Skip to main content
SpringerLink
Log in

Interaction of Uracil with LiF and Water Studied by Density Functional Theory Study on Anionic Complexes

  • Original Paper
  • Published:
Journal of Cluster Science Aims and scope Submit manuscript

Abstract

We investigated the interactions of uracil with LiF and water using density functional calculations and determined the structures of (Ura)−LiF(H2O)n (n = 0–6) complexes. In all clusters from n = 0 to 6, Li+ of LiF unit binds directly to the O4 site of uracil via electrostatic interaction. (Ura)−LiF connects one water molecule via F− to form a sandwich structure. When the water number reaches 2, the interaction strength between uracil and LiF decreased significantly. Li+ and F− always stay together that exist as contact ion pairs. Excess electrons were found on C6, C4, and both O sites of uracil in NPA charge studies.

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
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Data Availability

All data generated or analyzed during this study are included in this published article and in the Supplementary Material.

References

  1. A. Savelyev and A. D. MacKerell (2015). J. Phys. Chem. Lett. 6, 212.

    Article  CAS  PubMed  Google Scholar 

  2. S. Sardar, E. Jabeen, A. Mumtaz, M. Yasinzai, and J.-M. Leveque (2020). Synth. J. Mol. Liq. 300, 112–255.

    Google Scholar 

  3. C. Kalaivanan, M. Sankarganesh, M. Y. Suvaikin, G. B. Karthi, S. Gurusamy, R. Subramanian, and R. N. Asha (2020). J. Mol. Liq. 320, 114423.

    Article  CAS  Google Scholar 

  4. X. Hu, H. Li, L. Zhang, and S. Han (2007). J. Phys. Chem. B. 111, 9347.

    Article  CAS  PubMed  Google Scholar 

  5. I. Morfin, F. Horkay, P. J. Basser, F. Bley, A.-M. Hecht, C. Rochas, and E. Geissler (2004). Biophys. J. 87, 2897.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. V. Andrushchenko and P. Bouř (2009). J. Phys. Chem. B. 113, 283.

    Article  CAS  PubMed  Google Scholar 

  7. J. Burda, J. Šponer, and J. Leszczynski (Computational Approach, 2012), pp. 1277–1308.

  8. M. Kabeláč and P. Hobza (2006). J. Phys. Chem. B. 110, 14515.

    Article  PubMed  Google Scholar 

  9. C. Trujillo, A. M. Lamsabhi, O. Mó, M. Yáñez, and J.- Y. Salpin (2011). Int. J. Mass. Spectrom. 306, 27.

  10. N. Russo, M. Toscano, and A. Grand (2001). J. Am. Chem. Soc. 123, 10272.

    Article  CAS  PubMed  Google Scholar 

  11. B. A. Cerda and C. Wesdemiotis (1996). J. Am. Chem. Soc. 118, 11884.

    Article  CAS  Google Scholar 

  12. R. Ghiasi, M. Monajjem, F. Asadian, and H. Passdar (2004). J. Chem. Res. 2004, 445.

    Article  Google Scholar 

  13. W. Zhu, X. Luo, C. M. Puah, X. Tan, J. Shen, J. Gu, K. Chen, and H. Jiang (2004). J. Phys. Chem. A. 108, 4008.

    Article  CAS  Google Scholar 

  14. A. A. Zinchenko and K. Yoshikawa (2005). Biophys. J. 88, 4118.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. D. E. Draper, D. Grilley, and A. M. Soto (2005). Annu. Rev. Bioph. Biom. 34, 221.

    Article  CAS  Google Scholar 

  16. K. J. Koch, T. Aggerholm, S. C. Nanita, and R. G. Cooks (2002). J. Mass. Spectrom. 37, 676.

    Article  CAS  PubMed  Google Scholar 

  17. S. Rochut, C. Pepe, J.-P. Paumard, and J.-C. Tabet (2004). Rapid Commun. Mass. Sp. 18, 1686.

    Article  CAS  Google Scholar 

  18. K. Rajabi, E. A. L. Gillis, and T. D. Fridgen (2010). J. Phys. Chem. A. 114, 3449.

    Article  CAS  PubMed  Google Scholar 

  19. M. T. Rodgers and P. B. Armentrout (2000). J. Am. Chem. Soc. 122, 8548.

    Article  CAS  Google Scholar 

  20. Z. Yang and M. T. Rodgers (2004). J. Am. Chem. Soc. 126, 16217.

    Article  CAS  PubMed  Google Scholar 

  21. Z. Yang and M. T. Rodgers (2006). J. Phys. Chem. A. 110, 1455.

    Article  CAS  PubMed  Google Scholar 

  22. Z. Yang and M. T. Rodgers (2012). Phys. Chem. Chem. Phys. 14, 4517.

    Article  CAS  PubMed  Google Scholar 

  23. E. A. L. Gillis, M. Demireva, K. Nanda, G. Beran, E. R. Williams, and T. D. Fridgen (2012). Phys. Chem. Chem. Phys. 14, 3304.

