1
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Galeas DM, Tolbatov I, Colacino E, Maseras F. Computational study on the mechanism for the synthesis of active pharmaceutical ingredients nitrofurantoin and dantrolene in both solution and mechanochemical conditions. Phys Chem Chem Phys 2024; 26:24288-24293. [PMID: 39279546 DOI: 10.1039/d4cp01613k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
A combination of density functional theory (DFT) calculations and microkinetic simulations is applied to the study of condensation between N-acyl-hydrazides and aldehydes in acidic media to produce the active pharmaceutical ingredients (API) nitrofurantoin and dantrolene. Previous experimental reports have shown that the use of ball milling conditions leads to a reduction in the reaction time, which is associated with a significant reduction of waste. This result is reproduced by the current calculations, which additionally provide a detailed mechanistic explanation for this behavior.
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Affiliation(s)
- Dayana M Galeas
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans 16, 43007, Tarragona, Spain
| | - Iogann Tolbatov
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans 16, 43007, Tarragona, 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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2
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Deshmukh MA, Bakandritsos A, Zbořil R. Bimetallic Single-Atom Catalysts for Water Splitting. NANO-MICRO LETTERS 2024; 17:1. [PMID: 39317789 PMCID: PMC11422407 DOI: 10.1007/s40820-024-01505-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 08/10/2024] [Indexed: 09/26/2024]
Abstract
Green hydrogen from water splitting has emerged as a critical energy vector with the potential to spearhead the global transition to a fossil fuel-independent society. The field of catalysis has been revolutionized by single-atom catalysts (SACs), which exhibit unique and intricate interactions between atomically dispersed metal atoms and their supports. Recently, bimetallic SACs (bimSACs) have garnered significant attention for leveraging the synergistic functions of two metal ions coordinated on appropriately designed supports. BimSACs offer an avenue for rich metal-metal and metal-support cooperativity, potentially addressing current limitations of SACs in effectively furnishing transformations which involve synchronous proton-electron exchanges, substrate activation with reversible redox cycles, simultaneous multi-electron transfer, regulation of spin states, tuning of electronic properties, and cyclic transition states with low activation energies. This review aims to encapsulate the growing advancements in bimSACs, with an emphasis on their pivotal role in hydrogen generation via water splitting. We subsequently delve into advanced experimental methodologies for the elaborate characterization of SACs, elucidate their electronic properties, and discuss their local coordination environment. Overall, we present comprehensive discussion on the deployment of bimSACs in both hydrogen evolution reaction and oxygen evolution reaction, the two half-reactions of the water electrolysis process.
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Affiliation(s)
- Megha A Deshmukh
- Nanotechnology Centre, Centre for Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
| | - Aristides Bakandritsos
- Nanotechnology Centre, Centre for Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 241/27, 783 71, Olomouc - Holice, Czech Republic.
| | - Radek Zbořil
- Nanotechnology Centre, Centre for Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 241/27, 783 71, Olomouc - Holice, Czech Republic.
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3
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Di Matteo M, Gagliardi A, Pradal A, Veiros LF, Gallou F, Poli G. Pd-Catalyzed C(sp 2)-H/C(sp 2)-H Coupling of Limonene. J Org Chem 2024; 89:10451-10461. [PMID: 39025478 DOI: 10.1021/acs.joc.4c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Limonene undergoes a regioselective Pd(II)-catalyzed C(sp2)-H/C(sp2)-H coupling with acrylic acid esters and amides, α,β-unsaturated ketones, styrenes, and allyl acetate, affording novel 1,3-dienes. DFT computations gave results in accord with the experimental results and allowed for the formulation of a plausible mechanism. The postfunctionalization of one of the coupled products was achieved via a large-scale Sonogashira reaction conducted under micellar catalysis.
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Affiliation(s)
- Marco Di Matteo
- Institut Parisien de Chimie Moléculaire (IPCM), Faculté des Sciences et Ingénierie, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Anna Gagliardi
- Institut Parisien de Chimie Moléculaire (IPCM), Faculté des Sciences et Ingénierie, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Alexandre Pradal
- Institut Parisien de Chimie Moléculaire (IPCM), Faculté des Sciences et Ingénierie, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Luis F Veiros
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049 001 Lisboa, Portugal
| | | | - Giovanni Poli
- Institut Parisien de Chimie Moléculaire (IPCM), Faculté des Sciences et Ingénierie, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
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4
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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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5
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Sharma AK, Maseras F. The Subtle Mechanism of Nickel-Photocatalyzed C(sp 3)-H Cross-Coupling. Inorg Chem 2024; 63:13801-13806. [PMID: 39018463 DOI: 10.1021/acs.inorgchem.4c01763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
This computational study revises and reformulates the mechanism for the cross-coupling reaction between chlorobenzene and tetrahydrofuran catalyzed by a Ni complex with the assistance of an Ir photocatalyst. This is a representative process of transition-metal photocatalysis, and variations of it have been reported by different experimental authors. It has been also the subject of previous computational studies, which we revise and extend. Density functional theory (DFT) calculations and microkinetic modeling indicate that the most efficient mechanism takes place through an energy-transfer step and involves a NiIII complex.
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Affiliation(s)
- Akhilesh K Sharma
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avenida Països Catalans 16, Tarragona 43007, Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avenida Països Catalans 16, Tarragona 43007, Spain
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6
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Bhattacharyya HP, Sarma M. Efficiency Conceptualization Model: A Theoretical Method for Predicting the Turnover of Catalysts. Chemphyschem 2024; 25:e202400004. [PMID: 38619023 DOI: 10.1002/cphc.202400004] [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: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/16/2024]
Abstract
In recent times, the theoretical prediction of catalytic efficiency is of utmost urgency. With the advent of density functional theory (DFT), reliable computations can delineate a quantitative aspect of the study. To this state-of-the-art approach, valuable incorporation would be a tool that can acknowledge the efficiency of a catalyst. In the current work, we developed the efficiency conceptualization model (ECM) that utilizes the quantum mechanical tool to achieve efficiency in terms of turnover frequency (TOF). Twenty-six experimentally designed transition metal (TM) water oxidation catalysts were chosen under similar experimental conditions of temperature, pressure, and pH to execute the same. The computations conclude that the Fe-based [Fe(OTf)2(Me2Pytacn)] (MWOC-17) is a highly active catalyst and, therefore, can endure for more time in the catalytic cycle. Our results conclude that the Ir-based catalysts [Cp*Ir(κ2-N,O)X] with MWOC-23: X=Cl; and MWOC-24: X=NO3 report the highest computed turnover numbers (TONs),τ c o m p u t e d T O N 0 ${\tau _{computed\;TON}^0 }$ of 406 and 490 against the highest experimental TONs,τ e x p e r i m e n t a l T O N ${\tau _{experimental\;TON} }$ of 1200 and 2000 respectively, whereas the Co-based [Co(12-TMC)]2+ (MWOC-19) has the lowest TONs (τ c o m p u t e d T O N 0 ${\tau _{computed\;TON}^0 }$ =19, τexperimental TON=16) among the chosen catalysts and thereby successful in corroborating the previous experimental results.
