Comparison of the performance of exact-exchange-based density functional methods

Liu, Fenglai; Proynov, Emil; Yu, Jianguo; Furlani, Thomas R.; Kong, Jing

doi:10.1063/1.4752396

Cited by 36 publications

(46 citation statements)

References 61 publications

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“…69–72 The B3LYP functional predicts the correct mechanism and provides reasonable agreement with the experimental barrier (Δ G ǂ calc = 16.2 kcal/mol, which lowers to Δ G ǂ calc = 15.7 kcal/mol with Grimme empirical dispersion (D3) corrections; Δ G ǂ exp = 14.9 kcal/mol), although it underestimates the observed KIE (1.16 in B3LYP). Note that while a value of 1.7 is large for a secondary KIE, this reaction is measured at low temperatures, which can increase KIEs.…”

Section: Discussionsupporting

confidence: 52%

Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O₂ Reduction in Heme–Copper Oxidases

et al. 2017

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This study evaluates the reaction of a biomimetic heme–peroxo–copper complex, {[(DCHIm)(F8)-FeIII]–(O22−)–[CuII(AN)]}+ (1), with a phenolic substrate, involving a net H-atom abstraction to cleave the bridging peroxo O–O bond that produces FeIV=O, CuII—OH, and phenoxyl radical moieties, analogous to the chemistry carried out in heme–copper oxidases (HCOs). A 3D potential energy surface generated for this reaction reveals two possible reaction pathways: one involves nearly complete proton transfer (PT) from the phenol to the peroxo ligand before the barrier; the other involves O–O homolysis, where the phenol remains H-bonding to the peroxo OCu in the transition state (TS) and transfers the H+ after the barrier. In both mechanisms, electron transfer (ET) from phenol occurs after the PT (and after the barrier); therefore, only the interaction with the H+ is involved in lowering the O–O cleavage barrier. The relative barriers depend on covalency (which governs ET from Fe), and therefore vary with DFT functional. However, as these mechanisms differ by the amount of PT at the TS, kinetic isotope experiments were conducted to determine which mechanism is active. It is found that the phenolic proton exhibits a secondary kinetic isotope effect, consistent with the calculations for the H-bonded O–O homolysis mechanism. The consequences of these findings are discussed in relation to O–O cleavage in HCOs, supporting a model in which a peroxo intermediate serves as the active H+ acceptor, and both the H+ and e− required for O–O cleavage derive from the cross-linked Tyr residue present at the active site.

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Section: Discussionsupporting

confidence: 52%

Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O₂ Reduction in Heme–Copper Oxidases

et al. 2017

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“…These structures were assigned by comparison of their IR spectra with experimental data . More accurate single point calculations were carried out on the optimized geometries of the most stable clusters using the TPSSh functional and the DEF2‐TZVP basis set in conjunction with XDM dispersion correction . The (75,302) integration grid, as it is implemented in the Q‐Chem software, was applied in all cases.…”

Section: Methodsmentioning

confidence: 99%

Non‐covalent Interactions and Charge Transfer between Propene and Neutral Yttrium‐Doped and Pure Gold Clusters

Barabás

Vanbuel

Ferrari

et al. 2019

Chemistry A European J

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The dopant and size‐dependent propene adsorption on neutral gold (Aun) and yttrium‐doped gold (Aun−1Y) clusters in the n=5–15 size range are investigated, combining mass spectrometry and gas phase reactions in a low‐pressure collision cell and density functional theory calculations. The adsorption energies, extracted from the experimental data using an RRKM analysis, show a similar size dependence as the quantum chemical results and are in the range of ≈0.6–1.2 eV. Yttrium doping significantly alters the propene adsorption energies for n=5, 12 and 13. Chemical bonding and energy decomposition analysis showed that there is no covalent bond between the cluster and propene, and that charge transfer and other non‐covalent interactions are dominant. The natural charges, Wiberg bond indices, and the importance of charge transfer all support an electron donation/back‐donation mechanism for the adsorption. Yttrium plays a significant role not only in the propene binding energy, but also in the chemical bonding in the cluster‐propene adduct. Propene preferentially binds to yttrium in small clusters (n<10), and to a gold atom at larger sizes. Besides charge transfer, relaxation also plays an important role, illustrating the non‐local effect of the yttrium dopant. It is shown that the frontier molecular orbitals of the clusters determine the chemical bonding, in line with the molecular‐like electronic structure of metal clusters.

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“…All the meta-GGAs and LRC GGAs qualitatively fail the NO-dimer test. 133 With these explicitly nonlocal, exact-exchange-based functionals looking promising, it is tempting to proclaim that "universal" DFAs are in sight. But there is one more nonlocality to consider.…”

Section: Nonlocalitymentioning

confidence: 99%

“…If self-consistency is not desired, then post-LDA B05/B13 computations are a fast alternative. [133][134][135][136] The distributed Slater potential may also be computed in an indirect manner by a literal implementation of Slater's original orbital-averaged HF-potential concept (Sec. II).…”

Section: Into the Futurementioning

confidence: 99%

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Perspective: Fifty years of density-functional theory in chemical physics

Becke

2014

The Journal of Chemical Physics

1,245

943

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Since its formal inception in 1964-1965, Kohn-Sham density-functional theory (KS-DFT) has become the most popular electronic structure method in computational physics and chemistry. Its popularity stems from its beautifully simple conceptual framework and computational elegance. The rise of KS-DFT in chemical physics began in earnest in the mid 1980s, when crucial developments in its exchange-correlation term gave the theory predictive power competitive with welldeveloped wave-function methods. Today KS-DFT finds itself under increasing pressure to deliver higher and higher accuracy and to adapt to ever more challenging problems. If we are not mindful, however, these pressures may submerge the theory in the wave-function sea. KS-DFT might be lost. I am hopeful the Kohn-Sham philosophical, theoretical, and computational framework can be preserved. This Perspective outlines the history, basic concepts, and present status of KS-DFT in chemical physics, and offers suggestions for its future development. © 2014 AIP Publishing LLC.

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Comparison of the performance of exact-exchange-based density functional methods

Cited by 36 publications

References 61 publications

Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O₂ Reduction in Heme–Copper Oxidases

Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O₂ Reduction in Heme–Copper Oxidases

Non‐covalent Interactions and Charge Transfer between Propene and Neutral Yttrium‐Doped and Pure Gold Clusters

Perspective: Fifty years of density-functional theory in chemical physics

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Comparison of the performance of exact-exchange-based density functional methods

Cited by 36 publications

References 61 publications

Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O2 Reduction in Heme–Copper Oxidases

Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O2 Reduction in Heme–Copper Oxidases

Non‐covalent Interactions and Charge Transfer between Propene and Neutral Yttrium‐Doped and Pure Gold Clusters

Perspective: Fifty years of density-functional theory in chemical physics

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Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O₂ Reduction in Heme–Copper Oxidases

Phenol-Induced O–O Bond Cleavage in a Low-Spin Heme–Peroxo–Copper Complex: Implications for O₂ Reduction in Heme–Copper Oxidases