Advertisement

Theoretical Chemistry Accounts

, Volume 124, Issue 5–6, pp 319–330 | Cite as

Structural and electronic structure differences due to the O–H···O and O–H···S bond formation in selected benzamide derivatives: a first-principles molecular dynamics study

  • Aneta JezierskaEmail author
  • Jarosław J. Panek
  • Riccardo Mazzarello
Regular Article

Abstract

Density functional theory-based methods were employed to obtain static and dynamical descriptions of the molecular properties of 2-hydroxy-N-methylbenzamide and 2-hydroxy-N-methylthiobenzamide; compounds containing O–H···O and O–H···S strong, intramolecular hydrogen bonds. These compounds are important as analogues of commercial analgesic and antipyretic medicines. In the current study the classical Kohn–Sham method was applied to develop static models describing the geometric parameters and proton potentials. The topological analysis of the electron density was performed via atoms in molecules theory. Subsequently, Car–Parrinello molecular dynamics investigations were performed in vacuo and in the solid state. The geometric and spectroscopic properties were investigated and compared with available experimental data. The influence of quantum effects on the intramolecular hydrogen bond properties were studied via path integral molecular dynamics in the solid state for 2-hydroxy-N-methylbenzamide. We found that the proton behavior depends strongly on the type of acceptor: the sulfur-containing bridge has significantly smaller proton flexibility than the oxygen-bearing analogue, which is reflected in the electronic structure and bridge dynamics.

Keywords

Intramolecular hydrogen bond Atoms in molecules Car–Parrinello molecular dynamics (CPMD) Path integrals molecular dynamics (PIMD) 

Notes

Acknowledgments

We would like to thank Dr. Harald Forbert (Ruhr-Universität Bochum) for the program for dipole moment transformations. We also gratefully acknowledge the Academic Computer Center (TASK) in Gdańsk and the Poznań Supercomputing and Networking Center (PCSS) for providing CPU time and facilities.

Supplementary material

214_2009_612_MOESM1_ESM.pdf (189 kb)
Supplementary material 1 (PDF 190 kb)

