Hydrogen Bond Geometries from Electron Paramagnetic Resonance and Electron−Nuclear Double Resonance Parameters: Density Functional Study of Quinone Radical Anion−Solvent Interactions

Quantification of Quinones in Environmental Media by Chemical Tagging with Cysteine-Containing Peptides Coupled to Size Exclusionary Separation

Quinones are one of the most important redox-reactive organic compounds in natural environments, such as soil, water, and sediment, playing an important role in regulating the environmental processes and biogeochemical cycles of critical elements under climate change, including the influences of extreme events such as wildfires. However, to date, no existing methods can quantify quinones in complex environmental media. To overcome this challenge, a quantification method was developed by coupling chemical tagging of quinones by cysteine-containing nonaromatic peptides (Cpep) through a Michael addition reaction with size exclusionary chromatography (SEC) separation and ultraviolet (UV) analysis─leveraging on the characteristic absorbance of aromatic rings at 254 nm and molecular size of peptide. The method was demonstrated using model quinones, including 1,4-benzoquinone (BQ), 1,4-naphthoquinone (NQ), and 1,4-anthraquinone (AQ), with a detection limit of 3.3, 0.7, and 0.2 μM, respectively. Concentrations of quinones in water extractions of biochars, soils, and wildfire-derived ashes were determined to range from 0.8 to 14 μM and were positively correlated with their redox reactivity determined by a chemical assay. This method provides a novel rapid quantification of quinones in complex environmental media as well as a quick assessment for redox reactivity and opens up new avenues for studying environmental transformation and remediation of contaminants.

Controlling and exploiting intrinsic unpaired electrons in metalloproteins

Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in metalloproteins and enzymes that undergo oxidation-reduction reactions. In this chapter, we discuss the process from isolating the protein to acquiring and analyzing pulse EPR spectra, adopting a practical perspective. We start with considerations when preparing the protein sample, explain techniques and procedures available for determining the reduction potential of the redox-active center of interest and provide details on methodologies to trap a given paramagnetic state for detailed pulse EPR studies, with an emphasis on biochemical and spectroscopic tools available when multiple EPR-active species are present. We elaborate on some of the most commonly used pulse EPR techniques and the choices the user has to make, considering advantages and disadvantages and how to avoid pitfalls. Examples are provided throughout.

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 unified quantum model susceptible to elucidate the dissimilarity of IR spectral density of dicarboxylic acid crystals: Phthalic and terephthalic acid crystals cases

Over the last decades, several approaches have been developed for elucidating the infrared spectral density of dicarboxylic acid crystals, which has been served as prototype for determining hydrogen bonds dynamics. These approaches differ in how accurately the simulated spectra can superimpose the experimental ones. In this study, we present a superdimer quantum approach susceptible to elucidate the infrared spectral properties of some particular dicarboxylic acid crystals using a newly proposed algorithm, which favors the rule of Davydov coupling in the generation of the spectra. The approach, which is herein effectively applied to terephthalic and phthalic acid dimer crystals, ascribes the non-conventional IR spectral properties of these particular acid crystals to the existence of superdimer structure in their lattices. In this superdimer structure, a strong vibronic coupling mechanism, namely Davydov coupling, takes place between the proton stretching vibrations in the (COOH)₂ cycles. This strong coupling exciton, generated by the resonance arising in the two coupled (COOH)₂ cycles of the aromatic rings of the superdimer, in conjunction with the strong anharmonic coupling between the fast and slow modes of each hydrogen bonds provide a strong support basis for a common explanation of the physical properties of these two different crystalline systems. The numerical simulations, involving the implications of the superdimer model, are systematically correlated with the experimental spectra. A decent agreement between the evaluated spectra and the experimental bandshapes of terephthalic and phthalic dicarboxylic acid crystals was obtained using a set of physically sound parameters as inputs in the theoretical formulation. The superdimer quantum approach thereby underscore the potential of the dynamical cooperative interactions between "Davydov coupling" and "strong anharmonic coupling" mechanisms in the generation of the spectral features of terephthalic and phthalic dicarboxylic acid crystals, suggesting that the congregated effects of these two mechanisms can be considered as the most reliable source of the non-conventional IR spectral properties observed. It is therefore expected that this novel algorithm reduces the discrepancies between the simulated spectra compared to the experimental one and simplify the computation of spectra in more complex hydrogen bonded systems.

