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King-Smith E, Berritt S, Bernier L, Hou X, Klug-McLeod JL, Mustakis J, Sach NW, Tucker JW, Yang Q, Howard RM, Lee AA. Probing the chemical 'reactome' with high-throughput experimentation data. Nat Chem 2024; 16:633-643. [PMID: 38168924 PMCID: PMC10997498 DOI: 10.1038/s41557-023-01393-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
High-throughput experimentation (HTE) has the potential to improve our understanding of organic chemistry by systematically interrogating reactivity across diverse chemical spaces. Notable bottlenecks include few publicly available large-scale datasets and the need for facile interpretation of these data's hidden chemical insights. Here we report the development of a high-throughput experimentation analyser, a robust and statistically rigorous framework, which is applicable to any HTE dataset regardless of size, scope or target reaction outcome, which yields interpretable correlations between starting material(s), reagents and outcomes. We improve the HTE data landscape with the disclosure of 39,000+ previously proprietary HTE reactions that cover a breadth of chemistry, including cross-coupling reactions and chiral salt resolutions. The high-throughput experimentation analyser was validated on cross-coupling and hydrogenation datasets, showcasing the elucidation of statistically significant hidden relationships between reaction components and outcomes, as well as highlighting areas of dataset bias and the specific reaction spaces that necessitate further investigation.
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Affiliation(s)
- Emma King-Smith
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | | | - Xinjun Hou
- Pfizer Research and Development, Cambridge, MA, USA
| | | | | | - Neal W Sach
- Pfizer Research and Development, La Jolla, CA, USA
| | | | - Qingyi Yang
- Pfizer Research and Development, Cambridge, MA, USA
| | | | - Alpha A Lee
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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2
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Pahlavan F, Moosavi SS, Zolghadr AR, Iranpoor N. Electronic origins of the stereochemistry in β-lactam formed through the Staudinger reaction catalyzed by a nucleophile. RSC Adv 2023; 13:33654-33667. [PMID: 38020014 PMCID: PMC10653035 DOI: 10.1039/d3ra05286a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
This paper evaluates the electronic effects of molecular substituents on the stereoselectivity of the umpolung Staudinger catalytic reaction. This is especially important because experimental studies on constructing the β-lactam ring, a core structure of most antibiotics, through catalyzed Staudinger reactions have been massively progressing over the last century. Yet, there is a necessity for an in-depth understanding of the reaction mechanisms to help chemists, working on the well-established discoveries, improve these to optimize the stereoselectivity and yield of synthetic methods. Access to practical and effective advancements in forming optically pure β-lactam is paramount in the field of medical chemistry. This paper specifically investigates how changing the N-protecting group in the imine fragment can switch the stereoselectivity of the PPY-catalyzed Staudinger reaction. To do so, we employed the density functional theory (DFT) for geometry optimization and electronic analysis at the B3LYP/6-31G(d) level of theory to examine and compare the role of N-tosyl (N-Ts) and N-triflyl (N-Tf) imine on the mechanism pathways, i.e., imine-first or ketene-first, and stereochemistry of the reaction, i.e., cis or trans β-lactam. Our results show that the reaction mechanism pathway cannot be simply switched from ketene-first to imine-first by changing the substituent on the imine nitrogen atom, which is contrary to the reported experimental results, and both imines go through the ketene-first mechanism with different stereochemistries, which is cis selective for imine-Ts and trans selective for imine-Tf. Based on electronic analyses, the reversal in diastereoselectivity in the N-triflyl imine system could be attributed to the charge transfers and electron-density distribution over the transition states. Therefore, the cis/trans selectivity of the PPY-catalyzed Staudinger reaction could be effectively controlled by the electronic characteristics of the molecular substituents in the reactants. A N-protecting group in imine with a more electron-withdrawing nature seems to accelerate the stereo-determining step, ring closure, and increase the stabilization charge transfers in the transition state, leading to a preference for trans β-lactam formation. It seems that using a N-substituent with a higher electron-withdrawing nature can initially activate the imine by the nucleophilic catalyst in competition with ketene, i.e., imine-first versus ketene-first. These results can provide an insight into select proper substituents for the fragments to synthesis β-lactam with a desired stereochemistry. Also, a comprehensive comparison was performed between calculations with and without dispersion.
