Multiscale NEB-TS for transition states#
多尺度 NEB-TS 用于过渡态研究

Now let us go for an even more advanced use of the multilevel methods and combine it with another important ORCA feature: the NEB-TS method to automatically find transitions states. Please check the previous tutorial "Finding Transition States with NEB-TS" if still don't know what that is, from now on we will assume it is already understood.
现在让我们进一步探索多级方法的高级应用，并将其与另一个重要的 ORCA 功能——自动寻找过渡态的 NEB-TS 方法相结合。如果您还不了解 NEB-TS 方法，请查阅之前的教程“使用 NEB-TS 寻找过渡态”，从现在开始，我们将假设您已理解该方法。

In this tutorial we will find the transition state and compute its energy barrier using a mixture of regular r²SCAN-3c and XTB. To try to make things not so simple and a little bit more interesting: our target reaction will be the Diels-Alder reaction presented below:
在本教程中，我们将通过结合常规 r ² SCAN-3c 和 XTB 方法，寻找过渡态并计算其能垒。为了使问题不那么简单且更具趣味性，我们的目标反应将是下面展示的 Diels-Alder 反应：

The r2SCAN-3c is another recent "3c" method developed by the group of Stefan Grimme, based on the meta-GGA functional r²SCAN, which is already implemented in ORCA and has shown some really good benchmark results [Grimme2021].
r2SCAN-3c 是 Stefan Grimme 团队开发的另一种近期“3c”方法，基于已集成于 ORCA 并展现出优异基准测试结果的 meta-GGA 泛函 r ² SCAN [Grimme2021]。

Preparing our input for the NEB-TS calculation#
为 NEB-TS 计算准备输入数据

In order to run the NEB-TS, we need the reactant and product, preferably already optimized using some method. One can take the structures from the end of the page and optimize with:
为了运行 NEB-TS，我们需要反应物和产物，最好已经使用某种方法进行了优化。可以从页面末尾获取结构并使用以下方法进行优化：

!R2SCAN-3C OPT FREQ
* XYZ 0 1

and they should converge after a few steps. The whole optimization plus frequencies here took only about 25 minutes for each using !PAL16.
并且它们应在几步之后收敛。整个优化加上频率计算在此处每项仅耗时约 25 分钟，使用的是!PAL16。

So we have the reactants, positioned as an educt, and the product. As shown before, the first challenge on a successful ONIOM calculation is the choice of the QM1 and QM2 regions. Since our reaction occurs between the diene and the dienophile, it is reasonable to include both in the higher level r²SCAN-3c region. Here is a 3D image showing the ORCA numbering for one of these:
因此，我们有反应物，作为反应物定位，以及产物。如前所述，成功进行 ONIOM 计算的首要挑战是选择 QM1 和 QM2 区域。由于我们的反应发生在二烯和亲二烯体之间，因此将两者都纳入更高级别的 r ² SCAN-3c 区域是合理的。以下是其中一个的 ORCA 编号的三维图像：

Please notice that here we are also including the ester electron withdrawing-group bound to the ethene subunit. There is a strong electronic connection between them and removing it from the main QM1 region would not be a smart decision in this case.
请注意，这里我们还包括了与乙烯单元相连的酯类电子吸引基团。它们之间存在强烈的电子关联，在这种情况下将其从主 QM1 区域移除并非明智之举。

Running a NEB-TS with ONIOM#
使用 ONIOM 运行 NEB-TS

The ORCA input for the NEB-TS is then simple as always, except that the %QMATOMS must be explicitly assigned:
NEB-TS 的 ORCA 输入一如既往地简单，只需显式指定%QMATOMS：

!QM/XTB R2SCAN-3C NEB-TS NUMFREQ
%QMMM QMATOMS {0:6 8 22:31} END END
%NEB PREOPT TRUE PRODUCT "product.xyz" END
* XYZFILE 0 1 reactant.xyz

Some important remarks here:
这里有一些重要说明：

We have to use NUMFREQ, for there is no analytic Hessian with the ONIOM method in ORCA yet, and we want to compute the frequencies in the end to confirm that we have found a transition state.
我们必须使用 NUMFREQ，因为在 ORCA 中，ONIOM 方法尚无解析 Hessian 可用，而我们最终需要计算频率以确认已找到过渡态。

Our reactant/product structures were optimized using pure r²SCAN-3c. Since now we are using ONIOM, which represents a different potential energy surface, it makes sense to reoptimize these before the NEB, thus we set PREOPT TRUE.
我们的反应物/产物结构采用纯 r ² SCAN-3c 进行了优化。由于现在使用的是 ONIOM 方法，其代表不同的势能面，因此在进行 NEB 计算前重新优化这些结构是合理的，因此我们设定 PREOPT 为 TRUE。

