Evaluating the predictive character of the method of Constrained Geometries Simulate External Force with Density Functional Theory.
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## Abstract from [1]: Mechanochemistry is a fast-developing field of interdisciplinary research with a growing number of applications. Therefore, many theoretical methods have been developed to quickly predict the outcome of mechanically induced reactions. Constrained geometries simulate External Force (CoGEF) is one of the earlier methods in this field. It is easily implemented and can be conducted with most DFT codes. However, recently, we observed totally different predictions for model systems of epoxy resins in different conformations and with different density functionals. To better understand the conformational and functional dependence in typical CoGEF calculations we present a systematic evaluation of the CoGEF method for different model systems covering homolytic and heterolytic bond cleavage reactions, electrocyclic ring opening reactions and scission of non-covalent interactions in hydrogen-bond complexes. From our calculations we observe that many mechanochemical descriptors strongly depend on the functional used, however, a systematic trend exists for the relative maximum Force. In general, we observe that the CoGEF procedure is forcing the system to high energetic regions on the molecular potential energy profiles, which can lead to unexpected and uncorrelated predictions of mechanochemical reactions. This is questioning the true predictive character of the method. ## Contact Christian R. Wick Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Faculty of Science, Department of Physics, PULS Group, Interdisciplinary Center for Nanostructured Films (IZNF), Cauerstrasse 3, 91058, Germany ## License Creative Commons Attribution 4.0 International ## Context Dataset to paper [1] ## Contents All COGEF trajectories in xyz format. All CoGEF distances and DFT Energies in csv format. compounds.json: JSON file, containing SMILES, InChI and InChIKey descriptors for all compounds investigated as dictionary The following DFT levels of theory were investigated: B3LYP/6-31G(d) B3LYP-D3BJ/def2-SVP BP86-D3/def2-SVP PBE1PBE/def2-SVP M06-D3/def2-SVP ## Folder structure - compound_X : data set for compound number X (numbering corresponds to the numbering scheme in [1]) the xyz trajectories follow the following naming convention: "DFT_method"_"unrestricted/restricted".xyz the csv files follow the naming convention: "DFT_method"_"unrestricted/restricted".xyz.csv ## Software ### COGEFF calculations: COGEF.py v1.8.0 Zenodo release: https://doi.org/10.5281/zenodo.7079733 ### DFT calculations: Gaussian 16 Rev B [2] ## Funding This research was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 377472739/GRK 2423/1-2019 FRASCAL. ## References [1] C. R. Wick, E. Topraksal, D. M. Smith, A.-S. Smith, "Evaluating the predictive character of the method of Constrained Geometries Simulate External Force with Density Functional Theory.", Forces in Mechanics, 9, 100143; doi:10.1016/j.finmec.2022.100143 [2] Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; et al. Gaussian 16 Rev. B.01, 2016.
## 摘要 引自文献[1]： 机械化学（Mechanochemistry）是一门快速发展的交叉研究领域，应用场景日益丰富。为此，学界已开发出诸多理论方法以快速预测机械诱导反应的结果。约束几何模拟外力法（Constrained Geometries Simulate External Force，简称CoGEF）是该领域早期方法之一，其实现难度低，可兼容绝大多数密度泛函理论（Density Functional Theory，DFT）程序。然而，近期我们针对不同构象、使用不同密度泛函的环氧树脂模型体系开展研究时，得到了完全相悖的预测结果。为更好地理解典型CoGEF计算中构象与泛函的依赖性，我们针对多类模型体系系统性评估了CoGEF方法，涵盖均裂与异裂键断裂反应、电环开环反应以及氢键复合物中非共价相互作用的断裂过程。计算结果表明，诸多机械化学描述符强烈依赖于所选用的泛函，但相对最大力存在系统性变化趋势。总体而言，CoGEF流程会将体系强制推至分子势能面的高能量区域，这可能导致机械化学反应的预测结果出现意外且无关联的情况，进而对该方法的真实预测性能提出了质疑。 ## 联系方式 克里斯蒂安·R·威克（Christian R. Wick） 埃尔朗根-纽伦堡弗里德里希-亚历山大大学（Friedrich-Alexander-University Erlangen-Nürnberg，简称FAU）理学院物理系PULS课题组、纳米结构薄膜跨学科中心（Interdisciplinary Center for Nanostructured Films，简称IZNF），德国考厄大街3号，邮编91058 ## 授权协议 知识共享署名4.0国际许可协议（Creative Commons Attribution 4.0 International） ## 数据集说明 本数据集对应文献[1]的研究工作 ## 数据集内容 所有CoGEF轨迹文件均采用XYZ坐标格式存储。 所有CoGEF距离与DFT能量数据均采用逗号分隔值（Comma-Separated Values，CSV）格式存储。 compounds.json：JSON格式文件，以字典形式收录所有研究化合物的SMILES（Simplified Molecular-Input Line-Entry System，SMILES）、InChI（International Chemical Identifier，InChI）以及InChIKey（InChIKey）描述符。 本次研究涉及的DFT理论级别如下： B3LYP/6-31G(d) B3LYP-D3BJ/def2-SVP BP86-D3/def2-SVP PBE1PBE/def2-SVP M06-D3/def2-SVP ## 文件夹结构 - compound_X：编号为X的化合物对应数据集（编号规则与文献[1]一致） XYZ轨迹文件的命名规则为："DFT_method"_"unrestricted/restricted".xyz CSV数据文件的命名规则为："DFT_method"_"unrestricted/restricted".xyz.csv ## 所用软件 ### CoGEF计算：COGEF.py v1.8.0 泽诺多（Zenodo）存档链接：https://doi.org/10.5281/zenodo.7079733 ### DFT计算： 高斯16修订版B（Gaussian 16 Rev B）[2] ## 资助信息 本研究由德国研究基金会（Deutsche Forschungsgemeinschaft，简称DFG）资助——项目编号377472739/GRK 2423/1-2019 FRASCAL。 ## 参考文献 [1] C. R. Wick, E. Topraksal, D. M. Smith, A.-S. Smith, "Evaluating the predictive character of the method of Constrained Geometries Simulate External Force with Density Functional Theory.", Forces in Mechanics, 9, 100143; doi:10.1016/j.finmec.2022.100143 [2] Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; et al. Gaussian 16 Rev. B.01, 2016.