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Affiliation(s)
| | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
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7
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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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8
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Kalikadien AV, Mirza A, Hossaini AN, Sreenithya A, Pidko EA. Paving the road towards automated homogeneous catalyst design. Chempluschem 2024; 89:e202300702. [PMID: 38279609 DOI: 10.1002/cplu.202300702] [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: 11/29/2023] [Revised: 12/20/2023] [Indexed: 01/28/2024]
Abstract
In the past decade, computational tools have become integral to catalyst design. They continue to offer significant support to experimental organic synthesis and catalysis researchers aiming for optimal reaction outcomes. More recently, data-driven approaches utilizing machine learning have garnered considerable attention for their expansive capabilities. This Perspective provides an overview of diverse initiatives in the realm of computational catalyst design and introduces our automated tools tailored for high-throughput in silico exploration of the chemical space. While valuable insights are gained through methods for high-throughput in silico exploration and analysis of chemical space, their degree of automation and modularity are key. We argue that the integration of data-driven, automated and modular workflows is key to enhancing homogeneous catalyst design on an unprecedented scale, contributing to the advancement of catalysis research.
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Affiliation(s)
- Adarsh V Kalikadien
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Adrian Mirza
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Aydin Najl Hossaini
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Avadakkam Sreenithya
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Evgeny A Pidko
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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9
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Miao L, Jia W, Cao X, Jiao L. Computational chemistry for water-splitting electrocatalysis. Chem Soc Rev 2024; 53:2771-2807. [PMID: 38344774 DOI: 10.1039/d2cs01068b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Electrocatalytic water splitting driven by renewable electricity has attracted great interest in recent years for producing hydrogen with high-purity. However, the practical applications of this technology are limited by the development of electrocatalysts with high activity, low cost, and long durability. In the search for new electrocatalysts, computational chemistry has made outstanding contributions by providing fundamental laws that govern the electron behavior and enabling predictions of electrocatalyst performance. This review delves into theoretical studies on electrochemical water-splitting processes. Firstly, we introduce the fundamentals of electrochemical water electrolysis and subsequently discuss the current advancements in computational methods and models for electrocatalytic water splitting. Additionally, a comprehensive overview of benchmark descriptors is provided to aid in understanding intrinsic catalytic performance for water-splitting electrocatalysts. Finally, we critically evaluate the remaining challenges within this field.
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Affiliation(s)
- Licheng Miao
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Wenqi Jia
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Xuejie Cao
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Lifang Jiao
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China.
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10
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Resende LF, Pliego JR. Modeling the alkylation of amines with alkyl bromides: explaining the low selectivity due to multiple alkylation. J Mol Model 2024; 30:107. [PMID: 38492112 DOI: 10.1007/s00894-024-05902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
CONTEXT Nucleophilic substitution reactions of aliphatic amines with alkyl halides represent a simple and direct mechanism for obtaining higher-order aliphatic amines. However, it is well known that these reactions suffer from low selectivity due to multiple alkylations, which is attributed to the higher reactivity of the newly formed amine. In order to provide a detailed explanation for this kind of system, we have investigated the reactivity of primary and secondary amines with 1-bromopropane and 2-bromopropane. The free energy profile in acetonitrile solution was obtained and a detailed microkinetic analysis was needed to analyze this complex reaction system. We have found that the product of the first alkylation is an ion pair corresponding to the protonated secondary amine and the bromide ion, which can transfer the proton to the reactant primary amine. Then, the newly formed secondary amine can also react, leading to a second alkylation to produce a tertiary protonated amine. Our modeling points out that both the proton transfer equilibria and the similar reactivity of the primary and secondary amines produce reduced selectivity. The proton transfer equilibria also contribute to slowing down the kinetics of the first alkylation. METHODS The exploration of the mechanism was done by geometry optimization using the CPCM/X3LYP/ma-def2-SVP method, followed by harmonic frequency calculation at this same level of theory. A composite approach was used to obtain the free energy profile, using the more accurate ωB97X-D3/ma-def2-TZVPP level of theory for electronic energy and the SMD model for the solvation free energy. These calculations were performed with the ORCA 4 program. The detailed microkinetic analysis was done using the Kintecus program.
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Affiliation(s)
- Luis F Resende
- Departamento de Ciências Naturais, Universidade Federal de São João del Rei, São João del Rei, MG, 36301-160, Brazil
| | - Josefredo R Pliego
- Departamento de Ciências Naturais, Universidade Federal de São João del Rei, São João del Rei, MG, 36301-160, Brazil.
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11
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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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12
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Monti A, López-Serrano J, Prieto A, Nicasio MC. Broad-Scope Amination of Aryl Sulfamates Catalyzed by a Palladium Phosphine Complex. ACS Catal 2023; 13:10945-10952. [PMID: 37614522 PMCID: PMC10443792 DOI: 10.1021/acscatal.3c03166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/20/2023] [Indexed: 08/25/2023]
Abstract
Among phenol-derived electrophiles, aryl sulfamates are attractive substrates since they can be employed as directing groups for C-H functionalization prior to catalysis. However, their use in C-N coupling is limited only to Ni catalysis. Here, we describe a Pd-based catalyst with a broad scope for the amination of aryl sulfamates. We show that the N-methyl-2-aminobiphenyl palladacycle supported by the PCyp2ArXyl2 ligand (Cyp = cyclopentyl; ArXyl2 = 2,6-bis(2,6-dimethylphenyl)phenyl) efficiently catalyzes the C-N coupling of aryl sulfamates with a variety of nitrogen nucleophiles, including anilines, primary and secondary alkyl amines, heteroaryl amines, N-heterocycles, and primary amides. DFT calculations support that the oxidative addition of the aryl sulfamate is the rate-determining step. The C-N coupling takes place through a cationic pathway in the polar protic medium.
