Skip to main content
SpringerLink
Log in

Theoretically describing the 17O magnetic shielding constant of biomolecular systems: uracil and 5-fluorouracil in water environment

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

Abstract

The nuclear magnetic resonance chemical shielding of 17O is of great importance for biomolecular characterization in water environment. In these systems, oxygen atoms occupy important positions and are involved in hydrogen bonds with the water environment. In this work, different solvation models are used for the theoretical determination of the 17O chemical shielding of the nucleobase uracil and the substituted 5-fluorouracil in aqueous environment. Continuum, discrete and explicit solvent models are used, and an analysis is made of the role played by the solute polarization due the solvent. The best results are obtained using the sequential quantum mechanics/molecular mechanics methodology using an iterative procedure for the solute polarization, but a good compromise is obtained by using the electronic polarization provided by the polarizable continuum model. Quantum mechanical calculations of the chemical shieldings are made using density-functional theory in two different exchange–correlation approximations. Using an iterative procedure for the solute polarization and the mPW1PW91/aug-pcS-2 model in the electrostatic approximation, we obtained magnetic shielding constants for the two O atoms of uracil within 2 ppm of the experimental results. For 5-fluorouracil, the theoretical results, with the same model, are again in good agreement with the experimental values. An analysis of the influence of the solute–solvent hydrogen bonds in the chemical shielding of uracil case is also made, and it is concluded that the most important contribution to the calculated shielding derives from the electrostatic contribution to the solute–solvent interaction.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Macomber RS (1997) A complete introduction to modern NMR spectroscopy. Wiley, New Jersey

    Google Scholar 

  2. Gerothanassis IP (2010) Prog Nucl Magn Reson Spectrosc 56:95

    Article  CAS  Google Scholar 

  3. Gerothanassis IP (2010) Prog Nucl Magn Reson Spectrosc 57:1

    Article  CAS  Google Scholar 

  4. Klemperer WG (1978) Angew Chem Int Ed Engl 17:246

    Article  Google Scholar 

  5. Wu G, Dong S, Ida R, Reen N (2002) J Am Chem Soc 124:1768

    Article  CAS  Google Scholar 

  6. Longley DB, Harkin DP, Jonhston PG (2003) Nat Rev Cancer 3:330

    Article  CAS  Google Scholar 

  7. Chandrasekaran S, Wilson WD, Boykin DW (1985) J Org Chem 50:829

    Article  CAS  Google Scholar 

  8. Bednarek E, Dobrowolski JCz, Dobrosz-Teperek K, Kozerski L, Lewandowski W, Mazurek AP (2000) J Mol Struct 554:233

    Article  CAS  Google Scholar 

  9. Coutinho K, Canuto S, Zerner MC (2000) J Chem Phys 112:9874

    Article  CAS  Google Scholar 

  10. Rivelino R, Cabral BJC, Coutinho K, Canuto S (2005) Chem Phys Lett 407:13

    Article  CAS  Google Scholar 

  11. Coutinho K, Rivelino R, Georg HC, Canuto S (2008) In: Canuto S (ed) Solvation effects on molecules and biomolecules. Computational methods and applications. Springer, New York

