Advertisement

Theoretical Chemistry Accounts

, 135:251 | Cite as

Theoretical determination of aqueous acid–base pK values: electronic structure calculations and steered molecular dynamic simulations

  • S. TolosaEmail author
  • J. A. Sansón
  • A. Hidalgo
  • N. Mora-DiezEmail author
Regular Article

Abstract

The equilibrium constant (K) of several acid–base equilibria involving isomers of acetohydroxamic acid in aqueous solution is studied from a theoretical point of view applying electronic structure methods (at the M06-2X-SMD/6-311++G(d,p) and MP2-PCM/6-311++G(d,p) levels of theory) and steered molecular dynamic (SMD) simulations. The similarity of the results obtained indicates that SMD simulations can be successfully used to evaluate Gibbs energy changes in acid–base reactions in solution and pK values since these properties are in agreement with those found with quantum calculation and thermodynamic cycles. In the process of proton transfer from the imide isomers (the ZI and EI structures) toward the anion Z-amide, the deprotonation of the ZI(COH) molecule is the most favorable process kinetically and thermodynamically. It is observed that pK values are slightly higher for E-isomers and, particularly, for the deprotonation from the oxime group EI(NOH). Finally, we must emphasize the goodness of SMD simulations in solution to calculate this property as an alternative to using continuum solvation methods.

Keywords

Aqueous pK calculations Acid–base equilibria SMD simulations M06-2X MP2 

Notes

Acknowledgments

This research was sponsored by the Consejería de Infraestructuras y Desarrollo Tecnológico de la Junta de Extremadura (Project GR15003) and the Natural Sciences and Engineering Research Council of Canada (NSERC).

Supplementary material

214_2016_2008_MOESM1_ESM.docx (32 kb)
Tables S1 and S2 collects the thermodynamic data. Table S3 presents the Cartesian coordinates for each molecule calculate at M06-2X-SMD and MP2-PCM levels, and Table S3 shows the Cartesian coordinates of transition state and product systems from SMD simulations (DOCX 32 kb)

