晶体测试案例151(降低Rint-光源选择和曝光时间)

DJ_Tokyo

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晶体测试案例151(降低Rint-光源选择和曝光时间)

最近，某课题组利用吲哚骨架手性配体与三甲基硅基亚甲基亚铜 [1]（[CuCH2SiMe3]4, CCDC [2]: 1214451）以四氢呋喃 [3]（THF, tetrahydrofuran, CAS: 109-99-9, CCDC: 1116822–1116823 [3a], 1116824–1116825 [3b]）为溶剂进行反应，脱去四甲基硅烷（SiMe4, tetramethylsilane, CAS: 75-76-3），以期得到该配体参与配位成键的铜配合物，如图1所示（由ChemBioDraw[4]绘制）。

▲图1 反应式

反应后处理所得产物利用甲苯 [5]（Tol,toluene, CAS: 108-88-3, CCDC: 1273751 [5a], 1273752 [5b], 1273753 [5c], 725245 [5d], 1430464–1430470 [5e], 2377542 [5f]）作为溶剂进行结晶，所得晶体进行单晶X射线衍射（SC-XRD, single-crystal X-ray diffraction）实验，得到晶体数据，找笔者帮忙解析。

第一个数据是用铜靶测试，曝光时间5秒，共46轮数据，6833帧衍射图，总大小为10.3 GB，其衍射图如图2所示（由APEX6 [6]呈现）。

▲图2 铜靶数据衍射图

第一次处理，结构没解出来（后来发现是晶胞定错了），该铜靶数据共46轮数据，绝大数轮数据都没有衍射点，考虑到结构中含有比硅（Si）更大的原子，因此其绝对结构可以用钼靶测试（参阅推文“精修程序提示-绝对结构无法可靠确定(补充)”），故而将情况反馈并给出建议，如图3所示。

▲图3 情况反馈和建议

后来按照正确晶胞处理，是可以得到结构的，只是数据很差，如图4所示（由Olex2[7]呈现），Rint非常高（123.46%），不过表征绝对结构的参数Hooft y [8]、Parson's q [9]和Flack x [10]都还比较小。

▲图4 铜靶数据结果

情况反馈和建议后，对方表示在铜靶数据之前，其实有一个钼靶测试的数据，曝光时间为2秒，共8轮数据，2070帧衍射图，总大小为3.13 GB，其衍射图如图5所示，在该曝光时间下，衍射弱，分辨率低。

▲图5 钼靶数据衍射图

对其进行数据还原，也能够解出结构，只是Rint很高（35.08%），远高于18%（参阅推文“CheckCIF-Rint值触发警报的界限”），该数据有一个A级警报PLAT020（参阅推文“CheckCIF-PLAT020”），以及三个B级警报PLAT090（参阅推文“CheckCIF-PLAT090”）、PLAT342（参阅推文“CheckCIF-PLAT342”）和PLAT987（参阅推文“CheckCIF-PLAT987”）（验证报告由PLATON [11]呈现），如图6所示。

▲图6 钼靶数据结果

钼靶的这个数据，显然比铜靶数据好多了，只是曝光时间短了些，导致衍射弱，最终结果数据指标不理想，于是建议其增加曝光时间，用钼靶重新测个数据，如图7所示。

▲图7 建议

后来用钼靶重新测试，曝光时间设置为15秒，测定晶胞后，Bravais Lattice选择Monoclinic P，对称性选择Chiral (2)来计算数据收集策略，总共9轮数据，2484帧衍射图，总大小4.05 GB，其衍射图如图8所示。

▲图8 增加曝光时间重新测试的钼靶数据衍射图

重测数据结果如图9所示，数据各项指标都非常好。

▲图9 增加曝光时间重新测试的钼靶数据结果

三个数据对比如下表：

项目	260723k	260723i	260724j
辐射光源	铜靶	钼靶	钼靶
衍射图轮数	46	8	9
衍射图帧数	6833	2070	2484
衍射图大小	10.3 GB	3.13 GB	4.05 GB
分辨率（d min）/Å	0.83	0.84	0.74
信噪比（I/σ(I)）	2.0	5.7	44.1
Rint	123.46%	35.08%	2.91%
完整度（completeness）	98.5%	99.0%	99.8%
Max Peak/e·Å–3	3.4	1.5	0.5
Min Peak/e·Å–3	-4.3	-1.2	-0.2
拟合优度（GooF）	1.117	1.026	1.032
R1	20.64%	9.84%	2.41%
wR2	48.93%	26.23%	6.43%

由此可见，选择合适的辐射光源，设置适当的曝光时间，才能够得到良好的数据结果。

关于结构，由于[CuCH2SiMe]4是通过碘化亚铜 [12]（CuI, Copper(I) iodide, CAS: 7681-65-4; CCDC: 1594151 [12a], 1600048 [12b], 1600783–1600784 [12c], 1602525 [12d], 1604540–1604544 [12e], 1604707 [12f], 1606466–1606471 [12g], 1608909[12h], 1624288 [12i], 1637167 [12j], 1638550–1638554 [12k], 1640440–1640481 [12l], 1644229[12m], 1673978–1673979 [12n], 1679593–1679618 [12o], 1679963–1679964 [12p],1713334–1713337 [12q], 2149217 [12r]）和三甲基硅基亚甲基锂 [13]（LiCH2SiMe3）（LiCH2SiMe3 [13b], [(Trimethylsilyl)methyl]lithium, CAS:1822-00-0; 晶体结构表明三甲基硅基亚甲基锂有四聚体和六聚体形式：(LiCH2SiMe3)4 [13a, 13d], CAS:14322-84-0, 210177-05-2; (LiCH2SiMe3)6 [13c, 13e-h], CAS:110558-46-8; CCDC: 1181797 [13c], 1960466 [13h]）合成的，可能是后处理没有分离干净，导致所合成的[CuCH2SiMe]4不纯，含有原料CuI或LiCH2SiMe3，因此所得结构中含有碘或锂，如图10–12所示。

▲图10 结构问题讨论

▲图11 结构问题讨论

▲图12 结构问题讨论

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