Building a consistent and reproducible database for adsorption evaluation in Covalent-Organic Frameworks

We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal's postcombustion flue gases. This workflow is applied to a database of 324 covalent−organic frameworks (COFs) reported in the literature, to characterize their CO2 adsorption properties using the following steps:
(1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory,
(2) fitting atomic point charges based on the electron density,
(3) characterizing the pore geometry of the structures before and after optimization,
(4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally,
(5) assessing the CO2 parasitic energy via process modeling.

The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the automatically generated provenance graph of our calculations are made available on the Materials Cloud, allowing peers to inspect every input parameter and result along the workflow, download structures and files at intermediate stages, and start their research right from where this work has left off. In particular, our set of CURATED (Clean, Uniform, and Refined with Automatic Tracking from Experimental Database) COFs, having optimized geometry and high-quality DFT-derived point charges, are available for further investigations of gas adsorption properties. We plan to update the database as new COFs are being reported.

*** UPDATE December 2019 ***
- Database extended to include 417 COFs (from papers published until September 1st 2019)
- Migration to AiiDA-v1.0.0
- Using the publicly available plugin aiida-lsmo

*** UPDATE February 2020 ***
- Database extended to include 505 COFs (from papers published until February 1st 2020)
- Including AiiDA Groups for quick interactive visualization

*** UPDATE June 2020 ***
- Database extended to include 574 COFs (from papers published until June 1st 2020)

*** UPDATE September 2020 ***
- Include other applications than CCS, considering the same set of 574 COFs

*** UPDATE October 2020 ***
- Database extended to include 626 COFs (from papers published until October 1st 2020)

*** UPDATE February 2021 ***
- Database extended to include 632 COFs (from papers published until February 1st 2021). We added a total of 61 new structures but we discarded 55: see CURATED-COFs GitHub for more details.

*** UPDATE June 2021 ***
- Database extended to include 648 valid COFs (from papers published until June 1st 2021) plus 80 discarded: see CURATED-COFs GitHub for more details.

*** UPDATE July 2022 ***
- Database extended to include 871 valid COFs (from papers published until July 1st 2022) plus 110 discarded: see CURATED-COFs GitHub for more details.

我们提出一套工作流，可完整追踪从晶体材料体相结构到评估其在燃煤后烟气碳捕获中应用性能的全路径。本工作流被应用于文献报道的324个共价有机框架（covalent−organic frameworks, COFs）数据库，通过以下步骤表征其二氧化碳吸附性能：
(1) 利用密度泛函理论（density functional theory）优化晶体结构（原子位置与晶胞参数）；
(2) 基于电子密度拟合原子点电荷；
(3) 表征优化前后结构的孔道几何特征；
(4) 采用基于经验相互作用势的巨正则蒙特卡洛（grand canonical Monte Carlo）模拟计算二氧化碳与氮气吸附等温线；
(5) 通过过程建模（process modeling）评估二氧化碳捕集的寄生能耗。

整套工作流已在计算科学自动化交互基础设施与数据库（Automated Interactive Infrastructure and Database for Computational Science, AiiDA）中完成编码。本工作流与我们计算过程自动生成的溯源图均已发布至材料云（Materials Cloud），便于同行检视工作流中每一项输入参数与结果、下载中间阶段的结构与文件，并可直接基于本研究的成果开展后续研究。尤为值得关注的是，我们整理的CURATED（Clean, Uniform, and Refined with Automatic Tracking from Experimental Database，即源自实验数据库的清洁、统一、经自动追踪优化的）COFs集合，包含优化后的几何结构与高质量密度泛函理论衍生的原子点电荷，可用于后续气体吸附性能的相关研究。我们将随新的COFs文献报道持续更新该数据库。

*** 2019年12月更新 ***
- 数据库扩容至417个COFs（涵盖截至2019年9月1日发表的相关文献）
- 迁移至AiiDA-v1.0.0版本
- 采用公开可用的aiida-lsmo插件

*** 2020年2月更新 ***
- 数据库扩容至505个COFs（涵盖截至2020年2月1日发表的相关文献）
- 新增AiiDA分组以支持快速交互式可视化

*** 2020年6月更新 ***
- 数据库扩容至574个COFs（涵盖截至2020年6月1日发表的相关文献）

*** 2020年9月更新 ***
- 针对该574个COFs集合，拓展其应用场景至碳捕获以外的领域

*** 2020年10月更新 ***
- 数据库扩容至626个COFs（涵盖截至2020年10月1日发表的相关文献）

*** 2021年2月更新 ***
- 数据库扩容至632个COFs（涵盖截至2021年2月1日发表的相关文献）。本次新增61个结构，同时剔除55个结构，详细信息请参见CURATED-COFs GitHub仓库。

*** 2021年6月更新 ***
- 数据库包含648个有效COFs（涵盖截至2021年6月1日发表的相关文献），另有80个被剔除的结构，详细信息请参见CURATED-COFs GitHub仓库。

*** 2022年7月更新 ***
- 数据库包含871个有效COFs（涵盖截至2022年7月1日发表的相关文献），另有110个被剔除的结构，详细信息请参见CURATED-COFs GitHub仓库。