Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data.

The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOx complex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.

Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II.

Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.

Reaction Center Excitation in Photosystem II: From Multiscale Modeling to Functional Principles.

Oxygenic photosynthesis is the fundamental energy-converting process that utilizes sunlight to generate molecular oxygen and the organic compounds that sustain life. Protein-pigment complexes harvest light and transfer excitation energy to specialized pigment assemblies, reaction centers (RC), where electron transfer cascades are initiated. A molecular-level understanding of the primary events is indispensable for elucidating the principles of natural photosynthesis and enabling development of bioinspired technologies. The primary enzyme in oxygenic photosynthesis is Photosystem II (PSII), a membrane-embedded multisubunit complex, that catalyzes the light-driven oxidation of water. The RC of PSII consists of four chlorophyll a and two pheophytin a pigments symmetrically arranged along two core polypeptides; only one branch participates in electron transfer. Despite decades of research, fundamental questions remain, including the origin of this functional asymmetry, the nature of primary charge-transfer states and the identity of the initial electron donor, the origin of the capability of PSII to enact charge separation with far-red photons, i.e., beyond the "red limit" where individual chlorophylls absorb, and the role of protein conformational dynamics in modulating charge-separation pathways.In this Account, we highlight developments in quantum-chemistry based excited-state computations for multipigment assemblies and the refinement of protocols for computing protein-induced electrochromic shifts and charge-transfer excitations calibrated with modern local correlation coupled cluster methods. We emphasize the importance of multiscale atomistic quantum-mechanics/molecular-mechanics and large-scale molecular dynamics simulations, which enabled direct and accurate modeling of primary processes in RC excitation at the quantum mechanical level.Our findings show how differential protein electrostatics enable spectral tuning of RC pigments and generate functional asymmetry in PSII. A chlorophyll pigment on the active branch (ChlD1) has the lowest site energy in PSII and is the primary electron donor. The complete absence of low-lying charge-transfer states within the central pair of chlorophylls excludes a long-held assumption about the initial charge separation. Instead, we identify two primary charge separation pathways, both with the same pheophytin acceptor (PheoD1): a fast pathway with ChlD1 as the primary electron donor (short-range charge-separation) and a slow pathway with PD1PD2 as the initial donor (long-range charge separation). The low-energy spectrum is dominated by two states with significant charge-transfer character, ChlD1δ+PheoD1δ- and PD1δ+PheoD1δ-. The conformational dynamics of PSII allows these charge-transfer states to span wide energy ranges, pushing oxygenic photosynthesis beyond the "red limit". These results provide a quantum mechanical picture of the primary events in the RC of oxygenic photosynthesis, forming a solid basis for interpreting experimental observations and for extending photosynthesis research in new directions.

Exploring Electrophilic Hydrophosphination via Metal Phosphenium Intermediates.

Two Mo(0) phosphenium complexes containing ancillary secondary phosphine ligands have been investigated with respect to their ability to participate in electrophilic addition at unsaturated substrates and subsequent P-H hydride transfer to "quench" the resulting carbocations. These studies provide stoichiometric "proof of concept" for a proposed new metal-catalyzed electrophilic hydrophosphination mechanism. The more strongly Lewis acidic phosphenium complex, [Mo(CO)4(PR2H)(PR2)]+ (R=Ph, Tolp), cleanly hydrophosphinates 1,1-diphenylethylene, benzophenone, and ethylene, while other substrates react rapidly to give products resulting from competing electrophilic processes. A less Lewis acidic complex, [Mo(CO)3(PR2H)2(PR2)]+, generally reacts more slowly but participates in clean hydrophosphination of a wider range of unsaturated substrates, including styrene, indene, 1-hexene, and cyclohexanone, in addition to 1,1-diphenylethylene, benzophenone, and ethylene. Mechanistic studies are described, including stoichiometric control reactions and computational and kinetic analyses, which probe whether the observed P-H addition actually does occur by the proposed electrophilic mechanism, and whether hydridic P-H transfer in this system is intra- or intermolecular. Preliminary reactivity studies indicate challenges that must be addressed to exploit these promising results in catalysis.

Does Serial Femtosecond Crystallography Depict State-Specific Catalytic Intermediates of the Oxygen-Evolving Complex?