The complete calculation, using !PAL8 and including the numerical frequencies took only about 1h and 20 mins, which is impressively fast for such a calculation all the way from finding the transition state to computing frequencies. Finally, the transition state was found with a single negative frequency of $- 358.36$ $c m^{- 1}$ .
使用!PAL8 进行完整计算，并包含数值频率分析，整个过程仅耗时约 1 小时 20 分钟，从寻找过渡态到计算频率，如此快速的计算令人印象深刻。最终，过渡态以单一负频率 $- 358.36$ $c m^{- 1}$ 被成功确定。

Here is an animated version of the Minimum Energy Path (MEP) found:
以下是找到的最小能量路径（MEP）的动画版本：

and also the vibrational mode with the imaginary frequency, clearly indicating the expected coordinate for the Diels-Alder reaction:
并且还存在具有虚频的振动模式，明确指示了预期的 Diels-Alder 反应坐标：

As part of the output of the NEB-TS, together with the energy of the MEP we get the reaction energy, which in this case is $E_{b a r r i e r}^{O N I O M} = 9.37$ $k c a l / m o l$ :
作为 NEB-TS 输出的一部分，连同 MEP 的能量，我们得到了反应能，在此情况下为 $E_{b a r r i e r}^{O N I O M} = 9.37$ $k c a l / m o l$ ：

                      PATH SUMMARY FOR NEB-TS
---------------------------------------------------------------
All forces in Eh/Bohr. Global forces for TS.

Image     E(Eh)   dE(kcal/mol)  max(|Fp|)  RMS(Fp)
  0    -495.04184     0.00       0.00007   0.00003
  1    -495.04118     0.41       0.00204   0.00031
  2    -495.03976     1.31       0.00375   0.00057
  3    -495.03781     2.53       0.00454   0.00071
  4    -495.03476     4.44       0.00318   0.00052
  5    -495.02943     7.78       0.00166   0.00032
  6    -495.02579    10.07       0.00173   0.00033 <= CI
 TS    -495.02690     9.37       0.00063   0.00009 <= TS
  7    -495.03697     3.06       0.00168   0.00046
  8    -495.07669   -21.87       0.00524   0.00143
  9    -495.08248   -25.50       0.00009   0.00002

Comparison with the full DFT result#
与完整 DFT 结果的比较

We can also compare the ONIOM results with the full DFT result just for checking:
我们还可以将 ONIOM 结果与完整 DFT 结果进行比较，仅用于验证：

!R2SCAN-3C NEB-TS FREQ
%NEB PRODUCT "product.xyz" END
* XYZFILE 0 1 reactant.xyz

After the NEB convergence, the transition state is found and an energy barrier of $E_{b a r r i e r}^{O N I O M} = 10.25$ $k c a l / m o l$ is found. This means our ONIOM presented only a 10 % error with respect to the full calculation in this case.
NEB 收敛后，找到了过渡态，并发现能量势垒为 $E_{b a r r i e r}^{O N I O M} = 10.25$ $k c a l / m o l$ 。这意味着在此情况下，我们采用的 ONIOM 方法仅产生了相对于全计算 10%的误差。

Taking these ONIOM structures and recomputing the DFT energies results in a barrier of $E_{b a r r i e r}^{D F T / O N I O M} = 10.63$ $k c a l / m o l$ , which is then quite close to the exact result.
采用这些 ONIOM 结构并重新计算 DFT 能量，得到的能垒为 $E_{b a r r i e r}^{D F T / O N I O M} = 10.63$ $k c a l / m o l$ ，这与精确结果相当接近。

Overlaying both structures of the transition states found also show that the results are quite similar:
叠加两种过渡态结构的结果也显示出相当的一致性：

To conclude this section, the full DFT frequency found for the transition state is $- 370.80$ $c m^{- 1}$ , also in agreement with the previous result found using multiscale.
综上所述，过渡态的完整 DFT 频率为 $- 370.80$ $c m^{- 1}$ ，与之前使用多尺度方法得到的结果一致。

A large example from literature#
文学中的一个大型实例

In order to show how the multiscale would perform on a very large system, let's take as an example a recent paper from a collaboration of the group of Prof. Frank Neese and Prof. Benjamin List (the 2022 Chemistry Nobel prize winner!).
为了展示多尺度方法在处理极大规模系统时的表现，我们以 Frank Neese 教授和 Benjamin List 教授（2022 年诺贝尔化学奖得主！）合作的一篇近期论文为例。

The group from Prof. List is known for their reactions using organic molecules as catalysts, and one of these reactions is the stereoselective Diels-Alder reaction below [Bistoni2020]:
List 教授课题组以其利用有机分子作为催化剂的反应而闻名，其中之一便是下述的立体选择性 Diels-Alder 反应[Bistoni2020]：

The article describes the study of this reaction using DFT and DLPNO-CCSD(T) in great detail. We will not try to reproduce any of its results, but simply show how one could use NEB-TS together with ORCA's ONIOM, to find the transition state of this 206-atom large system.
文章详细描述了使用 DFT 和 DLPNO-CCSD(T)对该反应的研究。我们不试图重现其任何结果，而是简单展示如何结合 NEB-TS 与 ORCA 的 ONIOM，来寻找这个包含 206 个原子的大型系统的过渡态。

