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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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2
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Rastetter U, Jacobi von Wangelin A, Herrmann C. Redox-active ligands as a challenge for electronic structure methods. J Comput Chem 2023; 44:468-479. [PMID: 36326153 DOI: 10.1002/jcc.27013] [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: 03/04/2022] [Revised: 07/27/2022] [Accepted: 08/19/2022] [Indexed: 11/06/2022]
Abstract
To improve the catalytic activity of 3d transition metal catalysts, redox-active ligands are a promising tool. These ligands influence the oxidation state of the metal center as well as the ground spin-state and make the experimental determination of both properties challenging. Therefore, first-principles calculations, in particular employing density functional theory with a proper choice of exchange-correlation (xc) functional, are crucial. Common xc functionals were tested on a simple class of metal complexes: homoleptic, octahedral tris(diimine) iron(II) complexes. The spin-state energy splittings for most of these complexes showed the expected linear dependence on the amount of exact exchange included in the xc functionals. Even though varying redox-activity affects the electronic structure of the complexes considerably, the sensitivity of the spin-state energetics to the exact exchange admixture is surprisingly small. For iron(II) complexes with highly redox-active ligands and for a broad range of ligands in the reduced tris(diimine) iron(I) complexes, self-consistent field convergence to local minima was observed, which differ from the global minimum in the redox state of the ligand. This may also result in convergence to a molecular structure that corresponds to an energetically higher-lying local minimum. One criterion to detect such behavior is a change in the sign of the slope for the dependence of the spin-state energy splittings on the amount of exact exchange. We discuss possible protocols for dealing with such artifacts in cases in which a large number of calculations makes checking by hand unfeasible.
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Affiliation(s)
- Ursula Rastetter
- Department of Chemistry, University of Hamburg, Hamburg, Germany
| | | | - Carmen Herrmann
- Department of Chemistry, University of Hamburg, Hamburg, Germany
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3
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Díaz-Ruiz M, Urbina A, Llor N, Bosch J, Amat M, Maseras F. Origin of the selectivity in the ring-closing metathesis step of the synthesis of (−)-callyspongiolide: Formation of fourteen-versus eight-membered rings. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Epton RG, Unsworth WP, Lynam JM. DFT Studies of Au(I) Catalysed Reactions: Anion Effects and Reaction Selectivity. Isr J Chem 2022. [DOI: 10.1002/ijch.202200033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ryan G. Epton
- Department of Chemistry University of York Heslington, York YO10 5DD UK
| | | | - Jason M. Lynam
- Department of Chemistry University of York Heslington, York YO10 5DD UK
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5
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Grotjahn R, Kaupp M. A Look at Real‐World Transition‐Metal Thermochemistry and Kinetics with Local Hybrid Functionals. Isr J Chem 2022. [DOI: 10.1002/ijch.202200021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Robin Grotjahn
- Technische Universität Berlin Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7 Straße des 17. Juni 135 D-10623 Berlin Germany
| | - Martin Kaupp
- Technische Universität Berlin Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7 Straße des 17. Juni 135 D-10623 Berlin Germany
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Study on Rh(I)-o-aminophenol Catalyst Catalyzed Carbonylation of Methanol to Acetic Acid. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-022-06936-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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7
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Wang Y, Liao W, Wang Y, Jiao L, Yu ZX. Mechanism and Stereochemistry of Rhodium-Catalyzed [5 + 2 + 1] Cycloaddition of Ene-Vinylcyclopropanes and Carbon Monoxide Revealed by Visual Kinetic Analysis and Quantum Chemical Calculations. J Am Chem Soc 2022; 144:2624-2636. [PMID: 35130434 DOI: 10.1021/jacs.1c11030] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Previously, we developed a rhodium-catalyzed [5 + 2 + 1] cycloaddition of ene-vinylcyclopropanes (ene-VCPs) and carbon monoxide to synthesize eight-membered carbocycles. The efficiency of this reaction can be appreciated from its application in the synthesis of several natural products. Herein we report the results of a 15-year investigation into the mechanism of the [5 + 2 + 1] cycloaddition by applying visual kinetic analysis and high-level quantum chemical calculations at the DLPNO-CCSD(T)//BMK level. According to the kinetic measurements, the resting state of the catalyst possesses a dimeric structure (with two rhodium centers) whereas the active catalytic species is monomeric (with one rhodium center). The catalytic cycle consists of cyclopropane cleavage (the turnover-limiting step), alkene insertion, CO insertion, reductive elimination, and catalyst transfer steps. Other reaction pathways have also been considered but then have been ruled out. The steric origin of the diastereoselectivity (cis versus trans) was revealed by comparing the alkene insertion transition states. In addition, how the double-bond configuration of the VCPs (Z versus E) affects the substrate reactivity and the origins of chemoselectivity ([5 + 2 + 1] versus [5 + 2]) were also investigated. The present study will provide assistance in understanding other carbonylative annulations catalyzed by transition metals.