References

  1. 1.
    Soldatos CR, Kales A, Bixler EO, Scharf MB, Kales JD (1978) Pharmacol 16:193–198CrossRefGoogle Scholar
  2. 2.
    Kirk RE, Othmer DF (1997) Kirk-Othmer encyclopedia of chemical technology, vol 21, 4th edn. Wiley, New York, pp 601–626Google Scholar
  3. 3.
    Way EL, Takemori AE, Smith GE Jr, Anderson HH, Brodie DC (1953) J Pharmacol Exp Ther 108:450–460Google Scholar
  4. 4.
    Fuente De La R, Sonawane ND, Arumainayagam D, Verkman AS (2006) Br J Pharmacol 149:551–559CrossRefGoogle Scholar
  5. 5.
    Zhu X-F, Wang J-S, Cai L-L, Zeng Y-X, Yang D (2006) Cancer Sci 97:84–89CrossRefGoogle Scholar
  6. 6.
    Agrawal VK, Sharma S (1984) Pharmazie 39:373–378Google Scholar
  7. 7.
    Brown ME, Fitzner JN, Stevens T, Chin W, Wright CD, Boyce JP (2008) Bioorg Med Chem 16:8760–8764CrossRefGoogle Scholar
  8. 8.
    Wagner G, Singer D, Weuffen W (1966) Pharmazie 21:161–166Google Scholar
  9. 9.
    Weuffen W, Wagner G, Singer D, Hellmuth L (1966) Pharmazie 21:477–482Google Scholar
  10. 10.
    Sur K, Shome SC (1971) Anal Chim Acta 57:201–208CrossRefGoogle Scholar
  11. 11.
    Sur K, Mazumdar M, Shome SC (1972) Anal Chim Acta 59:306–310CrossRefGoogle Scholar
  12. 12.
    Banerjee K, Raychaudhury S (1982) Bull Chem Soc Jpn 55:3621–3624CrossRefGoogle Scholar
  13. 13.
    Hay BP, Dixon DA, Vargas R, Garza J, Raymond KN (2001) Inorg Chem 40:3922–3935CrossRefGoogle Scholar
  14. 14.
    Padwa A, Beall LS, Heidelbaugh TM, Liu B, Sheehan SM (2000) J Org Chem 65:2684–2695CrossRefGoogle Scholar
  15. 15.
    Price SL (2009) Acc Chem Res 42:117–126CrossRefGoogle Scholar
  16. 16.
    Jeffrey GA (1997) An introduction to hydrogen bonding. Oxford University Press, New YorkGoogle Scholar
  17. 17.
    Grabowski S (2006) Hydrogen bonding—new insights. Challenges and advances in computational chemistry and physics 3. Springer, DordrechtGoogle Scholar
  18. 18.
    Hobza P, Havlas Z (2000) Chem Rev 100:4253CrossRefGoogle Scholar
  19. 19.
    Saam J, Tajkhorshid E, Hayashi S, Schulten K (2002) Biophys J 83:3097–3112CrossRefGoogle Scholar
  20. 20.
    Haas AH, Lancaster CRD (2004) Biophys J 87:4298–4315CrossRefGoogle Scholar
  21. 21.
    Betzel C, Gourinath S, Kumar P, Kaur P, Perbandt M, Eschenburg S, Singh TP (2001) Biochemistry 40:3080–3088CrossRefGoogle Scholar
  22. 22.
    Bertolasi V, Gilli P, Ferretti V, Gilli G (1996) Chem Eur J 2:925–934CrossRefGoogle Scholar
  23. 23.
    Tour JM, Kozaki M, Seminario JM (1998) J Am Chem Soc 120:8486–8493CrossRefGoogle Scholar
  24. 24.
    Alarcón SH, Olivieri AC, Sanz D, Claramunt RM, Elguero J (2004) J Mol Struct 705:1–9CrossRefGoogle Scholar
  25. 25.
    Sobczyk L, Grabowski SJ, Krygowski TM (2005) Chem Rev 105:3513–3560CrossRefGoogle Scholar
  26. 26.
    Hammes-Schiffer S (2001) Acc Chem Res 34:273–281CrossRefGoogle Scholar
  27. 27.
    Peters KS (2009) Acc Chem Res 42:89–96CrossRefGoogle Scholar
  28. 28.
    Iordanova N, Hammes-Schiffer S (2002) J Am Chem Soc 124:4848–4856CrossRefGoogle Scholar
  29. 29.
    Szatyłowicz H, Krygowski TM, Hobza P (2007) J Phys Chem A 111:170–175CrossRefGoogle Scholar
  30. 30.
    Szatyłowicz H, Krygowski TM, Zachara-Horeglad JE (2007) J Chem Inf Model 47:875–886CrossRefGoogle Scholar
  31. 31.
    Szatyłowicz H (2008) J Phys Org Chem 21:897–914CrossRefGoogle Scholar
  32. 32.
    Gilli G, Bellucci F, Ferretti V, Bertolasi V (1989) J Am Chem Soc 111:1023–1028CrossRefGoogle Scholar
  33. 33.
    Gilli P, Bertolasi V, Ferretti V, Gilli G (1994) J Am Chem Soc 116:909–915CrossRefGoogle Scholar
  34. 34.
    Jezierska A, Panek JJ (2009) J Comput Chem 30:1241–1250CrossRefGoogle Scholar
  35. 35.
    Steiner T (1998) Chem Commun 411–412Google Scholar
  36. 36.
    Pertlik F (1992) Z Kristallogr 202:17–23CrossRefGoogle Scholar
  37. 37.
    Steinwender E, Mikenda W (1990) Monatsh Chem 121:809–820CrossRefGoogle Scholar
  38. 38.
    Mikenda W, Pertlik F, Steinwender E (1993) Monatsh Chem 124:867–875CrossRefGoogle Scholar
  39. 39.
    Mikenda W, Steinwender E, Mereiter K (1995) Monatsh Chem 126:495–504CrossRefGoogle Scholar
  40. 40.
    Pertlik F (1990) Monatsh Chem 121:129–139CrossRefGoogle Scholar