As always, for NEB-TS we need a reactant and a product. These structures, kindly provided by the authors, were pre-optimized and the starting structures are printed by the end of this page.
一如既往，对于 NEB-TS，我们需要一个反应物和一个产物。这些结构由作者慷慨提供，并已预先优化，起始结构列于本页末尾。

Setting up our more complex input - the charges#
设置更复杂的输入 - 电荷 #

Now we can run a NEB-TS calculation to find the transition state involved in this reaction. Using the QM/XTB approach and a PBE/def2-SVP as QM method, the input looks like:
现在我们可以运行 NEB-TS 计算来寻找该反应涉及的过渡态。采用 QM/XTB 方法和 PBE/def2-SVP 作为 QM 方法，输入如下：

! QM/XTB PBE D3BJ def2-SVP NEB-TS NUMFREQ
%NEB
 product "product.xyz"
 preopt true
END
%QMMM
 QMAtoms { 151:205 } end
 Charge_Total 0
END
* XYZFILE 1 1 reactant.xyz

Which corresponds to a division of regions as shown in the image below, with the solid balls representing the higher-level DFT region:
这对应于下图所示的区域划分，其中实心球体代表更高级别的 DFT 区域：

Some important points here:
这里有一些重要点：

We use !NEB-TS together with !NUMFREQ?, so that the frequencies are calculated in the end to verify the transition state. Remember that ORCA currently can only do numerical frequencies for multiscale calculations.
我们使用!NEB-TS 与 !NUMFREQ? 结合，以便最终计算频率以验证过渡态。请记住，ORCA 目前仅能对多尺度计算进行数值频率计算。

It is recommended to use PREOPT TRUE, in order to preoptimize the reactant and product since they were previously optimized using a different method.
建议使用 PREOPT TRUE ，以便对反应物和产物进行预优化，因为它们之前已采用不同方法进行了优化。

Please note that now, after the QMAtoms, we also have Charge_Total 0. This is the charge of the total system (QM1 + QM2, or DFT + XTB), which in this case is neutral. On the Lewis structure above, it is shown that the reactant is actually a cation and the catalyst is an anion.

The total charge is zero, however since we chose the reactant educt as the higher-level QM region, the charge given at the end of the input, after xyzfile has to be +1. There one has to add the total charge of the higher-level QM system, and the charge of the lower-level XTB will be deduced from that and the Charge_Total.

Important 重要

The charge that goes together with the multiplicity in the coordinate section, is always the one of the highest-level region. The same applies to the multiplicity, which can be set for the total system using Mult_Total under %QMMM, and has to be also set for the higher-level system.

Note 注释

If no Charge_Total or Mult_Total is given, a neutral system with all paired electrons is assumed.

Using !PAL16 for 16 cores, this calculation took 15 hours and only one negative frequency was found, of $- 384.94$ $c m^{- 1}$ . The overall result for the NEB-TS is:

---------------------------------------------------------------
                      PATH SUMMARY FOR NEB-TS
---------------------------------------------------------------
All forces in Eh/Bohr. Global forces for TS.

Image     E(Eh)   dE(kcal/mol)  max(|Fp|)  RMS(Fp)
  0   -1627.03519     0.00       0.00012   0.00002
  1   -1627.03314     1.29       0.00380   0.00030
  2   -1627.03058     2.90       0.00195   0.00026
  3   -1627.02792     4.56       0.00318   0.00036
  4   -1627.02388     7.10       0.00578   0.00058
  5   -1627.01743    11.15       0.00186   0.00027 <= CI
 TS   -1627.02210     8.22       0.00009   0.00001 <= TS
  6   -1627.02306     7.62       0.00419   0.00055
  7   -1627.03571    -0.32       0.01194   0.00094
  8   -1627.05101    -9.93       0.00263   0.00029
  9   -1627.05229   -10.73       0.00009   0.00001

with a predicted electronic energy barrier of $E_{b a r r i e r}^{O N I O M} = 8.22$ $k c a l / m o l$ . The minimum energy path, saved as basename_MEP_trj.xyz is shown below:

Reducing the size of the active region#
缩小有源区尺寸

You can see from the MEP above, that most of the action in practice occurs very close to the reactant educt. That is expected, since the catalyst in this case is only there to bring together and properly position the reactants. One could go one step further in terms of approximations and also limit the Active Region of this optimization.

By Active Region here we mean the parts of the molecule/system that will actually move and be optimized. For larger systems with localized bond breaking/forming, we could essentially ignore the surroundings in terms of the geometry optimization and only take the central relevant part into the NEB-TS.

