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Villegas-Escobar N. Insights into the variations of kinetic and potential energies in a multi-bond reaction: the reaction electronic flux perspective. J Mol Model 2024; 30:262. [PMID: 38990414 DOI: 10.1007/s00894-024-06024-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
CONTEXT The debate over whether kinetic energy (KE) or potential energy (PE) are the fundamental energy components that contribute to forming covalent bonds has been enduring and stimulating over time. However, the supremacy of these energy components in reactions where multiple bonds are simultaneously formed or broken has yet to be explored. In this study, we use the reaction electronic flux (REF), an effective tool for investigating changes in driving electronic activity when bond formation or dissociation occurs in a chemical reaction, to examine the fluctuations in the KE and PE in a multi-bond reaction. To that end, the activation of CO2 by low-valent group 14 catalysts through a concerted σ -bond metathesis mechanism is analyzed. The findings of this preliminary study suggest that the REF can be utilized as a tool to rationalize alterations in the KE and PE in a multi-bond reaction. Specifically, analyses across the reaction coordinate reveal that changes in the KE and PE precede activation in the REF, stimulating the electronic activity where bond formation or dissociation processes dominate. METHODS The activation of CO2 by the low-valent LEH catalysts (L = N,N'-bis(2,6-diisopropyl phenyl)- β -diketiminate; E = Si, Ge, Sn, and Pb) was studied along the reaction coordinate at the M06-2X/6-31 G(d,p)-LANL2DZ(E) level of theory. The respective minimum energy path calculations were obtained using the intrinsic reaction coordinate (IRC) procedure. The reaction electronic flux (REF) was calculated through the computation of the electronic chemical potential using the frontier molecular orbital approximation. Mayer bond orders along the reaction coordinate have been determined using the NBO 3.1 program in Gaussian16. Most of the reaction coordinate quantities reported in this study (REF, KE, PE, among others) have been determined using the Kudi program and custom Python scripts.
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Affiliation(s)
- Nery Villegas-Escobar
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, 4070139, Chile.
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2
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Barrales-Martínez C, Jaque P. A deeper analysis of the role of synchronicity on the Bell-Evans-Polanyi plot in multibond chemical reactions: a path-dependent reaction force constant. Phys Chem Chem Phys 2022; 24:14772-14779. [PMID: 35686531 DOI: 10.1039/d2cp01460b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the degree of synchronicity in the formation of the new single-bonds in a large set of 1,3-dipolar cycloadditions and its relation in the fulfilment of the classical Bell-Evans-Polanyi principle and Hammond-Leffler postulate are deeply investigated. Our results confirm that asynchronicity is an important path-dependent factor to be taken into account: (i) the Bell-Evans-Polanyi is fulfilled as the degree of (a)synchronicity is quite the same, and a linear relationship between reorganisation energy and asynchronicity is found; (ii) the asynchronicity is the origin of deviations of this classical principle of chemical reactivity since any decrease of the energy barrier is due to an increase of asynchronicity at the same exothermicity; and (iii) the less exothermic the reaction is, the more asynchronous the mechanism is, at the same energy barrier. Thus, this implies that TS imbalance decreases the reorganisation energy, consequently affecting the reaction exothermicity as well.
