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Na+, K+ and Tl+ hydration from QM/MM computations and MD simulations with a polarizable force field

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Abstract

The hydration of three different monovalent cations was studied with a number of theoretical approaches ranging from classical MD simulations to MD simulations with a polarizable force field and finally to QM/MM MD. A particular emphasis was put on the development of a novel polarizable potential function for studies of Tl+ hydration enabling the ability to reproduce key features observed in QM/MM simulations. We extended the CHARMM-deMon interface developed previously to studies of ion hydration with QM/MM simulations. All simulations reproduce experimental data on the Radial Distribution Function (RDF) accurately. However, notable differences start to emerge in the description of probabilities for coordination states of an ion if explicit account of polarization is included.

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References

  1. Adcock, S.A., McCammon, J.A. 2006. Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews 106, 1589–1615.

    Article  CAS  PubMed  Google Scholar 

  2. Asthagiri, D., Ashbaugh, H.S., Piryatinski, A., Paulaitis, M.E., Pratt, L.R. 2007. Non-van der waals treatment of the hydrophobic solubilities of CF4. Journal of the American Chemical Society 129, 10133–10140.

    Article  CAS  PubMed  Google Scholar 

  3. Becke, A.D. 1988. Density-functional exchange-energy approximation with correct asymptotic-behavior. Physical Review A 38, 3098–3100.

    Article  CAS  PubMed  Google Scholar 

  4. Boudker, O., Ryan, R.M., Yernool, D., Shimamoto, K., Gouaux, E. 2007. Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature 445, 387–393.

    Article  CAS  PubMed  Google Scholar 

  5. Brooks, B.R., Brooks, C.L., Mackerell, A.D., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A.R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R.W., Post, C.B., Pu, J.Z., Schaefer, M., Tidor, B., Venable, R.M., Woodcock, H.L., Wu, X., Yang, W., York, D.M., Karplus, M. 2009. CHARMM: The biomolecular simulation program. Journal of Computational Chemistry 30, 1545–1614.

    Article  CAS  PubMed  Google Scholar 

  6. Cao, J.S., Voth, G.A. 1994. The formulation of quantum-statistical mechanics based on the feynman path centroid density. 1. Equilibrium Properties. Journal of Chemical Physics 100, 5093–5105.

    Article  CAS  Google Scholar 

  7. Chen, B., Ivanov, I., Klein, M.L., Parrinello, M. 2003. Hydrogen bonding in water. Physical Review Letters 91, Art: 215503.

    Google Scholar 

  8. Christen, M., Hunenberger, P.H., Bakowies, D., Baron R., Burgi R., Geerke, D.P., Heinz, T.N., Kastenholz, M.A., Krautler, V., Oostenbrink C., Peter, C., Trzesniak, D., Van Gunsteren, W.F. 2005. The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry 26, 1719–1751.

    Article  CAS  PubMed  Google Scholar 

  9. Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., Karplus, M. 2001. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. Journal of Physical Chemistry B 105, 569–585.

    Article  CAS  Google Scholar 

  10. Field, M.J. 2002. Simulating enzyme reactions: Challenges and perspectives. Journal of Computational Chemistry 23, 48–58.

    Article  CAS  PubMed  Google Scholar 

  11. Galvan-Arzate, S., Santamaria, A. 1998. Thallium toxicity. Toxicology Letters 99, 1–13.

    Article  CAS  PubMed  Google Scholar 

  12. Glezakou, V.A., Chen, Y.S., Fulton, J.L., Schenter, G.K., Dang, L.X. 2006. Electronic structure, statistical mechanical simulations, and EXAFS spectroscopy of aqueous potassium. Theoretical Chemistry Accounts 115, 86–99.

    Article  CAS  Google Scholar 

  13. Gouaux, E., Mackinnon, R. 2005. Principles of selective ion transport in channels and pumps. Science 310, 1461–1465.

    Article  CAS  PubMed  Google Scholar 

  14. Grossfield, A., Ren, P.Y., Ponder, J.W. 2003. Ion solvation thermodynamics from simulation with a polarizable force field. Journal of the American Chemical Society 125, 15671–15682.

    Article  CAS  PubMed  Google Scholar 

  15. Harder, E., Anisimov, V.M., Vorobyov, I.V., Lopes, P.E.M., Noskov, S.Y., Mackerell, A.D., Roux, B. 2006. Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator. Journal of Chemical Theory and Computation 2, 1587–1597.

    Article  CAS  Google Scholar 

  16. Hermann, J.C., Hensen, C., Ridder, L., Mulholland, A.J., Holtje, H.D. 2005. Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin. Journal of the American Chemical Society 127, 4454–4465.

    Article  CAS  PubMed  Google Scholar 

  17. Hess, B., Kutzner, C., Van Der Spoel, D., Lindahl, E. 2008. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 4, 435–447.

