Theoretical Chemistry Accounts

, Volume 125, Issue 3–6, pp 253–268 | Cite as

Hydrogen bonding in the urea dimers and adenine–thymine DNA base pair: anharmonic effects in the intermolecular H-bond and intramolecular H-stretching vibrations

Regular Article


The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different (cyclic and asymmetric) urea dimers and for the adenine–thymine DNA base pair system have been studied using the second-order Møller–Plesset perturbation theory (MP2) method and different density functional theory (DFT) exchange–correlation (XC) functionals (BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V++** basis sets. The widely used a posteriori Boys–Bernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.


Urea dimer Adenine–thymine base pairs Anharmonic corrections H-stretching vibration BSSE effect 



This work was supported by the Grant of Romanian Ministry of Education and Research for young researcher, No: CEEX ET-30/08.10.2005, for which A.B. is gratefully acknowledged. A. B. is also thankful for the Grant of German Cancer Research Center (DKFZ) and for its support during his visit to carrying out this work. The author thanks Prof. Dr. Sándor Suhai for helpful comments on the manuscript.

Supplementary material

214_2009_645_MOESM1_ESM.pdf (893 kb)
Supplementary material 1 (PDF 892 kb)


  1. 1.
    Rose G, Fleming P, Banavar J, Martin A (2006) PNAS 103:16623CrossRefGoogle Scholar
  2. 2.
    Deechongkit S, Nguyen H, Dawson PE, Gruebele M, Kelly JW (2004) Nature 403:101CrossRefGoogle Scholar
  3. 3.
    Bende A, Suhai S (2005) Int J Quantum Chem 103(6):841CrossRefGoogle Scholar
  4. 4.
    Masunov A, Dannenberg JJ (1999) J Phys Chem A 103:178CrossRefGoogle Scholar
  5. 5.
    Masunov A, Dannenberg JJ (2000) J Phys Chem B 104:806CrossRefGoogle Scholar
  6. 6.
    Belosludov RV, Li Z-Q, Kawazoe Y (1999) Mol Eng 8:105CrossRefGoogle Scholar
  7. 7.
    Skurski P, Simons J (2001) J Chem Phys 115:10731CrossRefGoogle Scholar
  8. 8.
    Gavezzotti A (2003) CrystEngComm 5(76):429CrossRefGoogle Scholar
  9. 9.
    Caballero-Herrera A, Nilsson L (2006) J Mol Struct (THEOCHEM) 785(2-3):139CrossRefGoogle Scholar
  10. 10.
    Shukla A, Isaacs ED, Hamann DR, Platzman PM (2001) Phys Rev B 64:052101CrossRefGoogle Scholar
  11. 11.
    Rousseau B, Van Alsenoy C, Keuleers R, Desseyn HO (1998) J Phys Chem A 102:6540CrossRefGoogle Scholar
  12. 12.
    Keuleers R, Desseyn HO, Rousseau B, Van Alsenoy C (1999) J Phys Chem A 103:4621CrossRefGoogle Scholar
  13. 13.
    Wu K, Snijders JG, Lin C (2002) J Phys Chem B 106:8954CrossRefGoogle Scholar
  14. 14.
    Skurski P, Simons J (2001) J Chem Phys 115:8373CrossRefGoogle Scholar
  15. 15.
    Skurski P, Simons J (2002) J Chem Phys 116(14):6118CrossRefGoogle Scholar
  16. 16.
    Caballero-Herrera A, Nordstrand K, Berndt KD, Nilsson L (2005) Biophys J 89:842CrossRefGoogle Scholar
  17. 17.
    Šponer J, Jurečka P, Hobza P (2004) J Am Chem Soc 126:10142CrossRefGoogle Scholar
  18. 18.
    Podolyan Y, Nowak MJ, Lapinski L, Leszczynski J (2005) J Mol Struct 744–747:19CrossRefGoogle Scholar
  19. 19.
    Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (2000) J Am Chem Soc 122:4117CrossRefGoogle Scholar
  20. 20.
    Giese TJ, Sherer EC, Cramer CJ, York DM (2005) J Chem Theory Comput 1:1275CrossRefGoogle Scholar
  21. 21.
    Brauer B, Gerber RB, Kabeláč M, Hobza P, Bakker JM, Riziq AGA, de Vries MS (2005) J Phys Chem A 109:6974CrossRefGoogle Scholar
  22. 22.
    Bakker JM, Compagnon I, Meijer G, von Helden G, Kabeláč M, Hobza P, de Vries MS (2004) Phys Chem Chem Phys 6:2810CrossRefGoogle Scholar
