Two‐Color Valence‐to‐Core X‐ray Emission Spectroscopy Tracks Cofactor Protonation State in a Class I Ribonucleotide Reductase

Proton transfer reactions are of central importance to a wide variety of biochemical processes, though determining proton location and monitoring proton transfers in biological systems is often extremely challenging. Herein, we use two‐color valence‐to‐core X‐ray emission spectroscopy (VtC XES) to identify protonation events across three oxidation states of the O₂‐activating, radical‐initiating manganese–iron heterodinuclear cofactor in a class I‐c ribonucleotide reductase. This is the first application of VtC XES to an enzyme intermediate and the first simultaneous measurement of two‐color VtC spectra. In contrast to more conventional methods of assessing protonation state, VtC XES is a more direct probe applicable to a wide range of metalloenzyme systems. These data, coupled to insight provided by DFT calculations, allow the inorganic cores of the Mn^IVFe^IV and Mn^IVFe^III states of the enzyme to be assigned as Mn^IV(μ‐O)₂Fe^IV and Mn^IV(μ‐O)(μ‐OH)Fe^III, respectively.     

Kβ X‐Ray Emission Spectroscopic Study of a Second‐Row Transition Metal (Mo) and Its Application to Nitrogenase‐Related Model Complexes

In recent years, X‐ray emission spectroscopy (XES) in the Kβ (3p‐1s) and valence‐to‐core (valence‐1s) regions has been increasingly used to study metal active sites in (bio)inorganic chemistry and catalysis, providing information about the metal spin state, oxidation state and the identity of coordinated ligands. However, to date this technique has been limited almost exclusively to first‐row transition metals. In this work, we present an extension of Kβ XES (in both the 4p‐1s and valence‐to‐1s [or VtC] regions) to the second transition row by performing a detailed experimental and theoretical analysis of the molybdenum emission lines. It is demonstrated in this work that Kβ₂ lines are dominated by spin state effects, while VtC XES of a 4d transition metal provides access to metal oxidation state and ligand identity. An extension of Mo Kβ XES to nitrogenase‐relevant model complexes shows that the method is sufficiently sensitive to act as a spectator probe for redox events that are localized at the Fe atoms. Mo VtC XES thus has promise for future applications to nitrogenase, as well as a range of other Mo‐containing biological cofactors. Further, the clear assignment of the origins of Mo VtC XES features opens up the possibility of applying this method to a wide range of second‐row transition metals, thus providing chemists with a site‐specific tool for the elucidation of 4d transition metal electronic structure.     

Kβ X-Ray Emission Spectroscopic Study of a Second-Row Transition Metal (Mo) and Its Application to Nitrogenase-Related Model Complexes

In recent years, X-ray emission spectroscopy (XES) in the Kβ (3p-1s) and valence-to-core (valence-1s) regions has been increasingly used to study metal active sites in (bio)inorganic chemistry and catalysis, providing information about the metal spin state, oxidation state and the identity of coordinated ligands. However, to date this technique has been limited almost exclusively to first-row transition metals. In this work, we present an extension of Kβ XES (in both the 4p-1s and valence-to-1s [or VtC] regions) to the second transition row by performing a detailed experimental and theoretical analysis of the molybdenum emission lines. It is demonstrated in this work that Kβ₂ lines are dominated by spin state effects, while VtC XES of a 4d transition metal provides access to metal oxidation state and ligand identity. An extension of Mo Kβ XES to nitrogenase-relevant model complexes shows that the method is sufficiently sensitive to act as a spectator probe for redox events that are localized at the Fe atoms. Mo VtC XES thus has promise for future applications to nitrogenase, as well as a range of other Mo-containing biological cofactors. Further, the clear assignment of the origins of Mo VtC XES features opens up the possibility of applying this method to a wide range of second-row transition metals, thus providing chemists with a site-specific tool for the elucidation of 4d transition metal electronic structure.     