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Affiliation(s)
- Andrea Monti
- Departamento
de Química Inorgánica, Universidad
de Sevilla, Aptdo 1203, 41071 Sevilla, Spain
| | - Joaquín López-Serrano
- Instituto
de Investigaciones Químicas (IIQ), Departamento de Química
Inorgánica and Centro de Innovación Química Avanzada
(ORFEO-CINQA), Universidad de Sevilla and
CSIC, 41092 Sevilla, Spain
| | - Auxiliadora Prieto
- Laboratorio
de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro
de Investigación en Química Sostenible and Departamento
de Química, Universidad de Huelva, Campus de El Carmen s/n, 21007 Huelva, Spain
| | - M. Carmen Nicasio
- Departamento
de Química Inorgánica, Universidad
de Sevilla, Aptdo 1203, 41071 Sevilla, Spain
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13
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Rama RJ, Maya C, Molina F, Nova A, Nicasio MC. Important Role of NH-Carbazole in Aryl Amination Reactions Catalyzed by 2-Aminobiphenyl Palladacycles. ACS Catal 2023; 13:3934-3948. [PMID: 36970467 PMCID: PMC10029719 DOI: 10.1021/acscatal.3c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/25/2023] [Indexed: 03/09/2023]
Abstract
2-Aminobiphenyl palladacycles are among the most successful precatalysts for Pd-catalyzed cross-coupling reactions, including aryl amination. However, the role of NH-carbazole, a byproduct of precatalyst activation, remains poorly understood. Herein, the mechanism of the aryl amination reactions catalyzed by a cationic 2-aminobiphenyl palladacycle supported by a terphenyl phosphine ligand, PCyp2ArXyl2 (Cyp = cyclopentyl; ArXyl2 = 2,6-bis(2,6-dimethylphenyl)phenyl), P1, has been thoroughly investigated. Combining computational and experimental studies, we found that the Pd(II) oxidative addition intermediate reacts with NH-carbazole in the presence of the base (NaO t Bu) to yield a stable aryl carbazolyl Pd(II) complex. This species functions as the catalyst resting state, providing the amount of monoligated LPd(0) species required for catalysis and minimizing Pd decomposition. In the case of a reaction with aniline, an equilibrium between the carbazolyl complex and the on-cycle anilido analogue is established, which allows for a fast reaction at room temperature. In contrast, heating is required in a reaction with alkylamines, whose deprotonation involves coordination to the Pd center. A microkinetic model was built combining computational and experimental data to validate the mechanistic proposals. In conclusion, our study shows that despite the rate reduction observed in some reactions by the formation of the aryl carbazolyl Pd(II) complex, this species reduces catalyst decomposition and could be considered an alternative precatalyst in cross-coupling reactions.
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Affiliation(s)
- Raquel J. Rama
- Departamento de Química Inorgánica, Universidad de Sevilla, Aptdo 1203, 41071 Sevilla, Spain
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences and Centre for Materials Science and Nanotechnology, University of Oslo, N-0315 Oslo, Norway
| | - Celia Maya
- Instituto de Investigaciones Químicas (IIQ), Departamento de Química Inorgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Sevilla, Avenida Américo Vespucio 49, 41092 Sevilla, Spain
| | - Francisco Molina
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química, Universidad de Huelva, 21071 Huelva, Spain
| | - Ainara Nova
- Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences and Centre for Materials Science and Nanotechnology, University of Oslo, N-0315 Oslo, Norway
| | - M. Carmen Nicasio
- Departamento de Química Inorgánica, Universidad de Sevilla, Aptdo 1203, 41071 Sevilla, Spain
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14
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Schneider FSS, Caramori GF. Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions. J Comput Chem 2023; 44:209-217. [PMID: 35404515 DOI: 10.1002/jcc.26861] [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: 01/23/2022] [Revised: 03/07/2022] [Accepted: 03/23/2022] [Indexed: 12/31/2022]
Abstract
Today's demand for precisely predicting chemical reactions from first principles requires research to go beyond Gibbs' free energy diagrams and consider other effects such as concentrations and quantum tunneling. The present work introduces overreact, a novel Python package for propagating chemical reactions over time using data from computational chemistry only. The overreact code infers all differential equations and parameters from a simple input that consists of a set of chemical equations and quantum chemistry package outputs for each chemical species. We evaluate some applications from the literature: gas-phase eclipsed-staggered isomerization of ethane, gas-phase umbrella inversion of ammonia, gas-phase degradation of methane by chlorine radical, and three solvation-phase reactions. Furthermore, we comment on a simple solvation-phase acid-base equilibrium. We show how it is possible to achieve reaction profiles and information matching experiments.
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Affiliation(s)
- Felipe S S Schneider
- Department of Chemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Giovanni F Caramori
- Department of Chemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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15
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Dowman LJ, Kulkarni SS, Alegre-Requena JV, Giltrap AM, Norman AR, Sharma A, Gallegos LC, Mackay AS, Welegedara AP, Watson EE, van Raad D, Niederacher G, Huhmann S, Proschogo N, Patel K, Larance M, Becker CFW, Mackay JP, Lakhwani G, Huber T, Paton RS, Payne RJ. Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine. Nat Commun 2022; 13:6885. [PMID: 36371402 PMCID: PMC9653470 DOI: 10.1038/s41467-022-34530-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.
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Affiliation(s)
- Luke J Dowman
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Sameer S Kulkarni
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Juan V Alegre-Requena
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Andrew M Giltrap
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Alexander R Norman
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Ashish Sharma
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Liliana C Gallegos
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Adarshi P Welegedara
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Emma E Watson
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Damian van Raad
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Gerhard Niederacher
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Susanne Huhmann
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Nicholas Proschogo
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Mark Larance
- Charles Perkins Centre and School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Christian F W Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Girish Lakhwani
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia.