  23. 23.
    Gorb L, Podolyan Y, Dziekonski P, Sokalski WA, Leszczynski J (2004) J Am Chem Soc 126:10119CrossRefGoogle Scholar
  24. 24.
    Müller A, Talbot F, Leutwyler S (2002) J Am Chem Soc 124:14486CrossRefGoogle Scholar
  25. 25.
    Hobza P, Halvas Z (2000) Chem Rew 100:4253CrossRefGoogle Scholar
  26. 26.
    Hobza P, Špirko V (2003) Phys Chem Chem Phys 5:1290CrossRefGoogle Scholar
  27. 27.
    Bende A, Vibók Á, Halász GJ, Suhai S (2004) Int J Quantum Chem 99(5):585CrossRefGoogle Scholar
  28. 28.
    Wang NX, Venkatesh K, Wilson AK (2006) J Phys Chem A 110:779CrossRefGoogle Scholar
  29. 29.
    Simon S, Bertran J, Sodupe M (2001) J Phys Chem A 105:4359CrossRefGoogle Scholar
  30. 30.
    Rekik N, Oujia B, Wójcik MJ (2008) Chem Phys 352:65CrossRefGoogle Scholar
  31. 31.
    Pelel L, Gerber RB (2008) J Chem Phys 128:165105CrossRefGoogle Scholar
  32. 32.
    Watanabe Y, Maeda S, Ohno K (2008) J Chem Phys 129:074315CrossRefGoogle Scholar
  33. 33.
    Lundell J, Latajka Z (2008) J Mol Struct 887:179CrossRefGoogle Scholar
  34. 34.
    Cremer D (2001) Mol Phys 99:1899CrossRefGoogle Scholar
  35. 35.
    Toulouse J, Colonna F, Savin A (2005) J Chem Phys 122:014110CrossRefGoogle Scholar
  36. 36.
    Chao SD, Li AH-T (2007) J Phys Chem A 111:9586CrossRefGoogle Scholar
  37. 37.
    van Mourik T, Gdanitz RJ (2002) J Chem Phys 116:9620CrossRefGoogle Scholar
  38. 38.
    Ireta J, Neugebauer J, Scheffler M (2004) J Phys Chem A 108:5692CrossRefGoogle Scholar
  39. 39.
    Johnson ER, Wolkow RA, Di Labio GA (2004) Chem Phys Lett 394:334CrossRefGoogle Scholar
  40. 40.
    Kang JK, Musgrave CB (2001) J Chem Phys 115:11040CrossRefGoogle Scholar
  41. 41.
    Hamprecht FA, Cohen AJ, Tozer DJ, Handy NC (1998) J Chem Phys 109:6264Google Scholar
  42. 42.
    Boese AD, Doltsinis NL, Handy NC, Sprik M (2000) J Chem Phys 112:1670Google Scholar
  43. 43.
    Boese AD, Handy NC (2001) J Chem Phys 114:5497; see also the supplementary material: EPAPS Document No. EGoogle Scholar
  44. 44.
    Perdew JP, Burke K, Ernzerhof M (1996) Phys Rev Lett 77:3865Google Scholar
  45. 45.
    Perdew JP, Burke K, Ernzerhof M (1997) Phys Rev Lett 78:1396Google Scholar
  46. 46.
    Jansen HB, Ros P (1969) Chem Phys Lett 3:140; Boys SB, Bernardi F (1970) Mol Phys 19:553Google Scholar
  47. 47.
    Gaussian 03, Revision C.02, 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, 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, Gaussian, Inc., Wallingford CT, 2004Google Scholar
  48. 48.
    Clabo DA Jr, Allen WD, Remington RB, Yamaguchi Y, Schaefer HF III (1988) Chem Phys 123:187CrossRefGoogle Scholar
  49. 49.
    Barone V (2005) J Chem Phys 122:014108CrossRefGoogle Scholar
  50. 50.
    Dunning TH Jr, Hay PJ (1976) In: Schaefer HF III (ed) Modern theoretical chemistry, vol 3. Plenum, New York, pp 1–28Google Scholar
  51. 51.
    Carbonniere P, Lucca T, Pouchan C, Rega N, Barone V (2005) J Comput Chem 26:384CrossRefGoogle Scholar
  52. 52.
    Begue D, Carbonniere P, Pouchan C (2005) J Phys Chem A 109:4611CrossRefGoogle Scholar
  53. 53.
    Barone V (2004) J Phys Chem A 108:4146CrossRefGoogle Scholar
  54. 54.
    Barone V (2004) Chem Phys Lett 383:528CrossRefGoogle Scholar
  55. 55.
    Pulay P (1983) Chem Phys Lett 100:151CrossRefGoogle Scholar
  56. 56.
    Hetzer G, Pulay P, Werner H-J (1998) Chem Phys Lett 290:143CrossRefGoogle Scholar
  57. 57.
    Schütz M, Hetzer G, Werner H-J (1999) J Chem Phys 111:5691CrossRefGoogle Scholar
  58. 58.