In order to do it, the following input has to be used:
为了实现这一目标，必须使用以下输入：

! QM/XTB PBE D3BJ def2-SVP NEB-TS NUMFREQ
%NEB
 product "product.xyz"
 preopt true
END
%QMMM
 QMAtoms { 151:205 } end
 ActiveAtoms {151:205} end
 Charge_Total 0
END
* XYZFILE 1 1 reactant.xyz

which is essentially the same, except that now there is also a list of ActiveAtoms. In this case, we chose it to be the same as the higher-level DFT, but in principle it can be anything. Now, looking back to the final part of the QMMM output:
这本质上是一样的，只是现在还增加了一个 ActiveAtoms 列表。在这种情况下，我们选择它与更高层次的 DFT 相同，但原则上它可以是任何内容。现在，回顾 QMMM 输出的最后部分：

Size of region for optimizer           ... 59
        optimized atoms = activeRegion ... 55
        fixed atoms (distance cutoff)  ... 4 ( 1.0)
Composition of different systems (atoms start counting at 0):
QM1 Subsystem                          ... 151 152 153 154 155 156 157 158 159 160
                                           161 162 163 164 165 166 167 168 169 170
                                           171 172 173 174 175 176 177 178 179 180
                                           181 182 183 184 185 186 187 188 189 190
                                           191 192 193 194 195 196 197 198 199 200
                                           201 202 203 204 205
Active atoms                           ... 151 152 153 154 155 156 157 158 159 160
                                           161 162 163 164 165 166 167 168 169 170
                                           171 172 173 174 175 176 177 178 179 180
                                           181 182 183 184 185 186 187 188 189 190
                                           191 192 193 194 195 196 197 198 199 200
                                           201 202 203 204 205
Fixed atoms used in optimizer          ... 104 106 109 143

You can see that the number of Active atoms correspond to what we chose, but another 4 Fixed atoms will be added to the optimizer. These are selected based on their distance to the active atoms, and are important to stabilize the geometry optimization. They are just atoms for which the Cartesian coordinates will be fully constrained.
可以看到，活跃原子的数量与我们选择的相符，但优化器中还会额外添加 4 个固定原子。这些固定原子是根据它们与活跃原子的距离选定的，对于稳定几何优化至关重要。它们只是那些笛卡尔坐标将被完全约束的原子。

In principle, these four extra atoms won't make much of a difference, in some cases it could be even much more, but they are really necessary to avoid having the Active atoms moving to a region of space were the ignored atoms are. There is no need to play around with these, but more information can be found on the ORCA manual.
原则上，这四个额外原子不会造成太大差异，某些情况下甚至可能更为显著，但它们确实有必要，以防止活性原子移动到被忽略原子所在的区域。无需对此进行调整，更多信息可参阅 ORCA 手册。

This calculation with 16 cores now takes only about three hours, including the frequencies! The imaginary mode is essentially the same, with $- 372.29$ $c m^{- 1}$ and the MEP is shown below:
使用 16 核计算现在仅需约三小时，包括频率计算！虚模态基本相同， $- 372.29$ $c m^{- 1}$ ，MEP 如下所示：

The summary for the NEB-TS is:
NEB-TS 的摘要为：

---------------------------------------------------------------
                      PATH SUMMARY FOR NEB-TS
---------------------------------------------------------------
All forces in Eh/Bohr. Global forces for TS.

Image     E(Eh)   dE(kcal/mol)  max(|Fp|)  RMS(Fp)
  0   -1626.95773     0.00       0.05123   0.00546
  1   -1626.95627     0.92       0.05121   0.00547
  2   -1626.95362     2.58       0.05120   0.00548
  3   -1626.95029     4.67       0.05113   0.00549
  4   -1626.94563     7.59       0.05094   0.00552
  5   -1626.94303     9.23       0.05056   0.00547 <= CI
 TS   -1626.94483     8.10       0.05053   0.00547 <= TS
  6   -1626.94614     7.27       0.05034   0.00547
  7   -1626.95464     1.94       0.05001   0.00563
  8   -1626.97407   -10.25       0.04976   0.00564
  9   -1626.97568   -11.26       0.04984   0.00541

with an electronic barrier of $E_{b a r r i e r}^{O N I O M, r e d u c e d} = 8.10$ $k c a l / m o l$ , which is extremely close to the one we found using the whole molecule as the active region.
具有 $E_{b a r r i e r}^{O N I O M, r e d u c e d} = 8.10$ $k c a l / m o l$ 的电子势垒，这与我们将整个分子作为活性区域时所发现的势垒极为接近。

Important 重要

Choosing the active region might be crucial for a good result in you calculation. If it makes sense to reduce it, there is no reason why not to do it as long as you keep being critical.
选择活动区域可能对你的计算结果至关重要。如果缩小活动区域有意义，只要保持批判性思维，就没有理由不这样做。