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Affiliation(s)
- César Barrales-Martínez
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile. .,Centro de Modelamiento Molecular, Biofísica y Bioinformática, CM2B2, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
| | - Pablo Jaque
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile. .,Centro de Modelamiento Molecular, Biofísica y Bioinformática, CM2B2, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
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New Insights into the (A)Synchronicity of Diels–Alder Reactions: A Theoretical Study Based on the Reaction Force Analysis and Atomic Resolution of Energy Derivatives. Molecules 2022; 27:molecules27051546. [PMID: 35268648 PMCID: PMC8911883 DOI: 10.3390/molecules27051546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/31/2022] [Accepted: 02/08/2022] [Indexed: 02/04/2023] Open
Abstract
In the present manuscript, we report new insights into the concept of (a)synchronicity in Diels–Alder (DA) reactions in the framework of the reaction force analysis in conjunction with natural population calculations and the atomic resolution of energy derivatives along the intrinsic reaction coordinate (IRC) path. Our findings suggest that the DA reaction transitions from a preferentially concerted mechanism to a stepwise one in a 0.10 Å window of synchronicity indices ranging from 0.90 to 1.00 Å. We have also shown that the relative position of the global minimum of the reaction force constant with respect to the TS is an alternative and quantifiable indicator of the (a)synchronicity in DA reactions. Moreover, the atomic resolution of energy derivatives reveals that the mechanism of the DA reaction involves two inner elementary processes associated with the formation of each of the two C-C bonds. This resolution goes on to indicate that, in asynchronous reactions, the driving and retarding components of the reaction force are mostly due to the fast and slow-forming C-C bonds (elementary processes) respectively, while in synchronous reactions, both elementary processes retard and drive the process concomitantly and equivalently.
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. The Phosphorus Bond, or the Phosphorus-Centered Pnictogen Bond: The Covalently Bound Phosphorus Atom in Molecular Entities and Crystals as a Pnictogen Bond Donor. Molecules 2022; 27:molecules27051487. [PMID: 35268588 PMCID: PMC8911988 DOI: 10.3390/molecules27051487] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a nucleophile in another, or the same, molecular entity. It is the second member of the family of pnictogen bonds, formed by the second member of the pnictogen family of the periodic table. In this overview, we provide the reader with a snapshot of the nature, and possible occurrences, of phosphorus-centered pnictogen bonding in illustrative chemical crystal systems drawn from the ICSD (Inorganic Crystal Structure Database) and CSD (Cambridge Structural Database) databases, some of which date back to the latter part of the last century. The illustrative systems discussed are expected to assist as a guide to researchers in rationalizing phosphorus-centered pnictogen bonding in the rational design of molecular complexes, crystals, and materials and their subsequent characterization.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence:
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
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Barrales-Martínez C, Gutiérrez-Oliva S, Toro-Labbé A, Pendás ÁM. Interacting Quantum Atoms Analysis of the Reaction Force: A Tool to Analyze Driving and Retarding Forces in Chemical Reactions. Chemphyschem 2021; 22:1976-1988. [PMID: 34293240 DOI: 10.1002/cphc.202100428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Indexed: 12/22/2022]
Abstract
The analysis of the reaction force and its topology has provided a wide range of fruitful concepts in the theory of chemical reactivity over the years, allowing to identify chemically relevant regions along a reaction profile. The reaction force (RF), a projection of the Hellmann-Feynman forces acting on the nuclei of a molecular system onto a suitable reaction coordinate, is partitioned using the interacting quantum atoms approach (IQA). The exact IQA molecular energy decomposition is now shown to open a unique window to identify and quantify the chemical entities that drive or retard a chemical reaction. The RF/IQA coupling offers an extraordinarily detailed view of the type and number of elementary processes that take reactants into products, as tested on two sets of simple reactions.
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Affiliation(s)
- César Barrales-Martínez
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Departamento de Química-Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Departamento de Química-Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain
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Hernández Mancera JP, Núñez-Zarur F, Gutiérrez-Oliva S, Toro-Labbé A, Vivas-Reyes R. Diels-Alder reaction mechanisms of substituted chiral anthracene: A theoretical study based on the reaction force and reaction electronic flux. J Comput Chem 2020; 41:2022-2032. [PMID: 32585758 DOI: 10.1002/jcc.26360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/02/2020] [Indexed: 11/08/2022]
Abstract
Quantum chemical calculations were used to study the mechanism of Diels-Alder reactions involving chiral anthracenes as dienes and a series of dienophiles. The reaction force analysis was employed to obtain a detailed scrutiny of the reaction mechanisms, it has been found that thermodynamics and kinetics of the reactions are quite consistent: the lower the activation energy, the lower the reaction energy, thus following the Bell-Evans-Polanyi principle. It has been found that activation energies are mostly due to structural rearrangements that in most cases represented more than 70% of the activation energy. Electronic activity mostly due to changes in σ and π bonding were revealed by the reaction electronic flux (REF), this property helps identify whether changes on σ or π bonding drive the reaction. Additionally, new global indexes describing the behavior of the electronic activity were introduced and then used to classify the reactions in terms of the spontaneity of their electronic activity. Local natural bond order electronic population analysis was used to check consistency with global REF through the characterization of specific changes in the electronic density that might be responsible for the activity already detected by the REF. Results show that reactions involving acetoxy lactones are driven by spontaneous electronic activity coming from bond forming/strengthening processes; in the case of maleic anhydrides and maleimides it appears that both spontaneous and non-spontaneous electronic activity are quite active in driving the reactions.