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Affiliation(s)
- Yi Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Wei Liao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Yuanyuan Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Lei Jiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Zhi-Xiang Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
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Sameera W, Takeda Y, Ohki Y. Transition metal catalyzed cross-coupling and nitrogen reduction reactions: Lessons from computational studies. ADVANCES IN ORGANOMETALLIC CHEMISTRY 2022. [DOI: 10.1016/bs.adomc.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Catalyzed stereo-selective hydrogenation of ynamides to give enamines: Ethanol as a hydrogen donor. J Organomet Chem 2021. [DOI: 10.1016/j.jorganchem.2021.122024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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10
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Matsuzawa A, Harvey JN, Himo F. On the Importance of Considering Multinuclear Metal Sites in Homogeneous Catalysis Modeling. Top Catal 2021. [DOI: 10.1007/s11244-021-01507-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractIn this short review, we provide an account of a number of computational studies of catalytic reaction mechanisms carried out in our groups. We focus in particular on studies in which we came to realize during the course of the investigation that the active catalytic species was a bimetallic complex, rather a monometallic one as previously assumed. In some cases, this realization was in part prompted by experimental observations, but careful exploration based on computation of the speciation of the metal precursor also provided a powerful guide: it is often possible to predict that bimetallic species (intermediates or transition states) lie lower in free energy than a priori competitive monometallic species. In this sense, we argue that in organometallic catalysis, the rule whereby “two is better than one” turns out to be relevant much more often than one might expect.
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Kaneko M, Nakashima S. Density Functional Theory Study on the 193Ir Mössbauer Spectroscopic Parameters of Vaska's Complexes and Their Oxidative Adducts. Inorg Chem 2021; 60:12740-12752. [PMID: 34410705 DOI: 10.1021/acs.inorgchem.1c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the present study, density functional theory (DFT) calculation was applied to Vaska's complexes of formula trans-[IrIX(CO)(PPh3)2] and their oxidative adducts with small molecules (YZ) including H2, i.e., trans-[IrIIIClYZ(CO)(PPh3)2], to successfully correlate the electronic states of the complexes with the corresponding 193Ir Mössbauer spectroscopic parameters. After confirming the reproducibility of the DFT methods for elucidating the equilibrium structures and 193Ir Mössbauer isomer shifts of the octahedral Ir complexes, the isomer shifts and quadrupole splitting values of Vaska's complexes and their oxidative adducts were calculated. A bond critical point analysis revealed that the tendency in the isomer shifts was correlated with the strength of the covalent interaction in the coordination bonds. In an electric field gradient (EFG) analysis of the oxidative adducts, the sign of the principal axis was found to be positive for the complex with YZ = Cl2 and negative for the complex with YZ = H2. This reversal of the sign of the EFG principal axis was caused by the difference in the electron density distribution for the coordination bonds between Ir and YZ, according to a density of states analysis.
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Affiliation(s)
- Masashi Kaneko
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4, Shirakata, Tokai-mura, Ibaraki 319-1195, Japan
| | - Satoru Nakashima
- Natural Science Center for Basic Research and Development, Hiroshima University, 1-4-2, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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12
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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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13
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Young TA, Silcock JJ, Sterling AJ, Duarte F. autodE: Automated Calculation of Reaction Energy Profiles— Application to Organic and Organometallic Reactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tom A. Young
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Joseph J. Silcock
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Alistair J. Sterling
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
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Abstract
The design of heterogeneous catalysts relies on understanding the fundamental surface kinetics that controls catalyst performance, and microkinetic modeling is a tool that can help the researcher in streamlining the process of catalyst design. Microkinetic modeling is used to identify critical reaction intermediates and rate-determining elementary reactions, thereby providing vital information for designing an improved catalyst. In this review, we summarize general procedures for developing microkinetic models using reaction kinetics parameters obtained from experimental data, theoretical correlations, and quantum chemical calculations. We examine the methods required to ensure the thermodynamic consistency of the microkinetic model. We describe procedures required for parameter adjustments to account for the heterogeneity of the catalyst and the inherent errors in parameter estimation. We discuss the analysis of microkinetic models to determine the rate-determining reactions using the degree of rate control and reversibility of each elementary reaction. We introduce incorporation of Brønsted-Evans-Polanyi relations and scaling relations in microkinetic models and the effects of these relations on catalytic performance and formation of volcano curves are discussed. We review the analysis of reaction schemes in terms of the maximum rate of elementary reactions, and we outline a procedure to identify kinetically significant transition states and adsorbed intermediates. We explore the application of generalized rate expressions for the prediction of optimal binding energies of important surface intermediates and to estimate the extent of potential rate improvement. We also explore the application of microkinetic modeling in homogeneous catalysis, electro-catalysis, and transient reaction kinetics. We conclude by highlighting the challenges and opportunities in the application of microkinetic modeling for catalyst design.