References

  1. 1.
    Warshel A (1991) Computer modeling of chemical reactions in enzymes and solutions. Wiley, New YorkGoogle Scholar
  2. 2.
    Muller A, Ratjczak H, Junge W (1992) Electron and proton transfer in chemistry and biology. Elsevier, AmsterdamGoogle Scholar
  3. 3.
    Cramer CJ, Truhlar DG (1994) Structure and reactivity in aqueous solution: characterization of chemical and biological systems. American Chemical Society, WashingtonCrossRefGoogle Scholar
  4. 4.
    Bala P, Grocowski P, Lesyg B, McCammon JA (1995) Quantum mechanical simulation methods for studying biological systems. Springer, BerlinGoogle Scholar
  5. 5.
    Aqvist J (1997) Modelling of proton transfer reactions in enzymes. In: Naray-Szabó G, Warshel A (eds) Computational approaches to biochemical reactivity. Kluwer Academic Publisher, Netherlands, pp 341–362Google Scholar
  6. 6.
    Náray-Szabó G, Warshel A (2002) Computational approaches to biochemical reactivity. Springer, BerlinCrossRefGoogle Scholar
  7. 7.
    Tapia O, Bertrán J (2003) Solvent effects and chemical reactivity. Springer, BerlinGoogle Scholar
  8. 8.
    Binder K, Ciccotti G, Ferrario M (2006) Computer simulations in condensed matter systems: from materials to chemical biology, vol 2. Springer, BerlinGoogle Scholar
  9. 9.
    Kotz JC, Treichel PM, Townsend J (2009) Chemistry and chemical reactivity. Thomson Higher Education, BelmontGoogle Scholar
  10. 10.
    Ho J, Coote ML (2010) Theor Chem Acc 125:3–21CrossRefGoogle Scholar
  11. 11.
    Ho J, Klamt A, Coote ML (2010) J Phys Chem A 2010(114):13442–13444CrossRefGoogle Scholar
  12. 12.
    Stumm W, Morgan JJ (1996) Aquatic chemistry: chemical equilibria and rates in natural waters. Wiley-Interscience, New YorkGoogle Scholar
  13. 13.
    Thomas G (2000) Medicinal chemistry: an introduction. Wiley, West SussexGoogle Scholar
  14. 14.
    Shields GC, Seybold PG (2014) Computational approaches for the prediction of pK a values. CRC Press Taylor & Francis Group, Boca RatonGoogle Scholar
  15. 15.
    Casasnovas R, Ortega-Castro J, Frau J, Donoso J, Muñoz F (2014) Int J Quant Chem 114:1350–1363CrossRefGoogle Scholar
  16. 16.
    Tolosa S, Mora-Diez N, Hidalgo A, Sansón J (2014) RSC Adv. 4:44757–44768CrossRefGoogle Scholar
  17. 17.
    Brown TN, Mora-Diez N (2006) J Phys Chem B 110:9270–9279CrossRefGoogle Scholar
  18. 18.
    Pliego JR, Riveros JM (2002) J Phys Chem A 106:7434–7439CrossRefGoogle Scholar
  19. 19.
    Bryantsev VS, Diallo MS, Goddard WA (2008) J Phys Chem B 112:9709–9719CrossRefGoogle Scholar
  20. 20.
    Karelson M, Lobanov VS, Katritzky AR (1996) Chem Rev 96:1027–1044CrossRefGoogle Scholar
  21. 21.
    Hennemann M, Clark T (2002) J Mol Model 8:95–101CrossRefGoogle Scholar
  22. 22.
    Soriano E, Cerdán S, Ballesteros P (2004) J Mol Struct (THEOCHEM) 684:121–128CrossRefGoogle Scholar
  23. 23.
    Brown TN, Mora-Diez N (2006) J Phys Chem B 110:20546–20554CrossRefGoogle Scholar
  24. 24.
    Poliak P (2014) Acta Chimica Slovaca 7:25–30. doi: 10.2478/acs-2014-0005 CrossRefGoogle Scholar
  25. 25.
    Sastre S, Casasnovas R, Muñoz F, Frau J (2013) Theor. Chem. Acc. 132:1310CrossRefGoogle Scholar
  26. 26.
    Biswas AK, Lo R, Ganguly B (2013) Synlett 24:2519–2524CrossRefGoogle Scholar
  27. 27.
    Derbel N, Clarot I, Mourer M, Regnouf-de-Vains J, Ruiz-Lopez MF (2012) J Phys Chem A 116:9404–9411CrossRefGoogle Scholar
  28. 28.
    Govender KK, Cukrowski I (2010) J Phys Chem A 114:1868–1878CrossRefGoogle Scholar
  29. 29.
    Govender KK, Cukrowski I (2009) J Phys Chem A 113:3639–3647CrossRefGoogle Scholar
  30. 30.
    Li GS, Ruiz-Lopez MF, Maigret B (1997) J Phys Chem A 101:7885–7892CrossRefGoogle Scholar
  31. 31.
    Hehre WJ, Ditchfield R, Radom L, Pople JA (1970) J Am Chem Soc 92:4796–4801CrossRefGoogle Scholar
  32. 32.
    Ponomarev DA, Takhistov VV (1997) J Chem Ed 74:201–203CrossRefGoogle Scholar
  33. 33.