    Google Scholar 

  12. Manzoni V, Lyra ML, Gester RM, Coutinho K, Canuto S (2010) Phys Chem Chem Phys 12:14023

    Article  CAS  Google Scholar 

  13. Gester RM, Georg HC, Fonseca TL, Provasi PF, Canuto S (2012) Theory Chem Acc 131:1220

    Article  Google Scholar 

  14. Gester RM, Georg HC, Canuto S, Caputo MC, Provasi PF (2009) J Phys Chem A 113:14936

    Article  CAS  Google Scholar 

  15. Manzoni V, Lyra ML, Coutinho K, Canuto S (2011) J Chem Phys 135:144103

    Article  Google Scholar 

  16. Fonseca TL, Coutinho K, Canuto S (2008) J Chem Phys 129:34502

    Article  Google Scholar 

  17. Kongsted J, Mennucci B (2007) J Phys Chem A 111:9890

    Article  CAS  Google Scholar 

  18. Mennucci B, Martinez JM (2005) J Phys Chem B 109:9830

    Article  CAS  Google Scholar 

  19. Fileti EE, Georg HC, Coutinho K, Canuto S (2007) J Braz Chem Soc 18:74

    Article  CAS  Google Scholar 

  20. Esrafili MD, Alizadeh V (2011) Struct Chem 22:1195

    Article  CAS  Google Scholar 

  21. Karami L, Behzadi H, Hadipour NL, Mousavi-Khoshdel M (2011) Comput Theor Chem 965:137

    Article  CAS  Google Scholar 

  22. Esrafili MD, Alizadeh V (2011) Comput Theor Chem 974:66

    Article  CAS  Google Scholar 

  23. Claramunt RM, Pérez-Torralba M, Santa María D, Sanz D, Elena B, Alkorta I, Elguero J (2010) J Magn Reson 206:274

    Article  CAS  Google Scholar 

  24. Amini SK, Shaghaghi H, Bain AD, Chabok A, Tafazzoli M (2010) Solid State Nucl Magn Reson 37:13

    Article  CAS  Google Scholar 

  25. Alkorta I, Blanco F, Elguero J (2009) Magn Reson Chem 47:249

    Article  CAS  Google Scholar 

  26. Del Bene JE, Bartlett RJ (2000) J Am Chem Soc 122:10480

    Article  Google Scholar 

  27. Miertuš S, Scrocco E, Tomasi J (1981) Chem Phys 55:117

    Article  Google Scholar 

  28. Mennucci B, Cammi R (eds) Continuum solvation models In: Chemical physics (2007) John Wiley, New Jersey

  29. Marenich AV, Olson RM, Chamberlin AC, Cramer CJ, Truhlar DG (2007) J Chem Theory Comput 3:2055

    Article  CAS  Google Scholar 

  30. Kongsted J, Osted A, Mikkelsen KV, Christiansen O (2002) Mol Phys 100:1813

    Article  CAS  Google Scholar 

  31. McDonald NA, Carlson HA, Jorgensen WL (1997) J Phys Org Chem 10:563

    Article  CAS  Google Scholar 

  32. Xie W, Gao J (2007) J Chem Theory Comput 3:1890

    Article  CAS  Google Scholar 

  33. Öhrn A, Karlström G (2007) J Chem Theory Comput 3:1993

    Article  Google Scholar 

  34. Georg HC, Coutinho K, Canuto S (2006) Chem Phys Lett 429:119

    Article  CAS  Google Scholar 

  35. Bistafa C, Canuto S (2013) Theor Chem Acc 132:1299

    Article  Google Scholar 

  36. Pranata TJ, Wierchke SG, Jorgensen WL (1991) J Am Chem Soc 113:2810

    Article  CAS  Google Scholar 

  37. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926

    Article  CAS  Google Scholar 

  38. Breneman CM, Wiberg KB (1990) J Comput Chem 11:361

    Article  CAS  Google Scholar 

  39. Coutinho K, Guedes RC, Cabral BJC, Canuto S (2003) Chem Phys Lett 369:345

    Article  CAS  Google Scholar 

  40. Coutinho K, Canuto S (2010) DICE (version 2.9): a Monte Carlo program for molecular liquid simulation, version 2.9. University of São Paulo, São Paulo

    Google Scholar 

  41. Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Oxford University Press, Oxford

