晶体数据审稿意见-保留原始衍射照片的重要性2

DJ_Tokyo · 发表于 2025-4-28 07:48:28

晶体数据审稿意见-保留原始衍射照片的重要性2

文献案例：Dalton Trans. 2023, 52, 13146–13153

论文主页：https://pubs.rsc.org/en/Content/ArticleLanding/2023/DT/D3DT02460A

有关晶体数据的审稿意见如下：

有关CCDC2262742晶体数据的审稿意见主要是有关分辨率的问题，用Olex2[1]查看其I/σ(I) vs. Resolution图（此图查看方式见推文“审稿意见-晶体数据的“真实分辨率””），如图1所示，可知在2θ大约45°开始的数据都是噪音（即I/σ(I)小于3）。

▲图1 CCDC 2262742投稿时的晶体数据

这个审稿意见比较好处理，可使用SHELXL指令中的OMIT指令或SHEL指令将这些噪音从精修中剔除，也可重新进行数据还原，在数据还原阶段对分辨率进行截断（具体可见推文“审稿意见-晶体数据的“真实分辨率””）。本案例中使用APEX4[2]采取重新还原的处理方法，将分辨率截断在I/σ(I) ≥ 2处，而不是I/σ(I) ≥ 3处，由于该结构CCDC号为2262742，所以最终处理后将数据的文件名和数据名均改为2262742，最终结果如图2所示。

▲图2 CCDC 2262742重新处理的晶体数据

有关CCDC2262744晶体数据的审稿意见，首先提到查看HKLF指令可知晶胞在最初的积分后发生了改变（这应该是结构解析过程中进行了升空间群导致的），并建议在正确的晶胞下重新进行积分，也就是在正确的晶胞下重新进行数据还原，这就需要原始衍射照片了（好在作者保留了原始衍射照片，所以可以进行重新还原）。再者就是和上一个数据相同的分辨率问题。该数据还有一个PLAT414的A级警报，该警报指出结构中有两个氢原子（H2和H27）之间的距离为1.61 Å（小于2.1 Å）。最后是溶剂分子二氯甲烷的Ueq太大，可能存在无序。上述问题具体表现见图3–5。

▲图3 CCDC 2262744包含转换矩阵的HKLF指令

▲图4 CCDC 2262744结构中距离太近（小于2.1 Å）的氢原子

▲图5 CCDC 2262744结构中二氯甲烷原子的Ueq

Ueq的查看：在Olex2中，将鼠标悬停在原子上，随后显示的方框中Ueq后的数值；或用记事本打开lst文件，搜素关键词Ueq即可查看，如图5所示。

拿到原始衍射照片文件后进行重新还原处理：查看提交的数据，发现该数据最初按三斜还原，最后解析出来是单斜空间群P21/c，所以中间经过了空间群变换，HKLF指令中才会留有转换矩阵，对此，在重新进行数据还原时，经过选取合适的衍射照片来收集衍射点定晶胞（参见推文“定晶胞选择衍射照片案例1”和“定晶胞选择衍射照片案例2”），按单斜还原，并将分辨率截断在I/σ(I) ≥ 2处，随后在结构解析和精修中对配体中的部分基团以及二氯甲烷做了无序处理，如图6所示，图中红色为无序的第二组分原子。

▲图6 CCDC 2262744重新处理的晶体数据

有关CCDC2262745晶体数据的审稿意见，同样发现晶胞在数据还原后发生了改变，且加入了孪晶法则进行精修，而且整个配体无序，审稿人建议检查空间群，并重新进行数据还原，因此该数据也是需要原始衍射照片进行重新数据还原来处理。

▲图7 CCDC 2262745投稿时的晶体数据

拿到原始衍射照片文件后，经重新数据还原处理，发现确如审稿人所说，最初定的空间群（第26号空间群Pmc21）不对，正确空间群为更高的第62号空间群Pnma，在正确的空间群下Rint值更低，而且也不需要添加孪晶法则进行精修，不对称单元中只有一个分子且不存在无序，最终结果如图8所示。

▲图8 CCDC 2262745重新处理的晶体数据

最后，编者处理完这些数据后，针对审稿意见撰写了一个初步的回复，如下：

Commentsto the Author

Thereare 3 Structures in this paper. We examined this file: 2262742-2262745

Thereare a few issues that need to be addressed prior to publication, although theseshould be able to be done fairly easily.

Theexperimental should include information on the hydrogen atom treatment, anyrestraints or constraints used and any twinning present.

Answer: The information on the hydrogen atom treatment, restraintsand constraints used in the refinement of all the structures have been added tothe experimental section in the revised manuscript.

Structure4 (CCDC 2262742): C23 H32 Cl2 Co N2

-The I/sigma drops below 3 at ~2theta = 45. The data should be truncated hereand a note added to the experimental.

Answer: Effective data standards (I/sigma above 2) were applied tothe new data integration process, thus the data were truncated by 0.84 Å (2θ =50°). The new cif file havebeen updated in CCDC.

Structure230222d-iPr-NH (CCDC 2262744): C30 H46 Cl4 Co N2

-Looking at the HKLF instruction it seems that the cell has been changed afterthe initial integration, the data should really be reintegrated in the correctcell. This may also help to improve the Rint. Again the I/sigma drops below 3at ~2theta = 45, if this remains the case after reintegration the data shouldbe truncated here and a note added to the experimental.