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16
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Ismail I, Chantreau Majerus R, Habershon S. Graph-Driven Reaction Discovery: Progress, Challenges, and Future Opportunities. J Phys Chem A 2022; 126:7051-7069. [PMID: 36190262 PMCID: PMC9574932 DOI: 10.1021/acs.jpca.2c06408] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/22/2022] [Indexed: 11/29/2022]
Abstract
Graph-based descriptors, such as bond-order matrices and adjacency matrices, offer a simple and compact way of categorizing molecular structures; furthermore, such descriptors can be readily used to catalog chemical reactions (i.e., bond-making and -breaking). As such, a number of graph-based methodologies have been developed with the goal of automating the process of generating chemical reaction network models describing the possible mechanistic chemistry in a given set of reactant species. Here, we outline the evolution of these graph-based reaction discovery schemes, with particular emphasis on more recent methods incorporating graph-based methods with semiempirical and ab initio electronic structure calculations, minimum-energy path refinements, and transition state searches. Using representative examples from homogeneous catalysis and interstellar chemistry, we highlight how these schemes increasingly act as "virtual reaction vessels" for interrogating mechanistic questions. Finally, we highlight where challenges remain, including issues of chemical accuracy and calculation speeds, as well as the inherent challenge of dealing with the vast size of accessible chemical reaction space.
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Affiliation(s)
- Idil Ismail
- Department of Chemistry, University
of Warwick, CoventryCV4 7AL, United Kingdom
| | | | - Scott Habershon
- Department of Chemistry, University
of Warwick, CoventryCV4 7AL, United Kingdom
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17
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Li M, Liao RZ. Water Oxidation Catalyzed by a Bioinspired Tetranuclear Manganese Complex: Mechanistic Study and Prediction. CHEMSUSCHEM 2022; 15:e202200187. [PMID: 35610183 DOI: 10.1002/cssc.202200187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Density functional theory calculations were utilized to elucidate the water oxidation mechanism catalyzed by polyanionic tetramanganese complex a [MnIII 3 MnIV O3 (CH3 COO)3 (A-α-SiW9 O34 )]6- . Theoretical results indicated that catalytic active species 1 (Mn4 III,III,IV,IV ) was formed after O2 formation in the first turnover. From 1, three sequential proton-coupled electron transfer (PCET) oxidations led to the MnIV -oxyl radical 4 (Mn4 IV,IV,IV,IV -O⋅). Importantly, 4 had an unusual butterfly-shaped Mn2 O2 core for the two substrate-coordinated Mn sites, which facilitated O-O bond formation via direct coupling of the oxyl radical and the adjacent MnIV -coordinated hydroxide to produce the hydroperoxide intermediate Int1 (Mn4 III,IV,IV,IV -OOH). This step had an overall energy barrier of 24.9 kcal mol-1 . Subsequent PCET oxidation of Int1 to Int2 (Mn4 III,IV,IV,IV -O2 ⋅) enabled the O2 release in a facile process. Furthermore, apart from the Si-centered complex, computational study suggested that tetramanganese polyoxometalates with Ge, P, and S could also catalyze the water oxidation process, where those bearing P and S likely present higher activities.
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Affiliation(s)
- Man Li
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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18
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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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19
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Xiao B, Sun TY, Wu YD. Study of Pd-catalyzed Selective Mono- and Di-C(sp 3)-H Bond Activation: A Bi-ligand Model. J Org Chem 2022; 87:10958-10966. [PMID: 35901268 DOI: 10.1021/acs.joc.2c01235] [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
Controlling the number of C-H bond activation is a long-standing challenge in organic synthesis. Recently, Yu's group demonstrated that in Pd-catalyzed alanine's arylation, pyridine-type ligands favor a mono-C-H bond activation, while quinoline-type ligands favor a di-C-H bond activation. To disclose the underlying principles, a theoretical study (density functional theory (DFT)) has been carried out. Our study indicates that a mono-ligand model, which is generally adopted in the community, does not reproduce the experimentally observed mono-/di-selectivity, while a bi-ligand model can rationalize the experimental observations well, including the observed diastereoselectivity in diarylation. The electron-rich pyridine-type ligands with less steric congestion can promote the C-H bond activation reaction of alanine derivatives. The quinoline-type ligands have a better π back-donation interaction with the metal, which makes a more active C-H bond activation than the pyridine-type ligands for this reaction. This bi-ligand model, which is a necessity, allows the understanding and future design of a dual ligand effect in C-H bond activation.
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Affiliation(s)
- Bo Xiao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Computational Chemistry and Drug Design, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Computational Chemistry and Drug Design, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.,Shenzhen Bay Laboratory, Shenzhen 518132, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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20
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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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21
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Ismail I, Robertson C, Habershon S. Successes and challenges in using machine-learned activation energies in kinetic simulations. J Chem Phys 2022; 157:014109. [DOI: 10.1063/5.0096027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The prediction of the thermodynamic and kinetic properties of chemical reactions is increasingly being addressed by machine-learning (ML) methods such as artificial neural networks (ANNs). While a number of recent studies have reported success in predicting chemical reaction activation energies, less attention has focused on how the accuracy of ML predictions filter through to predictions of macroscopic observables. Here, we consider the impact of the uncertainty associated with ML prediction of activation energies on observable properties of chemical reaction networks, as given by microkinetics simulations based on ML-predicted reaction rates. After training an ANN to predict activation energies given standard molecular descriptors for reactants and products alone, we performed microkinetics simulations of three different prototypical reaction networks: formamide decomposition, aldol reactions and decomposition of 3-hydroperoxypropanal. We find that the kinetic modelling predictions can be in excellent agreement with corresponding simulations performed with ab initio calculations, but this is dependent on the inherent energetic landscape of the networks. We use these simulations to suggest some guidelines for when ML-based activation energies can be reliable, and when one should take more care in applications to kinetics modelling.
