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通过无监督学习实现有限温度下的光学和电子性质的快速途径。

An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning.

机构信息

Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy.

Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy.

出版信息

Molecules. 2023 Apr 12;28(8):3411. doi: 10.3390/molecules28083411.

Abstract

Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time dependent density functional theory and ab initio molecular dynamics (MD) have become very powerful in this field, although they require still a large number of computations for a detailed reproduction of electronic properties, such as band shapes. Besides the ongoing research in more traditional computational chemistry fields, data analysis and machine learning methods have been increasingly employed as complementary approaches for efficient data exploration, prediction and model development, starting from the data resulting from MD simulations and electronic structure calculations. In this work, dataset reduction capabilities by unsupervised clustering techniques applied to MD trajectories are proposed and tested for the ab initio modeling of electronic absorption spectra of two challenging case studies: a non-covalent charge-transfer dimer and a ruthenium complex in solution at room temperature. The K-medoids clustering technique is applied and is proven to be able to reduce by ∼100 times the total cost of excited state calculations on an MD sampling with no loss in the accuracy and it also provides an easier understanding of the representative structures (medoids) to be analyzed on the molecular scale.

摘要

电子性质和吸收光谱是研究分子电子态及其与环境相互作用的基础。为了理解分子并设计光活性材料和传感器的策略,需要对模型和计算进行研究。然而,这些性质的解释需要昂贵的计算,并需要处理在有限温度下发色团的电子激发态与复杂基质(即溶剂、生物分子、晶体)中构象自由度的相互作用。将含时密度泛函理论和从头算分子动力学(MD)相结合的计算方案在该领域变得非常强大,尽管它们仍然需要大量的计算来详细再现电子性质,例如能带形状。除了在更传统的计算化学领域进行的研究外,数据分析和机器学习方法也越来越多地被用作补充方法,用于有效地探索、预测和开发模型,这些方法从 MD 模拟和电子结构计算产生的数据开始。在这项工作中,提出并测试了通过无监督聚类技术对 MD 轨迹进行数据集缩减的能力,以用于两个具有挑战性的案例研究的从头算电子吸收光谱建模:非共价电荷转移二聚体和室温下溶液中的钌配合物。应用了 K-medoids 聚类技术,证明它能够将 MD 采样上激发态计算的总成本减少约 100 倍,而不会降低准确性,并且它还提供了一种更容易理解要在分子尺度上分析的代表性结构(质心)的方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3e50/10144358/80c513535a27/molecules-28-03411-g001.jpg

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