Recent advances in serial femtosecond crystallography (SFX) of photosystem II (PSII), enabled by X-ray free electron lasers (XFEL), provided the first geometric models of distinct intermediates in the catalytic S-state cycle of the oxygen-evolving complex (OEC). These models are obtained by flash-advancing the OEC from the dark-stable state (S1) to more oxidized intermediates (S2 and S3), eventually cycling back to the most reduced S0. However, the interpretation of these models is controversial because geometric parameters within the Mn4CaO5 cluster of the OEC do not exactly match those expected from coordination chemistry for the spectroscopically verified manganese oxidation states of the distinct S-state intermediates. Here we focus on the first catalytic transition, S1 → S2, which represents a one-electron oxidation of the OEC. Combining geometric and electronic structure criteria, including a novel effective oxidation state approach, we analyze existing 1-flash (1F) SFX-XFEL crystallographic models that should depict the S2 state of the OEC. We show that the 1F/S2 equivalence is not obvious, because the Mn oxidation states and total unpaired electron counts encoded in these models are not fully consistent with those of a pure S2 state and with the nature of the S1 → S2 transition. Furthermore, the oxidation state definition in two-flashed (2F) structural models is practically impossible to elucidate. Our results advise caution in the extraction of electronic structure information solely from the literal interpretation of crystallographic models and call for re-evaluation of structural and mechanistic interpretations that presume exact correspondence of such models to specific catalytic intermediates of the OEC.

Nature of S-States in the Oxygen-Evolving Complex Resolved by High-Energy Resolution Fluorescence Detected X-ray Absorption Spectroscopy.

Photosystem II, the water splitting enzyme of photosynthesis, utilizes the energy of sunlight to drive the four-electron oxidation of water to dioxygen at the oxygen-evolving complex (OEC). The OEC harbors a Mn4CaO5 cluster that cycles through five oxidation states Si (i = 0-4). The S3 state is the last metastable state before the O2 evolution. Its electronic structure and nature of the S2 → S3 transition are key topics of persisting controversy. Most spectroscopic studies suggest that the S3 state consists of four Mn(IV) ions, compared to the Mn(III)Mn(IV)3 of the S2 state. However, recent crystallographic data have received conflicting interpretations, suggesting either metal- or ligand-based oxidation, the latter leading to an oxyl radical or a peroxo moiety in the S3 state. Herein, we utilize high-energy resolution fluorescence detected (HERFD) X-ray absorption spectroscopy to obtain a highly resolved description of the Mn K pre-edge region for all S-states, paying special attention to use chemically unperturbed S3 state samples. In combination with quantum chemical calculations, we achieve assignment of specific spectroscopic features to geometric and electronic structures for all S-states. These data are used to confidently discriminate between the various suggestions concerning the electronic structure and the nature of oxidation events in all observable catalytic intermediates of the OEC. Our results do not support the presence of either peroxo or oxyl in the active configuration of the S3 state. This establishes Mn-centered storage of oxidative equivalents in all observable catalytic transitions and constrains the onset of the O-O bond formation until after the final light-driven oxidation event.

Structure and Flexibility of Copper-Modified DNA G-Quadruplexes Investigated by 19 F ENDOR Experiments at 34†GHz.

DNA G-quadruplexes (GQs) are of great interest due to their involvement in crucial biological processes such as telomerase maintenance and gene expression. Furthermore, they are reported as catalytically active DNAzymes and building blocks in bio-nanotechnology. GQs exhibit remarkable structural diversity and conformational heterogeneity, necessitating precise and reliable tools to unravel their structure-function relationships. Here, we present insights into the structure and conformational flexibility of a unimolecular GQ with high spatial resolution via electron-nuclear double resonance (ENDOR) experiments combined with Cu(II) and fluorine labeling. These findings showcase the successful application of the 19 F-ENDOR methodology at 34 GHz, overcoming the limitations posed by the complexity and scarcity of higher-frequency spectrometers. Importantly, our approach retains both sensitivity and orientational resolution. This integrated study not only enhances our understanding of GQs but also expands the methodological toolbox for studying other macromolecules.

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory.

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II.

Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.

Copper Complexes with Diazoolefin Ligands and their Photochemical Conversion into Alkenylidene Complexes.

Homometallic copper complexes with alkenylidene ligands are discussed as intermediates in catalysis but the isolation of such complexes has remained elusive. Herein, we report the structural characterization of copper complexes with bridging and terminal alkenylidene ligands. The compounds were obtained by irradiation of CuI complexes with N-heterocyclic diazoolefin ligands. The complex with a terminal alkenylidene ligand required isolation in a crystalline matrix, and its structural characterization was enabled by in crystallo photolysis at low temperature.

Functional Water Networks in Fully Hydrated Photosystem II.

