1
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Husbands DR, Tanner T, Whitwood AC, Hodnett NS, Wheelhouse KMP, Fairlamb IJS. Revealing the Hidden Complexity and Reactivity of Palladacyclic Precatalysts: The P( o-tolyl) 3 Ligand Enables a Cocktail of Active Species Utilizing the Pd(II)/Pd(IV) and Pd(0)/Pd(II) Pathways for Efficient Catalysis. ACS Catal 2024; 14:12769-12782. [PMID: 39263545 PMCID: PMC11385352 DOI: 10.1021/acscatal.4c02585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 09/13/2024]
Abstract
The ligand, P(o-tolyl)3, is ubiquitous in applied synthetic chemistry and catalysis, particularly in Pd-catalyzed processes, which typically include Pd(OAc)2 (most commonly used as Pd3(OAc)6) as a precatalyst. The Herrmann-Beller palladacycle [Pd(C^P)(μ2-OAc)]2 (where C^P = monocyclopalladated P(o-tolyl)3) is easily formed from reaction of Pd(OAc)2 with P(o-tolyl)3. The mechanisms by which this precatalyst system operates are inherently complex, with studies previously implicating Pd nanoparticles (PdNPs) as reservoirs for active Pd(0) species in arylative cross-coupling reactions. In this study, we reveal the fascinating, complex, and nontrivial behavior of the palladacyclic group. First, in the presence of hydroxide base, [Pd(C^P)(μ2-OAc)]2 is readily converted into an activated form, [Pd(C^P)(μ2-OH)]2, which serves as a conduit for activation to catalytically relevant species. Second, palladacyclization imparts unique stability for catalytic species under reaction conditions, bringing into play a Pd(II)/Pd(IV) cross-coupling mechanism. For a benchmark Suzuki-Miyaura cross-coupling (SMCC) reaction, there is a shift from a mononuclear Pd catalytic pathway to a PdNP-controlled catalytic pathway during the reaction. The activation pathway of [Pd(C^P)(μ2-OH)]2 has been studied using an arylphosphine-stabilized boronic acid and low-temperature NMR spectroscopic analysis, which sheds light on the preactivation step, with water and/or acid being critical for the formation of active Pd(0) and Pd(II) species. In situ reaction monitoring has demonstrated that there is a sensitivity to the structure of the arylboron species in the presence of pinacol. This work, taken together, highlights the mechanistic complexity accompanying the use of palladacyclic precatalyst systems. It builds on recent findings involving related Pd(OAc)2/PPh3 precatalyst systems which readily form higher order Pdn clusters and PdNPs under cross-coupling reaction conditions. Thus, generally, one needs to be cautious with the assumption that Pd(OAc)2/tertiary phosphine mixtures cleanly deliver mononuclear "Pd(0)Ln" species and that any assessment of individual phosphine ligands may need to be taken on a case-by-case basis.
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Affiliation(s)
- David R Husbands
- Department of Chemistry, University of York, York, Heslington YO10 5DD, United Kingdom
| | - Theo Tanner
- Department of Chemistry, University of York, York, Heslington YO10 5DD, United Kingdom
| | - Adrian C Whitwood
- Department of Chemistry, University of York, York, Heslington YO10 5DD, United Kingdom
| | - Neil S Hodnett
- Medicine Development & Supply, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Katherine M P Wheelhouse
- Medicine Development & Supply, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian J S Fairlamb
- Department of Chemistry, University of York, York, Heslington YO10 5DD, United Kingdom
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2
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Damián Burgoa J, Álvarez-Miguel L, Mosquera MEG, Hamilton A, Whiteoak CJ. Binary and Halide-free Catalyst Systems Based on Al/Ga/In Aminopyridylbisphenolate Complexes for the Cycloaddition of Epoxides and CO 2. Inorg Chem 2024; 63:15376-15387. [PMID: 39093822 PMCID: PMC11337169 DOI: 10.1021/acs.inorgchem.4c02352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Group 13 complexes bearing an aminopyridylbisphenol ligand have been prepared [ML-X; L = ligand, M = Al (X = Cl and Br), Ga (X = Cl, Br, and I), or In (X = Cl)]. The structures of the complexes containing the chloride ligand (ML-Cl; M = Al, Ga, and In) have been directly compared through an X-ray crystallography study, with differences in the monomeric or dimeric nature of their structures observed. All of the complexes obtained have been studied as potential catalysts for the synthesis of cyclic carbonates from epoxides and CO2. It has been found that the indium complex, as part of a traditional binary catalyst system (catalyst + tetra-butylammonium halide cocatalyst), displays the highest catalytic activity and is active under rather mild reaction conditions (balloon pressure of CO2). Meanwhile, it has been found that the GaL-I complex is a competent single-component catalyst (no need for addition of a cocatalyst) at more elevated reaction temperatures and pressures. A full substrate scope has been performed with both developed catalyst systems to demonstrate their applicability. In addition to the experimental results, a density functional theory study was performed on both catalyst systems. These results explain both why the indium catalyst is the most active under binary catalyst system conditions and how the gallium catalyst with an iodide (GaL-I) is able to act as a single-component catalyst in contrast to the indium-based complex.
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Affiliation(s)
- Jesús Damián Burgoa
- Departamento
de Química Orgánica y Química Inorgánica,
Facultad de Farmacia and Instituto de Investigación Química
Andrés M. del Río (IQAR), Universidad de Alcalá, Grupo SOSCATCOM, Campus Universitario, Ctra. Madrid-Barcelona
Km. 33,600, Alcalá de Henares 28871, Madrid, Spain
| | - Lucía Álvarez-Miguel
- Departamento
de Química Orgánica y Química Inorgánica,
Facultad de Farmacia and Instituto de Investigación Química
Andrés M. del Río (IQAR), Universidad de Alcalá, Grupo SOSCATCOM, Campus Universitario, Ctra. Madrid-Barcelona
Km. 33,600, Alcalá de Henares 28871, Madrid, Spain
| | - Marta E. G. Mosquera
- Departamento
de Química Orgánica y Química Inorgánica,
Facultad de Farmacia and Instituto de Investigación Química
Andrés M. del Río (IQAR), Universidad de Alcalá, Grupo SOSCATCOM, Campus Universitario, Ctra. Madrid-Barcelona
Km. 33,600, Alcalá de Henares 28871, Madrid, Spain
| | - Alex Hamilton
- Biomolecular
Sciences Research Centre (BMRC) and Department of Biosciences and
Chemistry, College of Health, Wellbeing and Life Sciences Howard Street, Sheffield Hallam University, Sheffield S1 1WB, U.K.
| | - Christopher J. Whiteoak
- Departamento
de Química Orgánica y Química Inorgánica,
Facultad de Farmacia and Instituto de Investigación Química
Andrés M. del Río (IQAR), Universidad de Alcalá, Grupo SOSCATCOM, Campus Universitario, Ctra. Madrid-Barcelona
Km. 33,600, Alcalá de Henares 28871, Madrid, Spain
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3
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Huth SE, Tampellini N, Guerrero MD, Miller SJ. Catalytic Enantioselective Sulfoxidation of Functionalized Thioethers Mediated by Aspartic Acid-Containing Peptides. Org Lett 2024; 26:6872-6877. [PMID: 39102356 PMCID: PMC11329351 DOI: 10.1021/acs.orglett.4c02452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
A peptide-catalyzed enantioselective oxidation of sulfides to yield pharmaceutically relevant chiral sulfoxides is reported. Experimental evidence suggesting that a hydrogen bond-donating moiety must be present in the substrate to achieve high levels of enantioinduction is supported by computational modeling of transition states. These models also indicate that dual points of contact between the peptidic catalyst and substrate are likely responsible for the formation of one desired sulfoxide in 94:6 er.
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Affiliation(s)
- Susannah E. Huth
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Nicolò Tampellini
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Maria D. Guerrero
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
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4
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Gantzer P, Staub R, Harabuchi Y, Maeda S, Varnek A. Chemography-guided analysis of a reaction path network for ethylene hydrogenation with a model Wilkinson's catalyst. Mol Inform 2024:e202400063. [PMID: 39121023 DOI: 10.1002/minf.202400063] [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: 02/21/2024] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 08/11/2024]
Abstract
Visualization and analysis of large chemical reaction networks become rather challenging when conventional graph-based approaches are used. As an alternative, we propose to use the chemical cartography ("chemography") approach, describing the data distribution on a 2-dimensional map. Here, the Generative Topographic Mapping (GTM) algorithm - an advanced chemography approach - has been applied to visualize the reaction path network of a simplified Wilkinson's catalyst-catalyzed hydrogenation containing some 105 structures generated with the help of the Artificial Force Induced Reaction (AFIR) method using either Density Functional Theory or Neural Network Potential (NNP) for potential energy surface calculations. Using new atoms permutation invariant 3D descriptors for structure encoding, we've demonstrated that GTM possesses the abilities to cluster structures that share the same 2D representation, to visualize potential energy surface, to provide an insight on the reaction path exploration as a function of time and to compare reaction path networks obtained with different methods of energy assessment.
