晶体数据审稿意见-精修细节描述文献案例(Nat. Chem.)

DJ_Tokyo · 发表于 3 天前

晶体数据审稿意见-精修细节描述文献案例(Nat. Chem.)

案例来源：Nat. Chem. 2024, 16,1788–1793. DOI[1]: 10.1038/s41557-024-01597-8. CCDC[2]: 2320937‒2320946.

经论文作者同意，该论文有关晶体方面的审稿意见及其回复罗列如下（笔者进行了翻译以及一些格式的整理编辑）：

Reviewer: In general, the structures in the article have been correctly determined, however there are some issues that should be resolved before publication, as noted below for the individual structures. 1a: This structure has no problems. 2a: This structure has no problems. 2b: This structure has no problems. 3: This structure has no problems. 6: This structure has no problems.	审稿人：总的来说，文章中的结构已经正确确定，但在发表之前，仍有一些问题需要解决，如下所述。 1a：此结构没问题。 2a：此结构没问题。 2b：此结构没问题。 3：此结构没问题。 6：此结构没问题。
Response: We thank the reviewer for thoroughly evaluating the crystallographic data and useful suggestions (see below).	答复：我们感谢审稿人对晶体学数据的全面评估和有用的建议（见下文）。

Reviewer: 1b: This structure is correctly determined, however a more complete description of the disorder modelling should include in the _refine_special_details section of the CIF. As an example, for this structure it should read something similar to:	审稿人：1b：该结构已正确确定，但CIF[3]的_refine_special_details部分应包含对无序建模的更完整描述。例如，对于该结构，它应该读起来类似于：
_refine_special_details ; The toluene solvent molecule is disordered over two orientations. The occupancies of the two disorder components were refined competitively converging to a ratio of 0.62:0.38. Aromatic C-C 1,2- and 1,3-distances of the toluene molecules were restrained to be approximately equal, and each toluene molecule was restrained to approximately flat geometry. Rigid bond and similarity restraints were applied to the thermal parameters of the disordered atoms. ;	（_refine_special_details内容大意）甲苯溶剂分子在两个方向上无序。两个无序组分的占有率经过竞争性精修收敛为0.62:0.38的比例。甲苯中芳香碳碳1,2-距离和1,3-距离限制为近似相等，每个甲苯分子几何结构限制为近似平面。对无序原子的热参数应用刚性键和相似性限制。
Response: We have added the following description into the _refine_special_details section of the cif file of 1b: “The toluene solvent molecule is disordered over two orientations. The occupancies of the two disorder components were refined competitively converging to a ratio of 0.618(9):0.382(9). Aromatic C-C 1,2- and 1,3-distances of the toluene molecules were restrained to be approximately equal as well as the Me-C 1,2- and 1,3-distances. Each toluene molecule was restrained to approximately flat geometry. Rigid bond and similarity restraints were applied to the anisotropic displacement parameters of the disordered atoms.”	答复：我们将以下描述添加到1b的CIF文件中_refine_special_details部分：（内容大意）甲苯溶剂分子在两个方向上无序。两个无序组分的占有率经过竞争性精修收敛为0.618(9):0.382(9)的比例。甲苯中芳香碳碳1,2-距离和1,3-距离以及Me-C键键长限制为近似相等，每个甲苯分子几何结构限制为近似平面。对无序原子的热参数应用刚性键和相似性限制。

Reviewer: 4: This structure has been correctly determined, however the same remarks regarding explanation of the disorder modelling for 1b apply to this structure as well.

审稿人：4：该结构已被正确确定，然而，关于1b的无序建模的解释同样适用于该结构。

Response: We have added the following description into the _refine_special_details section of the cif file of 4:

“The OPh group is disordered over two positions. All equivalent 1,2- and 1,3-distances were restrained to be approximately equal. The occupancies of the two disorder components were refined competitively converging to a ratio of 0.869(3):0.131(3). Rigid bond and similarity restraints were applied to the anisotropic displacement parameters of the disordered atoms.”

答复：我们将以下描述添加到4的CIF文件中_refine_special_details部分：

（内容大意）

苯氧基在两个位置无序。所有等效1,2-距离和1,3-距离被限制为近似相等。两个无序组分的占有率经过竞争性精修收敛为0.869(3):0.131(3)的比例。对无序原子的热参数应用刚性键和相似性限制。

Reviewer: 5a: This structure has been correctly determined, however the same remarks regarding explanation of the disorder modelling for 1b apply to this structure as well.