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Affiliation(s)
- Farideh Pahlavan
- Department of Chemistry, School of Science, Shiraz University Shiraz 71454 Iran
| | | | - Amin Reza Zolghadr
- Department of Chemistry, School of Science, Shiraz University Shiraz 71454 Iran
| | - Nasser Iranpoor
- Department of Chemistry, School of Science, Shiraz University Shiraz 71454 Iran
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3
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Jacquemin D, Kossoski F, Gam F, Boggio-Pasqua M, Loos PF. Reference Vertical Excitation Energies for Transition Metal Compounds. J Chem Theory Comput 2023. [PMID: 37965941 DOI: 10.1021/acs.jctc.3c01080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
To enrich and enhance the diversity of the quest database of highly accurate excitation energies [Véril, M.; et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2021, 11, e1517], we report vertical transition energies in transition metal compounds. Eleven diatomic molecules with a singlet or doublet ground state containing a fourth-row transition metal (CuCl, CuF, CuH, ScF, ScH, ScO, ScS, TiN, ZnH, ZnO, and ZnS) are considered, and the corresponding excitation energies are computed using high-level coupled-cluster (CC) methods, namely, CC3, CCSDT, CC4, and CCSDTQ, as well as multiconfigurational methods such as CASPT2 and NEVPT2. In many cases, to provide more comprehensive benchmark data, we also provide full configuration interaction estimates computed with the configuration interaction using a perturbative selection made iteratively (CIPSI) method. Based on these calculations, theoretical best estimates of the transition energies are established in both the aug-cc-pVDZ and aug-cc-pVTZ basis sets. This allows us to accurately assess the performance of the CC and multiconfigurational methods for this specific set of challenging transitions. Furthermore, comparisons with experimental data and previous theoretical results are also reported.
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Affiliation(s)
- Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Franck Gam
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
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4
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Hayashi H, Maeda S, Mita T. Quantum chemical calculations for reaction prediction in the development of synthetic methodologies. Chem Sci 2023; 14:11601-11616. [PMID: 37920348 PMCID: PMC10619630 DOI: 10.1039/d3sc03319h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/29/2023] [Indexed: 11/04/2023] Open
Abstract
Quantum chemical calculations have been used in the development of synthetic methodologies to analyze the reaction mechanisms of the developed reactions. Their ability to estimate chemical reaction pathways, including transition state energies and connected equilibria, has led researchers to embrace their use in predicting unknown reactions. This perspective highlights strategies that leverage quantum chemical calculations for the prediction of reactions in the discovery of new methodologies. Selected examples demonstrate how computation has driven the development of unknown reactions, catalyst design, and the exploration of synthetic routes to complex molecules prior to often laborious, costly, and time-consuming experimental investigations.
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Affiliation(s)
- Hiroki Hayashi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
- Department of Chemistry, Faculty of Science, Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Tsuyoshi Mita
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
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5
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Zheng H, Cai L, Pan M, Uyanik M, Ishihara K, Xue XS. Catalyst-Substrate Helical Character Matching Determines the Enantioselectivity in the Ishihara-Type Iodoarenes Catalyzed Asymmetric Kita-Dearomative Spirolactonization. J Am Chem Soc 2023; 145:7301-7312. [PMID: 36940192 DOI: 10.1021/jacs.2c13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Catalyst design has traditionally focused on rigid structural elements to prevent conformational flexibility. Ishihara's elegant design of conformationally flexible C2-symmetric iodoarenes, a new class of privileged organocatalysts, for the catalytic asymmetric dearomatization (CADA) of naphthols is a notable exception. Despite the widespread use of the Ishihara catalysts for CADAs, the reaction mechanism remains the subject of debate, and the mode of asymmetric induction has not been well established. Here, we report an in-depth computational investigation of three possible mechanisms in the literature. Our results, however, reveal that this reaction is best rationalized by a fourth mechanism called "proton-transfer-coupled-dearomatization (PTCD)", which is predicted to be strongly favored over other competing pathways. The PTCD mechanism is consistent with a control experiment and further validated by applying it to rationalize the enantioselectivities. Oxidation of the flexible I(I) catalyst to catalytic active I(III) species induces a defined C2-symmetric helical chiral environment with a delicate balance between flexibility and rigidity. A match/mismatch effect between the active catalyst and the substrate's helical shape in the dearomatization transition states was observed. The helical shape match allows the active catalyst to adapt its conformation to maximize attractive noncovalent interactions, including I(III)···O halogen bond, N-H···O hydrogen bond, and π···π stacking, to stabilize the favored transition state. A stereochemical model capable of rationalizing the effect of catalyst structural variation on the enantioselectivities is developed. The present study enriches our understanding of how flexible catalysts achieve high stereoinduction and may serve as an inspiration for the future exploration of conformational flexibility for new catalyst designs.
