PyntaAn Automated Workflow for Calculation of Surface and Gas–Surface Kinetics

Many important industrial processes
rely on heterogeneous catalytic
systems. However, given all possible catalysts and conditions of interest,
it is impractical to optimize most systems experimentally. Automatically
generated microkinetic models can be used to efficiently consider
many catalysts and conditions. However, these microkinetic models
require accurate estimation of many thermochemical and kinetic parameters.
Manually calculating these parameters is tedious and error prone,
involving many interconnected computations. We present Pynta, a workflow
software for automating the calculation of surface and gas–surface
reactions. Pynta takes the reactants, products, and atom maps for
the reactions of interest, generates sets of initial guesses for all
species and saddle points, runs all optimizations, frequency, and
IRC calculations, and computes the associated thermochemistry and
rate coefficients. It is able to consider all unique adsorption configurations
for both adsorbates and saddle points, allowing it to handle high
index surfaces and bidentate species. Pynta implements a new saddle
point guess generation method called harmonically forced saddle point
searching (HFSP). HFSP defines harmonic potentials based on the optimized
adsorbate geometries and which bonds are breaking and forming that
allow initial placements to be optimized using the GFN1-xTB semiempirical
method to create reliable saddle point guesses. This method is reaction
class agnostic and fast, allowing Pynta to consider all possible adsorbate
site placements efficiently. We demonstrate Pynta on 11 diverse reactions
involving monodenate, bidentate, and gas-phase species, many distinct
reaction classes, and both a low and a high index facet of Cu. Our
results suggest that it is very important to consider reactions between
adsorbates adsorbed in all unique configurations for interadsorbate
group transfers and reactions on high index surfaces.

诸多重要的工业过程均依赖于多相催化体系。然而，若要针对所有候选催化剂与目标反应条件开展优化，通过实验手段对绝大多数催化体系进行优化并不现实。自动生成的微观动力学模型（microkinetic model）可用于高效筛选大量催化剂与反应条件，但这类模型需要精准估算众多热化学与动力学参数。手动计算这类参数不仅繁琐冗长，还极易引入误差，且涉及大量相互关联的计算步骤。本研究推出了一款名为Pynta的工作流软件，用于自动化计算表面反应与气-表面界面反应。Pynta可接收目标反应的反应物、产物与原子映射关系，为所有反应物种与鞍点（saddle point）生成初始猜测集，完成全部优化、频率分析与内禀反应坐标（Intrinsic Reaction Coordinate, IRC）计算，并同步计算相关热化学参数与速率系数。该软件可覆盖吸附质与鞍点的所有独特吸附构型，因此能够处理高指数晶面与双齿物种。Pynta还实现了一种全新的鞍点初始猜测生成方法，命名为谐波强制鞍点搜索（harmonically forced saddle point searching, HFSP）。HFSP基于优化后的吸附质几何结构与待断裂/形成的化学键定义谐波势，可通过GFN1-xTB半经验方法对初始位点布局进行优化，从而生成可靠的鞍点初始猜测。该方法不依赖反应类别且运算高效，可使Pynta高效遍历所有可能的吸附质位点布局。本研究通过11种不同反应验证了Pynta的性能，这些反应涵盖单齿、双齿与气相物种，包含多种不同反应类别，且同时涉及铜的低指数与高指数晶面。研究结果表明，在吸附质间基团转移反应以及高指数晶面上的反应中，考虑所有独特吸附构型下的吸附质之间的反应至关重要。