Structures# 结构

Reactant - second reaction

206

P   0.916540   -1.446915    -0.319940
O   2.371689   -0.759534     0.092738
O   0.757312   -2.624241     0.830064
C   3.424107   -1.513413     0.600201
C   4.601756   -1.616396    -0.198660
C   5.654349   -2.382135     0.279295
C   5.574035   -3.072225     1.519527
C   6.644233   -3.895980     1.976074
C   6.542851   -4.603066     3.163608
C   5.353751   -4.519092     3.933852
C   4.300040   -3.714908     3.523431
C   4.381496   -2.952449     2.320644
C   3.309095   -2.106095     1.858576
C   2.086336   -1.901706     2.682513
C   2.149623   -1.371833     4.020418
C   3.357817   -0.872255     4.590832
C   3.377330   -0.354237     5.878000
C   2.197907   -0.343563     6.669067
C   1.005220   -0.811527     6.138662
C   0.939076   -1.301039     4.800643
C   -0.29459    -1.71597      4.22743
C   -0.37893    -2.16984      2.91371
C   0.834583   -2.225332     2.158796
C   4.710423   -0.920983    -1.507929
H   6.573936   -2.466560    -0.319659
H   7.551361   -3.968163     1.356325
H   7.373611   -5.239805     3.502683
H   5.262066   -5.102616     4.862336
H   3.381935   -3.672022     4.124449
H   4.276104   -0.882571     3.989665
H   4.316741    0.048319     6.284977
H   2.231999    0.042133     7.699243
H   0.081163   -0.799654     6.735099
H   -1.20194    -1.68274      4.84936
C   -1.66996    -2.64261      2.35073
C   4.650292    0.482034    -1.582299
C   4.830403    1.135713    -2.813629
C   5.054553    0.401861    -3.984779
C   5.080086   -1.001951    -3.917445
C   4.919055   -1.661606    -2.691409
C   -2.86470    -1.94773      2.62676
C   -4.10108    -2.46212      2.20367
C   -4.16805    -3.66753      1.48952
C   -2.98138    -4.35769      1.20172
C   -1.74308    -3.84912      1.62007
H   4.470387    1.065209    -0.668426
H   5.182774    0.918236    -4.945377
H   4.907411   -2.758422    -2.648989
H   -2.82717    -0.99836      3.18032
H   -5.13604    -4.07516      1.17340
H   -0.82670    -4.41393      1.40619
N   -0.13760    -0.30734     -0.10383
P   -1.11716     0.84307     -0.52955
O   -0.86292     2.21936      0.36552
O   -2.57781     0.33507      0.05903
C   -0.99952     2.14893      1.74493
C   0.187340    2.254363     2.537791
C   0.059383    2.089838     3.914637
C   -1.19602     1.81551      4.52419
C   -1.30988     1.61067      5.93106
C   -2.52824     1.28457      6.50764
C   -3.68590     1.15709      5.69466
C   -3.61931     1.40154      4.33045
C   -2.38345     1.75042      3.70931
C   -2.27530     1.99194      2.29410
C   -3.47851     2.08063      1.42171
C   -4.51475     3.05388      1.66124
C   -4.43717     4.03015      2.69741
C   -5.46126     4.94562      2.89566
C   -6.61363     4.93236      2.06746
C   -6.70810     4.01382      1.03394
C   -5.66792     3.06852      0.79414
C   -5.73701     2.16335     -0.30057
C   -4.71616     1.26354     -0.57110
C   -3.59436     1.24775      0.31211
C   1.497070    2.633715     1.943844
H   0.948307    2.186260     4.556414
H   -0.40307     1.70365      6.54660
H   -2.59970     1.11782      7.59310
H   -4.64531     0.86440      6.14649
H   -4.51949     1.30450      3.70928
H   -3.54674     4.06077      3.33952
H   -5.37453     5.69262      3.69908
H   -7.42132     5.65978      2.23806
H   -7.58590     4.00681      0.36940
H   -6.62166     2.18859     -0.95500
C   -4.74641     0.37537     -1.75661
C   1.587359    3.721436     1.044844
C   2.835496    4.184339     0.608214
C   4.018065    3.557099     1.034349
C   3.934033    2.469870     1.913820
C   2.685175    2.007033     2.365504
C   -5.04627     0.89481     -3.03265
C   -5.04801     0.05656     -4.15897
C   -4.74087    -1.30622     -4.03597
C   -4.42670    -1.81895     -2.77042
C   -4.43782    -0.99326     -1.63800
H   0.675241    4.231162     0.709859
H   4.994598    3.919111     0.688111
H   2.634057    1.154539     3.057707
H   -5.22010     1.97400     -3.14419
H   -4.71726    -1.95250     -4.92191
