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Kjeldal FØ, Eriksen JJ. Properties of Local Electronic Structures. J Chem Theory Comput 2023; 19:9228-9238. [PMID: 38051663 DOI: 10.1021/acs.jctc.3c00963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The simulation of intrinsic contributions to molecular properties holds the potential to allow for chemistry to be directly inferred from changes to electronic structures at the atomic level. In the present study, we demonstrate how such local properties can be readily derived from suitable molecular orbitals to yield effective fingerprints of various types of atoms in organic molecules. In contrast, corresponding inferences from schemes that instead make use of individual atomic orbitals for this purpose are generally found to fail in expressing much uniqueness in atomic environments. By further studying the extent to which entire chemical reactions may be decomposed into meaningful and continuously evolving atomic contributions, schemes based on molecular rather than atomic orbitals are once again found to be the more consistent, even allowing for intricate differences between seemingly uniform nucleophilic substitutions to be probed.
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Affiliation(s)
- Frederik Ø Kjeldal
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, 2800 Kgs. Lyngby, Denmark
| | - Janus J Eriksen
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, 2800 Kgs. Lyngby, Denmark
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2
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Kossaka Macedo G, Haiduke RLA. The performance of exchange-correlation functionals in describing electron density parameters of saddle point structures along chemical reactions. J Comput Chem 2022; 43:1830-1838. [PMID: 36053978 DOI: 10.1002/jcc.26985] [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: 11/10/2021] [Revised: 05/26/2022] [Accepted: 08/03/2022] [Indexed: 11/07/2022]
Abstract
This work is focused on evaluating the performance of exchange-correlation functionals from density functional theory in providing descriptor values derived from the electron density of saddle point structures (transition states) in chemical reactions. The properties investigated were obtained from the quantum theory of atoms in molecules, including atomic charges and electron density topological data at the bond critical points. In addition, parameters from the Interacting quantum atom energy partition were used as well in this comparative study. The reference values are attained in coupled cluster calculations with iterative single and double excitations (CCSD). Six elementary reactions are considered here: CO + H2 ↔ H2 CO, CO + H2 O ↔ HCOOH, HCN ↔ HNC, H + F2 ↔ HF + F, H + N2 ↔ HN2 , and H + CO ↔ HCO. In general, the BB1K functional (hybrid-meta-generalized gradient approximation) provides the best description of these properties. Our study indicates that an intermediate percentage of nonlocal exact exchange, around 40%-55% (perhaps even larger), is probably required for attaining more accurate values with actual functionals, although this condition is not able of explaining all the trends observed.
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Affiliation(s)
- Gabriel Kossaka Macedo
- Department of Chemistry and Molecular Physics, São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Roberto Luiz Andrade Haiduke
- Department of Chemistry and Molecular Physics, São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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3
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Alkorta I, Elguero J. The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction. Struct Chem 2021. [DOI: 10.1007/s11224-021-01805-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThis communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.
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Elguero J, Alkorta I. The extraordinary richness of the reaction between diazomethane and tetracyanoethylene: can computational calculations shed light on old papers? NEW J CHEM 2019. [DOI: 10.1039/c9nj00824a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the quest of the structure of the intermediate between Δ1- and Δ2-pyrazolines, the reactivity of these molecules tetrasubstituted by cyano groups in adjacent positions (3,3,4,4 or 4,4,5,5) has been explored in their neutral and protonated forms.
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Affiliation(s)
- José Elguero
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
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5
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Vannay L, Meyer B, Petraglia R, Sforazzini G, Ceriotti M, Corminboeuf C. Analyzing Fluxional Molecules Using DORI. J Chem Theory Comput 2018; 14:2370-2379. [PMID: 29570294 DOI: 10.1021/acs.jctc.7b01176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Density Overlap Region Indicator (DORI) is a density-based scalar field that reveals covalent bonding patterns and noncovalent interactions in the same value range. This work goes beyond the traditional static quantum chemistry use of scalar fields and illustrates the suitability of DORI for analyzing geometrical and electronic signatures in highly fluxional molecular systems. Examples include a dithiocyclophane, which possesses multiple local minima with differing extents of π-stacking interactions and a temperature dependent rotation of a molecular rotor, where the descriptor is employed to capture fingerprints of CH-π and π-π interactions. Finally, DORI serves to examine the fluctuating π-conjugation pathway of a photochromic torsional switch (PTS). Attention is also placed on postprocessing the large amount of generated data and juxtaposing DORI with a data-driven low-dimensional representation of the structural landscape.
