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Towards a converged strategy for including microsolvation in reaction mechanism calculations

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Abstract

A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent–solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges—a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pKa values and a mechanistic study of the methanol mediated Morita–Baylis–Hillman reaction.

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References

  1. Tajti A, Szalay PG, Csaszar AG, Kallay M, Gauss J, Valeev EF, Flowers BA, Vazquez J, Stanton JF (2004) J Chem Phys 121:11599

    Article  CAS  PubMed  Google Scholar 

  2. Bomble YJ, Vazquez J, Kallay M, Michauk C, Szalay PG, Csaszar AG, Gauss J, Stanton JF (2006) J Chem Phys 125:064108

    Article  Google Scholar 

  3. Harding ME, Vazquez J, Ruzcic B, Wilson AK, Gauss J, Stanton JF (2008) J Chem Phys 128:114111

    Article  PubMed  Google Scholar 

  4. Marx D, Hutter J (2009) Ab initio molecular dynamics. Cambridge

  5. Warshel A, Levitt M (1976) J Mol Biol 103:227–249

    Article  CAS  PubMed  Google Scholar 

  6. Chandler D, Andersen HC (1972) J Chem Phys 57:1930–1937

    Article  CAS  Google Scholar 

  7. Ikeguchi M, Doi JJ (1995) Chem Phys 103:5011

    CAS  Google Scholar 

  8. Beglov D, Roux B (1997) J Phys Chem B 101:7821

    Article  CAS  Google Scholar 

  9. Du Q, Beglov D, Roux B (2000) J Phys Chem B 104:796

    Article  CAS  Google Scholar 

  10. Kovalenko A, Hirata F (1998) Chem Phys Lett 290:237

    Article  CAS  Google Scholar 

  11. Hoffgaard F, Heil J, Kast SM (2013) J Chem Theory Comput 9:4718–4726

    Article  CAS  PubMed  Google Scholar 

  12. Tomasi J, Mennucci B, Cammi R (2005) Chem Rev 105:2999–3093

    Article  CAS  PubMed  Google Scholar 

  13. Miertus S, Scrocco E, Tomasi J (1981) Chem Phys 55:117

    Article  CAS  Google Scholar 

  14. Tomasi J, Persico M (2027) Chem Rev 1994:94

    Google Scholar 

  15. Tomasi J, Cammi R, Menucci B (1999) Int J Quantum Chem 75:767

    Article  Google Scholar 

  16. Cancès E, Menucci B, Tomasi J (1997) J Chem Phys 107:3032–3041

    Article  Google Scholar 

  17. Foresman JB, Keith TA, Wiberg KB, Snoonian J, Frisch MJ (1996) J Phys Chem 100:16098–16104

    Article  CAS  Google Scholar 

  18. Marenich AV, Cramer CJ, Truhlar DG (2009) J Phys Chem B 113:6378–6396

    Article  CAS  PubMed  Google Scholar 

  19. Cramer CJ, Truhlar DG (2008) Acc Chem Res 41:760

    Article  CAS  PubMed  Google Scholar 

  20. Cramer CJ, Truhlar DG (2009) Acc Chem Res 42:493

    Article  CAS  Google Scholar 

  21. Marenich AV, Cramer CJ, Truhlar DG (2009) J Phys Chem B 113:4538–4543

    Article  CAS  PubMed  Google Scholar 

  22. Klamt A, Schüürmann G (1993) J Chem Soc Perkin Trans II:799

    Article  Google Scholar 

  23. Maurizio Cossi M, CarloAdamo C, Barone V (1998) Chem Phys Lett 297:1–7

    Article  Google Scholar 

  24. Tao DJ, Slutskyy Y, Muuronen M, Le A, Kohler P, Overman L (2018) J Am Chem Soc 140(8):3091–3102

    Article  CAS  PubMed  Google Scholar 

  25. Klamt A (1995) J Phys Chem 99:2224–2235

    Article  CAS  Google Scholar 

  26. Eckert F, Klamt A (2002) AIChE J 48:369–385

    Article  CAS  Google Scholar 

  27. Ashcraft RW, Raman S, Green WH (2008) J Phys Chem 112:7577

    Article  CAS  Google Scholar 

  28. Deglmann P, Müller I, Becker F, Schäfer A, Hungenberg K-D, Weiß H (2009) Macromol React Eng 3:496

    Article  CAS  Google Scholar 

  29. Deglmann P, Schenk S (2012) J Comput Chem 33:1304

    Article  CAS  PubMed  Google Scholar 

