Transition State Conformers#
过渡态构象 #
After we successfully searched for a TS with NEB-TS, we should consider its conformational flexibility via a fully automatic conformer search with GOAT.
This is important as the conformation of the TS structure can influence the resulting reaction barrier significantly. Often, the TS is even more affected than minimum structures of the reactants and products
due to the sterically crowded situation of adjacent substituents and ligands.
在成功使用 NEB-TS 搜索到过渡态后，我们应通过 GOAT 进行全自动构象搜索来考虑其构象灵活性。这一点至关重要，因为过渡态结构的构象会显著影响最终的反应能垒。通常，过渡态受到的影响甚至比反应物和产物的最小结构更大，这是由于相邻取代基和配体的空间拥挤情况所致。
Figure: Schematic energy diagram of the conformational space of reactant, TS, and product.
图：反应物、过渡态和产物的构象空间示意图能级图。#
Per default, GOAT would search for the relaxed global minimum structures and respective conformers. For a TS conformer search, we typically want to keep the atoms fixed that are directly
involved in the chemical transformation. To do so, we can use the constraint functionality within ORCA to modify our GOAT procedure.
默认情况下，GOAT 会搜索松弛的全局最小结构及其相应构象。对于过渡态构象搜索，我们通常希望固定那些直接参与化学转化的原子。为此，我们可以利用 ORCA 中的约束功能来调整 GOAT 流程。
!XTB GOAT
%GEOM
Constraints
{C 0 C} # Constrain Cartesian coordinate of atom 0
{B 0 1 C} # Constrain bond of atoms 0 and 1
{A 0 1 2 C } # Constrain angle between atoms 0, 1, and 2
{D 0 1 2 3 C } # Constrain dihedral angle between atoms 0, 1, 2, and 3
END
END
*XYZFILE 0 1 ts.xyz
Warning 警告
Note, that ORCA starts counting at 0! Therefore, the first atom in your XYZ file will be atom 0.
注意，ORCA 从 0 开始计数！因此，XYZ 文件中的第一个原子将是原子 0。
Example: Olefin Metathesis#
示例：烯烃复分解反应
In this example, we will search for conformers of the transition state of a olefin metathesis reaction by a Schrock metathesis catalyst.
在此示例中，我们将通过 Schrock 烯烃复分解催化剂搜索烯烃复分解反应过渡态的构象。
Figure: TS of an olefin metathesis at a Schrock catalyst. Hydrogens are omitted for clarity.
图：在 Schrock 催化剂作用下的烯烃复分解反应过渡态。为清晰起见，氢原子未显示。#
The transition state of this reaction was found and optimized using the NEB-TS procedure with the GFN2-xTB method. In this case, the important atoms that are involved
in our reaction are the central molybdenum and the adjacent carbon atoms of the previous carbene ligand and the attacking alkene. We could also also include the
通过使用 GFN2-xTB 方法的 NEB-TS 程序，我们找到了并优化了该反应的过渡态。在此情况下，反应中涉及的关键原子是中心的钼原子、前卡宾配体的相邻碳原子以及进攻的烯烃。我们还可以包括烯烃的
!XTB GOAT
%PAL
NPROCS 16
END
%GEOM
Constraints
{ C 0 C }
{ C 1 C }
{ C 2 C }
END
END
*XYZFILE 0 1 ts.xyz
Note 注释
Note, that we increased the number of processing cores to 16 to benefit from the high parallelity of the GOAT approach. Conformational searches for large, flexible molecules can be
very time consuming. Therefore, a combination of fast semi-empirical methods like GFN2-xTB and an increased number of cores is recommended.
注意，我们将处理核心数量增加到 16，以充分利用 GOAT 方法的高度并行性。对于大型、柔性分子的构象搜索可能非常耗时。因此，建议结合使用 GFN2-xTB 等快速半经验方法并增加核心数量。
We now run the GOAT conformer search with constrained Cartesian coordinates of the respective atoms Mo0, C1, and C2. After a successful GOAT run, it will give us a list of generated conformers ordered
by increasing energy with respect to the newly found global minimum structure.
我们现在使用受限的笛卡尔坐标对相应原子 Mo0、C1 和 C2 进行 GOAT 构象搜索。成功运行 GOAT 后，将为我们提供一个按能量递增顺序排列的生成构象列表，相对于新发现的全局最小结构。
Global minimum found!
Writing structure to orca.globalminimum.xyz
# Final ensemble info #
Conformer Energy Degen. % total % cumul.
(kcal/mol)
------------------------------------------------------
0 0.000 1 24.18 24.18
1 0.390 1 12.52 36.70
2 0.440 1 11.51 48.21
3 0.457 1 11.18 59.40
4 0.595 1 8.86 68.26
5 0.743 1 6.90 75.15
6 0.838 1 5.88 81.03
7 1.007 1 4.42 85.45
8 1.186 1 3.26 88.72
9 1.423 1 2.19 90.91
10 1.640 1 1.52 92.43
11 1.649 1 1.50 93.92
12 1.867 1 1.03 94.96
13 2.105 1 0.69 95.65
14 2.205 1 0.59 96.23
[...]
Important 重要
As we employed constraints in our GOAT run, the produced conformers are no fully optimized transition state structures! In any case, they should be finally optimized using the OptTS keyword.
This will also influence the energetic ranking. In general, the conformer ensemble should be refined afterwards using more accurate DFT or WFT methods to obtain more reliable results.
