ORCA 5.0 过渡态官方教程（搬运）

找了会，百度上没有，谷歌搜到了，有条件的可以去原文看，主要是为了方便做同样工作的人能看到。使用 NEB-TS 查找过渡状态 - ORCA 5.0 教程 --- Finding transition states with NEB-TS - ORCA 5.0 tutorials (faccts.de)

Finding transition states with NEB-TS
使用 NEB-TS# 查找转换状态

Suppose you wanted to predict the transition state (TS) for the hydrolysis of methyl-acetate into acetic acid and methanol:
假设您要预测乙酸甲酯水解成乙酸和甲醇的过渡态 （TS）：

Maybe you need to investigate the mechanism, or even to compute the ΔG† and try to predict reaction rates. How could one do that using theory?
也许你需要研究机制，甚至计算 ΔG† 并尝试预测反应速率。如何用理论来做到这一点呢？

In ORCA there is a black box method called NEB-TS (from Nudged Elastic Band with TS optimization), that can find the TS structure only from the geometries of the reactants and products!
在 ORCA 中，有一种称为 NEB-TS 的黑盒方法（来自 Nudged Elastic Band with TS optimization），它只能从反应物和产物的几何形状中找到 TS 结构！

Defining your reactants and products
定义反应物和产物#

So the first step is to optimize the "reactants" and "products". Please, have in mind that here it means everything that is left and right of the arrow, the collection of molecules. First, for the reactant, after drawing the initial guess and doing a Geometry optimization using:
所以第一步是优化 “反应物” 和 “产物”。请记住，这里它指的是箭头左右的一切，即分子的集合。首先，对于反应物，在绘制初始猜测并使用以下方法进行几何优化后：

!B3LYP DEF2-SVP OPT D4 

one gets, for instance, the following geometry:
例如，可以得到以下 Geometry：

with the nucleophilic water making a hydrogen bond with the carbonyl group. Rearranging the atoms to make a guess product structure, and after optimizing with the same method, one gets:
与亲核水与羰基形成氢键。重新排列原子以猜测产品结构，使用相同的方法进行优化后，可以得到：

and we are ready to find the transition state.
我们已准备好查找 transition 状态。

Important 重要

In order for the NEB-TS to work, the atom numbering in both reactant and product geometries must be the same. Which means that a given carbon on the reactant, should have the same order in the xyz table in the product. The best way to guarantee this is to start from one geometry, make a copy and move the atoms to draw the next structure.
为了使 NEB-TS 工作，反应物和产物几何形状中的原子编号必须相同。这意味着反应物上的给定碳在产物的 xyz 表中应该具有相同的顺序。保证这一点的最佳方法是从一种几何结构开始，复制并移动原子以绘制下一个结构。

Note 注意

If using Avogadro, you have to disable the Adjust Hydrogen feature, otherwise atoms will be automatically placed when a bond is broken, and not necessarily where you want them to be.
如果使用 Avogadro，则必须禁用 Adjust Hydrogen 功能，否则当键断裂时，原子将自动放置，而不一定是您想要的位置。

Note 注意

The idea is not to optimize all molecules separately and just join then in a single file, but rather already build your "reactant" and "product" adducts in a certain orientation that makes sense with respect to the expected reaction, like done in the example.
这个想法不是单独优化所有分子，然后加入一个文件，而是已经在某个方向构建你的 “反应物 ”和 “产物 ”加合物，这对预期的反应是有意义的，就像在例子中所做的那样。

Making the NEB-TS input
进行 NEB-TS 输入#

The NEB-TS input is quite simple, one has to add only NEB-TS in the main input, and give the name of the product xyz file on the %NEB options:
NEB-TS 输入非常简单，只需在主输入中添加 NEB-TS，并在 %NEB 选项上给出产品 xyz 文件的名称：

!B3LYP DEF2-SVP D4 NEB-TS FREQ %NEB NEB_END_XYZFILE "product.xyz" END * XYZFILE 0 1 reactant.xyz 

In case you have a guess structure for the TS as well, that can be included as:
如果您也有 TS 的猜测结构，则可以将其包含在内：

!B3LYP DEF2-SVP D4 NEB-TS FREQ %NEB NEB_END_XYZFILE "product.xyz" NEB_TS_XYZFILE "guessTS.xyz" END * XYZFILE 0 1 reactant.xyz 

and you can already run it.
你已经可以运行它了。

Note 注意

The reactant and products will not be optimized during the default run, so make sure you are using the same method you chose for the previous optimization. If you want to reoptimize them, set PREOPT_ENDS TRUE under %NEB.
在默认运行期间，反应物和产物不会进行优化，因此请确保您使用与之前优化相同的方法。如果要重新优化它们，请在 %NEB 下设置 PREOPT_ENDS TRUE。

