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晶体数据审稿意见-原子编号和排序 最近，B站有小伙伴留言遇到如图1所示审稿意见。 ▲图1 问题描述 该审稿意见大意如下： 原子名称尚未从SHELXL[1]中的初始解中更新。按照合理的顺序给原子起化学上有意义的名称。 出现这个审稿意见，大概率是用SHELX结构解析程序SHELXT[2]解析结构模型后，没有对SHELXT程序赋予原子的名称（编号或标签）进行修改，即审稿人所说的化学上有意义的名称。 那么什么是化学上有意义的原子编号呢？ 其实很多特定骨架会有特定的编号，例如吲哚的编号如图2所示（由ChemBioDraw[3]绘制）。 ▲图2 吲哚的编号 因此在晶体结构中，如果需要按照特定骨架进行编号，那就按照该骨架约定俗成的编号进行原子编号即可。 不过，像这样的骨架特定编号有时并不包含所有原子，例如上述吲哚骨架中，两个环共用的两个碳原子就没有编号，但晶体结构中每个原子都必须有编号，例如对于论文“Sci.China Chem. 2023, 66, 117‒126. DOI[4]: 10.1007/s11426-022-1396-x.”中CCDC[5]存储号为2152655的结构，其非氢原子编号如图3所示（由Olex2[6]呈现），吲哚骨架原子编号并未采取吲哚的编号，而是整体结构采用具有一定顺利逻辑的编号。 ▲图3 CCDC 2152655结构原子编号 如图是用SHELXT解析的结构模型，则SHELXT会赋予每个原子四个字符满编的混乱无序没有逻辑的原子编号，如图4所示，对于这种情况，需要自己设计一种有序的、有逻辑的和有（化学）意义的原子编号，否则就有可能得到上述审稿意见。 ▲图4 SHELXT程序给原子赋予的原子编号 视频讲解请参阅： 晶体数据审稿意见-原子编号和排序：https://www.bilibili.com/video/BV1BAkkYFEdN 相关推文： 参考文献 [1] (a) Sheldrick, G. M. SHELXL-2019/3,Program for Crystal Structure Refinement,University of Göttingen, Germany, 2019. (b) Sheldrick, G. M. A Short History of SHELX. Acta Cryst. 2008, A64, 112–122. DOI: 10.1107/S0108767307043930. (c) Sheldrick, G. M. CrystalStructure Refinement with SHELXL. Acta Cryst. 2015, C71, 3–8. DOI:10.1107/S2053229614024218. (d) Lübben, J.; Wandtke, C. M.; Hübschle, C. B.; Ruf, M.;Sheldrick, G. M.; Dittrich, B. Aspherical Scattering Factors for SHELXL – Model, Implementation andApplication. Acta Cryst. 2019, A75, 50–62. DOI:10.1107/S2053273318013840. [2] Sheldrick, G. M. SHELXT – Integrated Space-Group and Crystal StructureDetermination. Acta Cryst. 2015, A71, 3–8. DOI: 10.1107/S2053273314026370. [3] (a) Klein, F. M. CS ChemDraw Pro,1 Version3.1 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] (a) International Organization forStandardization (2012). ISO 26324:2012. Informationand 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[5] (a) Allen, F. H. The Cambridge StructuralDatabase: A Quarter of a Million Crystal Structures and 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 III2021, 413–437. DOI: 10.1016/B978-0-12-409547-2.14829-2. [6] 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. 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：晶体数据审稿意见-原子编号和排序.pdf
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