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Ion-Water Cluster Molecular Dynamics Using a Semiempirical Intermolecular Potential

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Computational Science and Its Applications -- ICCSA 2015 (ICCSA 2015)

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Abstract

Classical Molecular Dynamics (MD) simulations have been performed to describe structural and dynamical properties of the water clusters forming around the Na\(^{+}\) and K\(^{+}\). The dynamics of K\(^{+}\) and Na\(^{+}\) was investigated for small water clusters [K(H\(_{2}\)O)\(_{n}\)]\(^{+}\) and [Na(H\(_{2}\)O)\(_{n}\)]\(^{+}\) (n = 3 - 8), isolated in gas phase following the structure transformation through isomerizations between the accessible energy minima. The extent to which a classical molecular simulation accurately predicts properties depends on the quality of the force field used to model the interactions in the fluid. This has been explored by exploiting the flexibility of the Improved Lennard-Jones (ILJ) function in describing the long-range interaction of ionic water systems.

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References

  1. Dunand, F., Helm, L., Merbach, A.: Solvent exchange on metal ions. Advances in Inorganic Chemistry 54, 1–69 (2003)

    Google Scholar 

  2. Helm, L., Merbach, A.E.: Applications of advanced experimental techniques: high pressure nmr and computer simulations. J. Chem. Soc., Dalton Trans. 5, 633–641 (2002)

    Article  Google Scholar 

  3. Helm, L., Merbach, A.E.: Inorganic and bioinorganic solvent exchange mechanisms. Chemical Reviews 105, 1923–1960 (2005). PMID: 15941206

    Article  Google Scholar 

  4. Helm, L., Nicolle, G.M., Merbach, A.E.: Water and proton exchanges processes on metal ions. Adv. Inorg. Chem. 57, 327–379 (2005)

    Google Scholar 

  5. Lincoln, S.F., Merbach, A.E.: Substitution reactions of solvated metal ions. 42, 1–88 (1995)

    Google Scholar 

  6. Marcus, Y.: Effect of ions on the structure of water: Structure making and breaking. Chemical Reviews 109, 1346–1370 (2009). PMID: 19236019

    Article  Google Scholar 

  7. Doyle, D.A., Cabral, J.M., Pfuetzner, R.A., Kuo, A., Gulbis, J.M., Cohen, S.L., Chait, B.T., MacKinnon, R.: The structure of the potassium channel: Molecular basis of k+ conduction and selectivity. Science 280, 69–77 (1998)

    Article  Google Scholar 

  8. Guidoni, L., Torre, V., Carloni, P.: Potassium and sodium binding to the outer mouth of the k+ channel. Biochemistry 38, 8599–8604 (1999). PMID: 10393534

    Article  Google Scholar 

  9. Laio, A., Torre, V.: Physical origin of selectivity in ionic channels of biological membranes. Biophysical Journal 76, 129–148 (1999)

    Article  Google Scholar 

  10. Mooney, B.L., Corrales, L.R., Clark, A.E.: Novel analysis of cation solvation using a graph theoretic approach. The Journal of Physical Chemistry B 116, 4263–4275 (2012). PMID: 22417120

    Article  Google Scholar 

  11. Faginas-Lago, N., Lombardi, A., Albertí, M., Grossi, G.: Accurate analytic intermolecular potential for the simulation of na\(^{+}\) and k\(^{+}\) ion hydration in liquid water. Journal of Molecular Liquids 204, 192–197 (2015)

    Article  Google Scholar 

  12. Neilson, G.W., Mason, P.E., Ramos, S., Sullivan, D.: Neutron and x–ray scattering studies of hydration in aqueous solutions. Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences 359, 1575–1591 (2001)

    Article  Google Scholar 

  13. Soper, A.K., Weckström, K.: Ion solvation and water structure in potassium halide aqueous solutions. Biophysical Chemistry 124(3), 180–191 (2006). http://www.sciencedirect.com/science/article/pii/S0301462206001207

    Article  Google Scholar 

  14. Glezakou, V.A., Chen, Y., Fulton, J., Schenter, G., Dang, L.: Electronic structure, statistical mechanical simulations, and exafs spectroscopy of aqueous potassium. Theoretical Chemistry Accounts 115, 86–99 (2006)