H   -4.18767    -1.41095     -0.65409
N   0.873504   -2.167366    -1.757367
N   -1.09279     1.26973     -2.07667
S   1.808817   -3.398539    -2.225292
O   2.092018   -3.259925    -3.678636
O   2.928958   -3.743659    -1.317722
S   -1.75776     2.59220     -2.73710
O   -1.68433     2.45266     -4.21201
O   -3.02132     3.05419     -2.11734
C   -0.52341     3.99163     -2.33414
C   0.644415   -4.882681    -2.101455
F   0.729296    3.514442    -2.290286
F   -0.60864     4.92727     -3.29108
F   -0.83052     4.55556     -1.16036
F   -0.45331    -4.69511     -2.84683
F   0.288702   -5.064743    -0.823796
F   1.291438   -5.968586    -2.540237
C   5.192754    1.796225     2.408800
C   2.934804    5.460725    -0.200433
C   4.721390    2.641232    -2.852077
C   5.234315   -1.781031    -5.203879
F   5.206130    1.701634     3.762311
F   6.309693    2.455705     2.034292
F   5.302189    0.524016     1.931633
F   3.076358    6.529362     0.627439
F   1.833844    5.688669    -0.950334
F   4.006422    5.459748    -1.025178
F   3.460905    3.044032    -2.523146
F   4.992896    3.152663    -4.075670
F   5.563898    3.224405    -1.967565
F   4.215300   -1.499275    -6.066313
F   6.382445   -1.451951    -5.845450
F   5.238364   -3.113368    -5.006944
C   -3.02552    -5.69794      0.49584
C   -5.36705    -1.70698      2.53462
C   -3.97906    -3.24648     -2.59146
C   -5.30714     0.66172     -5.51911
F   -5.33625    -0.27572     -6.49940
F   -6.48519     1.32707     -5.55472
F   -4.34016     1.55585     -5.85334
F   -4.74679    -3.91115     -1.69246
F   -4.01076    -3.95377     -3.75008
F   -2.70307    -3.28314     -2.12987
F   -5.49414    -0.58164      1.77722
F   -6.47562    -2.44985      2.32760
F   -5.38043    -1.30188      3.83003
F   -4.29137    -6.15315      0.35700
F   -2.33063    -6.62953      1.19617
F   -2.47472    -5.64864     -0.73929
C   1.155646    0.166147    -5.793662
C   2.721219    2.452084    -8.138136
C   -0.41783     2.72241     -8.42839
H   -0.60514     1.77909     -8.94466
H   -0.15917     3.44935     -9.19924
C   1.010667    3.674443    -5.732567
H   0.036290    3.566447    -5.254043
O   0.813838    0.848100    -6.820561
O   1.508592    0.873232    -4.748569
Si  1.038945    2.501060    -7.217859
H   2.976447    3.453654    -8.483171
H   2.639880    1.830136    -9.031107
C   1.646025    0.286420    -3.465817
H   0.669869   -0.023013    -3.092706
H   2.322221   -0.567760    -3.472660
H   2.025061    1.075376    -2.822243
C   -1.70568     3.17588     -7.73771
H   -2.53448     3.17848     -8.44248
H   -1.96035     2.52627     -6.90597
H   -1.59330     4.18195     -7.34479
C   3.864246    1.922008    -7.274127
H   3.648258    0.906989    -6.945738
H   4.794725    1.905611    -7.838628
H   4.005370    2.554371    -6.401758
C   1.233311    5.141535    -6.099683
H   2.228596    5.291075    -6.511106
H   0.507994    5.472241    -6.837522
H   1.129038    5.766357    -5.216856
H   1.752137    3.385937    -4.986940
C   1.249962   -1.251680    -5.902304
C   0.908114   -1.820168    -7.137152
C   -1.51427    -2.31699     -6.73757
C   -1.70407    -0.47019     -5.35988
C   -1.91187    -0.99093     -6.69137
C   -1.23208    -1.49189     -4.55096
H   -2.05199    -3.41513     -4.99108
H   -1.00323    -1.43925     -3.47532
H   -1.86082     0.57669     -5.04595
H   -2.28337    -0.39909     -7.53878
H   -1.60264    -2.99563     -7.59713
C   -1.21260    -2.76653     -5.33724
H   -0.30867    -3.38863     -5.18320
H   1.617135   -1.859476    -5.052770
H   0.564628   -1.132627    -7.928863
C   1.241506   -3.174011    -7.575174
C   1.838539   -4.115887    -6.730312
C   1.052550   -3.496709    -8.924919
C   2.264638   -5.326977    -7.239584
H   1.996561   -3.893845    -5.687836
C   1.483944   -4.707408    -9.424893
H   0.584062   -2.776219    -9.580217
C   2.099227   -5.623783    -8.584070
H   2.741592   -6.039624    -6.584255
H   1.353008   -4.938006   -10.471775
H   2.449888   -6.565802    -8.977882