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Affiliation(s)
- Ali Hussain Motagamwala
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - James A Dumesic
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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15
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Recent advances in theoretical studies on ligand-controlled selectivity of nickel- and palladium-catalyzed cross-coupling reactions. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Young TA, Silcock JJ, Sterling AJ, Duarte F. autodE: Automated Calculation of Reaction Energy Profiles— Application to Organic and Organometallic Reactions. Angew Chem Int Ed Engl 2020; 60:4266-4274. [DOI: 10.1002/anie.202011941] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Tom A. Young
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Joseph J. Silcock
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Alistair J. Sterling
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
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17
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Computational mechanistic study on molecular catalysis of water oxidation by cyclam ligand-based iron complex. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02664-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Sahharova LT, Gordeev EG, Eremin DB, Ananikov VP. Pd-Catalyzed Synthesis of Densely Functionalized Cyclopropyl Vinyl Sulfides Reveals the Origin of High Selectivity in a Fundamental Alkyne Insertion Step. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Liliya T. Sahharova
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
| | - Evgeniy G. Gordeev
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
| | - Dmitry B. Eremin
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
- The Bridge@USC, University of Southern California, 1002 Childs Way, Los Angeles, California 90089-3502, United States
| | - Valentine P. Ananikov
- Zelinsky institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow 119991, Russia
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Takeda Y, Sameera WMC, Minakata S. Palladium-Catalyzed Regioselective and Stereospecific Ring-Opening Cross-Coupling of Aziridines: Experimental and Computational Studies. Acc Chem Res 2020; 53:1686-1702. [PMID: 32786337 DOI: 10.1021/acs.accounts.0c00395] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Aziridines, i.e., the smallest saturated N-heterocycles, serve as useful building blocks in synthetic organic chemistry. Because of the release of the large ring strain energy accommodated in the small ring, (ca. 27 kcal/mol), aziridines undergo ring-opening reactions with a variety of nucleophiles. Therefore, among the synthetic reactions utilizing aziridines, regioselective ring-opening substitutions of aziridines with nucleophiles, such as heteroatomic nucleophiles (e.g., amines, alcohols, and thiols) and carbonaceous nucleophiles (e.g., carbanions, organometallic reagents, and electron-rich arenes), constitute a useful synthetic methodology to synthesize biologically relevant β-functionalized alkylamines. However, the regioselection in such traditional ring-opening substitutions of aziridines is highly dependent on the substrate combination, and stereochemical control is challenging to achieve, especially in the case of Lewis acid-promoted variants. Therefore, the development of robust catalytic ring-opening functionalization methods that enable precise prediction of regioselectivity and stereochemistry is desirable. In this direction, our group focused on the highly regioselective and stereospecific nature of the stoichiometric oxidative addition elementary step of 2-substituted aziridines into Pd(0) complexes in an SN2 fashion. In conjunction with the recent advancements in transition-metal-catalyzed cross-coupling reactions of alkyl pseudohalides containing a C(sp3)-Q (Q = O, N, S, etc.) bond, aziridines can be used as nonclassical alkyl pseudohalides in regioselective and stereospecific cross-couplings.In this Account, starting from the background of transition-metal-catalyzed ring-opening functionalization of aziridines, our contributions to the palladium-catalyzed regioselective and stereoinvertive cross-couplings of aziridines with organoboron reagents to form C(sp3)-C, C(sp3)-B, and C(sp3)-Si bonds have been compiled. The developed methods allow the syntheses of medicinally important amine compounds, e.g., enantioenriched β-phenethylamines, β-amino acids, and their boron and silyl surrogates, from readily available enantiopure aziridine substrates. Notably, the regioselectivity of the ring opening can be switched by appropriate selection of the catalyst (i.e., Pd/NHC vs Pd/PR3 systems). Computational studies rationalized the detailed mechanisms of the full catalytic cycle and the regioselectivity and stereospecificity of the reactions. The computational results suggested that the interactions operating between the Pd catalyst and aziridine substrate play important roles in determining the regioselection of the aziridine ring-opening event (i.e., oxidative addition). Also, the computational results rationalized the role of water molecules in promoting the transmetalation step through the formation of a Pd-hydroxide active intermediate. This Account evidences the benefits of synergistic collaborations between experimental and computational methods in developing novel transition-metal-catalyzed cross-coupling reactions.
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Affiliation(s)
- Youhei Takeda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan
| | - W. M. C. Sameera
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, North 19 West 8, Sapporo, Hokkaido 060-0819, Japan
| | - Satoshi Minakata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan
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DFT Study on Mechanisms of the N2O Direct Catalytic Decomposition over Cu-ZSM-5: The Detailed Investigation on NO Formation Mechanism. Catalysts 2020. [DOI: 10.3390/catal10060646] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nitrous oxide (N2O) is an industrial emission that causes the greenhouse effect and damages the ozone layer. Density functional theory study on the N2O direct catalytic decomposition over Cu–ZSM-5 has been performed in this paper. Two possible reaction mechanisms for N2O direct catalytic decomposition over Cu-ZSM-5 were proposed (O2 formation mechanism and Nitric oxide (NO) formation mechanism). The geometrical parameters, vibration frequency and thermodynamic data of the intermediate states in each step have been examined. The results indicate that N2O can be adsorbed on active site Cu in two ways (O-terminal or N-terminal), and N2O decomposition reactions can occur in both cases. The NO formation mechanism exhibits higher N2O dissociation reaction due to lower energy barrier.
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21
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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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22
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de Aguirre A, Fernandez-Alvarez VM, Maseras F. Computational Modeling of Selected Photoactivated Processes. TOP ORGANOMETAL CHEM 2020. [DOI: 10.1007/3418_2020_50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Mai BK, Himo F. Mechanisms of Metal-Catalyzed Electrophilic F/CF3/SCF3 Transfer Reactions from Quantum Chemical Calculations. TOP ORGANOMETAL CHEM 2020. [DOI: 10.1007/3418_2020_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Hydrogen Production from Formic Acid Attained by Bimetallic Heterogeneous PdAg Catalytic Systems. ENERGIES 2019. [DOI: 10.3390/en12214027] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The production of H2 from the so-called Liquid Organic Hydrogen Carriers (LOHC) has recently received great focus as an auspicious option to conventional hydrogen storage technologies. Among them, formic acid, the simplest carboxylic acid, has recently emerged as one of the most promising candidates. Catalysts based on Pd nanoparticles are the most fruitfully investigated, and, more specifically, excellent results have been achieved with bimetallic PdAg-based catalytic systems. The enhancement displayed by PdAg catalysts as compared to the monometallic counterpart is ascribed to several effects, such as the formation of electron-rich Pd species or the increased resistance against CO-poisoning. Aside from the features of the metal active phases, the properties of the selected support also play an important role in determining the final catalytic performance. Among them, the use of carbon materials has resulted in great interest by virtue of their outstanding properties and versatility. In the present review, some of the most representative investigations dealing with the design of high-performance PdAg bimetallic heterogeneous catalysts are summarised, paying attention to the impact of the features of the support in the final ability of the catalysts towards the production of H2 from formic acid.