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Affiliation(s)
- Philippe Gantzer
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Ruben Staub
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
- Laboratory of Chemoinformatics, UMR 7140, CNRS, University of Strasbourg, Strasbourg, 67081, France
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5
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Díaz-Ruiz M, Nieto-Rodríguez M, Maseras F. Revealing the Mechanistic Features of an Electrosynthetic Catalytic Reaction and the Role of Redox Mediators through DFT Calculations and Microkinetic Modeling. Chemphyschem 2024; 25:e202400402. [PMID: 38739104 DOI: 10.1002/cphc.202400402] [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: 04/09/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
Abstract
Organic electrosynthesis is an emerging field that provides original selectivity while adding features of atom economy, sustainability, and selectivity. Electrosynthesis is often enhanced by redox mediators or electroauxiliaries. The mechanistic understanding of organic electrosynthesis is however often limited by the low lifetime of intermediates and its difficult detection. In this work, we report a computational analysis of the mechanism of an appealing reaction previously reported by Mei and co-workers which is catalyzed by copper and employs iodide as redox mediator. Our scheme combines DFT calculations with microkinetic modeling and covers both the reaction in solution and the electrodic steps. A detailed mechanistic scheme is obtained which reproduces well experimental data and opens perspectives for the general treatment of these processes.
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Affiliation(s)
- Marina Díaz-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països, Catalans 16, 43007, Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel⋅lí Domingo s/n, Tarragona, 43007, Spain
| | - Marc Nieto-Rodríguez
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països, Catalans 16, 43007, Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel⋅lí Domingo s/n, Tarragona, 43007, Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països, Catalans 16, 43007, Tarragona, Spain
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6
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Laplaza R, Wodrich MD, Corminboeuf C. Overcoming the Pitfalls of Computing Reaction Selectivity from Ensembles of Transition States. J Phys Chem Lett 2024; 15:7363-7370. [PMID: 38990895 DOI: 10.1021/acs.jpclett.4c01657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The prediction of reaction selectivity is a challenging task for computational chemistry, not only because many molecules adopt multiple conformations but also due to the exponential relationship between effective activation energies and rate constants. To account for molecular flexibility, an increasing number of methods exist that generate conformational ensembles of transition state (TS) structures. Typically, these TS ensembles are Boltzmann weighted and used to compute selectivity assuming Curtin-Hammett conditions. This strategy, however, can lead to erroneous predictions if the appropriate filtering of the conformer ensembles is not conducted. Here, we demonstrate how any possible selectivity can be obtained by processing the same sets of TS ensembles for a model reaction. To address the burdensome filtering task in a consistent and automated way, we introduce marc, a tool for the modular analysis of representative conformers that aids in avoiding human errors while minimizing the number of reoptimization computations needed to obtain correct reaction selectivity.
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Affiliation(s)
- Ruben Laplaza
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Matthew D Wodrich
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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7
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Okoročenkova J, Filgas J, Khan NM, Slavíček P, Klán P. Thermal Truncation of Heptamethine Cyanine Dyes. J Am Chem Soc 2024; 146:19768-19781. [PMID: 38995720 PMCID: PMC11273355 DOI: 10.1021/jacs.4c02116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
Cyanine dyes are a class of organic, usually cationic molecules containing two nitrogen centers linked through conjugated polymethine chains. The synthesis and reactivity of cyanine derivatives have been extensively investigated for decades. Unlike the recently described phototruncation process, the thermal truncation (chain shortening) reaction is a phenomenon that has rarely been reported for these important fluorophores. Here, we present a systematic investigation of the truncation of heptamethine cyanines (Cy7) to pentamethine (Cy5) and trimethine (Cy3) cyanines via homogeneous, acid-base-catalyzed nucleophilic exchange reactions. We demonstrate how different substituents at the C3' and C4' positions of the chain and different heterocyclic end groups, the presence of bases, nucleophiles, and oxygen, solvent properties, and temperature affect the truncation process. The mechanism of chain shortening, studied by various analytical and spectroscopic techniques, was verified by extensive ab initio calculation, implying the necessity to model catalytic reactions by highly correlated wave function-based methods. In this study, we provide critical insight into the reactivity of cyanine polyene chains and elucidate the truncation mechanism and methods to mitigate side processes that can occur during the synthesis of cyanine derivatives. In addition, we offer alternative routes to the preparation of symmetrical and unsymmetrical meso-substituted Cy5 derivatives.
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Affiliation(s)
- Jana Okoročenkova
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Josef Filgas
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, 16628 Prague 6, Czech Republic
| | - Nasrulla Majid Khan
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, 16628 Prague 6, Czech Republic
| | - Petr Klán
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
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8
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Meng F, Sun L, Liu Y, Li X, Tan H, Yuan C, Li X. Theoretical investigation of the reaction mechanism of THP oxidative rearrangement catalysed by BBOX. Phys Chem Chem Phys 2024. [PMID: 39015023 DOI: 10.1039/d4cp01661k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a non-heme FeII/2OG dependent enzyme that is able to perform two different kinds of catalytic reactions on 3-(2,2,2-trimethylhydrazinium) propionate (THP) to produce distinct catalytic products. Although the structure of BBOX complexed with THP has been resolved, the details of its catalytic mechanism are still elusive. In this study, by employing molecular dynamics (MD) simulations and density functional theory (DFT) calculations, the mechanism of the THP oxidative rearrangement reactions catalysed by BBOX was investigated. Our calculations revealed how the enzyme undergoes a conformational conversion to initiate the catalytic reactions. In the first catalytic step, BBOX performs hydrogen abstraction from the substrate THP as a common non-heme iron enzyme. Due to the structure of the substrate stabilizing the radical species and polarizing the adjacent N-N bond, in the next step, THP takes the pathway for N-N bond homolysis but not regular hydroxyl rebounding. The cleaved ammonium radical could either react with the hydroxyl group on the iron centre of the enzyme or recombine with the other cleaved fragment of the substrate to generate the rearranged product. This study revealed the catalytic mechanism of BBOX, detailing how the enzyme and the substrate regulated the hydroxyl rebound process to generate various products.
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Affiliation(s)
- Fanqi Meng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Lu Sun
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Yueying Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xiang Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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9
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Worakul T, Laplaza R, Das S, Wodrich MD, Corminboeuf C. Microkinetic Molecular Volcano Plots for Enhanced Catalyst Selectivity and Activity Predictions. ACS Catal 2024; 14:9829-9839. [PMID: 38988648 PMCID: PMC11232097 DOI: 10.1021/acscatal.4c01175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Molecular volcano plots, which facilitate the rapid prediction of the activity and selectivity of prospective catalysts, have emerged as powerful tools for computational catalysis. Here, we integrate microkinetic modeling into the volcano plot framework to develop "microkinetic molecular volcano plots". The resulting unified computational framework allows the influence of important reaction parameters, including temperature, reaction time, and concentration, to be quickly incorporated and more complex situations, such as off-cycle resting states and coupled catalytic cycles, to be tackled. Compared to previous generations of molecular volcanoes, these microkinetic counterparts offer a more comprehensive understanding of catalytic behavior, in which selectivity and product ratios can be explicitly determined by tracking the evolution of each product concentration over time. This is demonstrated by examining two case studies, rhodium-catalyzed hydroformylation and metal-catalyzed hydrosilylation, in which the unique insights provided by microkinetic modeling, as well as the ability to simultaneously screen catalysts and reaction conditions, are highlighted. To facilitate the construction of these plots/maps, we introduce mikimo, a Python program that seamlessly integrates with our previously developed automated volcano builder, volcanic.
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Affiliation(s)
- Thanapat Worakul
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fedéralé
de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Rubén Laplaza
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fedéralé
de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National
Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne
(EPFL), 1015 Lausanne, Switzerland
| | - Shubhajit Das
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fedéralé
de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matthew D. Wodrich
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fedéralé
de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National
Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne
(EPFL), 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory
for Computational Molecular Design, Institute of Chemical Sciences
and Engineering, Ecole Polytechnique Fedéralé
de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National
Center for Competence in Research-Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne
(EPFL), 1015 Lausanne, Switzerland
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10
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Rieder GS, Duarte T, Delgado CP, Rodighiero A, Nogara PA, Orian L, Aschner M, Dalla Corte CL, Da Rocha JBT. Interplay between diphenyl diselenide and copper: Impact on D. melanogaster survival, behavior, and biochemical parameters. Comp Biochem Physiol C Toxicol Pharmacol 2024; 281:109899. [PMID: 38518983 DOI: 10.1016/j.cbpc.2024.109899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 03/24/2024]
Abstract
Copper (Cu2+) is a biologically essential element that participates in numerous physiological processes. However, elevated concentrations of copper have been associated with cellular oxidative stress and neurodegenerative diseases. Organo‑selenium compounds such as diphenyl diselenide (DPDS) have in vitro and in vivo antioxidant properties. Hence, we hypothesized that DPDS may modulate the toxicity of Cu2+ in Drosophila melanogaster. The acute effects (4 days of exposure) caused by a high concentration of Cu2+ (3 mM) were studied using endpoints of toxicity such as survival and behavior in D. melanogaster. The potential protective effect of low concentration of DPDS (20 μM) against Cu2+ was also investigated. Adult flies aged 1-5 days post-eclosion (both sexes) were divided into four groups: Control, DPDS (20 μM), CuSO4 (3 mM), and the combined exposure of DPDS (20 μM) and CuSO4 (3 mM). Survival, biochemical, and behavioral parameters were determined. Co-exposure of DPDS and CuSO4 increased acetylcholinesterase (AChE) activity and the generation of reactive oxygen species (ROS as determined by DFCH oxidation). Contrary to our expectation, the co-exposure reduced survival, body weight, locomotion, catalase activity, and cell viability in relation to control group. Taken together, DPDS potentiated the Cu2+ toxicity.