One Electron Multiple Proton Transfer in Model Organic Donor-Acceptor Systems: Implications for High Frequency EPR

EPR spectroscopy is an important spectroscopic method for identification and characterization of radical species involved in many biological reactions. The tyrosyl radical is one of the most studied amino acid radical intermediates in biology. Often in conjunction with histidine residues, it is involved in many fundamental biological electron and proton transfer processes, such as in the water oxidation in photosystem II. As biological processes are typically extremely complicated and hard to control, molecular bio-mimetic model complexes are often used to clarify the mechanisms of the biological reactions. Here we present theoretical calculations to investigate the sensitivity of magnetic resonance parameters to proton-coupled electron transfer events, as well as conformational substates of the molecular constructs which mimic the tyrosine-histidine (Tyr-His) pairs found in a large variety of proteins. Upon oxidation of the phenol, the Tyr analogue, these complexes can perform not only one-electron one-proton transfer (EPT), but also one-electron two-proton transfers (E2PT). It is shown that in aprotic environment the g_X-components of the electronic g-tensor are extremely sensitive to the first proton transfer from the phenoxyl oxygen to the imidazole nitrogen (EPT product), leading to a significant increase of the g_X-value of up to 0.003, but are not sensitive to the second proton transfer (E2PT product). In the latter case the change of the g_X-value is much smaller (ca. 0.0001), which is too small to be distinguished even by high frequency EPR. The ¹⁴N hyperfine values are also too similar to allow differentiation between the different protonation states in EPT and E2PT. The magnetic resonance parameters were also calculated as a function of the rotation angles around single bonds. It was demonstrated that rotation of the phenoxyl group results in large positive changes (>0.001) in the g_X-values. Analysis of the data reveals that the main source of these changes is related to the strength of the H-bond between phenoxyl oxygen and the proton(s) on N₁ and N₂ positions of the imidazole.

1,2H hyperfine spectroscopy and DFT modeling unveil the demethylmenasemiquinone binding mode to E. coli nitrate reductase A (NarGHI)

The quinol oxidation site Q_D in E. coli respiratory nitrate reductase A (EcNarGHI) reacts with the three isoprenoid quinones naturally synthesized by the bacterium, i.e. ubiquinones (UQ), menaquinones (MK) and demethylmenaquinones (DMK). The binding mode of the demethylmenasemiquinone (DMSK) intermediate to the EcNarGHI Q_D quinol oxidation site is analyzed in detail using ^1,2H hyperfine (hf) spectroscopy in combination with H₂O/D₂O exchange experiments and DFT modeling, and compared to the menasemiquinone one bound to the Q_D site (MSK_D) previously studied by us. DMSK_D and MSK_D are shown to bind in a similar and strongly asymmetric manner through a short (~1.7 Å) H-bond. The origin of the specific hf pattern resolved on the DMSK_D field-swept EPR spectrum is unambiguously ascribed to slightly inequivalent contributions from two β-methylene protons of the isoprenoid side chain. DFT calculations show that their large isotropic hf coupling constants (A_iso ~12 and 15 MHz) are consistent with both (i) a specific highly asymmetric binding mode of DMSK_D and (ii) a near in-plane orientation of its isoprenyl chain at Cβ relative to the aromatic ring, which differs by ~90° to that predicted for free or NarGHI-bound MSK. Our results provide new insights into how the conformation and the redox properties of different natural quinones are selectively fine-tuned by the protein environment at a single Q site. Such a fine-tuning most likely contributes to render NarGHI as an efficient and flexible respiratory enzyme to be used upon rapid variations of the Q-pool content.