Water channels and networks within photosystem II (PSII) of oxygenic photosynthesis are critical for enzyme structure and function. They control substrate delivery to the oxygen-evolving center and mediate proton transfer at both the oxidative and reductive endpoints. Current views on PSII hydration are derived from protein crystallography, but structural information may be compromised by sample dehydration and technical limitations. Here, we simulate the physiological hydration structure of a cyanobacterial PSII model following a thorough hydration procedure and large-scale unconstrained all-atom molecular dynamics enabled by massively parallel simulations. We show that crystallographic models of PSII are moderately to severely dehydrated and that this problem is particularly acute for models derived from X-ray free electron laser (XFEL) serial femtosecond crystallography. We present a fully hydrated representation of cyanobacterial PSII and map all water channels, both static and dynamic, associated with the electron donor and acceptor sides. Among them, we describe a series of transient channels and the attendant conformational gating role of protein components. On the acceptor side, we characterize a channel system that is absent from existing crystallographic models but is likely functionally important for the reduction of the terminal electron acceptor plastoquinone QB. The results of the present work build a foundation for properly (re)evaluating crystallographic models and for eliciting new insights into PSII structure and function.

Mechanism of the Aryl-F Bond-Forming Step from Bi(V) Fluorides.

In this article, we describe a combined experimental and theoretical mechanistic investigation of the C(sp2)-F bond formation from neutral and cationic high-valent organobismuth(V) fluorides, featuring a dianionic bis-aryl sulfoximine ligand. An exhaustive assessment of the substitution pattern in the ligand, the sulfoximine, and the reactive aryl on neutral triarylbismuth(V) difluorides revealed that formation of dimeric structures in solution promotes facile Ar-F bond formation. Noteworthy, theoretical modeling of reductive elimination from neutral bismuth(V) difluorides agrees with the experimentally determined kinetic and thermodynamic parameters. Moreover, the addition of external fluoride sources leads to inactive octahedral anionic Bi(V) trifluoride salts, which decelerate reductive elimination. On the other hand, a parallel analysis for cationic bismuthonium fluorides revealed the crucial role of tetrafluoroborate anion as fluoride source. Both experimental and theoretical analyses conclude that C-F bond formation occurs through a low-energy five-membered transition-state pathway, where the F anion is delivered to a C(sp2) center, from a BF4 anion, reminiscent of the Balz-Schiemann reaction. The knowledge gathered throughout the investigation permitted a rational assessment of the key parameters of several ligands, identifying the simple sulfone-based ligand family as an improved system for the stoichiometric and catalytic fluorination of arylboronic acid derivatives.

Decoding the Ambiguous Electron Paramagnetic Resonance Signals in the Lytic Polysaccharide Monooxygenase from Photorhabdus luminescens.

Understanding the structure and function of lytic polysaccharide monooxygenases (LPMOs), copper enzymes that degrade recalcitrant polysaccharides, requires the reliable atomistic interpretation of electron paramagnetic resonance (EPR) data on the Cu(II) active site. Among various LPMO families, the chitin-active PlAA10 shows an intriguing phenomenology with distinct EPR signals, a major rhombic and a minor axial signal. Here, we combine experimental and computational investigations to uncover the structural identity of these signals. X-band EPR spectra recorded at different pH values demonstrate pH-dependent population inversion: the major rhombic signal at pH 6.5 becomes minor at pH 8.5, where the axial signal dominates. This suggests that a protonation change is involved in the interconversion. Precise structural interpretations are pursued with quantum chemical calculations. Given that accurate calculations of Cu g-tensors remain challenging for quantum chemistry, we first address this problem via a thorough calibration study. This enables us to define a density functional that achieves accurate and reliable prediction of g-tensors, giving confidence in our evaluation of PlAA10 LPMO models. Large models were considered that include all parts of the protein matrix surrounding the Cu site, along with the characteristic second-sphere features of PlAA10. The results uniquely identify the rhombic signal with a five-coordinate Cu ion bearing two water molecules in addition to three N-donor ligands. The axial signal is attributed to a four-coordinate Cu ion where only one of the waters remains bound, as hydroxy. Alternatives that involve decoordination of the histidine brace amino group are unlikely based on energetics and spectroscopy. These results provide a reliable spectroscopy-consistent view on the plasticity of the resting state in PlAA10 LPMO as a foundation for further elucidating structure-property relationships and the formation of catalytically competent species. Our strategy is generally applicable to the study of EPR parameters of mononuclear copper-containing metalloenzymes.

The Electronic Origin of Far-Red-Light-Driven Oxygenic Photosynthesis.

Photosystem-II uses sunlight to trigger charge separation and catalyze water oxidation. Intrinsic properties of chlorophyll a pigments define a natural "red limit" of photosynthesis at ≈680 nm. Nevertheless, charge separation can be triggered with far-red photons up to 800 nm, without altering the nature of light-harvesting pigments. Here we identify the electronic origin of this remarkable phenomenon using quantum chemical and multiscale simulations on a native Photosystem-II model. We find that the reaction center is preorganized for charge separation in the far-red region by specific chlorophyll-pheophytin pairs, potentially bypassing the light-harvesting apparatus. Charge transfer can occur along two distinct pathways with one and the same pheophytin acceptor (PheoD1 ). The identity of the donor chlorophyll (ChlD1 or PD1 ) is wavelength-dependent and conformational dynamics broaden the sampling of the far-red region by the two charge-transfer states. The two pathways rationalize spectroscopic observations and underpin designed extensions of the photosynthetically active radiation limit.

