Diels-Alder reaction mechanisms of substituted chiral anthracene: A theoretical study based on the reaction force and reaction electronic flux

A comprehensive study of the influence of non-covalent interactions on electron density redistribution during the reaction between acetic acid and methylamine

CONTEXT

A chemical reaction can be described, from a physicochemical perspective, as a redistribution of electron density. Additionally, non-covalent interactions locally modify the electron density distribution. This study aims to characterize the modification of reactivity caused by the presence of non-covalent interactions such as hydrogen bonds, in a reaction involving the formation of two bonds and the breaking of two others: CH₃COOH + NH₂CH₃ → CH₃CONHCH₃.

METHODS

In this work, we will follow the how a reaction mechanism involving the formation of two chemical bonds and the breaking of two other chemical bonds is affected by non-covalent interaction. To this end, the reaction force will be used to define the region of the reagents, the region of the transition state, and the region of the products. We will analyze the redistributions of electron density and electron pairs in each of the regions of the reaction mechanisms, using QTAIM and ELF, topological analyses, respectively, for the reaction between methylamine and acetic acid, in the presence of 0 to 4 water molecules. DFT calculations were carried out at the LC-ωPBE/6-311 + + G(d,p) + GD3BJ level along the intrinsic reaction coordinate of the one-step reaction leading to the formation of methylacetamide.

How does dopamine convert into norepinephrine? Insights on the key step of the reaction

CONTEXT

Dopamine β -monooxygenase (D β M) is an essential enzyme in the organism that regioselectively converts dopamine into R-norepinephrine, the key step of the reaction, studied in this paper, is a hydrogen atom transfer (HAT) from dopamine to a superoxo complex on D β M, forming a hydroperoxo intermediate and dopamine radical. It was found that the formation of a hydrogen bond between dopamine and the D β M catalyst strengthens the substrate-enzyme interaction and facilitates the HAT which takes place selectively to give the desired enantiomeric form of the product. Six reactions leading to the hydroperoxo intermediate were analyzed in detail using theoretical and computational tools in order to identify the most probable reaction mechanism. The reaction force analysis has been used to demonstrate that the nature of the activation energy is mostly structural and largely due to the initial approach of species in order to get closer to each other to facilitate the hydrogen abstraction. On the other hand, the reaction electronic flux revealed that electronic activity driving the reactions is triggered by polarization effects and, in the most probable reaction among the six studied, it takes place in a concerted and non-spontaneous way. Chemical events driving the reaction have been identified and the energy absorbed or delivered by each one was quantified in detail.

METHODS

The dopamine and a computational model of the copper superoxo complex on D β M were optimized at B3LYP-D3(BJ)/6-311 G(d,p) level theory in the Gaussian 16 software package. Optimization and IRC calculations were performed in the gas phase and through the PCM solvation model to mimic the protein medium. Non-covalent interactions were plotted using the NCI-plot software.

Description of changes in chemical bonding along the pathways of chemical reactions by deformation of the molecular electrostatic potential

CONTEXT

The analysis of the changes in the electronic structure along intrinsic reaction coordinate (IRC) paths for model reactions: (i) ethylene + butadiene cycloaddition, (ii) prototype SN2 reaction Cl- + CH3Cl, (iii) HCN/CNH isomerization assisted by water, (iv) CO + HF → C(O)HF was performed, in terms of changes in the deformation density (Δr) and the deformation of MEP (ΔMEP). The main goal was to further examine the utility of the ΔMEP as a descriptor of chemical bonding, and to compare the pictures resulting from Δr and ΔMEP. Both approaches clearly show that the main changes in the electronic structure occur in the TS region. The ΔMEP picture is fully consistent with that based on Δρ for the reactions of the neutral species leading to the neutral products without large charge transfer between the fragments. In the case of reactions with large electron density displacements, the ΔMEP picture is dominated by charge transfer leading to more clear indication of charge shifts than the analysis of Δr.

METHODS

All the calculations were performed using the ADF package. The Becke-Perdew exchange-correlation functional was used with the Grimme's dispersion correction (D3 version) with Becke-Johnson damping. The Slater TZP basis sets defined within the ADF program were applied. For the analysed reactions, the stationary points were determined and verified by frequency calculations, and the IRC was determined. Further analysis was performed for the structures of reactants, TS, products, and the points corresponding to the minimum and maximum of the reaction force. For each point, two fragments, A and B, corresponding to the reactants were considered. The deformation density was calculated as the difference between the electron density of the system AB and the sum of densities of A and B, Δ ρ r = ρ AB r - ρ A r - ρ B r , with the same fragment definition as in the ETS-NOCV method. Correspondingly, deformation in MEP was determined as Δ V r = V AB r - V A r - V B r .

