含过渡金属和柔性配体催化体系的构象搜索

doi:10.6023/cjoc202207021

摘要/Abstract

采用密度泛函理论对含有过渡金属和柔性配体的分子进行优化时, 通常只能将初始结构优化到势能面上的局部最小点, 而确定反应势能面上各中间体和过渡态的最低能量构象是准确描述一个催化反应最优路径的关键. 使用Cr/ PCCP体系催化乙烯选择性三聚/四聚反应路径中的关键过渡态(TS1, TS2, TS3)作为分子模型, 对基于Tinker软件包和CREST软件包的两种构象搜索方法进行了对比测试. 使用两种构象搜索方法均成功找到了三个分子模型的最低能量构象, 并且两种方法获得的构象数量总数相差不大. 与基于Tinker软件包的构象搜索方法相比, 使用CREST软件包进行构象搜索的计算流程更加简单, 并且大大减少了计算时间.

关键词: 过渡金属配合物, 柔性配体, 构象搜索, 密度泛函理论(DFT)

A geometry optimization on a molecular system containing a transition metal center and a flexible ligand will certainly yield a minimum on the potential energy surface (PES). However, there is no guarantee that the optimized structure is a global minimum on the PES, but a local minimum in most cases. The searching for the global minimum of each intermediate and the transition state is of crucial importance for mechanistic understanding on a specific reaction. In this work, three transition states (TS1, TS2, TS3) for the Cr/PCCP catalyzed ethylene tri-/tetramerization were selected as the molecular models, which were subjected to a sophisticated conformational search using Tinker program and CREST program, respectively. With a careful analysis, the global minimum for each of these three transition states was successfully located using either Tinker program or CREST program, and both methods generated a similar number of conformers in this study. Compared with Tinker program, the conformational screening using CREST program is more straightforward and easier to use.

Key words: transition metal complex, flexible ligand, conformational screening, density function theory (DFT)

引用此文

钟绪琴, 刘振. 含过渡金属和柔性配体催化体系的构象搜索[J]. 有机化学, 2023, 43(2): 734-741.

Xuqin Zhong, Zhen Liu. Conformational Screening of the Catalyst System Containing Transition Metal and Flexible Ligand[J]. Chinese Journal of Organic Chemistry, 2023, 43(2): 734-741.

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参考文献 22

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Entry	Molecular dynamics				GFN0-xTB	DFT calculation
Entry	Fixed atom	Steps	Temperature/K	Initial conformer ensemble	Refined conformer ensemble	Final conformer ensemble	Energy window/ (kJ•mol^-1)
1	1,2	100000000	473	10000	1453	11	59.1
2	1,2	100000000	573	10000	2125	13	37.6
3	1,2	100000000	673	10000	2901	6	16.0

Entry	Molecular dynamics				GFN0-xTB	DFT calculation
Entry	Fixed atom	Steps	Temperature/K	Initial conformer ensemble	Refined conformer ensemble	Final conformer ensemble	Energy window/ (kJ•mol^-1)
1	1,2	100000000	473	10000	1453	11	59.1
2	1,2	100000000	573	10000	2125	13	37.6
3	1,2	100000000	673	10000	2901	6	16.0

Number of conformers	Free energy/Hartree	Moments of inertia/(amu•Å²)			Bond length/nm
Number of conformers	Free energy/Hartree	I_x	I_y	I_z	β-H-Cr	γ-H-Cr	δ-H-Cr	β'-H-Cr
T-TS1-01	-2278.749756	4352	5753	7316	0.191	0.403	0.370	0.408
T-TS1-02	-2278.749149	4370	5802	7342	0.191	0.405	0.371	0.409
T-TS1-03	-2278.748547	4343	5903	7374	0.192	0.426	0.470	0.335
T-TS1-04	-2278.748273	4335	6034	7546	0.202	0.433	0.472	0.336
T-TS1-05	-2278.748137	4313	5945	7473	0.194	0.427	0.471	0.334
T-TS1-06	-2278.746676	4332	6022	7578	0.201	0.433	0.473	0.335
T-TS1-07	-2278.743619	4482	5545	7000	0.190	0.427	0.458	0.408
T-TS1-08	-2278.743565	4250	5962	7446	0.274	0.457	0.329	0.406
T-TS1-09	-2278.743516	4153	5952	7590	0.193	0.376	0.369	0.351
T-TS1-10	-2278.740752	4245	6005	7155	0.421	0.378	0.402	0.189
T-TS1-11	-2278.740313	4112	6761	8227	0.423	0.508	0.484	0.335
T-TS1-12	-2278.739514	4240	6048	7161	0.420	0.380	0.401	0.189
T-TS1-13	-2278.739294	4458	5460	6831	0.303	0.209	0.421	0.321
T-TS1-14	-2278.738767	4513	5428	6810	0.300	0.208	0.424	0.338
T-TS1-15	-2278.738175	4181	5995	7251	0.407	0.463	0.431	0.191
T-TS1-16	-2278.738063	4190	6023	7261	0.406	0.461	0.429	0.190
T-TS1-17	-2278.732524	4298	5554	6822	0.339	0.425	0.206	0.335