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Affiliation(s)
- Hanliang Zheng
- Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Liu Cai
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Ming Pan
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Muhammet Uyanik
- Graduate School of Engineering, Nagoya University Furocho, Chikusaku, Nagoya 464-8603, Japan
| | - Kazuaki Ishihara
- Graduate School of Engineering, Nagoya University Furocho, Chikusaku, Nagoya 464-8603, Japan
| | - Xiao-Song Xue
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, P. R. China
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6
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Hashemi A, Bougueroua S, Gaigeot MP, Pidko EA. ReNeGate: A Reaction Network Graph-Theoretical Tool for Automated Mechanistic Studies in Computational Homogeneous Catalysis. J Chem Theory Comput 2022; 18:7470-7482. [PMID: 36321652 DOI: 10.1021/acs.jctc.2c00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Exploration of the chemical reaction space of chemical transformations in multicomponent mixtures is one of the main challenges in contemporary computational chemistry. To remove expert bias from mechanistic studies and to discover new chemistries, an automated graph-theoretical methodology is proposed, which puts forward a network formalism of homogeneous catalysis reactions and utilizes a network analysis tool for mechanistic studies. The method can be used for analyzing trajectories with single and multiple catalytic species and can provide unique conformers of catalysts including multinuclear catalyst clusters along with other catalytic mixture components. The presented three-step approach has the integrated ability to handle multicomponent catalytic systems of arbitrary complexity (mixtures of reactants, catalyst precursors, ligands, additives, and solvents). It is not limited to predefined chemical rules, does not require prealignment of reaction mixture components consistent with a reaction coordinate, and is not agnostic to the chemical nature of transformations. Conformer exploration, reactive event identification, and reaction network analysis are the main steps taken for identifying the pathways in catalytic systems given the starting precatalytic reaction mixture as the input. Such a methodology allows us to efficiently explore catalytic systems in realistic conditions for either previously observed or completely unknown reactive events in the context of a network representing different intermediates. Our workflow for the catalytic reaction space exploration exclusively focuses on the identification of thermodynamically feasible conversion channels, representative of the (secondary) catalyst deactivation or inhibition paths, which are usually most difficult to anticipate based solely on expert chemical knowledge. Thus, the expert bias is sought to be removed at all steps, and the chemical intuition is limited to the choice of the thermodynamic constraint imposed by the applicable experimental conditions in terms of threshold energy values for allowed transformations. The capabilities of the proposed methodology have been tested by exploring the reactivity of Mn complexes relevant for catalytic hydrogenation chemistry to verify previously postulated activation mechanisms and unravel unexpected reaction channels relevant to rare deactivation events.
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Affiliation(s)
- Ali Hashemi
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Sana Bougueroua
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE) UMR8587, Universite Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes 91025, France
| | - Marie-Pierre Gaigeot
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE) UMR8587, Universite Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes 91025, France
| | - Evgeny A Pidko
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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7
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Bhaskararao B, Rotella ME, Kim DY, Kee JM, Kim KS, Kozlowski MC. Ir and NHC Dual Chiral Synergetic Catalysis: Mechanism and Stereoselectivity in γ-Butyrolactone Formation. J Am Chem Soc 2022; 144:16171-16183. [PMID: 36006026 PMCID: PMC9620864 DOI: 10.1021/jacs.2c07376] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cooperative dual catalysis is a powerful strategy for achieving unique reactivity by combining catalysts with orthogonal modes of action. This approach allows for independent control of the absolute and relative stereochemistry of the product. Despite its potential utility, the combination of N-heterocyclic carbene (NHC) organocatalysis and transition metal catalysis has remained a formidable challenge as NHCs readily coordinate metal centers. This characteristic also makes it difficult to rationalize or predict the stereochemical outcomes of these reactions. Herein, we use quantum mechanical calculations to investigate formation of γ-butyrolactones from aldehydes and allyl cyclic carbonates by means of an NHC organocatalyst and an iridium catalyst. Stereoconvergent activation of the racemic allyl cyclic carbonate forms an Ir-π-allyl intermediate and activation of an unsaturated aldehyde forms an NHC enolate, the latter of which is rate-limiting. Union of the two fragments leads to stereodetermining C-C bond formation and ultimately ring closure to generate the product lactone. Notably, CO2 loss occurs after formation of the C-C bond and Et3NH+ plays a key role in stabilizing carboxylate intermediates and in facilitating proton transfer to form the NHC enolate. The computed pathways agree with the experimental findings in terms of the absolute configuration, the enantiomer excess, and the different diastereomers seen with the (R)- and (S)-spiro-phosphoramidite combined with the NHC catalyst. Calculations reveal the lowest energy pathway includes both an NHC ligand and a phosphoramidite ligand on the iridium center. However, the stereochemical features of this Ir-bound NHC were found to not contribute to the selectivity of the process.