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Affiliation(s)
- G S Rieder
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil. https://twitter.com/RiederSchmitt
| | - T Duarte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil. https://twitter.com/tttamie
| | - C P Delgado
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil. https://twitter.com/cassiapdelgado
| | - A Rodighiero
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - P A Nogara
- Instituto Federal de Educação, Ciência e Tecnologia Sul-rio-grandense (IFSul), Av. Leonel de Moura Brizola, 2501, 96418-400 Bagé, RS, Brazil. https://twitter.com/nogara_pablo
| | - L Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy. https://twitter.com/_LauraOrian
| | - M Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - C L Dalla Corte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - J B T Da Rocha
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil; Department of Biochemistry, Institute of Basic Health Science, Federal University of Rio Grande do Sul, Porto Alegre, RS 90035-003, Brazil.
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11
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D'Anania O, Romano E, Barone V, Talarico G. Predicting the propene stereoselectivity on transition metal catalysts: A daunting task for density functional theory. J Comput Chem 2024; 45:1483-1492. [PMID: 38470153 DOI: 10.1002/jcc.27343] [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: 12/27/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024]
Abstract
Thanks to recent developments in hardware and software, quantum chemical methods are increasingly used for interpreting the complex mechanisms underlying polymerization reaction by homogeneous catalysis. Unfortunately, the dimensions of even the smallest realistic models are too large to permit the use of state-of-the-art composite wave function methods. Under these circumstances, density functional theory still offers the best compromise between cost and accuracy. However, comprehensive benchmarks of different functionals are not yet available for this important research field. The main aim of the present paper is to fill this gap by performing an unbiased comparison of several density functionals and continuum solvent models for the stereo-control in the propylene polymerization on prototypical catalysts inducing different reaction mechanisms. While it was not possible to define a unique computational protocol providing the best results in all the situations, the B3PW91 functional in conjunction with D3 empirical dispersions and the solvent model density solvent model performs remarkably well for three out of the four investigated catalysts. Under such circumstances, it is recommended to compare the results delivered by different models when approaching additional classes of catalysts.
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Affiliation(s)
- Olga D'Anania
- Scuola Superiore Meridionale, Napoli, Italy
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Eugenio Romano
- Scuola Superiore Meridionale, Napoli, Italy
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | | | - Giovanni Talarico
- Scuola Superiore Meridionale, Napoli, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Napoli, Italy
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12
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Tampellini N, Mercado BQ, Miller SJ. Scaffold-Oriented Asymmetric Catalysis: Conformational Modulation of Transition State Multivalency during a Catalyst-Controlled Assembly of a Pharmaceutically Relevant Atropisomer. Chemistry 2024; 30:e202401109. [PMID: 38507249 PMCID: PMC11132932 DOI: 10.1002/chem.202401109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/22/2024]
Abstract
A new class of superbasic, bifunctional peptidyl guanidine catalysts is presented, which enables the organocatalytic, atroposelective synthesis of axially chiral quinazolinediones. Computational modeling unveiled the conformational modulation of the catalyst by a novel phenyl urea N-cap, that preorganizes the structure into the active, folded state. A previously unanticipated noncovalent interaction involving a difluoroacetamide acting as a hybrid mono- or bidentate hydrogen bond donor emerged as a decisive control element inducing atroposelectivity. These discoveries spurred from a scaffold-oriented project inspired from a fascinating investigational BTK inhibitor featuring two stable chiral axes and relies on a mechanistic framework that was foreign to the extant lexicon of asymmetric catalysis.
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Affiliation(s)
- Nicolò Tampellini
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511 (USA)
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511 (USA)
| | - Scott J. Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511 (USA)
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13
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Souza JPA, Jacobs AK, Piovan L, Campos RB. Exploring the mechanism of the reductive amination of acetophenones via the Borch approach: the role of the acid catalyst. Org Biomol Chem 2024; 22:3926-3932. [PMID: 38659303 DOI: 10.1039/d4ob00160e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The energetic viability of several mechanistic variations of the reductive amination of acetophenones via the Borch approach was re-examined through density functional theory calculations. The crucial involvement of the acid catalyst is evident not only in the elimination of water, but also in the initial nucleophilic step. This role increases with the electron-donating capability of the substituent positioned at the para-position of acetophenone.
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Affiliation(s)
- João P A Souza
- Departamento de Química, Universidade Federal do Paraná (UFPR), Curitiba, PR, CP 19081, CEP 81531-990, Brazil
| | - Amanda K Jacobs
- Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Rua Deputado Heitor de Alencar Furtado, 5000, 81280-340, Curitiba, Brazil.
| | - Leandro Piovan
- Departamento de Química, Universidade Federal do Paraná (UFPR), Curitiba, PR, CP 19081, CEP 81531-990, Brazil
| | - Renan B Campos
- Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Rua Deputado Heitor de Alencar Furtado, 5000, 81280-340, Curitiba, Brazil.
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14
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Steiner M, Reiher M. A human-machine interface for automatic exploration of chemical reaction networks. Nat Commun 2024; 15:3680. [PMID: 38693117 PMCID: PMC11063077 DOI: 10.1038/s41467-024-47997-9] [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: 08/31/2023] [Accepted: 04/15/2024] [Indexed: 05/03/2024] Open
Abstract
Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible intermediates is computationally too demanding. This renders brute-force explorations unfeasible, while explorations with completely pre-defined intermediates or hard-wired chemical constraints, such as element-specific coordination numbers, are not flexible enough for complex chemical systems. Here, we introduce a STEERING WHEEL to guide an otherwise unbiased automated exploration. The STEERING WHEEL algorithm is intuitive, generally applicable, and enables one to focus on specific regions of an emerging network. It also allows for guiding automated data generation in the context of mechanism exploration, catalyst design, and other chemical optimization challenges. The algorithm is demonstrated for reaction mechanism elucidation of transition metal catalysts. We highlight how to explore catalytic cycles in a systematic and reproducible way. The exploration objectives are fully adjustable, allowing one to harness the STEERING WHEEL for both structure-specific (accurate) calculations as well as for broad high-throughput screening of possible reaction intermediates.
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Affiliation(s)
- Miguel Steiner
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Markus Reiher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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15
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Grochowska-Tatarczak M, Koteras K, Kazimierczuk K, Malinowski PJ. Hydrosilylation of Olefins Activated on Highly Lewis-Acidic Calcium Cation. Chemistry 2024:e202401322. [PMID: 38660917 DOI: 10.1002/chem.202401322] [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: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/26/2024]
Abstract
The report introduces simple yet highly reactive calcium salt, Ca[Al(ORF)4]2 (RF=C(CF3)3), 1, which effectively catalyses olefin hydrosilylation through an unusual mechanism involving the activation of the alkene molecule. Upon dissolution in o-difluorobenzene (oDFB), 1 forms a highly Lewis acidic [Ca(oDFB)6]2+ complex. Our DFT calculations reveal that fluoride ion affinity is comparable to SbF5. Reactivity tests show that it effectively catalyses the hydrosilylation of olefins with high regioselectivity, also in reactions involving sterically demanding substrates like (iPr)3SiH or tetrasubstituted olefins. Experimental and computational results point to the mechanism where the olefin molecule forms a complex with Ca2+, which significantly facilitates the attack of H-SiR3 on the C=C double bond.
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Affiliation(s)
| | - K Koteras
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-093, Warsaw, Poland
| | - K Kazimierczuk
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-093, Warsaw, Poland
| | - P J Malinowski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-093, Warsaw, Poland
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16
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Kótai B, Laczkó G, Hamza A, Pápai I. Stereocontrol via Propeller Chirality in FLP-Catalyzed Asymmetric Hydrogenation. Chemistry 2024; 30:e202400241. [PMID: 38294415 DOI: 10.1002/chem.202400241] [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: 01/19/2024] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/01/2024]
Abstract
Utilization of chiral frustrated Lewis pairs as catalysts in enantioselective hydrogenation of unsaturated molecules represents a promising approach in asymmetric synthesis. In our effort to improve our current understanding of the factors governing the stereoselectivity in these catalytic processes, herein we examined the mechanism of direct hydrogenation of aromatic enamines catalyzed by a binaphthyl-based chiral amino-borane. Our computational analysis reveals that only one particular conformer of the key borohydride reaction intermediate can be regarded as a reactive form of this species. This borohydride conformer has a well-defined chiral propeller shape, which induces facial selectivity in the hydride transfer to pro-chiral iminium intermediates. The propeller chirality of the reactive borohydride conformer is generated by the axially chiral binaphthyl scaffold of the amino-borane catalyst through stabilizing π-π stacking interactions. This new computational insight can be readily used to interpret the high degree of stereoinduction observed for these reactions. We expect that the concept of chirality relay could be further exploited in catalyst design endeavors.