    Article  Google Scholar 

  15. Varma, S., Rempe, S.B.: Coordination numbers of alkali metal ions in aqueous solutions. Biophysical Chemistry 124, 192–199 (2006). Ion Hydration Special Issue

    Article  Google Scholar 

  16. Caminiti, R., Licheri, G., Paschina, G., Piccaluga, G., Pinna, G.: Interactions and structure in aqueous nano3 solutions. The Journal of Chemical Physics 72, 4522–4528 (1980)

    Article  Google Scholar 

  17. Skipper, N.T., Neilson, G.W.: X-ray and neutron diffraction studies on concentrated aqueous solutions of sodium nitrate and silver nitrate. J. Phys. Condens. Matter 1, 4141–4154 (1989)

    Article  Google Scholar 

  18. Michaelian, K.H., Moskovits, M.: Tetrahedral hydration of ions in solution. Nature 273, 135–136 (1978)

    Article  Google Scholar 

  19. Ohtaki, H., Radnai, T.: Structure and dynamics of hydrated ions. Chemical Reviews 93, 1157–1204 (1993)

    Article  Google Scholar 

  20. Köpfer, D.A., Song, C., Gruene, T., Sheldrick, G.M., Zachariae, U., de Groot, B.L.: Ion permeation in k\(_{+}\) channels occurs by direct coulomb knock-on. Science 346, 352–355 (2014)

    Article  Google Scholar 

  21. Shafei, R.A.M.: Theoretical Study of Ion Water Interaction Ab Initio and Classical Molecular Dynamics, September 2014

    Google Scholar 

  22. Pirani, F., Cappelletti, D., Liuti, G.: Range, strength and anisotropy of intermolecular forces in atom-molecule systems: an atom-bond pairwise additivity approach. Chem. Phys. Lett. 350, 286–296 (2001)

    Article  Google Scholar 

  23. Albertí, M., Castro, A., Laganà, A., Pirani, F., Porrini, M., Cappelletti, D.: Properties of an atom-bond additive representation of the interaction for benzene-argon clusters. Chemical Physics Letters 392, 514–520 (2004)

    Article  Google Scholar 

  24. Bartolomei, M., Pirani, F., Lagan, A., Lombardi, A.: A full dimensional grid empowered simulation of the co\(_{2}\) + co\(_{2}\) processes. Journal of Computational Chemistry 33, 1806–1819 (2012)

    Article  Google Scholar 

  25. Lombardi, A., Faginas-Lago, N., Pacifici, L., Costantini, A.: Modeling of energy transfer from vibrationally excited co\(_{2}\) molecules: Cross sections and probabilities for kinetic modeling of atmospheres, flows, and plasmas. J. Phys. Chem. A 117, 11430–11440 (2013)

    Article  Google Scholar 

  26. Lago, N.F., Albertí, M., Laganà, A., Lombardi, A., Pacifici, L., Costantini, A.: The molecular stirrer catalytic effect in methane ice formation. In: Murgante, B., Misra, S., Rocha, A.M.A.C., Torre, C., Rocha, J.G., Falcão, M.I., Taniar, D., Apduhan, B.O., Gervasi, O. (eds.) ICCSA 2014, Part I. LNCS, vol. 8579, pp. 585–600. Springer, Heidelberg (2014)

