Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding

X-ray absorption spectroscopy systematics at the tungsten L-edge

A series of mononuclear six-coordinate tungsten compounds spanning formal oxidation states from 0 to +VI, largely in a ligand environment of inert chloride and/or phosphine, has been interrogated by tungsten L-edge X-ray absorption spectroscopy. The L-edge spectra of this compound set, comprised of [W<sup>0</sup>(PMe<sub>3</sub>)<sub>6</sub>], [W<sup>II</sup>Cl<sub>2</sub>(PMePh<sub>2</sub>)<sub>4</sub>], [W<sup>III</sup>Cl<sub>2</sub>(dppe)<sub>2</sub>][PF<sub>6</sub>] (dppe = 1,2-bis(diphenylphosphino)ethane), [W<sup>IV</sup>Cl<sub>4</sub>(PMePh<sub>2</sub>)<sub>2</sub>], [W<sup>V</sup>(NPh)Cl<sub>3</sub>(PMe<sub>3</sub>)<sub>2</sub>], and [W<sup>VI</sup>Cl<sub>6</sub>] correlate with formal oxidation state and have usefulness as references for the interpretation of the L-edge spectra of tungsten compounds with redox-active ligands and ambiguous electronic structure descriptions. The utility of these spectra arises from the combined correlation of the estimated branching ratio (EBR) of the L<sub>3,2</sub>-edges and the L<sub>1</sub> rising-edge energy with metal Z<sub>eff</sub>, thereby permitting an assessment of effective metal oxidation state. An application of these reference spectra is illustrated by their use as backdrop for the L-edge X-ray absorption spectra of [W<sup>IV</sup>(mdt)<sub>2</sub>(CO)<sub>2</sub>] and [W<sup>IV</sup>(mdt)<sub>2</sub>(CN)<sub>2</sub>]<sup>2–</sup> (mdt<sup>2–</sup> = 1,2-dimethylethene-1,2-dithiolate), which shows that both compounds are effectively W<sup>IV</sup> species. Use of metal L-edge XAS to assess a compound of uncertain formulation requires: 1) Placement of that data within the context of spectra offered by unambiguous calibrant compounds, preferably with the same coordination number and similar metal ligand distances. Such spectra assist in defining upper and/or lower limits for metal Z<sub>eff</sub> in the species of interest; 2) Evaluation of that data in conjunction with information from other physical methods, especially ligand K-edge XAS; 3) Increased care in interpretation if strong π-acceptor ligands, particularly CO, or π-donor ligands are present. The electron-withdrawing/donating nature of these ligand types, combined with relatively short metal-ligand distances, exaggerate the difference between formal oxidation state and metal Z<sub>eff</sub> or, as in the case of [W<sup>IV</sup>(mdt)<sub>2</sub>(CO)<sub>2</sub>], add other subtlety by modulating the redox level of other ligands in the coordination sphere

Density functional theory

Density functional theory (DFT) finds increasing use in applications related to biological systems. Advancements in methodology and implementations have reached a point where predicted properties of reasonable to high quality can be obtained. Thus, DFT studies can complement experimental investigations, or even venture with some confidence into experimentally unexplored territory. In the present contribution, we provide an overview of the properties that can be calculated with DFT, such as geometries, energies, reaction mechanisms, and spectroscopic properties. A wide range of spectroscopic parameters is nowadays accessible with DFT, including quantities related to infrared and optical spectra, X-ray absorption and Mössbauer, as well as all of the magnetic properties connected with electron paramagnetic resonance spectroscopy except relaxation times. We highlight each of these fields of application with selected examples from the recent literature and comment on the capabilities and limitations of current methods

Multiple Core and Vibronic Coupling Effects in Attosecond Stimulated X-Ray Raman Spectroscopy

Attosecond Stimulated X-ray Raman Spectroscopy (SXRS) is a promising technique for investigating molecular electronic structure and photochemical processes with high spatial and temporal resolution. We present a theoretical study of SXRS from multiple core excitation sites of the same element. Two issues are addressed: interference between pathways contributing the signals from different sites; and how nuclear vibrations influence the signals. Taking furan as a model system, which contains two types of carbons Cα and Cβ, we performed time-dependent density functional theory calculations and computed the SXRS signals with two pulses tuned at the carbon K-edge. Our simulations demonstrate that the SXRS signal from the Cα and Cβ sites are non-additive, owing to the significant mixed contributions (Cα 1s excitations by the pump pulse followed by Cβ 1s excitations by the probe, or vice verse). Harmonic vibrations linearly coupled to the electronic transitions are incorporated using the cumulant expansion. The nuclei act as a bath for electronic transitions which accelerate the decay of time-domain signal. The frequency-domain spectrum is modified by a small red shift and high-resolution fine-structure features are introduced

Calibration of Scalar Relativistic Density Functional Theory for the Calculation of Sulfur K-Edge X-ray Absorption Spectra

Sulfur K-edge X-ray absorption spectroscopy has been proven to be a powerful tool for investigating the electronic structures of sulfur-containing coordination complexes. The full information content of the spectra can be developed through a combination of experiment and time-dependent density functional theory (TD-DFT). In this work, the necessary calibration is carried out for a range of contemporary functionals (BP86, PBE, OLYP, OPBE, B3LYP, PBE0, TPSSh) in a scalar relativistic (0th order regular approximation, ZORA) DFT framework. It is shown that with recently developed segmented all-electron scalar relativistic (SARC) basis sets one obtains results that are as good as with large, uncontracted basis sets. The errors in the calibrated transition energies are on the order of 0.1 eV. The error in calibrated intensities is slightly larger, but the calculations are still in excellent agreement with experiment. The behavior of full TD-DFT linear response versus the Tamm−Dancoff approximation has been evaluated with the result that two methods are almost indistinguishable. The inclusion of relativistic effects barely changes the results for first row transition metal complexes, however, the contributions become visible for second-row transition metals and reach a maximum (of an ∼10% change in the calibration parameters) for third row transition metal species. The protocol developed here is ∼10 times more efficient than the previously employed protocol, which was based on large, uncontracted basis sets. The calibration strategy followed here may be readily extended to other edges

Prediction of Iron K-Edge Absorption Spectra Using Time-Dependent Density Functional Theory

Iron K-edge X-ray absorption pre-edge features have been calculated using a time-dependent density functional approach. The influence of functional, solvation, and relativistic effects on the calculated energies and intensities has been examined by correlation of the calculated parameters to experimental data on a series of 10 iron model complexes, which span a range of high-spin and low-spin ferrous and ferric complexes in Oh to Td geometries. Both quadrupole and dipole contributions to the spectra have been calculated. We find that good agreement between theory and experiment is obtained by using the BP86 functional with the CP(PPP) basis set on the Fe and TZVP one of the remaining atoms. Inclusion of solvation yields a small improvement in the calculated energies. However, the inclusion of scalar relativistic effects did not yield any improved correlation with experiment. The use of these methods to uniquely assign individual spectral transitions and to examine experimental contributions to backbonding is discussed