strong interactions of TMAO and water stabilize the water structure, which counteracts the effects of urea indirectly.
- Urea,
- Trimethylamine-N-oxide,
- Carbon nanotube,
- Hydration,
- Molecular dynamics
1. [1]
  (1) Kresheck, G. C.; Scheraga, H. A. J. Phys. Chem. 1965, 69 (5), 1704. doi: 10.1021/j100889a043
2. [2]
  (2) Camilloni, C.; Rocco, A. G.; Eberini, I.; Gianazza, E.; Broglia, R. A.; Tiana, G. Biophys. J. 2008, 94 (12), 4654. doi: 10.1529/biophysj.107.125799
3. [3]
  (3) Moglich, A.; Krieger, F.; Kiefhaber, T. J. Mol. Biol. 2005, 345 (1), 153. doi: 10.1016/j.jmb.2004.10.036
4. [4]
  (4) Das, A.; Mukhopadhyay, C. J. Phys. Chem. B 2008, 112 (26), 7903. doi: 10.1021/jp800370e
5. [5]
  (5) Soper, A. K.; Finney, J. L. Phys. Rev. Lett. 1993, 71 (26), 4346. doi: 10.1103/PhysRevLett.71.4346
6. [6]
  (6) Turner, J.; Soper, A. K.; Finney, J. L. Mol. Phys. 1990, 70 (4), 679. doi: 10.1080/00268979000102661
7. [7]
  (7) Bolen, D. W.; Rose, G. D. Annu. Rev. Biochem. 2008, 77, 339. doi: 10.1146/annurev.biochem.77.061306.131357
8. [8]
  (8) Stumpe, M. C.; Grubmuller, H. J. Am. Chem. Soc. 2007, 129 (51), 16126. doi: 10.1021/ja076216j
9. [9]
  (9) Stumpe, M. C.; Grubmuller, H. J. Phys. Chem. B 2007, 111 (22), 6220. doi: 10.1021/jp066474n
10. [10]
  (10) Canchi, D. R.; Garcia, A. E. Annual Review of Physical Chemistry 2013, 64, 273. doi: 10.1146/annurev-physchem-040412-110156
11. [11]
  (11) Lin, T. Y.; Timasheff, S. N. Biochemistry 1994, 33 (42), 12695. doi: 10.1021/bi00208a021
12. [12]
  (12) Auton, M.; Bolen, D. W. Proc. Natl. Acad. Sci. U. S. A. 2005, 102 (42), 15065. doi: 10.1073/pnas.0507053102
13. [13]
  (13) Gluick, T. C.; Yadav, S. J. Am. Chem. Soc. 2003, 125 (15), 4418. doi: 10.1021/ja0292997
14. [14]
  (14) Venkatesu, P.; Lin, H. M.; Lee, M. J. Thermochim. Acta 2009, 491 (1–2), 20. doi: 10.1016/j.tca.2009.02.017
15. [15]
  (15) Venkatesu, P.; Lee, M. J.; Lin, H. M. J. Phys. Chem. B 2009, 113 (15), 5327. doi: 10.1021/jp8113013
16. [16]
  (16) Krywka, C.; Sternemann, C.; Paulus, M.; Tolan, M.; Royer, C.; Winter, R. ChemPhysChem 2008, 9 (18), 2809. doi: 10.1002/cphc.200800522
17. [17]
  (17) Robinson, D. R.; Jencks, W. P. J. Am. Chem. Soc. 1965, 87 (11), 2462. doi: 10.1021/ja01089a028
18. [18]
  (18) Lim, W. K.; Rosgen, J.; Englander, S. W. Proc. Natl. Acad. Sci. U. S. A. 2009, 106 (8), 2595. doi: 10.1073/pnas.0812588106
19. [19]
  (19) Hua, L.; Zhou, R. H.; Thirumalai, D.; Berne, B. J. Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (44), 16928. doi: 10.1073/pnas.0808427105
20. [20]
  (20) Das, P.; Zhou, R. H. J. Phys. Chem. B 2010, 114 (16), 5427. doi: 10.1021/jp911444q
21. [21]
  (21) Zangi, R.; Zhou, R. H.; Berne, B. J. J. Am. Chem. Soc. 2009, 131 (4), 1535. doi: 10.1021/ja807887g
22. [22]
  (22) Wetlaufer, D. B.; Coffin, R. L.; Malik, S. K.; Stoller, L. J. Am. Chem. Soc. 1964, 86 (3), 508. doi: 10.1021/ja01057a045
23. [23]