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Affiliation(s)
- B Kótai
- Institute of Organic Chemistry, Research Centre for Natural Sciences, H-1117, Budapest, Magyar tudósok körútja 2
- Hevesy György Ph.D. School of Chemistry, Eötvös Loránd University, P.O. Box 32, H-1518, Budapest, Hungary
| | - G Laczkó
- Institute of Organic Chemistry, Research Centre for Natural Sciences, H-1117, Budapest, Magyar tudósok körútja 2
- Hevesy György Ph.D. School of Chemistry, Eötvös Loránd University, P.O. Box 32, H-1518, Budapest, Hungary
| | - A Hamza
- Institute of Organic Chemistry, Research Centre for Natural Sciences, H-1117, Budapest, Magyar tudósok körútja 2
| | - I Pápai
- Institute of Organic Chemistry, Research Centre for Natural Sciences, H-1117, Budapest, Magyar tudósok körútja 2
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17
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Kundu A, Mandal B, Maji B, Adhikari D. DFT-Guided Mechanistic Insights into Chemodivergence: A Mixed Explicit-Implicit Solvent Description to Dictate the Chemoselectivity. J Phys Chem A 2023; 127:10068-10074. [PMID: 37990876 DOI: 10.1021/acs.jpca.3c04458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Herein we report a density functional theory (DFT)-guided mechanistic investigation of the nitrile reduction reaction, which exhibits a solvent-dependent chemodivergence. This study reveals an interesting mechanistic picture, highlighting the exact role of a protic solvent, isopropanol, in regulating the reaction outcome. The explicit solvent effect involving polar protic isopropanol favors imine metathesis by proton hopping through stepwise addition and elimination steps and thus produces a secondary amine as the final product. In contrast, the nonpolar solvent n-hexane is incapable of facilitating the proton migration and stops the solvent-assisted imine metathesis. As a result, only primary amines are obtained as the final product. This DFT study provides a recipe for the choice of solvents that can dictate chemoselectivity in product formation.
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Affiliation(s)
- Abhishek Kundu
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, SAS Nagar 140306, India
| | - Baishanal Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, SAS Nagar 140306, India
| | - Biplab Maji
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Debashis Adhikari
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, SAS Nagar 140306, India
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18
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Martínez-Vivas S, Gusev DG, Poyatos M, Peris E. Tuning the Catalytic Activity of a Pincer Complex of Rhodium(I) by Supramolecular and Redox Stimuli. Angew Chem Int Ed Engl 2023; 62:e202313899. [PMID: 37792812 DOI: 10.1002/anie.202313899] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023]
Abstract
We report the rhodium(I) complex [Rh(CNC-NDI)(CO)]+ , in which CNC-NDI refers to a pincer-CNC ligand decorated with a naphthalenediimide moiety. Due to the presence of the planar CNC ligand and the naphthalenediimide moiety, the electronic nature of the complex can be modulated by means of supramolecular and redox stimuli, respectively. The metal complex shows a strong π-π-stacking interaction with coronene. This interaction has an impact on the electron-richness of the metal, as demonstrated by the shifting of the ν(CO) stretching band to a lower frequency. The addition of tetrabutylammonium fluoride facilitates the sequential one- and two-electron reduction of the NDI moiety of the ligand, thus resulting in a situation in which the ligand can increase its electron-donor strength in two levels. The nature of the interaction with the fluoride anion was studied computationally. The catalytic activity of the [Rh(CNC-NDI)(CO)]+ complex was tested in the cycloisomerization of alkynoic acids, where it is observed that the activity of the catalyst can be modulated between four levels of activity, which correspond to i) the use of the unmodified catalyst, ii) catalyst+coronene, iii) catalyst+2 equivalents of fluoride, and iv) catalyst+5 equivalents of fluoride.
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Affiliation(s)
- Sebastián Martínez-Vivas
- Institute of Advanced Materials (INAM), Universitat Jaume I, Av. Vicente Sos Baynat s/n., Castellón, E-12071, Spain
| | - Dmitry G Gusev
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, 75 University Avenue West, Waterloo, Ontario, N2 L 3 C5, Canada
| | - Macarena Poyatos
- Institute of Advanced Materials (INAM), Universitat Jaume I, Av. Vicente Sos Baynat s/n., Castellón, E-12071, Spain
| | - Eduardo Peris
- Institute of Advanced Materials (INAM), Universitat Jaume I, Av. Vicente Sos Baynat s/n., Castellón, E-12071, Spain
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19
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Talmazan RA, Podewitz M. PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent. J Chem Inf Model 2023; 63:5400-5407. [PMID: 37606893 PMCID: PMC10498442 DOI: 10.1021/acs.jcim.3c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Indexed: 08/23/2023]
Abstract
We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge.
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Affiliation(s)
- R. A. Talmazan
- Institute
of Materials Chemistry, TU Wien, Getreidemarkt 9, A-1060 Wien, Austria
| | - M. Podewitz
- Institute
of Materials Chemistry, TU Wien, Getreidemarkt 9, A-1060 Wien, Austria
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20
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Petrus E, Garay-Ruiz D, Reiher M, Bo C. Multi-Time-Scale Simulation of Complex Reactive Mixtures: How Do Polyoxometalates Form? J Am Chem Soc 2023; 145:18920-18930. [PMID: 37496164 DOI: 10.1021/jacs.3c05514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Understanding the dynamics of reactive mixtures still challenges both experiments and theory. A relevant example can be found in the chemistry of molecular metal-oxide nanoclusters, also known as polyoxometalates. The high number of species potentially involved, the interconnectivity of the reaction network, and the precise control of the pH and concentrations needed in the synthesis of such species make the theoretical/computational treatment of such processes cumbersome. This work addresses this issue relying on a unique combination of recently developed computational methods that tackle the construction, kinetic simulation, and analysis of complex chemical reaction networks. By using the Bell-Evans-Polanyi approximation for estimating activation energies, and an accurate and robust linear scaling for correcting the computed pKa values, we report herein multi-time-scale kinetic simulations for the self-assembly processes of polyoxotungstates that comprise 22 orders of magnitude, from tens of femtoseconds to months of reaction time. This very large time span was required to reproduce very fast processes such as the acid/base equilibria (at 10-12 s), relatively slow reactions such as the formation of key clusters such as the metatungstate (at 103 s), and the very slow assembly of the decatungstate (at 106 s). Analysis of the kinetic data and of the reaction network topology shed light onto the details of the main reaction mechanisms, which explains the origin of kinetic and thermodynamic control followed by the reaction. Simulations at alkaline pH fully reproduce experimental evidence since clusters do not form under those conditions.
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Affiliation(s)
- Enric Petrus
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Avenida Països Catalans, 16, Tarragona 43007, Spain
| | - Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Avenida Països Catalans, 16, Tarragona 43007, Spain
| | - Markus Reiher
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich 8093, Switzerland
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Avenida Països Catalans, 16, Tarragona 43007, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel•li Domingo s/n, Tarragona 43007, Spain
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21
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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22
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Chang X, Liu XT, Li F, Yang Y, Chung LW, Wang CJ. Electron-rich benzofulvenes as effective dipolarophiles in copper(i)-catalyzed asymmetric 1,3-dipolar cycloaddition of azomethine ylides. Chem Sci 2023; 14:5460-5469. [PMID: 37234882 PMCID: PMC10207880 DOI: 10.1039/d3sc00435j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
A series of benzofulvenes without any electron-withdrawing substituents were employed as 2π-type dipolarophiles for the first time to participate in Cu(i)-catalyzed asymmetric 1,3-dipolar cycloaddition (1,3-DC) reactions of azomethine ylides. An intrinsic non-benzenoid aromatic characteristic from benzofulvenes serves as a key driving force for activation of the electron-rich benzofulvenes. Utilizing the current methodology, a wide range of multi-substituted chiral spiro-pyrrolidine derivatives containing two contiguous all-carbon quaternary centers were formed in good yield with exclusive chemo-/regioselectivity and high to excellent stereoselectivity. Computational mechanistic studies elucidate the origin of the stereochemical outcome and the chemoselectivity, in which the thermostability of these cycloaddition products is the major factor.
