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

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

An alternative evolutionary strategy to optimize photoreaction quantum yields

Photoisomerization of a protein bound chromophore is the basis of light sensing of many photoreceptors. We tracked Z-to-E photoisomerization of Cph1 phytochrome chromophore PCB in the Pr form in real-time. Two different phycocyanobilin (PCB) ground state geometries with different ring D orientations have been identified. The pre-twisted and hydrogen bonded PCBa geometry exhibits a time constant of 30 ps and a quantum yield of photoproduct formation of 29%, about six times slower and ten times higher than that for the non-hydrogen bonded PCBb geometry. This new mechanism of pre-twisting the chromophore by protein-cofactor interaction optimizes yields of slow photoreactions and provides a scaffold for photoreceptor engineering

Evaluación del carbón activado obtenido a partir de la vaina de malinche para absorción de fenol del agua residual de Laboratorio CIDEA-UCA.

La investigación a borda sobre la capacidad de adsorción del carbón activado, para remover o adsorber fenol en aguas residuales de Laboratorio Instituto de Capacitación e Investigación y Desarrollo Ambiental de la Universidad Centroamericana, obtenido a partir de la vaina de malinche. Este estudio abarca la preparación del carbón consiste en recolección, selección, lavado, reducción de tamaño y molienda de la vaina de malinche hasta una granulometría de 106 micrómetros (um), la cual es impregnada con NaOH, como agente activante, con una relación de impregnación optima de 1:1.5 durante 10 minutos siendo acompañada de una agitación constante, posteriormente se pirolizo a 350 C en una mufla durante 30 minutos

Fortalecimiento de los criterios de semejanzas de triángulos mediante la integración de las TIC para mejorar el componente geométrico

El siguiente trabajo pretende fortalecer los criterios de semejanza de triángulo mediante la integración de las TIC. Se desarrolla a través del diseño e implementación de una secuencia didáctica compuesta por siete sesiones, las cuales contiene actividades variadas con material concreto, construcciones con instrumentos geométricos y desarrollo de guías con el software Geogebra, además de la utilización de la plataforma Edmodo. Esta secuencia se desarrolló con los estudiantes del grado noveno de la Institución Educativa Cultural las Malvinas de Barranquilla, evidenciándose que con la implementación de esta estrategia pedagógica se obtiene mejores resultados que utilizando los métodos tradicionales, tanto en el manejo de los conceptos como en el ámbito actitudinal y motivacional de los estudiantes. Para la investigación se tuvo en cuenta un enfoque Investigación –acción – educativa el cual propende hacia la búsqueda del mejoramiento de la práctica docente vista como un proceso de desarrollo continua a través de la reflexión que hace el docente de su quehacer diario