Skip to main content
SpringerLink
Log in

Barrier-free molecular reorientations in polyhedral water clusters

  • Original Research
  • Published:
Structural Chemistry Aims and scope Submit manuscript

Abstract

The structural stability of the weakest bonded configurations of water clusters in the form of gas hydrate cavities D and T, as well as in the form of Kelvin’s polyhedron, was tested using the local geometric optimization with the polarizable force field AMOEBA. A number of different barrier-free molecular rearrangements were observed. Most of the configurations changed their shapes, forming surface defects of the same type. But the main attention is paid to the concerted molecular reorientations leading to the proton shift along hydrogen bonds. A number of statements about the topology of the hydrogen-bonded network are rigorously proved. It is concluded that the structural stability of configurations and the features of structural transformations are basically determined by the arrangement of the homodromic hydrogen-bonded water rings. The stability of the configurations, which retained their original shape during local geometric optimization, was studied by the molecular dynamics method with a gradual increase in temperature. Some interesting effects were found. This is the stabilizing locking of the most polarized configurations, as well as very intense amplitude oscillations of the free OH group at the end of two-bond flips.

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
Fig. 9

Similar content being viewed by others

Availability of data and material

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Code availability

The code used can be accessed in the TINKER Software Tools for Molecular Design. Version 6.2, VMD 1.9.3.

References

  1. Debenedetti PG (2003) Supercooled and glassy water. J Phys Condens Matter 15:R1669–R1726. https://doi.org/10.1063/1.1595053

    Article  CAS  Google Scholar 

  2. Smith JD, Cappa CD, Wilson KR, Messer BM, Cohen RC, Saykally RC (2004) Energetics of hydrogen bond network rearrangements in liquid water. Science 306:851–853. https://doi.org/10.1126/science.1102560

    Article  CAS  PubMed  Google Scholar 

  3. Malenkov G (2009) Liquid water and ices: understanding the structure and physical properties. J Phys: Condens Matter 21:283101. https://doi.org/10.1088/0953-8984/21/28/283101

    Article  CAS  PubMed  Google Scholar 

  4. Gallo P, Arnann-Winkel K, Angell CA et al (2016) Water: a tale of two liquids. Chem Rev 116:7463–7500. https://doi.org/10.1021/acs.jpca.1c08020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Shephard JJ, Slater B, Harvey P, Hart M, Bull CL, Bramwell ST, Salzmann CG (2018) Doping-induced disappearance of ice II from water’s phase diagram. Nat Phys 14:569–572. https://doi.org/10.1038/s41567-018-0094-z

    Article  CAS  Google Scholar 

  6. Gohlke M, Moessner R, Pollmann F (2019) Polarization plateaus in hexagonal water ice Ih. Phys Rev B 100:014206. https://doi.org/10.1073/pnas.2018837118

    Article  CAS  Google Scholar 

  7. Drechsel-Grau C, Marx D (2014) Quantum simulation of collective proton tunneling in hexagonal ice crystals. Phys Rev Lett 112:148302. https://doi.org/10.1103/PhysRevLett.112.148302

    Article  CAS  PubMed  Google Scholar 

  8. Bernal JD, Fowler RH (1933) A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions. J Chem Phys 1:515–548. https://doi.org/10.1063/1.1749327

    Article  CAS  Google Scholar 

  9. Pauling L (1935) The structure and entropy of ice and of other crystals with some randomness of atomic arrangement. J Am Chem Soc 57:2680–2684. https://doi.org/10.1021/ja01315a102

    Article  CAS  Google Scholar 

  10. Sloan ED Jr (1998) Clathrate Hydrates of Natural Gases. Marcel Dekker, New York

    Google Scholar 

  11. Kirov MV (1994) Residual entropy of polyhedral water clusters. Exact relations. J Struct Chem 35:126–128. https://doi.org/10.1007/BF02578511

    Article  Google Scholar 

  12. McDonald S, Ojamae L, Singer SJ (1998) Graph theoretical generation and analysis of hydrogen-bonded structures with applications to the neutral and protonated water cube and dodecahedral clusters. J Phys Chem 102:2824–2832. https://doi.org/10.1021/jp9803539

    Article  CAS  Google Scholar 

  13. Anick DJ (2002) Polyhedral water clusters, I: formal consequences of the ice rules. THEOCHEM 587:87–96. https://doi.org/10.1016/S0166-1280(02)00101-X

    Article  CAS  Google Scholar 

  14. Anick DJ (2002) Polyhedral water clusters, II: correlations of connectivity parameters with electronic energy and hydrogen bond lengths. THEOCHEM 587:97–110. https://doi.org/10.1016/S0166-1280(02)00100-8

    Article  CAS  Google Scholar 

  15. Kirov MV, Fanourgakis GS, Xantheas SS (2008) Identifying the most stable networks in polyhedral water clusters. Chem Phys Lett 461:180–188. https://doi.org/10.1016/j.cplett.2008.04.079

    Article  CAS  Google Scholar 

  16. Laage D, Hynes JT (2006) A molecular jump mechanism of water reorientation. Science 311:832–835. https://doi.org/10.1126/science.1122154

    Article  CAS  PubMed  Google Scholar 

  17. Leone SR, Cremer PS, Groves JT, Johnson MA (2011) Reorientation and allied dynamics in water and aqueous solutions. Annu Rev Phys Chem 62:395–416. https://doi.org/10.1146/annurev.physchem.012809.103503

    Article  CAS  Google Scholar 

  18. Hassanali A, Giberti F, Cuny J, Kühne TD (2013) Parrinello, M. Proton transfer through the water gossamer. Proc Natl Acad Sci 110:13723–13728. https://doi.org/10.1073/pnas.1306642110