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25
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Takeda Y, Matsuno T, Sharma AK, Sameera WMC, Minakata S. Asymmetric Synthesis of β
2
‐Aryl Amino Acids through Pd‐Catalyzed Enantiospecific and Regioselective Ring‐Opening Suzuki–Miyaura Arylation of Aziridine‐2‐carboxylates. Chemistry 2019; 25:10226-10231. [DOI: 10.1002/chem.201902009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/01/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Youhei Takeda
- Department of Applied ChemistryGraduate School of EngineeringOsaka University Yamadaoka 2-1 Suita Osaka 565-0871 Japan
| | - Tetsuya Matsuno
- Department of Applied ChemistryGraduate School of EngineeringOsaka University Yamadaoka 2-1 Suita Osaka 565-0871 Japan
| | - Akhilesh K. Sharma
- Fukui Institute for Fundamental ChemistryKyoto University Takano-Nishishiraki-cho 34-4 Sakyo-ku Kyoto 606-8103 Japan
| | - W. M. C. Sameera
- Institute of Low Temperature ScienceHokkaido University Kita-ku, North 19 West 8 Sapporo Hokkaido 060-0819 Japan
| | - Satoshi Minakata
- Department of Applied ChemistryGraduate School of EngineeringOsaka University Yamadaoka 2-1 Suita Osaka 565-0871 Japan
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26
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Sanjosé-Orduna J, Mudarra ÁL, Martínez de Salinas S, Pérez-Temprano MH. Sustainable Knowledge-Driven Approaches in Transition-Metal-Catalyzed Transformations. CHEMSUSCHEM 2019; 12:2882-2897. [PMID: 31094085 DOI: 10.1002/cssc.201900914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/10/2019] [Indexed: 06/09/2023]
Abstract
The sustainable synthesis of relevant scaffolds for their use in the pharmaceutical, agrochemical, and materials sectors constitutes one of the most urgent challenges that the chemical community needs to overcome. In this context, the development of innovative and more efficient catalytic processes based on a fundamental understanding of the underlying reaction mechanisms remains a largely unresolved challenge for academic and industrial chemists. Herein, selected examples of computational and experimental knowledge-driven approaches for the rational design of transition-metal-catalyzed transformations are discussed.
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Affiliation(s)
- Jesús Sanjosé-Orduna
- Institute of Chemical Research of Catalonia, ICIQ), Avgda. Països Catalans 16, 43007, Tarragona, Spain
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, C/ Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
| | - Ángel L Mudarra
- Institute of Chemical Research of Catalonia, ICIQ), Avgda. Països Catalans 16, 43007, Tarragona, Spain
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, C/ Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
| | - Sara Martínez de Salinas
- Institute of Chemical Research of Catalonia, ICIQ), Avgda. Països Catalans 16, 43007, Tarragona, Spain
| | - Mónica H Pérez-Temprano
- Institute of Chemical Research of Catalonia, ICIQ), Avgda. Països Catalans 16, 43007, Tarragona, Spain
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27
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Chan B, Gill PMW, Kimura M. Assessment of DFT Methods for Transition Metals with the TMC151 Compilation of Data Sets and Comparison with Accuracies for Main-Group Chemistry. J Chem Theory Comput 2019; 15:3610-3622. [PMID: 31150234 DOI: 10.1021/acs.jctc.9b00239] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In the present study, we have gathered a collection (that we term TMC151) of accurate reference data for transition-metal reactions for the assessment of quantum chemistry methods. It comprises diatomic dissociation energies and reaction energies and barriers for prototypical transition-metal reactions. Our assessment of a diverse range of different types of DFT methods shows that the most accurate functionals include ωB97M-V, ωB97X-V, MN15, and B97M-rV. Notably, they have also been previously validated to be highly robust for main-group chemistry. Nevertheless, even these methods show substantially worse accuracies for transition metals than for main-group chemistry. For less accurate methods, there is not a good correlation between their accuracies for main-group and transition-metal chemistries. Thus, in the development of new DFT, it is important to assess the accuracies for both types of data. In this regard, we have formulated the TMC34 model for efficient assessment of the performance for transition metals, which complements our previously developed MG8 model for main-group chemistry. Together, they provide a cost-effective means for initial assessment of new methodologies.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan
| | - Peter M W Gill
- Research School of Chemistry , Australian National University , Canberra , Australian Capital Territory 2601 , Australia
| | - Masanari Kimura
- Graduate School of Engineering , Nagasaki University , Bunkyo 1-14 , Nagasaki 852-8521 , Japan
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28
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Sharma AK, Sameera WMC, Takeda Y, Minakata S. Computational Study on the Mechanism and Origin of the Regioselectivity and Stereospecificity in Pd/SIPr-Catalyzed Ring-Opening Cross-Coupling of 2-Arylaziridines with Arylboronic Acids. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Akhilesh K. Sharma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishishiraki-cho, 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - W. M. C. Sameera
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido 060-0819, Japan
| | - Youhei Takeda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan
| | - Satoshi Minakata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka 565-0871, Japan
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29
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Abstract
The presence of single-electron transfer (SET) steps in water oxidation processes catalyzed by first-row transition metal complexes has been recently recognized, but the computational characterization of this type of process is not trivial. We report a systematic theoretical study based on density functional theory (DFT) calculations on the reactivity of a specific copper complex active in water oxidation that reacts through two consecutive single-electron transfers. Both inner-sphere (through transition state location) and outer-sphere (through Marcus theory) mechanisms are analyzed. The first electron transfer is found to operate through outer-sphere, and the second one through inner-sphere. The current work proposes a scheme for the systematic study of single-electron transfer in water oxidation catalysis and beyond.
