Skip to main content
SpringerLink
Log in

Molecular modeling of dipeptide and its analogous systems with water

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Intermolecular hydrogen-bond interactions in the monohydrated complexes of formamide, N-methylacetamide and glycylglycine have been studied using ab initio and DFT methods. The geometries were optimized using second-order Møller–Plesset perturbation theory and the B3LYP DFT functional with the 6-311++G** basis set. It is observed that hydrogen-bond interactions at the carbonyl group of the peptide moiety are stronger than those at the amino group of the formamide and N-methylacetamide molecules. Because of the presence of cyclic hydrogen-bonding interactions in glycylglycine, the interaction at the amino group is higher than at the carbonyl. The 13C and 15N NMR shielding values were calculated for the non-hydrated and monohydrated complexes. Condensed Fukui functions have also been calculated for non-hydrated formamide, N-methylacetamide and glycylglycine molecules at the B3LYP/6-311++G** level of theory, and the results are discussed.

Figure Structure of hydrated glycylglycine dipeptide

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

Similar content being viewed by others

References

  1. Jarrold ME (1999) Acc Chem Res 32:360–367

    Article  CAS  Google Scholar 

  2. Daune M (1999) Molecular biophysics. Oxford University Press, Oxford

  3. Lovas FJ, Suenram RD, Fraser GT (1988) J Chem Phys 88:722–729

    Article  CAS  Google Scholar 

  4. Fraser GT, Suenram RD, Lovas FJ (1988) J Mol Struct 189:165–172

    Article  CAS  Google Scholar 

  5. Engdahl A, Nelander B, Astrand PO (1993) J Chem Phys 99:4894–4907

    Article  CAS  Google Scholar 

  6. Sieler G, Schweitzer-Stenner R (1997) J Am Chem Soc 119:1720–1726

    Article  CAS  Google Scholar 

  7. Kameda T, Takeda N, Ando S, Ando I, Hashizume D, Ohashi Y (1998) Biopolymers 45:333–339

    Article  CAS  Google Scholar 

  8. Manas ES, Getahun Z, Wright WW, de Grado WF, Vanderkooi JM (2000) J Am Chem Soc 122:9883–9890

    Article  CAS  Google Scholar 

  9. Dixon DA, Dobbs KD, Valentini JJ (1994) J Phys Chem 98:13435–13439

    CAS  Google Scholar 

  10. Besley NA, Hirst JD (1999) J Am Chem Soc 121:8559–8566

    Article  CAS  Google Scholar 

  11. Weir AF, Lowery AH, Williams RW (2001) Biopolymers 58:577–591

    Article  CAS  PubMed  Google Scholar 

  12. Nemukhin AV, Grigorenko BL, Bochenkova AV, Topol IA, Burt SK (2002) J Mol Struct (Theochem) 581:167–175

    Google Scholar 

  13. Fu A, Du D, Zhou Z (2003) J Mol Struct 623:315–325

    Article  CAS  Google Scholar 

  14. Lecomte F, Lucas G, Gregoire G, Schermann JP, Desfrancois C (2002) Eur Phys J D 20:449-457

    Article  CAS  Google Scholar 

  15. Tazaki K, Shimizu K (1998) J Phys Chem B 102:6419–6424

    Article  CAS  Google Scholar 

  16. Apostolakis J, Ferrara P, Caflisch A (1999) J Chem Phys 110:2099–2108

    Article  CAS  Google Scholar 

  17. Kalko SG, Guardia E, Padro JA (1999) J Phys Chem B 103:3935–3941

    Article  CAS  Google Scholar 

  18. Abramov YA, Volkov A, Wu G, Coppens P (2000) J Phys Chem B 104:2183–2188

    Article  CAS  Google Scholar 

  19. Chaudhuri P, Canuto S (2002) J Mol Struct (Theochem) 577:267–279

    Google Scholar 

  20. Møller C, Plesset MS (1934) Phys Rev 46:618–622

    Article  Google Scholar 

  21. Becke AD (1993) J Chem Phys 98:5648–5652

    CAS  Google Scholar 

  22. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789

    Article  CAS  Google Scholar 

  23. Boys SF, Bernardi F (1970) Mol Phys 19:553–566

    Google Scholar 

  24. Sedano PS (2001) Doctoral dissertation. Universitat de Girona, Spain

  25. Kulkarni SA, Bartolotti LJ, Pathak RK, (2003) Chem Phys Lett 372:620–626

    Article  CAS  Google Scholar 

  26. Ditchfield R (1974) Mol Phys 27:789–807

    CAS  Google Scholar 

  27. Wolinski K, Hinton JF, Pulay P (1990) J Am Chem Soc 112:8251–8260

    CAS  Google Scholar 

  28. Yang W, Mortier WJ (1986) J Am Chem Soc 108:5708–5711

    CAS  Google Scholar 

  29. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery Jr JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels JD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Rega N, Salvador P, Dannenberg JJ, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (2001) Gaussian 98, Revision A.11.2. Gaussian, Pittsburgh, PA

  30. Schaftenaar G, Noordik JH (2000) J Comput-Aided Mol Des 14:123–134

    Google Scholar 

  31. Scheiner S (1997) Hydrogen bonding: a theoretical perspective. Oxford University Press, New York

    Google Scholar 

  32. MacArthur MW, Thorton JM (1996) J Mol Biol 264:1180–1195

    Article  CAS  PubMed  Google Scholar 

  33. Senthilkumar K, Kolandaivel P (2002) Mol Phys 100:3817–3822

    Article  CAS  Google Scholar 

  34. Basch H, Stevens WJ (1990) Chem Phys Lett 169:275–280

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank Department of Science and Technology, Government of India, (DST) for financial assistance in the form of project (SP/S1/H-27/99) to complete this work.

Author information

Authors and Affiliations

  1. Department of Physics, Bharathiar University, Coimbatore, 641 046, India

    Paranthaman Selvarengan & Ponmalai Gounder Kolandaivel

Authors
  1. Paranthaman Selvarengan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ponmalai Gounder Kolandaivel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ponmalai Gounder Kolandaivel.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Selvarengan, P., Kolandaivel, P.G. Molecular modeling of dipeptide and its analogous systems with water. J Mol Model 10, 198–203 (2004). https://doi.org/10.1007/s00894-004-0184-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-004-0184-y

Keywords

Search

Navigation