    Article  CAS  Google Scholar 

  18. Hu, H., Lu, Z.Y., Yang, W.T. 2007. QM/MM minimum free-energy path: Methodology and application to triosephosphate isomerase. Journal of Chemical Theory and Computation 3, 390–406.

    Article  CAS  PubMed  Google Scholar 

  19. Ikeuchi, H., Fujita, Y., Iwai, K., Sato, G.P. 1976. Precise measurement of ionic-diffusion coefficients with a hanging mercury drop electrode. Bulletin of the Chemical Society of Japan 49, 1883–1887.

    Article  CAS  Google Scholar 

  20. Krishnamurthy, H., Piscitelli, C.L., Gouaux, E. 2009. Unlocking the molecular secrets of sodium-coupled transporters. Nature 459, 347–355.

    Article  CAS  PubMed  Google Scholar 

  21. Lameijer, W., Vanzwieten, P.A. 1976. Acute cardiovascular toxicity of thallium (I) ions. Archives of Toxicology 35, 49–61.

    Article  CAS  PubMed  Google Scholar 

  22. Lamoureux, G., Faraldo-Gomez, J.D., Krupin, S., Noskov, S.Y. 2009. Polarizable model of chloroform based on classical Drude oscillators. Chemical Physics Letters 468, 270–274.

    Article  CAS  Google Scholar 

  23. Lamoureux, G., Harder, E., Vorobyov, I.V., Roux, B., Mackerell, A.D. 2006. A polarizable model of water for molecular dynamics simulations of biomolecules. Chemical Physics Letters 418, 245–249.

    Article  CAS  Google Scholar 

  24. Lamoureux, G., Roux, B. 2003. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm. Journal of Chemical Physics 119, 3025–3039.

    Article  CAS  Google Scholar 

  25. Lamoureux G., Roux B. 2006. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. Journal of Physical Chemistry B 110, 3308–3322.

    Article  CAS  Google Scholar 

  26. Lev, B., Zhang, R., De La Lande, A., Salahub, D.R., Noskov S.Y. 2010. The QM-MM interface for CHARMM-deMon. Journal of Computational Chemistry, In Press, DOI: 10.1002/jcc.21387.

  27. Lin, H., Truhlar, D.G. 2007. QM/MM: what have we learned, where are we, and where do we go from here? Theoretical Chemistry Accounts 117, 185–199.

    Article  CAS  Google Scholar 

  28. Lopes, P.E.M., Roux, B., Mackerell, A.D. 2009. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications. Theoretical Chemistry Accounts 124, 11–28.

    Article  CAS  Google Scholar 

  29. Maple, J.R., Cao, Y.X., Damm, W.G., Halgren, T.A., Kaminski, G.A., Zhang, L.Y., Friesner, R.A. 2005. A polarizable force field and continuum solvation methodology for modeling of protein-ligand interactions. Journal of Chemical Theory and Computation 1, 694–715.

    Article  CAS  Google Scholar 

  30. Marcus, Y. 1988. Ionic-radii in aqueous-solutions. Chemical Reviews 88, 1475–1498.

    Article  CAS  Google Scholar 

  31. Maurizio, C., D’acapito, F., Ghibaudo, E., Broquin, J.E. 2008. Tl ion-exchange borosilicate glass: Investigation of the Tl site by X-ray absorption spectroscopy. Journal of Non-Crystalline Solids 354, 124–128.

    Article  CAS  Google Scholar 

  32. Mudring, A.V., Rieger, F. 2005. Lone pair effect in thallium(I) macrocyclic compounds. Inorganic Chemistry 44, 6240–6243.

    Article  CAS  PubMed  Google Scholar 

  33. Mulkey, J.P., Oehme, F.W. 1993. A review of thallium toxicity. Veterinary and Human Toxicology 35, 445–453.

    CAS  PubMed  Google Scholar 

  34. Noskov, S.Y., Berneche, S., Roux, B. 2004. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431, 830–834.

    Article  CAS  PubMed  Google Scholar 

  35. Persson, I., Jalilehvand, F., Sandstrom, M. 2002. Structure of the solvated thallium(I) ion in aqueous, dimethyl sulfoxide, N,N′-dimethylpropyleneurea, and N,N′-dimethylthioformamide solution. Inorganic Chemistry 41, 192–197.

    Article  CAS  PubMed  Google Scholar 

  36. Pratt, L.R., Laviolette, R.A. 1998. Quasi-chemical theories of associated liquids. Molecular Physics 94, 909–915.

    Article  CAS  Google Scholar 

  37. Rempe, S.B., Asthagiri, D., Pratt, L.R. 2004. Inner shell definition and absolute hydration free energy of K+(aq) on the basis of quasi-chemical theory and ab initio molecular dynamics. Physical Chemistry Chemical Physics 6, 1966–1969.

