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探究结构和能量调整的 QM/MM 键合的适用范围 II:密度泛函紧束缚方法的优化键合参数。

Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches.

机构信息

Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria.

出版信息

J Comput Chem. 2022 Apr 30;43(11):746-756. doi: 10.1002/jcc.26830. Epub 2022 Mar 3.

DOI:10.1002/jcc.26830
PMID:35239208
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9314059/
Abstract

Optimized link bond parameters for the C C bond of 22 different capped amino acid model systems have been determined at SCC DFTB/mio (self-consistent charge density functional tight-binding), SCC DFTB/3ob and GFNn-xTB (n = 0, 1, and 2) level in conjunction with the AMBER 99SB, 14SB, and 19B force fields. The resulting parameter sets have been compared to newly calculated reference data obtained via resolution-of-identity 2nd order Møller-Plesset perturbation theory. The data collected in this work suggests that the optimized values in this study provide a more suitable setup of the QM/MM link bonds compared to the use of a single global setting applied to every amino acid fragmented by the QM/MM interface. The results also imply that a transfer of the ideal link bond settings between different levels of theory is not advised. In contrast, virtually identical parameters were obtained in calculations employing different variants of the AMBER force field. Considering the increasing success of tight binding based approaches being inter alia a results of their exceptional accuracy/effort ratio the provided collection of link atoms parameters provides a valuable resource for QM/MM studies of biomacromolecular systems as demonstrated in an exemplary QM/MM MD simulation of the β-amyloid/Zn complex.

摘要

已在 SCC DFTB/mio(自洽电荷密度泛函紧束缚)、SCC DFTB/3ob 和 GFNn-xTB(n = 0、1 和 2)水平上,针对 22 种不同封端氨基酸模型体系的 C C 键,确定了优化的键参数。结合 AMBER 99SB、14SB 和 19B 力场,将得到的参数集与通过身份分辨的 2 阶 Møller-Plesset 微扰理论新计算的参考数据进行了比较。这项工作收集的数据表明,与使用应用于通过 QM/MM 界面碎片化的每个氨基酸的单个全局设置相比,本研究中优化的值提供了 QM/MM 键的更合适的设置。结果还表明,不建议在不同理论水平之间转移理想的键参数设置。相反,在使用不同 AMBER 力场变体的计算中,几乎获得了相同的参数。考虑到基于紧束缚的方法越来越成功,尤其是由于其出色的准确性/努力比,提供的键原子参数集合为生物大分子系统的 QM/MM 研究提供了有价值的资源,如β-淀粉样蛋白/Zn 配合物的 QM/MM MD 模拟示例所示。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/ad45bee14a1e/JCC-43-746-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/9cb197253b9e/JCC-43-746-g003.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/a1a85e0fadc9/JCC-43-746-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/05b2fa047253/JCC-43-746-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/b3359750b578/JCC-43-746-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/ad45bee14a1e/JCC-43-746-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/9cb197253b9e/JCC-43-746-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/2a5da4739d46/JCC-43-746-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/b6c090cece33/JCC-43-746-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/70e3b59402a9/JCC-43-746-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/a1a85e0fadc9/JCC-43-746-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/05b2fa047253/JCC-43-746-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f473/9314059/b3359750b578/JCC-43-746-g004.jpg
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本文引用的文献

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ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.
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