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Affiliation(s)
- Bangaru Bhaskararao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Madeline E. Rotella
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Dong Yeon Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jung-Min Kee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kwang Soo Kim
- Center for Superfunctional Materials, Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Marisa C. Kozlowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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8
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Jain P, Kumar N, Avasare V. A Shuttle Catalysis: Elucidating a True Reaction Mechanism Involved in the Palladium Xantphos-Assisted Transposition of Aroyl Chloride and Aryl Iodide Functional Groups. J Org Chem 2022; 87:12547-12557. [PMID: 35584056 DOI: 10.1021/acs.joc.2c00193] [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
A thorough DFT study was performed to unravel the true mechanism involved in the Pd(0)-catalyzed functional group transposition between aroyl chlorides and aryl iodides. Two different experimental groups proposed different mechanisms for the functional group transposition reaction. A careful assessment of experimental findings and thorough computational studies endorsed that the functional group transposition proceeds via phosphonium salt formation and ligand-enabled C-P bond metathesis, leading to the formation of the PhI and the intermediate 2. After the formation of the intermediate 2, the transposition of functional groups takes place through the interpalladium ligand exchange mechanism, where two palladium centers act as shuttle catalysts. In short, both C-P bond metathesis and interpalladium ligand exchange steps are crucial in the functional group transposition mechanism.
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Affiliation(s)
- Pooja Jain
- Department of Chemistry, Indian Institution of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Nitesh Kumar
- Department of Chemistry, Sir Parashurambhau College, Pune, Maharashtra 411030, India
| | - Vidya Avasare
- Department of Chemistry, Sir Parashurambhau College, Pune, Maharashtra 411030, India.,Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
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9
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Eisenstein O. From the Felkin‐Anh Rule to the Grignard Reaction: an Almost Circular 50 Year Adventure in the World of Molecular Structures and Reaction Mechanisms with Computational Chemistry**. Isr J Chem 2022. [DOI: 10.1002/ijch.202100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Odile Eisenstein
- ICGM, Univ. Montpellier, CNRS, ENSCM, Montpellier, 34095 France Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences University of Oslo Oslo 0315 Norway
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10
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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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11
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Abstract
Transition metal catalysts play a vital role in a wide range of industrial organic processes. The large-scale production of chemicals relying on catalyzed organic reactions represents a sustainable approach to supply society with end products for many daily life applications. Homogeneous (mainly for academic uses) and heterogeneous (crucial in industrial processes) metal-based catalysts have been developed for a plethora of organic reactions. The search for more sustainable strategies has led to the development of a countless number of metal-supported catalysts, nanosystems, and electrochemical and photochemical catalysts. In this work, although a vast number of transition metals can be used in this context, special attention is devoted to Ir- and Pd-based catalysts in the industrial manufacture of pharmaceutical drugs. Pd is by far the most widely used and versatile catalyst not only in academia but also in industry. Moreover, Ir-based complexes have emerged as attractive catalysts, particularly in asymmetric hydrogenation reactions. Ir- and Pd-based asymmetric reductions, aminations, cross-coupling reactions, and C–H activation are covered herein in the production of biologically active compounds or precursors; adaptation to bulk conditions is particularly highlighted.
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12
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Kunchur HS, Balakrishna MS. Platinum Assisted Tandem P-C Bond Cleavage and P-N Bond Formation in Amide Functionalized Bisphosphine o-Ph 2PC 6H 4C(O)N(H)C 6H 4PPh 2- o: Synthesis, Mechanistic, and Catalytic Studies. Inorg Chem 2022; 61:857-868. [PMID: 34978187 DOI: 10.1021/acs.inorgchem.1c02515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The reactions of amide functionalized bisphosphine o-Ph2PC6H4C(O)N(H)C6H4PPh2-o (1) with platinum salts are described. Treatment of 1 with [Pt(COD)Cl2] yielded a chelate complex, [PtCl2{o-Ph2PC6H4C(O)N(H)C6H4PPh2-o}κ2-P,P] (2), which on subsequent treatment with LiHMDS formed a novel 1,2-azaphospholene-phosphine complex [Pt(C6H5)Cl{o-C6H4{C(O)N(o-PPh2(C6H4))P(Ph)}}κ2-P,P] (3) involving a tandem P-C bond cleavage and P-N bond formation. The same complex 3 on passing dry HCl gas afforded the dichloro complex [PtCl2{o-C6H4{C(O)N(o-PPh2(C6H4))P(Ph)}}κ2-P,P] (5). Complex 2 upon refluxing in toluene or treatment of 1 with [Pt(COD)Cl2] in the presence of a base at room temperature resulted in the pincer complex [PtCl{o-Ph2PC6H4C(O)N(C6H4PPh2-o)}κ3-P,N,P] (4). Reaction of 1 with [Pt(COD)ClMe] at room temperature also afforded the pincer complex [PtMe{o-Ph2PC6H4C(O)N(C6H4PPh2-o)}κ3-P,N,P] (6). Mechanistic studies on 1,2-azaphospholene formation showed the reductive elimination of LiCl to form a phosphonium salt that readily adds one of the P-C bonds oxidatively to the in situ generated Pt0 species to form a chelate complex 3. The analogous palladium complex [PdCl2{o-C6H4{C(O)N(o-PPh2(C6H4))P(Ph)}}κ2-P,P] (7) showed excellent catalytic activity toward N-alkylation of amines with alcohols with a very low catalyst loading (0.05 mol %), and the methodology is very efficient toward the gram-scale synthesis of many N-alkylated amines.
