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在微波光谱学、量子化学和人工智能的帮助下进行无偏构象浴的解缠:同型半胱氨酸的难题。

Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry, and artificial intelligence: The puzzling case of homocysteine.

机构信息

Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005 Valladolid, Spain.

SMART Laboratory, Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy.

出版信息

J Chem Phys. 2022 Aug 21;157(7):074107. doi: 10.1063/5.0102841.

Abstract

An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel the possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the "surviving" conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic α-amino acid. The synergism of the integrated strategy allowed for the characterization of five conformers stabilized by bifurcated N-H⋯O=C hydrogen bonds, together with an additional conformer involving a more conventional HN⋯H-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.

摘要

提出了一种综合实验计算策略,用于准确描述柔性生物分子构建块的构象景观。该策略基于旋转光谱学与人工智能工具引导的量子化学计算相结合。该策略的第一步是通过进化算法进行构象搜索和相对稳定性评估。在此步骤中,利用半经验方法和混合密度泛函、双杂化密度泛函联合探索最后一代方法。接下来,评估控制低能构象之间转化的势垒,以揭示可能的快速松弛途径。然后,使用最先进的复合方案来细化“幸存”构象的相对稳定性和光谱参数。通过包括振动和热效应,可以进一步提高计算过程的可靠性。该策略的最后一步是在不进行任何特殊调整的情况下进行实验与理论之间的比较,这允许根据不同的构象及其光谱参数对光谱特征进行无偏分配。该方法已在高度灵活的非蛋白质α-氨基酸同型半胱氨酸中进行了测试和验证。综合策略的协同作用允许对由分叉 N-H⋯O=C 氢键稳定的五个构象进行特征描述,同时还包括涉及更常规 HN⋯H-O 氢键的附加构象。从实验强度估计的稳定性顺序以及在气相中观察到的构象的数量和类型与理论预测完全一致。同样,在光谱参数方面也找到了很好的匹配。

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