  30. Gadre SR, Yeole SD, Sahu N (2014) Chem Rev 114:12132–12173

    Article  CAS  PubMed  Google Scholar 

  31. Pliego Jr, JR, Riveros JM (2001) J Chem Phys A 105:7241–7247

    Article  Google Scholar 

  32. Pliego Jr JR, Riveros JM (2002) J Chem Phys A 106:7434–7439

    Article  Google Scholar 

  33. Pliego Jr JR, Riveros JM (2004) Chem Phys 306:273–280

    Article  Google Scholar 

  34. Eckert F, Diedenhofen M, Klamt A (2010) Mol Phys 108:229–241

    Article  CAS  Google Scholar 

  35. Ho J, Coote M (2010) Theor Chem Acc 125:3–21

    Article  CAS  Google Scholar 

  36. Ho J, Ertem MZ (2016) J Phys Chem B 120:1319–1329

    Article  CAS  PubMed  Google Scholar 

  37. Kelly CP, Cramer CJ, Truhlar DG (2005) J Chem Theory Comput 1:1133–1152

    Article  CAS  PubMed  Google Scholar 

  38. Basdogan Y, Keith JA (2018) Chem Sci 9:5341–5346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Hadad C, Florez E, Acelas N, Merino G, Restreppo A (2019) Int J Quant Chem 119:e25766

    Article  Google Scholar 

  40. Florez E, Acelas N, Ramirez F, Hadad C, Restreppo A (2018) Phys Chem Chem Phys 20:8909–8916

    Article  CAS  PubMed  Google Scholar 

  41. Ahlrichs R, Armbruster MK, Bär M, Baron H-P, Bauernschmitt R, Crawford N, Deglmann P, Ehrig M, Eichkorn K, Elliott S, Furche F, Haase F, Häser M, Hättig C, Hellweg A, Horn H, Huber C, Huniar U, Kattannek M, Kölmel C, Kollwitz M, May K, Nava P, Ochsenfeld C, Öhm H, Patzelt H, Rappoport D, Rubner O, Schäfer A, Schneider U, Sierka M, Treutler O, Unterreiner B, von Arnim M, Weigend F, Weis P, Weiss H (2018) TURBOMOLE 7.3, Universität Karlsruhe. http://www.turbomole.com.

  42. Furche F, Ahlrichs R, Hättig C, Klopper W, Sierka M, Weigend F (2014) WIREs Comput Mol Sci 4:91–100

    Article  CAS  Google Scholar 

  43. Tao J, Perdew J, Staroverov V, Scuseria G (2003) Phys Rev Lett 91:146401

    Article  PubMed  Google Scholar 

  44. Weigend F, Ahlrichs R (2005) Phys Chem Chem Phys 7:3297–3305

    Article  CAS  PubMed  Google Scholar 

  45. Grimme S, Antony J, Ehrlich S, Krieg H (2010) J Chem Phys 132:154104

    Article  PubMed  Google Scholar 

  46. Johnson ER, Becke AD (2005) J Chem Phys 123:24101

    Article  PubMed  Google Scholar 

  47. Becke AD, Johnson ER (2005) J Chem Phys 123:154101

    Article  PubMed  Google Scholar 

  48. Eckert F, Klamt A (2018) COSMOtherm, Version C3.0, Release 18.01; COSMOlogic GmbH & Co. KG, Leverkusen, Germany

  49. Perdew JP (1986) Phys Rev B 33:8822–8824

    Article  CAS  Google Scholar 

  50. Becke AD (1988) Phys Rev A 38:3098–3100

    Article  CAS  Google Scholar 

  51. Schäfer A, Huber C, Ahlrichs R (1994) J Chem Phys 100:5829–5235

    Article  Google Scholar 

  52. Staroverov VN, Scuseria GE, Tao J, Perdew JP (2003) J Chem Phys 119:12129

    Article  CAS  Google Scholar 

  53. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785

    Article  CAS  Google Scholar 

  54. Vosko SH, Wilk L, Nusair M (1980) Can J Phys 58:1200

    Article  CAS  Google Scholar 

  55. Stephens PJ, Devlin FJ, Chabalowski CF, Frisch MJ (1994) J Phys Chem 98:11623

    Article  CAS  Google Scholar 

  56. Zhao Y, Truhlar DG (2008) Theor Chem Acc 120:215

    Article  CAS  Google Scholar 

  57. Eichkorn K, Treutler O, Öm H, Häser M, Ahlrichs R (1995) Chem Phys Lett 242:652–660

    Article  CAS  Google Scholar 

  58. Weigend F (2006) Phys Chem Chem Phys 8:1057–1065

    Article  CAS  PubMed  Google Scholar 

  59. Treutler O, Ahlrichs R (1995) J Chem Phys 102:346

    Article  CAS  Google Scholar 

  60. Plata RE, Singleton DA (2015) J Am Chem Soc 137:3811

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Jensen J (2015) PhysChemChemPhys 17:12441