Coupled Methyl Group Rotation in FMN Radicals Revealed by Selective Deuterium Labeling

Flavin semiquinones are common intermediate redox states in flavoproteins, and thus, knowledge of their electronic structure is essential for fully understanding their chemistry and chemical versatility. In this contribution, we use a combination of high-field electron nuclear double resonance spectroscopy and selective deuterium labeling of flavin mononucleotide (FMN) with subsequent incorporation as cofactor into a variant Avena sativa LOV domain to extract missing traits of the electronic structure of a protein-bound FMN radical. From these experiments, precise values of small proton hyperfine and deuterium nuclear quadrupole couplings could be extracted. Specifically, isotropic hyperfine couplings of -3.34, -0.11, and +0.91 MHz were obtained for the protons H(6), H(9), and H(7α), respectively. These values are discussed in the light of specific protein-cofactor interactions. Furthermore, the temperature behavior of the H(7α) methyl-group rotation elicited by its energy landscape was analyzed in greater detail. Pronounced interplay between the two methyl groups at C(7) and C(8) of FMN could be revealed. Most strikingly, this rotational behavior could be modulated by selective deuterium editing.

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.

Towards accurate infrared spectral density of weak H-bonds in absence of relaxation mechanisms

Following the previous theoretical developments to completely reproduce the IR spectra of weak hydrogen bond complexes within the framework of the linear response theory (LRT), the quantum theory of the high stretching mode spectral density (SD) of weak H-bonds is reconsidered. Within the LRT theory, the SD is the one sided Fourier transform of the autocorrelation function (ACF) of the high stretching mode dipole moment operator. In order to provide more accurate theoretical bandshapes, we have explored the equivalence between the SDs given in previous studies with respect to a new quantum one, and revealed that in place of the basic equations used in the precedent works for which the SD I_Old(ω)=2Re∫₀^∞G_Old(t)e^-iωtdt where the ACF G_Old(t) = ⟨μ(0)μ(t)⁺⟩ = tr {ρ {μ(0)} {μ(t)}⁺}, one can use a new expression for the SD, given by I_New(ω)=2ωRe∫₀^∞G_New(t)e^-iωtdt where G_New(t)=μ(0)μ(t)⁺=1βtrρ_B∫₀^βμ(0)μ(t+iλℏ)⁺dλ. Here ρ_B is the Boltzmann density operator, μ(0) the dipole moment operator at initial time and μ(t) the dipole moment operator at time t in the Heisenberg picture, ℏ is the Planck constant, β is the inverse of the Boltzmann factor k_BT where T is the absolute temperature and k_B the Boltzmann constant. Using this formalism, we demonstrated that the new quantum approach gives the same final SD as used by previous models, and reduces to the Franck-Condon progression appearing in the Maréchal and Witkowski's pioneering approach when the relaxation mechanisms are ignored. Results of this approach shed light on the equivalence between the quantum and classical IR SD approaches for weak H-bonds in absence of medium surroundings effect, which has been a subject of debate for decades.

Accurate spin-densities based on the domain-based local pair-natural orbital coupled-cluster theory

Exploiting locality in the electron correlation reduces the computational cost for solving the Coupled-Cluster (CC) equations. This is important for making CC theory applicable to routine computational chemistry applications where it promises to deliver results of "gold-standard" quality. Recently, we have proposed a series of CC formulations in the domain-based local pair-natural orbital framework [DLPNO-coupled-cluster with singles and doubles (CCSD) and DLPNO-coupled-cluster singles and doubles with perturbative triples] which are designed to reproduce approximately 99.9% of the canonical correlation energy. In our previous work, the DLPNO-CCSD method has been extended to the high-spin open-shell reference and shown to possess comparable accuracy to the closed-shell counterpart [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)]. The so-called Λ-equations have been formulated in the DLPNO framework for the closed-shell species as an exact derivative of the DLPNO-CCSD Lagrangian with respect to the PNO-based cluster amplitudes [D. Datta et al., J. Chem. Phys. 145, 114101 (2016)]. In this paper, we extend the DLPNO-based Lagrangian scheme to the high-spin open-shell reference cases, thus enabling the accurate computation of the electron- and spin-densities for large open-shell species. We apply this newly developed approach to various first-order electronic and magnetic properties such as isotropic and anisotropic components in the hyperfine coupling interactions and the electric field gradient. We demonstrate that the DLPNO-CCSD results converge toward the respective canonical CC density and also that the DLPNO-CCSD-based properties are more accurate than the conventional density functional theory (DFT) results in real-life applications. The additional computational cost is not more than one energy evaluation in the DLPNO-CCSD framework.

