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The any particle molecular orbital/molecular mechanics approach

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Abstract

A computational scheme is proposed to broaden the range of applications of multicomponent methodologies for the study of local properties of big molecular systems existing in the gas phase and in solvated environments. This scheme extends the any particle molecular orbital (APMO) approach in the quantum mechanics/molecular mechanics (QM/MM) framework. As a first assessment of the performance of the proposed approach, we estimate the proton affinities (PAs) of seventy amines in the gas phase and the proton binding energies (PBEs) in the gas phase and in an explicitly solvated environment of the sixty-one protons present in the chignolin protein. These calculations are performed with the QM/MM versions of the APMO second-order proton propagator (APMO-PP2) and the APMO extended Koopmans’ theorem (APMO-KT) approaches. Calculated PAs and PBEs show significant reductions in the computational effort with a reduced loss in accuracy. These results suggest that the APMO/MM scheme might be used as a low-cost multi-component alternative for studies of local properties in big molecular systems.

QMMM regions and CPU times for the APMO/MM approach

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References

  1. Kolos W, Wolniewicz L (1963) Rev Mod Phys 35(3):473

    CAS  Google Scholar 

  2. Kolos W, Wolniewicz L (1967) J Chem Phys 46(4):1426

    CAS  Google Scholar 

  3. Kozlowski PM, Adamowicz L (1991) J Chem Phys 95(9):6681

    CAS  Google Scholar 

  4. Shigeta Y, Takahashi H, Yamanaka S, Mitani M, Nagao H, Yamaguchi K (1998) Int J Quantum Chem 70:659

    CAS  Google Scholar 

  5. Tachikawa M, Mori K, Suzuki K, Iguchi K (1998) Int J Quantum Chem 70:491

    CAS  Google Scholar 

  6. Kinghorn DB, Adamowicz L (2000) J Chem Phys 113(10):4203

    CAS  Google Scholar 

  7. Nakai H (2002) Int J Quantum Chem 86(6):511

    CAS  Google Scholar 

  8. Tachikawa M (2002) Chem Phys Lett 360(5-6):494

    CAS  Google Scholar 

  9. Webb SP, Iordanov T, Hammes-Schiffer S (2002) J Chem Phys 117(9):4106

    CAS  Google Scholar 

  10. Cafiero M, Bubin S, Adamowicz L, Cafiero M, Adamowicz L (2003) Phys Chem Chem Phys 5 (8):1491

    CAS  Google Scholar 

  11. Gonzȧlez SA, Aguirre NF, Reyes A (2008) Int J Quantum Chem 108(10):1742

    Google Scholar 

  12. Goli M, Shahbazian S (2011) Theor Chem Acc 129:235

    CAS  Google Scholar 

  13. Bubin S, Pavanello M, Tung WC, Sharkey KL, Adamowicz L (2013) Chem Rev 113(1):36

    CAS  PubMed  Google Scholar 

  14. Udagawa T, Ishimoto T, Tokiwa H, Tachikawa M, Nagashima U (2004) Chem Phys Lett 389 (4):236

    CAS  Google Scholar 

  15. Nakai H, Hoshino M, Miyamoto K, Hyodo S (2005) J Chem Phys 122:164101

    PubMed  Google Scholar 

  16. Takayoshi I, Masanori T, Hiroaki T, Umpei N (2005) Chem Phys 314(1):231

    Google Scholar 

  17. Ishimoto T, Tachikawa M, Nagashima U (2006) J Chem Phys 125(14):144103

    PubMed  Google Scholar 

  18. Ishimoto T, Tachikawa M, Nagashima U (2006), vol 124

  19. Udagawa T, Ishimoto T, Tokiwa H, Tachikawa M, Nagashima U (2006) J Phys Chem A 110 (22):7279

    CAS  PubMed  Google Scholar 

  20. Nakai H, Ikabata Y, Tsukamoto Y, Imamura Y, Miyamoto K, Hoshino M (2007) Mol Phys 105(19–22):2649

    CAS  Google Scholar 

  21. Itou Y, Mori S, Udagawa T, Tachikawa M, Ishimoto T, Nagashima U (2007) J Phys Chem A 111(2):261

    CAS  PubMed  Google Scholar 

  22. Ishimoto T, Tachikawa M, Nagashima U (2008) J Chem Phys 128(16):164118

    PubMed  Google Scholar 