Manganese Kβ X-ray emission spectroscopy as a probe of metal-ligand interactions

A systematic series of high-spin mononuclear Mn(II), Mn(III), and Mn(IV) complexes has been investigated by manganese Kβ X-ray emission spectroscopy (XES). The factors contributing to the Kβ main line and the valence to core region are discussed. The Kβ main lines are dominated by 3p-3d exchange correlation (spin state) effects, shifting to lower energy upon oxidation of Mn(II) to Mn(III) due to the decrease in spin state from S = 5/2 to S = 2, whereas the valence to core region shows greater sensitivity to the chemical environment surrounding the Mn center. A density functional theory (DFT) approach has been used to calculate the valence to core spectra and assess the contributions to the energies and intensities. The valence spectra are dominated by manganese np to 1s electric dipole-allowed transitions and are particularly sensitive to spin state and ligand identity (reflected primarily in the transition energies) as well as oxidation state and metal-ligand bond lengths (reflected primarily in the transition intensities). The ability to use these methods to distinguish different ligand contributions within a heteroleptic coordination sphere is highlighted. The similarities and differences between the current Mn XES study and previous studies of Fe XES investigations are discussed. These findings serve as an important calibration for future applications to manganese active sites in biological and chemical catalysis.     

Operando soft x-ray emission spectroscopy of LiMn2O4 thin film involving Li–ion extraction/insertion reaction

We developed an electrochemical in situ cell for soft x-ray emission spectroscopy (XES) to accurately investigate the redox reaction and electronic structure of transition metals in the cathode materials for Li–ion battery. The in situ cell consists of a Li–metal counter electrode, an organic electrolyte solution, and a cathode on a membrane window which separates the liquid electrolyte from high vacuum and can pass the incoming and emitted photons. In this study, the Mn 3d electronic structure of LiMn₂O₄ thin-film electrode was clarified by the operando XES. At the charged state, the XES spectrum changed significantly from the open-circuit-voltage (OCV) state, suggesting oxidation of the Mn^3 + component through Li–ion extraction. Upon discharge up to 3.0 V vs. Li/Li⁺, the XES spectrum almost returned to its profile at the OCV state with small difference, indicating the valence change of Mn: Mn^3.6 + → Mn^4 + → Mn^3.3 + corresponding to the OCV, charged, and discharged states.     

Kβ X-ray emission spectroscopy offers unique chemical bonding insights: revisiting the electronic structure of ferrocene

Kβ X-ray emission spectroscopy (XES) is emerging as a powerful tool for the study of chemical bonding. Analyses of the Kβ XES of ferrocene (Fc) and ferrocenium (Fc(+)) are presented as further demonstrations of the capabilities of the technique. Assignments of the valence to core (V2C) region of these spectra as electric dipole-allowed cyclopentadienyl (Cp) → Fe 1s transitions demonstrate that XES affords electronic structural insight into the energetics of ligand-based molecular orbitals (MOs). Combined with K-edge X-ray absorption spectroscopy (XAS), we show that XES can provide analogous information to photoemission spectroscopy (PES). Density functional theory (DFT) analyses reveal that the V2C transitions in Fc/Fc(+) derive their intensity from Fe 4p admixture (on the order of 5-10%) into the Cp-based MOs from which they originate. These 4p admixtures confer bonding character to the Cp-based a(2u) and e(1u) MOs to at least the extent of backbonding contributions to frontier MOs from higher-lying Cp π* MOs.     

Identification of a single light atom within a multinuclear metal cluster using valence-to-core X-ray emission spectroscopy

Iron valence-to-core Fe Kβ X-ray emission spectroscopy (V2C XES) is established as a means to identify light atoms (C, N, O) within complex multimetallic frameworks. The ability to distinguish light atoms, particularly in the presence of heavier atoms, is a well-known limitation of both crystallography and EXAFS. Using the sensitivity of V2C XES to the ionization potential of the bound ligand, energetic shifts of ~10 eV in the ligand 2s ionization energies of bound C, N, and O may be observed. As V2C XES is a high-energy X-ray method, it is readily applicable to samples in any physical form. This method thus has great potential for application to multimetallic inorganic frameworks involved in both small molecule storage and activation.     