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Alkorta I, Thacker JCR, Popelier PLA. An interacting quantum atom study of model S N 2 reactions (X - ···CH 3 X, X = F, Cl, Br, and I). J Comput Chem 2018; 39:546-556. [PMID: 29125196 PMCID: PMC5836863 DOI: 10.1002/jcc.25098] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/25/2017] [Accepted: 10/17/2017] [Indexed: 12/30/2022]
Abstract
The quantum chemical topology method has been used to analyze the energetic profiles in the X- + CH3 X → XCH3 + X- SN 2 reactions, with X = F, Cl, Br, and I. The evolution of the electron density properties at the BCPs along the reaction coordinate has been analysed. The interacting quantum atoms (IQA) method has been used to evaluate the intra-atomic and interatomic energy variations along the reaction path. The different energetic terms have been examined by the relative energy gradient method and the ANANKE program, which enables automatic and unbiased IQA analysis. Four of the six most important IQA energy contributions were needed to reproduce the reaction barrier common to all reactions. The four reactions considered share many common characteristics but when X = F a number of particularities occur. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3Madrid28006Spain
| | - Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, M1 7DN, Great Britain, and School of Chemistry, University of Manchester, Oxford RoadManchesterM13 9PLGreat Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, M1 7DN, Great Britain, and School of Chemistry, University of Manchester, Oxford RoadManchesterM13 9PLGreat Britain
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7
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Uggerud E. The Factors Determining Reactivity in Nucleophilic Substitution. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Tognetti V, Bouzbouz S, Joubert L. A theoretical study of the diastereoselective allylation of aldehydes with new chiral allylsilanes. J Mol Model 2016; 23:5. [DOI: 10.1007/s00894-016-3173-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/16/2016] [Indexed: 11/24/2022]
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Andrés J, Berski S, Silvi B. Curly arrows meet electron density transfers in chemical reaction mechanisms: from electron localization function (ELF) analysis to valence-shell electron-pair repulsion (VSEPR) inspired interpretation. Chem Commun (Camb) 2016; 52:8183-95. [DOI: 10.1039/c5cc09816e] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The displacement of the nuclei along the reaction path provides an explanatory interpretation of the electron density transfers making possible to understand chemical reactions.
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Affiliation(s)
- Juan Andrés
- Departament de Ciències Experimentals Universitat Jaume I
- 12080 Castelló
- Spain
| | | | - Bernard Silvi
- Sorbonne Universités
- UPMC
- Univ Paris 06
- UMR 7616
- Laboratoire de Chimie Théorique
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10
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Minyaev RM, Quapp W, Schmidt B, Getmanskii IV, Koval VV. Unusual reaction paths of SN2 nucleophile substitution reactions CH4+H−→CH4+H− and CH4+F−→CH3F+H−: Quantum chemical calculations. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Wu P, Chaudret R, Hu X, Yang W. Noncovalent Interaction Analysis in Fluctuating Environments. J Chem Theory Comput 2013; 9:2226-2234. [PMID: 23894230 DOI: 10.1021/ct4001087] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnson et al developed a NonCovalent Interaction (NCI) index to characterize and visualize different types of weak interactions. To apply the NCI analysis to fluctuating environments as in solution phase, we here develop a new Averaged NonCovalent Interaction (i.e., aNCI) index along with a fluctuation index to characterize magnitude of interactions and fluctuations. We applied aNCI for various systems including solute-solvent and ligand-protein noncovalent interactions. For water and benzene molecules in aqueous solution, solvation structures and the specific hydrogen bond patterns were visualized clearly. For the Cl-+CH3Cl SN2 reaction in aqueous solution, charge reorganization influences over solvation structure along SN2 reaction were revealed. For ligand-protein systems, aNCI can recover several key fluctuating hydrogen bond patterns that have potential applications for drug design. Therefore, aNCI, as a complementary approach to the original NCI method, can extract and visualize noncovalent interactions from thermal noise in fluctuating environments.
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Affiliation(s)
- Pan Wu
- Department of Chemistry, Duke University, Durham, NC 27708
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12
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Giri S, Echegaray E, Ayers PW, Nuñez AS, Lund F, Toro-Labbé A. Insights into the mechanism of an S(N)2 reaction from the reaction force and the reaction electronic flux. J Phys Chem A 2012; 116:10015-26. [PMID: 22974407 DOI: 10.1021/jp3076707] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The mechanism of a simple S(N)2 reaction, viz; OH(-) + CH(3)F = CH(3)OH + F(-) has been studied within the framework of reaction force and reaction electronic flux. We have computationally investigated three different types of reaction mechanisms with two different types of transition states, leading to two different products. The electronic transfer contribution of the reaction electronic flux was found to play a crucial role in this reaction. Natural bond order analysis and dual descriptor provide additional support for elucidating the mechanism of this reaction.
