Determination of the Complete Spin Density Distribution in 13C-Labeled Protein-Bound Radical Intermediates Using Advanced 2D Electron Paramagnetic Resonance Spectroscopy and Density Functional Theory

Overcoming Challenges in Density Functional Theory-Based Calculations of Hyperfine Coupling Constants for Heavy Heteroatom Radicals

This study assesses density functional theory (DFT) methods for their accuracy in calculating hyperfine coupling constants (HFCCs) of heavy heteroatom radicals with heteroatoms including Sb, Bi, In, Tl, and Sn. Given the essential role of electron paramagnetic resonance spectroscopy in characterization of these species, it is crucial that theoretical models can predict HFCCs accurately for heavy elements. This work presents a computational approach that addresses crucial factors: selection of basis set, hybrid exchange-correlation functional, higher Hartree-Fock (HF) exchange, and the Gaussian description of nuclear charge. The relativistic effects are introduced using one-component linear response theory with the second-order Douglas-Kroll-Hess formalism and the fully relativistic four-component Dirac-Kohn-Sham method. The findings show that, while one-component DFT is accurate for the 4th-row elements, the four-component method is more precise for the 5th-row radicals and the one-component approach fails for the 6th-row congeners. Increasing HF exchange significantly improves HFCC predictions. The developed framework for accurate HFCC calculations will enhance the understanding of electronic and magnetic properties of heavy element radicals and can be used by computational chemists and experimentalists alike.

Pulsed Electron-Nuclear Double Resonance in the Fourier Regime

Nuclear magnetic resonance (NMR) spectroscopy provides atomic-level molecular structural information. However, in molecules containing unpaired electron spins, NMR signals are difficult to measure directly. In such cases, data is obtained using the electron-nuclear double resonance (ENDOR) method, where nuclei are detected through their interaction with nearby unpaired electron spins. Unfortunately, electron spins spread the ENDOR signals, which challenges current acquisition techniques, often resulting in low spectral resolution that provides limited structural details. Here, we show that by using miniature microwave resonators to detect a small number of electron spins, integrated with miniature NMR coils, one can excite and detect a wide bandwidth of ENDOR data in a single pulse. This facilitates the measurement of ENDOR spectra with narrow lines spread over a large frequency range at much better spectral resolution than conventional approaches, which helps reveal details of the paramagnetic molecules' chemical structure that were not accessible before.

o-Semiquinone radical anion isolated as an amorphous porous solid

The use of metal cations is a commonly applied strategy to create S > 1/2 stable molecular systems containing semiquinone radicals. Persistent mono-semiquinonato complexes of diamagnetic metal ions (S = 1/2) have been hitherto less common and mostly limited to the complexes of heavy metal ions. In this work, a mono-semiquinonato complex of aluminum, derived from 1,2-dihydroxybenzene, is obtained using a surprisingly short and uncomplicated procedure. The isolated product is an amorphous and porous solid that exhibits very good stability under ambient conditions. To characterise its molecular and electronic structure, 9.7, 34 and 406 GHz EPR spectroscopy was used in concert with computational techniques (DFT and DLPNO-CCSD). It was revealed that the radical complex is composed of two chemically equivalent aluminum cations and two catechol-like ligands with the unpaired electron uniformly distributed between the two organic molecules. The good stability and porous structure make this complex applicable in heterogeneous aerobic reactions.

A sensitivity leap for X-band EPR using a probehead with a cryogenic preamplifier

Inspired by the considerable success of cryogenically cooled NMR cryoprobes, we present an upgraded X-band EPR probehead, equipped with a cryogenic low-noise preamplifier. Our setup suppresses source noise, can handle the high microwave powers typical in X-band pulsed EPR, and is compatible with the convenient resonator coupling and sample access found on commercially available spectrometers. Our approach allows standard pulsed and continuous-wave EPR experiments to be performed at X-band frequency with significantly increased sensitivity compared to the unmodified setup. The probehead demonstrates a voltage signal-to-noise ratio (SNR) enhancement by a factor close to 8× at a temperature of 6 K, and remains close to 2× at room temperature. By further suppressing room-temperature noise at the expense of reduced microwave power (and thus minimum π-pulse length), the factor of SNR improvement approaches 15 at 6 K, corresponding to an impressive 200-fold reduction in EPR measurement time. We reveal the full potential of this probehead by demonstrating such SNR improvements using a suite of typical hyperfine and dipolar spectroscopy experiments on exemplary samples.

Two-dimensional 67Zn HYSCORE spectroscopy reveals that a Zn-bacteriochlorophyll aP′ dimer is the primary donor (P840) in the type-1 reaction centers of Chloracidobacterium thermophilum

Using pulsed EPR spectroscopy and isotopic labeling we demonstrate that reaction centers of Chloracidobacterium thermophilum have an unusual primary donor that is a dimer of Zn-bacteriochlorophyll a_P′ molecules.

How accurate is density functional theory in predicting spin density? An insight from the prediction of hyperfine coupling constants

Electron paramagnetic resonance (EPR) spectroscopy has been proven to be an important technique for studying paramagnetic systems. Probably, the most accessible EPR parameter and the one that provides a significant amount of information about molecular structure and spin density is the hyperfine coupling constant (HFCC). Hence, accurate quantum-chemical modeling of HFCCs is frequently essential to the adequate interpretation of EPR spectra. It requires the precise spin density, which is the difference between the densities of α- and β-electrons, and thus, its quality is expected to reflect the quality of the total electron density. The question of which approximate exchange-correlation density functional yields sufficiently accurate HFCCs, and thus, the spin density remains open. To assess the performance of well-established density functionals for calculating HFCCs, we used a series of 26 small paramagnetic species and compared the obtained results to the CCSD reference values. The performance of DFT was also tested on EPR-studied o-semiquinone radical interacting with water molecules and Mg²⁺ cation. The HFCCs were additionally calculated by the DLPNO-CCSD method, and this wave function-based technique was found superior to all functionals we tested. Although some functionals were found, on average, to be fairly efficient, we found that the most accurate functional is system-dependent, and therefore, the DLPNO-CCSD method should be preferred for theoretical investigations of the HFCCs and spin density.

The Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Accommodates Menaquinone and Stabilizes a Functional Menasemiquinone

Cytochrome bo₃, one of three terminal oxygen reductases in the aerobic respiratory chain of Escherichia coli, has been well characterized as a ubiquinol oxidase. The ability of cytochrome bo₃ to catalyze the two-electron oxidation of ubiquinol-8 requires the enzyme to stabilize the one-electron oxidized ubisemiquinone species that is a transient intermediate in the reaction. Cytochrome bo₃ has been shown recently to also utilize demethylmenaquinol-8 as a substrate that, along with menaquinol-8, replaces ubiquinol-8 when E. coli is grown under microaerobic or anaerobic conditions. In this work, we show that its steady-state turnover with 2,3-dimethyl-1,4-naphthoquinol, a water-soluble menaquinol analogue, is just as efficient as with ubiquinol-1. Using pulsed electron paramagnetic resonance spectroscopy, we demonstrate that the same residues in cytochrome bo₃ that stabilize the semiquinone state of ubiquinone also stabilize the semiquinone state of menaquinone, with the hydrogen bond strengths and the distribution of unpaired spin density accommodated for the different substrate. Catalytic function with menaquinol is more tolerant of mutations at the active site than with ubiquinol. A mutation of one of the stabilizing residues (R71H in subunit I) that eliminates the ubiquinol oxidase activity of cytochrome bo₃ does not abolish activity with soluble menaquinol analogues.