X‐Ray Emission Spectroscopy: A Spectroscopic Measure for the Determination of NO Oxidation States in Fe–NO Complexes

Extensive study of the electronic structure of Fe‐NO complexes using a variety of spectroscopic methods was attempted to understand how iron controls the binding and release of nitric oxide. The comparable energy levels of NO π* orbitals and Fe 3d orbitals complicate the bonding interaction within Fe? NO complexes and puzzle the quantitative assignment of NO oxidation state. Enemark–Feltham notation, {Fe(NO)_x}ⁿ, was devised to circumvent this puzzle. This 40‐year puzzle is revisited using valence‐to‐core X‐ray emission spectroscopy (V2C XES) in combination with computational study. DFT calculation establishes a linear relationship between ΔE_σ2s*‐σ2p of NO and its oxidation state. V2C Fe XES study of Fe? NO complexes reveals the ΔE_σ2s*‐σ2p of NO derived from NO σ_2s*/σ_2p→Fe_1s transitions and determines NO oxidation state in Fe? NO complexes. Quantitative assignment of NO oxidation state will correlate the feasible redox process of nitric oxide and Fe‐nitrosylation biology.     

Light-triggered proton and electron transfer in flavin cofactors

The pH dependent behavior of two flavin cofactors, flavin-adenine dinucleotide (FAD) and flavin mononucleotide (FMN), has been characterized using femtosecond transient absorption spectroscopy for the first time. The flavin excited state was characterized in three states of protonation (Fl(-), Fl, and FlH(+)). We found that Fl and Fl(-) exhibit the same excited state absorption but that the lifetime of Fl(-) is much shorter than that of Fl. The transient absorption spectrum of FlH(+) is significantly different from Fl and Fl(-), suggesting that the electronic properties of the flavin chromophore become appreciably modified by protonation. We further studied the excited state protonation of the flavin and found that the protonation sites of the flavin in the ground and excited state are not equivalent. In the case of FAD, its excited state dynamics are controlled by the two conformations it adopts. At low and high pH, FAD adopts an "open" conformation and behaves the same as FMN. In a neutral pH range, FAD undergoes a fast excited state deactivation due to the "stacked" conformer. The transition from stacked to open conformer occurs at pH ～ 3 (because of adenine protonation) and pH ～ 10 (because of flavin deprotonation).     

GAS SEPARATION PROPERTIES OF FREESTANDING FILM OF POLYANILINE

The gas separation properties of free- standing film of polyaniline (PANI) for gas pairs of He/N2, H_2/N_2. CO_2/N_2 and CO_2/CH_4 at room temperature were measured as a function of the protonation state. Variation of the gas permeabilities coefficient of PANI with an insulator to metal transition upon the protonation processes was observed, which might be due to a change in both gas solubility coefficient and diffusion coefficient with the protonation state.     

Site-specific intermolecular interaction in α-phase crystalline films of phthalocyanines studied by soft x-ray emission spectroscopy

The local electronic structures of crystalline and amorphous films of zinc phthalocyanine (ZnPc) and metal-free phthalocyanine (H(2)Pc) have been studied by soft x-ray emission spectroscopy (XES). We found a clear crystalline structure dependence of the elastic-peak shape in the resonant XES spectra. The elastic peaks of both ZnPc and H(2)Pc are found to show an asymmetric shape due to resonant inelastic x-ray scattering (RIXS) at the nitrogen sites for the α-crystalline films, but not for the amorphous films. The observed RIXS feature is ascribed to the charge transfer excitation due to the Raman-active intermolecular interaction, which dominates the excited-electron dynamics in α-crystalline phthalocyanine films.     

Solvation of p-coumaric acid in water

The photoactive yellow protein (PYP) is an important model protein for many (photoactive) signaling proteins. Key steps in the PYP photocycle are the isomerization and protonation of its chromophore, p-coumaric acid (pCA). In the ground state of the protein, this chromophore is in the trans configuration with its phenolic oxygen deprotonated. For this paper, we studied four different configurations of pCA solvated in water with ab initio molecular dynamics simulations as implemented in CP2K/Quickstep. We researched the influence of the protonation and isomerization state of pCA on its hydrogen-bonding properties and on the Mulliken charges of the atoms in the simulation. The chromophore isomerization state influenced the hydrogen-bonding less than its protonation state. In general, more charge yielded a higher hydrogen-bond coordination number. Where deprotonation increases both the coordination number and the residence time of the water molecules around the chromophore, protonation showed a somewhat lower coordination number on two of the three pCA oxygens but much higher residence times on all of them. This could be explained by the increased polarization of the OH groups of the molecule. The presence of the chromophore also influenced the charge and polarization of the water molecules around it. This effect was different in the four systems studied and mainly localized in the first solvation shell. We also performed a proton-transfer reaction from hydronium through various other water molecules to the chromophore. In this small charge-separated system, the protonation occurred within 6.5 ps. We identified the transition state for the final step in this protonation series.     