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Affiliation(s)
| | | | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ricardo Vivas-Reyes
- Grupo de Química Cuántica y Teórica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.,Grupo CipTec, Fundación Universitaria Tecnológico de Comfenalco, Facultad de Ingenierías, Programa de Ingeniería Industrial, Cartagena de Indias, Bolivar, Colombia
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Yepes D, Munarriz J, Daniel l'Anson, Contreras-Garcia J, Jaque P. Real-Space Approach to the Reaction Force: Understanding the Origin of Synchronicity/Nonsynchronicity in Multibond Chemical Reactions. J Phys Chem A 2020; 124:1959-1972. [PMID: 32058718 DOI: 10.1021/acs.jpca.9b10508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this article, we present a complementary analysis based on the reaction force F(ξ)/reaction force constant κ(ξ) and noncovalent interactions (NCI) index to characterize the energetics (kinetic and thermodynamics) and mechanistic pathways of two sets of multibond chemical reactions, namely, two double-proton transfer and two Diels-Alder cycloaddition reactions. This approach offers a very straightforward and useful way to delve into a deeper understanding of this type of process. While F(ξ) allows the partition of the whole pathway into three regions or phases, κ(ξ) describes how orchestrated are the bond-breaking and bond-formation events. In turn, NCI indicates how the inter- and intramolecular bonds evolve. The most innovative aspect is the inclusion of the formation of the reactant complex along the pathway, which, by means of NCI, unveils the early molecular recognition and the comprehension of its role in determining the degree of the synchronicity/nonsynchronicity of one-step processes. This approach should be a useful and alternative tool to characterize the energetics and the mechanism of general chemical reactions.
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Affiliation(s)
- Diana Yepes
- Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 275, Santiago, Chile
| | - Julen Munarriz
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, CC 137-4, place Jussieu, F-75252 Paris Cedex 05, France
| | - Daniel l'Anson
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, CC 137-4, place Jussieu, F-75252 Paris Cedex 05, France
| | - Julia Contreras-Garcia
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, CC 137-4, place Jussieu, F-75252 Paris Cedex 05, France
| | - Pablo Jaque
- Departamento de Quı́mica Orgánica y Fisicoquı́mica, Facultad de Ciencias Quı́micas y Farmacéuticas, Universidad de Chile, Olivos, 1007 Santiago, Chile
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Durán R, Herrera B. Theoretical Study of the Mechanism of Catalytic Enanteoselective N-H and O-H Insertion Reactions. J Phys Chem A 2020; 124:2-11. [PMID: 31809051 DOI: 10.1021/acs.jpca.9b07274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Theoretical density functional theory (DFT) calculations were carried out to study bond insertion reactions using a copper(I)-Box-carbenoid as a bond activator. In order to understand the reaction mechanism where N-H and O-H bonds actively participate, the reaction force (RF) and activation strain model (ASM) were used. Results indicate that the first step of the reaction is barrierless for both bond insertions (N-H and O-H), and the second step of the insertion reaction in the phenol (O-H bond) is favored kinetically and thermodynamically with regard to the aniline substrate (N-H bond). The enantioselectivity is driven by the ligand of the catalyst by steric repulsion, favoring the formation of the R isomer. The analysis of the reaction force and ASM exhibited that the higher energy barrier in aniline is mainly due to a higher W2 contribution together with repulsive interactions, which hinders the insertion process.