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Affiliation(s)
- Xin Chang
- Engineering Research Center of Organosilicon Compounds & Materials, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry Shanghai 230021 China
| | - Xue-Tao Liu
- Engineering Research Center of Organosilicon Compounds & Materials, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry Shanghai 230021 China
| | - Fangfang Li
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Shenzhen 518055 China
| | - Yuhong Yang
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Shenzhen 518055 China
| | - Lung Wa Chung
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Shenzhen 518055 China
| | - Chun-Jiang Wang
- Engineering Research Center of Organosilicon Compounds & Materials, Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University Wuhan 430072 China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry Shanghai 230021 China
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23
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Ariai J, Gellrich U. The entropic penalty for associative reactions and their physical treatment during routine computations. Phys Chem Chem Phys 2023; 25:14005-14015. [PMID: 37161492 DOI: 10.1039/d3cp00970j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 ΔrG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol-1 (classic) and underestimated by 2 kcal mol-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol-1 lower than barriers obtained with WFT.
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Affiliation(s)
- Jama Ariai
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
| | - Urs Gellrich
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
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24
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Schwiedrzik L, Rajkovic T, González L. Regeneration and Degradation in a Biomimetic Polyoxometalate Water Oxidation Catalyst. ACS Catal 2023; 13:3007-3019. [PMID: 36910868 PMCID: PMC9990072 DOI: 10.1021/acscatal.2c06301] [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: 12/21/2022] [Revised: 01/30/2023] [Indexed: 02/16/2023]
Abstract
Complete understanding of catalytic cycles is required to advance the design of water oxidation catalysts, but it is difficult to attain, due to the complex factors governing their reactivity and stability. In this study, we investigate the regeneration and degradation pathways of the highly active biomimetic water oxidation catalyst [Mn3+ 2Mn4+ 2V4O17(OAc)3]3-, thereby completing its catalytic cycle. Beginning with the deactivated species [Mn3+ 4V4O17(OAc)2]4- left over after O2 evolution, we scrutinize a network of reaction intermediates belonging to two alternative water oxidation cycles. We find that catalyst regeneration to the activated species [Mn4+ 4V4O17(OAc)2(OH)(H2O)]- proceeds via oxidation of each Mn center, with one water ligand being bound during the first oxidation step and a second water ligand being bound and deprotonated during the final oxidation step. ΔΔG values for this last oxidation are consistent with previous experimental results, while regeneration within an alternative catalytic cycle was found to be thermodynamically unfavorable. Extensive in silico sampling of catalyst structures also revealed two degradation processes: cubane opening and ligand dissociation, both of which have low barriers at highly reduced states of the catalyst due to the presence of Jahn-Teller effects. These mechanistic insights are expected to spur the development of more efficient and stable Mn cubane water oxidation catalysts.
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Affiliation(s)
- Ludwig Schwiedrzik
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.,Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, 1090 Vienna, Austria
| | - Tina Rajkovic
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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25
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Cabrera DJ, Lewis RD, Díez-Poza C, Álvarez-Miguel L, Mosquera MEG, Hamilton A, Whiteoak CJ. Group 13 salphen compounds (In, Ga and Al): a comparison of their structural features and activities as catalysts for cyclic carbonate synthesis. Dalton Trans 2023; 52:5882-5894. [PMID: 36852925 DOI: 10.1039/d3dt00089c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Many complexes based on group 13 elements have been successfully applied as catalysts for the synthesis of cyclic carbonates from epoxides and CO2 and to date these have provided some of the most active catalysts developed. It is notable that most reports have focused on the use of aluminium-based compounds likely because of the well-established Lewis acidity of this element and its cost. In comparison, relatively little attention has been paid to the development of catalysts based on the heavier group 13 elements, despite their known Lewis acidic properties. This study describes the synthesis of aluminium, gallium and indium compounds supported by a readily prepared salphen ligand and explores both their comparative structures and also their potential as catalysts for the synthesis of cyclic carbonates. In addition, the halide ligand which forms a key part of the compound has been systematically varied and the effect of this change on the structure and catalytic activity is also discussed. It is demonstrated that the indium compounds are actually, and unexpectedly, the most active for cyclic carbonate synthesis, despite their lower Lewis acidity when compared to their aluminium congeners. The experimental observations from this work are fully supported by a Density Functional Theory (DFT) study, which provides important insights into the reasons as to why the indium catalyst with bromide, [InBr(salphen)], is most active.
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Affiliation(s)
- Diego Jaraba Cabrera
- Universidad de Alcalá, Grupo SOSCATCOM, Departamento de Química Orgánica y Química Inorgánica, Facultad de Farmacia and Instituto de Investigación Química Andrés M. del Río (IQAR), Campus Universitario, Ctra. Madrid-Barcelona Km. 33, 600, 28871 Alcalá de Henares, Madrid, Spain.
| | - Ryan D Lewis
- Sheffield Hallam University, Biomolecular Sciences Research Centre (BMRC) and Department of Biosciences and Chemistry, College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Howard Street, Sheffield, S1 1WB, UK
| | - Carlos Díez-Poza
- Universidad de Alcalá, Grupo SOSCATCOM, Departamento de Química Orgánica y Química Inorgánica, Facultad de Farmacia and Instituto de Investigación Química Andrés M. del Río (IQAR), Campus Universitario, Ctra. Madrid-Barcelona Km. 33, 600, 28871 Alcalá de Henares, Madrid, Spain.
| | - Lucía Álvarez-Miguel
- Universidad de Alcalá, Grupo SOSCATCOM, Departamento de Química Orgánica y Química Inorgánica, Facultad de Farmacia and Instituto de Investigación Química Andrés M. del Río (IQAR), Campus Universitario, Ctra. Madrid-Barcelona Km. 33, 600, 28871 Alcalá de Henares, Madrid, Spain.
| | - Marta E G Mosquera
- Universidad de Alcalá, Grupo SOSCATCOM, Departamento de Química Orgánica y Química Inorgánica, Facultad de Farmacia and Instituto de Investigación Química Andrés M. del Río (IQAR), Campus Universitario, Ctra. Madrid-Barcelona Km. 33, 600, 28871 Alcalá de Henares, Madrid, Spain.
| | - Alex Hamilton
- Sheffield Hallam University, Biomolecular Sciences Research Centre (BMRC) and Department of Biosciences and Chemistry, College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Howard Street, Sheffield, S1 1WB, UK
| | - Christopher J Whiteoak
- Universidad de Alcalá, Grupo SOSCATCOM, Departamento de Química Orgánica y Química Inorgánica, Facultad de Farmacia and Instituto de Investigación Química Andrés M. del Río (IQAR), Campus Universitario, Ctra. Madrid-Barcelona Km. 33, 600, 28871 Alcalá de Henares, Madrid, Spain.
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26
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Kee CW. Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities. Molecules 2023; 28:molecules28041715. [PMID: 36838703 PMCID: PMC9966076 DOI: 10.3390/molecules28041715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/25/2023] Open
Abstract
Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.
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Affiliation(s)
- Choon Wee Kee
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
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Abstract
Reactivity scales are useful research tools for chemists, both experimental and computational. However, to determine the reactivity of a single molecule, multiple measurements need to be carried out, which is a time-consuming and resource-intensive task. In this Tutorial Review, we present alternative approaches for the efficient generation of quantitative structure-reactivity relationships that are based on quantum chemistry, supervised learning, and uncertainty quantification. First published in 2002, we observe a tendency for these relationships to become not only more predictive but also more interpretable over time.
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Affiliation(s)
- Maike Vahl
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany.
| | - Jonny Proppe
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany.
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28
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Solvent Coordination Effect on Copper-Based Molecular Catalysts for Controlled Radical Polymerization. Catalysts 2022. [DOI: 10.3390/catal12121656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The equilibrium of copper-catalyzed atom transfer radical polymerization was investigated in silico with the aim of finding an explanation for the experimentally observed solvent effect. Various combinations of alkyl halide initiators and copper complexes in acetonitrile (MeCN) and dimethyl sulfoxide (DMSO) were taken into consideration. A continuum model for solvation, which does not account for the explicit interactions between the solvent and metal complex, is not adequate and does not allow the reproduction of the experimental trend. However, when the solvent molecules are included in the coordination sphere of the copper(I,II) species and the continuum description of the medium is still used, a solvent dependence of process thermodynamics emerges, in fair agreement with experimental trends.