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Affiliation(s)
| | | | - Scott Habershon
- Department of Chemistry, University of Warwick, United Kingdom
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22
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Garay-Ruiz D, Bo C. Chemical reaction network knowledge graphs: the OntoRXN ontology. J Cheminform 2022; 14:29. [PMID: 35637523 PMCID: PMC9153116 DOI: 10.1186/s13321-022-00610-x] [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: 04/01/2022] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a novel ontology describing the reaction networks constructed from computational chemistry calculations. Under our paradigm, these networks are handled as undirected graphs, without assuming any traversal direction. From there, we propose a core class structure including reaction steps, network stages, chemical species, and the lower-level entities for the individual computational calculations. These individual calculations are founded on the OntoCompChem ontology and on the ioChem-BD database, where information is parsed and stored in CML format. OntoRXN is introduced through several examples in which knowledge graphs based on the ontology are generated for different chemical systems available on ioChem-BD. Finally, the resulting knowledge graphs are explored through SPARQL queries, illustrating the power of the semantic approach to standardize the analysis of intricate datasets and to simplify the development of complex workflows.
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Affiliation(s)
- Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel . lí Domingo s/n, 43007 Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel . lí Domingo s/n, 43007 Tarragona, Spain
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23
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Harper DR, Kulik HJ. Computational Scaling Relationships Predict Experimental Activity and Rate-Limiting Behavior in Homogeneous Water Oxidation. Inorg Chem 2022; 61:2186-2197. [PMID: 35037756 DOI: 10.1021/acs.inorgchem.1c03376] [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
While computational screening with first-principles density functional theory (DFT) is essential for evaluating candidate catalysts, limitations in accuracy typically prevent the prediction of experimentally relevant activities. Exemplary of these challenges are homogeneous water oxidation catalysts (WOCs) where differences in experimental conditions or small changes in ligand structure can alter rate constants by over an order of magnitude. Here, we compute mechanistically relevant electronic and energetic properties for 19 mononuclear Ru transition-metal complexes (TMCs) from three experimental water oxidation catalysis studies. We discover that 15 of these TMCs have experimental activities that correlate with a single property, the ionization potential of the Ru(II)-O2 catalytic intermediate. This scaling parameter allows the quantitative understanding of activity trends and provides insight into the rate-limiting behavior. We use this approach to rationalize differences in activity with different experimental conditions, and we qualitatively analyze the source of distinct behavior for different electronic states in the other four catalysts. Comparison to closely related single-atom catalysts and modified WOCs enables rationalization of the source of rate enhancement in these WOCs.
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Affiliation(s)
- Daniel R Harper
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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24
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Heitkämper J, Herrmann J, Titze M, Bauch SM, Peters R, Kästner J. Asymmetric Hydroboration of Ketones by Cooperative Lewis Acid–Onium Salt Catalysis: A Quantum Chemical and Microkinetic Study to Combine Theory and Experiment. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juliane Heitkämper
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Justin Herrmann
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Marvin Titze
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Soeren M. Bauch
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - René Peters
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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25
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Tamosiunaite N, Logie LC, Neale SE, Singh K, Davies DL, Macgregor SA. Experimental and Computational Studies on the Acetate-Assisted C-H Activation of N-Aryl Imidazolium Salts at Rhodium and Iridium: A Chloride Additive Changes the Selectivity of C-H Activation. J Org Chem 2021; 87:1445-1456. [PMID: 34967215 DOI: 10.1021/acs.joc.1c02756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Combined experimental and computational mechanistic studies of the reactions of unsymmetrical, para-substituted N-aryl imidazolium salts, L2-R1,R2, at [MCl2Cp*]2 (M = Rh, Ir) in the presence of NaOAc are reported. These proceed via intermediate N-heterocyclic carbene complexes that then allow an internal competition between two differently substituted aryl rings toward C-H activation to be monitored. At 348 K in dichloroethane C-H activation of the aryl with the more electron-withdrawing substituents is generally favored. DFT calculations show similar barriers for proton transfer and dissociative HOAc/Cl- ligand substitution, with proton transfer favoring electron-donating substituents, and ligand substitution favoring electron-withdrawing substituents. Microkinetic simulations reproduce the experimental preference implying that the ligand substitution step dominates selectivity. For several substrates, notably L2-F,OMe and L2-F,H, running the C-H activation reactions at 298 K in the presence of added [Et4N]Cl reverses the selectivity. The greater availability of chloride in solution makes an alternative dissociative interchange ligand substitution mechanism accessible, leaving proton transfer as selectivity determining and so favoring electron-donating substituents. Our results highlight the potential importance of the ligand substitution step in the interpretation of substituent effects and demonstrate how a simple additive, [Et4N]Cl, can have a dramatic effect on selectivity by changing the mechanism of ligand substitution.
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Affiliation(s)
| | - Lauren C Logie
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, U.K
| | - Samuel E Neale
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, U.K
| | - Kuldip Singh
- Department of Chemistry, University of Leicester, Leicester, LE1 7RH, U.K
| | - David L Davies
- Department of Chemistry, University of Leicester, Leicester, LE1 7RH, U.K
| | - Stuart A Macgregor
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, U.K
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26
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Artús Suàrez L, Balcells D, Nova A. Computational Studies on the Mechanisms for Deaminative Amide Hydrogenation by Homogeneous Bifunctional Catalysts. Top Catal 2021. [DOI: 10.1007/s11244-021-01542-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractThe deaminative hydrogenation of amides is one of the most convenient pathways for the synthesis of amines and alcohols. The ideal source of reducing equivalents for this reaction is molecular hydrogen, though, in practice, this approach requires high pressures and temperatures, with many catalysts achieving only small turnover numbers and frequencies. Nonetheless, during the last ten years, this field has made major advances towards larger turnovers under milder conditions thanks to the development of bifunctional catalysts. These systems promote the heterolytic cleavage of hydrogen into proton and hydride by combining a basic ligand with an acidic metal centre. The present review focuses on the computational study of the reaction mechanism underlying bifunctional catalysis. This review is structured around the fundamental steps of this mechanism, namely the C=O and C–N hydrogenation of the amide, the C–N protonolysis of the hemiaminal, the C=O hydrogenation of the aldehyde, and the competition between hydrogen activation and catalyst deactivation. In line with the complexity of the mechanism, we also provide a perspective on the use of microkinetic models. Both Noyori- and Milstein-type catalysts are discussed and compared.
