What is the Real Nature of Ferrous Soybean Lipoxygenase-1? A New Two-Conformation Model Based on Combined ONIOM(DFT:MM) and Multireference Configuration Interaction Characterization

The geometric and spectral features of the ferrous resting state of soybean lipoxygenase-1 (SLO-1) have remained puzzling. We have theoretically characterized ferrous SLO-1 by means of the ONIOM(DFT:MM), TDDFT, and CASSCF/SORCI methods, taking explicitly into account the effect of the protein environment. Two conformations found theoretically in this study, Conf-A and Conf-B, have almost equal stability but have quite different geometries, with short and long Fe−O₆₉₄ distances, respectively. While neither of the geometries agreed well with the crystal structure of the enzyme, an averaged geometry showed excellent agreement. Therefore, we propose that the crystal structure reflects a mixture of these two conformations. The calculated circular dichroism (CD) spectra for Conf-A and Conf-B were found to agree well with the two experimental spectra obtained previously for “six-coordinate” and “five-coordinate” forms of ferrous SLO-1, respectively

ONIOM (DFT:MM) Study of the Catalytic Mechanism of <i>myo</i>-Inositol Monophosphatase: Essential Role of Water in Enzyme Catalysis in the Two-Metal Mechanism

<i>myo</i>-Inositol monophosphatase (IMPase), a putative target of lithium therapy for bipolar disorder, is an enzyme that catalyzes the hydrolysis of <i>myo</i>-inositol-1-phosphate (Ins­(1)­P) into <i>myo</i>-inositol (MI) and inorganic phosphate. It is known that either two or three Mg²⁺ ions are used as cofactors in IMPase catalysis; however, the detailed catalytic mechanism and the specific number of Mg²⁺ ions required have long remained obscure. To obtain a clearer view of the IMPase reaction, we undertook extensive ONIOM hybrid quantum mechanics and molecular mechanics (QM/MM) calculations, to evaluate the reaction with either three or two Mg²⁺ ions. Our calculations show that the three-metal mechanism is energetically unfavorable; the initial inline attack of a hydroxide ion on the Ins(1)P substrate markedly destabilized the system without producing any stable transition state or intermediate. By contrast, for the two-metal mechanism, a favorable pathway was obtained from QM/MM calculations. In our proposed two-metal mechanism, the phosphoryl oxygen of the substrate acts as an acid–base catalyst, activating a water molecule in the first step, and the resultant hydroxide ion attacks the substrate in an inline fashion. A second water molecule, bound to a Mg²⁺ ion, was found to play an essential role in the final proton-transfer step that leads to the formation of an MI product; this is achieved by lowering the energy barrier by 2.5 kcal/mol compared with the barrier for the mechanism that does not use this water molecule. Our results should advance our understanding of the IMPase mechanism, and this could have profound implications for the treatment of disease in the central nervous system

Effect of Protein Environment within Cytochrome P450cam Evaluated Using a Polarizable-Embedding QM/MM Method

Metalloenzymes accommodate cofactors and substrates in their active sites, thereby exerting powerful catalytic effects. Understanding the key elements of the mechanism via which such binding is accomplished using a number of atoms in a protein is a fundamental challenge. To address this issue computationally, here we used mechanical-embedding (ME), electronic-embedding (EE), and polarizable-embedding (PE) hybrid quantum mechanics and molecular mechanics (QM/MM) methods and performed an energy decomposition analysis (EDA) of the nonbonding protein environmental effect in the “compound I” intermediate state of cytochrome P450cam. The B3LYP and AMBER99/QP302 methods were used to deal with the QM and MM subsystems, respectively, and the nonbonding interaction energy between these subsystems was decomposed into electrostatic, van der Waals, and polarization contributions. The PE-QM/MM calculation was performed using polarizable force fields that were capable of describing induced dipoles within the MM subsystem, which arose in response to the electric field generated by QM electron density, QM nuclei, and MM point charges. The present QM/MM EDA revealed that the electrostatic term constituted the largest stabilizing interaction between the QM and MM subsystems. When proper adjustment was made for the point charges of the MM atoms located at the QM–MM boundary, EE-QM/MM and PE-QM/MM calculations yielded similar QM electron density distributions, indicating that the MM polarization effect does not have a significant influence on the extent of QM polarization in this particular enzyme system

Estrogen Formation via H‑Abstraction from the O–H Bond of <i>gem</i>-Diol by Compound I in the Reaction of CYP19A1: Mechanistic Scenario Derived from Multiscale QM/MM Calculations

Recent experiments suggested that, contrary to traditional belief, the third step of aromatase-catalyzed estrogen formation should be effected by compound I (Cpd I), rather than by ferric peroxide. We performed QM/MM calculations to address the question of how Cpd I drives the aromatization process. Surprisingly, the calculations show that the reaction begins with hydrogen abstraction from the O–H bond of a <i>gem</i>-diol substrate, which is followed by barrierless homolytic C–C bond cleavage and then 1β-H-abstraction. Proton-coupled electron transfer enables the cleavage of the strong O–H bond. Another product, carboxylic acid, can be formed from either the <i>gem</i>-diol or aldehyde

Pivotal Role of Water in Terminating Enzymatic Function: A Density Functional Theory Study of the Mechanism-Based Inactivation of Cytochromes P450

