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[审稿意见] 晶体数据审稿意见-混合类型无序(跟着文献学习无序处理)

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声明:本文仅代表个人观点,笔者学识有限,资料整理过程中难免存在疏漏谬误,请不吝指正。
晶体数据审稿意见-混合类型无序(跟着文献学习无序处理)
案例来源:CCDC [1] 2374582. Nature 2025, 641,106–111. DOI [2]: 10.1038/s41586-025-08841-2.
案例结构如1所示(由ChemBioDraw [3]绘制)。
1 案例结构
审稿意见:
8: I do appreciate the effort the authors havegone through in attempting to model the disorder in this structure. Hower, isit obvious to me that this is indeed disorder, but rather a modelling of(potentially) something else: maybe the crystal data presented some degree oftwinning and what they are modelling is simply ghosting from a secondarycomponent? Or perhaps there is an issue with the absorption correction method?I should clarify that the disorder treatment is not intrinsically wrong and I'mnot totally against their approach, but the position of the ring, Os centresand phosphine ligands do not reflect their treatment – i.e. the ring hasrotational disorder, whilst the other fragments are displaced by roughly 0.3 Å,so these two are not the same disorder component (if classic crystallographicdisorder was indeed present). I wouldn't recommend solely focusing on obtainingthe lowest R1, but rather present a more realistic model.
大意:
化合物8:我非常赞赏作者在试图建模该结构中的无序方面所做的努力。然而,在我看来,这的确是一种无序,而是对(潜在的)其他事物的建模:也许晶体数据呈现出某种程度的孪晶,而他们所建模的只是次要组分的重影?或者,吸收校正方法可能存在问题?我应该澄清的是,这种无序处理在本质上并没有错,我也不完全反对他们的做法,但环的位置、锇中心和膦配体并不能反映他们的处理——即环具有旋转无序,而其他片段被移位了大约0.3 Å,因此这两个片段不是同一种无序成分(如果经典的晶体学无序确实存在的话)。我不建议只关注获得最低的R1,而是提出一个更真实的模型。
该数据笔者最初帮忙处理的是整体做位移无序,如2所示(由Olex2 [4]呈现)。
2 整体无序处理
该结构最终发表状态如3所示。
3 发表状态
各个无序组分如4–6所示。
4 无序第一组分(配体环旋转无序),占有率为0.514(4)
5 无序第二组分(配体环旋转无序),占有率为0.486(4)
6 无序第三组分(P-Os-P的平移无序),占有率为0.0925(9)
经上述处理后,回应如下:
We greatly appreciate your suggestions and wecompletely agree with you. In order to solve this problem, we grew new singlecrystals and collected the data again. We analyzed the new data and excludedthe reasons of twinning and absorption correction. In our opinion, there may betwo kinds of disorder in this crystal. One is the rotational disorder relatedto the C1 to C15 ring, and the other involves a whole molecular displacement.The two parts of the rotational disorder of the ring (set as part 1 and part 2)have occupancies of 0.51369 and 0.48631, respectively. The two parts of thedisplacement disorder (set as part 1 and part 3) have occupancies of 0.90753and 0.09247, respectively. Due to the small occupancy of part 3, only Os and Patoms with large electron density could be assigned, and the residual electrondensity peaks of C atoms in the displaced part are too small to refine withconfidence. Indeed, we tried to refine all the C atoms in part 3, but a lot ofrestraints had to be applied. The resulting structure looks "messy"and is not helpful in terms of confirming the molecular structure. Therefore,we only refined the Os and P atoms in part 3.