    CAS  Google Scholar 

  62. Zimmerman PM (2013) J Chem Theory Comput 9:3043–3050

    Article  CAS  PubMed  Google Scholar 

  63. Zimmerman PM (2013) J Chem Phys 138:184102

    Article  PubMed  Google Scholar 

  64. Zimmerman PM (2015) Comput Chem 36:601

    Article  CAS  Google Scholar 

  65. Legault CY (2009) CYLview, b.; Université de Sherbrooke. http://www.cylview.org

  66. Kildgaard JV, Mikkelsen KV, Bilde M, Elm J (2018) J Phys Chem A 122:5026

    Article  CAS  PubMed  Google Scholar 

  67. Kildgaard JV, Mikkelsen KV, Bilde M, Elm J (2018) Phys Chem A 122:8549

    Article  CAS  Google Scholar 

  68. Simm GN, Türtscher PL, Reiher M (2020) J Comput Chem 41:1144–1155

    Article  CAS  PubMed  Google Scholar 

  69. Bruice TC, Schmir GL (1958) J Am Chem Soc 80:148

    Article  CAS  Google Scholar 

  70. Robiette R, Aggarwal VK, Harvey JN (2007) J Am Chem Soc 129:15513

    Article  CAS  PubMed  Google Scholar 

  71. Cantillo D, Kappe CO (2010) J Org Chem 75:8615

    Article  CAS  PubMed  Google Scholar 

  72. Xu J (2006) J Mol Struct Theochem 767:61

    Article  CAS  Google Scholar 

  73. Fan J-F, Yang C-H, He L-J (2009) Int J Quantum Chem 74:3031

    Google Scholar 

  74. Li J, Jiang W-Y (2010) J Theor Comput Chem 9:65

    Article  CAS  Google Scholar 

  75. Dong L, Qin S, Su Z, Yang H, Hu C (2010) Org Biomol Chem 8:3985

    Article  CAS  PubMed  Google Scholar 

  76. Roy D, Sunoj RB (2007) Org Lett 9:4873

    Article  CAS  PubMed  Google Scholar 

  77. Harvey JN (2010) Faraday Discuss 145:487

    Article  CAS  Google Scholar 

  78. Martelli G, Orena M, Rinaldi S (2012) Eur J Org Chem 2012:4140

    Article  CAS  Google Scholar 

  79. Roy D, Sunoj RB (2008) Chem Eur J 14:10530

    Article  CAS  PubMed  Google Scholar 

  80. Roy D, Patel C, Sunoj RB (2009) J Org Chem 74:6936

    Article  CAS  PubMed  Google Scholar 

  81. Liu Z, Patel C, Harvey JN, Sunoj RB (2017) Phys Chem Chem Phys 19:30647–30657

    Article  CAS  PubMed  Google Scholar 

  82. Goerigk L, Hansen A, Bauer CA, Ehrlich S, Najibi A, Grimme S (2017) Phys Chem Chem Phys 19:32184

    Article  CAS  PubMed  Google Scholar 

  83. Check CE, Gilbert TM (2005) J Org Chem 70:9828–9834

    Article  CAS  PubMed  Google Scholar 

  84. Grimme S (2012) Chem Eur J 18:9955–9964

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors thank Stefan Grimme for providing the code to compute the vibrational entropy with the quasi-rigid-rotor-harmonic-oscillator approach, Oliver Welz and Mikko Muuronen for helpful discussions, and the reviewers for their thorough work.

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MM and AP carried out preliminary studies. PD performed the computations for the introduction and the section “general strategy” and RS performed those for the acid–base reactions and the MBH mechanism. RS and PD wrote the manuscript.

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Correspondence to Rebecca Sure.

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Sure, R., el Mahdali, M., Plajer, A. et al. Towards a converged strategy for including microsolvation in reaction mechanism calculations. J Comput Aided Mol Des 35, 473–492 (2021). https://doi.org/10.1007/s10822-020-00366-2

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