容易无序的分子片段3

DJ_Tokyo

容易无序的分子片段3

本次带来的案例分子片段是2,5-二取代噻唑并[5,4-d]噻唑，如图1所示（由ChemBioDraw[1]绘制）。

▲图1 2,5-二取代噻唑并[5,4-d]噻唑分子片段

该分子片段对呈中心对称，水平方向双键中心为对称中心，像这样具有较高对称性的片段无序的可能性很高，如图2所示（由Olex2[2]呈现）为某个晶体结构中含有的2,5-二取代噻唑并[5,4-d]噻唑结构片段，从差值电子密度图来看，显然存在取向无序，第二组分无序的硫原子（重原子）靠近第一组分无序的氮原子（轻原子），受此影响导致氮原子非正定。

▲图2 2,5-二取代噻唑并[5,4-d]噻唑及其附近差值电子密度图

对于这种情况，可设计二组分取向无序，如图3所示。

▲图3 无序方案

按照上述无序方案对该2,5-二取代噻唑并[5,4-d]噻唑结构片段做二组分无序处理，并用SHELXL[3]指令SIMU（参阅推文“SHELXL指令之SIMU”）对两个无序组分原子（包括与之直接相连的有序原子）各向异性位移参数进行相似性限制，结果如图4所示，两个无序组分原子椭球均正常，并且差值电子密度图也非常干净。

▲图4 2,5-二取代噻唑并[5,4-d]噻唑二组分取向无序处理结果

两个无序组分单独显示如图5所示。

▲图5 2,5-二取代噻唑并[5,4-d]噻唑二组分取向无序组分

视频讲解请参阅：

容易无序的分子片段3：https://www.bilibili.com/video/BV14R35zwEWv

参考文献

[1]    (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.

[2]    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.

[3]    (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. Crystal Structure 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 ScatteringFactors for SHELXL – Model,Implementation and Application. ActaCryst. 2019, A75, 50–62. DOI:10.1107/S2053273318013840.

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：容易无序的分子片段3.pdf

链接: https://pan.baidu.com/s/1fEXejW4QVEV7yIGbksHrdg 提取码: ugxm