Low-scaling first-order properties within second-order Møller-Plesset perturbation theory using Cholesky decomposed density matrices

An efficient implementation of energy gradients and of hyperfine coupling constants in second-order Møller-Plesset perturbation theory (MP2) is presented based on our fully atomic orbital (AO)-based approach. For the latter, an unrestricted AO-based MP2 formulation is introduced. A reduction in the dependency of the computational efficiency on the size of the basis set is achieved by a Cholesky decomposition and the prefactor is reduced by the resolution-of-the-identity approximation. Significant integral contributions are selected based on distance-including integral estimates (denoted as QQR-screening) and its reliability as a fully controlled screening procedure is demonstrated. The rate-determining steps are shown via model computations to scale cubically in the computation of energy gradients and quadratically in the case of hyperfine coupling constants. Furthermore, a significant speed-up of the computational time with respect to the canonical formulation is demonstrated.

Equivalence between the Classical and Quantum IR Spectral Density Approaches of Weak H-Bonds in the Absence of Damping

The aim of this paper is to overhaul the quantum elucidation of the spectral density (SD) of weak H-bonds treated without taking into account any of the damping mechanisms. The reconsideration of the SD is performed within the framework the linear response theory. Working in the setting of the strong anharmonic coupling theory and the adiabatic approximation, the simplified expression of the classical SD, in the absence of dampings, is equated to be I_Cl(ω) = Re[∫₀^∞G_Cl(t)e^-iΩt dt] in which the classical-like autocorrelation function (ACF), G_Cl(t), is given by G_Cl(t) = tr{ρ(β){μ(0)}{μ(t)}^†}. With this consideration, we have shown that the classical SD is equivalent to the line shape obtained by F(ω) = ΩI_Cl(ω), which in turn is equivalent to the quantum SD given by I_Qu(ω) = Re[∫₀^∞G_Qu(t)e^-iΩt dt], where G_Qu(t) is the corresponding quantum ACF having for expression G_Qu(t) = (1/β) tr{ρ∫₀^β[μ(0)}{μ(t + iλℏ)}^† dλ}. Thus, we have shown that for weak H-bonds dealt without dampings, the SDs obtained by the quantum approaches are equivalent to the SDs geted by the classical approach in which the incepation ACF is, however, of quantum nature and where the line shape is the Fourier transform of the ACF times the angular frequency. It is further shown that the classical approach dealing with the SD of weak H-bonds leads identically to the result found by Maréchal and Witkowski in their pioneering quantum treatment where they ignored the linear response theory and dampings.

A Comparison of Experimental and Broken Symmetry Density Functional Theory (BS-DFT) Calculated Electron Paramagnetic Resonance (EPR) Parameters for Intermediates Involved in the S2 to S3 State Transition of Nature's Oxygen Evolving Complex