    Article  PubMed  PubMed Central  Google Scholar 

  19. Vaillant CL, Wales DJ, Althorpe SC (2019) Tunneling splittings in water clusters from path integral molecular dynamics. J Phys Chem Lett 10:7300–7304. https://doi.org/10.1021/acs.jpclett.9b02951

    Article  CAS  PubMed  Google Scholar 

  20. Anick DJ (2003) Application of database methods to the prediction of B3LYP-optimized polyhedral water cluster geometries and electronic energies. J Chem Phys 119:12442. https://doi.org/10.1063/1.1625631

    Article  CAS  Google Scholar 

  21. Chihaia V, Adams S, Kuhs WF (2004) Influence of water molecules arrangement on structure and stability of 512 and 51262 buckyball water clusters. A theoretical study. Chem Phys 297:271–287. https://doi.org/10.1016/j.chemphys.2003.10.032

    Article  CAS  Google Scholar 

  22. Ren P, Ponder JW (2003) Polarizable atomic multipole water model for molecular mechanics simulation. J Phys Chem B 107:5933–5947. https://doi.org/10.1021/jp027815+

    Article  CAS  Google Scholar 

  23. Kirov MV (1996) Conformational combinatorial analysis of polyhedral water clusters J. Struct Chem 37:84–91. https://doi.org/10.1007/BF02578574

    Article  Google Scholar 

  24. Anick DJ (2010) Topology-energy relationships and lowest energy configurations for pentagonal dodecahedral (H2O)20X clusters, X=empty, H2O, NH3, H3O+: The importance of O-topology. J Chem Phys 132:164311. https://doi.org/10.1063/1.3397812

    Article  CAS  PubMed  Google Scholar 

  25. Parkkinen P, Riikonen S, Halonen L (2013) (H2O)20 water clusters at finite temperatures. J Phys Chem A 117:9985–9998. https://doi.org/10.1021/jp4003092

    Article  CAS  PubMed  Google Scholar 

  26. Iwata S, Akase D, Aida M, Xantheas SS (2016) Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24. Phys Chem Chem Phys 18:19746–19756. https://doi.org/10.1039/C6CP02487D

    Article  CAS  PubMed  Google Scholar 

  27. Kuo JL, Ciobanu CV, Ojamae L, Shavitt I, Singer SJ (2003) Short H-bonds and spontaneous self-dissociation in (H2O)20: effects of H-bond topology. J Chem Phys 118:3583–3588. https://doi.org/10.1063/1.1538240

    Article  CAS  Google Scholar 

  28. Ponder JW (2012) TINKER Software Tools for Molecular Design. Version 6.2. Washington University School of Medicine, Saint Louis, MO. http://dasher.wustl.edu/tinker. Accessed 6 Sept 2021

  29. Berendsen HJC, Postma JPM, Van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690. https://doi.org/10.1063/1.448118

    Article  CAS  Google Scholar 

  30. Kirov MV (2002) Sequential orientation of cycles in gas hydrate frameworks. J Struct Chem 43:274–283. https://doi.org/10.1023/a:1019600524366

    Article  CAS  Google Scholar 

  31. Stallings JR (1987) In: Gersten SM, Stallings JR (eds) Combinational Group Theory and Topology. Princeton Univ. Press, Princeton, p. 145—156

  32. Wales DJ, Walsh TR (1996) Theoretical study of the water pentamer. J Chem Phys 105:6957–6971. https://doi.org/10.1063/1.471987

    Article  CAS  Google Scholar 

  33. Gudkovskikh SV, Kirov MV (2021) Thermal stability of water polyhedra with square faces. J Mol Model 27:366. https://doi.org/10.1007/s00894-021-04996-7

    Article  CAS  PubMed  Google Scholar 

  34. Kirov MV (2020) Energetics of water polyhedra with square faces. J Phys Chem A 124:4463–4470. https://doi.org/10.1021/acs.jpca.0c02835

    Article  CAS  PubMed  Google Scholar 

  35. Inoue KI, Ahmed M, Nihonyanagi S et al (2020) Reorientation-induced relaxation of free OH at the air/water interface revealed by ultrafast heterodyne-detected nonlinear spectroscopy. Nat Commun 11:5344. https://doi.org/10.1038/s41467-020-19143-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Kirov MV (2016) Classification of hydrogen bond flips in small water polyhedra applied to concerted proton tunneling. Phys Chem Chem Phys 18:27351–27357. https://doi.org/10.1039/C6CP04960E

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This research was carried out according to state assignment no. 121041600040–3 and was supported by the Russian Science Foundation (grant number 22–23-00092).

Author information

Authors and Affiliations

  1. RAS, Earth Cryosphere Inst Tyumen SC SB, Malygina Str 86, Tyumen, 625026, Russia

    Sergey V. Gudkovskikh & Mikhail V. Kirov

Authors
  1. Sergey V. Gudkovskikh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mikhail V. Kirov
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

MVK: conceptualization, methodology, writing–review, editing. SVG: calculation, data curation, formal analysis, investigation.

Corresponding author

Correspondence to Mikhail V. Kirov.

Ethics declarations

Ethics approval

Not applicable.

Consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

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 (AVI 1039 KB)

Supplementary file2 (AVI 1325 KB)

Supplementary file3 (AVI 1999 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gudkovskikh, S.V., Kirov, M.V. Barrier-free molecular reorientations in polyhedral water clusters. Struct Chem 34, 553–563 (2023). https://doi.org/10.1007/s11224-022-01997-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11224-022-01997-x

Keywords

Search

Navigation