Valence-to-core X-ray emission spectroscopy: a sensitive probe of the nature of a bound ligand

The sensitivity of iron Kβ X-ray emission spectroscopy (XES) to the nature of the bound ligands (σ-donating, π-donating, and π-accepting) has been explored. A combination of experiment and theory has been employed, with a DFT approach being utilized to elucidate ligand effects on the spectra and to assign the spectral intensity mechanisms. Knowledge of the various contributions to the spectra allows for a deeper understanding of spectral features and demonstrates the sensitivity of this method to the identity of the interacting ligands. The potential of XES for identifying intermediate species in nonheme iron enzymes is highlighted.     

Mn K-edge XANES and Kbeta XES studies of two Mn-oxo binuclear complexes: investigation of three different oxidation states relevant to the oxygen-evolving complex of photosystem II.

Two structurally homologous Mn compounds in different oxidation states were studied to investigate the relative influence of oxidation state and ligand environment on Mn K-edge X-ray absorption near-edge structure (XANES) and Mn Kbeta X-ray emission spectroscopy (Kbeta XES). The two manganese compounds are the di-mu-oxo compound [L'2Mn(III)O2Mn(IV)L'2](ClO4)3, where L' is 1,10-phenanthroline (Cooper, S. R.; Calvin, M. J. Am. Chem. Soc. 1977, 99, 6623-6630) and the linear mono-mu-oxo compound [LMn(III)OMn(III)L](ClO4)2, where L- is the monoanionic N,N-bis(2-pyridylmethyl)-N'-salicylidene-1,2-diaminoethane ligand (Horner, O.; Anxolabéhère-Mallart, E.; Charlot, M. F.; Tchertanov, L.; Guilhem, J.; Mattioli, T. A.; Boussac, A.; Girerd, J.-J. Inorg. Chem. 1999, 38, 1222-1232). Preparative bulk electrolysis in acetonitrile was used to obtain higher oxidation states of the compounds: the Mn(IV)Mn(IV) species for the di-mu-oxo compound and the Mn(III)Mn(IV) and Mn(IV)Mn(IV) species for the mono-mu-oxo compound. IR, UV/vis, EPR, and EXAFS spectra were used to determine the purity and integrity of the various sample solutions. The Mn K-edge XANES spectra shift to higher energy upon oxidation when the ligand environment remains similar. However, shifts in energy are also observed when only the ligand environment is altered. This is achieved by comparing the di-mu-oxo and linear mono-mu-oxo Mn-Mn moieties in equivalent oxidation states, which represent major structural changes. The magnitude of an energy shift due to major changes in ligand environment can be as large as that of an oxidation-state change. Therefore, care must be exercised when correlating the Mn K-edge energies to manganese oxidation states without taking into account the nature of the ligand environment and the overall structure of the compound. In contrast to Mn K-edge XANES, Kbeta XES spectra show less dependence on ligand environment. The Kbeta1,3 peak energies are comparable for the di-mu-oxo and mono-mu-oxo compounds in equivalent oxidation states. The energy shifts observed due to oxidation are also similar for the two different compounds. The study of the different behavior of the XANES pre-edge and main-edge features in conjunction with Kbeta XES provides significant information about the oxidation state and character of the ligand environment of manganese atoms.     

Epik: a software program for pK<Subscript><Emphasis Type="Italic">a</Emphasis></Subscript> prediction and protonation state generation for drug-like molecules

Epik is a computer program for predicting pK_a values for drug-like molecules. Epik can use this capability in combination with technology for tautomerization to adjust the protonation state of small drug-like molecules to automatically generate one or more of the most probable forms for use in further molecular modeling studies. Many medicinal chemicals can exchange protons with their environment, resulting in various ionization and tautomeric states, collectively known as protonation states. The protonation state of a drug can affect its solubility and membrane permeability. In modeling, the protonation state of a ligand will also affect which conformations are predicted for the molecule, as well as predictions for binding modes and ligand affinities based upon protein–ligand interactions. Despite the importance of the protonation state, many databases of candidate molecules used in drug development do not store reliable information on the most probable protonation states. Epik is sufficiently rapid and accurate to process large databases of drug-like molecules to provide this information. Several new technologies are employed. Extensions to the well-established Hammett and Taft approaches are used for pK_a prediction, namely, mesomer standardization, charge cancellation, and charge spreading to make the predicted results reflect the nature of the molecule itself rather just for the particular Lewis structure used on input. In addition, a new iterative technology for generating, ranking and culling the generated protonation states is employed. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