A broken symmetry density functional theory (BS-DFT) magnetic analysis of the S₂, S₂Y_Z^•, and S₃ states of Nature's oxygen evolving complex is performed for both the native Ca and Sr substituted forms. Good agreement with experiment is observed between the tyrosyl calculated g-tensor and ¹H hyperfine couplings for the native Ca form. Changes in the hydrogen bonding environment of the tyrosyl radical in S₂Y_Z^• caused by Sr substitution lead to notable changes in the calculated g-tensor of the tyrosyl radical. Comparison of calculated and experimental ⁵⁵Mn hyperfine couplings for the S₃ state presently favors an open cubane form of the complex with an additional OH ligand coordinating to Mn_D. In Ca models, this additional ligation can arise by closed-cubane form deprotonation of the Ca ligand W3 in the S₂Y_Z^• state accompanied by spontaneous movement to the vacant Mn coordination site or by addition of an external OH group. For the Sr form, no spontaneous movement of W3 to the vacant Mn coordination site is observed in contrast to the native Ca form, a difference which may lead to the reduced catalytic activity of the Sr substituted form. BS-DFT studies on peroxo models of S₃ as indicated by a recent X-ray free electron laser (XFEL) crystallography study give rise to a structural model compatible with experimental data and an S = 3 ground state compatible with EPR studies.

Interplay between CN- Ligands and the Secondary Coordination Sphere of the H-Cluster in [FeFe]-Hydrogenases

The catalytic cofactor of [FeFe]-hydrogenses (H-cluster) is composed of a generic cubane [4Fe-4S]-cluster (4Fe_H) linked to a binuclear iron-sulfur cluster (2Fe_H) that has an open coordination site at which the reversible conversion of protons to molecular hydrogen occurs. The (2Fe_H) subsite features a diatomic coordination sphere composed of three CO and two CN^- ligands affecting its redox properties and providing excellent probes for FTIR spectroscopy. The CO stretch vibrations are very sensitive to the redox changes within the H-cluster occurring during the catalytic cycle, whereas the CN^- signals seem to be relatively inert to these effects. This could be due to the more structural role of the CN^- ligands tightly anchoring the (2Fe_H) unit to the protein environment through hydrogen bonding. In this work we explore the effects of structural changes within the secondary ligand sphere affecting the CN^- ligands on FTIR spectroscopy and catalysis. By comparing the FTIR spectra of wild-type enzyme and two mutagenesis variants, we are able to assign the IR signals of the individual CN^- ligands of the (2Fe_H) site for different redox states of the H-cluster. Moreover, protein film electrochemistry reveals that targeted manipulation of the secondary coordination sphere of the proximal CN^- ligand (i.e., closest to the (4Fe_H) site) can affect the catalytic bias. These findings highlight the importance of the protein environment for re-adjusting the catalytic features of the H-cluster in individual enzymes and provide valuable information for the design of artificial hydrogenase mimics.

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli

The respiratory cytochrome bo₃ ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQ_H), which is a transient intermediate during the electron-mediated reduction of O₂ to water. It is known that SQ_H is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQ_H was investigated with orientation-selective Q-band (∼34 GHz) pulsed ¹H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo₃ in a H₂O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor T_z' = 11.8 MHz, whereas for H2, T_z' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo₃ Q_H site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.

Electron Transfer Rate Maxima at Large Donor-Acceptor Distances

Because of their low mass, electrons can transfer rapidly over long (>15 Å) distances, but usually reaction rates decrease with increasing donor-acceptor distance. We report here on electron transfer rate maxima at donor-acceptor separations of 30.6 Å, observed for thermal electron transfer between an anthraquinone radical anion and a triarylamine radical cation in three homologous series of rigid-rod-like donor-photosensitizer-acceptor triads with p-xylene bridges. Our experimental observations can be explained by a weak distance dependence of electronic donor-acceptor coupling combined with a strong increase of the (outer-sphere) reorganization energy with increasing distance, as predicted by electron transfer theory more than 30 years ago. The observed effect has important consequences for light-to-chemical energy conversion.

