甲苯无序处理和理解案例1

DJ_Tokyo

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甲苯无序处理和理解案例1

案例来源：CCDC [1]: 2239523, 2532656.DOI [2]:10.5517/ccdc.csd.cc2f5dpq, 10.5517/ccdc.csd.cc2r0flt. (J. Mol. Struct. 2025,1339, 142404. DOI: 10.1016/j.molstruc.2025.142404.)

如图1所示（由Olex2 [3]呈现），四个共面残余峰形成类似硝酸根形状，其中Q1、Q2和Q3颜色较深，Q4颜色较浅。

▲图1 四个残余峰

在Olex2左下角命令行输入grow（大小写均可）并回车，结果如图2所示，由Q1-Q4对称操作产生的另外四个残余峰组成的片段看起来像是对二甲苯 [4]（pTol, para-Xylene, CAS: 106-42-3, CCDC: 1201987 [4a], 1318981 [4b], 1318982 [4c], 200340(pTol-d10,deuterated para-xylene, CAS: 41051-88-1) [4d], 2154572–2154580(pTol-d10)[4e], 2151091 [4e]），但该配合物培养晶体用的溶剂并非对二甲苯，而是甲苯 [5]（Tol, toluene, CAS: 108-88-3, CCDC: 1273751 [5a], 1273752 [5b], 1273753 [5c], 725245 [5d], 1430464–1430470 [5e], 2377542 [5f]），Q4颜色更浅（即峰强更弱）也表明Q4要么是比其他Q峰更小的原子或更小的占有率，而从培养晶体所用溶剂可以判定其为甲苯，即所有Q峰均为碳原子，所以Q4是比其他Q峰具有更小的占有率。

▲图2 四个Q峰+对称操作产生的四个Q峰组成的片段

将这些Q峰定为碳原子，并查看差值电子密度图（Olex2中按Ctrl+M快捷组合键，参阅推文“Olex2快捷键总结”），如图3所示，甲基碳原子处为负的差值电子密度（红色），表明该碳原子为部分占据，而非全占位。

▲图3 差值电子密度

用Mercury [6]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4所示，该甲苯分子处于倒**心对称元素。

▲图4 查看对称元素

对于本案例处于倒**心对称元素上的甲苯分子，有两种处理方式，普通无序处理和特殊无序处理。

>>普通无序处理

普通无序处理很简单，对甲基碳进行分组，并将其占有率设为0.5，在Olex2中选中甲基碳，输入“part 1 10.5”并回车，然后精修，加氢即可，结果如图5所示，左侧为不对称单元（ASU, asymmetric unit）结构，右侧为生长得到的完整结构。

▲图5 普通无序处理结果

如果查看单独两个无序组分完整结构，如图6所示，第一组分是半个对二甲苯，第二组分是半个苯 [7]（C6H6, benzene, CAS: 71-43-2,CCDC: 1108749–1108750 [7a], 1108751 [7b], 1108752 [7c], 1108753 [7d], 1108754 [7e], 1108755–1108756(C6D6,deuterated benzene, CAS: 1076-43-3) [7f], 1108757–1108759 [7g], 298305–298307 [7h], 682617 [7i], 757059–757061 [7j], 725244 [7k], 1454032 [7l], 1423904 [7m], 1579553 [7n], 1579564 [7n], 1581798 [7n], 1581824 [7n], 1843296 [7o], 1843297 [7p], 1913527 [q7], 2201163 [7r]）。

▲图6 普通无序处理的两个无序组分

如图7所示，该处于倒**心对称元素的无序甲苯差值电子密度形状形似对二甲苯，在不对称单元中只有一半的甲苯，其无序表现为甲基和氢的无序，两者所连的苯环碳由于不对称单元中只有半个甲苯而重合为同一个碳，因此做无序组分对称操作后，两个组分表观上看起来是半个对二甲苯和半个苯（0.5(C8H10) + 0.5(C6H6)= C7H8），但不能做此理解，应当理解为底部的实际结构，即甲基朝向相反的两个半个甲苯（0.5(C7H8) + 0.5(C7H8)= C7H8）。

▲图7 普通无序处理结果理解

>>特殊无序处理

特殊无序处理则是将对称操作产生的原子用“part -c”指令（“part”和“-c”之间有一个空格，c必须为小写）固定下来，然后删去其中一个甲基碳，对剩下的甲苯骨架用“part -1 10.5”进行分组和占有率设置，结果如图8所示。

▲图8 甲苯特殊无序处理结果（不对称单元）

其另外一个组分如图9所示，两个组分苯环六个碳错位分布。

▲图9 甲苯特殊无序处理结果（完整结构）

上述两种处理均可，只不过普通无序处理结果理解上需要绕个弯，而特殊无序处理结构更加容易理解，从晶体学角度以及简洁的角度来说，普通无序处理结果更佳，因其参数更少，故而数据参数比更高，例如本案例中普通无序处理结果数据参数比为14.7，特殊无序处理结果数据参数比则为13.4，如果数据参数比太低，可能会触发警报PLAT088（参阅推文“CheckCIF-PLAT088”）、PLAT089（参阅推文“CheckCIF-PLAT089”）或PLAT090（参阅推文“CheckCIF-PLAT090”）。

相关视频：

单晶结构解析练习746(文献案例-数据还原-无序处理)：https://www.bilibili.com/video/BV1MUwFzqEvM

如需数据进行练习，请从以下链接下载：

链接：https://pan.baidu.com/s/1JpfZkmOE5hsYckL3P7_K8w?pwd=migi

提取码：migi

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