Principal active species of horseradish peroxidase, compound I: a hybrid quantum mechanical/molecular mechanical study

The active species, Compound I, of horseradish peroxidase (HRP) has been investigated by quantum mechanical/molecular mechanical (QM/MM) calculations using 10 different QM regions. In accord with experimental data, the lowest doublet and quartet states are found to be virtually degenerate, with two unpaired electrons on the FeO moiety and one localized on the porphyrin in an a(2u)-dominant orbital with a minor, but nonnegligible, a(1u) component. The proximal ligand appears to be imidazole rather than imidazolate. The hydrogen-bonding network around the FeO moiety (i.e., Arg38 and His42) has significant influence on the axial bonds and the spin density distribution in the FeO moiety. Including this network in the QM region was found to be essential for reproducing the experimental M?ssbauer parameters. The protein environment shapes most of the subtle features of Compound I of HRP.     

Valence bond calculations of hydrogen transfer reactions: a general predictive pattern derived from theory

Hydrogen abstraction reactions of the type X(*) + H-H' --> X-H + H'(*) (X = F, Cl, Br, I) are studied by ab initio valence bond methods and the VB state correlation diagram (VBSCD) model. The reaction barriers and VB parameters of the VBSCD are computed by using the breathing orbital valence bond and valence bond configuration interaction methods. The combination of the VBSCD model and semiempirical VB theory leads to analytical expressions for the barriers and other VB quantities that match the ab initio VB calculations fairly well. The barriers are influenced by the endo- or exothermicity of the reaction, but the fundamental factor of the barrier is the average singlet-triplet gap of the bonds that are broken or formed in the reactions. Some further approximations lead to a simple formula that expresses the barrier for nonidentity and identity hydrogen abstraction reactions as a function of the bond strengths of reactants and products. The semiempirical expressions are shown to be useful not only for the model reactions that are studied in this work, but also for other nonidentity and identity hydrogen abstraction reactions that have been studied in previous articles.     

Thermal and X-ray diffraction investigations of some lanthanum(III) and neodymium(III) oxide-alkali persulfate binary systems

Different molar ratios of La₂O₃ or Nd₂O₃:Na₂/K₂S₂O₈ have been prepared, and the results of their TG and DTA investigations, under an atmosphere of static air, are reported. The effects of either La₂O₃ or Nd₂O₃ on the thermal decomposition of the persulfates from ambient to 1050°C, using a derivatograph, have been studied. It has been found that La₂O₃ lowers the initial decomposition temperatures of these alkali persulfates through catalytic activity. Nd₂O₃ shows little or no catalytic effect and therefore it acts as an insulator. Intermediate and final products are identified by X-ray diffraction analysis. The stoichiometric molar ratios of the solid state reactions are 1:3::R₂O₃:M₂S₂O₈. (R = La or Nd. M = Na or K), which give double salts of formulae: NaLa(So₄)₂, KLa(SO₄)₂, NaNd(SO₄)₂, and KNd(SO₄)₂. No sulfates or oxysulfates of lanthanum or neodymium have been identified.     

Revealing the relationship between photoelectrochemical performance and interface hole trapping in CuBi2O4 heterojunction photoelectrodes

p-Type CuBi₂O₄ is considered a promising metal oxide semiconductor for large-scale, economic solar water splitting due to the optimal band structure and low-cost fabrication. The main challenge in utilizing CuBi₂O₄ as a photoelectrode for water splitting, is that it must be protected from photo-corrosion in aqueous solutions, an inherent problem for Cu-based metal oxide photoelectrodes. In this work, several buffer layers (CdS, BiVO₄, and Ga₂O₃) were tested between CuBi₂O₄ and conformal TiO₂ as the protection layer. RuO_x was used as the co-catalyst for hydrogen evolution. Factors that limit the photoelectrochemical performance of the CuBi₂O₄/TiO₂/RuO_x, CuBi₂O₄/CdS/TiO₂/RuO_x, CuBi₂O₄/BiVO₄/TiO₂/RuO_x and CuBi₂O₄/Ga₂O₃/TiO₂/RuO_x heterojunction photoelectrodes were revealed by comparing photocurrents, band offsets, and directed charge transfer measured by modulated surface photovoltage spectroscopy. For CuBi₂O₄/Ga₂O₃/TiO₂/RuO_x photoelectrodes, barriers for charge transfer strongly limited the performance. In CuBi₂O₄/CdS/TiO₂/RuO_x, the absence of hole traps resulted in a relatively high photocurrent density and faradaic efficiency for hydrogen evolution despite the presence of pronounced deep defect states at the CuBi₂O₄/CdS interface. Hole trapping limited the performance moderately in CuBi₂O₄/BiVO₄/TiO₂/RuO_x and strongly in CuBi₂O₄/TiO₂/RuO_x photoelectrodes. For the first time, our results show that hole trapping is a key factor that must be addressed to optimize the performance of CuBi₂O₄-based heterojunction photoelectrodes.

CdS, BiVO₄, and Ga₂O₃ buffer layers were tested between CuBi₂O₄ and TiO₂ in heterojunction photoelectrodes. Photoelectrochemical analysis and modulated surface photovoltage spectroscopy revealed that interface hole traps impacted device performance.     

Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor

The hydrogen abstraction reaction of camphor in cytochrome P450(cam) has been investigated in the native enzyme environment by combined quantum mechanical/molecular mechanical (QM/MM) calculations and in the gas phase by density functional calculations. This work has been motivated by contradictory published QM/MM results. In an attempt to pinpoint the origin of these discrepancies, we have systematically studied the factors that may affect the computed barriers, including the QM/MM setup, the optimization procedures, and the choice of QM region, basis set, and protonation states. It is found that the ChemShell and QSite programs used in the published QM/MM calculations yield similar results at given geometries, and that the discrepancies mainly arise from two technical issues (optimization protocols and initial system preparation) that need to be well controlled in QM/MM work. In the course of these systematic investigations, new mechanistic insights have been gained. The crystallographic water 903 placed near the oxo atom of Compound I lowers the hydrogen abstraction barrier by ca. 4 kcal/mol, and thus acts as a catalyst for this reaction. Spin density may appear at the A-propionate side chain of the heme if the carboxylate group is not properly screened, which might be expected to happen during protein dynamics, but not in static equilibrium situations. There is no clear correlation between the computed A-propionate spin density and the hydrogen abstraction barrier, and hence, no support for a previously proposed side-chain mediated transition state stabilization mechanism. Standard QM/MM optimizations yield an A-propionate environment close to the X-ray structure only for protonated Asp297, and not for deprotonated Asp297, but the computed barriers are similar in both cases. An X-ray like A-propionate environment can also be obtained when deprotonated Asp297 is included in the QM region and His355 is singly protonated, but this Compound II-type species with a closed-shell porphyrin ring has a higher hydrogen abstraction barrier and should thus not be mechanistically relevant.