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Affiliation(s)
- Harish S Kunchur
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Maravanji S Balakrishna
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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13
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Sunoj RB. Coming of Age of Computational Chemistry from a Resilient Past to a Promising Future. Isr J Chem 2021. [DOI: 10.1002/ijch.202100106] [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)
- Raghavan B. Sunoj
- Department of Chemistry Indian Institute of Technology Bombay, Powai Mumbai 400076 India
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14
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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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15
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Late-stage C–H functionalization offers new opportunities in drug discovery. Nat Rev Chem 2021; 5:522-545. [PMID: 37117588 DOI: 10.1038/s41570-021-00300-6] [Citation(s) in RCA: 261] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 12/24/2022]
Abstract
Over the past decade, the landscape of molecular synthesis has gained major impetus by the introduction of late-stage functionalization (LSF) methodologies. C-H functionalization approaches, particularly, set the stage for new retrosynthetic disconnections, while leading to improvements in resource economy. A variety of innovative techniques have been successfully applied to the C-H diversification of pharmaceuticals, and these key developments have enabled medicinal chemists to integrate LSF strategies in their drug discovery programmes. This Review highlights the significant advances achieved in the late-stage C-H functionalization of drugs and drug-like compounds, and showcases how the implementation of these modern strategies allows increased efficiency in the drug discovery process. Representative examples are examined and classified by mechanistic patterns involving directed or innate C-H functionalization, as well as emerging reaction manifolds, such as electrosynthesis and biocatalysis, among others. Structurally complex bioactive entities beyond small molecules are also covered, including diversification in the new modalities sphere. The challenges and limitations of current LSF methods are critically assessed, and avenues for future improvements of this rapidly expanding field are discussed. We, hereby, aim to provide a toolbox for chemists in academia as well as industrial practitioners, and introduce guiding principles for the application of LSF strategies to access new molecules of interest.
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16
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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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17
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Catalytic cycle and off-cycle steps in the palladium-catalyzed fluorination of aryl bromide with biaryl monophosphine ligands: Theoretical free energy profile. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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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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19
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Qi T, Fu S, Zhang X, Liu TH, Li QZ, Gou C, Li JL. Theoretical insight into the origins of chemo- and diastereo-selectivity in the palladium-catalysed (3 + 2) cyclisation of 5-alkenyl thiazolones. Org Chem Front 2021. [DOI: 10.1039/d1qo01071a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The mechanism of the palladium-catalysed (3 + 2) cyclisation of 5-alkenyl thiazolones and VECs has been investigated from a computational perspective, and the origins of unique chemoselectivity and excellent diastereoselectivity have been disclosed.
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Affiliation(s)
- Ting Qi
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, 610106, China
| | - Shuai Fu
- College of Chemical Engineering, Sichuan University, Chengdu, Sichuan, 610065, P.R. China
| | - Xiang Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, 610106, China
| | - Ting-Hao Liu
- College of Chemical Engineering, Sichuan University, Chengdu, Sichuan, 610065, P.R. China
| | - Qing-Zhu Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, 610106, China
| | - Chuan Gou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, 610106, China
| | - Jun-Long Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, Sichuan, 610106, China
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20
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Urabe D, Fukaya K. Systematic Search for Transition States in Complex Molecules: Computational Analyses of Regio- and Stereoselective Interflavan Bond Formation in Flavan-3-ols. HETEROCYCLES 2021. [DOI: 10.3987/rev-20-943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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21
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Ingman VM, Schaefer AJ, Andreola LR, Wheeler SE. QChASM
: Quantum chemistry automation and structure manipulation. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1510] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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22
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Lam YH, Abramov Y, Ananthula RS, Elward JM, Hilden LR, Nilsson Lill SO, Norrby PO, Ramirez A, Sherer EC, Mustakis J, Tanoury GJ. Applications of Quantum Chemistry in Pharmaceutical Process Development: Current State and Opportunities. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00222] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu-hong Lam
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yuriy Abramov
- Pfizer Worldwide Research & Development, Groton, Connecticut 06340, United States
| | - Ravi S. Ananthula
- Small Molecule Design and Development, Eli Lilly and Company, Bangalore 560103, India
| | - Jennifer M. Elward
- Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Lori R. Hilden
- Small Molecule Design and Development, Eli Lilly and Company, Indianapolis, Indiana 46221, United States