  23. Kikuta Y, Ishimoto T, Nagashima U (2008) Chem Phys 354:218

    CAS  Google Scholar 

  24. Kikuta Y, Ishimoto T, Nagashima U (2008) B Chem Soc Jpn 81(7):820

    CAS  Google Scholar 

  25. Ishimoto T, Tachikawa M, Nagashima U (2009) Int J Quantum Chem 109:2677

    CAS  Google Scholar 

  26. Ikabata Y, Imamura Y, Nakai H (2011) J Phys Chem A 115(8):1433

    CAS  PubMed  Google Scholar 

  27. Kikuta Y, Ishimoto T, Nagashima U (2011) Comp Theo Chem 975(1):138

    CAS  Google Scholar 

  28. Romero J, Posada E, Flores-Moreno R, Reyes A (2012) J Chem Phys 137:074105

    PubMed  Google Scholar 

  29. Moncada F, Uribe LS, Romero J, Reyes A (2013) Int J Quantum Chem 113(10):1556

    CAS  Google Scholar 

  30. Romero J, Restrepo A, Reyes A (2014) Mol Phys 112(3–4):518

    CAS  Google Scholar 

  31. Moncada F, Flores-Moreno R, Reyes A (2017) J Mol Model 23:90

    PubMed  Google Scholar 

  32. Sugimoto H, Tachikawa M, Udagawa T (2018) Int J Quantum Chem 119(10):e25895

    Google Scholar 

  33. Ishibashi R, Tachikawa M, Udagawa T (2019) B Chem Soc Jpn 92(3):592

    CAS  Google Scholar 

  34. Swalina C, Pak MV, Chakraborty A, Hammes-Schiffer S (2006) J Phys Chem A 110(33):9983

    CAS  PubMed  Google Scholar 

  35. Imamura Y, Kiryu H, Nakai H (2008) J Comput Chem 29(5):735

    CAS  PubMed  Google Scholar 

  36. Sirjoosingh A, Pak MV, Hammes-Schiffer S (2011) J Chem Theor Comp 7(9):2689

    CAS  Google Scholar 

  37. Goli M, Shahbazian S (2013) Theor Chem Acc 132:1410

    Google Scholar 

  38. Udagawa T, Tsuneda T, Tachikawa M (2014) Phys Rev A 89:052519

    Google Scholar 

  39. Brorsen KR, Yang Y, Hammes-Schiffer S (2017) J Phys Chem Lett 8(15):3488

    CAS  PubMed  Google Scholar 

  40. Pak MV, Hammes-Schiffer S (2004) Phys Rev Lett 92(10):103002

    PubMed  Google Scholar 

  41. Swalina C, Pak MV, Hammes-Schiffer S (2005) Chem Phys Lett 404(4-6):394

    CAS  Google Scholar 

  42. Moncada F, Cruz D, Reyes A (2012) Chem Phys Lett 539–540:209

    Google Scholar 

  43. Moncada F, Cruz D, Reyes A (2013) Chem Phys Lett 570:16

    CAS  Google Scholar 

  44. Posada E, Moncada F, Reyes A (2014) J Phys Chem A 118(40):9491

    CAS  PubMed  Google Scholar 

  45. Goli M, Shahbazian S (2014) Phys Chem Chem Phys 16:6602

    CAS  PubMed  Google Scholar 

  46. Goli M, Shahbazian S (2015) Phys Chem Chem Phys 17:7023

    CAS  PubMed  Google Scholar 

  47. Goli M, Shahbazian S (2015) Phys Chem Chem Phys 17:245

    CAS  PubMed  Google Scholar 

  48. Goli M, Shahbazian S (2016) Chem-Eur J 22(7):2525

    CAS  PubMed  Google Scholar 

  49. Goli M, Jalili S (2018) Int J Quantum Chem 118(22):e25758

    Google Scholar 

  50. Posada E, Moncada F, Reyes A (2018) J Chem Phys 148(8):084113

    PubMed  Google Scholar 

  51. Tachikawa M, Mori K, Nakai H, Iguchi K (1998) Chem Phys Lett 290(4-6):437

    CAS  Google Scholar 

  52. Tachikawa M (2001) Chem Phys Lett 350(3):269

    CAS  Google Scholar 

  53. Adamson PE, Duan XF, Burggraf LW, Pak MV, Swalina C, Hammes-Schiffer S (2008) J Phys Chem A 112(6):1346

    CAS  PubMed  Google Scholar 

  54. Tachikawa M, Kita Y, Buenker R J (2011) Phys Chem Chem Phys 13:2701

    CAS  PubMed  Google Scholar 

  55. Swalina C, Pak MV, Hammes-Schiffer S (2012) J Chem Phys 136(16):164105

    PubMed  Google Scholar 

  56. Sirjoosingh A, Pak MV, Swalina C, Hammes-Schiffer S (2013) J Chem Phys 139(3):034103

    PubMed  Google Scholar 

  57. Charry J, Romero J, Varella M TD N, Reyes A (2014) Phys Rev A 89:052709

    Google Scholar 

  58. Romero J, Charry J, Flores-Moreno R, do M, Varella N, Reyes A (2014) J Chem Phys 141 (11):114103

    PubMed  Google Scholar 

