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Benítez FJ, Gutiérrez-Oliva S, Herrera B, Toro-Labbé A. Basis Electronic Activity of Molecular Systems. A Theory of Bond Reactivity. J Phys Chem A 2024. [PMID: 38437616 DOI: 10.1021/acs.jpca.4c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
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.
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Affiliation(s)
- Francisca J Benítez
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Bárbara Herrera
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
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Hernández-Mancera JP, Rojas-Valencia N, Núñez-Zarur F. Rationalizing the Substituent Effects in Diels-Alder Reactions of Triazolinediones with Anthracene. J Phys Chem A 2022; 126:6657-6667. [PMID: 36122186 DOI: 10.1021/acs.jpca.2c04970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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, ΔEint, 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.
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Affiliation(s)
| | - Natalia Rojas-Valencia
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 no. 30-65, 050026 Medellín, Colombia
| | - Francisco Núñez-Zarur
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 no. 30-65, 050026 Medellín, Colombia
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Forero-Girón AC, Toro-Labbé A. How Does Electronic Activity Drive Chemical Reactions? Insights from the Reaction Electronic Flux for the Conversion of Dopamine into Norepinephrine. J Phys Chem A 2022; 126:4156-4163. [PMID: 35748576 DOI: 10.1021/acs.jpca.2c01469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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.
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Affiliation(s)
- Angie Carolay Forero-Girón
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago de Chile, 7820436, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago de Chile, 7820436, Chile
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Isamura BK, Lobb KA. AMADAR: a python-based package for large scale prediction of Diels-Alder transition state geometries and IRC path analysis. J Cheminform 2022; 14:39. [PMID: 35706060 PMCID: PMC9202188 DOI: 10.1186/s13321-022-00618-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/25/2022] [Indexed: 12/28/2022] Open
Abstract
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}
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\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}
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\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}
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\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.
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Affiliation(s)
- Bienfait K Isamura
- Department of Chemistry, Rhodes University, Makhanda, 6140, South Africa
| | - Kevin A Lobb
- Department of Chemistry, Rhodes University, Makhanda, 6140, South Africa. .,Research Unit in BioInformatics (RUBi), Rhodes University, Makhanda, 6140, South Africa.
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Rehman U, Mansha A, Zahid M, Asim S, Zahoor AF, Rehan ZA. Quantum mechanical modeling unveils the effect of substitutions on the activation barriers of the Diels–Alder reactions of an antiviral compound 7H-benzo[a]phenalene. Struct Chem 2022. [DOI: 10.1007/s11224-022-01948-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ćoćić D, Petrović B, Puchta R, Chrzanowska M, Katafias A, van Eldik R. Investigation of water substitution at Ru II complexes by conceptual density function theory approach. J Comput Chem 2022; 43:1161-1175. [PMID: 35484985 DOI: 10.1002/jcc.26878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/08/2022]
Abstract
In this paper, we investigated water exchange reactions and substitution of aqua RuII 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.
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Affiliation(s)
- Dušan Ćoćić
- Department of Chemistry, Faculty of Science, University of Kragujevac, Kragujevac
| | - Biljana Petrović
- Department of Chemistry, Faculty of Science, University of Kragujevac, Kragujevac
| | - Ralph Puchta
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany.,Central Institute for Scientific Computing (CISC), University of Erlangen-Nuremberg, Erlangen, Germany.,Computer Chemistry Center, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Marta Chrzanowska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń
| | - Anna Katafias
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń
| | - Rudi van Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany.,Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń
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Rojas-Valencia N, Núñez-Zarur F. The origin of the high reactivity of triazolinediones (TADs) in Diels-Alder reactions from a theoretical perspective. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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