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Affiliation(s)
- Rocío Durán
- Laboratorio de Química Teórica Computacional (QTC), Departamento de Química-Física, Facultad de Química y de Farmacia , Pontificia Universidad Católica de Chile , Av. Vicuña Mackenna, 4860 Macul, Santiago , Chile
| | - Barbara Herrera
- Laboratorio de Química Teórica Computacional (QTC), Departamento de Química-Física, Facultad de Química y de Farmacia , Pontificia Universidad Católica de Chile , Av. Vicuña Mackenna, 4860 Macul, Santiago , Chile
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9
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Paredes-Gil K, Mendizábal F, Jaque P. Further understanding of the Ru-centered [2+2] cycloreversion/cycloaddition involved into the interconversion of ruthenacyclobutane using the Grubbs catalysts from a reaction force analysis. J Mol Model 2019; 25:305. [PMID: 31494753 DOI: 10.1007/s00894-019-4150-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/08/2019] [Indexed: 11/28/2022]
Abstract
The chemical reactivity of the first- and second-generation Grubbs catalysts has always been a significant issue in olefin metathesis. In the present work, we study the [2+2] cycloreversion/cycloaddition and the alkylidene rotation involved into the interconversion of the ruthenacyclobutane intermediate, through the reaction force and reaction force constant analysis. It has been found that the structural contribution controls the barrier energy in the interconversion of ruthenacyclobutane via [2+2] cycloreversion/cycloaddition, which is slightly lower in the second generation of Grubbs catalysts while its electronic contribution is slightly higher, which unveils a major rigidity and donor/acceptor properties of the NHC. This finding explains a greater structural contribution in the rate constant. Moreover, on the basis of the reaction force constant, the process can be classified as "two-stage"-concerted reactions, noting a more asynchronous process when the first generation is used as a catalyst.Finally, a similar analysis into the alkylidene rotation was performed. It was determined that [2+2] cycloreversion and alkylidene rotations take place in a sequential manner, the energy barrier is again controlled by structural reorganization, and the pathway is less asynchronous.
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Affiliation(s)
- Katherine Paredes-Gil
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O. Box 8940577, San Joaquín, Santiago, Chile.
| | - Fernando Mendizábal
- Facultad de Ciencias, Departamento de Química, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Pablo Jaque
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Santiago, Chile
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Zhang X. Mechanistic study on the intramolecular oxa-[4 + 2] cycloaddition of substituted o-divinylbenzenes. J Mol Model 2019; 25:14. [PMID: 30607638 DOI: 10.1007/s00894-018-3883-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/28/2018] [Indexed: 12/13/2022]
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Yepes D, Valenzuela J, Martínez-Araya JI, Pérez P, Jaque P. Effect of the exchange–correlation functional on the synchronicity/nonsynchronicity in bond formation in Diels–Alder reactions: a reaction force constant analysis. Phys Chem Chem Phys 2019; 21:7412-7428. [DOI: 10.1039/c8cp02284d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The performance of 24 KS-DFT-based methods (GGA, MGGA, HGGA, HMGGA, and DHGGA) was assessed, finding that M11 and M06-2X (HMGGA) predicting reliable TS geometries, energetics, and (a)synchronicities in Diels–Alder reactions.
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Affiliation(s)
- Diana Yepes
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Joel Valenzuela
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Jorge I. Martínez-Araya
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Patricia Pérez
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Pablo Jaque
- Departamento de Química Orgánica y Fisicoquímica
- Facultad de Ciencias Químicas y Farmacéuticas
- Universidad de Chile
- Santiago
- Chile
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Ortega DE, Cortés-Arriagada D, Toro-Labbé A. Mechanistic details of ethylene polymerization reaction using methallyl nickel(ii) catalysts. Phys Chem Chem Phys 2018; 20:22915-22925. [DOI: 10.1039/c8cp03955k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a mechanistic study of the ligand functionalization of bulky boron co-activators on neutral methallyl Ni(ii) catalysts for polyethylene production. This provides a blueprint for the development and design of catalysts with a high degree of tunability in a more efficient way.