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27
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Siradze S, Poissonnier J, Frøseth M, Stensrød RE, Heyn RH, Thybaut JW. Kinetics Assessment of the Homogeneously Catalyzed Hydroformylation of Ethylene on an Rh Catalyst. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c02572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sébastien Siradze
- Laboratory for Chemical Technology, Ghent University, Technologiepark 125, 9052 Ghent, Belgium
| | - Jeroen Poissonnier
- Laboratory for Chemical Technology, Ghent University, Technologiepark 125, 9052 Ghent, Belgium
| | - Morten Frøseth
- SINTEF Industry, P.O. Box 124 Blindern, 0314 Oslo, Norway
| | | | | | - Joris W. Thybaut
- Laboratory for Chemical Technology, Ghent University, Technologiepark 125, 9052 Ghent, Belgium
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28
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Li X, Panetier JA. Computational Study for CO 2-to-CO Conversion over Proton Reduction Using [Re[bpyMe(Im-R)](CO) 3Cl] + (R = Me, Me 2, and Me 4) Electrocatalysts and Comparison with Manganese Analogues. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaohui Li
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States
| | - Julien A. Panetier
- Department of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States
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29
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Younas SL, Streuff J. Kinetic Analysis Uncovers Hidden Autocatalysis and Inhibition Pathways in Titanium(III)-Catalyzed Ketone-Nitrile Couplings. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Sara L. Younas
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Jan Streuff
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
- Department of Chemistry—BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
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30
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Nandy A, Duan C, Taylor MG, Liu F, Steeves AH, Kulik HJ. Computational Discovery of Transition-metal Complexes: From High-throughput Screening to Machine Learning. Chem Rev 2021; 121:9927-10000. [PMID: 34260198 DOI: 10.1021/acs.chemrev.1c00347] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transition-metal complexes are attractive targets for the design of catalysts and functional materials. The behavior of the metal-organic bond, while very tunable for achieving target properties, is challenging to predict and necessitates searching a wide and complex space to identify needles in haystacks for target applications. This review will focus on the techniques that make high-throughput search of transition-metal chemical space feasible for the discovery of complexes with desirable properties. The review will cover the development, promise, and limitations of "traditional" computational chemistry (i.e., force field, semiempirical, and density functional theory methods) as it pertains to data generation for inorganic molecular discovery. The review will also discuss the opportunities and limitations in leveraging experimental data sources. We will focus on how advances in statistical modeling, artificial intelligence, multiobjective optimization, and automation accelerate discovery of lead compounds and design rules. The overall objective of this review is to showcase how bringing together advances from diverse areas of computational chemistry and computer science have enabled the rapid uncovering of structure-property relationships in transition-metal chemistry. We aim to highlight how unique considerations in motifs of metal-organic bonding (e.g., variable spin and oxidation state, and bonding strength/nature) set them and their discovery apart from more commonly considered organic molecules. We will also highlight how uncertainty and relative data scarcity in transition-metal chemistry motivate specific developments in machine learning representations, model training, and in computational chemistry. Finally, we will conclude with an outlook of areas of opportunity for the accelerated discovery of transition-metal complexes.
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Affiliation(s)
- Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael G Taylor
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Fang Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam H Steeves
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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31
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Sciortino G, Maseras F. Computational Study of Homogeneous Multimetallic Cooperative Catalysis. Top Catal 2021. [DOI: 10.1007/s11244-021-01493-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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32
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Goossen LJ, Koley D, De S, Sivendran N. Isomerization of Functionalized Olefins Using the Dinuclear Catalyst [PdI(μ-Br)(PtBu3)]2: A Mechanistic Study. Chemistry 2021; 27:15226-15238. [PMID: 34387372 PMCID: PMC8596456 DOI: 10.1002/chem.202102554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 11/13/2022]
Abstract
In a combined experimental and computational study, the isomerization activity of the dinuclear palladium(I) complex [PdI(μ‐Br)(PtBu3)]2 towards allyl arenes, esters, amides, ethers, and alcohols has been investigated. The calculated energy profiles for catalyst activation for two alternative dinuclear and mononuclear catalytic cycles, and for catalyst deactivation are in good agreement with the experimental results. Comparison of experimentally observed E/Z ratios at incomplete conversion with calculated kinetic selectivities revealed that a substantial amount of product must form via the dinuclear pathway, in which the isomerization is promoted cooperatively by two palladium centers. The dissociation barrier towards mononuclear Pd species is relatively high, and once the catalyst enters the energetically more favorable mononuclear pathway, only a low barrier has to be overcome towards irreversible deactivation.
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Affiliation(s)
- Lukas J Goossen
- Ruhr-Universität Bochum, Organische Chemie I, Universitätsstraße 150, ZEMOS 2/27, 44801, 44801 Bochum, GERMANY
| | - Debasis Koley
- IISER-K: Indian Institute of Science Education and Research Kolkata, Chemical Sciences, Campus Rd, 741 246, Mohanpur, Nadia, INDIA
| | - Sriman De
- IISER-K: Indian Institute of Science Education and Research Kolkata, Chemical Sciences, Campus Rd, 741 246, Mohanpur, Nadia, INDIA
| | - Nardana Sivendran
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Chemistry and Biochemistry, Universitätsstr. 150, ZEMOS, 44795, Bochum, GERMANY
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33
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Krieger AM, Pidko EA. The Impact of Computational Uncertainties on the Enantioselectivity Predictions: A Microkinetic Modeling of Ketone Transfer Hydrogenation with a Noyori-type Mn-diamine Catalyst. ChemCatChem 2021; 13:3517-3524. [PMID: 34589158 PMCID: PMC8453751 DOI: 10.1002/cctc.202100341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/23/2021] [Indexed: 12/26/2022]
Abstract
Selectivity control is one of the most important functions of a catalyst. In asymmetric catalysis the enantiomeric excess (e.e.) is a property of major interest, with a lot of effort dedicated to developing the most enantioselective catalyst, understanding the origin of selectivity, and predicting stereoselectivity. Herein, we investigate the relationship between predicted selectivity and the uncertainties in the computed energetics of the catalytic reaction mechanism obtained by DFT calculations in a case study of catalytic asymmetric transfer hydrogenation (ATH) of ketones with an Mn-diamine catalyst. Data obtained from our analysis of DFT data by microkinetic modeling is compared to results from experiment. We discuss the limitations of the conventional reductionist approach of e.e. estimation from assessing the enantiodetermining steps only. Our analysis shows that the energetics of other reaction steps in the reaction mechanism have a substantial impact on the predicted reaction selectivity. The uncertainty of DFT calculations within the commonly accepted energy ranges of chemical accuracy may reverse the predicted e.e. with the non-enantiodetermining steps contributing to e.e. deviations of up to 25 %.
