Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

Journal of Chemical Physics

Volumn 140, Issue 9, 2014, Pages

  Nawrocki, Grzegorz ^a   Cieplak, Marek ^a  

^a INSTITUTE OF PHYSICS   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; COVALENT BONDS; HYDROGEN BONDS; II-VI SEMICONDUCTORS; MOLECULAR DYNAMICS; MORSE POTENTIAL; OXIDE MINERALS; PROTEINS; SEMICONDUCTOR QUANTUM DOTS; ZINC OXIDE; ZINC SULFIDE; ZNS NANOPARTICLES;

AMINO ACIDS AND PROTEINS; DENSITY PROFILE; DISULFIDE BONDS; MOLECULAR DYNAMICS SIMULATIONS; POTENTIAL WELLS; POTENTIALS OF MEAN FORCES; UMBRELLA SAMPLING; ZNS(110) SURFACES;

SULFUR COMPOUNDS;

AMINO ACID; PROTEIN; SULFIDE; WATER; ZINC DERIVATIVE; ZINC SULFIDE;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; SURFACE PROPERTY;

AMINO ACIDS; MOLECULAR DYNAMICS SIMULATION; PROTEINS; SULFIDES; SURFACE PROPERTIES; WATER; ZINC COMPOUNDS;

EID: 84896763586     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4866763     Document Type: Article

References (61)