TheseCheckCif A and B alerts are raised by this structure. This is for yourinformation only - you may wish to address these issues before re-submittingyour cif file to the CCDC.

414_ALERT_2_AShort Intra D—H..H-X H2 ..H27 1.61 Ang.

TheUeq values of the following atoms are extremely large(Ueq = > 0.15). Eitherthe occupancy is set too high for these atom, or you might need to explore thepossibility that these atoms are involved in some form of disorder: Cl3 Cl4C30.

Answer: Effective data standards (I/sigma above 2) were applied tothe new data integration process, thus the data were truncated by 0.91 Å (2θ =45°). The disordereddichloromethane (labeled as Cl3 Cl4 C30) has been treated properly. The alert"414_ALERT_2_A Short Intra D—H..H-X H2 ..H27 1.61 Ang." have beensolved. A new alert "THETM01_ALERT_3_AThe value of sine(theta_max)/wavelength is less than 0.550 Calculatedsin(theta_max)/wavelength = 0.5477" was raised due to the data truncationand a proper author response was added into the new cif file, which have beenupdated in CCDC.

Structure2 (CCDC 2262745): C50 H72 Cl4 Co2 N4

-Again looking at the HKLF instruction it seems that the cell has been changedafter the initial integration, the data should really be reintegrated in thecorrect cell. This may also help to improve the Rint and reduce the number ofreflections needing to be omitted. Given that the BASF is 0.5 it would be worthchecking the space group when reintegrating and checking that one of the cellaxes is not currently doubled.

-Removing the restraints suggests that perhaps there is some unmodelled disorderpresent in the ethyl chains that should be modelled, if still the case once thedata have been reintegrated.

Answer: The data have been reintegrated and the space group wascorrected to be Pnma, and thus no twin law needed in the refinement. And thenew cif file have been updated in CCDC.

另外还需要在支撑材料中晶体部分添加如下内容：

Refinement of 2262742: The data were truncatedby 0.84 angstrom due to the I/sigma drops below 2 at about 2theta = 50 (ca. 0.84 Å). No significant disorderfound in this structure. The hydrogen atom (H2) on the nitrogen atom (N2) ofamine group was located by difference Fourier syntheses and was refined freely.All of the other hydrogen atoms were placed at the calculated positions andwere refined as riding model. The isotropic Uvalue of hydrogen atoms (Uiso)were refined as: Uiso(N−H)= 1.2 Ueq(N), Uiso(Csp2−H) = 1.2Ueq(Csp2), Uiso(Csp3−H) = 1.2Ueq(C), and Uiso(CH3) = 1.2 Ueq(C). The residual electrondensities were of no chemical significance.

Refinement of 2262744: The data were truncatedby 0.93 angstrom due to the I/sigma drops below 2 at about 2theta = 45 (ca. 0.93 Å). The linker fragment [C(CH3)C(CH3)2,labeled as C13, C14, C15, C16, and C17) between two nitrogen atoms of the imineligand were refined as two-components-disorder (C13~C17 and C13A~C17A) over twosites with occupancies 0.892:0.108, as well as the hydrogen atoms on thenitrogen atom of amine group. The methyl groups in one isopropyl of the twodiisopropylphenyl (dipp) group were refined as two-components-disorder (C8~C9/C8A~C9Aand C28~C29/C28A~C29A) over two sites with occupancies 0.542:0.458 and0.412:0.588, respectively. The methylene and one chloride atom of the freesolvent dichloromethane were refined as two-components-disorder (C30, Cl3 andC30A, Cl3A) over two sites with occupancies 0.646:0.354. The hydrogen atoms on thenitrogen atom of amine group cannot be located by difference Fourier synthesesdue to disorder, and thus were placed at the calculated positions and wererefined as riding model. The isotropic Uvalue of hydrogen atoms (Uiso)were refined as: Uiso(N−H)= 1.2 Ueq(N), Uiso(Csp2−H) = 1.2Ueq(Csp2), Uiso(Csp3−H) = 1.2Ueq(C), and Uiso(CH3) = 1.2 Ueq(C). Necessaryrestraints/constraints (SADI, DFIX, FLAT, RIGU and SIMU) were applied toprevent deformation of the disordered fragments and maintain its anisotropicdisplacement parameters within a reasonable range. The residual electrondensities were of no chemical significance.

Refinement of 2262745: The whole structure wason mirror plane leading to a special disorder of the entire ligand acrosssymmetry element wit occupancies of 0.5. The hydrogen atoms on the nitrogenatom of amine group cannot be located by difference Fourier syntheses due todisorder, and thus were placed at the calculated positions and were refined asriding model. The isotropic U valueof hydrogen atoms (Uiso)were refined as: Uiso(N−H)= 1.2 Ueq(N), Uiso(Csp2−H) = 1.2Ueq(Csp2), Uiso(Csp3−H) = 1.2Ueq(C), and Uiso(CH3) = 1.2 Ueq(C). Necessaryrestraints/constraints (DFIX, RIGU and SIMU) were applied to preventdeformation of the disordered fragments and maintain its anisotropicdisplacement parameters within a reasonable range. The residual electrondensities were of no chemical significance.

[审稿意见] 晶体数据审稿意见-保留原始衍射照片的重要性2

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