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Affiliation(s)
- Annika M. Krieger
- Inorganic Systems EngineeringDepartment of Chemical EngineeringFaculty of Applied SciencesDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
| | - Evgeny A. Pidko
- Inorganic Systems EngineeringDepartment of Chemical EngineeringFaculty of Applied SciencesDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
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34
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Pladevall BS, de Aguirre A, Maseras F. Understanding Ball Milling Mechanochemical Processes with DFT Calculations and Microkinetic Modeling. CHEMSUSCHEM 2021; 14:2763-2768. [PMID: 33843150 DOI: 10.1002/cssc.202100497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Mechanochemistry is an emerging field with many potential applications in sustainable chemistry. But despite the growing interest in the field, its underlying mechanistic foundations are not fully understood yet. This work presents the application of computational tools, such as DFT calculations in continuum and microkinetic modeling, to the analysis of mechanically activated procedures. Two reactions reported in previous experimental publications were studied: (i) a series of Diels-Alder reactions and (ii) the synthesis of sulfonylguanidines. Calculations succeed in reproducing experimentally reported reaction times. The procedures were mostly standard, coupled with some sensitive choices in terms of starting concentrations and dielectric constant. This means that these particular reactions accelerated by ball milling followed the same mechanism as the equivalent reactions in solution. The implications of this result on the general picture of mechanochemical processes are discussed.
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Affiliation(s)
- Bruna S Pladevall
- Institute of Chemical Research of Catalonia, The Barcelona Institute for Science and Technology, Avgda. Països Catalans, 16, Tarragona, 43007, Catalonia, Spain
| | - Adiran de Aguirre
- Institute of Chemical Research of Catalonia, The Barcelona Institute for Science and Technology, Avgda. Països Catalans, 16, Tarragona, 43007, Catalonia, Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia, The Barcelona Institute for Science and Technology, Avgda. Països Catalans, 16, Tarragona, 43007, Catalonia, Spain
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35
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Kuznetsov ML, Pombeiro AJ. Metal-free and iron(II)-assisted oxidation of cyclohexane to adipic acid with ozone: A theoretical mechanistic study. J Catal 2021. [DOI: 10.1016/j.jcat.2021.04.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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36
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Affiliation(s)
- Agustí Lledós
- Departament de Química Universitat Autònoma de Barcelona Campus UAB 08193 Cerdanyola del Vallès Catalonia Spain
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37
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Clark JA, Thacker PJ, McGill CJ, Miles JR, Westmoreland PR, Efimenko K, Genzer J, Santiso EE. DFT Analysis of Organotin Catalytic Mechanisms in Dehydration Esterification Reactions for Terephthalic Acid and 2,2,4,4-Tetramethyl-1,3-cyclobutanediol. J Phys Chem A 2021; 125:4943-4956. [PMID: 34101445 DOI: 10.1021/acs.jpca.1c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyesters synthesized from 2,2,4,4-tetramethyl-1,3-cyclobutanediol (TMCD) and terephthalic acid (TPA) are improved alternatives to toxic polycarbonates based on bisphenol A. In this work, we use ωB97X-D/LANL2DZdp calculations, in the presence of a benzaldehyde polarizable continuum model solvent, to show that esterification of TMCD and TPA will reduce and subsequently dehydrate a dimethyl tin oxide catalyst, becoming ligands on the now four-coordinate complex. This reaction then proceeds most plausibly by an intramolecular acyl-transfer mechanism from the tin complex, aided by a coordinated proton donor such as hydronium. These findings are a key first step in understanding polyester synthesis and avoiding undesirable side reactions during production.
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Affiliation(s)
- Jennifer A Clark
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Pranav J Thacker
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Charles J McGill
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jason R Miles
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Phillip R Westmoreland
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Kirill Efimenko
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jan Genzer
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Erik E Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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38
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Legnani L, Darù A, Jones AX, Blackmond DG. Mechanistic Insight into the Origin of Stereoselectivity in the Ribose-Mediated Strecker Synthesis of Alanine. J Am Chem Soc 2021; 143:7852-7858. [PMID: 33979125 DOI: 10.1021/jacs.1c03552] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enantioenriched amino acids are produced in a hydrolytic kinetic resolution of racemic aminonitriles mediated by chiral pentose sugars. Experimental kinetic and spectroscopic results combined with DFT computational studies and microkinetic modeling help to identify the nature of the intermediate species and provide insight into the stereoselectivity of their hydrolysis in the prebiotically relevant ribose-alanine system. These studies support a synergistic role for sugars and amino acids in the emergence of homochirality in biological molecules.
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Affiliation(s)
- Luca Legnani
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Andrea Darù
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Alexander X Jones
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Donna G Blackmond
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
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39
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Pliego JR. Diradical character of the bond breaking in the reaction of Br2 with benzene: Reliable barriers using the CR-CC(2,3) method. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Gan H, Peng L, Gu FL. Mechanistic understanding of the Cu( i)-catalyzed domino reaction constructing 1-aryl-1,2,3-triazole from electron-rich aryl bromide, alkyne, and sodium azide: a DFT study. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00123j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism of the Cu(i)-catalyzed domino reaction furnishing 1-aryl-1,2,3-triazole assisted by CuI and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) is explored with density functional theory (DFT) calculations.