大意:
我们非常感谢您的建议,我们完全同意您的意见。为了解决这个问题,我们培育了新的单晶并再次收集了数据。我们分析了新的数据,排除了孪晶和吸收校正的原因。我们认为,这种晶体中可能存在两种无序。一种是与C1C15环相关的旋转无序,另一种涉及整个分子位移。环的旋转无序的两个部分(设置为part 1part 2)的占有率分别为0.513690.48631。位移无序的两个部分(设置为part 1part 3)的占有率分别为0.907530.09247。由于part 3的占有率很小,只能分配电子密度较大的锇和磷原子,而位移部分中碳原子的残余电子密度峰太小,无法可靠地精修。事实上,我们试图在part 3中精修所有的碳原子,但必须施加很多限制。由此产生的结构看起来“混乱”,对确认分子结构没有帮助。因此,我们在part 3中仅对锇和磷原子进行了精修。
相关视频:
单晶结构解析练习576(文献案例-数据还原-无序处理)https://www.bilibili.com/video/BV1u1VPzLEmv
数据下载:
提取码: c4by
参考文献
[1]    (a) Allen, F. H.The Cambridge Structural Database: A Quarter of a Million Crystal Structuresand Rising. Acta Cryst. 2002, B58, 380–388. DOI:10.1107/S0108768102003890. (b) Groom, C. R.; Bruno, I. J.; Lightfoot, M.P.; Ward, S. C. The Cambridge Structural Database. Acta Cryst. 2016, B72, 171–179. DOI:10.1107/S2052520616003954. (c) Mitchell, J.; Robertson, J. H.; Raithby,P. R. Cambridge Crystallographic Data Centre (CCDC). Comprehensive Coordination Chemistry III 2021, 413–437. DOI: 10.1016/B978-0-12-409547-2.14829-2.
[2]    (a) InternationalOrganization for Standardization (2012). ISO 26324:2012. Information and Documentation – Digital Object Identifier System.http://www.iso.org/iso/catalogue_detail.htm?csnumber=43506. (b) McDonald J. D.;Levine-Clark, M. Encyclopedia of Libraryand Information Sciences. Fourth Edition, CRC Press, 2017. DOI: 10.1081/e-elis4. (c) Liu, J. Digital ObjectIdentifier (DOI) and DOI Services: An Overview. Libri 2021, 71, 349‒360. DOI:10.1515/libri-2020-0018. (d) International Organization forStandardization (2022). ISO 26324:2022. Informationand Documentation – Digital Object Identifier System.https://www.iso.org/standard/81599.html
[3]    (a) Klein, F. M.CS ChemDraw Pro,1 Version 3.1 for Windows. J.Chem. Inf. Comput. Sci. 1995, 35, 166–167. DOI: 10.1021/ci00023a026. (b)Cousins, K. R. ChemDraw 6.0 Ultra CambridgeSoft Corporation, 100 Cambridge ParkDrive, Cambridge, MA 02140. http://www.camsoft.com. Commercial Price:  $1395.Academic Price:  $699. J. Am. Chem. Soc. 2000, 122, 10257–10258. DOI: 10.1021/ja0047572.(c) Buntrock, R. E. ChemOffice Ultra 7.0. J.Chem. Inf. Comput. Sci. 2002, 42, 1505–1506. DOI: 10.1021/ci025575p. (d) Li, Z.; Wan, H.; Shi, Y.;Ouyang, P. Personal Experience with Four Kinds of Chemical Structure DrawingSoftware: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch. J. Chem.Inf. Comput. Sci. 2004, 44, 1886–1890. DOI: 10.1021/ci049794h.(e) Mendelsohn, L. D. ChemDraw8 Ultra, Windows and Macintosh Versions. J.Chem. Inf. Comput. Sci. 2004, 44, 2225–2226. DOI: 10.1021/ci040123t. (f) Cousins, K. R. ChemDrawUltra 9.0. CambridgeSoft, 100 CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. See Web site for pricing options. J. Am. Chem. Soc. 2005, 127, 4115–4116. DOI:10.1021/ja0410237. (g) Zielesny, A. Chemistry Software PackageChemOffice Ultra 2005. J. Chem. Inf.Model. 2005, 45, 1474–1477. DOI:10.1021/ci050273j. (h) Mills, N. ChemDraw Ultra 10.0 CambridgeSoft, 100CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. CommercialPrice:  $1910 for download, $2150 for CD-ROM; Academic Price:  $710 fordownload, $800 for CD-ROM. J. Am. Chem.Soc. 2006, 128, 13649–13650. DOI: 10.1021/ja0697875. (i) Kerwin, S. M.ChemBioOffice Ultra 2010 Suite. J. Am. Chem.Soc. 2010, 132, 2466–2467. DOI: 10.1021/ja1005306. (j) Milne, G. W. A. SoftwareReview of ChemBioDraw 12.0. J. Chem. Inf.Model. 2010, 50, 2053. DOI:10.1021/ci100385n. (k) Narayanaswamy, V. K.; Rissdörfer, M.; Odhav, B.Review on CambridgeSoft ChemBioDraw Ultra 13.0v. Int. J. Theor. Appl. Sci. 2013,5, 43–49.

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