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Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods.凝聚相中的分子间相互作用:半经验量子力学方法的评估。
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3
A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1-86).一种用于所有 spd 区元素(Z=1-86)的大体系结构、振动频率和非共价相互作用的强韧且精确的紧束缚量子化学方法。
J Chem Theory Comput. 2017 May 9;13(5):1989-2009. doi: 10.1021/acs.jctc.7b00118. Epub 2017 Apr 24.
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Metal Ion Modeling Using Classical Mechanics.使用经典力学的金属离子建模
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Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.水中及蛋白质中的铜氧化/还原:基于DFTB3/MM和VALBOND分子动力学模拟的研究
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探索密度泛函紧束缚方法对过渡金属离子的适用性。采用自旋极化DFTB3模型对镍进行参数化。

Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

作者信息

Vujović Milena, Huynh Mioy, Steiner Sebastian, Garcia-Fernandez Pablo, Elstner Marcus, Cui Qiang, Gruden Maja

机构信息

Center for Computational Chemistry and Bioinformatics, Faculty of Chemistry, University of Belgrade, Studentski trg 12-16 11001, Belgrade, Serbia.

Departments of Chemistry, Physics, Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts.

出版信息

J Comput Chem. 2019 Jan 15;40(2):400-413. doi: 10.1002/jcc.25614. Epub 2018 Oct 9.

DOI:10.1002/jcc.25614
PMID:30299559
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6294695/
Abstract

In this work, we explore the applicability and limitations of the current third order density functional tight binding (DFTB3) formalism for treating transition metal ions using nickel as an example. To be consistent with recent parameterization of DFTB3 for copper, the parametrization for nickel is conducted in a spin-polarized formulation and with orbital-resolved Hubbard parameters and their charge derivatives. The performance of the current parameter set is evaluated based on structural and energetic properties of a set of nickel-containing compounds that involve biologically relevant ligands. Qualitatively similar to findings in previous studies of copper complexes, the DFTB3 results are more reliable for nickel complexes with neutral ligands than for charged ligands; nevertheless, encouraging agreement is noted in comparison to the reference method, B3LYP/aug-cc-pVTZ, especially for structural properties, including cases that exhibit Jahn-Teller distortions; the structures also compare favorably to available X-ray data in the Cambridge Crystallographic Database for a number of nickel-containing compounds. As to limitations, we find it is necessary to use different d shell Hubbard charge derivatives for Ni(I) and Ni(II), due to the distinct electronic configurations for the nickel ion in the respective complexes, and substantial errors are observed for ligand binding energies, especially for charged ligands, d orbital splitting energies and splitting between singlet and triplet spin states for Ni(II) compounds. These observations highlight that future improvement in intra-d correlation and ligand polarization is required to enable the application of the DFTB3 model to complex transition metal ions. © 2018 Wiley Periodicals, Inc.

摘要

在这项工作中,我们以镍为例,探讨了当前三阶密度泛函紧束缚(DFTB3)形式体系在处理过渡金属离子方面的适用性和局限性。为了与最近针对铜的DFTB3参数化保持一致,对镍的参数化是在自旋极化形式体系中进行的,并采用了轨道分辨的哈伯德参数及其电荷导数。基于一组包含与生物相关配体的含镍化合物的结构和能量性质,对当前参数集的性能进行了评估。与之前对铜配合物的研究结果定性相似,DFTB3对具有中性配体的镍配合物的结果比对带电荷配体的结果更可靠;然而,与参考方法B3LYP/aug-cc-pVTZ相比,仍有令人鼓舞的一致性,特别是对于结构性质,包括表现出 Jahn-Teller 畸变的情况;对于许多含镍化合物,其结构与剑桥晶体学数据库中可用的 X 射线数据相比也很有利。至于局限性,我们发现由于各自配合物中镍离子的电子构型不同,有必要对Ni(I)和Ni(II)使用不同的d壳层哈伯德电荷导数,并且观察到配体结合能存在大量误差,特别是对于带电荷配体、d轨道分裂能以及Ni(II)化合物单重态和三重态自旋态之间的分裂。这些观察结果突出表明,未来需要在d内相关性和配体极化方面进行改进,以使DFTB3模型能够应用于复杂的过渡金属离子。© 2018威利期刊公司。