The importance of the mechanism-based inactivation (MBI) of enzymes, which has a variety of physiological effects and therapeutic implications, has been garnering appreciation. Density functional theory calculations were undertaken to gain a clear understanding of the MBI of a cytochrome P450 enzyme (CYP2B4) by <i>tert</i>-butylphenylacetylene (tBPA). The results of calculations suggest that, in accordance with previous proposals, the reaction proceeds via a ketene-type metabolic intermediate. Once an oxoiron­(IV) porphyryn π-cation radical intermediate (compound I) of P450 is generated at the heme reaction site, ketene formation is facile, as the terminal acetylene of tBPA can form a C–O bond with the oxo unit of compound I with a relatively low reaction barrier (14.1 kcal/mol). Unexpectedly, it was found that the ketene-type intermediate was not very reactive. Its reaction with the hydroxyl group of a threonine (Thr302) to form an ester bond required a substantial barrier (38.2 kcal/mol). The high barrier disfavored the mechanism by which these species react directly. However, the introduction of a water molecule in the reaction center led to its active participation in the reaction. The water was capable of donating its proton to the tBPA molecule, while accepting the proton of threonine. This water-mediated mechanism lowered the reaction barrier for the formation of an ester bond by about 20 kcal/mol. Therefore, our study suggests that a water molecule, which can easily gain access to the threonine residue through the proton-relay channel, plays a critical role in enhancing the covalent modification of threonine by terminal acetylene compounds. Another type of MBI by acetylenes, <i>N</i>-alkylation of the heme prosthetic group, was less favorable than the threonine modification pathway

Electrochemical Properties of Phenols and Quinones in Organic Solvents are Strongly Influenced by Hydrogen-Bonding with Water

The electrochemical behavior of several phenols, quinones and hydroquinone in acetonitrile (CH₃CN) with varying amounts of water were investigated to understand the effect of hydrogen-bonding on their voltammetric responses. Karl Fischer coulometric titrations were performed to obtain an accurate reading of the water concentrations. The solvent/electrolyte mixture was carefully dried using 3 Å molecular sieves to obtain an initial water content that was close to the substrate concentration (∼1 × 10^–3 M), and higher water contents were then achieved via the addition from microliter syringes. It was found that small changes in what is often considered “trace” amounts of water were sufficient to substantially change the potential and in some cases the appearance of the voltammetric waves observed during the oxidation of the phenols/hydroquinones and reduction of the quinones. Density functional theory calculations were performed on the reduced/oxidized species in the presence of varying numbers of water molecules to better understand the hydrogen-bonding interactions at the molecular level. The results highlight the importance of accurately knowing the trace water content of organic solvents when used for voltammetric experiments

Pd-Catalyzed Conversion of Alkynyl‑λ³‑iodanes to Alkenyl‑λ³‑iodanes via Stereoselective 1,2-Iodine(III) Shift/1,1-Hydrocarboxylation

Alkynyl-λ³-iodanes have been established as alkynyl cation equivalents for the alkynylation of carbon- and heteroatom-based nucleophiles. Herein, we report an unprecedented reaction mode of this compound class, which features a Pd­(II)-assisted 1,2-I­(III) shift of an alkynylbenziodoxole. A Pd­(II) catalyst mediates this shift and the subsequent interception of the transient vinylidene species with carboxylic acid (1,1-hydro­carboxylation). The product of this stereoselective rearrangement–addition reaction, β-oxyalkenyl­benziodoxole, represents a novel and useful building block for further synthetic transformations

Co²⁺/Co⁺ Redox Tuning in Methyltransferases Induced by a Conformational Change at the Axial Ligand

Density functional theory and quantum mechanics/molecular mechanics computations predict cob­(I)­alamin (Co⁺Cbx), a universal B₁₂ intermediate state, to be a pentacoordinated square pyramidal complex, which is different from the most widely accepted viewpoint of its tetracoordinated square planar geometry. The square pyramidality of Co⁺Cbx is inspired by the fact that a Co⁺ ion, which has a dominant d⁸ electronic configuration, forms a distinctive Co⁺--H interaction because of the availability of appropriately oriented filled d orbitals. This uniquely H-bonded Co⁺Cbx may have catalytic relevance in the context of thermodynamically uphill Co²⁺/Co⁺ reduction that constitutes an essential component in a large variety of methyltransferases

Pd-Catalyzed Conversion of Alkynyl‑λ³‑iodanes to Alkenyl‑λ³‑iodanes via Stereoselective 1,2-Iodine(III) Shift/1,1-Hydrocarboxylation

Alkynyl-λ³-iodanes have been established as alkynyl cation equivalents for the alkynylation of carbon- and heteroatom-based nucleophiles. Herein, we report an unprecedented reaction mode of this compound class, which features a Pd­(II)-assisted 1,2-I­(III) shift of an alkynylbenziodoxole. A Pd­(II) catalyst mediates this shift and the subsequent interception of the transient vinylidene species with carboxylic acid (1,1-hydro­carboxylation). The product of this stereoselective rearrangement–addition reaction, β-oxyalkenyl­benziodoxole, represents a novel and useful building block for further synthetic transformations

Gold(I)/Gold(III)-Catalyzed Selective Synthesis of <i>N</i>‑Sulfonyl Enaminone Isomers from Sulfonamides and Ynones via Two Distinct Reaction Pathways

Au-catalyzed chemoselective methods for synthesizing <i>N</i>-sulfonyl enaminones are developed. Two different isomers are obtained in a chemocontrolled manner by employing the different properties of Au­(I) and Au­(III) catalysts. Hydroamidation and proton-assisted carbonyl activation followed by Meyer–Schuster rearrangement are proposed as the working mechanisms for the reactions. A wide range of substrates afforded moderate to excellent yields and selectivities. These reactions represent the first examples of transition-metal-catalyzed enamine synthesis from sulfonamides and alkynes