Basis Electronic Activity of Molecular Systems. A Theory of Bond Reactivity

In this paper, we present a new finding, the basis electronic activity (BEA) of molecular systems; it corresponds to the significant, although nonreactive, vibrationally induced electronic activity that takes place in any molecular system. Although the molecule's BEA is composed of an equal number of local contributions as the vibrational degrees of freedom, our results indicate that only stretching modes contribute to it. To account for this electronic activity, a new descriptor, the bond electronic flux (BEF), is introduced. The BEF combined with the force constant of the potential well hosting the electronic activity gives rise to the effective bond reactivity index (EBR), which turns out to be the first density functional theory-based descriptor that simultaneously accounts for structural and electronic effects. Besides quantifying the bond reactivity, EBR provides a basis to compare the reactivities of bonds inserted in different chemical environments and paves the way for the exertion of selective control to enhance or inhibit their reactivities. The new concepts formulated in this paper and the associated computational tools are illustrated with characterization of the BEA of a set of representative molecules. In all cases, the BEFs follow the same linear pattern, whose slopes indicate the intensity of the electronic activity and quantify the reactivity of chemical bonds.

Rationalizing the Substituent Effects in Diels-Alder Reactions of Triazolinediones with Anthracene

In this work we tackle the problem of the substituent effects in the Diels-Alder cycloadditions between triazolinediones (TADs) and anthracene. Experiments showed that aryl TADs substituted with electron-withdrawing groups (EWG) are more reactive than those substituted with electron-donating (EDG) or alkyl groups. However, the molecular origin of this preference is not yet understood. By a combination of methods including the activation strain model (ASM), energy decomposition analysis (EDA), molecular orbital (MO) theory, and conceptual density functional theory (CDFT), we disclosed the substituent effects of TADs. First, ASM/EDA analysis revealed that the reactivity of alkyl and aryl-substituted TADs is controlled by interaction energies, ΔE_int, which are ultimately defined by orbital interactions between frontier molecular orbitals. Moreover, alkyl-TADs are also controlled by the extent of strain at the transition state. The MO analysis suggested that the rate acceleration for EWG-substituted TADs is due to a more favorable orbital interaction between the HOMO of anthracene and the LUMO of the TADs, which is corroborated by calculations of charge transfer at the transition states. From CDFT, the chemical potential of anthracene is higher than those of TADs, indicating a flow of electron density from anthracene to TADs, in agreement with the results from the electrophilicity index.

How Does Electronic Activity Drive Chemical Reactions? Insights from the Reaction Electronic Flux for the Conversion of Dopamine into Norepinephrine

Hydrogen atom transfer (HAT) is a crucial step in the physiological conversion of dopamine into norepinephrine catalyzed by dopamine β-monooxygenase. The way the reaction takes place is unclear, and a rational explanation on how the electronic activity drives the HAT seems to be necessary. In this work, we answer this question using the reaction electronic flux (REF), a DFT-based descriptor of electronic activity. Two reaction mechanisms will be analyzed using the REF's decomposition in polarization and electron transfer effects. Results show that both mechanisms proceed as follows: (1) polarization effects initiate the reactions producing structural distortions; (2) electron transfer processes take over near the transition states, triggering specific chemical events such as bond forming and breaking which are responsible to push the reactions toward the products; (3) after passing the transition state, polarization shows up again and drives the relaxation process toward the product. Similar polarization effects were observed in both reactions, but they present an opposite behavior of the electronic transfer flux disclosing the fact that electron transfer phenomena govern the reaction mechanisms.

AMADAR: a python-based package for large scale prediction of Diels-Alder transition state geometries and IRC path analysis

Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication reports technical details and preliminary results of a python-based tool (AMADAR) designed to generate any Diels–Alder (DA) transition state geometry (TS) and analyze determined IRC paths in a (quasi-)automated fashion, given the product SMILES. Two modules of the package are devoted to performing, from IRC paths, reaction force analyses (RFA) and atomic (fragment) decompositions of the reaction force F and reaction force constant \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\kappa$$\end{document}κ. The performance of the protocol has been assessed using a dataset of 2000 DA cycloadducts retrieved from the ZINC database. The sequential location of the corresponding TSs was achieved with a success rate of 95%. RFA plots confirmed the reaction force constant \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\kappa$$\end{document}κ to be a good indicator of the (non)synchronicity of the associated DA reactions. Moreover, the atomic decomposition of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\kappa$$\end{document}κ allows for the rationalization of the (a)synchronicity of each DA reaction in terms of contributions stemming from pairs of interacting atoms. The source code of the AMADAR tool is available on GitHub [CMCDD/AMADAR(github.com)] and can be used directly with minor customizations, mostly regarding the local working environment of the user.

Investigation of water substitution at RuII complexes by conceptual density function theory approach

In this paper, we investigated water exchange reactions and substitution of aqua Ru^II complexes of general formula [Ru(terpy)(N^N)(H₂ O)]²⁺ (where N^N = ethylenediamine (en), 1,2-(aminomethyl)pyridine (ampy) and 2,2'-bipyridine (bipy)) by ammonia and thioformaldehyde. These reactions were studied in detail by applying conceptual density functional theory. This approach enabled us to gain further insight into the underlying reaction mechanism at the microscopic level (involving only direct participants of the reaction, without the influence of the solvent) and to put the concept of reaction mechanism on a quantitative basis. The course of the chemical reaction along the reaction coordinate ξ, is rationalized in terms of reaction energy, force, dipole moment, and reaction electronic flux (REF). The results yield and characterize the significant influence of an intermolecular hydrogen bond formed between the entering and the spectator ligand to the overall energy barrier of the reactions.