| | - Sten O. Nilsson Lill
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal 431 50, Sweden
| | - Per-Ola Norrby
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal 431 50 Sweden
| | - Antonio Ramirez
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Edward C. Sherer
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jason Mustakis
- Pfizer Worldwide Research & Development, Groton, Connecticut 06340, United States
| | - Gerald J. Tanoury
- Process Chemistry, Vertex Pharmaceuticals, 50 Northern Avenue, Boston, Massachusetts 02210, United States
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23
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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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24
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Pliego JR. Theoretical free energy profile and benchmarking of functionals for amino-thiourea organocatalyzed nitro-Michael addition reaction. Phys Chem Chem Phys 2020; 22:11529-11536. [PMID: 32393952 DOI: 10.1039/d0cp00481b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Amino-thiourea organocatalysis is an important catalytic process for enantioselective conjugate addition reactions. The interaction of the reactants with the catalyst has a substantial effect of dispersion forces and is a challenge for a reliable description when applying density functional theory. In this report, the classical addition of acetylacetone to β-nitro-styrene catalyzed by Takemoto's catalyst in toluene was studied using the PBE functional for geometry optimization and the DLPNO-CCSD(T) benchmark method for single point energy. The complete free energy profile calculated for the reaction was able to explain all experimental observations, including the fact that the carbon-carbon bond formation step is rate-determining. The overall barrier was calculated to be 22.8 kcal mol-1 (experimental value approximately 20 kcal mol-1), and the enantiomeric excess was calculated to be 88% (experimental value in the range of 84 to 92%). Some functionals were tested for single point energy. The hybrid B3LYP presented a high mean absolute deviation (MAD) from the DLPNO-CCSD(T) benchmark method by approximately 20 kcal mol-1. The inclusion of empirical dispersion correction in the B3LYP method decreased the MAD to 6 kcal mol-1. Even the double-hybrid mPW2-PLYP and B2GP-PLYP methods had MAD values of approximately 5 kcal mol-1. The inclusion of the dispersion correction decreased the MAD to 3.6 kcal mol-1. M06-2X and ωB97X-D3 were the most accurate among the tested functionals, with MADs of 2.5 kcal mol-1 and 1.8 kcal mol-1, respectively. Additivity approximation of the correlation energy was also tested and presented a MAD of only 0.6 kcal mol-1.
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Affiliation(s)
- Josefredo R Pliego
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, 36301-160, São João del-Rei, MG, Brazil.
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25
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Heck arylation of acyclic olefins employing arenediazonium salts and chiral N,N ligands: new mechanistic insights from quantum-chemical calculations. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02588-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Teixeira ES, Morales JA. Electron nuclear dynamics with plane wave basis sets: complete theory and formalism. Theor Chem Acc 2020; 139:73. [PMID: 32913423 PMCID: PMC7480945 DOI: 10.1007/s00214-020-2578-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/29/2020] [Indexed: 11/30/2022]
Abstract
Electron nuclear dynamics (END) is an ab initio quantum dynamics method that adopts a time-dependent, variational, direct, and non-adiabatic approach. The simplest-level (SL) END (SLEND) version employs a classical mechanics description for nuclei and a Thouless single-determinantal wave function for electrons. A higher-level END version, END/Kohn-Sham density functional theory, improves the electron correlation description of SLEND. While both versions can simulate various types of chemical reactions, they have difficulties to simulate scattering/capture of electrons to/from the continuum due to their reliance on localized Slater-type basis functions. To properly describe those processes, we formulate END with plane waves (PWs, END/PW), basis functions able to represent both bound and unbound electrons. As extra benefits, PWs also afford fast algorithms to simulate periodic systems, parametric independence from nuclear positions and momenta, and elimination of basis set linear dependencies and orthogonalization procedures. We obtain the END/PW formalism by extending the Thouless wave function and associated electron density to periodic systems, expressing the energy terms as functionals of the latter entities, and deriving the energy gradients with respect to nuclear and electronic variables. END/ PW has a great potential to simulate electron processes in both periodic (crystal) and aperiodic (molecular) systems (the latter in a supercell approach). Following previous END studies, END/PW will be applied to electron scattering processes in proton cancer therapy reactions.
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Affiliation(s)
- Erico S. Teixeira
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock 79409-1061, USA
- Present Address: CESAR School, Avenida Cais do Apolo, 77, Recife, PE CEP 50030-220, Brazil
| | - Jorge A. Morales
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock 79409-1061, USA
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27
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Jain P, Shukla RK, Pal S, Avasare V. Hydrogen bonding and non-covalent interaction assisted nickel(0) catalysed reversible alkenyl functional group swapping: a computational study. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02486g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An extensive DFT study is carried out to explore the mechanistic pathways involved in nickel(0) catalysed functional group swapping, where the less substituted N-tosyl allylamine transforms into a more substituted N-tosyl allylamine product.
