Ghanavati Reza, Escobosa Alma C, Manz Thomas A
Chemical & Materials Engineering, New Mexico State University Las Cruces NM 88001 USA
RSC Adv. 2024 Jul 19;14(31):22714-22762. doi: 10.1039/d4ra01859a. eCollection 2024 Jul 12.
In this work, forcefield flexibility parameters were constructed and validated for more than 100 metal-organic frameworks (MOFs). We used atom typing to identify bond types, angle types, and dihedral types associated with bond stretches, angle bends, dihedral torsions, and other flexibility interactions. Our work used Manz's angle-bending and dihedral-torsion model potentials. For a crystal structure containing in its unit cell, the number of independent flexibility interactions is 3( - 1). Because the number of bonds, angles, and dihedrals is normally much larger than 3( - 1), these internal coordinates are redundant. To reduce (but not eliminate) this redundancy, our protocol prunes dihedral types in a way that preserves symmetry equivalency. Next, each dihedral type is classified as non-rotatable, hindered, rotatable, or linear. We introduce a smart selection method that identifies which particular torsion modes are important for each rotatable dihedral type. Then, we computed the force constants for all flexibility interactions together LASSO regression (, regularized linear least-squares fitting) of the training dataset. LASSO automatically identifies and removes unimportant forcefield interactions. For each MOF, the reference dataset was quantum-mechanically-computed in VASP DFT with dispersion and included: (i) finite-displacement calculations along every independent atom translation mode, (ii) geometries randomly sampled molecular dynamics (AIMD), (iii) the optimized ground-state geometry using experimental lattice parameters, and (iv) rigid torsion scans for each rotatable dihedral type. After training, the flexibility model was validated across geometries that were not part of the training dataset. For each MOF, we computed the goodness of fit (-squared value) and the root-mean-squared error (RMSE) separately for the training and validation datasets. We compared flexibility models with and without bond-bond cross terms. Even without cross terms, the model yielded -squared values of 0.910 (avg across all MOFs) ± 0.018 (st. dev.) for atom-in-material forces in the validation datasets. Our SAVESTEPS protocol should find widespread applications to parameterize flexible forcefields for material datasets. We performed molecular dynamics simulations using these flexibility parameters to compute heat capacities and thermal expansion coefficients for two MOFs.
在这项工作中，构建并验证了100多种金属有机框架（MOF）的力场灵活性参数。我们使用原子类型识别与键伸缩、角弯曲、二面角扭转及其他灵活性相互作用相关的键类型、角类型和二面角类型。我们的工作使用了曼兹的角弯曲和二面角扭转模型势。对于其晶胞中包含的晶体结构，独立灵活性相互作用的数量为3( - 1)。由于键、角和二面角的数量通常远大于3( - 1)，这些内坐标是冗余的。为了减少（但不是消除）这种冗余，我们的方案以保持对称等效性的方式修剪二面角类型。接下来，将每个二面角类型分类为不可旋转、受阻、可旋转或线性。我们引入了一种智能选择方法，以确定哪些特定的扭转模式对每个可旋转二面角类型很重要。然后，我们通过对训练数据集进行LASSO回归（，正则化线性最小二乘拟合）来一起计算所有灵活性相互作用的力常数。LASSO会自动识别并去除不重要的力场相互作用。对于每个MOF，参考数据集是在VASP DFT中通过量子力学计算得到的，包括色散：(i) 沿每个独立原子平移模式的有限位移计算，(ii) 通过分子动力学（AIMD）随机采样的几何结构，(iii) 使用实验晶格参数优化的基态几何结构，以及(iv) 对每个可旋转二面角类型的刚性扭转扫描。训练后，在不属于训练数据集的几何结构上验证了灵活性模型。对于每个MOF，我们分别计算了训练和验证数据集的拟合优度（平方值）和均方根误差（RMSE）。我们比较了有无键 - 键交叉项的灵活性模型。即使没有交叉项，该模型在验证数据集中对于材料中原子力的平方值为0.910（所有MOF的平均值）±0.018（标准差）。我们的SAVESTEPS方案应该会在为材料数据集参数化灵活力场方面得到广泛应用。我们使用这些灵活性参数进行分子动力学模拟，以计算两种MOF的热容和热膨胀系数。