Product - second reaction

206

P   0.916540    -1.446915    -0.319940
O   2.371689    -0.759534     0.092738
O   0.757312    -2.624241     0.830064
C   3.424107    -1.513413     0.600201
C   4.601756    -1.616396    -0.198660
C   5.654349    -2.382135     0.279295
C   5.574035    -3.072225     1.519527
C   6.644233    -3.895980     1.976074
C   6.542851    -4.603066     3.163608
C   5.353751    -4.519092     3.933852
C   4.300040    -3.714908     3.523431
C   4.381496    -2.952449     2.320644
C   3.309095    -2.106095     1.858576
C   2.086336    -1.901706     2.682513
C   2.149623    -1.371833     4.020418
C   3.357817    -0.872255     4.590832
C   3.377330    -0.354237     5.878000
C   2.197907    -0.343563     6.669067
C   1.005220    -0.811527     6.138662
C   0.939076    -1.301039     4.800643
C   -0.29459     -1.71597      4.22743
C   -0.37893     -2.16984      2.91371
C   0.834583    -2.225332     2.158796
C   4.710423    -0.920983    -1.507929
H   6.573936    -2.466560    -0.319659
H   7.551361    -3.968163     1.356325
H   7.373611    -5.239805     3.502683
H   5.262066    -5.102616     4.862336
H   3.381935    -3.672022     4.124449
H   4.276104    -0.882571     3.989665
H   4.316741     0.048319     6.284977
H   2.231999     0.042133     7.699243
H   0.081163    -0.799654     6.735099
H   -1.20194     -1.68274      4.84936
C   -1.66996     -2.64261      2.35073
C   4.650292     0.482034    -1.582299
C   4.830403     1.135713    -2.813629
C   5.054553     0.401861    -3.984779
C   5.080086    -1.001951    -3.917445
C   4.919055    -1.661606    -2.691409
C   -2.86470     -1.94773      2.62676
C   -4.10108     -2.46212      2.20367
C   -4.16805     -3.66753      1.48952
C   -2.98138     -4.35769      1.20172
C   -1.74308     -3.84912      1.62007
H   4.470387     1.065209    -0.668426
H   5.182774     0.918236    -4.945377
H   4.907411    -2.758422    -2.648989
H   -2.82717     -0.99836      3.18032
H   -5.13604     -4.07516      1.17340
H   -0.82670     -4.41393      1.40619
N   -0.13760     -0.30734     -0.10383
P   -1.11716      0.84307     -0.52955
O   -0.86292      2.21936      0.36552
O   -2.57781      0.33507      0.05903
C   -0.99952      2.14893      1.74493
C   0.187340     2.254363     2.537791
C   0.059383     2.089838     3.914637
C   -1.19602      1.81551      4.52419
C   -1.30988      1.61067      5.93106
C   -2.52824      1.28457      6.50764
C   -3.68590      1.15709      5.69466
C   -3.61931      1.40154      4.33045
C   -2.38345      1.75042      3.70931
C   -2.27530      1.99194      2.29410
C   -3.47851      2.08063      1.42171
C   -4.51475      3.05388      1.66124
C   -4.43717      4.03015      2.69741
C   -5.46126      4.94562      2.89566
C   -6.61363      4.93236      2.06746
C   -6.70810      4.01382      1.03394
C   -5.66792      3.06852      0.79414
C   -5.73701      2.16335     -0.30057
C   -4.71616      1.26354     -0.57110
C   -3.59436      1.24775      0.31211
C   1.497070     2.633715     1.943844
H   0.948307     2.186260     4.556414
H   -0.40307      1.70365      6.54660
H   -2.59970      1.11782      7.59310
H   -4.64531      0.86440      6.14649
H   -4.51949      1.30450      3.70928
H   -3.54674      4.06077      3.33952
H   -5.37453      5.69262      3.69908
H   -7.42132      5.65978      2.23806
H   -7.58590      4.00681      0.36940
H   -6.62166      2.18859     -0.95500
C   -4.74641      0.37537     -1.75661
C   1.587359     3.721436     1.044844
C   2.835496     4.184339     0.608214
C   4.018065     3.557099     1.034349
C   3.934033     2.469870     1.913820
C   2.685175     2.007033     2.365504
C   -5.04627      0.89481     -3.03265
C   -5.04801      0.05656     -4.15897
C   -4.74087     -1.30622     -4.03597
C   -4.42670     -1.81895     -2.77042
C   -4.43782     -0.99326     -1.63800
H   0.675241     4.231162     0.709859
H   4.994598     3.919111     0.688111
H   2.634057     1.154539     3.057707
H   -5.22010      1.97400     -3.14419
H   -4.71726     -1.95250     -4.92191
H   -4.18767     -1.41095     -0.65409
N   0.873504    -2.167366    -1.757367
N   -1.09279      1.26973     -2.07667
S   1.808817    -3.398539    -2.225292
O   2.092018    -3.259925    -3.678636
O   2.928958    -3.743659    -1.317722
S   -1.75776      2.59220     -2.73710
O   -1.68433      2.45266     -4.21201
O   -3.02132      3.05419     -2.11734
C   -0.52341      3.99163     -2.33414
C   0.644415    -4.882681    -2.101455