    Google Scholar 

  42. Coutinho K, Georg HC, Fonseca TL, Ludwig V, Canuto S (2007) Chem Phys Lett 437:148

    Article  CAS  Google Scholar 

  43. Galván IF, Sánchez ML, Martín ME, del Valle FJO, Aguilar MA (2003) Comput Phys Commun 155:244

    Article  Google Scholar 

  44. Stillinger FH, Rahman A (1972) J Chem Phys 57:1281

    Article  CAS  Google Scholar 

  45. Mezei M, Beveridge DL (1981) J Chem Phys 74:622

    Article  CAS  Google Scholar 

  46. Coutinho K, Canuto S (2000) Int J Quantum Chem 77:192

    Article  Google Scholar 

  47. Helgaker T, Jaszunski M, Ruud K (1999) Chem Rev 99:293

    Article  CAS  Google Scholar 

  48. Auer AA (2009) Chem Phys Lett 467:230

    Article  CAS  Google Scholar 

  49. Ozimiski WP, Garnuszek P, Bednarek E, Dobrowolski JCz (2007) Inorg Chim Acta 360:1902

    Article  Google Scholar 

  50. Keal TW, Helgaker T, Salek P, Tozer DJ (2006) Chem Phys Lett 425:163

    Article  CAS  Google Scholar 

  51. Becke AD (1993) J Chem Phys 98:5648

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  53. Adamo C, Barone V (1998) J Chem Phys 108:664

    Article  CAS  Google Scholar 

  54. Burke K, Perdew JP, Wang Y (1998) In: Dobson JF, Vignale G, Das MP (eds) Electronic density functional theory: recent progress and new directions. Plenum, Berlin

    Google Scholar 

  55. Jensen F (2008) J Chem Theory Comput 4:719

    Article  CAS  Google Scholar 

  56. London F (1937) J Phys Radium 8:397

    Article  CAS  Google Scholar 

  57. McWeeny R (1962) Phys Rev 126:1028

    Article  Google Scholar 

  58. Ditchfield R (1974) Mol Phys 27:789

    Article  CAS  Google Scholar 

  59. Wolinski K, Hilton JF, Pulay P (1990) J Am Chem Soc 112:8251

    Article  CAS  Google Scholar 

  60. Gauss J (1993) J Chem Phys 99:3629

    Article  CAS  Google Scholar 

  61. Cheeseman JR, Trucks GW, Keith TA, Frisch MJ (1996) J Chem Phys 104:5497

    Article  CAS  Google Scholar 

  62. Wasylishen RE, Bryce DL (2002) J Chem Phys 117:10061

    Article  CAS  Google Scholar 

  63. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, revision D01. Gaussian Inc, Wallingford

    Google Scholar 

  64. Ludwig V, Coutinho K, Canuto S (2007) Phys Chem Chem Phys 9:4907

    Article  CAS  Google Scholar 

  65. Millefiori S, Alparone A (2004) Chem Phys 303:27

    Article  CAS  Google Scholar 

  66. Brown RD, Godfrey PD, McNaughton D, Pierlot AP (1988) J Am Chem Soc 110:2329

    Article  CAS  Google Scholar 

  67. Witanowski M, Biedrzycka Z, Sicinska W, Grabowski Z (2003) J Magn Reson 164:212

    Article  CAS  Google Scholar 

  68. Karplus M, Pople JA (1963) J Chem Phys 38:2803

    Article  CAS  Google Scholar 

  69. Del Bene JE (1981) J Comput Chem 2:188

    Article  Google Scholar 

  70. Schwarz HM, MacCross M, Danyluk SS (1983) J Am Chem Soc 105:5901

    Article  Google Scholar 

Download references

Acknowledgments

This work has been partially supported by FAPESP, CAPES, CNPq, INCT-FCx and N-BioNet.

Author information

Authors and Affiliations

  1. Instituto de Física, Universidade de São Paulo, CP 66318, São Paulo, SP, 05315-970, Brazil

    Rodrigo M. Gester, Carlos Bistafa, Kaline Coutinho & Sylvio Canuto

  2. Instituto de Física, Universidade Federal de Goiás, CP 131, Goiânia, GO, 74001-970, Brazil

    Herbert C. Georg

  3. Faculdade de Física, Universidade Federal do Pará, Marabá, PA, 68505-080, Brazil

    Rodrigo M. Gester

Authors
  1. Rodrigo M. Gester
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carlos Bistafa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Herbert C. Georg
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kaline Coutinho
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sylvio Canuto
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sylvio Canuto.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gester, R.M., Bistafa, C., Georg, H.C. et al. Theoretically describing the 17O magnetic shielding constant of biomolecular systems: uracil and 5-fluorouracil in water environment. Theor Chem Acc 133, 1424 (2014). https://doi.org/10.1007/s00214-013-1424-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00214-013-1424-y

Keywords

Search

Navigation