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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。 特殊无序晶体结构绘图案例2(文献案例) 最近在B站有小伙伴私信如图1所示问题，即如何在Olex2 [1]中将图示穿过对称轴的无序（特殊无序）的两个无序组分都显示出来，以及该案例如何用Diamond [2]绘图，并通过邮箱将论文和晶体数据CIF [3]文件发了过来，如图2所示。 ▲图1 问题描述 ▲图2 数据发送 案例数据为CCDC [4]: 1885425，来自论文“CrystEngComm 2019, 21, 5095–5105. DOI [5]: 10.1039/c9ce00661c.”，其结构为5-氟脲嘧啶 [6]（5FU, 5-fluorouracil, CAS: 51-21-8, CCDC:1161431 [6a], 250467–250468 [6b], 257856 [6b], 1161432–1161441 [6b], 873160 [6c], 1997262 [6d], 616141–616143 [6e],）和水杨酸（SA, salicylic acid, CAS: 69-72-7, CCDC: 1254506[7a], 1254507 [7b], 1254508–1254509 [7c], 1254510–1254511 [7d], 297104 [7e], 276208 [7f], 871047 [7g], 737930 [7h], 836668 [7i], 1423858 [7j], 1557027 [7k], 1545143 [7l], 1962102–1962105 [7m], 2161488 [7n], 2412885 [7o], 2431098 [7p], [7q], [7r], [7s],[7t],）2:1共晶，分子式为C15H12F2N4O7，如图3所示（由ChemBioDraw[8]绘制）。 ▲图3 CCDC 1885425结构 以下简单介绍Olex2、Diamond和Mercury [9]三个软件绘图操作步骤。 >>Olex2绘图步骤 用Olex2打开1885425.cif文件，显示不对称单元（ASU, asymmetric unit）结构，如图4所示，黑色标签为原子编号方案，在Work选项卡下ToolboxWork展开栏Labels下拉菜单中选择Parts，水杨酸上除了C7之外的所有原子均有绿色“-1”标签，表明水杨酸除了C7之外均作了特殊无序处理。 ▲图4 CCDC 1885425不对称单元结构 由于C7未作无序处理，因此在Olex2左下角命令行输入“grow”并回车，可得水杨酸的第二个无序组分，如图5所示。 ▲图5 水杨酸第二无序组分显示 随后，再输入“grow -w”（注：“grow”和“-w”之间有一个空格）并回车，得到另一个5-氟脲嘧啶，如图6所示，随后即可按照正常流程绘图并输出图片。（参阅视频“Olex2基操-Grow主体分子后接着Grow溶剂分子：https://www.bilibili.com/video/BV1YP411K7zf”。） ▲图6 预期效果 在此处讲解一下该结构中水杨酸的无序，在Mercury中查看对称元素（参阅视频“Mercury基操-查看对称元素：https://www.bilibili.com/video/BV1U44y1U7ZF”），如图7所示，水杨酸处于2次轴（2-foldaxis）上（C7处于2次轴上，故而C7未做无序处理，其他原子做了无序处理（特殊无序处理），即PART -1 10.50000），由于水杨酸处于2次轴上，因此水杨酸在空间上存在两个方向（取向）排布，比例为50%:50%（因为处于2次轴上）。 ▲图7 用Mercury查看对称元素 对于本案例5-氟脲嘧啶和水杨酸2:1共晶结构，如图8所示，仅从化学意义上来看，就是5-氟脲嘧啶和水杨酸2:1共晶结构，水杨酸羟基上的质子和羧酸基团的羰基氧形成分子内氢键，羧酸基团上的质子和5-氟脲嘧啶的羰基氧形成分子间氢键，而5-氟脲嘧啶和水杨酸比例为2:1，这意味着晶体中有一半（50%）的5-氟脲嘧啶并不与水杨酸形成分子间氢键，晶体中5-氟脲嘧啶是有序的，其实际结构为：有50%的水杨酸和左边的5-氟脲嘧啶形成分子间氢键（不与右边的5-氟脲嘧啶形成分子间氢键），另外50%的水杨酸和右边的5-氟脲嘧啶形成分子间氢键（不与左边的5-氟脲嘧啶形成分子间氢键）。 ▲图8 无序结构理解 >>Diamond绘图步骤 用Diamond打开1885425.cif文件，如图9所示。 ▲图9 Diamond打开1885425.cif文件 点击底部的直接填充配位球（FillCoordination Spheres）按钮（或按快捷组合键Shift+Ctrl+S）直至得到完整的水杨酸无序组分，如图10所示。 ▲图10 得到全部水杨酸无序组分 选中右侧羧酸基团的质子，然后点击底部的创建所选原子的邻近原子（Create Atoms' Neighbouring Atoms）按钮（或按快捷组合键Shift+Ctrl+X），得到该质子邻近的一个氧、一个氢和一个氟，如图11所示。 ▲图11 创建所选原子的邻近原子 然后选中上述步骤创建的三个原子，接着按补全片段（Complete Fragments）按钮（或按快捷组合键Shift+Ctrl+F），得到完整的5-氟脲嘧啶分子，如图12所示。 ▲图12 得到完整结构 随后删除水杨酸无序组分之间的键，再添加氢键，如图13所示，之后设置原子和键的样式，输出图片即可。 ▲图13 最终效果 >>Mercury绘图步骤 用Mercury打开1885425.cif文件，如图14所示，程序直接显示水杨酸的全部无序组分。 ▲图14 Mercury打开1885425.cif文件 勾选底部的“H-Bond”，结果如图15所示。 ▲图15 Display Options>>Display>>H-Bond 点击右侧虚线所连氧原子（红色箭头所指）得到右侧完整5-氟脲嘧啶分子，如图16所示。 ▲图16 得到另一个5-氟脲嘧啶分子 随后取消勾选“H-Bond”，结果如图17所示。 ▲图17 完整结构 随后，在顶部菜单Edit下拉菜单中选择Edit Structure，在弹出的Edit Structure对话框下Add功能区点击Bonds使其激活，从其右侧下拉菜单中选择Pi，然后点击水杨酸羧酸基团的质子和5-氟脲嘧啶上的氧，插入虚线，如图18所示。（注：经笔者摸索，发现应先添加虚线，再通过“H-Bond”得到右侧5-氟脲嘧啶分子，否则添加虚线后该分子自动消失。） ▲图18 最终效果 视频讲解和操作演示请参阅： 特殊无序晶体结构绘图案例2(文献案例)：https://www.bilibili.com/video/BV1QBAfzGEhG 如需论文PDF和CIF文件，请从以下链接下载： 提取码: 6jwg 参考文献 [1] Dolomanov,O. 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