The Keto–Enol Tautomerism of Biliverdin in Bacteriophytochrome: Could it Explain the Bathochromic Shift in the Pfr Form?

Phytochromes are ubiquitous photoreceptors found in plants, eukaryotic algae, bacteria and fungi. Particularly, when bacteriophytochrome is irradiated with light, a Z‐to‐E (photo)isomerization takes place in the biliverdin chromophore as part of the Pr‐to‐Pfr conversion. This photoisomerization is concomitant with a bathochromic shift in the Q‐band. Based on experimental evidence, we studied a possible keto–enol tautomerization of BV, as an alternative reaction channel after its photoisomerization. In this contribution, the noncatalyzed and water‐assisted reaction pathways for the lactam–lactim interconversion through consecutive keto–enol tautomerization of a model BV species were studied deeply. It was found that in the absence of water molecules, the proton transfer reaction is unable to take place at normal conditions, due to large activation energies, and the endothermic formation of lactim derivatives prevents its occurrence. However, when a water molecule assists the process by catalyzing the proton transfer reaction, the activation free energy lowers considerably. The drastic lowering in the activation energy for the keto–enol tautomerism is due to the stabilization of the water moiety through hydrogen bonds along the reaction coordinate. The absorption spectra were computed for all tautomers. It was found that the UV–visible absorption bands are in reasonable agreement with the experimental data. Our results suggest that although the keto–enol equilibrium is likely favoring the lactam tautomer, the equilibrium could eventually be shifted in favor of the lactim, as it has been reported to occur in the dark reversion mechanism of bathy phytochromes

Description of the Reaction Intermediate Stabilization for the Zimmerman Di-π-methane Rearrangement on the Basis of a Parametric Diabatic Analysis

The mechanism of the Zimmerman di-π-methane rearrangement has been studied using a parametric diabatic analysis (PDA) on which the diagonal elements on the effective Hamiltonian defining the energies of the diabatic electronic states have been parametrized and modeled upon the use of the vertex form of a parabolic function. The PDA requires two inputs: the energy local minimum of an optimized structure along the intrinsic reaction coordinate and the maximum gradients associated with the barriers for the transition states. In the present work, the PDA was used to gain novel insights into the mechanism of the triplet di-π-methane rearrangement of substituted dibenzobarrelenes. Our results suggest that, when using an electron-withdrawing group as substituent, the activation energy for the rate-determining step is directly modulated by the stabilization of the biradical intermediate on the triplet surface. This mechanistic feature was thoroughly analyzed and discussed within the conceptual framework provided by the diabatic model of intermediate stabilization (DMIS)

Exploring the Nature of the Energy Barriers on the Mechanism of the Zirconocene-Catalyzed Ethylene Polymerization: A Quantitative Study from Reaction Force Analysis

Ethylene polymerization mediated by methyl-bis(cyclopentadienyl)-zirconium or zirconocene catalyst, [ZrCp₂CH₃]⁺, is one of the most popular catalytic reaction for polyethylene production. Rationalizing the major effects that control the polymer growth result in a challenge for computational studies. Through quantum chemical calculations, we characterized the zirconocene ethylene polymerization reaction mechanism: chain initiation (I; first ethylene insertion) [ZrCp₂CH₂CH₂CH₃]⁺, chain propagation (P; from second (P₁) to ninth (P₉) ethylene insertion) [ZrCp₂ (CH₂)₂₀CH₃]⁺, and chain termination processes (T; β-hydrogen elimination from P₅ or P₉) [ZrHCp₂ (H₂C═CH(CH₂)₁₈CH₃]⁺ are analyzed through the potential energy surface (PES) and reaction force analysis (RFA). The RFA approach involves pulling out the portion of an activation barrier that corresponds to distorting reactants into the geometries they adopt in a transition state structure until it reaches the structural relaxation toward the equilibrium geometry of the product. Because the interactions between the zirconocene and the ethylene molecule are influenced by a combination of several kinds of steric and electronic effects, it is indispensable to understanding these interactions in order to rationalize and predict in a quantitative manner the reaction barrier heights and the concomitant polymer growth. In the present work, we employ a simple procedure within the framework of the RFA and the density functional steric energy decomposition analysis (EDA) approach to quantitatively separate the different types of interactions; steric (ΔE_s), electrostatic (ΔE_e), and quantum (ΔE_q) effects in order to predict the impact of each factor on the course of the polymerization process as well as for the polymer control and design