Plasticity in the High Affinity Menaquinone Binding Site of the Cytochrome aa3-600 Menaquinol Oxidase from Bacillus subtilis

Cytochrome aa3-600 is a terminal oxidase in the electron transport pathway that contributes to the electrochemical membrane potential by actively pumping protons. A notable feature of this enzyme complex is that it uses menaquinol as its electron donor instead of cytochrome c when it reduces dioxygen to water. The enzyme stabilizes a menasemiquinone radical (SQ) at a high affinity site that is important for catalysis. One of the residues that interacts with the semiquinone is Arg70. We have made the R70H mutant and have characterized the menasemiquinone radical by advanced X- and Q-band EPR. The bound SQ of the R70H mutant exhibits a strong isotropic hyperfine coupling (a(14)N ≈ 2.0 MHz) with a hydrogen bonded nitrogen. This nitrogen originates from a histidine side chain, based on its quadrupole coupling constant, e(2)qQ/h = 1.44 MHz, typical for protonated imidazole nitrogens. In the wild-type cyt aa3-600, the SQ is instead hydrogen bonded with Nε from the Arg70 side chain. Analysis of the (1)H 2D electron spin echo envelope modulation (ESEEM) spectra shows that the mutation also changes the number and strength of the hydrogen bonds between the SQ and the surrounding protein. Despite the alterations in the immediate environment of the SQ, the R70H mutant remains catalytically active. These findings are in contrast to the equivalent mutation in the close homologue, cytochrome bo3 ubiquinol oxidase from Escherichia coli, where the R71H mutation eliminates function.

The first tyrosyl radical intermediate formed in the S2-S3 transition of photosystem II

The EPR "split signals" represent key intermediates of the S-state cycle where the redox active D1-Tyr161 (YZ) has been oxidized by the reaction center of the photosystem II enzyme to its tyrosyl radical form, but the successive oxidation of the Mn4CaO5 cluster has not yet occurred (SiYZ˙). Here we focus on the S2YZ˙ state, which is formed en route to the final metastable state of the catalyst, the S3 state, the state which immediately precedes O-O bond formation. Quantum chemical calculations demonstrate that both isomeric forms of the S2 state, the open and closed cubane isomers, can form states with an oxidized YZ˙ residue without prior deprotonation of the Mn4CaO5 cluster. The two forms are expected to lie close in energy and retain the electronic structure and magnetic topology of the corresponding S2 state of the inorganic core. As expected, tyrosine oxidation results in a proton shift towards His190. Analysis of the electronic rearrangements that occur upon formation of the tyrosyl radical suggests that a likely next step in the catalytic cycle is the deprotonation of a terminal water ligand (W1) of the Mn4CaO5 cluster. Diamagnetic metal ion substitution is used in our calculations to obtain the molecular g-tensor of YZ˙. It is known that the gx value is a sensitive probe not only of the extent of the proton shift between the tyrosine-histidine pair, but also of the polarization environment of the tyrosine, especially about the phenolic oxygen. It is shown for PSII that this environment is determined by the Ca(2+) ion, which locates two water molecules about the phenoxyl oxygen, indirectly modulating the oxidation potential of YZ.

The structure and function of quinones in biological solar energy transduction: a cyclic voltammetry, EPR, and hyperfine sub-level correlation (HYSCORE) spectroscopy study of model naphthoquinones

Quinones function as electron transport cofactors in photosynthesis and cellular respiration. The versatility and functional diversity of quinones is primarily due to the diverse midpoint potentials that are tuned by the substituent effects and interactions with surrounding amino acid residues in the binding site in the protein. In the present study, a library of substituted 1,4-naphthoquinones are analyzed by cyclic voltammetry in both protic and aprotic solvents to determine effects of substituent groups and hydrogen bonds on the midpoint potential. We use continuous-wave electron paramagnetic resonance (EPR) spectroscopy to determine the influence of substituent groups on the electronic properties of the 1,4-naphthoquinone models in an aprotic solvent. The results establish a correlation between the presence of substituent group(s) and the modification of electronic properties and a corresponding shift in the midpoint potential of the naphthoquinone models. Further, we use pulsed EPR spectroscopy to determine the effect of substituent groups on the strength and planarity of the hydrogen bonds of naphthoquinone models in a protic solvent. This study provides support for the tuning of the electronic properties of quinone cofactors by the influence of substituent groups and hydrogen bonding interactions.

