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Mutually polarizable QM/MM model with in situ optimized localized basis functions

Abstract

We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repul- sive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl−. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface.

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Articles
Type:
artykuł w czasopiśmie wyróżnionym w JCR
Published in:
JOURNAL OF CHEMICAL PHYSICS no. 150, pages 1 - 24,
ISSN: 0021-9606
Language:
English
Publication year:
2019
Bibliographic description:
Dziedzic J., Head-Gordon T., Head-Gordon M., Skylaris C.: Mutually polarizable QM/MM model with in situ optimized localized basis functions// JOURNAL OF CHEMICAL PHYSICS. -Vol. 150, (2019), s.1-24
DOI:
Digital Object Identifier (open in new tab) 10.1063/1.5080384
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  1. W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem., Int. Ed. 29, 992 (1990). open in new tab
  2. O. Demerdash, L.-P. Wang, and T. Head-Gordon, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 8, e1355 (2018). open in new tab
  3. P. S. Nerenberg and T. Head-Gordon, Curr. Opin. Struct. Biol. 49, 129 (2018), Theory and simulation-Macromolecular assemblies. open in new tab
  4. O. Demerdash, Y. Mao, T. Liu, M. Head-Gordon, and T. Head-Gordon, J. Chem. Phys. 147, 161721 (2017). open in new tab
  5. Y. Mao, O. Demerdash, M. Head-Gordon, and T. Head-Gordon, J. Chem. Theory Comput. 12, 5422 (2016). open in new tab
  6. W. L. Jorgensen, J. Chem. Theory Comput. 3, 1877 (2007). open in new tab
  7. O. Demerdash, E.-H. Yap, and T. Head-Gordon, Annu. Rev. Phys. Chem. 65, 149 (2014). open in new tab
  8. S. W. Rick and S. J. Stuart, Rev. Comput. Chem. 18, 89 (2002). open in new tab
  9. P. Cieplak, F.-Y. Dupradeau, Y. Duan, and J. Wang, J. Phys.: Condens. Matter 21, 333102 (2009). open in new tab
  10. G. Lamoureux, A. D. MacKerell, and B. Roux, J. Chem. Phys. 119, 5185 (2003). open in new tab
  11. D. P. Geerke and W. F. van Gunsteren, J. Phys. Chem. B 111, 6425 (2007). open in new tab
  12. A. C. T. van Duin, S. Dasgupta, F. Lorant, and W. A. Goddard III, J. Phys. Chem. A 105, 9396 (2001). open in new tab
  13. D.-X. Zhao, C. Liu, F.-F. Wang, C.-Y. Yu, L.-D. Gong, S.-B. Liu, and Z.-Z. Yang, J. Chem. Theory Comput. 6, 795 (2010). open in new tab
  14. G. A. Kaminski, H. A. Stern, B. J. Berne, R. A. Friesner, Y. X. Cao, R. B. Murphy, R. Zhou, and T. A. Halgren, J. Comput. Chem. 23, 1515 (2002). open in new tab
  15. P. Ren and J. W. Ponder, J. Comput. Chem. 23, 1497 (2002). open in new tab
  16. P. Ren and J. W. Ponder, J. Phys. Chem. B 107, 5933 (2003). open in new tab
  17. P. Ren, C. Wu, and J. W. Ponder, J. Chem. Theory Comput. 7, 3143 (2011). open in new tab
  18. J. W. Ponder, C. Wu, P. Ren, V. S. Pande, J. D. Chodera, M. J. Schnieders, I. Haque, D. L. Mobley, D. S. Lambrecht, J. R. A. DiStasio, M. Head-Gordon, ARTICLE scitation.org/journal/jcp open in new tab
  19. G. N. I. Clark, M. E. Johnson, and T. Head-Gordon, J. Phys. Chem. B 114, 2549 (2010). open in new tab
