Kernel-Based Minimal Distributed Charges: A Conformationally Dependent ESP-Model for Molecular Simulations,Journal of Chemical Theory and Computation

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Kernel-Based Minimal Distributed Charges: A Conformationally Dependent ESP-Model for Molecular Simulations
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2024-09-04 , DOI: 10.1021/acs.jctc.4c00759
Eric Boittier ₁ , Kai Töpfer ₁ , Mike Devereux ₁ , Markus Meuwly ₁

Affiliation

A kernel-based method (kernelized minimal distributed charge model (kMDCM)) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges is introduced. The positions of the charges adapt to the molecular geometry and allow the description of intramolecular charge flow. Using Gaussian kernels and atom–atom distances as the features, the ESPs for water and methanol are shown to improve by at least a factor of 2 compared with point charge models fit to an ensemble of structures. The conformationally fluctuating molecular dipole moment of water is reproduced almost twice as accurately using kMDCM compared with static PCs, despite not fitting to the dipole directly. The role of hyperparameters in the kernelization is investigated and their implication on model performance and simulation stability is discussed. Combining kMDCM for the electrostatics and reproducing kernels for the bonded terms allows energy-conserving simulations of 2000 water molecules with periodic boundary conditions on the nanosecond time scale. These MD simulations sample geometries outside the training set but remain stable, which demonstrates the robustness of the model and its implementation.

中文翻译：

基于内核的最小分布式电荷：用于分子模拟的构象相关 ESP 模型

引入了一种基于核的方法（核化最小分布电荷模型（kMDCM）），以偏心点电荷的形式表示分子静电势（ESP）。电荷的位置适应分子几何形状并允许描述分子内电荷流。使用高斯核和原子间距离作为特征，与适合结构集合的点电荷模型相比，水和甲醇的 ESP 至少提高了 2 倍。尽管不直接拟合偶极子，但与静态 PC 相比，使用 kMDCM 再现水的构象波动分子偶极矩的准确度几乎是静态 PC 的两倍。研究了超参数在核化中的作用，并讨论了它们对模型性能和仿真稳定性的影响。将静电学的 kMDCM 与键合项的再现核相结合，可以在纳秒时间尺度上对具有周期性边界条件的 2000 个水分子进行节能模拟。这些 MD 模拟对训练集之外的几何形状进行采样，但保持稳定，这证明了模型及其实现的稳健性。

更新日期：2024-09-04

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