Skip to main content
SpringerLink
Log in

Density functional theory study of 1:1 glycine-water complexes in the gas phase and in solution

  • Articles
  • Published:
Science China Chemistry Aims and scope Submit manuscript

Abstract

We present a systematic study of 1:1 glycine-water complexes involving all possible glycine conformers. The complex geometries are fully optimized for the first time both in the gas phase and in solution using three DFT methods (B3LYP, PBE1PBE, X3LYP) and the MP2 method. We calculate the G3 energies and use them as the reference data to gauge hydrogen bond strength in the gas phase. The solvent effects are treated via the integral equation formalism-polarizable continuum model (IEF-PCM). Altogether, we locate fifty-two unique nonionized (N) structures and six zwitterionic (Z) structures in the gas phase, and fifty-five N structures and thirteen Z structures in solution. Both correlation and solvation are shown to be important in geometry determination. We found that in the gas phase, a water molecule binds more strongly to the carboxylic acid group of glycine than to its amine group, whereas in solution phase the reverse is true. The most stable Z structure is isoenergetic with the most stable N structure.

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

Similar content being viewed by others

References

  1. Zhang H, Zhou Z, Shi Y. Density functional theory study of the hydrogen-bonding interaction of 1:1 complexes of alanine with water. J Phys Chem A, 2004, 108: 6735–6743

    Article  CAS  Google Scholar 

  2. Degtyarenko IM, Jalkanen KJ, Gurtovenko AA, Nieminen RM. L-alanine in a droplet of water: A density-functional molecular dynamics study. J Phys Chem B, 2007, 111: 4227–4234

    Article  CAS  Google Scholar 

  3. Ji N, Shen YR. Sum frequency vibrational spectroscopy of leucine molecules adsorbed at air-water interface. J Chem Phys, 2004, 120: 7107–7112

    Article  CAS  Google Scholar 

  4. Zhang P, Han SH, Zhang Y, Ford RC, Li JC. Neutron spectroscopic and Raman studies of interaction between water and proline. Chem Phys, 2008, 345: 196–199

    Article  CAS  Google Scholar 

  5. Furić K, Mohaček V, Bonifačić M, Štefanić I. Raman-spectroscopic study of H2O and D2O water solutions of glycine. J Mol Struct, 1992, 267: 39–44

    Article  Google Scholar 

  6. Khurgin YI, Kudryashova VA, Zavizion VA. Study of intermolecular interactions in aqueous solutions by millimeter spectroscopy. 6. Negative hydration of the glycine zwitterions. Russ Chem Bull, 1997, 46: 1248–1250

    Article  CAS  Google Scholar 

  7. Sasaki M, Kameda Y, Yaegashi M, Usuki T. Hydration structure around the methylene group of glycine molecule. Bull Chem Soc Jpn, 2003, 76: 2293–2299

    Article  CAS  Google Scholar 

  8. Kameda Y, Ebata H, Usuki T, Uemura O, Misawa M. Hydration structure of glycine molecules in concentrated aqueous solutions. Bull Chem Soc Jpn, 1994, 67: 3159–3164

    Article  CAS  Google Scholar 

  9. Parsons MT, Koga Y. Hydration number of glycine in aqueous solution: An experimental estimate. J Chem Phys, 2005, 123: 234504

    Article  CAS  Google Scholar 

  10. Alonso JL, Cocinero EJ, Lesarri A, Sanz ME, Lopez JC. The glycine-water complex. Angew Chem Int Ed, 2006, 45: 3471–3474

    Article  CAS  Google Scholar 

  11. Ramaekers R, Pajak J, Lambie B, Maes G. Neutral and zwitterionic glycine.H2O complexes: A theoretical and matrix-isolation Fourier transform infrared study. J Chem Phys, 2004, 120: 4182–4193

    Article  CAS  Google Scholar 

  12. Jensen JH, Gordon MS. On the number of water molecules necessary to stabilize the glycine zwitterion. J Am Chem Soc, 1995, 117: 8159–8170

    Article  CAS  Google Scholar 

  13. Basch H, Stevens WJ. The structure of glycine water H-bonded complexes. Chem Phys Lett, 1990, 169: 275–280

    Article  CAS  Google Scholar 

  14. Tortonda FR, Pascual-Ahuir JL, Silla E, Tuñón I. Why is glycine a zwitterion in aqueous solution? A theoretical study of solvent stabilizing factors. Chem Phys Lett, 1996, 260: 21–26