Crystalline Germanium(I) and Tin(I) Centered Radical Anions.

An isostructural series of heavy Group 14 E(I) radical anions (Ge, Sn, Pb), stabilized by a bulky xanthene-based diamido ligand are reported. The radical anions were synthesised by the one-electron reduction of their corresponding E(II) precursor complexes with sodium naphthalenide in THF, yielding the radical anions as charge-separated sodium salts. The series of main group radicals have been comprehensively characterized by EPR spectroscopy, X-ray crystallography and DFT analysis, which reveal that in all cases, the spin density of the unpaired electron almost exclusively resides in a p-orbital of π symmetry located on the Group 14 center.

How expectations of pain elicited by consciously and unconsciously perceived cues unfold over time.

Expectation can shape the perception of pain within a fraction of time, but little is known about how perceived expectation unfolds over time and modulates pain perception. Here, we combine magnetoencephalography (MEG) and machine learning approaches to track the neural dynamics of expectations of pain in healthy participants with both sexes. We found that the expectation of pain, as conditioned by facial cues, can be decoded from MEG as early as 150 ms and up to 1100 ms after cue onset, but decoding expectation elicited by unconsciously perceived cues requires more time and decays faster compared to consciously perceived ones. Also, results from temporal generalization suggest that neural dynamics of decoding cue-based expectation were predominately sustained during cue presentation but transient after cue presentation. Finally, although decoding expectation elicited by consciously perceived cues were based on a series of time-restricted brain regions during cue presentation, decoding relied on the medial prefrontal cortex and anterior cingulate cortex after cue presentation for both consciously and unconsciously perceived cues. These findings reveal the conscious and unconscious processing of expectation during pain anticipation and may shed light on enhancing clinical care by demonstrating the impact of expectation cues.

Electrophysiological Decoding of Spatial and Color Processing in Human Prefrontal Cortex.

The prefrontal cortex (PFC) plays a pivotal role in goal-directed cognition, yet its representational code remains an open problem with decoding techniques ineffective in disentangling task-relevant variables from PFC. Here we applied regularized linear discriminant analysis to human scalp EEG data and were able to distinguish a mental-rotation task versus a color-perception task with 87% decoding accuracy. Dorsal and ventral areas in lateral PFC provided the dominant features dissociating the two tasks. Our findings show that EEG can reliably decode two independent task states from PFC and emphasize the PFC dorsal/ventral functional specificity in processing the where rotation task versus the what color task.

Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations.

The determination of the diiron core intermediate structures involved in the catalytic cycle of soluble methane monooxygenase (sMMO), the enzyme that selectively catalyzes the conversion of methane to methanol, has been a subject of intense interest within the bioinorganic scientific community. Particularly, the specific geometry and electronic structure of the intermediate that precedes methane binding, known as intermediate Q (or MMOHQ), has been debated for over 30 years. Some reported studies support a bis-µ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer Fe-Fe distance. The lack of consensus calls for a thorough re-examination and reinterpretation of the spectroscopic data available on the MMOHQ intermediate. Herein, we report extensive simulations based on a hybrid quantum mechanics/molecular mechanics approach (QM/MM) approach that takes into account the complete enzyme to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum chemical approaches are used to correlate specific structural motifs with geometric parameters for comparison with crystallographic and EXAFS data, as well as with spectroscopic data from Mössbauer spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy (HERFD XAS), and resonance Raman 16O-18O difference spectroscopy. The results provide strong support for an open-core-type configuration in MMOHQ, with the most likely topology involving mono-oxo-bridged Fe ions and alternate terminal Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen bonding. The implications of an open-core intermediate Q on the reaction mechanism of sMMO are discussed.

Characterization of a Triplet Vinylidene.

Singlet vinylidenes (R2C═C:) are proposed as intermediates in a series of organic reactions, and very few have been studied by matrix isolation or gas-phase spectroscopy. Triplet vinylidenes, however, featuring two unpaired electrons at a monosubstituted carbon atom are thus far only predicted as electronically excited-state species and represent an unexplored class of carbon-centered diradicals. We report the photochemical generation and low-temperature EPR/ENDOR characterization of the first ground-state high-spin (triplet) vinylidene. The zero-field splitting parameters (D = 0.377 cm-1 and |E|/D = 0.028) were determined, and the 13C hyperfine coupling tensor was obtained by 13C-ENDOR measurements. Most strikingly, the isotropic 13C hyperfine coupling constant (50 MHz) is far smaller than the characteristic values of triplet carbenes, demonstrating a unique electronic structure which is supported by quantum chemical calculations.