Number of conformers	Free energy/Hartree	Moments of inertia/(amu•Å²)			Bond length/nm
Number of conformers	Free energy/Hartree	I_x	I_y	I_z	β-H-Cr	γ-H-Cr	δ-H-Cr	β'-H-Cr
T-TS1-01	-2278.749756	4352	5753	7316	0.191	0.403	0.370	0.408
T-TS1-02	-2278.749149	4370	5802	7342	0.191	0.405	0.371	0.409
T-TS1-03	-2278.748547	4343	5903	7374	0.192	0.426	0.470	0.335
T-TS1-04	-2278.748273	4335	6034	7546	0.202	0.433	0.472	0.336
T-TS1-05	-2278.748137	4313	5945	7473	0.194	0.427	0.471	0.334
T-TS1-06	-2278.746676	4332	6022	7578	0.201	0.433	0.473	0.335
T-TS1-07	-2278.743619	4482	5545	7000	0.190	0.427	0.458	0.408
T-TS1-08	-2278.743565	4250	5962	7446	0.274	0.457	0.329	0.406
T-TS1-09	-2278.743516	4153	5952	7590	0.193	0.376	0.369	0.351
T-TS1-10	-2278.740752	4245	6005	7155	0.421	0.378	0.402	0.189
T-TS1-11	-2278.740313	4112	6761	8227	0.423	0.508	0.484	0.335
T-TS1-12	-2278.739514	4240	6048	7161	0.420	0.380	0.401	0.189
T-TS1-13	-2278.739294	4458	5460	6831	0.303	0.209	0.421	0.321
T-TS1-14	-2278.738767	4513	5428	6810	0.300	0.208	0.424	0.338
T-TS1-15	-2278.738175	4181	5995	7251	0.407	0.463	0.431	0.191
T-TS1-16	-2278.738063	4190	6023	7261	0.406	0.461	0.429	0.190
T-TS1-17	-2278.732524	4298	5554	6822	0.339	0.425	0.206	0.335

Number of conformers	Free energy/Hartree	Moments of inertia/(amu•Å²)			Bond length/nm
Number of conformers	Free energy/Hartree	I_x	I_y	I_z	β-H-Cr	γ-H-Cr
C-TS1-01	-2278.749758	4352	5752	7315	0.191	0.403
C-TS1-02	-2278.749144	4370	5801	7342	0.191	0.405
C-TS1-03	-2278.748529	4343	5902	7373	0.192	0.426
C-TS1-04	-2278.748141	4313	5945	7473	0.194	0.427
C-TS1-05	-2278.744931	4436	5661	7292	0.197	0.430
C-TS1-06	-2278.744013	4479	5705	7226	0.198	0.431
C-TS1-07	-2278.743616	4482	5545	7000	0.190	0.427
C-TS1-08	-2278.743562	4533	5670	7164	0.199	0.433
C-TS1-09	-2278.743497	4153	5952	7590	0.193	0.376
C-TS1-10	-2278.743444	4457	5597	7154	0.191	0.428
C-TS1-11	-2278.742194	4166	5960	7603	0.192	0.377
C-TS1-12	-2278.741632	4476	5699	7288	0.200	0.433
C-TS1-13	-2278.739285	4458	5461	6831	0.303	0.209
C-TS1-14	-2278.73923	4616	5288	6739	0.298	0.219
C-TS1-15	-2278.735569	4424	5988	6845	0.199	0.414
C-TS1-16	-2278.734971	4444	6051	6819	0.199	0.413