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30
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Sameera WMC, Maseras F. Expanding the Range of Force Fields Available for ONIOM Calculations: The SICTWO Interface. J Chem Inf Model 2018; 58:1828-1835. [PMID: 30137980 DOI: 10.1021/acs.jcim.8b00332] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemical problems. The "Shell Interface for Combining Tinker With ONIOM" (SICTWO) program gives access to all force fields available in the Tinker molecular mechanics program from a Gaussian09 or Gaussian16 calculation. The first application presented is the geometry optimization of dithienobicyclo-[4.4.1]-undeca-3,8-diene-11-one ethylene glycol ketal. A variety of force fields were tested for the MM part, and the molecular structure using the ONIOM(B3LYP:OPLS-AA) method shows good agreement with the experimental results. The second problem is related with enantioselectivity of the vanadium-catalyzed asymmetric oxidation of 1,2-bis( tert-butyl)-disulfide. ONIOM(B3LYP:MM3) results, obtained with SICTWO, are consistent with those of a previous IMOMM(B3LYP:MM3) study. In the third application, we have combined AMOEBA09 polarizable force field with ONIOM to study a water molecule binding on water ice. Calculated ONIOM(ωB97X-D:AMOEBA09) binding energies are consistent with the ωB97X-D results. These studies show SICTWO as an easy-to-use tool that can further expand the use of the multiscale ONIOM method within computational chemistry and computational biology.
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Affiliation(s)
- W M C Sameera
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16 , 43007 , Tarragona , Spain.,Institute of Low Temperature Science , Hokkaido University , Sapporo , Hokkaido 060-0819 , Japan
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16 , 43007 , Tarragona , Spain.,Departament de Química , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
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31
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Toledo A, Funes-Ardoiz I, Maseras F, Albéniz AC. Palladium-Catalyzed Aerobic Homocoupling of Alkynes: Full Mechanistic Characterization of a More Complex Oxidase-Type Behavior. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01540] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Alberto Toledo
- IU CINQUIMA/Química Inorgánica, Universidad de Valladolid, 47071 Valladolid, Spain
| | - Ignacio Funes-Ardoiz
- Institute of Chemical Research of Catalonia (ICIQ). The Barcelona Institute of Science and Technology, Avda. Països Catalans 16, 43007 Tarragona, Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ). The Barcelona Institute of Science and Technology, Avda. Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ana C. Albéniz
- IU CINQUIMA/Química Inorgánica, Universidad de Valladolid, 47071 Valladolid, Spain
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32
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Besora M, Maseras F. Microkinetic modeling in homogeneous catalysis. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1372] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Maria Besora
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyBarcelonaSpain
- Departament de QuímicaUniversitat Autònoma de Barcelona (UAB)BarcelonaSpain
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33
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Bhattacharya S, Xu L, Thompson D. Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Liang Xu
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Damien Thompson
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
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34
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Pastor J, Rezabal E, Voituriez A, Betzer JF, Marinetti A, Frison G. Revised Theoretical Model on Enantiocontrol in Phosphoric Acid Catalyzed H-Transfer Hydrogenation of Quinoline. J Org Chem 2018; 83:2779-2787. [DOI: 10.1021/acs.joc.7b03248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Julien Pastor
- LCM,
CNRS, Ecole polytechnique, Université Paris-Saclay, 91128 Palaiseau, France
| | - Elixabete Rezabal
- LCM,
CNRS, Ecole polytechnique, Université Paris-Saclay, 91128 Palaiseau, France
- Kimika
Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi Spain
| | - Arnaud Voituriez
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-François Betzer
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Angela Marinetti
- Institut
de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Gilles Frison
- LCM,
CNRS, Ecole polytechnique, Université Paris-Saclay, 91128 Palaiseau, France
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35
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Affiliation(s)
- Ignacio Funes-Ardoiz
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Catalonia, Spain
| | - Feliu Maseras
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Catalonia, Spain
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
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36
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Chan B, Luo Y, Kimura M. Mechanism for Three-Component Ni-Catalyzed Carbonyl–Ene Reaction for CO2 Transformation: What Practical Lessons Do We Learn from DFT Modelling? Aust J Chem 2018. [DOI: 10.1071/ch17573] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present study, we use computational quantum chemistry to examine the nickel-catalyzed three-component coupling for transforming CO2 into a homoallylic alcohol. We find that the reaction is limited by several Ni-assisted atom transfer reactions in the catalytic cycle, in which a new product formation pathway is found from our calculations. Our results also point towards several key factors for an efficient reaction. Thus, substrates that would lead to a stabilized alkene facilitate a key step in the catalytic cycle. The optimal phosphine ligand should provide a good balance between directing stereochemistry with its steric bulk and enabling the reaction without being excessively bulky. Our calculations also highlight the importance of carefully chosen substrates and ligands in order to avoid potential side reactions, and that knowing the conformational preference in the substrate alone may not be sufficient for predicting the stereochemistry.
