eScholarship
收藏资源简介：
This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process
本研究构建了一套经整理筛选的数据库，收录了水环境中小型中性分子的实验与计算所得水合自由能数据，同时配套提供分子结构、输入文件、参考文献及注释信息，该数据库被命名为自由溶剂化数据库（Free Solvation Database，简称FreeSolv）。实验数据取自既往发表文献，且将持续开展整理筛选工作，随着新的实验参考文献与数据公开，将及时更新补充。计算值基于采用分子动力学模拟的炼金术式自由能计算（alchemical free energy calculations）得到，计算过程中使用了TIP3P（Transferable Intermolecular Interaction Potential 3-point）水模型下的GAFF（Generalized Amber Force Field）小分子力场与AM1-BCC（Austin Model 1 - Bond Charge Correction）电荷，并通过GROMACS（GROningen MAchine for Chemical Simulations）模拟软件包完成数值计算，完整细节可参见数据库内引用的相关文献。本数据库部分内容基于此前一套包含504个分子的同类数据库构建，但本研究对实验数据与计算值均开展了额外的整理筛选工作，目前数据库内的分子总数已增至643个。此外，数据库新增了多项信息，例如SMILES（Simplified Molecular Input Line Entry System）字符串、PubChem（PubChem Compound Database）化合物标识符、精准的参考文献DOI等。本文的补充材料（Supporting Information）中提供了该数据库的一个版本，但由于本数据库将持续更新，目前已实现版本化管理并在线托管。本研究除公开该数据库外，还详细阐述了其构建流程。