1. A. I. Ekimov and A. A. Onushchenko, JETP Lett. 34, 345 (1981).
2. M. A. Reed, J. N. Randall, R. J. Aggarwal, R. J. Matyi, T. M. Moore, and A. E. Wetsel, Phys. Rev. Lett. 60, 535 (1988). 10.1103/PhysRevLett.60.535
3. W. Y. Liang, Phys. Educ. 5, 226 (1970). 10.1088/0031-9120/5/4/003
4. Y. Wang and L. Chen, Nanomedicine 7, 385 (2011). 10.1016/j.nano.2010.12. 006
5. M. A. Walling, J. A. Novak, and J. R. E. Shepard, Int. J. Mol. Sci. 10, 441 (2009). 10.3390/ijms10020441
6. M. F. Frasco and N. Chaniotakis, Sensors 9, 7266 (2009). 10.3390/s90907266
7. P. Reiss, M. Protiere, and L. Li, Small 5, 154 (2009). 10.1002/smll.200800841
8. J. Wang, S. Han, D. Ke, and R. Wang, Nanomedicine 3, 83 (2008). 10.1155/2012/129041
9. B. O. Dabbousi, J. Rodriguez-Viejo, F. V. Mikulec, J. R. Heine, H. Mattoussi, R. Ober, K. F. Jensen, and M. G. Bawendi, J. Phys. Chem. B 101, 9463 (1997). 10.1021/jp971091y
10. U. Soni and S. Sapra, J. Phys. Chem. C 114, 22514 (2010). 10.1021/jp1091637
11. L. Cao, S. Huang, S. Lu, and J. Lin, J. Colloid Interface Sci. 284, 516 (2005). 10.1016/j.jcis.2004.10.066
12. M. Q. Zhu, E. Chang, J. Sun, and R. A. Drezek, J. Mater. Chem. 17, 800 (2007). 10.1039/b614432b
13. X. Zhang, S. Mohandessi, L. W. Millera, and P. T. Snee, Chem. Commun. 47, 3532 (2011). 10.1039/c0cc04549g
14. V. Brunetti, H. Chibli, R. Fiammengo, A. Galeone, M. A. Malvindi, G. Vecchio, R. Cingolani, J. L. Nadeaub, and P. P. Pompa, Nanoscale 5, 307 (2013). 10.1039/c2nr33024e
15. M. Hoefling, F. Iori, S. Corni, and K. E. Gottschalk, Langmuir 26, 8347 (2010). 10.1021/la904765u
16. A. V. Verde, J. M. Acres, and J. K. Maranas, Biomacromolecules 10, 2118 (2009). 10.1021/bm9002464
17. E. R. Cruz-Chu, A. Aksimentiev, and K. Schulten, J. Phys. Chem. B 110, 21497 (2006). 10.1021/jp063896o
18. G. Forte, A. Grassi, and G. Marletta, J. Phys. Chem. B 111, 11237 (2007). 10.1021/jp068803h
19. S. Monti and T. R. Walsh, J. Phys. Chem. C 114, 22197 (2010). 10.1021/jp107859q
20. Y. K. Gao, F. Traeger, O. Shekhah, H. Idriss, and C. Woll, J. Colloid Interface Sci. 338, 16 (2009). 10.1016/j.jcis.2009.06.008
21. G. Nawrocki and M. Cieplak, Phys. Chem. Chem. Phys. 15, 13628 (2013). 10.1039/c3cp52198b
22. R. A. Sperling and W. J. Parak, Philos. Trans. R. Soc. A 368, 1333 (2010). 10.1098/rsta.2009.0273
23. S. Kumar, M. Singhal, and J. K. Sharma, J. Mater. Sci. 24, 3875 (2013). 10.1007/s10854-013-1332-x
24. W. Baea and R. K. Mehra, J. Inorg. Biochem. 70, 125 (1998). 10.1016/S0162-0134(98)10008-9
25. F. Pinaud, D. King, H. P. Moore, and S. Weiss, J. Am. Chem. Soc. 126, 6115 (2004). 10.1021/ja031691c
26. Y. Li, J. Chen, C. Zhu, L. Wang, D. Zhao, S. Zhuo, and Y. Wu, Spectrochim. Acta, Part A 60, 1719 (2004). 10.1016/j.saa.2003.09.012
27. S. R. Whaley, D. S. English, E. L. Hu, P. F. Barbara, and A. M. Belcher, Nature (London) 405, 665 (2000). 10.1038/35015043
28. M. Bachmann, K. Goede, A. G. Beck-Sickinger, M. Grundmann, A. Irback, and W. Janke, Angew. Chem., Int. Ed. 49, 9530 (2010). 10.1002/anie.201000984
29. N. Yokoo, T. Togashi, M. Umetsu, K. Tsumoto, T. Hattori, T. Nakanishi, S. Ohara, S. Takami, T. Naka, H. Abe, I. Kumagai, and T. Adschiri, J. Phys. Chem. B 114, 480 (2010). 10.1021/jp907731b
30. J. Grzyb, Acta Phys. Pol., A 122, 279 (2012).
31. E. E. Oren, C. Tamerler, and M. Sarikaya, Nano Lett. 5, 415 (2005). 10.1021/nl048425x
32. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992). 10.1002/jcc.540130812
33. J. A. Lemkul and D. R. Bevan, J. Phys. Chem. B 114, 1652 (2010). 10.1021/jp9110794
34. L. B. Wright and T. R. Walsh, J. Phys. Chem. C 116, 2933 (2012). 10.1021/jp209554g
35. V. A. Basiuk and T. Y. Gromovoy, Adsorption 2, 145 (1996). 10.1007/BF00127044
36. R. B. Pandey, Z. Kuang, and B. L. Farmer, PLoS One 8, e70847 (2013). 10.1371/journal.pone.0070847
37. R. B. Pandey and B. L. Farmer, J. Chem. Phys. 139, 164901 (2013). 10.1063/1.4825370
38. D. Van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 26, 1701 (2005). 10.1002/jcc.20291
39. Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman, J. Comput. Chem. 24, 1999 (2003). 10.1002/jcc.10349
40. 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
41. D. R. Lide, CRC Handbook of Chemistry and Physics, 90th ed. (CRC Press, Cleveland, OH, 2009).
42. H. E. Swanson and R. K. Fuyat, Natl. Bur. Stand. Circ. (U.S.) 2, 25 (1953).
43. P. W. Tasker, J. Phys. C: Solid State Phys. 12, 4977 (1979). 10.1088/0022-3719/12/22/036
44. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995). 10.1063/1.470117
45. H. Q. Xie, Y. Zeng, W. Q. Huang, L. Peng, P. Peng, and T. H. Wang, Int. J. Phys. Sci. 5, 2672 (2010).
46. N. Dragneva, W. B. Floriano, D. Stauffer, R. C. Mawhinney, G. Fanchini, and O. Rubel, J. Chem. Phys. 139, 174711 (2013). 10.1063/1.4828437
47. J. G. Kirkwood, J. Chem. Phys. 3, 300 (1935). 10.1063/1.1749657
48. B. J. Hess, J. Chem. Phys. 116, 209 (2002). 10.1063/1.1421362
49. H. Zhang, J. R. Rustad, and J. F. Banfield, J. Phys. Chem. A 111, 5008 (2007). 10.1021/jp0688916
50. C. I. Chang, W. J. Lee, T. F. Young, S. P. Ju, C. W. Chang, H. L. Chen, and J. G. Chang, J. Chem. Phys. 128, 154703 (2008). 10.1063/1.2897931
51. S. R. V. Castrillo, N. Giovambattista, I. A. Aksay, and P. G. Debenedetti, J. Phys. Chem. B 113, 1438 (2009). 10.1021/jp809032n
52. M. Cieplak, J. Koplik, and J. R. Banavar, Physica A 274, 281 (1999). 10.1016/S0378-4371(99)00308-8
53. M. Cieplak, J. Koplik, and J. R. Banavar, Physica A 287, 153 (2000). 10.1016/S0378-4371(00)00353-8
54. J. Feng, R. B. Pandey, R. J. Berry, B. L. Farmer, R. R. Naikc, and H. Heinz, Soft Matter 7, 2113 (2011). 10.1039/c0sm01118e
55. A. Starzyk and M. Cieplak, J. Chem. Phys. 135, 235103 (2011). 10.1063/1.3665930
56. A. Starzyk and M. Cieplak, J. Chem. Phys. 139, 045102 (2013). 10.1063/1.4813854
57. J. Tsai, R. Taylor, C. Chothia, and M. Gerstein, J. Mol. Biol. 290, 253 (1999). 10.1006/jmbi.1999.2829
58. M. Sikora, J. I. Sułkowska, and M. Cieplak, PLoS Comp. Biol. 5, e1000547 (2009). 10.1371/journal.pcbi.1000547
59. A. P. Gondikas, E. K. Jang, and H. Hsu-Kim, J. Colloid Interface Sci. 347, 167 (2010). 10.1016/j.jcis.2010.03.051
60. D. Elbaum, private communication (2013).
61. A. Baranowska-Korczyc, PhD thesis, "Semiconducting sensors based on electrospun fibers," 2012, Institute of Physics, PAS, Warsaw, Poland, supervised by D. Elbaum.