晶体数据还原示例44(选点定晶胞)

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晶体数据还原示例44(选点定晶胞)

案例来源：CCDC[1] 2212724. Organometallics 2023, 42, 81‒90. DOI[2]:10.1021/acs.organomet.2c00524.

案例结构如图1所示（由ChemBioDraw[3]绘制）。

▲图1 案例结构

原始衍射图文件为4轮数据，共计1464个sfrm文件，总大小为384 MB。其衍射图如图2所示（由APEX4[4]呈现），钼靶测试，曝光时间为10秒。

▲图2 衍射图样

按照默认设置（10.00信噪比阈值，3轮数据，每轮20帧sfrm）共收集到837个衍射点，施加限制条件后剩下365个衍射点用于中指标化，得到的晶胞参数和Bravais Lattice结果如图3所示。

▲图3 默认设置收集衍射点结果

在XPREP[5]中给出空间群为第2号空间群Pī，如图4所示，不过注意到综合诊断指标CFOM（combined figure of merit）很高（24.55）。

▲图4 第14号空间群Pī

在Olex2[6]中运行SHELXT[7]解析初始结构模型，结果如图5所示，不对称单元ASU（asymmetry unit）中有1.5个分子结构。

▲图5 SHELXT解析结果

精修结果如图6所示，各项指标参数都很好（R1 = 1.96%, wR2 = 6.51%, GooF= 0.933），但不论如何精修，均无法收敛（Shift = -4.645），SHELXL[8]输出提示“Maximum = ‒4.645 for U23 Lu02”（金属Lu02的各向异性位移参数分量U23无法收敛）。

▲图6 SHELXL精修结果

PLATON[9]验证报告（Validation Report）如图7所示，PLAT110（参阅推文“CheckCIF-PLAT110”）、PLAT112（参阅推文“CheckCIF-PLAT112”）和PLAT113（参阅推文“CheckCIF-PLAT113”）等3个B级警报表明存在更高对称性。

▲图7 PLATON验证报告

于是用PLATON进行空间群变换，结果如图8所示，晶胞变小，晶胞参数为原来的1/3，然而HKLF4指令后变换矩阵均为非整数，导致非整数/无效密勒指数，致使25751个无效衍射点被移除，显然，这个需要重新还原（参阅视频“Olex2晶体解析与精修实例126(审稿意见)：https://www.bilibili.com/video/BV1ee411M7DZ”），虽然处理后残余峰降下来并且无AB级警报，如图9所示，不过Shift只能收敛至0.013，SHELXL提示“Maximum = 0.013 for z Lu01”（金属Lu01的z坐标无法收敛）。

▲图8 晶胞变换后出现的提示

▲图9 晶胞变换后精修结果

晶胞变换后，晶胞参数由

“a = 14.0702(10) Å, b= 16.1528(11) Å, c = 16.6864(12) Å, α = 80.618(1)°, β = 68.554(1)°, γ =65.675°, V = 3216.3(4) Å3”

变更为

“a = 8.8276(4) Å, b= 11.2622(6) Å, c = 11.4705(5) Å, α = 89.445(5)°, β = 86.745(6)°, γ = 70.338(4)°,V = 1072.10(9) Å3”。

返回APEX4，收集少一些衍射点，如422个衍射点，限制后剩下159个衍射用于指标化，得到上述空间群变换后相同的晶胞参数，如图10所示。

▲图10 数量较少的衍射点指标化结果

按照正确晶胞进行数据还原，结构精修收敛的很好，如图11所示。

▲图11 正确晶胞还原结果

视频操作：

单晶结构解析练习327(数据还原-文献案例)：https://www.bilibili.com/video/BV1HDiCYsEZm

数据下载：

论文PDF和CIF文件：

链接: https://pan.baidu.com/s/1zWFo37QFnu5zDe3azH5XTg

提取码: 37k4

2212724（Lu）：

链接:https://pan.baidu.com/s/13o0OnU75hhRdLBEslej7ZA

提取码: ja4m

参考文献

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