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迈向用于模拟大分子体系光谱性质的可行且全面的计算协议:采用降维/混合VPT2方法研究固态尿嘧啶的非谐红外光谱。

Toward feasible and comprehensive computational protocol for simulation of the spectroscopic properties of large molecular systems: the anharmonic infrared spectrum of uracil in the solid state by the reduced dimensionality/hybrid VPT2 approach.

作者信息

Fornaro Teresa, Carnimeo Ivan, Biczysko Malgorzata

机构信息

†Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.

‡Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy.

出版信息

J Phys Chem A. 2015 May 28;119(21):5313-26. doi: 10.1021/jp510101y. Epub 2014 Dec 18.

Abstract

Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra- and intermolecular interactions that may take place, the interpretation of experimental data becomes more and more difficult as the system under study increases in size or is placed in a complex environment, such as condensed phases. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes, with increasing complexity toward condensed phases and monolayers of biomolecules on solid supports. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work ( Phys. Chem. Chem. Phys. 2014 , 16 , 10112 - 10128 ) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended such computational protocol to simulate spectroscopic properties of a molecular solid, namely polycrystalline uracil. First we have selected a realistic molecular model for representing the spectroscopic properties of uracil in the solid state, the uracil heptamer, and then we have computed the relative anharmonic frequencies combining less demanding approaches such as the hybrid B3LYP-D3/DFTBA one, in which the harmonic frequencies are computed at a higher level of theory (B3LYP-D3/N07D) whereas the anharmonic shifts are evaluated at a lower level of theory (DFTBA), and the reduced dimensionality VPT2 (RD-VPT2) approach, where only selected vibrational modes are computed anharmonically along with the couplings with other modes. The good agreement between the theoretical results and the experimental findings allowed us to extend the interpretation of experimental data. Our results indicate that hybrid and reduced dimensionality models pave a way for the definition of system-tailored computational protocols able to provide more and more accurate results for very large molecular systems, such as molecular solids and molecules adsorbed on solid supports.

摘要

用于模拟大型复杂分子系统光谱性质的可行且全面的计算协议备受追捧。实际上,由于分子内和分子间可能发生的相互作用种类繁多,随着研究系统规模的增大或处于诸如凝聚相之类的复杂环境中,实验数据的解释变得越来越困难。在此框架下,我们正在积极开发一种全面且稳健的计算协议,旨在定量再现核酸碱基复合物的光谱,随着向凝聚相和固体支持物上生物分子单层的复杂性增加。我们采用了广义二阶振动微扰理论(GVPT2)方法内的全非谐量子力学计算,结合具有成本效益的B3LYP-D3方法,并结合双ζ加极化质量的基组。这种方法已在先前的工作(《物理化学化学物理》2014年,16卷,10112 - 10128页)中得到验证,用于模拟核碱基单体及其一些二聚体的红外光谱。在本论文中,我们将这种计算协议扩展到模拟分子固体(即多晶尿嘧啶)的光谱性质。首先,我们选择了一个现实的分子模型来表示固态尿嘧啶的光谱性质,即尿嘧啶七聚体,然后我们结合了要求较低的方法来计算相对非谐频率,例如混合B3LYP-D3/DFTBA方法,其中谐波频率在更高的理论水平(B3LYP-D3/N07D)下计算,而非谐位移在较低的理论水平(DFTBA)下评估,以及降维VPT2(RD-VPT2)方法,其中仅对选定的振动模式进行非谐计算以及与其他模式的耦合计算。理论结果与实验结果之间的良好一致性使我们能够扩展对实验数据的解释。我们的结果表明,混合模型和降维模型为定义能够为非常大的分子系统(如分子固体和吸附在固体支持物上的分子)提供越来越准确结果的系统定制计算协议铺平了道路。

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