Advertisement

DFT modelling of the infrared spectra for the isolated and the micro-hydrated forms of uracil

  • Claude PouchanEmail author
  • Sandrine Thicoipe
  • Marco De La Pierre
Regular Article
  • 39 Downloads

Abstract

This theoretical study provides the anharmonic vibrational spectra of isolated and micro-hydrated forms of uracil. The calculations were performed at the DFT B3LYP/6-31+G(d,p) level of theory using two different approaches for the treatment of the anharmonicity, namely a time-independent one (VPT2) and a time-dependent one (molecular dynamics). The wavenumbers obtained from both methods are compared to experimental data for the two forms. Globally, the VPT2 method appears slightly better to describe the mid-IR spectra in the fingerprint region between 500 and 1800 cm−1 for the two forms. It should be emphasized that the structural model for solvation of aqueous uracil, which combines an explicit solvent model with a polarizable continuum model gives excellent results, similar to the previously investigated cases of cytosine, thymine, guanine and adenine. As a complement, the role of solvation is discussed in comparison with the role of the chemical environment in the solid phase.

Keywords

Density functional theory Vibrational anharmonic calculations Solvation model IR spectroscopy Uracil micro-hydrated and solid 

Notes

References

  1. 1.
    Sivakova S, Rowan SJ (2005) Chem Soc Rev 34:9–21CrossRefGoogle Scholar
  2. 2.
    Szczesniak M, Nowak MJ, Rostkowska H, Szczepaniak K, Person WB, Shugar D (1983) J Am Chem Soc 105:5969–5976CrossRefGoogle Scholar
  3. 3.
    Chin S, Scott I, Szczepaniak K, Person WB (1984) J Am Chem Soc 106:3415–3422CrossRefGoogle Scholar
  4. 4.
    Rozenberg M, Shoham G, Reva I, Fausto R (2004) Spectrochim Acta Part A 60:2323–2336CrossRefGoogle Scholar
  5. 5.
    Choi MY, Miller RE (2005) Phys Chem Chem Phys 7:3565–3573CrossRefGoogle Scholar
  6. 6.
    Fornaro T, Brucato JR, Pace E, Cestelli Guidi M, Branciamore S, Pucci A (2013) Icarus 226:1068–1085 And references therein CrossRefGoogle Scholar
  7. 7.
    Barone V, Festa G, Grandi A, Rega N, Sanna N (2004) Chem Phys Lett 388:279–283CrossRefGoogle Scholar
  8. 8.
    Puzzarini C, Biczysko M, Barone V (2011) J Chem Theory Comput 7:3702–3710CrossRefGoogle Scholar
  9. 9.
    Barone V, Biczysko M, Bloino J, Borkowska-Panek M, Carnimeo I, Panek P (2012) Int J Quantum Chem 112:2185–2200CrossRefGoogle Scholar
  10. 10.
    Fornaro T, Biczysko M, Monti S, Barone V (2014) Phys Chem Chem Phys 16:10112–10128CrossRefGoogle Scholar
  11. 11.
    Singh JS (2014) Spectrochim Acta Part A 130:313–328CrossRefGoogle Scholar
  12. 12.
    Fornaro T, Burini D, Biczysko M, Barone V (2015) J Phys Chem A 119:4224–4236CrossRefGoogle Scholar
  13. 13.
    Fornaro T, Carnimeo I, Biczysko M (2015) J Phys Chem A 119:5313–5326CrossRefGoogle Scholar
  14. 14.
    Singh JS (2015) Spectrochim Acta Part A 137:625–640CrossRefGoogle Scholar
  15. 15.
    Krasnoshchekov SV, Vogt N, Stepanov NF (2015) J Phys Chem A 11:6723–6737CrossRefGoogle Scholar
  16. 16.
    Fornaro T, Biczysko M, Bloino J, Barone V (2016) Phys Chem Chem Phys 18:8479–8490CrossRefGoogle Scholar
  17. 17.
    De La Pierre M, Pouchan C (2018) Theor Chem Acc 137:25CrossRefGoogle Scholar
  18. 18.