  41. 41.
    Jezierska A, Novič M, Panek JJ (2009) Pol J Chem 83:799–819Google Scholar
  42. 42.
    Jezierska A, Panek JJ, Koll A (2008) Chem Phys Chem 9:839–846Google Scholar
  43. 43.
    Hohenberg P, Kohn W (1964) Phys Rev 136:B864–B871CrossRefGoogle Scholar
  44. 44.
    Kohn W, Sham LJ (1965) Phys Rev 140:A1133–A1138CrossRefGoogle Scholar
  45. 45.
    Car R, Parrinello M (1985) Phys Rev Lett 55:2471–2474CrossRefGoogle Scholar
  46. 46.
    Marx D, Parrinello M (1996) Science 271:179–181CrossRefGoogle Scholar
  47. 47.
    Becke AD (1993) J Chem Phys 98:5648–5652CrossRefGoogle Scholar
  48. 48.
    Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789CrossRefGoogle Scholar
  49. 49.
    Krishnan R, Binkley JS, Seeger R, Pople JA (1980) J Chem Phys 72:650–654CrossRefGoogle Scholar
  50. 50.
    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 C.02. Gaussian Inc., Wallingford, CTGoogle Scholar
  51. 51.
    Bader RFW (1990) Atoms in molecules. A quantum theory. Clarendon Press, OxfordGoogle Scholar
  52. 52.
    Bader RFW (1991) AIMPAC, suite of programs for the theory of atoms in molecules. McMaster University, Hamilton, ONGoogle Scholar
  53. 53.
    Perdew JP, Burke K, Ernzerhof M (1996) Phys Rev Lett 77:3865–3868CrossRefGoogle Scholar
  54. 54.
    Troullier N, Martins JL (1991) Phys Rev B 43:1993–2006CrossRefGoogle Scholar
  55. 55.
    Schlegel HB (1984) Theor Chim Acta 66:333–340CrossRefGoogle Scholar
  56. 56.
    Nosé S (1984) Mol Phys 52:255–268CrossRefGoogle Scholar
  57. 57.
    Nosé S (1984) J Chem Phys 81:511–519CrossRefGoogle Scholar
  58. 58.
    Hoover WG (1985) Phys Rev A 31:1695–1697CrossRefGoogle Scholar
  59. 59.
    Monkhorst HJ, Pack JD (1976) Phys Rev B 13:5188–5192CrossRefGoogle Scholar
  60. 60.
    Marx D, Parrinello M (1996) J Chem Phys 104:4077–4082CrossRefGoogle Scholar
  61. 61.
    Tuckerman ME, Marx D, Klein ML, Parrinello M (1996) J Chem Phys 104:5579–5588CrossRefGoogle Scholar
  62. 62.
    Tuckerman ME, Berne BJ, Martyna GJ, Klein ML (1993) J Chem Phys 99:2796–2808CrossRefGoogle Scholar
  63. 63.
    CPMD Copyright IBM Corp. 1990–2004, Copyright MPI fuer Festkoerperforschung Stuttgart 1997–2001Google Scholar
  64. 64.
    Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14:33–38CrossRefGoogle Scholar
  65. 65.
    Gnuplot, Copyright (C) 1986–1993, 1998, 2004 Williams T, Kelley C, Copyright (C) 2004–2007 Broeker HB, Campbell J, Cunningham R, Denholm D, Elber G, Fearick R, Grammes C, Hart L, Hecking L, Koenig T, Kotz D, Kubaitis E, Lang R, Lehmann A, Mai A, Steger C, Tkacik T, Van der Woude J, Van Zandt JR, Woo A, Merritt E, Mikulík P, Zellner JGoogle Scholar
  66. 66.
    Mennucci B, Tomasi J (1997) J Chem Phys 106:5151–5158CrossRefGoogle Scholar
  67. 67.
    Koch U, Popelier PLA (1995) J Phys Chem 99:9747–9754CrossRefGoogle Scholar
  68. 68.
    Biswal HS, Chakraborty S, Wategaonkar S (2008) J Chem Phys 129:184311CrossRefGoogle Scholar
  69. 69.
    Desiraju GR (2002) Acc Chem Res 35:565–573CrossRefGoogle Scholar
  70. 70.
    Goebel JR, Ault BS, Del Bene JE (2001) J Phys Chem A 105:11365–11370CrossRefGoogle Scholar
  71. 71.
    Posokhov Y, Gorski A, Spanget-Larsen J, Duus F, Hansen PE, Waluk J (2001) Chem Phys Lett 350:502–508CrossRefGoogle Scholar
  72. 72.
    Pauling LJ (1932) J Am Chem Soc 54:3570–3582CrossRefGoogle Scholar
  73. 73.
    Tangney P, Scandolo S (2002) J Chem Phys 116:14–24CrossRefGoogle Scholar
  74. 74.
    Wathelet V, Champagne B, Mosley DH, André J-M, Massidda S (1997) Chem Phys Lett 275:506–512CrossRefGoogle Scholar
  75. 75.
    Gaigeot M-P, Sprik M (2003) J Phys Chem B 107:10344–10358CrossRefGoogle Scholar
  76. 76.
    Benoit M, Marx D (2005) Chem Phys Chem 6:1738–1741Google Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Aneta Jezierska
    • 1
    • 2
    Email author
  • Jarosław J. Panek
    • 2
  • Riccardo Mazzarello
    • 3
  1. 1.National Institute of ChemistryLjubljanaSlovenia
  2. 2.Faculty of ChemistryUniversity of WrocławWrocławPoland
  3. 3.Computational Science, Department of Chemistry and Applied BiosciencesETH ZurichLuganoSwitzerland

Personalised recommendations