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29
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Qin C, Huang Z, Wu SB, Li Z, Yang Y, Xu S, Zhang X, Liu G, Wu YD, Chung LW, Huang Z. Breaking Conventional Site Selectivity in C–H Bond Activation: Selective sp 3 versus sp 2 Silylation by a Pincer-Based Pocket. J Am Chem Soc 2022; 144:20903-20914. [DOI: 10.1021/jacs.2c09356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chuan Qin
- The State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Zhidao Huang
- The State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Song-Bai Wu
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Zhuangxing Li
- The State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yuhong Yang
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Songgen Xu
- The State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xin Zhang
- The State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Guixia Liu
- The State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zheng Huang
- The State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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30
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de Lima Lopes Rocha P, dos Santos FM, Pinheiro S, Fiorot RG. Noncovalent interactions as a solution for the metal-free one-pot asymmetric synthesis of (S)-2-aryl-2,3-dihydro-4(1H)-quinolones. J Mol Model 2022; 28:369. [DOI: 10.1007/s00894-022-05361-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/20/2022] [Indexed: 11/29/2022]
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31
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Lan J, Zhang T, Yang Y, Li X, Chung LW. A Mechanistic Study of the Cobalt(I)-Catalyzed Amination of Aryl Halides: Effects of Metal and Ligand. Inorg Chem 2022; 61:18019-18032. [DOI: 10.1021/acs.inorgchem.2c02385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jialing Lan
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Tonghuan Zhang
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
- Lab of Computational Chemistry and Drug Design, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yuhong Yang
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
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32
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Talmazan RA, Refugio Monroy J, del Río‐Portilla F, Castillo I, Podewitz M. Encapsulation Enhances the Catalytic Activity of C-N Coupling: Reaction Mechanism of a Cu(I)/Calix[8]arene Supramolecular Catalyst. ChemCatChem 2022; 14:e202200662. [PMID: 36605358 PMCID: PMC9804476 DOI: 10.1002/cctc.202200662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/11/2022] [Indexed: 01/07/2023]
Abstract
Development of C-N coupling methodologies based on Earth-abundant metals is a promising strategy in homogeneous catalysis for sustainable processes. However, such systems suffer from deactivation and low catalytic activity. We here report that encapsulation of Cu(I) within the phenanthroyl-containing calix[8]arene derivative 1,5-(2,9-dimethyl-1,10-phenanthroyl)-2,3,4,6,7,8-hexamethyl-p-tert-butylcalix[8]arene (C8PhenMe6 ) significantly enhances C-N coupling activity up to 92 % yield in the reaction of aryl halides and aryl amines, with low catalyst loadings (2.5 % mol). A tailored multiscale computational protocol based on Molecular Dynamics simulations and DFT investigations revealed an oxidative addition/reductive elimination process of the supramolecular catalyst [Cu(C8PhenMe6)I]. The computational investigations uncovered the origins of the enhanced catalytic activity over its molecular analogues: Catalyst deactivation through dimerization is prevented, and product release facilitated. Capturing the dynamic profile of the macrocycle and the impact of non-covalent interactions on reactivity allows for the rationalization of the behavior of the flexible supramolecular catalysts employed.
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Affiliation(s)
- Radu A. Talmazan
- Institute of Materials ChemistryTU WienGetreidemarkt 91060ViennaAustria
- Institute of General, Inorganic, and Theoretical Chemistry and Center of Molecular BiosciencesUniversity of InnsbruckInnrain 80/826020InnsbruckAustria
| | - J. Refugio Monroy
- Instituto de QuímicaUniversidad Nacional Autónoma de MéxicoCircuito ExteriorCU, Ciudad de México04510México
- Present address: Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Strasse 212489BerlinGermany
| | - Federico del Río‐Portilla
- Instituto de QuímicaUniversidad Nacional Autónoma de MéxicoCircuito ExteriorCU, Ciudad de México04510México
| | - Ivan Castillo
- Instituto de QuímicaUniversidad Nacional Autónoma de MéxicoCircuito ExteriorCU, Ciudad de México04510México
| | - Maren Podewitz
- Institute of Materials ChemistryTU WienGetreidemarkt 91060ViennaAustria
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Bursch M, Mewes J, Hansen A, Grimme S. Best-Practice DFT Protocols for Basic Molecular Computational Chemistry. Angew Chem Int Ed Engl 2022; 61:e202205735. [PMID: 36103607 PMCID: PMC9826355 DOI: 10.1002/anie.202205735] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 01/11/2023]
Abstract
Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.
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Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| | - Jan‐Michael Mewes
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
| | - Andreas Hansen
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
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34
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Darù A, Martín-Fernández C, Harvey JN. Iron-Catalyzed Kumada Cross-Coupling Reaction Involving Fe 8Me 12– and Related Clusters: A Computational Study. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Darù
- Department of Chemistry, Scripps Research, La Jolla, California92037, United States
| | | | - Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, LeuvenB-3001, Belgium
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35
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Wititsuwannakul T, Hall MB, Gladysz JA. Mechanism of Coupling of Methylidene to Ethylene Ligands in Dimetallic Assemblies; Computational Investigation of a Model for a Key Step in Catalytic C 1 Chemistry. J Am Chem Soc 2022; 144:18672-18687. [PMID: 36174130 DOI: 10.1021/jacs.2c08886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methylidene complexes often couple to ethylene complexes, but the mechanistic insight is scant. The path by which two cations [(η5-C5H5)Re(NO)(PPh3)(═CH2)]+ (5+) transform (CH2Cl2/acetonitrile) to [(η5-C5H5)Re(NO)(PPh3)(H2C═CH2)]+ (6+) and [(η5-C5H5)Re(NO)(PPh3)(NCCH3)]+ is studied by density functional theory. Experiments provide a number of constraints such as the second-order rate in 5+; no prior ligand dissociation/exchange; a faster reaction of (S)-5+ with (S)-5+ than with (R)-5+ ("enantiomer self-recognition"). Although dirhenium dications with Re(μ-CH2)2Re cores represent energy minima, they are not accessible by 2 + 2 cycloadditions of 5+. Transition states leading to ReCH2CH2Re linkages are prohibitively high in energy. However, 5+ can give non-covalent SRe/SRe or SRe/RRe dimers with π interactions between the PPh3 ligands but long ReCH2···H2CRe and H2CRe···H2CRe distances (3.073-3.095 Å and 3.878-4.529 Å, respectively). In rate-determining steps, these afford [(η5-C5H5)Re(NO)(PPh3)(μ-η2:η2-H2C···CH2)(Ph3P)(ON)Re(η5-C5H5)]2+ (132+), in which one rhenium binds the bridging ethylene more tightly than the other (2.115-2.098 vs 2.431-2.486 Å to the centroid). In the SRe/RRe adduct, Dewar-Chatt-Duncanson optimization leads to unfavorable PPh3/PPh3 contacts. Ligand interactions are further dissected in the preceding transition states via component analyses, and ΔΔG‡ (1.2 kcal/mol, CH2Cl2) favors the SRe/SRe pathway, in accordance with the experiment. Acetonitrile then displaces 6+ from the more weakly bound rhenium of 132+. The formation of similar μ-H2C···CH2 intermediates is found to be rate-determining for varied coordinatively saturated M═CH2 species [M = Fe(d6)/Re(d4)/Ta(d2)], establishing generality and enhancing relevancy to catalytic CH4 and CO/H2 chemistry.
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Affiliation(s)
- Taveechai Wititsuwannakul
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - Michael B Hall
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - John A Gladysz
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
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36
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Rummel L, König HF, Hausmann H, Schreiner PR. Silyl Groups Are Strong Dispersion Energy Donors. J Org Chem 2022; 87:13168-13177. [PMID: 36166406 DOI: 10.1021/acs.joc.2c01633] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an experimental and computational study to investigate noncovalent interactions between silyl groups that are often employed as "innocent" protecting groups. We chose an extended cyclooctatetraene (COT)-based molecular balance comprising unfolded (1,4-disubstituted) and folded (1,6-disubstituted) valance bond isomers that typically display remote and close silyl group contacts, respectively. The thermodynamic equilibria were determined using nuclear magnetic resonance measurements. Additionally, we utilized Boltzmann weighted symmetry-adapted perturbation theory (SAPT) at the sSAPT0/aug-cc-pVDZ level of theory to dissect and quantify noncovalent interactions. Apart from the extremely bulky tris(trimethylsilyl)silyl "supersilyl" group, there is a preference for the folded 1,6-COT valence isomer, with London dispersion interactions being the main stabilizing factor. This makes silyl groups excellent dispersion energy donors, a finding that needs to be taken into account in synthesis planning.
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Affiliation(s)
- Lars Rummel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Henrik F König
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Heike Hausmann
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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37
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Bursch M, Mewes J, Hansen A, Grimme S. Best‐Practice DFT Protocols for Basic Molecular Computational Chemistry**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Jan‐Michael Mewes
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
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38
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Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes. Nat Protoc 2022; 17:2550-2569. [PMID: 35978038 DOI: 10.1038/s41596-022-00726-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 05/23/2022] [Indexed: 11/09/2022]
Abstract
Volcano plots and activity maps are powerful tools for studying homogeneous catalysis. Once constructed, they can be used to estimate and predict the performance of a catalyst from one or more descriptor variables. The relevance and utility of these tools has been demonstrated in several areas of catalysis, with recent applications to homogeneous catalysts having been pioneered by our research group. Both volcano plots and activity maps are built from linear free energy scaling relationships that connect the value of a descriptor variable(s) with the relative energies of other catalytic cycle intermediates/transition states. These relationships must be both constructed and postprocessed appropriately to obtain the resulting plots/maps; this process requires careful execution to obtain meaningful results. In this protocol, we provide a step-by-step guide to building volcano plots and activity maps using curated reaction profile data. The reaction profile data are obtained using density functional theory computations to model the catalytic cycle. In addition, we provide volcanic, a Python code that automates the steps of the process following data acquisition. Unlike the computation of individual reaction energy profiles, our tools lead to a holistic view of homogeneous catalyst performance that can be broadly applied for both explanatory and screening purposes.