    Article  CAS  PubMed  Google Scholar 

  24. J. E. D. Bene (1984). J. Phys. Chem. 88, 5927.

    Article  Google Scholar 

  25. M. T. Rodgers and P. B. Armentrout (2007). Int. J. Mass. Spectrom. 267, 167.

    Article  CAS  Google Scholar 

  26. N. Russo, M. Toscano, and A. Grand (2001). J. Phys. Chem. B 105, 4735.

    Article  CAS  Google Scholar 

  27. G.- Y. Lee (2002). B. Korean. Chem. Soc. 23, 1023.

  28. H. Farrokhpour and S. Khoshkhou (2021). Spectrochim. Acta. A. 244, 118862.

    Article  CAS  Google Scholar 

  29. E. A. L. Gillis, K. Rajabi, and T. D. Fridgen (2009). J. Phys. Chem. A. 113, 824.

    Article  CAS  PubMed  Google Scholar 

  30. M. Gebala, G. M. Giambaşu, J. Lipfert, N. Bisaria, S. Bonilla, G. Li, D. M. York, and D. Herschlag (2015). J. Am. Chem. Soc. 137, 14705.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. A. Savelyev and G. A. Papoian (2006). J. Am. Chem. Soc. 128, 14506.

    Article  CAS  PubMed  Google Scholar 

  32. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, and M. A. Robb (2009). Gaussian 09.

  33. S. Grimmean, J. Antony, S. Ehrlicdh, and H. Krieg (2010). J. Chem. Phys. 132, 154104.

    Article  Google Scholar 

  34. E. S. Kryachko, M. T. Nguyen, and T. Zeegers-Huyskens (2001). J. Phys. Chem. A. 105, 1288.

    Article  CAS  Google Scholar 

  35. R. D. Brown, P. D. Godfrey, D. McNaughton, and A. P. Pierlot (1988). J. Am. Chem. Soc. 110, 2329.

    Article  CAS  Google Scholar 

  36. O. A. Vydrov, J. Heyd, A. V. Krukau, and G. E. Scuseria (2006). J. Chem. Phys. 125, 074106.

    Article  PubMed  Google Scholar 

  37. O. A. Vydrov and G. E. Scuseria (2006). J. Chem. Phys. 125, 234109.

    Article  PubMed  Google Scholar 

  38. O. A. Vydrov, G. E. Scuseria, and J. P. Perdew (2007). J. Chem. Phys. 126, 154109.

    Article  PubMed  Google Scholar 

  39. J.-D. Chai and M. Head-Gordon (2008). Phys. Chem. Chem. Phys. 10, 6615.

    Article  CAS  PubMed  Google Scholar 

  40. E. R. Johnson, S. Keinan, P. Mori-Sánchez, J. Contreras-García, A. J. Cohen, and W. Yang (2010). J. Am. Chem. Soc. 132, 6498.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. R. F. W. Bader (1991). Chem. Rev. 91, 893.

    Article  CAS  Google Scholar 

  42. M. Z. Hopffgarten and G. Frenking (2012). Wires. Comput. Mol. Sci. 2, 43.

    Article  Google Scholar 

  43. T. Lu and F. Chen (2012). J. Comput. Chem. 33, 580.

    Article  PubMed  Google Scholar 

  44. R.-Z. Li, C.- W. Liu, Y. Q. Gao, H. Jiang, H.- G. Xu, and W.- J. Zheng (2013). J. Am. Chem. Soc. 135, 5190.

  45. J. Akola, M. Manninen, H. Häkkinen, U. Landman, X. Li, and L. S. Wang (2000). Phys. Rev. B 62, 13216.

    Article  CAS  Google Scholar 

  46. J. A. Sordo (2001). J. Mol. Struct. (Theochem) 537, 245.

    Article  CAS  Google Scholar 

  47. K. Vanommeslaeghe, P. Mignon, S. Loverix, D. Tourwé, and P. Geerlings (2006). J. Chem. Theory. Comput. 2, 1444.

    Article  CAS  PubMed  Google Scholar 

  48. R.-Z. Li, Y.-Y. Liu, and M. Yang (2017). Comput Theor. Chem. 1115, 119.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Natural Science Foundation of Shaanxi, China (Grant No. 2019JM-292). Part of the theoretical calculations was conducted on the ScGrid and DeepComp 7000 of the Supercomputing Center, Computer Network Information Center of the Chinese Academy of Sciences.

Author information

Authors and Affiliations

  1. School of Environmental and Chemical Engineering, Xi’an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi’an Polytechnic University, Xi’an, 710048, People’s Republic of China

    Xiao-Yang Xu, Ren-Zhong Li, Liang Lu & Yu Cheng

Authors
  1. Xiao-Yang Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ren-Zhong Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Liang Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yu Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ren-Zhong Li.

Ethics declarations

Conflict of interest

There are no conflicts of interest to declare.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 13186 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Xu, XY., Li, RZ., Lu, L. et al. Interaction of Uracil with LiF and Water Studied by Density Functional Theory Study on Anionic Complexes. J Clust Sci 34, 1249–1258 (2023). https://doi.org/10.1007/s10876-022-02296-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10876-022-02296-5

Keywords

Search

Navigation