  20. P. Cieplak, J. Caldwell, and P. Kollman, J. Comput. Chem. 22, 1048 (2001). open in new tab
  21. P. N. Day, J. H. Jensen, M. S. Gordon, S. P. Webb, W. J. Stevens, M. Krauss, D. Garmer, H. Basch, and D. Cohen, J. Chem. Phys. 105, 1968 (1996). open in new tab
  22. N. Gresh, G. A. Cisneros, T. A. Darden, and J.-P. Piquemal, J. Chem. Theory Comput. 3, 1960 (2007). open in new tab
  23. A. Holt, J. Boström, G. Karlström, and R. Lindh, J. Comput. Chem. 31, 1583 (2010). open in new tab
  24. K. Burke, J. Chem. Phys. 136, 150901 (2012). open in new tab
  25. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976). open in new tab
  26. J. Spence, Y. Huang, and O. Sankey, Acta Metall. Mater. 41, 2815 (1993). open in new tab
  27. X. Long, J. Nicholas, M. Guest, and R. Ornstein, J. Mol. Struct. 412, 121 (1997). open in new tab
  28. G. A. Cisneros, J.-P. Piquemal, and T. A. Darden, J. Phys. Chem. B 110, 13682 (2006). open in new tab
  29. J. Q. Broughton, F. F. Abraham, N. Bernstein, and E. Kaxiras, Phys. Rev. B 60, 2391 (1999). open in new tab
  30. H. Hu, Z. Lu, J. M. Parks, S. K. Burger, and W. Yang, J. Chem. Phys. 128, 034105 (2008). open in new tab
  31. S. Ogata, E. Lidorikis, F. Shimojo, A. Nakano, P. Vashishta, and R. K. Kalia, Comput. Phys. Commun. 138, 143 (2001). open in new tab
  32. G. Csányi, T. Albaret, M. C. Payne, and A. De Vita, Phys. Rev. Lett. 93, 175503 (2004). open in new tab
  33. D. Fang, R. E. Duke, and G. A. Cisneros, J. Chem. Phys. 143, 044103 (2015). open in new tab
  34. R. Khare, S. L. Mielke, J. T. Paci, S. Zhang, R. Ballarini, G. C. Schatz, and T. Belytschko, Phys. Rev. B 75, 075412 (2007). open in new tab
  35. F. Cui and H. Li, J. Chem. Phys. 138, 174114 (2013). open in new tab
  36. J. Dziedzic, M. Bobrowski, and J. Rybicki, Phys. Rev. B 83, 224114 (2011). open in new tab
  37. A. J. Sodt, Y. Mei, G. König, P. Tao, R. P. Steele, B. R. Brooks, and Y. Shao, J. Phys. Chem. A 119, 1511 (2015). open in new tab
  38. M. W. van der Kamp and A. J. Mulholland, Biochemistry 52, 2708 (2013). open in new tab
  39. H. M. Senn and W. Thiel, Angew. Chem., Int. Ed. 48, 1198 (2009). open in new tab
  40. N. Bernstein, J. R. Kermode, and G. Csányi, Rep. Prog. Phys. 72, 026501 (2009). open in new tab
  41. T. Schwabe, J. M. H. Olsen, K. Sneskov, J. Kongsted, and O. Christiansen, J. Chem. Theory Comput. 7, 2209 (2011). open in new tab
  42. M. Aida, H. Yamataka, and M. Dupuis, Int. J. Quantum Chem. 77, 199 (2000). open in new tab
  43. J. M. Olsen, K. Aidas, and J. Kongsted, J. Chem. Theory Comput. 6, 3721 (2010). open in new tab
  44. C. Curutchet, A. Muñoz-Losa, S. Monti, J. Kongsted, G. D. Scholes, and B. Mennucci, J. Chem. Theory Comput. 5, 1838 (2009). open in new tab
  45. S. Caprasecca, S. Jurinovich, L. Viani, C. Curutchet, and B. Mennucci, J. Chem. Theory Comput. 10, 1588 (2014). open in new tab
  46. C. B. Nielsen, O. Christiansen, K. V. Mikkelsen, and J. Kongsted, J. Chem. Phys. 126, 154112 (2007). open in new tab
  47. K. Sneskov, T. Schwabe, O. Christiansen, and J. Kongsted, Phys. Chem. Chem. Phys. 13, 18551 (2011). open in new tab
  48. S. Caprasecca, S. Jurinovich, L. Lagardère, B. Stamm, and F. Lipparini, J. Chem. Theory Comput. 11, 694 (2015). open in new tab
