Performances of DFT methods implemented in G09 for simulations of the dispersion-dominated CH-π in ligand–protein complex: A case study with glycerol-GDH
“…This basis set has been recommended by Xu et al for 3d transition metals and has also been found to provide reasonable results for the separation of hydrocarbons on Fe 2 (dobdc) in an earlier work. Since the B3LYP exchange–correlation functional has been widely used to study the Fe(IV)O chemistry, we did test calculations with it to see how it performs compared to M06-L; these results are shown and discussed in the Supporting Information (see Figures S7 and S8), where the discussion, consistent with previous work, − indicates that B3LYP is less reliable than M06-L for this problem. Spin densities were calculated from partial atomic charges determined by Charge Model 5 (CM5) using the CM5PAC package with a Hirshfeld population analysis as input.…”
Section: Structures
and Computational Methodssupporting
The catalytic properties of the metal-organic framework Fe2(dobdc), containing open Fe(II) sites, include hydroxylation of phenol by pure Fe2(dobdc) and hydroxylation of ethane by its magnesium-diluted analogue, Fe0.1Mg1.9(dobdc). In earlier work, the latter reaction was proposed to occur through a redox mechanism involving the generation of an iron(IV)-oxo species, which is an intermediate that is also observed or postulated (depending on the case) in some heme and nonheme enzymes and their model complexes. In the present work, we present a detailed mechanism by which the catalytic material, Fe0.1Mg1.9(dobdc), activates the strong C-H bonds of ethane. Kohn-Sham density functional and multireference wave function calculations have been performed to characterize the electronic structure of key species. We show that the catalytic nonheme-Fe hydroxylation of the strong C-H bond of ethane proceeds by a quintet single-state σ-attack pathway after the formation of highly reactive iron-oxo intermediate. The mechanistic pathway involves three key transition states, with the highest activation barrier for the transfer of oxygen from N2O to the Fe(II) center. The uncatalyzed reaction, where nitrous oxide directly oxidizes ethane to ethanol is found to have an activation barrier of 280 kJ/mol, in contrast to 82 kJ/mol for the slowest step in the iron(IV)-oxo catalytic mechanism. The energetics of the C-H bond activation steps of ethane and methane are also compared. Dehydrogenation and dissociation pathways that can compete with the formation of ethanol were shown to involve higher barriers than the hydroxylation pathway.
“…This basis set has been recommended by Xu et al for 3d transition metals and has also been found to provide reasonable results for the separation of hydrocarbons on Fe 2 (dobdc) in an earlier work. Since the B3LYP exchange–correlation functional has been widely used to study the Fe(IV)O chemistry, we did test calculations with it to see how it performs compared to M06-L; these results are shown and discussed in the Supporting Information (see Figures S7 and S8), where the discussion, consistent with previous work, − indicates that B3LYP is less reliable than M06-L for this problem. Spin densities were calculated from partial atomic charges determined by Charge Model 5 (CM5) using the CM5PAC package with a Hirshfeld population analysis as input.…”
Section: Structures
and Computational Methodssupporting
The catalytic properties of the metal-organic framework Fe2(dobdc), containing open Fe(II) sites, include hydroxylation of phenol by pure Fe2(dobdc) and hydroxylation of ethane by its magnesium-diluted analogue, Fe0.1Mg1.9(dobdc). In earlier work, the latter reaction was proposed to occur through a redox mechanism involving the generation of an iron(IV)-oxo species, which is an intermediate that is also observed or postulated (depending on the case) in some heme and nonheme enzymes and their model complexes. In the present work, we present a detailed mechanism by which the catalytic material, Fe0.1Mg1.9(dobdc), activates the strong C-H bonds of ethane. Kohn-Sham density functional and multireference wave function calculations have been performed to characterize the electronic structure of key species. We show that the catalytic nonheme-Fe hydroxylation of the strong C-H bond of ethane proceeds by a quintet single-state σ-attack pathway after the formation of highly reactive iron-oxo intermediate. The mechanistic pathway involves three key transition states, with the highest activation barrier for the transfer of oxygen from N2O to the Fe(II) center. The uncatalyzed reaction, where nitrous oxide directly oxidizes ethane to ethanol is found to have an activation barrier of 280 kJ/mol, in contrast to 82 kJ/mol for the slowest step in the iron(IV)-oxo catalytic mechanism. The energetics of the C-H bond activation steps of ethane and methane are also compared. Dehydrogenation and dissociation pathways that can compete with the formation of ethanol were shown to involve higher barriers than the hydroxylation pathway.
“…The new empirical potential must always be compared with trustworthy methods, which will act as benchmarks. ,− At first sight, CCSD(T) and MP2 methods can be suitable but too expensive for large systems. In this stream of thought, DFT functionals with third-order Grimme’s dispersion corrections (D3) and Becke–Johnson damping functions (BJ) seem to be a great candidate to benchmark these interactions.…”
The electronic effects in supramolecular systems are a great challenge for computational chemistry, and the understanding of ligand-protein interactions driven by halogen bonds can be limited by molecular mechanics point of view. In fact, the variations of the halogen bond acceptors, such as an aromatic ring and electrons lone pairs, restrict the classical approximations even more. Our work enhances the statement that halogen bonds are led mainly by orbital interactions via σ*. Nonetheless, we have pointed a straight relationship between the maximum ESP value on the σ-hole and the LUMO energy levels of the halogen bond donor. In line with this scenario, the current work introduces a new promising empirical potential based on quantum parametrizations able to describe general halogen bonded systems. The new parameters allow force fields to detect variations on the molecular electronic structure of halogenated organic compounds to improve the description of fluorine, chlorine, and bromine in halogen bonds.
“…However, detailed quantitative interaction strengths at the amnio acid level are still unknown for N501 related protein-protein interaction. We carried out QM/MM simulation, and then quantum mechanics (QM) Møller–Plesset perturbation theory of the second order (MP2)/-aug-cc-pvdz, calculation of intermolecular force between the S glycoprotein receptor binding domain (RBD) and the human-origin antibody B38 possessing neutralization ability ( Liu et al, 2015a , Liu et al, 2015b , Liu et al, 2011 ). Fig.…”
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