    Article  CAS  Google Scholar 

  15. Wang WZ, Zheng WX, Pu XM, Wong NB, Tian AM. The 1:1 glycine-water complex: some theoretical observations. J Mol Struct (Theochem), 2002, 618: 235–244

    Article  CAS  Google Scholar 

  16. Wang WZ, Pu XM, Zheng WX, Wong NB, Tian AM. Some theoretical observations on the 1:1 glycine zwitterion-water complex. J Mol Struct (Theochem), 2003, 626: 127–132

    Article  CAS  Google Scholar 

  17. Twari S, Mishra PC, Suhai S. Solvent effect of aqueous media on properties of glycine: Significance of specific and bulk solvent effects, and geometry optimization in aqueous media. Int J Quantum Chem, 2008, 108: 1004–1016

    Article  CAS  Google Scholar 

  18. Bachrach SM. Microsolvation of glycine: A DFT study. J Phys Chem A, 2008, 112: 3722–3730

    Article  CAS  Google Scholar 

  19. Aikens CM, Gordon MS. Incremental solvation of nonionized and zwitterionic glycine. J Am Chem Soc, 2006, 128: 12835–12850

    Article  CAS  Google Scholar 

  20. Mezei M, Mehrotra PK, Beveridge DL. Monte Carlo computer simulation of the aqueous hydration of the glycine zwitterion at 25 °C. J Biomol Struct Dyn, 1984, 2: 1–27

    CAS  Google Scholar 

  21. Ding Y, Krogh-Jespersen K. The 1:1 glycine zwitterion-water complex: An ab initio electronic structure study. J Comput Chem, 1996, 17: 338–349

    Article  CAS  Google Scholar 

  22. Bandyopadhyay P. Gordon MS. A combined discrete/continuum solvation model: Application to glycine. J Chem Phys, 2000, 113: 1104–1109

    Article  CAS  Google Scholar 

  23. Bandyopadhyay P, Gordon MS, Mennucci B, Tomasi J. An integrated effective fragment-polarizable continuum approach to solvation: Theory and application to glycine. J Chem Phys, 2002, 116: 5023–5032

    Article  CAS  Google Scholar 

  24. Cui Q. Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine. J Chem Phys, 2002, 117: 4720–4728

    Article  CAS  Google Scholar 

  25. Rzepa HS, Yi MY. An AM1 and PM3 molecular orbital and self-consistent reaction-field study of the aqueous solvation of glycine, alanine and proline in their neutral and zwitterionic forms. J Chem Soc Perkin Trans 2, 1991, 531–537

  26. Iijima K, Tanaka K, Onuma S. Main conformer of gaseous glycine: molecular structure and rotational barrier from electron diffraction data and rotational constants. J Mol Struct, 1991, 246: 257–266

    Article  CAS  Google Scholar 

  27. Suenram RD, Lovas FJ. Millimeter wave spectrum of glycine. A new conformer. J Am Chem Soc, 1980, 102: 7180–7184

    Article  CAS  Google Scholar 

  28. Albrecht G, Corey RB. The crystal structure of glycine. J Am Chem Soc, 1939, 61: 1087–1103

    Article  CAS  Google Scholar 

  29. Marsh RE. A refinement of the crystal structure of glycine. Acta Crystallogr, 1958, 11: 654–663

    Article  CAS  Google Scholar 

  30. Jönsson PG, Kvick Å. Precision neutron diffraction structure determination of protein and nucleic acid components. III. The crystal and molecular structure of the amino acid α-glycine. Acta Crystallogr Sect B, 1972, 28: 1827–1833

    Article  Google Scholar 

  31. Hückel W. Theoretical Principles of Organic Chemistry. Vol II. New York: Elsevier, 1958

    Google Scholar 

  32. Diken EG, Hammer NI, Johnson MA. Preparation and photoelectron spectrum of the glycine molecular anion: Assignment to a dipole-bound electron species with a high-dipole moment, non-zwitterionic form of the neutral core. J Chem Phys, 2004, 120, 9899–9902

    Article  CAS  Google Scholar 

  33. Teh CK, Sipior J, Sulkes M. Spectroscopy of tryptophan in supersonic expansions—addition of solvent molecules. J Phys Chem, 1989, 93, 5393–5400