  49. E. G. Kratz, A. R. Walker, L. Lagardère, F. Lipparini, J.-P. Piquemal, and G. Andrés Cisneros, J. Comput. Chem. 37, 1019 (2016). open in new tab
  50. S. Caprasecca, C. Curutchet, and B. Mennucci, J. Chem. Theory Comput. 8, 4462 (2012). open in new tab
  51. N. M. Thellamurege, D. Si, F. Cui, H. Zhu, R. Lai, and H. Li, J. Comput. Chem. 34, 2816 (2013). open in new tab
  52. J. Dziedzic, Y. Mao, Y. Shao, J. Ponder, T. Head-Gordon, M. Head-Gordon, and C.-K. Skylaris, J. Chem. Phys. 145, 124106 (2016). open in new tab
  53. Y. Mao, Y. Shao, J. Dziedzic, C.-K. Skylaris, T. Head-Gordon, and M. Head-Gordon, J. Chem. Theory Comput. 13, 1963 (2017). open in new tab
  54. M. Schwörer, C. Wichmann, and P. Tavan, J. Chem. Phys. 144, 114504 (2016). open in new tab
  55. D. Loco, E. Polack, S. Caprasecca, L. Lagardère, F. Lipparini, J.-P. Piquemal, and B. Mennucci, J. Chem. Theory Comput. 12, 3654 (2016). open in new tab
  56. D. Loco, L. Lagardère, S. Caprasecca, F. Lipparini, B. Mennucci, and J.-P. Piquemal, J. Chem. Theory Comput. 13, 4025 (2017). open in new tab
  57. R. A. Bryce, R. Buesnel, I. H. Hillier, and N. A. Burton, Chem. Phys. Lett. 279, 367 (1997). open in new tab
  58. F. Lipparini, C. Cappelli, and V. Barone, J. Chem. Theory Comput. 8, 4153 (2012). open in new tab
  59. F. Lipparini, C. Cappelli, and V. Barone, J. Chem. Phys. 138, 234108 (2013). open in new tab
  60. I. Carnimeo, C. Cappelli, and V. Barone, J. Comput. Chem. 36, 2271 (2015). open in new tab
  61. E. Boulanger and W. Thiel, J. Chem. Theory Comput. 10, 1795 (2014). open in new tab
  62. E. Boulanger and W. Thiel, J. Chem. Theory Comput. 8, 4527 (2012). open in new tab
  63. X. Pan, E. Rosta, and Y. Shao, Molecules 23, 2500 (2018). open in new tab
  64. A. H. Steindal, K. Ruud, L. Frediani, K. Aidas, and J. Kongsted, J. Phys. Chem. B 115, 3027 (2011). open in new tab
  65. C.-K. Skylaris, P. D. Haynes, A. A. Mostofi, and M. C. Payne, J. Chem. Phys. 122, 084119 (2005). open in new tab
  66. C. Zhang, C. Lu, Z. Jing, C. Wu, J.-P. Piquemal, J. W. Ponder, and P. Ren, J. Chem. Theory Comput. 14(4), 2084 (2018). open in new tab
  67. W. Kohn, Phys. Rev. Lett. 76, 3168 (1996). open in new tab
  68. C.-K. Skylaris, P. D. Haynes, A. A. Mostofi, and M. C. Payne, J. Phys.: Condens. Matter 17, 5757 (2005). open in new tab
  69. C.-K. Skylaris, A. A. Mostofi, P. D. Haynes, O. Diéguez, and M. C. Payne, Phys. Rev. B 66, 035119 (2002). open in new tab
  70. Q. Hill and C.-K. Skylaris, Proc. R. Soc. A 465, 669 (2009). open in new tab
  71. M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, and E. Kaxiras, J. Chem. Phys. 114, 5149 (2001). open in new tab
  72. B. Thole, Chem. Phys. 59, 341 (1981). open in new tab
  73. P. T. van Duijnen and M. Swart, J. Phys. Chem. A 102, 2399 (1998). open in new tab
  74. C. J. Burnham, J. Li, S. S. Xantheas, and M. Leslie, J. Chem. Phys. 110, 4566 (1999). open in new tab
  75. T. Halgren, J. Am. Chem. Soc. 114, 7827 (1992). open in new tab
  76. A. A. Mostofi, On Linear-Scaling Methods for Quantum Mechanical First- Principles Calculations (University of Cambridge, 2004).