    Hetzer G, Schütz M, Stoll H, Werner H-J (2000) J Chem Phys 113:9443CrossRefGoogle Scholar
  59. 59.
    Werner H-J, Manby FR, Knowles PJ (2003) J Chem Phys 118:8149CrossRefGoogle Scholar
  60. 60.
    MOLPRO, version 2008.1, a package of ab initio programs, Werner H-J, Knowles PJ, Lindh R, Manby FR, Schütz M, Celani P, Korona T, Mitrushenkov A, Rauhut G, Adler TB, Amos RD, Bernhardsson A, Berning A, Cooper DL, Deegan MJO, Dobbyn AJ, Eckert F, Goll E, Hampel C, Hetzer G, Hrenar T, Knizia G, Köppl C, Liu Y, Lloyd AW, Mata RA, May AJ, McNicholas SJ, Meyer W, Mura ME, Nicklass A, Palmieri P, Pflüger K, Pitzer R, Reiher M, Schumann U, Stoll H, Stone AJ, Tarroni R, Thorsteinsson T, Wang M and Wolf A.
  61. 61.
    Holroyd LF, van Mourik T (2007) Chem Phys Lett 442:42CrossRefGoogle Scholar
  62. 62.
    Shields AE, van Mourik T (2007) J Phys Chem A 111:13272CrossRefGoogle Scholar
  63. 63.
    Hill JG, Platts JA (2008) Phys Chem Chem Phys 10:2785CrossRefGoogle Scholar
  64. 64.
    Schütz M, Rauhut G, Werner H-J (1998) J Phys Chem 102:5197Google Scholar
  65. 65.
    Grimme S (2006) J Comp Chem 27:1787CrossRefGoogle Scholar
  66. 66.
    Zhao Y, Truhlar DG (2007) Theor Chem Acc 120:215CrossRefGoogle Scholar
  67. 67.
    “NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.1.1”, Bylaska EJ, de Jong WA, Govind N, Kowalski K, Straatsma TP, Valiev M, Wang D, Apra E, Windus TL, Hammond J, Nichols P, Hirata S, Hackler MT, Zhao Y, Fan P-D, Harrison RJ, Dupuis M, Smith DMA, Nieplocha J, Tipparaju V, Krishnan M, Vazquez-Mayagoitia A, Wu Q, Van Voorhis T, Auer AA, Nooijen M, Crosby LD, Brown E, Cisneros G, Fann GI, Fruchtl H, Garza J, Hirao K, Kendall R, Nichols JA, Tsemekhman K, Wolinski K, Anchell J, Bernholdt D, Borowski P, Clark T, Clerc D, Dachsel H, Deegan M, Dyall K, Elwood D, Glendening E, Gutowski M, Hess A, Jaffe J, Johnson B, Ju J, Kobayashi R, Kutteh R, Lin Z, Littlefield R, Long X, Meng B, Nakajima T, Niu S, Pollack L, Rosing M, Sandrone G, Stave M, Taylor H, Thomas G, van Lenthe J, Wong A, and Zhang Z, Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA (2009)Google Scholar
  68. 68.
    Korth M, Grimme S (2009) J Chem Theory Comput 5:993CrossRefGoogle Scholar
  69. 69.
    Molden 4.7, Schaftenaar G, Noordik JH (2000) J Comput-Aided Mol Design 14:123Google Scholar
  70. 70.
    Gabedit 2.1.11, Allouche A-R, “Gabedit is a free Graphical User Interface for computational chemistry packages.” Available from
  71. 71.
    Dunning TH Jr (1989) J Chem Phys 90:1007CrossRefGoogle Scholar
  72. 72.
    Kendall RA, Dunning TH Jr, Harrison RJ (1992) J Chem Phys 96:6796CrossRefGoogle Scholar
  73. 73.
    Jalkanen KJ, Stephens PJ (1991) J Phys Chem 95:5446CrossRefGoogle Scholar
  74. 74.
    Sinha P, Boesch SE, Gu C, Wheeler RA, Wilson AK (2004) J Phys Chem A 108:9213CrossRefGoogle Scholar
  75. 75.
    Shui X, McFail-Isom L, Hu GG, Williams LD (1998) Biochem 37:8341CrossRefGoogle Scholar
  76. 76.
    Krishnan GM, Kühn O (2007) Chem Phys Lett 435:132CrossRefGoogle Scholar
  77. 77.
    Kabeláč M, Hobza P (2001) J Phys Chem B 105:5804CrossRefGoogle Scholar
  78. 78.
    Plützer C, Hünig I, Kleinermanns K, Nir E, de Vries MS (2003) Chem Phys Chem 4:838Google Scholar
  79. 79.
    Heyne K, Krishnan GM, Kühn O (2008) J Phys Chem B 112:7909CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Molecular and Biomolecular Physics DepartmentNational Institute for R&D of Isotopic and Molecular TechnologiesCluj-NapocaRomania
  2. 2.Molecular Biophysics DepartmentGerman Cancer Research CentreHeidelbergGermany

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