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Affiliation(s)
- Pooja Jain
- Department of Chemistry
- Indian Institution of Technology Bombay
- Mumbai 400076
- India
| | - Rahul K. Shukla
- Department of Chemistry
- Indian Institution of Technology Bombay
- Mumbai 400076
- India
| | - Sourav Pal
- Department of Chemistry
- Indian Institution of Technology Bombay
- Mumbai 400076
- India
- Indian Institute of Science Education and Research Kolkata
| | - Vidya Avasare
- Department of Chemistry
- Sir Parashurambhau College
- Pune-411030
- India
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28
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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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29
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Villar P, González-Pérez AB, de Lera AR. Deciphering the Origin of Enantioselectivity on the Cis-Cyclopropanation of Styrene with Enantiopure Di-chloro,Di-gold(I)-SEGPHOS Carbenoids Generated from Propargylic Esters. J Org Chem 2019; 84:7664-7673. [PMID: 31095390 DOI: 10.1021/acs.joc.9b00250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The stereoselective synthesis of cis-disubstituted cyclopropanes by the Au(I)/PPh3-catalyzed cycloaddition of propargylic esters and styrene has been studied using density functional theory calculations. The computed mechanistic scheme involves the rate-limiting 1,2-rearrangement of the propargylic ester with the π-coordinated gold complex, followed by the (2 + 1)-cheletropic reaction of styrene with the alkenyl-Au(I) carbene intermediate to afford the cis-disubstituted cyclopropane derivative in a high cis/trans diastereomeric ratio. With a ( R)-di-chloro,di-gold-DTBM-SEGPHOS complex as the catalyst, computations are consistent with a rate-determining (2 + 1)-cheletropic reaction, in which facial discrimination is proposed to result from a combination of subtle steric and electronic effects in the SiRe facial approach transition structure, which favor the formation of the cis-cyclopropane diastereomer of 1 R,2 S absolute configuration, as experimentally observed.
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Affiliation(s)
- Pedro Villar
- Departamento de Química Orgánica, Facultade de Química and Centro de Investigacións Biomédicas (CINBIO) , Universidade de Vigo , Lagoas-Marcosende , 36310 Vigo , Spain
| | - Adán B González-Pérez
- Departamento de Química Orgánica, Facultade de Química and Centro de Investigacións Biomédicas (CINBIO) , Universidade de Vigo , Lagoas-Marcosende , 36310 Vigo , Spain
| | - Angel R de Lera
- Departamento de Química Orgánica, Facultade de Química and Centro de Investigacións Biomédicas (CINBIO) , Universidade de Vigo , Lagoas-Marcosende , 36310 Vigo , Spain
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30
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Harvey JN, Himo F, Maseras F, Perrin L. Scope and Challenge of Computational Methods for Studying Mechanism and Reactivity in Homogeneous Catalysis. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01537] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Catalonia, Spain
| | - Lionel Perrin
- Univ Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INSA Lyon, ICBMS, CNRS UMR 5246, 43 Bd. du 11 Novembre 1918, 69622 Villeurbanne, France
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31
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Li Y, Wu Z, Ling Z, Chen H, Zhang W. Mechanistic study of the solvent-controlled Pd(ii)-catalyzed chemoselective intermolecular 1,2-aminooxygenation and 1,2-oxyamination of conjugated dienes. Org Chem Front 2019. [DOI: 10.1039/c8qo01288a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The different coordination modes in MeCN and DMSO solvents could clarify the origin of chemoselectivity.
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Affiliation(s)
- Yunyi Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- P.R. China
| | - Zhengxing Wu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- P.R. China
| | - Zheng Ling
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- P.R. China
| | - Hongjin Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- P.R. China
| | - Wanbin Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- P.R. China
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32
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Bhaskararao B, Sunoj RB. Two chiral catalysts in action: insights into cooperativity and stereoselectivity in proline and cinchona-thiourea dual organocatalysis. Chem Sci 2018; 9:8738-8747. [PMID: 30627394 PMCID: PMC6289169 DOI: 10.1039/c8sc03078b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/17/2018] [Indexed: 12/13/2022] Open
Abstract
Increasing use of two chiral catalysts in cooperative asymmetric catalysis in recent years raises some fundamental questions on chiral compatibility between the catalysts, modes of activation, and relative disposition of substrates within the chiral environment of the catalysts for effective asymmetric induction. We present molecular insights into a one-pot catalytic Michael reaction cascade between a dicarbonyl compound (7-oxo-7-phenylhept-5-enal) and nitrostyrene, catalyzed by two chiral organocatalysts (proline and cinchona-thiourea), leading to a densely functionalized tetra-substituted cyclohexane product. The density functional theory (SMD(toluene)/M06-2X/6-31G**) computations helped us identify the role of the organocatalytic catalytic dyad in providing a lower energy pathway. The covalent activation of the aldehydic end by (S)-proline results in an enamine, which then adds to the noncovalently activated nitrostyrene in the first Michael addition to give a nitronate anion. The configuration at two of the four chiral centers of the product gets fixed in this step whereas that of the remaining two is determined by intramolecular cyclization between the nitronate and the enone. Important mechanistic features such as (a) a lower energy pathway as compared to a proline-only route for the formation of the syn-enamine and its participation in the first Michael addition and (b) the origin of the preferred prochiral faces in the C-C bond formation are traced to the active involvement of the cinchona-thiourea catalyst in conjunction with proline in each step of the reaction. The true cooperative action by both the catalysts is identified as enabled by a network of hydrogen bonding, and π···π stacking between the aryl ring of the cinchona-thiourea catalyst as well as other noncovalent interactions between the catalysts themselves, and that between the catalysts and substrate.
