Time-dependent density functional calculations of ligand K-edge X-ray absorption spectra

Abstract.Terminal high-valent metal-oxygen species are key reaction intermediates in the catalytic cycle of both enzymes (e.g., oxygenases) and synthetic oxidation catalysts. While tremendous efforts have been directed towards the characterization of the biologically relevant terminal manganese-oxygen and iron-oxygen species, the corresponding analogues based on late-transition metals such as cobalt, nickel or copper are relatively scarce. This is in part related to the "Oxo Wall" concept, which predicts that late transition elements cannot support a terminal oxido ligand in a tetragonal environment. Here, the nickel(II) complex (1) of the tetradentate macrocyclic ligand bearing a 2,6-pyridinedicarboxamidate unit is shown to be an effective catalyst in the chlorination and oxidation of C-H bonds with sodium hypochlorite as terminal oxidant in the presence of acetic acid (AcOH). Insight into the active species responsible for the observed reactivity was gained through the study of the reaction of 1 with ClO -at low temperature by UV/Vis absorption, resonance Raman, EPR, ESI-MS, and XAS analyses. DFT calculations aided the assignment of the trapped chromophoric species (3) as a nickel-hypochlorite species. Despite the fact that the formal oxidation state of the nickel in 3 is +4, experimental and computational analysis indicate that 3 is best formulated as a Ni III complex with one unpaired electron delocalized in the ligands surrounding the metal center. Most remarkably, 3 reacts rapidly with a range of substrates including those with strong aliphatic C-H bonds, indicating the direct involvement of 3 in the oxidation/chlorination reactions observed in the 1/ClO -

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“…46,70,71 Spin unrestricted, time-dependent calculations for XAS spectra were ) using acetonitrile as solvent.…”

Section: Computational Detailsmentioning

confidence: 99%

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

et al. 2016

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“…In addition, the present analysis enables us to quantify the magnitude of the heme doming in the unligated form (deoxyMb). Finally, the electronic structure is investigated using the pre-edge structures, analysed with time-dependent density functional theory (TD-DFT), 61,62 implemented within the ORCA quantum chemistry package. 63,64 We find that these features are predominantly 1s -d s and 1s -d p À p ligand * transitions, while 1s -d p transitions also weakly contribute for MbO 2 , metMb and deoxyMb.…”

Section: Introductionmentioning

confidence: 99%

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy

Lima

Penfold

Veen

et al. 2014

Phys. Chem. Chem. Phys.

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We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO 2 ), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-N e (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied d s and d p À p ligand * orbitals. 1s -d p transitions contribute weakly for MbO 2 , metMb and deoxyMb.However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s -4p) moment due to the low symmetry of the heme environment.

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“…The XAS spectra were calculated with time-dependent density-functional theory (TD-DFT) following the established methodology [32,34,47] for selectively targeting excitations from the Cu 1s orbital(s). Such restricted-channel TD-DFT calculations have been applied extensively for K-edge XAS spectra of transition metal complexes [19,38,[48][49][50][51][52][53][54].…”

Section: Computational Methodologymentioning

confidence: 99%

“…We note that an empirical, methoddependent constant shift has to be applied in order to align the calculated spectra with experiment [32,33]. Here, a consistent shift has been applied to all spectra calculated with the same method, even though different types of complexes (e.g., with different charge states) might require a different shift [33,34]. Therefore, the absolute energies of the peaks in the calculated spectra will not always precisely match the experimental ones.…”

Section: Interpretation Of Cu K-edge Xas Spectra: Copper Ammine Modelmentioning

confidence: 99%

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Revisiting the Dependence of Cu K-Edge X-Ray Absorption Spectra on Oxidation State and Coordination Environment

Rudolph¹,

Jacob²

2018

Preprint

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X-ray absorption spectroscopy (XAS) at the Cu K-edge is an important tool for probing the properties of copper centers in transition metal chemistry and catalysis.However, the interpretation of experimental XAS spectra requires a detailed understanding of the dependence of spectroscopic features on the local geometric and electronic structure, which can be established by theoretical X-ray spectroscopy.Here, we present a systematic computational study of the Cu K-edge XAS spectra of selected Cu complexes based on time-dependent density-functional theory in combination with a molecular orbital analysis of the relevant transitions. For a series of Cu ammine model complexes as well as a comprehensive test set of 12 Cu(I) and 5 Cu(II) complexes, we revisit the dependence of the pre-edge region in Cu K-edge XAS spectra on oxidation state and coordination geometry. While our calculations confirm earlier experimental assignments, we can also reveal additional signatures of the ligand orbitals and identify the underlying orbital interactions.The comprehensive picture provided by this study will provide a reliable basis for the interpretation of in situ Cu K-edge XAS spectra of catalytic intermediates.2

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Time-dependent density functional calculations of ligand K-edge X-ray absorption spectra

Cited by 206 publications

References 42 publications

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy

Revisiting the Dependence of Cu K-Edge X-Ray Absorption Spectra on Oxidation State and Coordination Environment

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