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37
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Dewyer AL, Zimmerman PM. Simulated Mechanism for Palladium-Catalyzed, Directed γ-Arylation of Piperidine. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01390] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Amanda L. Dewyer
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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38
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Kalek M, Himo F. Mechanism and Selectivity of Cooperatively Catalyzed Meyer–Schuster Rearrangement/Tsuji–Trost Allylic Substitution. Evaluation of Synergistic Catalysis by Means of Combined DFT and Kinetics Simulations. J Am Chem Soc 2017; 139:10250-10266. [DOI: 10.1021/jacs.7b01931] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Marcin Kalek
- Centre
of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
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39
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Isegawa M, Sameera WMC, Sharma AK, Kitanosono T, Kato M, Kobayashi S, Morokuma K. Copper-Catalyzed Enantioselective Boron Conjugate Addition: DFT and AFIR Study on Different Selectivities of Cu(I) and Cu(II) Catalysts. ACS Catal 2017. [DOI: 10.1021/acscatal.7b01152] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miho Isegawa
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - W. M. C. Sameera
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
- Department
of Chemistry, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo 060-0810, Japan
| | - Akhilesh K. Sharma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Taku Kitanosono
- Department
of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masako Kato
- Department
of Chemistry, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo 060-0810, Japan
| | - Shu̅ Kobayashi
- Department
of Chemistry, School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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40
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Dell'Amico L, Fernández‐Alvarez VM, Maseras F, Melchiorre P. Light-Driven Enantioselective Organocatalytic β-Benzylation of Enals. Angew Chem Int Ed Engl 2017; 56:3304-3308. [PMID: 28185401 PMCID: PMC5412672 DOI: 10.1002/anie.201612159] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Indexed: 11/06/2022]
Abstract
A photochemical organocatalytic strategy for the direct enantioselective β-benzylation of α,β-unsaturated aldehydes is reported. The chemistry capitalizes upon the light-triggered enolization of 2-alkyl-benzophenones to afford hydroxy-o-quinodinomethanes. These fleeting intermediates are stereoselectively intercepted by chiral iminium ions, transiently formed upon condensation of a secondary amine catalyst with enals. Density functional theory (DFT) studies provided an explanation for why the reaction proceeds through an unconventional Michael-type addition manifold, instead of a classical cycloaddition mechanism and subsequent ring-opening.
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Affiliation(s)
- Luca Dell'Amico
- ICIQ—Institute of Chemical Research of Catalonia the Barcelona Institute of Science and TechnologyAvenida Països Catalans 1643007TarragonaSpain
| | - Victor M. Fernández‐Alvarez
- ICIQ—Institute of Chemical Research of Catalonia the Barcelona Institute of Science and TechnologyAvenida Països Catalans 1643007TarragonaSpain
| | - Feliu Maseras
- Departament de QuimicaUniversitat Autònoma de Barcelona08193BellaterraSpain
- ICIQ—Institute of Chemical Research of Catalonia the Barcelona Institute of Science and TechnologyAvenida Països Catalans 1643007TarragonaSpain
| | - Paolo Melchiorre
- ICREA—Catalan Institution for Research and Advanced StudiesPasseig Lluís Companys 2308010BarcelonaSpain
- ICIQ—Institute of Chemical Research of Catalonia the Barcelona Institute of Science and TechnologyAvenida Països Catalans 1643007TarragonaSpain
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41
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Dell'Amico L, Fernández-Alvarez VM, Maseras F, Melchiorre P. Light-Driven Enantioselective Organocatalytic β-Benzylation of Enals. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612159] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Luca Dell'Amico
- ICIQ-Institute of Chemical Research of Catalonia the Barcelona Institute of Science and Technology; Avenida Països Catalans 16 43007 Tarragona Spain
| | - Victor M. Fernández-Alvarez
- ICIQ-Institute of Chemical Research of Catalonia the Barcelona Institute of Science and Technology; Avenida Països Catalans 16 43007 Tarragona Spain
| | - Feliu Maseras
- Departament de Quimica; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
- ICIQ-Institute of Chemical Research of Catalonia the Barcelona Institute of Science and Technology; Avenida Països Catalans 16 43007 Tarragona Spain
| | - Paolo Melchiorre
- ICREA - Catalan Institution for Research and Advanced Studies; Passeig Lluís Companys 23 08010 Barcelona Spain
- ICIQ-Institute of Chemical Research of Catalonia the Barcelona Institute of Science and Technology; Avenida Països Catalans 16 43007 Tarragona Spain
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42
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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43
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Sharma D, Sameera WMC, Andersson S, Nyman G, Paterson MJ. Computational Study of the Interactions between Benzene and Crystalline Ice Ih: Ground and Excited States. Chemphyschem 2016; 17:4079-4089. [DOI: 10.1002/cphc.201600660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Divya Sharma
- Institute of Chemical Sciences; School of Engineering and Physical Sciences; Heriot Watt University Edinburgh EH14 4AS United Kingdom
| | - W. M. C. Sameera
- Fukui Institute for Fundamental Chemistry; Kyoto University; Kyoto 606-8103 Japan
- University of Gothenburg; Department of Chemistry and Molecular Biology; Kemigården 4 412 96 Gothenburg Sweden
| | - Stefan Andersson
- University of Gothenburg; Department of Chemistry and Molecular Biology; Kemigården 4 412 96 Gothenburg Sweden
- SINTEF Materials and Chemistry; P.O. Box 4760 7465 Trondheim Norway
| | - Gunnar Nyman
- University of Gothenburg; Department of Chemistry and Molecular Biology; Kemigården 4 412 96 Gothenburg Sweden
| | - Martin J. Paterson