F   0.729296     3.514442    -2.290286
F   -0.60864      4.92727     -3.29108
F   -0.83052      4.55556     -1.16036
F   -0.45331     -4.69511     -2.84683
F   0.288702    -5.064743    -0.823796
F   1.291438    -5.968586    -2.540237
C   5.192754     1.796225     2.408800
C   2.934804     5.460725    -0.200433
C   4.721390     2.641232    -2.852077
C   5.234315    -1.781031    -5.203879
F   5.206130     1.701634     3.762311
F   6.309693     2.455705     2.034292
F   5.302189     0.524016     1.931633
F   3.076358     6.529362     0.627439
F   1.833844     5.688669    -0.950334
F   4.006422     5.459748    -1.025178
F   3.460905     3.044032    -2.523146
F   4.992896     3.152663    -4.075670
F   5.563898     3.224405    -1.967565
F   4.215300    -1.499275    -6.066313
F   6.382445    -1.451951    -5.845450
F   5.238364    -3.113368    -5.006944
C   -3.02552     -5.69794      0.49584
C   -5.36705     -1.70698      2.53462
C   -3.97906     -3.24648     -2.59146
C   -5.30714      0.66172     -5.51911
F   -5.33625     -0.27572     -6.49940
F   -6.48519      1.32707     -5.55472
F   -4.34016      1.55585     -5.85334
F   -4.74679     -3.91115     -1.69246
F   -4.01076     -3.95377     -3.75008
F   -2.70307     -3.28314     -2.12987
F   -5.49414     -0.58164      1.77722
F   -6.47562     -2.44985      2.32760
F   -5.38043     -1.30188      3.83003
F   -4.29137     -6.15315      0.35700
F   -2.33063     -6.62953      1.19617
F   -2.47472     -5.64864     -0.73929
C   1.141889     0.131145    -5.786190
C   2.713551     2.443019    -8.133458
C   -0.41688      2.71408     -8.42594
H   -0.60740      1.77839     -8.95444
H   -0.14737      3.44707     -9.18712
C   1.006055     3.661088    -5.734153
H   0.032637     3.558995    -5.253286
O   0.771942     0.823170    -6.811350
O   1.595724     0.850478    -4.774151
Si  1.032906     2.470258    -7.208538
H   2.958554     3.449220    -8.473849
H   2.636708     1.826117    -9.030304
C   1.671368     0.289183    -3.477331
H   0.678125     0.010405    -3.125420
H   2.323107    -0.583753    -3.447224
H   2.050708     1.078516    -2.834933
C   -1.70496      3.17165     -7.73953
H   -2.53320      3.17684     -8.44519
H   -1.96193      2.52374     -6.90705
H   -1.58981      4.17761     -7.34734
C   3.862498     1.919605    -7.273819
H   3.651734     0.903918    -6.945663
H   4.792115     1.908999    -7.840013
H   4.000709     2.551715    -6.400830
C   1.229923     5.126886    -6.107408
H   2.225624     5.275880    -6.517963
H   0.505323     5.457320    -6.846272
H   1.125640     5.754911    -5.226303
H   1.748089     3.376573    -4.987987
C   1.039692    -1.269981    -5.814425
C   0.493261    -1.897043    -7.055037
C   -1.10705     -2.23921     -6.80226
C   -1.72802     -0.46808     -5.40818
C   -1.83893     -0.95365     -6.70276
C   -1.07065     -1.46633     -4.61626
H   -2.08839     -3.27912     -5.15728
H   -0.88673     -1.40709     -3.53016
H   -1.96686      0.55345     -5.05936
H   -2.24083     -0.39216     -7.55665
H   -1.43992     -2.93808     -7.59118
C   -1.12471     -2.76034     -5.35603
H   -0.31741     -3.46601     -5.08773
H   1.560507    -1.880683    -5.053891
H   0.514749    -1.171637    -7.892292
C   1.134126    -3.191265    -7.549291
C   1.779904    -4.098173    -6.720714
C   1.014883    -3.490317    -8.904583
C   2.271965    -5.287102    -7.236108
H   1.924464    -3.891685    -5.673537
C   1.503691    -4.678257    -9.416381
H   0.534383    -2.785436    -9.568955
C   2.124281    -5.589447    -8.578538
H   2.767662    -5.983446    -6.576870
H   1.395670    -4.896729   -10.469020
H   2.491749    -6.526037    -8.971060

Multiscale NEB-TS for transition states#多尺度 NEB-TS 用于过渡态研究

Preparing our input for the NEB-TS calculation#为 NEB-TS 计算准备输入数据

Running a NEB-TS with ONIOM#使用 ONIOM 运行 NEB-TS

Comparison with the full DFT result#与完整 DFT 结果的比较

A large example from literature#文学中的一个大型实例

Setting up our more complex input - the charges#设置更复杂的输入 - 电荷 #

Reducing the size of the active region#缩小有源区尺寸

Structures# 结构

Multiscale NEB-TS for transition states#
多尺度 NEB-TS 用于过渡态研究

Preparing our input for the NEB-TS calculation#
为 NEB-TS 计算准备输入数据

Running a NEB-TS with ONIOM#
使用 ONIOM 运行 NEB-TS

Comparison with the full DFT result#
与完整 DFT 结果的比较

A large example from literature#
文学中的一个大型实例

Setting up our more complex input - the charges#
设置更复杂的输入 - 电荷 #

Reducing the size of the active region#
缩小有源区尺寸