审稿人：5a：该结构已被正确确定，然而，关于1b的无序建模的解释同样适用于该结构。

Response: We have added the following description into the _refine_special_details section of the cif file of 5a:

“The asymmetric unit contains two different complex molecules disordered at the same position. The two alternative complex molecules were refined with occupation factors of 0.518(10) for [Pd(CSiMe3)(PNP)]*N2 and 0.482(10) for [PdC(N2)SiMe3(PNP)]. Rigid bond and similarity restraints were applied to the anisotropic displacement parameters of the disordered atoms. The N-N distance of the N2 molecule is restrained to approximately 1.1 Å.”

答复：我们将以下描述添加到5a的CIF文件中_refine_special_details部分：

（内容大意）

非对称单元中包含处于同一位置无序的两个不同的配合物分子。两个替代配合物分子[Pd(CSiMe3)(PNP)]*N2和[PdC(N2)SiMe3(PNP)]的占有率精修为0.518(10)和0.482(10)。对无序原子的各向异性位移参数应用刚性键和相似性限制。N2分子的N-N距离限制为近似1.1 Å。

Reviewer: 5b: This structure is probably correctly determined, however some additional refinements need to be tested out by the authors, and the results included in structure description. The occupancy of the A toluene molecule has a lower bound of the occupancy of the free N2 molecule, however could refine to a higher occupancy – this should be tested by separate competitive refinement of the toluene molecule occupancy, and if the resulting occupancy of the A toluene is higher than that of the N2, that is likely the correct model. Whether it is or not, this needs to be tested, and the result included in the structure description and _refine_special_details section. In addition, the comments for 1b also apply to this structure.

审稿人：5b：该结构可能是正确确定的，但是作者需要测试一些额外的精修，并将结果包含在结构描述中。A甲苯分子的占有率具有游离N2分子占有率的下限，但可以精修到更高的占有率——这应该通过单独竞争性精修甲苯分子占有率来测试，如果A甲苯的占有率高于N2，则可能是正确的模型。无论是否如此，都需要对此进行测试，并将结果包含在结构描述和_refine_special_details部分中。此外，1b的评论也适用于此结构。

Response: We thank the reviewer for this suggestion. However, refinement without constraining the occupancies of the toluene disorder with the occupancies of the N2 disorder led to unreasonable results and an A alert appeared in the checkcif routine:

330_ALERT_2_A Large Aver Phenyl C-C Dist C2B--C7B 1.44 Ang.

The occupancy of toluene molecule B with a position too close to the N2 molecule became higher (0.59) as well as the occupancy of the N2 molecule (0.54). We added this results in the revised ESI under the structure description of 5b as following:

“Refinement without constraining the occupancies of the toluene disorder with the occupancies of the N2 disorder led to unreasonable results and an A alert appeared in the checkcif routine (330_ALERT_2_A Large Aver Phenyl C-C Dist C2B--C7B 1.44 Ang). The occupancy of toluene molecule B with a position too close to the N2 molecule became higher (0.59) as well as the occupancy of the N2 molecule (0.54).”

Furthermore, we have added the following description into the _refine_special_details section of the cif file of 5b:

“The asymmetric unit contains two different complex molecules disordered at the same position and one N2 molecule and one co-crystallized toluene molecule also disordered at the same position. The occupancies of the two alternative complex molecules refined to 0.459(10) for [Pt(CSiMe3)(PNP')]*N2 and 0.541(10) for [PtC(N2)SiMe3(PNP')]. Aromatic C-C 1,2- and 1,3-distances of the toluene molecules were restrained to be approximately equal as well as the Me-C 1,2 and 1,3-distances. Each toluene molecule was restrained to approximately flat geometry. Rigid bond and similarity restraints were applied to the anisotropic displacement parameters of the disordered atoms.”

答复：我们感谢审稿人的建议。然而，在不约束甲苯无序组分与N2无序组分的占有率的情况下进行精修导致了不合理的结果，并在checkcif程序中出现了A级警报：

330_ALERT_2_A Large Aver Phenyl C-C Dist C2B--C7B 1.44 Ang.