    Article  CAS  Google Scholar 

  34. Lee C, Yang W, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B, 1988, 37: 785–789

    Article  CAS  Google Scholar 

  35. Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A, 1988, 38: 3098–3100

    Article  CAS  Google Scholar 

  36. Becke AD. Density-functional for thermochemistry. III. The role of exact exchange. J Chem Phys, 1993, 98: 5648–5652

    Article  CAS  Google Scholar 

  37. Burke K, Ernzerhof M, Perdew JP. Generalized gradient approximation made simple. Phys Rev Lett, 1996, 77: 3865–3868

    Article  Google Scholar 

  38. Adamo C, Barone V. Toward reliable density functional methods without adjustable parameters: The PBE0 model. J Chem Phys, 1999, 110: 6158–6170

    Article  CAS  Google Scholar 

  39. Xu X, Zhang QS, Muller RP, Goddard III W A. An extended hybrid density functional X3LYP with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems. J Chem Phys, 2005, 122: 014105

    Article  CAS  Google Scholar 

  40. Xu X, Goddard III WA. The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. Proc Natl Acad Sci USA, 2004, 101: 2673–2677

    Article  CAS  Google Scholar 

  41. Xu X, Goddard III WA. Bonding properties of the water dimer: A comparative study of density functional theories. J Phys Chem A, 2004, 108: 2305–2313

    Article  CAS  Google Scholar 

  42. Su JT, Xu X, Goddard III WA. Accurate energies and structures for large water clusters using the X3LYP hybrid density functional. J Phys Chem A, 2004, 108: 10518–10526

    Article  CAS  Google Scholar 

  43. Curtiss LA, Raghavachari K, Redfern PC, Rassolov V, Pople JA. Gaussian-3 (G3) theory for molecules containing first and second-row atoms. J Chem Phys, 1998, 109: 7764–7776

    Article  CAS  Google Scholar 

  44. Mennucci B, Tomasi J. Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries. J Chem Phys, 1997, 106: 5151–5158

    Article  CAS  Google Scholar 

  45. Cancès MT, Mennucci B, Tomasi J. A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics. J Chem Phys, 1997, 107: 3032–3041

    Article  Google Scholar 

  46. Cossi M, Barone V, Mennucci B, Tomasi J. Ab initio study of ionic solutions by a polarizable continuum dielectric model. Chem Phys Lett, 1998, 286: 253–260

    Article  CAS  Google Scholar 

  47. Császár AG. Conformers of gaseous glycine. J Am Chem Soc, 1992, 114: 9568–9575

    Article  Google Scholar 

  48. Hariharan PC, Pople JA. The influence of polarization functions on molecular orbital hydrogenation energies. Theor Chim Acta, 1973, 28: 213–222

    Article  CAS  Google Scholar 

  49. Clark T, Chandrasekhar J, Spitznagel GW, Schleyer P v R. Efficient diffuse function-augmented basis sets for anion calculations. III. The 3–21+G basis set for first-row elements, Li-F. J Comput Chem, 1983, 4: 294–301

    Article  CAS  Google Scholar 

  50. Woon DE, Dunning TH. Gaussian basis sets for use in correlated molecular calculations. III. The atomic aluminum through argon. J Chem Phys, 1993, 98: 1358–1371

    Article  CAS  Google Scholar 

  51. Kendall RA, Dunning TH, Harrison RJ. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J Chem Phys, 1992, 96: 6796–6806

    Article  CAS  Google Scholar 

  52. Ke HW, Rao L, Xu X, Yan YJ. Theoretical study of glycine conformers. J Theor Comp Chem, 2008, 7: 889–909

    Article  CAS  Google Scholar 

  53. Rao L, Ke HW, Gang F, Xu X, Yan YJ. Performance of several density functional theory methods on describing hydrogen-bond interactions. J Comp Theor Chem, 2009, 5: 86–96

    Article  CAS  Google Scholar 

  54. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JAJr, 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. Gaussian 03, revision D.01, Gaussian, Inc., Wallingford CT, 2004

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China

    HongWei Ke & YiJing Yan

  2. State Key Laboratory for Physical Chemistry of Solid Surfaces and Department of Chemistry, Xiamen University, Xiamen, 361005, China

    Li Rao & Xin Xu

Authors
  1. HongWei Ke
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Li Rao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xin Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. YiJing Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Xin Xu or YiJing Yan.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ke, H., Rao, L., Xu, X. et al. Density functional theory study of 1:1 glycine-water complexes in the gas phase and in solution. Sci. China Chem. 53, 383–395 (2010). https://doi.org/10.1007/s11426-010-0065-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11426-010-0065-4

Keywords

Search

Navigation