  77. Q. Hill, "Development of more accurate computational methods within linear-scaling density functional theory," Ph.D. thesis, University of Southampton, Southampton, United Kingdom, 2010.
  78. J. Sala, E. Guàrdia, and M. Masia, J. Chem. Phys. 133, 234101 (2010). open in new tab
  79. A. Stone, Chem. Phys. Lett. 83, 233 (1981). open in new tab
  80. A. Stone and M. Alderton, Mol. Phys. 56, 1047 (1985). open in new tab
  81. Y. Shi, Z. Xia, J. Zhang, R. Best, C. Wu, J. W. Ponder, and P. Ren, J. Chem. Theory Comput. 9, 4046 (2013). open in new tab
  82. A. J. Stone, J. Chem. Theory Comput. 1, 1128 (2005). open in new tab
  83. A. J. Misquitta, A. J. Stone, and F. Fazeli, J. Chem. Theory Comput. 10, 5405 (2014). open in new tab
  84. E. R. Kuechler, T. J. Giese, and D. M. York, J. Chem. Phys. 143, 234111 (2015). open in new tab
  85. I. V. Yudanov, V. A. Nasluzov, K. M. Neyman, and N. Rösch, Int. J. Quantum Chem. 65, 975 (1997). open in new tab
  86. J.-P. Piquemal, G. A. Cisneros, P. Reinhardt, N. Gresh, and T. A. Darden, J. Chem. Phys. 124, 104101 (2006). open in new tab
  87. R. J. Wheatley and S. L. Price, Mol. Phys. 69, 507 (1990). open in new tab
  88. J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996). open in new tab
  89. N. Mardirossian and M. Head-Gordon, Phys. Chem. Chem. Phys. 16, 9904 (2014). open in new tab
  90. M. J. Gillan, D. Alfé, and A. Michaelides, J. Chem. Phys. 144, 130901 (2016). open in new tab
  91. I.-C. Lin, A. P. Seitsonen, I. Tavernelli, and U. Rothlisberger, J. Chem. Theory Comput. 8, 3902 (2012). open in new tab
  92. R. A. DiStasio, B. Santra, Z. Li, X. Wu, and R. Car, J. Chem. Phys. 141, 084502 (2014). open in new tab
  93. D. L. Mobley, K. L. Wymer, N. M. Lim, and J. P. Guthrie, J. Comput.-Aided Mol. Des. 28, 135 (2014). open in new tab
  94. ARTICLE scitation.org/journal/jcp open in new tab
  95. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, J. Comput. Chem. 25, 1157 (2004). open in new tab
  96. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). open in new tab
  97. T. Fox and P. A. Kollman, J. Phys. Chem. B 102, 8070 (1998). open in new tab
  98. I. S. Joung and T. E. Cheatham, J. Phys. Chem. B 112, 9020 (2008). open in new tab
  99. V. Vitale, J. Dziedzic, S. M.-M. Dubois, H. Fangohr, and C.-K. Skylaris, J. Chem. Theory Comput. 11, 3321 (2015). open in new tab
  100. P. J. Dyer and P. T. Cummings, J. Chem. Phys. 125, 144519 (2006). open in new tab
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