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39
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A Plausible Mechanism for the Iridium-Catalyzed Hydrogenation of a Bulky N-Aryl Imine in the (S)-Metolachlor Process. Molecules 2022; 27:molecules27165106. [PMID: 36014344 PMCID: PMC9414898 DOI: 10.3390/molecules27165106] [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: 07/18/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 01/06/2023] Open
Abstract
The hydrogenation of N-(2-ethyl-6-methylphenyl)-1-methoxypropan-2-imine is the largest-scale asymmetric catalytic process for the industrial production of agrochemical (S)-metolachlor. The challenging hydrogenation across the sterically crowded carbon–nitrogen double bond was achieved using a mixture of [IrCl(COD)]2, (R,SFc)-Xyliphos, NBu4I and acetic acid. Acetic acid was critical in achieving excellent productivity and activity. Despite its industrial significance, a mechanism that explains how the sterically hindered bond in the imine is reduced has yet to be proposed. We propose a plausible proton-first, outer-sphere mechanism based on density functional theory calculations that is consistent with the experimentally observed activity and the enantioselectivity of the industrial process. Key findings include transition states involving acetate-assisted dihydrogen splitting, and a hydride transfer from a five-coordinate iridium trihydride directed by a C-H∙∙∙Ir interaction. This article was submitted to a Special Issue in honor of Professor Henri Kagan.
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40
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Pliego JR. Copper-Catalyzed Aromatic Fluorination of 2-(2-bromophenyl)pyridine via Cu(I)/Cu(III) Mechanism in Acetonitrile Solvent: Cluster-Continuum Free Energy Profile and Microkinetic Analysis. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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Ouyang Q, Pang Y, Yuan C, Tan H, Li X, Chen G. Theoretical investigation on the reaction mechanism of UTP cyclohydrolase. Phys Chem Chem Phys 2022; 24:17641-17653. [PMID: 35833743 DOI: 10.1039/d2cp01740g] [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
Nucleoside triphosphate cyclohydrolase (UrcA) is a critical enzyme of the uracil catabolism pathway that catalyses the two-step hydrolysis of uridine triphosphate (UTP). Although the recently resolved X-ray structure of UrcA in complex with substrate analogue dUTP provided insights into the structural characteristics of the enzyme, the detailed catalytic mechanism, including how the reaction intermediate accomplishes conformational conversion in the active centre, remains unclear. In this study, extensive DFT calculations and MD simulations were performed to investigate the catalytic reaction process of UrcA. This study shows that the first hydrolytic reactions in UrcA follow a three-step mechanism, while the second hydrolytic reaction follows a two-step mechanism. Glu392 plays a critical role in deprotonating the lytic water in both hydrolytic reactions. The rate-limiting step of the first hydrolytic reaction lies in the cleavage of the uracil ring, in which an extraneous water molecule bridges the proton transfer from C6-OH to N1 to enable the reaction to go through a six-membered transition state with relatively low steric tension. In the second hydrolytic reaction, Glu392 abstracts protons from the lytic water and directly transfers them to the nitrogen atom of the cleaved C4-N3 bond so that the hydrolytic reaction is no longer rate-limited by the C-N bond cleavage step. MD simulations show that the reaction intermediate experiences spontaneous conformation overturn in the active site of UrcA under the assistance of the hydrogen bond interaction from Tyr307 to place its C4-N3 bond alongside the Zn2+ centre of the enzyme to trigger the second hydrolytic reaction.
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Affiliation(s)
- Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Yunjie Pang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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42
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Linnolahti M, Collins S. Thermodynamics of metallocene catalyst activation: alignment of theory and experiment. Dalton Trans 2022; 51:11152-11162. [PMID: 35801522 DOI: 10.1039/d2dt01711c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three equilibria involved in metallocene catalyst activation, including dissociation of R6Al2 (R = Me, Et or i-Bu) and related species such as [L2ZrMe2AlMe2][B(C6F5)4] (L2 = Cp2, 1,2-ethylenebis(η5-indenyl), Me2C(η5-C5H4)2) or [(L2ZrMe)2μ-Me][MePBB] (L2 = (h5-1,2-Me2C5H3)2, [MePBB]- = [MeB(ArF)3]- with ArF = o-C6F5-C6F4) are studied by DFT using various approaches to account for the enthalpy and entropy changes in gas and condensed phases. These studies reveal that both low energy vibrations and translational entropy conspire to cause significant deviations between theory and experiment when it comes to the free energy change in condensed or even gas phase. Alignment of theory with experiment requires in addition, consideration of specific solvation of reactants and products.
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Affiliation(s)
- Mikko Linnolahti
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, Yliopistokatu 7, FI-80100, Joensuu, Finland.
| | - Scott Collins
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, Yliopistokatu 7, FI-80100, Joensuu, Finland.
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43
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Fey N, Lynam JM. Computational mechanistic study in organometallic catalysis: Why prediction is still a challenge. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Natalie Fey
- School of Chemistry University of Bristol, Cantock's Close Bristol UK
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44
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Laplaza R, Sobez JG, Wodrich MD, Reiher M, Corminboeuf C. The (not so) simple prediction of enantioselectivity - a pipeline for high-fidelity computations. Chem Sci 2022; 13:6858-6864. [PMID: 35774159 PMCID: PMC9200111 DOI: 10.1039/d2sc01714h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
The computation of reaction selectivity represents an appealing complementary route to experimental studies and a powerful means to refine catalyst design strategies. Accurately establishing the selectivity of reactions facilitated by molecular catalysts, however, remains a challenging task for computational chemistry. The small free energy differences that lead to large variations in the enantiomeric ratio (er) represent particularly tricky quantities to predict with sufficient accuracy to be helpful for prioritizing experiments. Further complicating this problem is the fact that standard approaches typically consider only one or a handful of conformers identified through human intuition as pars pro toto of the conformational space. Obviously, this assumption can potentially lead to dramatic failures should key energetic low-lying structures be missed. Here, we introduce a multi-level computational pipeline leveraging the graph-based Molassembler library to construct an ensemble of molecular catalysts. The manipulation and interpretation of molecules as graphs provides a powerful and direct route to tailored functionalization and conformer generation that facilitates high-throughput mechanistic investigations of chemical reactions. The capabilities of this approach are validated by examining a Rh(iii) catalyzed asymmetric C-H activation reaction and assessing the limitations associated with the underlying ligand design model. Specifically, the presence of remarkably flexible chiral Cp ligands, which induce the experimentally observed high level of selectivity, present a rich configurational landscape where multiple unexpected conformations contribute to the reported enantiomeric ratios (er). Using Molassembler, we show that considering about 20 transition state conformations per catalysts, which are generated with little human intervention and are not tied to "back-of-the-envelope" models, accurately reproduces experimental er values with limited computational expense.
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Affiliation(s)
- Rubén Laplaza
- Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Jan-Grimo Sobez
- Laboratorium für Physikalische Chemie, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), ETH Zürich Vladimir-Prelog-Weg 1-5/10 8093 Zürich Switzerland
| | - Matthew D Wodrich
- Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), ETH Zürich Vladimir-Prelog-Weg 1-5/10 8093 Zürich Switzerland
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
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45
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Gorbachev V, Tsybizova A, Miloglyadova L, Chen P. Increasing Complexity in a Conformer Space Step-by-Step: Weighing London Dispersion against Cation-π Interactions. J Am Chem Soc 2022; 144:9007-9022. [PMID: 35549249 DOI: 10.1021/jacs.2c01381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report an evaluation of the importance of London dispersion in moderately large (up to 36 heavy atoms) organic molecules by means of a molecular torsion balance whose conformations "weigh" one interaction against another in the absence of solvents. The experimental study, with gas-phase cryogenic ion vibrational predissociation (CIVP) spectroscopy, solid-state Fourier transfer infrared (FT-IR), and single-crystal X-ray crystallography, is accompanied by density functional theory calculations, including an extensive search and analysis of accessible conformations. We begin with the unsubstituted molecular torsion balance, and then step up the complexity systematically by adding alkyl groups incrementally as dispersion energy donors (DEDs) to achieve a degree of chemical complexity comparable to what is typically found in transition states for many regio- and stereoselective reactions in organic and organometallic chemistry. We find clear evidence for the small attractive contribution by DEDs, as had been reported in other studies, but we also find that small individual contributions by London dispersion, when they operate in opposition to other weak noncovalent interactions, produce composite effects on the structure that are difficult to predict intuitively, or by modern quantum chemical calculations. The experimentally observed structures, together with a reasonable value for a reference cation-π interaction, indicate that the pairwise interaction between two tert-butyl groups, in the best case, is modest. Moreover, the visualization of the conformational space, and comparison to spectroscopic indicators of the structure, as one steps up the complexity of the manifold of noncovalent interactions, makes clear that in silico predictive ability for the structure of moderately large, flexible, organic molecules falters sooner than one might have expected.
