Complete Crystal Structures and Elastic Properties of the Uranyl Minerals Johannite, Pseudojohannite and Derriksite
Round 1
Reviewer 1 Report
In this manuscript, the authors report the determination of the full crystal structures of a series of minerals. More importantly, the position of hydrogen atoms, are determined using first principles solid-state methods based on density functional theory using plane wave basis sets and pseudopotentials. Overall, this is nice paper and the data is convincing and therefore I recommend its acceptance to Crystals. Before publications, the following minor points should be addressed:
1. The authors emphasize that they determinate the “full crystal structures”. I wander why the true meaning of “full” in this statement.
2. The unit cell parameters of johannite and derriksite minerals (see Table 1) showing large error between the experimental and DTF results. It is better to give some necessary discussion.
3. As shown in Figure. 2, comparison of the X-ray diffraction patterns of johannite, pseudojohannite and derriksite derived from the experimental and theoretical crystal structures were given in a simple way. It is better to give the result of Rietveld refinement bases on related powder polycrystalline.
4. The expression of hydrogen bonding structure (like Figures 3, 6, 8) seems a little chaos. It is better to redrawn them.
Author Response
We are grateful to the referee 1 for accepting to review this manuscript and the positive evaluation. The comments have allowed to improve the manuscript. A point-by-point response to the comments is given below.
Response to the comments of Reviewer 1:
In this manuscript, the authors report the determination of the full crystal structures of a series of minerals. More importantly, the position of hydrogen atoms, are determined using first principles solid-state methods based on density functional theory using plane wave basis sets and pseudopotentials. Overall, this is nice paper, and the data is convincing and therefore I recommend its acceptance to Crystals. Before publications, the following minor points should be addressed:
1) The authors emphasize that they determinate the “full crystal structures”. I wander why the true meaning of “full” in this statement.
Response:
The term “full crystal structures” means that the unit cell parameters and fractional coordinates of all atoms in the unit cell of this mineral are completely specified. The previous crystal structures lack the positions of the hydrogen atoms due to the insufficient quality of the X-ray diffraction patterns. Without these positions it is not possible to describe the forces holding together the atoms in the corresponding crystal structures because hydrogen bonding is one of the most important bonding forces in these minerals.
The meaning of the term “full crystal structure” has been given in a sentence included in the Introduction Section of the revised version of the manuscript:
“The term “full crystal structures” means that the unit cell parameters and fractional coordinates of all atoms in the unit cell of these minerals are completely specified. The previous crystal structures lack of the positions of the hydrogen atoms due to the insufficient quality of the X-ray diffraction patterns. Without these positions it is impossible to describe the forces holding together the atoms in the corresponding crystal structures because hydrogen bonding is one of the most important bonding forces in these minerals.”
2) The unit cell parameters of johannite and derriksite minerals (see Table 1) showing large error between the experimental and DTF results. It is better to give some necessary discussion.
Response:
The computed and experimental unit cell parameters of johannite and pseudojohannite are well reproduced theoretically, the unit cell volume being underestimated by 2.6% in johannite and overestimated by 2.4% in pseudojohannite. However, for derriksite, the differences of the computed unit cell parameters and their experimental counterparts are larger. The unit cell volume is overestimated by 5.5%. The larger differences may be due to the largest difficulty in the description of selenium containing minerals with respect to sulfur containing minerals. The most probable reason for this fact is the inferior quality and transferability of the norm-conserving pseudopotential employed to describe the inner electrons of selenium atom in derriksite. This has been discussed in Section 3.1.3 of the manuscript, where the following sentence has been added:
“The most probable reason for the larger differences in the computed unit cell parameters with respect to their experimental counterparts in derriksite with respect to those of johannite and pseudojohannite is the inferior quality and transferability of the norm-conserving pseudopotential employed to describe the inner electrons of selenium atom in derriksite.”
3) As shown in Figure. 2, comparison of the X-ray diffraction patterns of johannite, pseudojohannite and derriksite derived from the experimental and theoretical crystal structures were given in a simple way. It is better to give the result of Rietveld refinement bases on related powder polycrystalline.
For derriksite, the Rietveld refinement of its crystal structure allowed for the determination of the experimental full crystal structure of this mineral. The experimental structure is consistent with the structure determined using first principles methods. However, for johannite and pseudojohannite, the determination of the full crystal structures by refinement from X-ray diffraction data is not feasible due to the poor quality of the corresponding X-ray diffraction patterns. As shown in the present manuscript, in the cases of incompletely specified unit cells, the use of first principles solid-state methods are an extremely useful tool for obtaining the full crystal structures. Furthermore, its knowledge allows for the accurate determination of the physical properties of these minerals using first principles solid-state methods.
4) The expression of hydrogen bonding structure (like Figures 3, 6, 8) seems a little chaos. It is better to redrawn them.