The hydrogen-bonded dianion of vitamin K1 produced in aqueous-organic solutions exists in equilibrium with its hydrogen-bonded semiquinone anion radical

When the quinone, vitamin K1 (VK1), is electrochemically reduced in aqueous-acetonitrile solutions (CH3CN with 7.22 M H2O), it undergoes a two-electron reduction to form the dianion that is hydrogen-bonded with water [VK1(H2O)y(2–)]. EPR and voltammetry experiments have shown that the persistent existence of the semiquinone anion radical (also hydrogen-bonded with water) [VK1(H2O)x(–•)] in aqueous or organic–aqueous solutions is a result of VK1(H2O)y(2–) undergoing a net homogeneous electron transfer reaction (comproportionation) with VK1, and not via direct one-electron reduction of VK1. When 1 mM solutions of VK1 were electrochemically reduced by two electrons in aqueous-acetonitrile solutions, quantitative EPR experiments indicated that the amount of VK1(H2O)x(–•) produced was up to approximately 35% of all the reduced species. In situ electrochemical ATR-FTIR experiments on sequentially one- and two-electron bulk reduced solutions of VK1 (showing strong absorbances at 1664, 1598, and 1298 cm(–1)) in CH3CN containing <0.05 M H2O led to the detection of VK1(–•) with strong absorbances at 1710, 1703, 1593, 1559, 1492, and 1466 cm(–1) and VK1(H2O)y(2–) with strong absorbances at 1372 and 1342 cm(–1).

Pulse Q-band EPR and ENDOR spectroscopies of the photochemically generated monoprotonated benzosemiquinone radical in frozen alcoholic solution

Quinones are essential cofactors in many physiological processes, among them proton-coupled electron transfer (PCET) in photosynthesis and respiration. A key intermediate in PCET is the monoprotonated semiquinone radical. In this work we produced the monoprotonated benzosemiquinone (BQH(•)) by UV illumination of BQ dissolved in 2-propanol at cryogenic temperatures and investigated the electronic and geometric structures of BQH(•) in the solid state (80 K) using EPR and ENDOR techniques at 34 GHz. The g-tensor of BQH(•) was found to be similar to that of the anionic semiquinone species (BQ(•-)) in frozen solution. The peaks present in the ENDOR spectrum of BQH(•) were identified and assigned by (1)H/(2)H substitutions. The experiments reconfirmed that the hydroxyl proton (O-H) on BQH(•), which is abstracted from a solvent molecule, mainly originates from the central CH group of 2-propanol. They also showed that the protonation has a strong impact on the electron spin distribution over the quinone. This is reflected in the hyperfine couplings (hfc's) of the ring protons, which dramatically changed with respect to those typically observed for BQ(•-). The hfc tensor of the O-H proton was determined by a detailed orientation-selection ENDOR study and found to be rhombic, resembling those of protons covalently bound to carbon atoms in a π-system (i.e., α-protons). It was found that the O-H bond lies in the quinone plane and is oriented along the direction of the quinone oxygen lone pair orbital. DFT calculations were performed on different structures of BQH(•) coordinated by four, three, or zero 2-propanol molecules. The O-H bond length was found to be around 1.0 Å, typical for a single covalent O-H bond. Good agreement between experimental and DFT results were found. This study provides a detailed picture of the electronic and geometric structures of BQH(•) and should be applicable to other naturally occurring quinones.