- Institute of Chemical Sciences; School of Engineering and Physical Sciences; Heriot Watt University Edinburgh EH14 4AS United Kingdom
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44
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Sameera WMC, Kumar Sharma A, Maeda S, Morokuma K. Artificial Force Induced Reaction Method for Systematic Determination of Complex Reaction Mechanisms. CHEM REC 2016; 16:2349-2363. [PMID: 27492586 DOI: 10.1002/tcr.201600052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 01/07/2023]
Abstract
Nowadays, computational studies are very important for the elucidation of reaction mechanisms and selectivity of complex reactions. However, traditional computational methods usually require an estimated reaction path, mainly driven by limited experimental implications, intuition, and assumptions of stationary points. However, the artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy can be used for unbiased and automatic reaction path searches for complex reactions. In this account, we highlight applications of the AFIR method to a variety of reactions (organic, organometallic, enzymatic, and photochemical) of complex molecular systems. In addition, the AFIR method has been successfully used to rationalise the origin of stereo- and regioselectivity. The AFIR method can be applied from small to large molecular systems, and will be a very useful tool for the study of complex molecular problems in many areas of chemistry, biology, and material sciences.
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Affiliation(s)
- W M C Sameera
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | | | - Satoshi Maeda
- Department of Chemistry, Hokkaido University, Sapporo, 060-0810, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan.
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45
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Sousa SF, Ribeiro AJM, Neves RPP, Brás NF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1281] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sérgio Filipe Sousa
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - António J. M. Ribeiro
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Rui P. P. Neves
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Natércia F. Brás
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Nuno M. F. S. A. Cerqueira
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Pedro A. Fernandes
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Maria João Ramos
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
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46
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Santoro S, Kalek M, Huang G, Himo F. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology. Acc Chem Res 2016; 49:1006-18. [PMID: 27082700 DOI: 10.1021/acs.accounts.6b00050] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in solving complex problems and proposing new detailed reaction mechanisms that rationalize the experimental findings. For each of the considered reactions, a consistent mechanism is presented, the experimentally observed selectivities are reproduced, and their sources are identified. Reproducing selectivities requires high accuracy in computing relative transition state energies. As demonstrated by the results summarized in this Account, this accuracy is possible with the use of the presented methodology, benefiting of course from a large extent of cancellation of systematic errors. It is argued that as the employed models become larger, the number of rotamers and isomers that have to be considered for every stationary point increases and a careful assessment of their energies is therefore necessary in order to ensure that the lowest energy conformation is located. This issue constitutes a bottleneck of the investigation in some cases and is particularly important when analyzing selectivities, since small energy differences need to be reproduced.
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Affiliation(s)
- Stefano Santoro
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Marcin Kalek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Genping Huang
- Department of Chemistry,
School of Science, Tianjin University, Tianjin 300072, P. R. China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius
Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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Funes‐Ardoiz I, Sameera WMC, Romero RM, Martínez C, Souto JA, Sampedro D, Muñiz K, Maseras F. DFT Rationalization of the Diverse Outcomes of the Iodine(III)‐Mediated Oxidative Amination of Alkenes. Chemistry 2016; 22:7545-53. [DOI: 10.1002/chem.201600415] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Ignacio Funes‐Ardoiz
- Institute of Chemical Research of Catalonia (ICIQ) The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
| | - W. M. C. Sameera
- Institute of Chemical Research of Catalonia (ICIQ) The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
- Fukui Institute for Fundamental Chemistry Kyoto University 606-8103 Kyoto Japan
| | - R. Martín Romero
- Institute of Chemical Research of Catalonia (ICIQ) The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
| | - Claudio Martínez
- Institute of Chemical Research of Catalonia (ICIQ) The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
| | - José A. Souto
- Institute of Chemical Research of Catalonia (ICIQ) The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
| | - Diego Sampedro
- Departamento de Química Centro de Investigación en Síntesis Química (CISQ) Universidad de La Rioja C/Madre de Dios, 51 26006 Logroño Spain
| | - Kilian Muñiz
- Institute of Chemical Research of Catalonia (ICIQ) The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
- Catalan Institution for Research and Advanced Studies (ICREA) Pg. Lluís Companys 23 08010 Barcelona Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ) The Barcelona Institute of Science and Technology Av. Països Catalans 16 43007 Tarragona Spain
- Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra Spain
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48