    Article  CAS  Google Scholar 

  38. Rieger, F., Mudring, A.V. 2005. Inorganic supramolecular host architectures: [(M18c6)(2)][TII4]center dot 2H(2)O, M=0.5 Tl, (NH4,NH3), (H3O,H2O). Inorganic Chemistry 44, 9340–9346.

    Article  CAS  PubMed  Google Scholar 

  39. Sato, T., Indo, H., Kawabata, Y., Kobayashi, T., Suenaga, S., Iwashita, Y., Nitta, T., Sugihara, K., Majima, H.J. 2005. Thallium-201 chloride (Tl-201) accumulation and Na+/K+-ATPase expression in tumours of the head and neck. Dentomaxillofacial Radiology 34, 212–217.

    Article  CAS  Google Scholar 

  40. Senn, H.M., Thiel, W. 2009. QM/MM methods for biomolecular systems. Angewandte Chemie-International Edition 48, 1198–1229.

    Article  CAS  Google Scholar 

  41. Shah, J.K., Asthagiri, D., Pratt, L.R., Paulaitis, M.E. 2007. Balancing local order and long-ranged interactions in the molecular theory of liquid water. Journal of Chemical Physics 127, Art 144508.

  42. Soper, A.K., Weckstrom, K. 2006. Ion solvation and water structure in potassium halide aqueous solutions. Biophysical Chemistry 124, 180–191.

    Article  CAS  PubMed  Google Scholar 

  43. Tanaka, M., Siehl, H.U. 2008. An application of the consistent charge equilibration (CQEq) method to guanidinium ionic liquid systems. Chemical Physics Letters 457, 263–266.

    Article  CAS  Google Scholar 

  44. Urry, D.W., Trapane, T.L., Venkatachalam, C.M., Prasad, K.U. 1985. C-13 nuclear magnetic-resonance study of potassium and thallium ion binding to the gramicidin-a transmembrane channel. Canadian Journal of Chemistry-Revue Canadienne De Chimie 63, 1976–1981.

    Article  CAS  Google Scholar 

  45. Vchirawongkwin, V., Hofer, T.S., Randolf, B.R., Rode, B.M. 2007. Tl(I) — The strongest structure-breaking metal ion in water? A quantum mechanical/molecular mechanical simulation study. Journal of Computational Chemistry 28, 1006–1016.

    Article  CAS  PubMed  Google Scholar 

  46. Whitfield, T.W., Martyna, G.J. 2006. A unified formalism for many-body polarization and dispersion: The quantum Drude model applied to fluid xenon. Chemical Physics Letters 424, 409–413.

    Article  CAS  Google Scholar 

  47. Whitfield, T.W., Varma, S., Harder, E., Lamoureux, G., Rempe, S.B., Roux, B. 2007. Theoretical study of aqueous solvation of K+ comparing ab initio, polarizable, and fixed-charge models. Journal of Chemical Theory and Computation 3, 2068–2082.

    Article  CAS  Google Scholar 

  48. Woodcock, H.L., Hodoscek, M., Gilbert, A.T.B., Gill, P.M.W., Schaefer, H.F., Brooks, B.R. 2007. Interfacing Q-chem and CHARMM to perform QM/MM reaction path calculations. Journal of Computational Chemistry 28, 1485–1502.

    Article  CAS  PubMed  Google Scholar 

  49. Yang, L.J., Tan, C.H., Hsieh, M.J., Wang, J.M., Duan, Y., Cieplak, P., Caldwell, J., Kollman, P.A., Luo, R. 2006. New-generation amber united-atom force field. Journal of Physical Chemistry B 110, 13166–13176.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute for BioComplexity and Informatics (IBI), University of Calgary, 2500 University Drive, Calgary, AB, T2N 2N4, Canada

    Bogdan B. Lev, Dennis R. Salahub & Sergei Yu Noskov

  2. Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, AB, T2N 2N4, Canada

    Bogdan B. Lev & Sergei Yu Noskov

  3. Department of Chemistry, University of Calgary, 2500 University Drive, Calgary, AB, T2N 2N4, Canada

    Dennis R. Salahub

  4. Institute for Sustainable Energy, Environment and Economy (ISEEE), University of Calgary, 2500 University Drive, Calgary, AB, T2N 2N4, Canada

    Dennis R. Salahub

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  1. Bogdan B. Lev
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Correspondence to Sergei Yu Noskov.

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Lev, B.B., Salahub, D.R. & Noskov, S.Y. Na+, K+ and Tl+ hydration from QM/MM computations and MD simulations with a polarizable force field. Interdiscip Sci Comput Life Sci 2, 12–20 (2010). https://doi.org/10.1007/s12539-010-0097-7

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  • DOI: https://doi.org/10.1007/s12539-010-0097-7

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