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Affiliation(s)
- Daniela E. Ortega
- Laboratorio de Química Teórica Computacional (QTC), Pontificia Universidad Católica de Chile
- Santiago 9900087
- Chile
| | - Diego Cortés-Arriagada
- Programa Institucional de Fomento a la Investigación
- Desarrollo e Innovación
- Universidad Tecnológica Metropolitana
- Santiago
- Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Pontificia Universidad Católica de Chile
- Santiago 9900087
- Chile
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13
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Yepes D, Martínez-Araya JI, Jaque P. Solvent effect on the degree of (a)synchronicity in polar Diels-Alder reactions from the perspective of the reaction force constant analysis. J Mol Model 2017; 24:33. [PMID: 29288466 DOI: 10.1007/s00894-017-3563-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/03/2017] [Indexed: 11/30/2022]
Abstract
In this work, we computationally evaluated the influence of six different molecular solvents, described as a polarizable continuum model at the M06-2X/6-31+G(d,p) level, on the activation barrier/reaction rate, overall energy change, TS geometry, and degree of (a)synchronicity of two concerted Diels-Alder cycloadditions of acrolein (R1) and its complex with Lewis acid acrolein···BH3 (R2) to cyclopentadiene. In gas-phase, we found that both exothermicity and activation barrier are only reduced by about 2.0 kcal mol-1, and the asynchronicity character of the mechanism is accentuated when BH3 is included. An increment in the solvent's polarity lowers the activation energy of R1 by 1.3 kcal mol-1, while for R2 the reaction rate is enhanced by more than 2000 times at room temperature (i.e., the activation energy decreases by 4.5 kcal mol-1) if the highest polar media is employed. Therefore, a synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together. This effect was ascribed to the ability of the solvent to favor the encounter between cyclopentadiene and acrolein···BH3. This was validated by the asymmetry of the TS which becomes highly pronounced when either both or just BH3 is considered or the solvent's polarity is increased. Finally, the reaction force constant κ(ξ) reveals that an increment in the solvent's polarity is able to turn a moderate asynchronous mechanism of the formation of the new C-C σ-bonds into a highly asynchronous one. Graphical abstract A synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together: lowered energy barriers and increased asynchronicities.
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Affiliation(s)
- Diana Yepes
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 498, Santiago, Chile
| | - Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 498, Santiago, Chile
| | - Pablo Jaque
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 498, Santiago, Chile.
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14
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Talaga P, Brela MZ, Michalak A. ETS-NOCV decomposition of the reaction force for double-proton transfer in formamide-derived systems. J Mol Model 2017; 24:27. [PMID: 29273840 PMCID: PMC5741796 DOI: 10.1007/s00894-017-3564-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/04/2017] [Indexed: 11/17/2022]
Abstract
The analysis of the electronic-structure changes along IRC paths for double-proton-transfer reactions in the formamide dimer (R1), formamide–thioformamide system (R2), and the thioformamide dimer (R3) was performed based on the extended-transition-state natural orbitals for chemical valence (ETS-NOCV) partitioning of the reaction force, considering the intra-fragments strain and the inter-fragments interaction terms, and further—the electrostatic, Pauli-repulsion and orbital interaction components, with the latter being decomposed into the NOCV components. Two methods of the system partitioning into the fragments were considered (‘reactant perspective’/bond-formation, ‘product perspective’ / bond-breaking). In agreement with previous studies, the results indicate that the major changes in the electronic structure occur in the transition state region; the bond-breaking processes are, however, initiated already in the reactant region, prior to entering the TS region. The electrostatic contributions were identified as the main factor responsible for the increase in the activation barrier in the order R1 < R2 < R3.
