flexible molecules JCP2021

Configurations of azobenzene featuring a cis to trans thermal inversion through three channels: inversion, rotation, and rotation assisted by inversion; and configurations of glycine as a simpler comparison molecule. All calculations were performed in FHI-aims software using the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Tkatchenko-Scheffler (TS) method to account for van der Waals (vdW) interactions. The azobenzene sets contain calculations from several different MD simulations, including two long simulations initialized at 300 K; short simulations (300 steps) initialized at 300 K and shorter (.5fs) timestep; four simulations, two starting from each of cis and trans isomer, at 750 K (initialized at 3000 K); and simulations at 50 K (initialized at 300 K). The glycine isomerization set was built using one MD simulation starting from each of two different minima. Initializatin and simulation temperature were 500 K.

本数据集收录了亚胺基苯的结构配置，其特征在于通过三个通道实现顺式至反式的热反转：反转、旋转以及反转辅助下的旋转；同时，还包括甘氨酸的结构配置，作为比较分子。所有计算均在FHI-aims软件中完成，采用Perdew-Burke-Ernzerhof (PBE) 交换相关泛函，并运用Tkatchenko-Scheffler (TS) 方法来考虑范德华 (vdW) 相互作用。亚胺基苯集合包含来自多个不同分子动力学 (MD) 模拟的计算结果，包括两个在300 K下初始化的长时间模拟；300步的短模拟（在300 K下初始化）和更短的（0.5 fs时间步长）模拟；以及四个模拟，两个分别从顺式和反式异构体开始，在750 K下进行（初始化于3000 K）；还有在50 K下进行的模拟（初始化于300 K）。甘氨酸异构化集合是通过从两个不同的最小值开始，各自进行一次MD模拟构建而成。初始化和模拟的温度均为500 K。