We have tried to obtain better figures to describe the hydrogen bonding structure in these minerals. However, these figures are the best we have been able to obtain due to the complexity of the unit cells of johannite, pseudojohannite and derriksite minerals.
Reviewer 2 Report
The authors aim to determine the full crystal structures of the uranyl sul-13 fate minerals johannite (Cu(UO2)2(SO4)2(OH)2 ·8H2O), pseudojohannite 14 (Cu3(UO2)4(SO4)2O4(OH)2 ·12H2O) and the uranyl selenite mineral derriksite 15 (Cu4[((UO2)(SeO3)2(OH)6]) crystals combining with the structure analysis and theoretical study. In this study, the positiveness of the energy hessian matrix for these structures was also checked, where the geometry optimizations were performed using stringent convergence tolerances. In my opinion, this paper covers enough crystal structure information to readers and is worth to be published on Crystals journal. However, there are some points should be corrected or improved.
1) The space group for these crystals should be checked. Pmn21? Full manuscript should also be checked.
2) Elastic constants and mechanical stability. Some experimental results are encouraged to add into the discussion part if crystal samples can be obtained, which is a very important to support the theoretical calculation. For crystals with mm2 symmetry, it is not hard to measure part of the elastic constants.
3) The authors state that the positions of hydrogen atoms were ascertained from the difference-Fourier maps. The H atoms were refined using a mix of soft constraints on O-H distances and with the atomic displacement parameter, and Ueq value for each H was set to be 1.2 times that of the donor O atom. Are these values in agreement with the criteria used in theoretical study? (lines 166-175) Please clearify in the manuscript.
Author Response
We are grateful to the referee 2 for accepting to review this manuscript and the positive evaluation. The comments have allowed to improve the manuscript. A point-by-point response to the comments is given below.
Response to the comments of Reviewer 1:
The authors aim to determine the full crystal structures of the uranyl sulfate minerals johannite (Cu(UO2)2(SO4)2(OH)2 ·8H2O), pseudojohannite (Cu3(UO2)4(SO4)2O4(OH)2 ·12H2O) and the uranyl selenite mineral derriksite (Cu4[((UO2)(SeO3)2(OH)6]) crystals combining with the structure analysis and theoretical study. In this study, the positiveness of the energy hessian matrix for these structures was also checked, where the geometry optimizations were performed using stringent convergence tolerances. In my opinion, this paper covers enough crystal structure information to readers and is worth to be published on Crystals journal. However, there are some points should be corrected or improved.
1) The space group for these crystals should be checked. Pmn21? Full manuscript should also be checked.
Response: The space groups of the three minerals has been checked. The most frequent notation for the space group of derriksite (no. 31) is Pn21m (Ginderow, D.; Cesbron, F. Acta Crystallogr. C 1983, 39, 1605–1607; Gurzhiy, V.V.; et al. Crystals 2019, 9, 639; Gurzhiy et al., J. Geosci. 2020, 65, 249−259), although the notation Pmn21 has also be used frequently. Therefore, we have changed Pmn21 by Pn21m in the revised version of the manuscript (and in the Supplementary Materials). The notation for the space groups has been checked in the full manuscript.
2) Elastic constants and mechanical stability. Some experimental results are encouraged to add into the discussion part if crystal samples can be obtained, which is a very important to support the theoretical calculation. For crystals with mm2 symmetry, it is not hard to measure part of the elastic constants.
We agree with this comment from the reviewer. The elastic constants of these minerals or at least a part of them could be measured experimentally. However, the experimental determination of the elastic constants of these minerals is quite difficult since requires the acquisition of well-developed crystal samples of these minerals. Obtaining well developed crystals of uranium containing minerals is quite difficult and expensive. Furthermore, we have not access to the corresponding equipment and we are not expert in the measurement of elastic tensor constants.
3) The authors state that the positions of hydrogen atoms were ascertained from the difference-Fourier maps. The H atoms were refined using a mix of soft constraints on O-H distances and with the atomic displacement parameter, and Ueq value for each H was set to be 1.2 times that of the donor O atom. Are these values in agreement with the criteria used in theoretical study? (lines 166-175) Please clearify in the manuscript.
Response: In complex cases of uranyl minerals as the case of derriksite, we usually determine the positions of hydrogen atoms from the difference-Fourier maps using the described procedure. However, in the theoretical determination of the position of the hydrogen atoms no constraints or criteria are employed. From the initial positions of these atoms, free unconstrained optimizations are performed. This has been noted in Section 2.2 (First principles solid-state methods) of the revised version of the manuscript where the following sentence has been introduced:
“The hydrogen atoms were put at a distance from the water or hydroxyl oxygen atoms of about 1.1 Å. These distances are only used to provide reasonable initial position of the H atoms which are later submitted to unconstrained full optimization.”