  59. Ellis B, Aggarwal S, Chakraborty A (2016) J Chem Theory Comput 12(1):188

    CAS  PubMed  Google Scholar 

  60. Brorsen KR, Pak MV, Hammes-Schiffer S (2017) J Phys Chem A 121(2):515

    CAS  PubMed  Google Scholar 

  61. Charry J, Varella MTDN, Reyes A (2018) Angew Chemie Int Ed 57:8859

    CAS  Google Scholar 

  62. Auer B, Pak M V, Hammes-Schiffer S (2010) J Phys Chem C 114(12):5582

    CAS  Google Scholar 

  63. Tsukamoto Y, Ikabata Y, Romero J, Reyes A, Nakai H (2016) Phys Chem Chem Phys 18 (39):27422

    CAS  PubMed  Google Scholar 

  64. Zhang Y, Lee T, Yang W (1999) J Chem Phys 110(1):46

    CAS  Google Scholar 

  65. Gao J, Amara P, Alhambra C, Field M J (1998) J Phys Chem A 102(24):4714

    CAS  Google Scholar 

  66. Philipp D M, Friesner R A (1999) J Comput Chem 20(14):1468

    CAS  Google Scholar 

  67. Walker R, Crowley M, Case D (2008) J Comput Chem 29(7): 1019

    CAS  PubMed  Google Scholar 

  68. Pedraza-González L, Romero J, Torres JA, Reyes A (2016) Phys Chem Chem Phys 18:27185

    PubMed  Google Scholar 

  69. McNaught AD, Wilkinson A (1997) IUPAC compendium of chemical terminology, vol 1669, 2nd edn. Blackwell Scientific Publications, Oxford

  70. Dewar M, Dieter K (1986) J Am Chem Soc 108:8075

    CAS  Google Scholar 

  71. Bagno A, Scorrano G (1996) J Phys Chem-US 100:1536

    CAS  Google Scholar 

  72. Gronert S, Simpson DC, Conner KM (2009) J Am Soc Mass Spectr 20(11):2116

    CAS  Google Scholar 

  73. Deakyne C (2003) Int J Mass Spectrom 227:601

    CAS  Google Scholar 

  74. Jones C, Bernier M, Carson E, Colyer KE, Metz R, Pawlow A, Wischow ED, Webb I, Andriole EJ, Poutsma JC (2007) Int J Mass Spectrom 267(1–3):54

    CAS  Google Scholar 

  75. Díaz-Tinoco M, Romero J, Ortiz J, Reyes A, Flores-Moreno R (2013) J Chem Phys 138:194108

    PubMed  Google Scholar 

  76. Pedraza-González L, Charry J, Quintero W, Torres JA, Reyes A (2017) Phys Chem Chem Phys 19:25324

    PubMed  Google Scholar 

  77. Curtiss LA, McGrath MP, Blaudeau J, Davis NE, Binning RC, Radom L (1995) J Chem Phys 103(14):6104

    CAS  Google Scholar 

  78. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) J Comput Chem 25(9):1157

    CAS  Google Scholar 

  79. Honda S, Yamasaki K, Sawada Y, Morii H (2004) Structure 12:1512

    Google Scholar 

  80. Maier J, Martinez C, Kasavajhala K, Wickstrom L, Hauser K, Simmerling C (2015) J Chem Theory Comput 11(8):3696

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

J.F.G. and J.M.R. thank the Departmento Administrativo de Ciencia, Tecnología e Innovación COLCIENCIAS for the “Es Tiempo de Volver” and Doctoral “Francisco José de Caldas” scholarships.

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Authors and Affiliations

  1. Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 # 45–03, Bogotá, Colombia

    José M. Rodas, Johan F. Galindo & Andrés Reyes

  2. Department of Chemistry, Universidad de Caldas, Calle 65 # 26–10, Manizales, Colombia

    José M. Rodas

  3. Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA

    Adrian E. Roitberg

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  1. José M. Rodas
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Correspondence to Andrés Reyes.

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This paper belongs to Topical Collection QUITEL 2018 (44th Congress of Theoretical Chemists of Latin Expression)

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Rodas, J.M., Galindo, J.F., Roitberg, A.E. et al. The any particle molecular orbital/molecular mechanics approach. J Mol Model 25, 316 (2019). https://doi.org/10.1007/s00894-019-4153-x

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