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溶剂遮掩带来的麻烦事(审稿意见) 案例来源：CCDC[1] 2067413‒2067415. New J. Chem. 2022, 46, 2465–2471. DOI[2]: 10.1039/d1nj05548h. 案例结构如图1所示（由ChemBioDraw[3]绘制）。 ▲图1 案例结构 审稿意见如下： | 审稿意见 | | **complex_5** (CCDC 2067415) -- A solvent mask has been used, and it has found 50 electrons in 185A^3. What was masked? This is most probably THF -- but that requires only 40 electrons, and we've got 50! I strongly suspect that there is a water molecule in there as well (there is evidence of this from the residual density map -- also for some of the other structures in this set!). This will lead to this information ... | **complex_5** (CCDC 2067415) 该数据适用了溶剂遮掩，并且在185立方埃中找到50个电子。遮掩掉了什么？这最有可能是四氢呋喃——但它仅需40个电子，但此处找到50个！我强烈怀疑这里也存在一个水分子（残余密度图也有证据表明这一点——这组中的其他结构同样如此！）。 这将产生以下信息。。。 |
_chemical_formula_moiety 'C43 H58 Cl2 N3 O3 Yb,1[C4H8O], 1[H2O]' _chemical_formula_sum 'C47 H68 Cl2 N3 O5 Yb' _chemical_formula_weight 998.98 | ... which is uncountably more informative and correct than your current: | |
_chemical_formula_moiety 'C43 H58 Cl2 N3 O3 Yb' _chemical_formula_sum 'C43 H58 Cl2 N3 O3 Yb' _chemical_formula_weight 908.86 | Author responds: Actually, the complex is synthesized under strict anhydrous and oxygen free conditions, and it is impossible to contain water. In the revised CIF, there was no solvent mask used and the residual densities were modelled as a disordered THF, resulting a reasonable max peak of 0.6. | 作者回应：事实上，该配合物是在严格的无水无氧条件下合成的，不可能含水。在修订的CIF中，没有使用溶剂遮掩，残余密度被建模为无序的四氢呋喃，最终得到合理的最大残余峰为0.6。 |
| **complex_4** (CCDC 2067414), **20190303a** (CCDC 2067413) The same comments regarding the solvent mask that was made elsewhere applies here. | **complex_4** (CCDC 2067414), **20190303a** (CCDC 2067413) 其他地方对溶剂遮掩的评论也适用于此。 | Author responds: In the revised CIF (complex3, CCDC 2067413 and complex4, CCDC 2067414), there was no solvent mask used and the residual densities were modelled as a disordered THF. | 作者回应：在修订的CIF（complex3, CCDC 2067413和complex4, CCDC 2067414）中，没有使用溶剂遮掩，残余密度被建模为无序的四氢呋喃。 |
对于CCDC 2067415，用Olex2[4]中的Solvent Mask[5]将主体结构之外的结构部分遮掩掉，则在176立方埃体积中找出49个电子，1个四氢呋喃的电子数是40个，多出来9个电子可对应于1个水分子，1个水分子的电子数是10个，而使用PLATON[6]的SQUEEZE[7]将主体结构之外的结构部分挤压掉，则在160立方埃的体积中找到42个电子，如图2所示，较为符合1个四氢呋喃。（Solvent Mask和SQUEEZE算法不同，因此遮掩/挤压后计算得到的电子数/体积不同。） ▲图2 Olex2/Solvent Mask和PLATON/SQUEEZE结果 上述溶剂遮掩/挤压后Max Peak为0.5，而把溶剂建模出来（此处为四氢呋喃）后Max Peak为0.6，相差无几，也是非常合理的，如图3所示。 ▲图3 建模好溶剂的结果 视频讲解请参阅： 溶剂遮掩带来的麻烦事(审稿意见)：https://www.bilibili.com/video/BV1KqfBYuE4c 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 for Standardization(2022). ISO 26324:2022. Information andDocumentation – 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. [4] Dolomanov, O. V.;Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H. OLEX2: A Complete Structure Solution,Refinement and Analysis Program. J. Appl. Cryst. 2009, 42, 339–341. DOI: 10.1107/S0021889808042726. [5] Spek, A. L.; vander Sluis, P. BYPASS: An EffectiveMethod for the Refinement of Crystal Structures Containing Disordered SolventRegions. Acta Cryst. 1990, A46, 194–201. DOI:10.1107/S0108767389011189. [6] (a) Spek, A. L. Single-CrystalStructure Validation with the Program PLATON.J. Appl. Cryst. 2003, 36, 7–13. DOI: 10.1107/S0021889802022112.(b) Spek, A. L. StructureValidation in Chemical Crystallography. ActaCryst. 2009, D65, 148–155. DOI:10.1107/S090744490804362X. (c) Spek, A. L. What Makes a Crystal Structure Report Valid? Inorg. Chim. Acta 2018, 470, 232–237. DOI:10.1016/j.ica.2017.04.036. (d) Spek, A. L. checkCIFValidation ALERTS: What They Mean and How to Respond. Acta Cryst. 2020, E76, 1–11. DOI: 10.1107/S2056989019016244. [7] Spek, A. L. PLATON SQUEEZE: A Tool for theCalculation of the Disordered Solvent Contribution to the Calculated StructureFactors. Acta Cryst. 2015, C71, 9–18. DOI:10.1107/S2053229614024929. 声明：本文仅代表个人观点，笔者学识有限，资料整理过程中可能存在疏漏错误，请不吝指正。 如需PDF文档，请从以下链接下载： 通过网盘分享的文件：溶剂遮掩带来的麻烦事(审稿意见).pdf
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发表于 2025-8-20 07:54:19