Running the NEB
运行 NEB#

After the calculation starts, the first output is:
计算开始后，第一个输出为：

---------------------- NEB settings ---------------------- Method type .... climbing image Threshold for climbing image .... 2.00e-02 Eh/Bohr Free endpoints .... off Tangent type .... improved Number of intermediate images .... 8 Number of images free to move .... 8 Spring type for image distribution .... distance between adjacent images Spring constant .... energy weighted (0.0100 -to- 0.1000) Eh/Bohr^2 Spring force perp. to the path .... none Generation of initial path .... image dependent pair potential Initial path via TS guess .... off [...] 

which contains some details of the method. Then, comes the construction of a initial path:
其中包含该方法的一些详细信息。然后，构建一个初始路径：

Generation of the initial path: Minimize RMSD between reactant and product configurations .... done RMSD before minimization .... 2.1153 Bohr RMSD after minimization .... 1.6611 Bohr Performing linear interpolation .... done Interpolation using .... IDPP (Image Dependent Pair Potential) IDPP-Settings: Remove global transl. and rot. ... true Convergence tolerance .... 0.0100 1/Ang.^3 Max. numer of iterations .... 7000 Spring constant .... 1.0000 1/Ang.^4 Time step .... 0.0100 fs Max. movement per iteration .... 0.0500 Ang. Full print .... false idpp initial path generation successfully converged in 117 iterations Displacement along initial path: 11.6511 Bohr Writing initial trajectory to file .... NEBTS_initial_path_trj.xyz 

The idea here is to use a method called IDPP to create a series of images, from the reactant to products, that will be optimized together using the NEB formalism.
这里的想法是使用一种称为 IDPP 的方法创建一系列图像，从反应物到产物，这些图像将使用 NEB 形式一起优化。

The initial path is saved in basename_initial_path_trj.xyz, and it is recommended to check if that makes sense. In this case, we get the following sequence of eight "images":
初始路径保存在 basename_initial_path_trj.xyz 中，建议检查这是否有意义。在本例中，我们得到以下 8 个 “images” 序列：

which looks reasonable, with the proton being transferred from the water to the methanol as it leaves.
这看起来很合理，因为质子在离开时从水中转移到甲醇。

Note 注意

Trajectory files are simply multixyz files containing several structures one after the other. Chemcraft, Molden and some other software can open those directly. Avogadro requires going to "Extensions" -> "Animation..." and the file can be opened and even animated.
轨迹文件只是包含多个结构的 multixyz 文件。Chemcraft、Molden 和其他一些软件可以直接打开它们。Avogadro 需要转到 “Extensions” -> “Animation...”并且可以打开文件，甚至可以制作动画。

Then, the iterative process starts:
然后，迭代过程开始：

Starting iterations: Optim. Iteration HEI E(HEI)-E(0) max(|Fp|) RMS(Fp) dS Switch-on CI threshold 0.020000 LBFGS 0 5 0.297110 0.116137 0.026058 11.6511 LBFGS 1 5 0.277441 0.092448 0.021661 11.5993 LBFGS 2 6 0.262453 0.111904 0.022265 11.5925 LBFGS 3 6 0.252519 0.082144 0.017474 11.6060 

and after some convergence, a "climbing image" (CI) is found:
经过一番收敛后，发现了一个 “攀爬图像” （CI）：

Image 6 will be converted to a climbing image in the next iteration (max(|Fp|) < 0.0200) Optim. Iteration CI E(CI)-E(0) max(|Fp|) RMS(Fp) dS max(|FCI|) RMS(FCI) Convergence thresholds 0.020000 0.010000 0.002000 0.001000 LBFGS 23 6 0.160709 0.029259 0.004374 12.8932 0.030101 0.007764 LBFGS 24 6 0.159481 0.051391 0.006905 13.0230 0.054092 0.012911 LBFGS 25 6 0.156310 0.068675 0.009114 13.3077 0.072840 0.017253 LBFGS 26 6 0.153131 0.031865 0.004433 13.3046 0.031225 0.007908 