    Izrailev S, Stepaniants S, Isralewitz B, Kosztin D, Lu H, Molnar F, Wriggers W, Schulten K (1998) Steered molecular dynamics. In: Deuflhard P, Hermans J, Leimkuhler B, Mark AE, Reich S, Skell RD (eds) Computational molecular dynamics, challenges, methods, ideas, vol 4., Lectures Notes in Computational Science and EngineeringSpringer, Berlin, pp 39–65CrossRefGoogle Scholar
  34. 34.
    Isralewitz B, Gao M, Schulten K (2001) Curr Opin Struct Biol 11:224–230CrossRefGoogle Scholar
  35. 35.
    Kakkar R (2013) In: Gupta SP (ed) Hydroxamic acids: a unique family of chemicals with multiple biological activities. Springer, BerlinGoogle Scholar
  36. 36.
    Brown DA, Chidambaram MV (1982) Metal ions in biological systems. Marcel Dekker, New York, p 14Google Scholar
  37. 37.
    Sennet ML, Niño A, Muñoz Caro C, Ibeas S, García B, Leal JM, Secco F, Venturini M (2003) J Org Chem 68:6535–6542CrossRefGoogle Scholar
  38. 38.
    Mora-Diez N, Senent ML, García B (2006) Chem Phys 324:350–358CrossRefGoogle Scholar
  39. 39.
    Dissanayake DP, Sentilnithy R (2009) J Mol Struct (THEOCHEM) 910:93–98CrossRefGoogle Scholar
  40. 40.
    Bagno A, Comuzzi C, Scorrano G (1999) J Am Chem Soc 116:916–924CrossRefGoogle Scholar
  41. 41.
    Monzyk B, Crumbliss AL (1980) J Org Chem 45:4670–4675CrossRefGoogle Scholar
  42. 42.
    Brink CP, Fish LL, Crumbliss AL (1985) J Org Chem 50:2277–2281CrossRefGoogle Scholar
  43. 43.
    Wise WM, Brandt WW (1955) J Am Chem Soc 77:1058–1059CrossRefGoogle Scholar
  44. 44.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, Revision A.1. Gaussian, Wallingford, CTGoogle Scholar
  45. 45.
    Miertuš S, Tomasi J (1982) Chem Phys 65:239–245CrossRefGoogle Scholar
  46. 46.
    Scalmani G, Frisch MJ (2010) J Chem Phys 132:114110CrossRefGoogle Scholar
  47. 47.
    Mulliken RS (1955) J Chem Phys 23:1833–1840CrossRefGoogle Scholar
  48. 48.
    Zhao Y, Truhlar DG (2008) Theor Chem Acc 120:215–241CrossRefGoogle Scholar
  49. 49.
    Marenich AV, Cramer CJ, Truhlar DG (2009) J Phys Chem B 113:6378–6396CrossRefGoogle Scholar
  50. 50.
    Cramer CJ, Truhlar DG (2006) SMx continuum models for condensed phases. In: Maroulis G, Simos TE (eds) Trends and perspectives in modern computational science; Lecture series on computer and computational sciences, vol 6. Brill/VSP, Leiden, pp 112–140Google Scholar
  51. 51.
    Cornell WD, Cieplak P, Bayly CI, Gould IR, Mez KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179–5197CrossRefGoogle Scholar
  52. 52.
    Damm W, Frontera A, Tirado-Rives J, Jorgensen WL (1997) J Comp Chem 18:1955–1970CrossRefGoogle Scholar
  53. 53.
    Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225–11236CrossRefGoogle Scholar
  54. 54.
    Jorgensen WL, Tirado-Rives J (1988) J Am Chem Soc 110:1657–1666CrossRefGoogle Scholar
  55. 55.
    Kaminski G, Duffy EM, Matsui T, Jorgensen WL (1994) J Phys Chem 98:13077–13082CrossRefGoogle Scholar
  56. 56.
    Jarzynski C (1997) Phys Rev Lett 78:2690–2693CrossRefGoogle Scholar
  57. 57.
    Case DA, Darden TA, Cheatham ITE III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Mert KM, Roberts B, Hayik S, Roitberg A, Seabra G, Swails J, Götz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2012) AMBER 12. University of California, San FranciscoGoogle Scholar
  58. 58.
    Ewald P (1921) Ann Phys 64:253–287CrossRefGoogle Scholar
  59. 59.
    Frauenheim T, Porezag D, Elstner M, Jungnickel G, Elsner J, Haugk M, Sieck A, Seifert G (1998) Mat Res Soc Symp Proc 491:91–104CrossRefGoogle Scholar
  60. 60.
    Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Phys Rev B 58:7260–7268CrossRefGoogle Scholar
  61. 61.
    Seabra GM, Walker RC, Elstner M, Case DA, Roitberg AE (2007) J Phys Chem A 111:5655–5664CrossRefGoogle Scholar
  62. 62.
    Walker RC, Crowley MF, Case DA (2008) J Comp Chem 29:1019–1031CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Departamento de Ingeniería Química y Química FísicaUniversidad de ExtremaduraBadajozSpain
  2. 2.Department of ChemistryThompson Rivers UniversityKamloopsCanada

Personalised recommendations