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Sameera WMC, Maeda S, Morokuma K. Computational Catalysis Using the Artificial Force Induced Reaction Method. Acc Chem Res 2016; 49:763-73. [PMID: 27023677 DOI: 10.1021/acs.accounts.6b00023] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy is an automatic approach to explore all important reaction paths of complex reactions. Most traditional methods in computational catalysis require guess reaction paths. On the other hand, the AFIR approach locates local minima (LMs) and transition states (TSs) of reaction paths without a guess, and therefore finds unanticipated as well as anticipated reaction paths. The AFIR method has been applied for multicomponent organic reactions, such as the aldol reaction, Passerini reaction, Biginelli reaction, and phase-transfer catalysis. In the presence of several reactants, many equilibrium structures are possible, leading to a number of reaction pathways. The AFIR method in the GRRM strategy determines all of the important equilibrium structures and subsequent reaction paths systematically. As the AFIR search is fully automatic, exhaustive trial-and-error and guess-and-check processes by the user can be eliminated. At the same time, the AFIR search is systematic, and therefore a more accurate and comprehensive description of the reaction mechanism can be determined. The AFIR method has been used for the study of full catalytic cycles and reaction steps in transition metal catalysis, such as cobalt-catalyzed hydroformylation and iron-catalyzed carbon-carbon bond formation reactions in aqueous media. Some AFIR applications have targeted the selectivity-determining step of transition-metal-catalyzed asymmetric reactions, including stereoselective water-tolerant lanthanide Lewis acid-catalyzed Mukaiyama aldol reactions. In terms of establishing the selectivity of a reaction, systematic sampling of the transition states is critical. In this direction, AFIR is very useful for performing a systematic and automatic determination of TSs. In the presence of a comprehensive description of the transition states, the selectivity of the reaction can be calculated more accurately. For relatively large molecular systems, the computational cost of AFIR searches can be reduced by using the ONIOM(QM:QM) or ONIOM(QM:MM) methods. In common practice, density functional theory (DFT) with a relatively small basis set is used for the high-level calculation, while a semiempirical approach or a force field description is used for the low-level calculation. After approximate LMs and TSs are determined, standard computational methods (e.g., DFT with a large basis set) are used for the full molecular system to determine the true LMs and TSs and to rationalize the reaction mechanism and selectivity of the catalytic reaction. The examples in this Account evidence that the AFIR method is a powerful approach for accurate prediction of the reaction mechanisms and selectivities of complex catalytic reactions. Therefore, the AFIR approach in the GRRM strategy is very useful for computational catalysis.
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Affiliation(s)
- W. M. C. Sameera
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Satoshi Maeda
- Department
of Chemistry, Hokkaido University, Sapporo 060-0810, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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49
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Sperger T, Fisher HC, Schoenebeck F. Computationally deciphering palladium-catalyzed reaction mechanisms. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1244] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Theresa Sperger
- Institute of Organic Chemistry; RWTH Aachen University; Aachen Germany
| | - Henry C. Fisher
- Institute of Organic Chemistry; RWTH Aachen University; Aachen Germany
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Rohmann K, Hölscher M, Leitner W. Can Contemporary Density Functional Theory Predict Energy Spans in Molecular Catalysis Accurately Enough To Be Applicable for in Silico Catalyst Design? A Computational/Experimental Case Study for the Ruthenium-Catalyzed Hydrogenation of Olefins. J Am Chem Soc 2015; 138:433-43. [PMID: 26713773 DOI: 10.1021/jacs.5b11997] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The catalytic hydrogenation of cyclohexene and 1-methylcyclohexene is investigated experimentally and by means of density functional theory (DFT) computations using novel ruthenium Xantphos(Ph) (4,5-bis(diphenylphosphino)-9,9-dimethylxanthene) and Xantphos(Cy) (4,5-bis(dicyclohexylphosphino)-9,9-dimethylxanthene) precatalysts [Ru(Xantphos(Ph))(PhCO2)(Cl)] (1) and [Ru(Xantphos(Cy))(PhCO2)(Cl)] (2), the synthesis, characterization, and crystal structures of which are reported. The intention of this work is to (i) understand the reaction mechanisms on the microscopic level and (ii) compare experimentally observed activation barriers with computed barriers. The Gibbs free activation energy ΔG(⧧) was obtained experimentally with precatalyst 1 from Eyring plots for the hydrogenation of cyclohexene (ΔG(⧧) = 17.2 ± 1.0 kcal/mol) and 1-methylcyclohexene (ΔG(⧧) = 18.8 ± 2.4 kcal/mol), while the Gibbs free activation energy ΔG(⧧) for the hydrogenation of cyclohexene with precatalyst 2 was determined to be 21.1 ± 2.3 kcal/mol. Plausible activation pathways and catalytic cycles were computed in the gas phase (M06-L/def2-SVP). A variety of popular density functionals (ωB97X-D, LC-ωPBE, CAM-B3LYP, B3LYP, B97-D3BJ, B3LYP-D3, BP86-D3, PBE0-D3, M06-L, MN12-L) were used to reoptimize the turnover determining states in the solvent phase (DF/def2-TZVP; IEF-PCM and/or SMD) to investigate how well the experimentally obtained activation barriers can be reproduced by the calculations. The density functionals B97-D3BJ, MN12-L, M06-L, B3LYP-D3, and CAM-B3LYP reproduce the experimentally observed activation barriers for both olefins very well with very small (0.1 kcal/mol) to moderate (3.0 kcal/mol) mean deviations from the experimental values indicating for the field of hydrogenation catalysis most of these functionals to be useful for in silico catalyst design prior to experimental work.
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Affiliation(s)
- Kai Rohmann
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University , Worringerweg 2, 52074 Aachen, Germany
| | - Markus Hölscher
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University , Worringerweg 2, 52074 Aachen, Germany
| | - Walter Leitner
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen University , Worringerweg 2, 52074 Aachen, Germany.,Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim a.d. Ruhr, Germany
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