    Carbonniere P, Thicoipe S, Very T, Assfeld X (2012) Int J Quantum Chem 112:2221CrossRefGoogle Scholar
  19. 19.
    Thicoipe S, Carbonniere P, Pouchan C (2013) Phys Chem Chem Phys 15:11646CrossRefGoogle Scholar
  20. 20.
    Thicoipe S, Carbonniere P, Pouchan C (2014) Chem Phys Lett 591:243CrossRefGoogle Scholar
  21. 21.
    Thicoipe S, Carbonniere P, Pouchan C (2018) Theor Chem Acc 136:44CrossRefGoogle Scholar
  22. 22.
    Tomasi J, Persico M (1994) Chem Rev 94:2027CrossRefGoogle Scholar
  23. 23.
    Cammi R, Tomasi J (1995) J Comput Chem 16:1449CrossRefGoogle Scholar
  24. 24.
    Cancès E, Mennucci B, Tomasi J (1997) J Chem Phys 107:3032CrossRefGoogle Scholar
  25. 25.
    Begue D, Carbonniere P, Barone V, Pouchan C (2005) Chem Phys Lett 416:206CrossRefGoogle Scholar
  26. 26.
    Marchal R, Carbonniere P, Pouchan C (2009) J Chem Phys 131:114105CrossRefGoogle Scholar
  27. 27.
    Thicoipe S, Carbonniere P, Pouchan C (2013) J Phys Chem A 117:7236CrossRefGoogle Scholar
  28. 28.
    Frisch MJ, Trucks GW, Schelgel 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 J.M, Klene MJ, Knox E, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yasyev 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 O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, Revision A.1, Gaussian Inc., Wallingford, CTGoogle Scholar
  29. 29.
    Carbonniere P, Barone V (2004) Chem Phys Lett 399:226CrossRefGoogle Scholar
  30. 30.
    Carbonniere P, Lucca T, Pouchan C, Rega N, Barone V (2005) J Comput Chem 26:384CrossRefGoogle Scholar
  31. 31.
    Barone V, Carbonniere P, Pouchan C (2005) J Chem Phys 122:224308CrossRefGoogle Scholar
  32. 32.
    Raghavachari K, Trucks GW, Pople JA, Head-Gordon M (1989) Chem Phys Lett 157:479CrossRefGoogle Scholar
  33. 33.
    Becke AD (1993) J Chem Phys 98:5648CrossRefGoogle Scholar
  34. 34.
    Biczysko M, Panek P, Barone V (2009) Chem Phys Lett 475:105CrossRefGoogle Scholar
  35. 35.
    Barone V (2004) J Chem Phys 122:014108CrossRefGoogle Scholar
  36. 36.
    Pouchan C, Zaki K (1997) J Chem Phys 107:342CrossRefGoogle Scholar
  37. 37.
    Carbonnière P, Dargelos A, Pouchan C (2010) Theor Chem Acc 125:543CrossRefGoogle Scholar
  38. 38.
    Carbonnière P, Dargelos A, Pouchan C (2012) VCI-P code InterDeposit Digital N FR.001.090003.000.S.P.2012.000.31235, Interdeposit certification Feb 27, 2012, Paris, FranceGoogle Scholar
  39. 39.
    Schlegel HB, Iyengar SS, Li X, Millam JM, Voth GA, Scuseria GE, Frisch MJ (2002) J Chem Phys 117:8694CrossRefGoogle Scholar
  40. 40.
    Schlegel HB, Millam JM, Iyengar SS, Voth GA, Daniels AD, Scuseria GE, Frisch MJ (2001) J Chem Phys 114:9758CrossRefGoogle Scholar
  41. 41.
    Iyengar SS, Schlegel HB, Millam JM, Voth GA, Scuseria GE, Frisch MJ (2001) J Chem Phys 115:10291CrossRefGoogle Scholar
  42. 42.
    Schmitz M, Tavan P (2004) J Chem Phys 121:12233CrossRefGoogle Scholar
  43. 43.
    Schmitz M, Tavan P (2004) J Chem Phys 121:12247CrossRefGoogle Scholar
  44. 44.
    Carbonniere P, Dargelos A, Ciofini I, Adamo C, Pouchan C (2009) Phys Chem Chem Phys 11:4375CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.CNRS, UMR 5254, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les MatériauxUniversité de Pau et des Pays de l’AdourPauFrance
  2. 2.Department of Chemistry, Curtin Institute for ComputationCurtin UniversityPerthAustralia

Personalised recommendations