This is our first guess to the TS final structure.
这是我们对 TS 最终结构的第一次猜测。

Optimization of the TS
TS# 的优化

After some iterations, the NEB-CI converges:
经过一些迭代后，NEB-CI 收敛：

 .--------------------. ----------------------| CI-NEB convergence |------------------------- Item value Tolerance Converged --------------------------------------------------------------------- RMS(Fp) 0.0006879134 0.0100000000 YES MAX(|Fp|) 0.0032907070 0.0200000000 YES RMS(FCI) 0.0006591030 0.0010000000 YES MAX(|FCI|) 0.0016597640 0.0020000000 YES --------------------------------------------------------------------- The elastic band and climbing image have converged successfully to a MEP in 128 iterations! *********************H U R R A Y********************* *** THE NEB OPTIMIZATION HAS CONVERGED *** ***************************************************** 

and a transition state optimization starts. First, a guess Hessian matrix is built using information from the previous NEB and a saddle point search is initiated.
，然后 transition state optimization 开始。首先，使用来自先前 NEB 的信息构建猜测 Hessian 矩阵，并启动鞍点搜索。

If the TS is fully optimized, a summary for the whole NEB-TS is printed:
如果 TS 已完全优化，则会打印整个 NEB-TS 的摘要：

 ***********************HURRAY************************ *** THE TS OPTIMIZATION HAS CONVERGED *** ***************************************************** --------------------------------------------------------------- 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 0.000 -344.38971 0.00 0.00014 0.00003 1 2.024 -344.38507 2.91 0.00144 0.00053 2 3.395 -344.38062 5.70 0.00150 0.00055 3 4.863 -344.38237 4.61 0.00167 0.00064 4 5.663 -344.36742 13.98 0.00329 0.00102 5 6.043 -344.33717 32.97 0.00274 0.00097 6 6.336 -344.32049 43.44 0.00178 0.00058 <= CI 7 6.754 -344.34916 25.45 0.00260 0.00098 8 7.426 -344.38096 5.49 0.00143 0.00058 9 9.661 -344.38666 1.91 0.00023 0.00007 

and the frequencies of the TS are computed, to verify if that has only one negative frequency. The result for this case is:
并计算 TS 的频率，以验证它是否只有一个负频率。这种情况的结果是：

----------------------- VIBRATIONAL FREQUENCIES ----------------------- Scaling factor for frequencies = 1.000000000 (already applied!) 0: 0.00 cm**-1 1: 0.00 cm**-1 2: 0.00 cm**-1 3: 0.00 cm**-1 4: 0.00 cm**-1 5: 0.00 cm**-1 6: -1149.57 cm**-1 ***imaginary mode*** 7: 106.27 cm**-1 8: 135.34 cm**-1 9: 188.41 cm**-1 

proving that the optimized TS structure is indeed a saddle point.
证明优化的 TS 结构确实是一个鞍点。

The final trajectory from the reactants to products can be read from basename_MEP_trj.xyz, and the final transition state geometry, saved in basename_NEB-TS_converged.xyz is:
从 basename_MEP_trj.xyz 中可以读取从反应物到产物的最终轨迹，保存在 basename_NEB-TS_converged.xyz 中的最终过渡态几何为：

One can see that the TS has a tetrahedral carbon atom, as expected from the experimental mechanism, and there is a concerted transfer of proton to the leaving methoxy group.
可以看到 TS 有一个四面体碳原子，正如实验机制所预期的那样，并且质子协同转移到离开的甲氧基。

Note 注意

This calculation was run in gas phase to simplify the explanation. If one includes the solvent, the mechanism will be more complex and the proton transfer can occur, possibly, through an external water molecule.
该计算在气相中运行以简化解释。如果包括溶剂，则机制将更加复杂，并且质子转移可能通过外部水分子发生。

Possible intermediates
可能的中间体#

During the NEB-CI process, the following message could appear:
在 NEB-CI 过程中，可能会出现以下消息：

Possible intermediate minimum found at image(s): 7 => have a look at the .interp file. => it is often a good idea to divide the path calculation into smaller fragments. 

That was because a local minimum was detected along the reaction path. Actually, there could be even more than one.
这是因为沿反应路径检测到局部最小值。实际上，可能不止一个。

The energies following the reaction minimum energy path are printed in the "interp" files and can be plotted to have a better look at it:
反应最小能量路径之后的能量打印在 “interp” 文件中，可以绘制出来以便更好地查看它：

Here one clearly sees that there are two intermediates and one should optimize this structures as well in order to predict reaction energies correctly, and maybe rerun the NEB-TS with these new rectant and product guesses.
在这里，人们清楚地看到有两个中间体，人们也应该优化这种结构，以便正确预测反应能量，也许可以使用这些新的正对子和产物猜测重新运行 NEB-TS。