Identifying reactive normal modes and their effect on regioselectivity in Myers-Saito and Schmittel cyclization of enyne-allenes: a combined perspective between the reaction force constant and statistical tools.

This paper presents a theoretical study on the distinguishable regiodivergent C-C Myers-Saito and C-C Schmittel routes of benzannelated enyne-allene cycloaromatizations, in which substitutions on the terminal alkyne by alkyl (-CH, -CHCH, -CH(CH) and -C(CH)) and aryl (-CH and -CH(CH)) groups were included. Mechanistic differences were found between substituents attached to alkynes with and without α-H, whereas in the former the Schmittel cyclization proceeds together with 1,8-H migration, in the latter it does so as the sole primitive event. It was also observed that bulky substituents preferentially favor the C-C Schmittel route, and the statistical prediction of regioselectivity is greatly affected when the ratio of accessible vibrational microstates of the transition states is included, especially in highly competing routes, , ΔΔ → 0.

Characterization of the interaction between the Sec61 translocon complex and ppαF using optical tweezers.

The Sec61 translocon allows the translocation of secretory preproteins from the cytosol to the endoplasmic reticulum lumen during polypeptide biosynthesis. These proteins possess an N-terminal signal peptide (SP) which docks at the translocon. SP mutations can abolish translocation and cause diseases, suggesting an essential role for this SP/Sec61 interaction.

Hidden intermediate activation: a concept to elucidate the reaction mechanism of the Schmittel cyclization of enyne-allenes.

The mechanistic paradigm in which the Schmittel cyclization transitions from one-step to stepwise has been investigated through the stabilization of a full hidden intermediate in the framework of the Diabatic Model of Intermediate Stabilization. Hidden intermediate activation was studied employing quasi-classical trajectories and the Electron Localization Function. The stabilization of hidden intermediates achieved by substituting enyne-allenes with cyano and nitro groups generates the appearance of a partially hidden and an explicit intermediate, leading to one-step asynchronous biradical and stepwise biradical/zwitterionic mechanisms, respectively.

Trapping an unusual pentacoordinate carbon atom in a neutral trialuminum complex.

A neutral trialuminum complex incorporates a pentacoordinate carbon through a methylidene bridge linking the three metal atoms. The rigid electron-deficient Al core stabilizes the hypercoordinate carbon atom resulting in the shortest equatorial Al-C distance reported for such an Al-(μ-CH) unit.

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

A new iodide aluminum complex ({AlI(κ-naphbam)}, ) supported by a tetradentate amidinate ligand derived from a naphthalene-1,8-bisamidine precursor (naphbamH, ) was obtained in quantitative yield via reaction of the corresponding methyl aluminum complex ({AlMe(κ-naphbam)}, ) with 1 equiv of I in CHCl at room temperature. Complexes and were tested and found to be active as catalysts for the cyclic carbonate formation from epoxides at 80 °C and 1 bar of CO pressure. A first series of experiments were carried out with 1.

The Interaction of TRAF6 With Neuroplastin Promotes Spinogenesis During Early Neuronal Development.

Correct brain wiring depends on reliable synapse formation. Nevertheless, signaling codes promoting synaptogenesis are not fully understood. Here, we report a spinogenic mechanism that operates during neuronal development and is based on the interaction of tumor necrosis factor receptor-associated factor 6 (TRAF6) with the synaptic cell adhesion molecule neuroplastin.

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.

Meisenheimer complexes as hidden intermediates in the aza-SAr mechanism.

In this work we report a computational study about the aza-SNAr 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 SNAr process involving both activated benzenes and nitrogen-containing heterocycles.

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.

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.

Reaction Electronic Flux Perspective on the Mechanism of the Zimmerman Di-π-methane Rearrangement.

The reaction electronic flux (REF) offers a powerful tool in the analysis of reaction mechanisms. Noteworthy, the relationship between aromaticity and REF can eventually reveal subtle electronic events associated with reactivity in aromatic systems. In this work, this relationship was studied for the triplet Zimmerman di-π-methane rearrangement.

Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β.

Elucidating the catalytic mechanism of DNA polymerase is crucial for a progress in the understanding of the control of replication fidelity. This work tries to advance the mechanistic understanding by analyzing the observed effect of mutations of the acidic groups in the active site of Polymerase β as well as the pH effect on the rate constant. The analysis involves both empirical valence bond (EVB) free energy calculations and considerations of the observed pH dependence of the reaction.

Path Integral Simulation of the H/D Kinetic Isotope Effect in Monoamine Oxidase B Catalyzed Decomposition of Dopamine.

Brain monoamines regulate many centrally mediated body functions, and can cause adverse symptoms when they are out of balance. A starting point to address challenges raised by the increasing burden of brain diseases is to understand, at atomistic level, the catalytic mechanism of an essential amine metabolic enzyme-monoamine oxidase B (MAO B). Recently, we demonstrated that the rate-limiting step of MAO B catalyzed conversion of amines into imines represents the hydride anion transfer from the substrate α-CH2 group to the N5 atom of the flavin cofactor moiety.

Understanding the comparative molecular field analysis (CoMFA) in terms of molecular quantum similarity and DFT-based reactivity descriptors.

The three-dimensional quantitative structure-activity relationship (3D QSAR) models have many applications, although the inherent complexity to understand the results coming from 3D-QSAR arises the necessity of new insights in the interpretation of them. Hence, the quantum similarity field as well as reactivity descriptors based on the density functional theory were used in this work as a consistent approach to better understand the 3D-QSAR studies in drug design. For this purpose, the quantification of steric and electrostatic effects on a series of bicycle [4.

Theory of substituent effects on the regioselectivity of di-π-methane rearrangements of dibenzobarrelenes.

The regioselectivities of the di-π-methane rearrangements of unsymmetrically substituted dibenzobarrelenes have been explored with DFT (UM06-2X). Regioselectivity depends on the intramolecular hydrogen bonding and originates from specific stabilization of the triplet biradical intermediates.

Competition between concerted and stepwise dynamics in the triplet di-π-methane rearrangement.

The molecular dynamics of the triplet-state Zimmerman di-π-methane rearrangement of dibenzobarrelene were computed with B3LYP and M06-2X density functionals. All productive quasiclassical trajectories involve sequential formation and cleavage of C-C bonds and an intermediate with lifetimes ranging from 13 to 1160 fs. Both dynamically concerted and stepwise trajectories are found.

The triplet surface of the Zimmerman di-π-methane rearrangement of dibenzobarrelene.

High-level calculations: the Zimmerman di-π-methane rearrangement of dibenzobarrelene occurs via a triplet state to form dibenzosemibullvalene, overcoming two barriers connecting two biradicals. The shape of the triplet potential-energy surface shows that the rearrangement involves two transition states. The first triplet diradical intermediate may bypass in the passive of the alkene triplet to the final intermediate.

The chromophore structure of the cyanobacterial phytochrome Cph1 as predicted by time-dependent density functional theory.

The UV-vis absorption spectra of the photoreceptor chromophores biliverdin (BV) in the ZZZssa conformation and the phycocyanobilin (PCB) with conformations ZZZssa and ZZZasa have been investigated by means of time-dependent density functional theory (TD-DFT) with a polarized continuum model. The three systems are studied in different conditions to include protonation, solvation- and protein-environmental effects on gas phase and available X-ray structures. The crystal structures of BV in bacteriophytochrome of Deinococcus radiodurans and PCB in C-Phycocyanin serve to calibrate the performance of the TD-DFT method and allow estimating the spectral shifts created when gas phase structures instead of a proper environment are used.