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Affiliation(s)
- Hanlin Gan
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- School of Chemistry
- South China Normal University
- Guangzhou 51006
| | - Liang Peng
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- School of Chemistry
- South China Normal University
- Guangzhou 51006
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- School of Chemistry
- South China Normal University
- Guangzhou 51006
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41
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Besora M, Maseras F. Computational insights into metal-catalyzed asymmetric hydrogenation. ADVANCES IN CATALYSIS 2021. [DOI: 10.1016/bs.acat.2021.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Salamanca V, Albéniz AC. Faster palladium-catalyzed arylation of simple arenes in the presence of a methylketone: beneficial effect of an a priori interfering solvent in C–H activation. Org Chem Front 2021. [DOI: 10.1039/d1qo00236h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A methyl ketone accelerates the Pd-catalyzed C–H activation of simple arenes. A noninnocent solvent, it reacts in a reversible way without affecting the outcome of the reaction.
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Affiliation(s)
- Vanesa Salamanca
- IU CINQUIMA/Química Inorgánica. Universidad de Valladolid
- 47071 Valladolid
- Spain
| | - Ana C. Albéniz
- IU CINQUIMA/Química Inorgánica. Universidad de Valladolid
- 47071 Valladolid
- Spain
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43
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Guillamón E, Oliva M, Andrés J, Llusar R, Pedrajas E, Safont VS, Algarra AG, Basallote MG. Catalytic Hydrogenation of Azobenzene in the Presence of a Cuboidal Mo3S4 Cluster via an Uncommon Sulfur-Based H2 Activation Mechanism. ACS Catal 2020. [DOI: 10.1021/acscatal.0c05299] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Eva Guillamón
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain
| | - Mónica Oliva
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain
| | - Juan Andrés
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain
| | - Rosa Llusar
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain
| | - Elena Pedrajas
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain
| | - Vicent S. Safont
- Departament de Química Física i Analítica, Universitat Jaume I, Av. Sos Baynat s/n, 12071 Castelló, Spain
| | - Andres G. Algarra
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, Universidad de Cádiz, Apartado 40, 11510 Puerto Real, Cádiz, Spain
| | - Manuel G. Basallote
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, Universidad de Cádiz, Apartado 40, 11510 Puerto Real, Cádiz, Spain
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44
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Vandervelden CA, Khan SA, Peters B. Importance learning estimator for the site-averaged turnover frequency of a disordered solid catalyst. J Chem Phys 2020; 153:244120. [PMID: 33380094 DOI: 10.1063/5.0037450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For disordered catalysts such as atomically dispersed "single-atom" metals on amorphous silica, the active sites inherit different properties from their quenched-disordered local environments. The observed kinetics are site-averages, typically dominated by a small fraction of highly active sites. Standard sampling methods require expensive ab initio calculations at an intractable number of sites to converge on the site-averaged kinetics. We present a new method that efficiently estimates the site-averaged turnover frequency (TOF). The new estimator uses the same importance learning algorithm [Vandervelden et al., React. Chem. Eng. 5, 77 (2020)] that we previously used to compute the site-averaged activation energy. We demonstrate the method by computing the site-averaged TOF for a simple disordered lattice model of an amorphous catalyst. The results show that with the importance learning algorithm, the site-averaged TOF and activation energy can now be obtained concurrently with orders of magnitude reduction in required ab initio calculations.
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Affiliation(s)
- Craig A Vandervelden
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Salman A Khan
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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45
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Burrows LC, Jesikiewicz LT, Liu P, Brummond KM. Mechanism and Origins of Enantioselectivity in the Rh(I)-Catalyzed Pauson–Khand Reaction: Comparison of Bidentate and Monodentate Chiral Ligands. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03774] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lauren C. Burrows
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Luke T. Jesikiewicz
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Kay M. Brummond
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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46
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Rufino VC, Pliego JR. The role of carboxylic acid impurity in the mechanism of the formation of aldimines in aprotic solvents. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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47
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Neto DHC, Dos Santos AAM, Da Silva JCS, Rocha WR, Dias RP. Propene Hydroformylation Reaction Catalyzed by HRh(CO)(BISBI): A Thermodynamic and Kinetic Analysis of the Full Catalytic Cycle. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Daniel H. Cruz Neto
- Faculté des Sciences d'Orsay UFR Sciences Université Paris‐Saclay 91400 Orsay Île‐de‐France France
| | - Artur A. M. Dos Santos
- LQCBIO: Laboratório de Química Computacional e Modelagem de Biomoléculas Instituto de Química e Biotecnologia, IQB Universidade Federal de Alagoas Campus A. C. Simões 57072‐900 Maceió AL Brazil
| | - Júlio C. S. Da Silva
- LQCBIO: Laboratório de Química Computacional e Modelagem de Biomoléculas Instituto de Química e Biotecnologia, IQB Universidade Federal de Alagoas Campus A. C. Simões 57072‐900 Maceió AL Brazil
- eCsMoLab: Laboratório de Estudos Computacionais em Sistemas Moleculares Departamento de Química, ICEx Universidade Federal de Minas Gerais 31270‐901 Pampulha Belo Horizonte, MG Brazil
| | - Willian R. Rocha
- eCsMoLab: Laboratório de Estudos Computacionais em Sistemas Moleculares Departamento de Química, ICEx Universidade Federal de Minas Gerais 31270‐901 Pampulha Belo Horizonte, MG Brazil
| | - Roberta P. Dias
- eCsMoLab: Laboratório de Estudos Computacionais em Sistemas Moleculares Departamento de Química, ICEx Universidade Federal de Minas Gerais 31270‐901 Pampulha Belo Horizonte, MG Brazil
- GIMMM: Grupo Interdisciplinar de Modelagem Molecular e Simulação de Materiais Núcleo Interdisciplinar de Ciências Exatas e Inovação Tecnológica ‐ NICEN, Campus do Agreste Universidade Federal de Pernambuco 55002‐970 Caruaru PE Brazil
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48
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Garay-Ruiz D, Bo C. Revisiting Catalytic Cycles: A Broader View through the Energy Span Model. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, 43007 Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, 43007 Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel lí Domingo s/n, 43007 Tarragona, Spain
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49
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Benedek Z, Papp M, Oláh J, Szilvási T. Demonstrating the Direct Relationship between Hydrogen Evolution Reaction and Catalyst Deactivation in Synthetic Fe Nitrogenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zsolt Benedek
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Marcell Papp
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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50
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Cui CX, Chen H, Li SJ, Zhang T, Qu LB, Lan Y. Mechanism of Ir-catalyzed hydrogenation: A theoretical view. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213251] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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