Water behavior in the self-aggregation of the bilirubin molecules in presence and absence of carbon nanotubes: A Molecular Dynamics Simulation approach

Noshin Moghtaderi, Mohammad Reza Bozorgmehr, Hassan Ali Zamani


This study illustrates the behavior of water molecules in bilirubin (BR)-carbon nanotube (CNT) systems by detailed analysis of several molecular dynamics simulations from the perspective of diffusion coefficients (D) and hydrogen bonding (HB). These analysis provide further understanding on the water network properties in the process of BR adsorption to treat or prevent hepatitis, biliary disease, liver cancer and some neurological and brain disorders. The results show that presence of BR and CNT interrupts the water network by confining the water molecules and decreasing the number of HBs that can be established. The best water and HB networking can be developed at high BR concentrations when CNT (10, 10) is available. Also, the most significant factor on increasing the water D is temperature. At higher temperatures, the BR molecules are adsorbed on CNTs and the enhanced CNT diameter helps BR molecules to advantage from higher adsorption surface to eliminate BR molecules from the water passage paths and diffuse, freely.


Keywords: Bilirubin, Carbon nanotube, Water, Hydrogen bonding, Diffusion coefficient

Full Text:



Wang, J.W.; Robinson, C.V.; Edelman. I.S.; J. Am. Chem. Soc.1953; 75, 466-470,DOI: 10.1021/ja01098a061.

Pimentel, G.C.; McClellan, A.L., The Hydrogen Bond. W.H.Freeman: 1960, p 473.

Jeffrey, G.A.; Saenger, W., Hydrogen Bonding in Biological Structures. Springer:1994,p 569.

Bernholc, J.; Brenner, D.; Nardelli, M.B.; Meunier, V.; Roland, C.; Annu. Rev. Mater. Res.2002, 32,

,DOI: 10.1146/annurev.matsci.32.112601.134925.

Shenderova, O.A.; Zhirnov, V.V.; Brenner, D.W., Crit. Rev. Solid State: 2002, p227-356.

Baughman, R.H.; Zakhidov, A.A.; de Heer, W.A.; Science, 2002, 297, 787-792,DOI: 10.1126/science.1060928.

Martin, C.R.; Kohli, P.; Drug Discovery,2003, 2, 29-37,DOI: 10.1038/nrd988.

Cheng, H.S.; Cooper, A.C.; Pez, G.P.; Kostov, M.K.; Piotrowski, P.; Stuart,S.J.; J. Phys. Chem. B. 2005, 109,3780–3786, DOI: 10.1021/jp045358m.

Sansom, M.S.P.; Kerr, I.D.; Breed, J.; Sankararamakrishnan, R.; J. Biophys. 1996, 70, 693–702,DOI:10.1016/S0006-3495(96)79609-1.

Sansom, M.S.P.; Biggin, P.C.; Nature. 2001,414, 156-159,DOI:10.1038/35102651.

Floquet, N.; Coulomb, J.P.; Dufau, N.; J. Phys. Chem. B. 2004, 108,13107–13115,DOI: 10.1021/jp048687n.

Lu, D.Y.; Aksimentiev, A.; Shih, A.Y., Cruz-Chu, E.; Freddolino, P.L.; Arkhipov, A.; Schulten, K.; Phys. Biol. 2006, 3, 40-53, DOI: 10.1088/1478-3975/3/1/S05.

Lin, Y.; Taylor, S.; Li, H.; Fernando, K.S.; Qu, L.; Wang, W.; Zhou, B.; Sun. Y.P.; J. Mater. Chem. 2004,14, 41-527-541,DOI: 10.1039/B314481J.

Iijima, S.; Nature. 1991, 354, 56-58,DOI: 10.1038/354056a0.

Bulmer, AC.; Coombes, JS.; Blanchfield,JT., Br J Pharmacol. 2011, 164,1857–1870, DOI: 10.1111/j.1476-5381.2011.01413.x.