    Google Scholar 

  27. Lombardi, A., Laganà, A., Pirani, F., Palazzetti, F., Lago, N.F.: Carbon oxides in gas flows and earth and planetary atmospheres: state-to-state simulations of energy transfer and dissociation reactions. In: Murgante, B., Misra, S., Carlini, M., Torre, C.M., Nguyen, H.-Q., Taniar, D., Apduhan, B.O., Gervasi, O. (eds.) ICCSA 2013, Part II. LNCS, vol. 7972, pp. 17–31. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  28. Falcinelli, S., Rosi, M., Candori, P., Vecchiocattivi, F., Bartocci, A., Lombardi, A., Lago, N.F., Pirani, F.: Modeling the intermolecular interactions and characterization of the dynamics of collisional autoionization processes. In: Murgante, B., Misra, S., Carlini, M., Torre, C.M., Nguyen, H.-Q., Taniar, D., Apduhan, B.O., Gervasi, O. (eds.) ICCSA 2013, Part I. LNCS, vol. 7971, pp. 69–83. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  29. Lombardi, A., Lago, N.F., Laganà, A., Pirani, F., Falcinelli, S.: A bond-bond portable approach to intermolecular interactions: simulations for N-methylacetamide and carbon dioxide dimers. In: Murgante, B., Gervasi, O., Misra, S., Nedjah, N., Rocha, A.M.A.C., Taniar, D., Apduhan, B.O. (eds.) ICCSA 2012, Part I. LNCS, vol. 7333, pp. 387–400. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  30. Laganà, A., Lombardi, A., Pirani, F., Gamallo, P., Sayos, R., Armenise, I., Cacciatore, M., Esposito, F., Rutigliano, M.: Molecular physics of elementary processes relevant to hypersonics: atom-molecule, molecule-molecule and atom-surface processes. The Open Plasma Physics Journal 7, 48 (2014)

    Article  Google Scholar 

  31. Faginas-Lago, N., Albertí, M., Costantini, A., Laganà, A., Lombardi, A., Pacifici, L.: An innovative synergistic grid approach to the computational study of protein aggregation mechanisms. Journal of Molecular Modeling 20, 2226 (2014)

    Article  Google Scholar 

  32. Albert, M., Castro, A., Lagan, A., Moix, M., Pirani, F., Cappelletti, D., Liuti, G.: A molecular dynamics investigation of rare-gas solvated cation-benzene clusters using a new model potential. The Journal of Physical Chemistry A 109, 2906–2911 (2005). PMID: 16833608

    Article  Google Scholar 

  33. Albertí, M., Aguilar, A., Lucas, J., Pirani, F.: Static and dynamic properties of anionic intermolecular aggregates: the i-benzene-ar\(_{n}\) case. Theoretical Chemistry Accounts 123, 21–27 (2009)

    Article  Google Scholar 

  34. Faginas-Lago, N., Albertí, M., Laganà, A., Lombardi, A.: Water (H\(_{2}\)O)\(_{m}\) or benzene (C\(_{6}\)H\(_{6}\))\(_{n}\) Aggregates to Solvate the K\(^ \text{+ } \)? In: Murgante, B., Misra, S., Carlini, M., Torre, C.M., Nguyen, H.-Q., Taniar, D., Apduhan, B.O., Gervasi, O. (eds.) ICCSA 2013, Part I. LNCS, vol. 7971, pp. 1–15. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  35. Albertí, M.: Rare gas-benzene-rare gas interactions: Structural properties and dynamic behavior. The Journal of Physical Chemistry A 114, 2266–2274 (2010). PMID: 20104928

    Article  Google Scholar 

  36. Albertí, M., Aguilar, A., Lucas, J.M., Pirani, F., Cappelletti, D., Coletti, C., Re, N.: Atom-bond pairwise additive representation for cation-benzene potential energy surfaces: An ab initio validation study. The Journal of Physical Chemistry A 110, 9002–9010 (2006). PMID: 16836464

    Article  Google Scholar 

  37. Coletti, C., Re, N.: Theoretical study of alkali cation-benzene complexes: Potential energy surfaces and binding energies with improved results for rubidium and cesium. J. Phys. Chem. A 110, 6563 (2006)

    Article  Google Scholar 

  38. Liuti, G., Pirani, F.: Regularities in van der waals forces: correlation between the potential parameters and polarizability. Chem. Phys. Lett. 122, 245 (1985)

    Article  Google Scholar 

  39. Albertí, M., Lago, N.F.: Competitive solvation of K\(^{+}\) by C\(_{6}\)H\(_{6}\) and H\(_{2}\)O in the K\(^{+}\)-(C\(_{6}\)H\(_{6}\)) n-(H\(_{2}\)O)m (n = 1–4; m = 1–6) aggregates. European Physical Journal D 67(4), art. no. 73 (2013). http://www.scopus.com/inward/record.url?eid=2-s2.0-84879071541&partnerID=40&md5=d471977fe0c15ea412f5330514ec038c

  40. Pirani, F., Albertí, M., Castro, A., Moix, M., Cappelletti, D.: Atom-bond pairwise additive representation for intermolecular potential energy surfaces. Chem. Phys. Lett. 394, 37 (2004)