质子化和脱质子化对酞菁光谱的影响

系统地研究四异丙氧基酞菁的子化和脱质子化对吸收和发射光谱的影响，研究表明，三氟乙酸可对酞菁分子连续质子化，分别生成（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．Ｈ＾＋）＾和（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．２Ｈ＾＋）＾２＋，而硫酸可使酞菁形成（Ｈ２Ｐｃ（Ｏ＾ｉＰｒ）４．４Ｈ＾＋＾４＋此外，ＮａＯＨ／ＥｔＯＨ可使酞菁分子脱质子化生成（Ｐｃ（Ｏ＾ｉＰｒ）４）＾２－反应一步完成，表明分子中的两个吡咯－ＮＨ－同步酸解，质子化可使     

Protonation states of the catalytic dyad of β-secretase (BACE1) in the presence of chemically diverse inhibitors: a molecular docking study

In this molecular docking study, the protonation states of the catalytic Asp dyad of the beta-secretase (BACE1) enzyme in the presence of eight chemically diverse inhibitors have been predicted. BACE1 catalyzes the rate-determining step in the generation of Alzheimer amyloid beta peptides and is widely considered as a promising therapeutic target. All the inhibitors were redocked into their corresponding X-ray structures using a combination of eight different protonation states of the Asp dyad for each inhibitor. Five inhibitors were primarily found to favor two different monoprotonated states, and the remaining three favor a dideprotonated state. In addition, five of them exhibited secondary preference for a diprotonated state. These results show that the knowledge of a single protonation state of the Asp dyad is not sufficient to search for the novel inhibitors of BACE1 and the most plausible state for each inhibitor must be determined prior to conducting in-silico screening.     

Optochemical sensing of hydrogen chloride gas using meso-tetramesitylporphyrin deposited glass plate

Meso-tetramesitylporphyrin (MTMP) deposited glass plate (solid state sensor) was used to sense hydrogen chloride (HCl) gas based on optochemical method. Exposure of the solid state sensor to HCl vapor results in the formation of protonated meso-tetramesitylporphyrin (PMTMP). UV-vis and fluorescence spectral techniques were used to study the protonation of MTMP in dichloromethane-methanol mixture. The optical spectra of MTMP show an intense Soret band at 418 nm with a 14 nm red shift upon protonation by HCl. Ab-initio calculations were carried out to visualize the effect of protonation on planarity and stability of the porphyrin ring. The solid state sensor was characterized by UV-vis spectral technique. The sensor exhibits characteristic Soret and Q bands for the deposited MTMP with slight red shift when compared to MTMP in dichloromethane. The concentration of gaseous HCl was monitored from the changes in the absorbance of Soret band of PMTMP at 452 nm. The detection limit of the solid state sensor towards gaseous HCl was found to be 0.03 ppm. The present solid state sensor was highly stable for several months.     

Electronic structure of the nucleobases

We present a comparison between experimental and calculated soft X-ray spectra of DNA's nucleobases, adenine (A), guanine (G), cytosine (C), and thymine (T) using X-ray absorption spectroscopy (XAS) and soft X-ray emission spectroscopy (XES). Spectra of the 1s thresholds of carbon, nitrogen, and oxygen give a complete picture of the occupied and unoccupied partial density of states of the nucleobases. A combination of both Hartree-Fock and density functional theory calculations are used in the comparison to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of all bases. All spectral features are assigned. A comparison of the experimental highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps is made to the diverse values predicted in the literature.     

Experimental and theoretical investigation of the electronic structure of 5-fluorouracil compounds

We present a comparison between experimental and theoretical X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of 5-fluorouracil compounds, with an emphasis on the effects of the inclusion of nickel in the structure. By focusing on the 1s thresholds of carbon, nitrogen, oxygen, and fluorine it was possible to provide a complete picture of the occupied and unoccupied partial density of states of the 5-fluorouracil systems. Spectra calculated using density functional theory are compared to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of the compounds. All spectral features are assigned. Our results reveal that the nickel in the compound is coordinated with the nitrogen sites of the 5-fluorouracil ligands.