位置太靠近N2分子的甲苯分子B的占有率变得更高（0.59），N2分子的占有率也变高（0.54）。我们在修订后的ESI中，在5b的结构描述下添加了以下结果：

（内容大意）

在不约束无序甲苯占有率和N2无序组分的占有率的情况下精修导致不合理结果并在checkcif例程中出现A级警报（330_ALERT_2_A Large Aver Phenyl C-C Dist C2B--C7B 1.44 Ang）。位置太靠近N2分子的甲苯分子B的占有率变得更高（0.59），N2分子的占有率也变高（0.54）。

与此同时，我们在5b的CIF文件_refine_special_details部分添加了以下内容：

（内容大意）

非对称单元中包含处于同一位置无序的不同配合物分子，并且一个N2分子和一个共结晶甲苯分子也在同一位置无序。两个替代配合物分子[Pt(CSiMe3)(PNP')]*N2和[PtC(N2)SiMe3(PNP')]的占有率精修为0.459(10)和0.541(10)。甲苯中芳香碳碳1,2-距离和1,3-距离以及Me-C键键长限制为近似相等，每个甲苯分子几何结构限制为近似平面。对无序原子的各向异性位移参数应用刚性键和相似性限制。

Reviewer: 2b*/2b’: All previous structures have included a very basic explanation of the disorder modelling in the image caption in the supplementary materials, however this has been omitted in this case – this should be included. In addition, the same remarks regarding explanation of the disorder modelling for 1b apply to this structure as well.

审稿人：2b*/2b’：所有之前的结构都在补充材料的图像标题中包含了对无序建模的非常基本的解释，但在此例下被省略了——这应该包括在内。此外，关于1b的无序建模的解释同样适用于这种结构。

Response: As the reviewer suggested, the following description about the disorder modelling of 2b’ has been added into the revised ESI under the structure description of 2b’:

“The asymmetric unit contains two different complex molecules disordered at the same position and one co-crystallized toluene molecule also disordered connected to the disorder of the two complexes. The occupancies of the two alternative complex molecules refined to 0.436(8) for [Pt{CH(SiMe3)CH2CHMePiPr(1,2-C6H3-5-Me)N(1,2-C6H3-5-Me)PiPr2}] and 0.564(8) for [PtC(N2)SiMe3(PNP')]. The structure was refined using some restraints and constraints (SADI, RIGU, SIMU).”

Furthermore, the following description was added in the _refine_special_details section of the cif file of 2b’:

“The asymmetric unit contains two different complex molecules disordered at the same position and one co-crystallized toluene molecule also disordered connected to the disorder of the two complexes. The occupancies of the two alternative complex molecules refined to 0.436(8) for [Pt{CH(SiMe3)CH2CHMePiPr(1,2-C6H3-5-Me)N(1,2-C6H3-5-Me)PiPr2}] and 0.564(8) for [PtC(N2)SiMe3(PNP')]. All equivalent 1,2- and 1,3- distances of the disordered parts of the two complexes were restrained to be approximately equal. Aromatic C-C 1,2- and 1,3-distances of the toluene molecules were restrained to be approximately equal as well as the Me-C 1,2- and 1,3-distances. Each toluene molecule was restrained to approximately flat geometry. Rigid bond and similarity restraints were applied to the anisotropic displacement parameters of the disordered atoms.”

答复：正如审稿人所建议的，在修订后的ESI中，在2b’的结构描述下增加了以下关于2b’无序建模的描述：

（内容大意）

非对称单元中包含处于同一位置无序的不同配合物分子，以及一个与两个配合物无序连接的共结晶甲苯分子。两个替代配合物分子[Pt{CH(SiMe3)CH2CHMePiPr(1,2-C6H3-5-Me)N(1,2-C6H3-5-Me)PiPr2}]和[PtC(N2)SiMe3(PNP')]的占有率精修为0.436(8)和0.564(8)。结构的精修使用了一些限制和约束（SADI、RIGU、SIMU）。

与此同时，在2b’的CIF文件_refine_special_details部分添加了以下内容：

（内容大意）

非对称单元中包含处于同一位置无序的不同配合物分子，以及一个与两个配合物无序连接的共结晶甲苯分子。两个替代配合物分子[Pt{CH(SiMe3)CH2CHMePiPr(1,2-C6H3-5-Me)N(1,2-C6H3-5-Me)PiPr2}]和[PtC(N2)SiMe3(PNP')]的占有率精修为0.436(8)和0.564(8)。两个配合物中所有等效1,2-距离和1,3-距离被限制为近似相等。甲苯中芳香碳碳1,2-距离和1,3-距离以及Me-C键键长限制为近似相等。每个甲苯分子几何结构限制为近似平面。对无序原子的各向异性位移参数应用刚性键和相似性限制。

[单晶结构] 晶体数据审稿意见-精修细节描述文献案例(Nat. Chem.)

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