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无监督搜索具有光谱精度的低能构象:一种扎根于岛屿模型进化算法的两步算法。

Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm.

机构信息

Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.

Super Computing Applications and Innovation, CINECA, Via Magnanelli, 6/3, Casalecchio di Reno, BO, Italy.

出版信息

J Chem Phys. 2020 Sep 28;153(12):124110. doi: 10.1063/5.0018314.

DOI:10.1063/5.0018314
PMID:33003701
Abstract

The fruitful interplay of high-resolution spectroscopy and quantum chemistry has a long history, especially in the field of small, semi-rigid molecules. However, in recent years, the targets of spectroscopic studies are shifting toward flexible molecules, characterized by a large number of closely spaced energy minima, all contributing to the overall spectrum. Here, artificial intelligence comes into play since it is at the basis of powerful unsupervised techniques for the exploration of soft degrees of freedom. Integration of such algorithms with a two-stage QM/QM' (Quantum Mechanical) exploration/refinement strategy driven by a user-friendly graphical interface is the topic of the present paper. We will address in particular: (i) the performances of different semi-empirical methods for the exploration step and (ii) the comparison between stochastic and meta-heuristic algorithms in achieving a cheap yet complete exploration of the conformational space for medium sized chromophores. As test cases, we choose three amino acids of increasing complexity, whose full conformer enumeration has been reached only very recently. Next, we show that systems in condensed phases can be treated at the same level and with the same efficiency when employing a polarizable continuum description of the solvent. Finally, the challenging issue represented by the vibrational circular dichroism spectra of some rhodium complexes with flexible ligands has been addressed, showing that our fully unsupervised approach leads to remarkable agreement with the experiment.

摘要

高分辨率光谱学和量子化学的硕果累累的相互作用有着悠久的历史,特别是在小的、半刚性分子领域。然而,近年来,光谱学研究的目标转向了柔性分子,其特点是存在大量紧密间隔的能量极小值,所有这些都对整体光谱有贡献。在这里,人工智能发挥了作用,因为它是探索软自由度的强大无监督技术的基础。将这些算法与基于用户友好图形界面的两阶段 QM/QM'(量子力学)探索/细化策略相结合是本文的主题。我们将特别关注:(i)不同半经验方法在探索步骤中的性能,以及(ii)随机和元启发式算法在实现中等大小生色团构象空间的廉价但完整探索方面的比较。作为测试案例,我们选择了三个复杂度递增的氨基酸,其完整的构象枚举最近才得以实现。接下来,我们表明,当采用溶剂的极化连续体描述时,可以在相同的水平和相同的效率下处理凝聚相中的系统。最后,我们还解决了一些具有柔性配体的铑配合物的振动圆二色性光谱这一具有挑战性的问题,表明我们完全无监督的方法与实验结果非常吻合。

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