    Article  Google Scholar 

  41. Pirani, P., Brizi, S., Roncaratti, L., Casavecchia, P., Cappelletti, D., Vecchiocattivi, F.: Beyond the lennard-jones model: a simple and accurate potential function probed by high resolution scattering data useful for molecular dynamics simulations. Phys. Chem. Chem. Phys. 10, 5489 (2008)

    Article  Google Scholar 

  42. Albertí, M., Faginas-Lago, N., Laganà, A., Pirani, F.: A portable intermolecular potential for molecular dynamics studies of nma-nma and nma-h2o aggregates. Phys. Chem. Chem. Phys. 13, 8422–8432 (2011)

    Article  Google Scholar 

  43. Albertí, M., Aguilar, A., Lucas, J.M., Pirani, F., Coletti, C., Re, N.: Atom-bond pairwise additive representation for halide-benzene potential energy surfaces: an ab initio validation study. J. Phys. Chem. A 113, 14606 (2009)

    Article  Google Scholar 

  44. Albertí, M., Aguilar, A., Cappelletti, D., Laganà, A., Pirani, F.: On the development of an effective model potential to describe ater interaction in neutral and ionic clusters. Int. J. Mass Spec. 280, 50–56 (2009)

    Article  Google Scholar 

  45. Halgren, T.A.: The representation of van der waals (vdw) interactions in molecular mechanics force fields: potential form, combination rules, and vdw parameters. J. Am. Chem. Soc. 114, 7827 (1992)

    Article  Google Scholar 

  46. Albertí, M., Aguilar, A., Lucas, J.M., Pirani, F.: A generalized formulation of ion-electron interactions: Role of the nonelectrostatic component and probe of the potential parameter transferability. J. Phys. Chem. A 114, 11964–11970 (2010)

    Article  Google Scholar 

  47. Albertí, M., Aguilar, A., Lucas, J.M., Pirani, F.: Competitive role of ch\(_{4}\)-chxi\(_{4}\)4 and ch-\(\pi \) interactions in c\(_{6}\)h\(_{6}\)-(ch\(_{4}\))\(_{n}\) aggregates: The transition from dimer to cluster features. The Journal of Physical Chemistry A 116, 5480–5490 (2012). PMID: 22591040

    Article  Google Scholar 

  48. Gregory, J.K., Clary, D.C., Liu, K., Brown, M.G., Saykally, R.J.: 275, 814 (1997)

    Google Scholar 

  49. Albertí, M., Aguilar, A., Bartolomei, M., Cappelletti, D., Laganà, A., Lucas, J., Pirani, F.: A study to improve the van der waals component of the interaction in water clusters. Phys. Script. 78, 058108 (2008)

    Article  Google Scholar 

  50. Ikeda, T., Boero, M., Terakura, K.: J. Chem. Phys. 126, 034801 (2007)

    Article  Google Scholar 

  51. Manion, J.A., Huie, R.E., Levin Jr., R.D., D.R.B., Orkin, V.L., Tsang, W., McGivern, W.S., Hudgens, J.W., Knyazev, V.D., Atkinson, D.B., Chai, E., Tereza, A.M., Lin, C.Y., Allison, T.C., Mallard, W.G., Westley, F., Herron, J.T., Hampson, R.F., Frizzell, D.H.: Nist chemical kinetics database, nist standard reference database 17 (2013)

    Google Scholar 

  52. Smith, W., Yong, C., Rodger, P.: Dl\(_{-}\)poly: Application to molecular simulation. Molecular Simulation 28, 385–471 (2002)

    Article  MATH  Google Scholar 

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Faginas-Lago, N., Albertí, M., Laganà, A., Lombardi, A. (2015). Ion-Water Cluster Molecular Dynamics Using a Semiempirical Intermolecular Potential. In: Gervasi, O., et al. Computational Science and Its Applications -- ICCSA 2015. ICCSA 2015. Lecture Notes in Computer Science(), vol 9156. Springer, Cham. https://doi.org/10.1007/978-3-319-21407-8_26

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  • DOI: https://doi.org/10.1007/978-3-319-21407-8_26

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