| Literature DB >> 36071798 |
Michal L Chodkiewicz1, Roman Gajda1, Barbara Lavina2, Sergey Tkachev2, Vitali B Prakapenka3, Przemyslaw Dera3, Krzysztof Wozniak1.
Abstract
Water is an essential chemical compound for living organisms, and twenty of its different crystal solid forms (ices) are known. Still, there are many fundamental problems with these structures such as establishing the correct positions and thermal motions of hydrogen atoms. The list of ice structures is not yet complete as DFT calculations have suggested the existence of additional and - to date - unknown phases. In many ice structures, neither neutron diffraction nor DFT calculations nor X-ray diffraction methods can easily solve the problem of hydrogen atom disorder or accurately determine their anisotropic displacement parameters (ADPs). Here, accurate crystal structures of H2O, D2O and mixed (50%H2O/50%D2O) ice VI obtained by Hirshfeld atom refinement (HAR) of high-pressure single-crystal synchrotron and laboratory X-ray diffraction data are presented. It was possible to obtain O-H/D bond lengths and ADPs for disordered hydrogen atoms which are in good agreement with the corresponding single-crystal neutron diffraction data. These results show that HAR combined with X-ray diffraction can compete with neutron diffraction in detailed studies of polymorphic forms of ice and crystals of other hydrogen-rich compounds. As neutron diffraction is relatively expensive, requires larger crystals which can be difficult to obtain and access to neutron facilities is restricted, cheaper and more accessible X-ray measurements combined with HAR can facilitate the verification of the existing ice polymorphs and the quest for new ones. © Michal L. Chodkiewicz et al. 2022.Entities:
Keywords: Hirshfeld atom refinement; deuterated ice; quantum crystallography
Year: 2022 PMID: 36071798 PMCID: PMC9438488 DOI: 10.1107/S2052252522006662
Source DB: PubMed Journal: IUCrJ ISSN: 2052-2525 Impact factor: 5.588
Figure 1Scheme of the HAR procedure.
Figure 2Selected symmetry elements in the structure of ice VI. Glide planes and inversion centers were removed for clarity: (a) O2 and its closest environment, (b) O1 and its closest environment, (c) examples of water clusters selected out of 259 configurations used in the HAR.
Figure 3Disordered (a)–(d) D2O and (e)–(g) H2O molecules with their anisotropic thermal ellipsoids derived from (a) neutron diffraction, (b) HAR of synchrotron X-ray data, (c) HAR of laboratory X-ray source data, and (d) IAM refinement of synchrotron X-ray data, (e) neutron data, (f) HAR of laboratory source X-ray data, and (g) mixed ice (50%D2O/50%H2O) HAR of laboratory X-ray source data.
Comparison of bond lengths and hydrogen ADPs in ice VI
For ADP values see the supporting information. is the average absolute difference between ADP components, is an analogous value, taking into account the relative difference of each ADP but is divided by the average value and S12 is the average similarity index for the hyrogen ADPs.
| D2O ice VI | H2O | H2O:D2O (1:1) | |||||
|---|---|---|---|---|---|---|---|
| Radiation | Neutron | X-ray | Neutron | X-ray | X-ray | ||
| Source | Synchrotron | Laboratory | Synchrotron | Laboratory | In-house | ||
| Model | HAR | HAR | IAM | HAR | HAR | ||
| Bond lengths | |||||||
| O2—H2 (Å) | 0.932 (1) | 0.951 (15) | 0.913 (18) | 0.806 (13) | 0.932 (4) | 0.899 (20) | 0.927 (50) |
| O1—H1A (Å) | 0.942 (1) | 0.947 (12) | 0.930 (13) | 0.797 (9) | 0.942 (3) | 0.919 (15) | 0.997 (30) |
| O1—H1B | 0.945 (1) | 0.988 (15) | 0.932 (20) | 0.819 (13) | 0.947 (3) | 0.928 (20) | 0.967 (40) |
| O1—H1C | 0.932 (2) | 0.954 (15) | 0.917 (17) | 0.810 (13) | 0.938 (4) | 0.891 (20) | 0.886 (50) |
| Average difference in bond lengths between the neutron and X-ray structures (Å) | |||||||
| 0.019 | 0.016 | 0.133 | 0.031 | ||||
| Average difference in hydrogen ADPs in the neutron and X-ray structures | |||||||
|
| 0.0056 | 0.0040 | 0.0062 | 0.0075 | |||
|
| 0.23 | 0.17 | 0.23 | 0.28 | |||
| S12 | 1.48 | 0.61 | 2.65 | 1.52 | |||