【关键词】高估占有率，溶剂掩膜。over-assignment，solvent mask
【审稿意见】
Structure 1.
The residual density map clearly shows that there is disorder in the two phenyl molecules of solvation. It is maybe not worth modelling this, but it might be worth including the attached residual density map to your SI.
More importantly, a solvent mask has been used, but nothing regarding this mask has been reported in the moiety formula and the atoms of the masked entities are missing from the sum formula (and therefore many follow-on quantities as well). Please address this issue.
Structure 2.
All Cu atoms appear to have been over-assigned. When refined freely, these are their resulting occupancies:
Atom information
Atom Type X Y Z Ueq Um Uvol ChemOccu R-bond R-VdW
O8 O 0.330 0.498 0.597 0.029 0.029 0.020 1.000 0.66 1.52
Cu4 Cu 0.286 0.511 0.777 0.026 0.026 0.017 0.850 1.28 1.4
Cu3 Cu 0.724 0.810 0.764 0.027 0.027 0.018 0.870 1.28 1.4
Cu1 Cu 0.328 0.666 0.495 0.027 0.027 0.018 0.969 1.28 1.4
Cu2 Cu 0.417 0.951 0.775 0.027 0.026 0.018 0.902 1.28 1.4
Formula (chemical occupancy): Cu3.59093 O, e count: 112.137, mass: 244.187
What is the reason for this? Are these not Cu atoms? Are they really not fully occupied? What else could cause this?
Of course, Ga radiation is a very bad choice for Cu containing materials, but nevertheless: you must deal with this and ensure that the final residual density map is clean and won't show the strong over-assignment that it currently shows.
Please also make sure that a 'clean' Fobs vs Fcal will be achieved -- and not the rather deviating on that is currently presented.
Structure 3.
It looks very much like O5 is *not* protonated but O6 *is* protonated, or maybe the proton is disordered over these two positions. Please check this carefully.
In the MS, please provide at least one structural drawing showing ADPs of each structure. From these images, any disorder should be visible -- and the nature of the actual molecule must be easily discernible.
Please use CheckCif as a guide in the final preparation of these structures. There should be no CheckCif A or B alerts remaining, and if any of them do, you must provide relevant and meaningful vrf entries.
【分析回复】
在结构1中，审稿人指出残余电子云密度图清楚地表明，两个溶剂化的苯分子存在无序。无序的苯分子可能不值得精修，但可能值得将所附的残余电子云密度图包含到支持文件中。更重要的是，精修时已经使用了溶剂掩膜，但在分子式中没有关于该掩膜的溶剂分子任何报道（因此也缺少许多后续量）。
在结构2中，审稿人指出所有铜原子的占有率均被高估了。当铜原子的占有率被自由精修时，所有的铜原子的占有率明显降低了。于是审稿人祭出了连环问：这是为何？这些不是铜原子？铜原子不是全占据的？或者其他原因？当然，对于含铜材料来说，Ga靶是一个非常糟糕的选择，但尽管如此：你必须处理好这一问题，并确保最终的残余电子云密度图是干净的，不会显示出目前所显示的占有率均被高估的现象。还请确保实现“干净”的Fobs-Fcal图，而不是目前的有偏离很多的图。
在结构3中，审稿人指出O5看起来不是质子化的，但O6是质子化了，或者质子在这两个位置上是无序的。请仔细检查。
剩下的就是些比较通用套路的审稿意见了。在正文中，请至少提供一张结构图，显示每个结构的各向异性温度因子。从这些图像中，任何无序都应该是可见的——而且实际分子的性质必须很容易辨别。请在这些结构的最终准备过程中使用CheckCif作为指南。不应存在剩余的CheckCif A或B警报，如果其中任何警报存在，则必须提供相关且有意义的vrf条目。
审稿人指出的问题都比较中肯，还给出了解决的思路。套路意见也是很常见的意见，照着改即可。
结构1中只要将掩膜掉的溶剂分子的种类和个数加入到分子式中即可。
结构2中遇到的问题也不是什么稀奇的问题了，在之前的文章中也提到过。可见于审稿意见240602-Fo-Fc图和审稿意见240608-高估占有率。审稿人在这里给出了占有率被高估的两个原因，一是原子类型错误，二是共占据。在这个例子中是Ti和Cu共占据，只要把Ti和Cu进行共占据精修即可。而关于Fobs vs Fcal图的问题，Fobs vs Fcal图中有些离群点，但是个数不多。由于原始照片无法得到，无法探究其根本原因，只能说这些离群点对结果影响不大。
结构3中O5和O6加氢不合适，重新都加上氢即可。
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