Density functional theory study of nitrogen-14 nuclear quadrupole coupling parameters of L-histidine: hydrogen-bonded system

The calculations of nitrogen-14 nuclear quadrupole parameters, nuclear quadrupole coupling constant, χ, and asymmetry parameter, η, of L-His were done in two distinct environments: one as a free fully optimized molecule, an isolated molecule with the geometrical parameters taken from X-ray, and the other in the orthorhombic and monoclinic solid states. The most probable interacting molecules with the central molecule in the crystalline phase were considered in the hexameric clusters to include hydrogen-bonding effects in the calculations. The computations were performed with PW91P86/6-31++G** and B3LYP6-31++G** methods using the Gaussian 98 program. The good agreement between the nitrogen-14 quadrupole parameters of the free His and imidazole molecules with their microwave available data demonstrates that the applied level of theory and the 6-31++G** basis set are suitable to obtain reliable electric field gradient values. In the solid state, the shifts of quadrupole coupling parameters from the monomer to the solid phase are reasonably well reproduced for the amino and imino sites of imidazole ring in a hexameric cluster. That implies the fact that the hexameric cluster worked effectively to generate the results which are compatible with the experiment. The quadrupole coupling constant values of -N(+) H(3) group are in fair agreement with the experiment. This discrepancy is due to the absences of vibrational effects and the rotation of -N(+) H(3) group around N-C(α) bond.

A tunable general purpose Q-band resonator for CW and pulse EPR/ENDOR experiments with large sample access and optical excitation

We describe a frequency tunable Q-band cavity (34 GHz) designed for CW and pulse Electron Paramagnetic Resonance (EPR) as well as Electron Nuclear Double Resonance (ENDOR) and Electron Electron Double Resonance (ELDOR) experiments. The TE(011) cylindrical resonator is machined either from brass or from graphite (which is subsequently gold plated), to improve the penetration of the 100 kHz field modulation signal. The (self-supporting) ENDOR coil consists of four 0.8mm silver posts at 2.67 mm distance from the cavity center axis, penetrating through the plunger heads. It is very robust and immune to mechanical vibrations. The coil is electrically shielded to enable CW ENDOR experiments with high RF power (500 W). The top plunger of the cavity is movable and allows a frequency tuning of ±2 GHz. In our setup the standard operation frequency is 34.0 GHz. The microwaves are coupled into the resonator through an iris in the cylinder wall and matching is accomplished by a sliding short in the coupling waveguide. Optical excitation of the sample is enabled through slits in the cavity wall (transmission ∼60%). The resonator accepts 3mm o.d. sample tubes. This leads to a favorable sensitivity especially for pulse EPR experiments of low concentration biological samples. The probehead dimensions are compatible with that of Bruker flexline Q-band resonators and it fits perfectly into an Oxford CF935 Helium flow cryostat (4-300 K). It is demonstrated that, due to the relatively large active sample volume (20-30 μl), the described resonator has superior concentration sensitivity as compared to commercial pulse Q-band resonators. The quality factor (Q(L)) of the resonator can be varied between 2600 (critical coupling) and 1300 (over-coupling). The shortest achieved π/2-pulse durations are 20 ns using a 3 W microwave amplifier. ENDOR (RF) π-pulses of 20 μs ((1)H @ 51 MHz) were obtained for a 300 W amplifier and 7 μs using a 2500 W amplifier. Selected applications of the resonator are presented.

Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR

Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q(D)) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q(D) site (MSQ(D)) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with (1)H2O/2H2O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ(D) binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in 1H2O and 2H2O samples and by selective detection of the exchanged deuterons using Q-band 2H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b(D). Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q(D) site are discussed, in light of the unusually high thermodynamic stability of MSQ(D).

Predicting the ¹H and ¹³C NMR spectra of paramagnetic Ru(III) complexes by DFT

Nuclear shieldings, including the Fermi-contact and pseudocontact terms, have been calculated with density functional theory (DFT) (nonrelativistic and relativistic) methods in several Ru(III) complexes, thereby predicting (1)H and (13)C paramagnetic shifts. A fair agreement with experimental values is observed. Structural, magnetic and dynamic parameters have also been input to the Solomon-Bloembergen equation in order to predict signal lineshapes. It is shown that DFT-predicted paramagnetic shifts can greatly aid in obtaining and understanding NMR spectra of paramagnetic Ru(III) complexes.