Theoretical insights into the E1cB/E2 mechanistic dichotomy of elimination reactions

E1cB and E2 eliminations have been described as competing mechanisms that can even share a common pathway when the E1cB/E2 borderline mechanism operates. A suitable case study evincing such a mechanistic dichotomy corresponds to the elimination reaction of β-phenylmercaptoethyl phenolate, since its mechanism has been thought to be an E2 elimination. Nonetheless, according to the computational assessment of the substituents on the leaving group, we demonstrate that the reaction proceeds via a borderline E1cB mechanism. Stabilization of the carbanion was provided not only by substituent effects tuning the nucleofugality of the leaving group, but also by a base, since distortion/interaction–activation strain and Natural Bond Order (NBO) analyses suggest a stabilizing interaction between the base and C_β of the E1cB intermediate. In order to gain insights into these results in a more general context, we have rationalized them with a qualitative picture of the E1cB/E2 mechanistic dichotomy using simple relationships between diabatic parabolas modeling the potential wells of reactants, intermediates, and products. In this Diabatic Model of Intermediate Stabilization (DMIS), the borderline E1cB mechanism for the elimination reaction of β-phenylmercaptoethyl phenolate was discussed in terms of bonding and dynamic stepwise processes. The conceptual model presented herein should be useful for the analysis of any reaction comprising competing one- and two-step mechanisms

Meisenheimer complexes as hidden intermediates in the aza-S_NAr mechanism

In this work we report a computational study about the aza-S_NAr mechanism in fluorine- and chlorine-containing azines with the aim to unravel the physical factors that determine the reactivity patterns in these heterocycles towards propylamine. The nature of the reaction intermediate was analyzed in terms of its electronic structure based on a topological analysis framework in some non-stationary points along the reaction coordinate. The mechanistic dichotomy of a concerted or a stepwise pathway is interpreted in terms of the qualitative Diabatic Model of Intermediate Stabilization (DMIS) approach, providing a general mechanistic picture for the S_NAr process involving both activated benzenes and nitrogen-containing heterocycles. With the information collected, a unified vision of the Meisenheimer complexes as transition state, hidden intermediate or real intermediate was proposed

Meisenheimer complexes as hidden intermediates in the aza-S_NAr mechanism

In this work we report a computational study about the aza-S_NAr mechanism in fluorine- and chlorine-containing azines with the aim to unravel the physical factors that determine the reactivity patterns in these heterocycles towards propylamine. The nature of the reaction intermediate was analyzed in terms of its electronic structure based on a topological analysis framework in some non-stationary points along the reaction coordinate. The mechanistic dichotomy of a concerted or a stepwise pathway is interpreted in terms of the qualitative Diabatic Model of Intermediate Stabilization (DMIS) approach, providing a general mechanistic picture for the S_NAr process involving both activated benzenes and nitrogen-containing heterocycles. With the information collected, a unified vision of the Meisenheimer complexes as transition state, hidden intermediate or real intermediate was proposed

Toward a Neutral Single-Component Amidinate Iodide Aluminum Catalyst for the CO₂ Fixation into Cyclic Carbonates

A new iodide aluminum complex ({AlI(κ⁴-naphbam)}, 3) supported by a tetradentate amidinate ligand derived from a naphthalene-1,8-bisamidine precursor (naphbamH, 1) was obtained in quantitative yield via reaction of the corresponding methyl aluminum complex ({AlMe(κ⁴-naphbam)}, 2) with 1 equiv of I₂ in CH₂Cl₂ at room temperature. Complexes 2 and 3 were tested and found to be active as catalysts for the cyclic carbonate formation from epoxides at 80 °C and 1 bar of CO₂ pressure. A first series of experiments were carried out with 1.5 mol % of the alkyl complex 2 and 1.5 mol % of tetrabutylammonium iodide (TBAI) as a cocatalyst; subsequently, the reactions were carried out with 1.5 mol % of iodide complex 3 as a single-component catalyst. Compound 3 is one of the first examples of a nonzwitterionic halide single-component aluminum catalyst producing cyclic carbonates. The full catalytic cycle with characterization of all minima and transition states was characterized by quantum chemistry calculations (QCCs) using density functional theory. QCCs on the reaction mechanism support a reaction pathway based on the exchange of the iodine contained in the catalyst by 1 equiv of epoxide, with subsequent attack of I⁻ to the epoxide moiety producing the ring opening of the epoxide. QCCs triggered new insights for the design of more active halide catalysts in future explorations of the field