Hilder, T.A.; Hill, J.M.; Appl. Phys. 2008, 8, 258-261,DOI:10.1016/j.cap.2007.10.011.

Portney, N.G.; Ozkan, M.; Anal. Bioanal. Chem.2006, 384, 620-630,DOI:10.1007/s00216-005-0247-7.

Gordillo, M. C.; Martı,.J. Chem. Phys. Lett. 2000, 329, 341–345, DOI:10.1016/S0009-2614(00)01032-0.

Pedretti, A.; Villa, L.; Vistoli, G.; J. Comp. Aided Mol. Des. 2004, 18, 167-173, DOI: 10.1023/B:JCAM.0000035186.90683.f2

Jorgensen, W.L.; Tirado-Rives, J.; J. Am. Chem. Soc. 1988, 110, 66-1657-1666,DOI:10.1021/ja00214a001.

Jorgensen, W.L.; Maxwell, D.S.; Tirado-Rives. J.; J. Am. Chem. Soc. 1996, 118, 11225–11236,DOI: 10.1021/ja9621760.

Gomes, T.C.; da Silva J.V.; Jr, L.N.; Vidal, P.A.; Vazquez, R.E.; Bruns. Theoret. Chem. Accnts. 2008,121, 173-179,DOI:10.1007/s00214-008-0461-4.

Lindahl, E.; Hess, B.; Van Der Spoel, D.; J. Mol. Model. 2001, 7,306-317, DOI:10.1007/s008940100045.

Jorgensen, W.L.; Chandrasekhar, J.; Madura, J.D.; Impey, R.W.; Klein, M.L.; J. Chem. Phys. 1983, 79, 926-935, DOI:10.1063/1.445869.

Hess, B.; Bekker, H., Berendsen, H.J.; Fraaije, J.G.; J. Comput. Chem. 1997, 18,1463-1472,DOI:10.1002/(SICI)1096-987X(199709)18.

Darden, T.; York, D.; Pedersen, L.; J. Chem. Phys. 1993, 98, 92-10089,DOI: 10.1063/1.464397.

Essmann, U.; Perera, L.; Berkowitz, M.L.; Darden, T.; Lee, H.; Pedersen, L.G J. Chem. Phys. 1995, 103, 93-8577,DOI:10.1063/1.470117.

Baxter, R.J., Exactly solved models in statistical mechanics. Academic Press:1982, p 102-110.

Berendsen, H.J.; Postma, J.P.M.; van Gunsteren, W.F.; Haak, J.R.;. J. Chem. Phys. 1984, 81, 3684-3690,DOI:10.1063/1.448118.

Moloni, K.; Buss, M.R.; Andres, R.P., Ultramicroscopy. 1999, 35, 237-246,DOI:10.1016/S0304-3991(99)00107-2.

Li, J.; Cassell, A.M.; Dai, H.; Surface and Interface Analysis. 1999, 28, 8-11,DOI: 10.1002/(SICI)1096-9918(199908)28.

Green, M. S.; J. Chem. Phys. 1954, 22, 398-413,DOI:10.1063/1.1740082.

Eisenberg, D.; Kauzmann, W., The Structure and Properties of Water. Oxford: Clarendon Press:1969, p 123-127.

Orgensen, W. L.; Madura, J. D.; Mol. Phys. 1985, 56, 1381-1392,DOI:10.1080/00268978500103111.

Zielkiewicz, J.; J. Chem Phys.2005,123, 104501-104506,DOI: 10.1063/1.2018637.

Luzar, A.; Chandler, D.; Nature. 1996, 379, 55-57,DOI:10.1038/379055a0.

URN: http://nbn-resolving.de/urn:nbn:de:0000easl.v3i4.1200


  • There are currently no refbacks.

Copyright (c) 2017 Entomology and Applied Science Letters

<Entomology+Zoology+Allied Branches>Entomology and Applied Science Letters