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Affiliation(s)
- Santanab Giri
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile
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13
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González-Navarrete P, Domingo LR, Andrés J, Berski S, Silvi B. Electronic fluxes during diels-alder reactions involving 1,2-benzoquinones: mechanistic insights from the analysis of electron localization function and catastrophe theory. J Comput Chem 2012; 33:2400-11. [DOI: 10.1002/jcc.23085] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/02/2012] [Accepted: 07/10/2012] [Indexed: 01/06/2023]
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14
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Omar NYM, Rahman NA, Zain SMD. Enantioselective organocatalytic Diels-Alder reactions: a density functional theory and kinetic isotope effects study. J Comput Chem 2011; 32:1813-23. [PMID: 21455954 DOI: 10.1002/jcc.21763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 12/02/2010] [Accepted: 01/11/2011] [Indexed: 11/10/2022]
Abstract
The mechanism and enantioselectivity of the organocatalytic Diels-Alder reaction were computationally investigated by density functional theory at the B3LYP/6-31G(d) level of theory. The uncatalyzed Diels-Alder reaction was also studied to explore the effect of the organocatalyst on this reaction in terms of energetics, selectivity, and mechanism. The catalyzed reaction showed improved endo/exo selectivity, and the free energy of activation was significantly lowered in the presence of the catalyst. Both uncatalyzed and catalyzed reactions exhibited concerted asynchronous reaction mechanism with the degree of asynchronicity being more evident in the presence of the catalyst. The Corey's experimentally derived predictive selection rules for the outcome of the organocatalytic Diels-Alder reaction were also theoretically analyzed, and an excellent agreement was found between experiment and theory.
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Affiliation(s)
- Nasr Y M Omar
- Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
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15
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Tognetti V, Cortona P, Adamo C. Activation enthalpies of pericyclic reactions: the performances of some recently proposed functionals. Theor Chem Acc 2009. [DOI: 10.1007/s00214-008-0503-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Abstract
This article gives an overview of recently published literature on the factors that govern SN2 reactivity. By comparing reactivity in solution with that in the isolated gas phase, it has become possible to dissect the contribution of the solvent from that of the intrinsic molecular properties. This has proven to be an extremely important and fruitful step forward in obtaining key knowledge not available before. The gas-phase studies have made it clear that organic chemists need to revise radically their concepts and ideas about this crucial reaction type. This is particularly true with regard to the commonly used term "steric effect".
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Affiliation(s)
- Einar Uggerud
- 1Mass Spectrometry Laboratory and The Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
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Echegaray E, Toro-Labbé A. Reaction electronic flux: a new concept to get insights into reaction mechanisms. Study of model symmetric nucleophilic substitutions. J Phys Chem A 2008; 112:11801-7. [PMID: 18942822 DOI: 10.1021/jp805225e] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The present work is focused on studying chlorine and fluorine identity SN2 substitutions on a methyl center, within the framework of the newly introduced reaction electronic flux J(xi), that allows one to identify charge transfer and polarization mechanisms that take place along the reaction coordinate. The main results concern the discovery of different charge transfer mechanism, despite both reactions have the same energetic pattern with simultaneous bond breaking and formation. It turns out that the chlorine substitution is mainly driven by polarization effects and characterized by through bond interactions while intermolecular charge transfer dominates the fluorine exchange reaction, that is characterized by through space interactions.
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Affiliation(s)
- Eleonora Echegaray
- Facultad de Química, Laboratorio de Química Teórica Computacional, Pontificia Universidad Católica de Chile, Correo 22, Santiago, Chile
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18
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Polo V, Andrés J. Lewis Acid and Substituent Effects on the Molecular Mechanism for the Nazarov Reaction of Penta-1,4-dien-3-one and Derivatives. A Topological Analysis Based on the Combined Use of Electron Localization Function and Catastrophe Theory. J Chem Theory Comput 2007; 3:816-23. [DOI: 10.1021/ct7000304] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Victor Polo
- Departamento de Química Física y Analítica, Universidad Jaime I, Apartado 224, 12080, Castellón, Spain
| | - Juan Andrés
- Departamento de Química Física y Analítica, Universidad Jaime I, Apartado 224, 12080, Castellón, Spain
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19
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Jay AN, Daniel KA, Patterson EV. Atom-Centered Density Matrix Propagation Calculations on the Methyl Transfer from CH3Cl to NH3: Gas-Phase and Continuum-Solvated Trajectories. J Chem Theory Comput 2007; 3:336-43. [DOI: 10.1021/ct6002803] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ashley N. Jay
- Truman State University, Division of Science, 100 E. Normal St., Kirksville, Missouri 63501
| | - Kelly A. Daniel
- Truman State University, Division of Science, 100 E. Normal St., Kirksville, Missouri 63501
| | - Eric V. Patterson
- Truman State University, Division of Science, 100 E. Normal St., Kirksville, Missouri 63501
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