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Affiliation(s)
- Vladimir Gorbachev
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Alexandra Tsybizova
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Larisa Miloglyadova
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Peter Chen
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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46
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Liang H, Rio J, Perrin L, Payard PA. Salt-Enhanced Oxidative Addition of Iodobenzene to Pd: An Interplay Between Cation, Anion, and Pd-Pd Cooperative Effects. Inorg Chem 2022; 61:7935-7944. [PMID: 35522732 DOI: 10.1021/acs.inorgchem.2c00565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halide salts facilitate the oxidative addition of organic halides to Pd(0). This phenomenon originates from a combination of anionic, cationic, and Pd-Pd cooperative effects. Exhaustive computational exploration at the density functional theory level of the complexes obtained from [Pd0(PPh3)2] and a salt (NMe4Cl or LiCl) showed that chlorides promote phosphine release, leading to a mixture of mononuclear and dinuclear Pd(0) complexes. Anionic Pd(0) dinuclear complexes exhibit a cooperativity between Pd(0) centers, which favors the oxidative addition of iodobenzene. The higher activity of Pd(0) dimers toward oxidative addition rationalizes the previously reported kinetic laws. In the presence of Li+, the oxidative addition to mononuclear [Pd0L(Li2Cl2)] is estimated barrierless. LiCl coordination polarizes Pd(0), enlarging both the electrophilicity and the nucleophilicity of the complex, which promotes both coordination of the substrate and the subsequent insertion into the C-I bond. These conclusions are paving the way to the rational use of the salt effects in catalysis for the activation of more challenging bonds.
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Affiliation(s)
- Haosheng Liang
- Univ de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne cedex, France
| | - Jordan Rio
- Univ de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne cedex, France
| | - Lionel Perrin
- Univ de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne cedex, France
| | - Pierre-Adrien Payard
- Univ de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne cedex, France
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47
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Lan J, Li X, Yang Y, Zhang X, Chung LW. New Insights and Predictions into Complex Homogeneous Reactions Enabled by Computational Chemistry in Synergy with Experiments: Isotopes and Mechanisms. Acc Chem Res 2022; 55:1109-1123. [PMID: 35385649 DOI: 10.1021/acs.accounts.1c00774] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Homogeneous catalysis and biocatalysis have been widely applied in synthetic, medicinal, and energy chemistry as well as synthetic biology. Driven by developments of new computational chemistry methods and better computer hardware, computational chemistry has become an essentially indispensable mechanistic "instrument" to help understand structures and decipher reaction mechanisms in catalysis. In addition, synergy between computational and experimental chemistry deepens our mechanistic understanding, which further promotes the rational design of new catalysts. In this Account, we summarize new or deeper mechanistic insights (including isotope, dispersion, and dynamical effects) into several complex homogeneous reactions from our systematic computational studies along with subsequent experimental studies by different groups. Apart from uncovering new mechanisms in some reactions, a few computational predictions (such as excited-state heavy-atom tunneling, steric-controlled enantioswitching, and a new geminal addition mechanism) based on our mechanistic insights were further verified by ensuing experiments.The Zimmerman group developed a photoinduced triplet di-π-methane rearrangement to form cyclopropane derivatives. Recently, our computational study predicted the first excited-state heavy-atom (carbon) quantum tunneling in one triplet di-π-methane rearrangement, in which the reaction rates and 12C/13C kinetic isotope effects (KIEs) can be enhanced by quantum tunneling at low temperatures. This unprecedented excited-state heavy-atom tunneling in a photoinduced reaction has recently been verified by an experimental 12C/13C KIE study by the Singleton group. Such combined computational and experimental studies should open up opportunities to discover more rare excited-state heavy-atom tunneling in other photoinduced reactions. In addition, we found unexpectedly large secondary KIE values in the five-coordinate Fe(III)-catalyzed hetero-Diels-Alder pathway, even with substantial C-C bond formation, due to the non-negligible equilibrium isotope effect (EIE) derived from altered metal coordination. Therefore, these KIE values cannot reliably reflect transition-state structures for the five-coordinate metal pathway. Furthermore, our density functional theory (DFT) quasi-classical molecular dynamics (MD) simulations demonstrated that the coordination mode and/or spin state of the iron metal as well as an electric field can affect the dynamics of this reaction (e.g., the dynamically stepwise process, the entrance/exit reaction channels).Moreover, we unveiled a new reaction mechanism to account for the uncommon Ru(II)-catalyzed geminal-addition semihydrogenation and hydroboration of silyl alkynes. Our proposed key gem-Ru(II)-carbene intermediates derived from double migrations on the same alkyne carbon were verified by crossover experiments. Additionally, our DFT MD simulations suggested that the first hydrogen migration transition-state structures may directly and quickly form the key gem-Ru-carbene structures, thereby "bypassing" the second migration step. Furthermore, our extensive study revealed the origin of the enantioselectivity of the Cu(I)-catalyzed 1,3-dipolar cycloaddition of azomethine ylides with β-substituted alkenyl bicyclic heteroarenes enabled by dual coordination of both substrates. Such mechanistic insights promoted our computational predictions of the enantioselectivity reversal for the corresponding monocyclic heteroarene substrates and the regiospecific addition to the less reactive internal C═C bond of one diene substrate. These predictions were proven by our experimental collaborators. Finally, our mechanistic insights into a few other reactions are also presented. Overall, we hope that these interactive computational and experimental studies enrich our mechanistic understanding and aid in reaction development.
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Affiliation(s)
- Jialing Lan
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Yuhong Yang
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Xiaoyong Zhang
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry, and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
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48
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Sinha V, Khramenkova E, Pidko EA. Solvent-mediated outer-sphere CO 2 electro-reduction mechanism over the Ag111 surface. Chem Sci 2022; 13:3803-3808. [PMID: 35432905 PMCID: PMC8966634 DOI: 10.1039/d1sc07119j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/23/2022] [Indexed: 12/01/2022] Open
Abstract
The electrocatalytic CO2 reduction reaction (CO2RR) is one of the key technologies of the clean energy economy. Molecular-level understanding of the CO2RR process is instrumental for the better design of electrodes operable at low overpotentials with high current density. The catalytic mechanism underlying the turnover and selectivity of the CO2RR is modulated by the nature of the electrocatalyst, as well as the electrolyte liquid, and its ionic components that form the electrical double layer (EDL). Herein we demonstrate the critical non-innocent role of the EDL for the activation and conversion of CO2 at a high cathodic bias for electrocatalytic conversion over a silver surface as a representative low-cost model cathode. By using a multiscale modeling approach we demonstrate that under such conditions a dense EDL is formed, which hinders the diffusion of CO2 towards the Ag111 electrocatalyst surface. By combining DFT calculations and ab initio molecular dynamics simulations we identify favorable pathways for CO2 reduction directly over the EDL without the need for adsorption to the catalyst surface. The dense EDL promotes homogeneous phase reduction of CO2 via electron transfer from the surface to the electrolyte. Such an outer-sphere mechanism favors the formation of formate as the CO2RR product. The formate can undergo dehydration to CO via a transition state stabilized by solvated alkali cations in the EDL.
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Affiliation(s)
- Vivek Sinha
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology Delft The Netherlands
| | - Elena Khramenkova
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology Delft The Netherlands
| | - Evgeny A Pidko
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology Delft The Netherlands
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Eisenstein O. From the Felkin‐Anh Rule to the Grignard Reaction: an Almost Circular 50 Year Adventure in the World of Molecular Structures and Reaction Mechanisms with Computational Chemistry**. Isr J Chem 2022. [DOI: 10.1002/ijch.202100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Odile Eisenstein
- ICGM, Univ. Montpellier, CNRS, ENSCM, Montpellier, 34095 France Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo Oslo 0315 Norway
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50
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Steiner M, Reiher M. Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis. Top Catal 2022; 65:6-39. [PMID: 35185305 PMCID: PMC8816766 DOI: 10.1007/s11244-021-01543-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to catalysis: (i) automation allows one to consider orders of magnitude more structures in a systematic and open-ended fashion than what would be accessible by manual inspection. Eventually, full resolution in terms of structural varieties and conformations as well as with respect to the type and number of potentially important elementary reaction steps (including decomposition reactions that determine turnover numbers) may be achieved. (ii) Fast electronic structure methods with uncertainty quantification warrant high efficiency and reliability in order to not only deliver results quickly, but also to allow for predictive work. (iii) A high degree of autonomy reduces the amount of manual human work, processing errors, and human bias. Although being inherently unbiased, it is still steerable with respect to specific regions of an emerging network and with respect to the addition of new reactant species. This allows for a high fidelity of the formalization of some catalytic process and for surprising in silico discoveries. In this work, we first review the state of the art in computational catalysis to embed autonomous explorations into the general field from which it draws its ingredients. We then elaborate on the specific conceptual issues that arise in the context of autonomous computational procedures, some of which we discuss at an example catalytic system.
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Affiliation(s)
- Miguel Steiner
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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