由于我们在 GOAT 运行中采用了约束条件，生成的构象并非完全优化的过渡态结构！无论如何，它们最终应使用 OptTS 关键字进行优化。这也会影响能量排序。通常，随后应采用更精确的 DFT 或 WFT 方法对构象集合进行精炼，以获得更可靠的结果。
We can now visualize a selection of generated conformers that are stored in the basename.finalensemble.xyz file, and we see that the constrained atoms were perfectly kept in place during the GOAT run.
我们现在可以可视化存储在 basename.finalensemble.xyz 文件中的一部分生成的构象，并观察到在 GOAT 运行过程中，受约束的原子被完美地固定在原位。
Figure: a) Overlay of selected conformers. b) Structures of selected conformers with their respective relative energies in kcal·mol-1.
图：a) 选定构象的重叠图。b) 选定构象的结构及其相应的相对能量（单位：kcal·mol -1 ）。#
If we compare the energy of the yet unoptimized transition state conformers from our GOAT run with that of the input TS, we see that the new global minimum structure is 6.44 kcal·mol-1 lower
in energy even without further optimization! The respective absolute energies can be found in the second lines of the basename.xyz (starting structure) and the basename.globalminimum.xyz files.
如果我们比较 GOAT 运行中尚未优化的过渡态构象的能量与输入的过渡态能量，我们会发现新的全局最小结构即使在未进一步优化的情况下，能量也降低了 6.44 kcal·mol -1 ！相应的绝对能量可以在 basename.xyz （起始结构）和 basename.globalminimum.xyz 文件的第二行中找到。
Structures# 结构
Input TS 输入 TS
93
Mo 0.06370 -0.28863 0.17017
C 0.84164 1.72537 0.43582
C 1.52344 0.27689 -1.34600
N -1.30128 0.25044 -0.75171
H -0.26969 -1.66376 -2.17422
H -0.65136 -2.81825 -3.45835
O -0.13617 -0.25848 2.24034
O 0.24700 -2.21112 0.37092
C 0.29419 -3.38192 1.05902
C -0.87377 0.21756 3.27512
C 0.73152 -4.53803 0.11457
C 1.24180 -3.35491 2.26679
C -1.16124 -3.71156 1.51808
C -0.62468 -0.73377 4.47753
C -0.33212 1.61191 3.70153
C -2.38966 0.31326 3.01714
F 0.67837 -0.84486 4.76724
F -1.24454 -0.36792 5.60296
F -1.05256 -1.97058 4.20136
F 0.99985 1.62713 3.79032
F -0.67075 2.56002 2.81769
F -0.80967 2.02886 4.88113
F 2.05670 -4.54676 -0.07838
F 0.42022 -5.73790 0.61587
F 0.17337 -4.44442 -1.09317
F -1.85881 -4.38139 0.59326
F -1.22045 -4.43558 2.63398
F -1.83646 -2.57517 1.73710
H 2.26257 -3.19419 1.92236
H 0.95694 -2.53229 2.91766
H 1.18788 -4.28984 2.81931
H -2.95262 -0.12159 3.83922
H -2.69463 1.34778 2.89170
H -2.60955 -0.23578 2.10094
C -2.30522 0.64608 -1.56169
C -2.31329 -1.58274 -2.87226
C -2.75620 2.63558 -0.04011
C -2.96097 1.88302 -1.33234
C -3.85714 2.37242 -2.26668
H -4.33254 3.32585 -2.09507
C -4.15679 1.66152 -3.41221
H -4.83839 2.06440 -4.14567
C -3.61326 0.40151 -3.58016
H -3.90384 -0.18780 -4.43836
C -2.71552 -0.13773 -2.67274
H -2.84186 -1.93794 -3.76512
C -0.82057 -1.80188 -3.10903
C -2.79413 -2.41636 -1.68345
C -4.06179 2.62612 0.76321
H -1.98947 2.10961 0.53954
C -2.29648 4.07621 -0.27085
H -4.39467 1.60668 0.94350
H -3.91592 3.12527 1.71875
H -4.84819 3.14963 0.22481
H -3.09495 4.67580 -0.70105
H -2.00545 4.52545 0.67577
H -1.44668 4.10489 -0.94580
H -3.87192 -2.32720 -1.56684
H -2.54386 -3.46388 -1.83112
H -2.31650 -2.06604 -0.76688
H -0.44616 -1.10623 -3.85768
C 2.90286 -0.41337 -1.43789
H 1.11942 0.27361 -2.36973
C 4.99218 -0.19037 0.01947
C 2.72448 -1.89144 -1.82100
C 3.72866 0.24932 -2.55423
H 1.79980 -0.67614 1.01812
H 5.60296 -0.06676 -0.85992
H 2.32668 -1.97495 -2.83053
H 3.67714 -2.41650 -1.78103
H 2.03568 -2.38298 -1.13777
H 4.02883 1.25820 -2.28477
H 4.61939 -0.33310 -2.77684
H 3.13481 0.30194 -3.46420
C 3.61561 -0.36095 -0.09696
C 2.88995 -0.53016 1.07701
C 3.49166 -0.50057 2.32164
H 2.89321 -0.60913 3.21405
C 4.86110 -0.31730 2.41675
H 5.33886 -0.28974 3.38379
C 5.60582 -0.16932 1.26054
H 6.67517 -0.03056 1.32166
C 1.64388 1.74157 -0.87132
H 0.16714 2.58408 0.46987
H 1.52579 1.85802 1.28502
C 1.08544 2.72374 -1.90384
H 2.69155 2.00572 -0.68020
H 1.53608 2.51791 -2.87835
H 0.00676 2.55991 -1.99439
C 1.37514 4.17570 -1.53620
H 2.44819 4.35624 -1.53117
H 0.91955 4.85121 -2.25671
H 0.98893 4.41339 -0.54860