  (23) Finer, E. G.; Franks, F.; Tait, M. J. J. Am. Chem. Soc. 1972, 94 (13), 4424. doi: 10.1021/ja00768a004
24. [24]
  (24) Das, A.; Mukhopadhyay, C. J. Phys. Chem. B 2009, 113 (38), 12816. doi: 10.1021/jp906350s
25. [25]
  (25) Idrissi, A.; Cinar, E.; Longelin, S.; Damay, P. J. Mol. Liq. 2004, 110 (1–3), 201. doi: 10.1016/j.molliq.2003.09.015
26. [26]
  (26) Frank, H. S.; Franks, F. J. Chem. Phys. 1968, 48 (10), 4746. doi: 10.1063/1.1668057
27. [27]
  (27) Zou, Q.; Bennion, B. J.; Daggett, V.; Murphy, K. P. J. Am. Chem. Soc. 2002, 124 (7), 1192. doi: 10.1021/ja004206b
28. [28]
  (28) Sarma, R.; Paul, S. J. Chem. Phys. 2011, 135 (17), 174501. doi: 10.1063/1.3655672
29. [29]
  (29) Koishi, T.; Yasuoka, K.; Wilow, S. Y.; Fujikawa, S.; Zeng, X. C. J. Chem. Theory Comput. 2013, 9 (6), 2540. doi: 10.1021/ct3010968
30. [30]
  (30) Sarma, R.; Paul, S. J. Phys. Chem. B 2012, 116 (9), 2831. doi: 10.1021/jp2104402
31. [31]
  (31) Yang, L. J.; Gao, Y. Q. J. Am. Chem. Soc. 2010, 132 (2), 842. doi: 10.1021/ja9091825
32. [32]
  (32) Wei, H. Y.; Fan, Y. B.; Gao, Y. Q. J. Phys. Chem. B 2010, 114 (1), 557. doi: 10.1021/jp9084926
33. [33]
  (33) Wei, H. Y.; Yang, L. J.; Gao, Y. Q. J. Phys. Chem. B 2010, 114 (36), 11820. doi: 10.1021/jp103770y
34. [34]
  (34) Shao, Q.; Fan, Y. B.; Yang, L. J.; Gao, Y. Q. J. Chem. Phys. 2012, 136 (11), 115101. doi: 10.1063/1.3692801
35. [35]
  (35) Shao, Q.; Gao, Y. Q. J. Chem. Phys. 2012, 137 (14), 145101. doi: 10.1063/1.4757419
36. [36]
  (36) Shao, Q.; Fan, Y. B.; Yang, L. J.; Gao, Y. Q. J. Chem. Theory Comput. 2012, 8 (11), 4364. doi: 10.1021/ct3002267
37. [37]
  (37) Gao, Y. Q. J. Phys. Chem. B 2012, 116 (33), 9934. doi: 10.1021/jp305532h
38. [38]
  (38) Xie, W. J.; Gao, Y. Q. Faraday Discuss. 2013, 160, 191. doi: 10.1039/C2FD20065A
39. [39]
  (39) Xie, W. J.; Gao, Y. Q. J. Phys. Chem. Lett. 2013, 4 (24), 4247. doi: 10.1021/jz402072g
40. [40]
  (40) Hummer, G.; Rasaiah, J. C.; Noworyta, J. P. Nature 2001, 414 (6860), 188. doi: 10.1038/35102535
41. [41]
  (41) Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79 (2), 926. doi: 10.1063/1.445869
42. [42]
  (42) Duffy, E. M.; Kowalczyk, P. J.; Jorgensen, W. L. J. Am. Chem. Soc. 1993, 115 (20), 9271. doi: 10.1021/ja00073a050
43. [43]
  (43) Kast, K. M.; Brickmann, J.; Kast, S. M.; Berry, R. S. J. Phys. Chem. A 2003, 107 (27), 5342. doi: 10.1021/jp027336a
44. [44]
  (44) Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81 (8), 3684. doi: 10.1063/1.448118
45. [45]
  (45) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98 (12), 10089. doi: 10.1063/1.464397
46. [46]
  (46) Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23 (3), 327. doi: 10.1016/0021-9991(77)90098-5
47. [47]
  (47) Hummer, G. Mol. Phys. 2007, 105 (2–3), 201. doi: 10.1080/00268970601140784
48. [48]
  (48) Sarma, R.; Paul, S. J. Phys. Chem. B 2013, 117 (18), 5691. doi: 10.1021/jp401750v
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