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Affiliation(s)
- Piotr Talaga
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Mateusz Z Brela
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Artur Michalak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
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Šebesta F, Brela MZ, Diaz S, Miranda S, Murray JS, Gutiérrez-Oliva S, Toro-Labbé A, Michalak A, Burda JV. The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study. J Comput Chem 2017; 38:2680-2692. [PMID: 28925001 DOI: 10.1002/jcc.24911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/09/2017] [Accepted: 07/18/2017] [Indexed: 11/11/2022]
Abstract
This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg2+ , Zn2+ , and Hg2+ . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine. To proceed to the second stage, a structural change is needed to allow the negatively charged hydroxo ligand to abstract the N3 proton, which represents the final product of the PT reaction. In the presence of the selected hexaaqua cations, the activation barrier is at most 8 kcal/mol. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
| | - Mateusz Z Brela
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Silvia Diaz
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Sebastian Miranda
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, 70148
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - Artur Michalak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague, 112 16, Czech Republic
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16
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Villegas-Escobar N, Larsen née Vilhelmsen MH, Gutiérrez-Oliva S, Hashmi ASK, Toro-Labbé A. Double Gold Activation of 1-Ethynyl-2-(Phenylethynyl)Benzene Toward 5-exo
-dig and 6-endo
-dig Cyclization Reactions. Chemistry 2017; 23:13360-13368. [DOI: 10.1002/chem.201701595] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Nery Villegas-Escobar
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química; Pontificia Universidad Católica de Chile; Santiago Chile
| | | | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química; Pontificia Universidad Católica de Chile; Santiago Chile
| | - A. Stephen K. Hashmi
- Institute of Organic Chemistry; Heidelberg University; Heidelberg Germany
- Chemistry Department, Faculty of Science; King Abdulaziz University; Jeddah 21589 Saudi Arabia
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química; Pontificia Universidad Católica de Chile; Santiago Chile
- Freiburg Institute for Advanced Studies (FRIAS); Albert-Ludwigs-Universität Freiburg; Freiburg Germany
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17
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Díaz S, Brela MZ, Gutiérrez-Oliva S, Toro-Labbé A, Michalak A. ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water. J Comput Chem 2017; 38:2076-2087. [DOI: 10.1002/jcc.24856] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 05/15/2017] [Indexed: 01/07/2023]
Affiliation(s)
- Silvia Díaz
- Department of Theoretical Chemistry; Faculty of Chemistry, Jagiellonian University; Ingardena 3 Krakow 30-060 Poland
- Laboratorio de Química Teórica Computacional (QTC); Facultad de Química, Pontificia Universidad Católica de Chile; Avenida Vicuña Mackenna 4860 Macul Santiago Chile
| | - Mateusz Z. Brela
- Department of Theoretical Chemistry; Faculty of Chemistry, Jagiellonian University; Ingardena 3 Krakow 30-060 Poland
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC); Facultad de Química, Pontificia Universidad Católica de Chile; Avenida Vicuña Mackenna 4860 Macul Santiago Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC); Facultad de Química, Pontificia Universidad Católica de Chile; Avenida Vicuña Mackenna 4860 Macul Santiago Chile
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs Universität Freiburg; Albertstr. 19 Freiburg 79104 Germany
| | - Artur Michalak
- Department of Theoretical Chemistry; Faculty of Chemistry, Jagiellonian University; Ingardena 3 Krakow 30-060 Poland
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18
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Varadwaj A, Varadwaj PR, Jin BY. Can an entirely negative fluorine in a molecule, viz. perfluorobenzene, interact attractively with the entirely negative site(s) on another molecule(s)? Like liking like! RSC Adv 2016. [DOI: 10.1039/c5ra27039a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study presents the possibility for the formation of attractive intermolecular interactions between various entirely negative Lewis bases, leading to the formation of the thirteen isolated binary complexes examined.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan 10617
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering
- School of Engineering
- The University of Tokyo
- Japan 113-8656
| | - Bih-Yaw Jin
- Department of Chemistry
- National Taiwan University
- Taipei
- Taiwan 10617
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20
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Murray JS, Yepes D, Jaque P, Politzer P. Insights into some Diels–Alder cycloadditions via the electrostatic potential and the reaction force constant. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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