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Affiliation(s)
- Bangaru Bhaskararao
- Department of Chemistry , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India .
| | - Raghavan B Sunoj
- Department of Chemistry , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India .
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33
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Patel ND, Sieber JD, Tcyrulnikov S, Simmons BJ, Rivalti D, Duvvuri K, Zhang Y, Gao DA, Fandrick KR, Haddad N, Lao KS, Mangunuru HPR, Biswas S, Qu B, Grinberg N, Pennino S, Lee H, Song JJ, Gupton BF, Garg NK, Kozlowski MC, Senanayake CH. Computationally Assisted Mechanistic Investigation and Development of Pd-Catalyzed Asymmetric Suzuki-Miyaura and Negishi Cross-Coupling Reactions for Tetra- ortho-Substituted Biaryl Synthesis. ACS Catal 2018; 8:10190-10209. [PMID: 30450265 DOI: 10.1021/acscatal.8b02509] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Metal-catalyzed cross-coupling reactions are extensively employed in both academia and industry for the synthesis of biaryl derivatives for applications to both medicine and material science. Application of these methods to prepare tetra-ortho-substituted biaryls leads to chiral atropisomeric products that introduces the opportunity to use catalyst-control to develop asymmetric cross-coupling procedures to access these important compounds. Asymmetric Pd-catalyzed Suzuki-Miyaura and Negishi cross-coupling reactions to form tetra-ortho-substituted biaryls were studied employing a collection of P-chiral dihydrobenzooxaphosphole (BOP) and dihydrobenzoazaphosphole (BAP) ligands. Enantioselectivities of up to 95:5 and 85:15 er were identified for the Suzuki-Miyaura and Negishi cross-coupling reactions, respectively. Unique ligands for the Suzuki-Miyaura reaction vs the Negishi reaction were identified. A computational study on these Suzuki-Miyaura and Negishi cross-coupling reactions enabled an understanding in the differences between the enantiodiscriminating events between these two cross-coupling reactions. These results support that enantioselectivity in the Negishi reaction results from the reductive elimination step, whereas all steps in the Suzuki-Miyaura catalytic cycle contribute to the overall enantioselection with transmetalation and reductive elimination providing the most contribution to the observed selectivities.
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Affiliation(s)
- Nitinchandra D. Patel
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Joshua D. Sieber
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284-3028, United States
| | - Sergei Tcyrulnikov
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Bryan J. Simmons
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Daniel Rivalti
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, 601 Main Street, P.O. Box 843028, Richmond, Virginia 23284-3028, United States
| | - Krishnaja Duvvuri
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yongda Zhang
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Donghong A. Gao
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Keith R. Fandrick
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Nizar Haddad
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Kendricks So Lao
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Hari P. R. Mangunuru
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, 601 Main Street, P.O. Box 843028, Richmond, Virginia 23284-3028, United States
| | - Soumik Biswas
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Bo Qu
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Nelu Grinberg
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Scott Pennino
- Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Heewon Lee
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Jinhua J. Song
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - B. Frank Gupton
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, 601 Main Street, P.O. Box 843028, Richmond, Virginia 23284-3028, United States
| | - Neil K. Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Marisa C. Kozlowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Chris H. Senanayake
- Chemical Development, Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
- Astatech BioPharmaceutical Corporation, 488 Kelin West Road, Wengjiang, Chendu, Sichuan 611130, People’s Republic of China
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34
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Ma G, Yu H, Xu T, Wei X, Chen J, Lin H, Schüürmann G. Computational Insight into the Activation Mechanism of Carcinogenic N'-Nitrosonornicotine (NNN) Catalyzed by Cytochrome P450. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:11838-11847. [PMID: 30209943 DOI: 10.1021/acs.est.8b02795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tobacco-specific N'-nitrosonornicotine (NNN), a genotoxic nitrosamine classified as Group 1 carcinogen, is also present in atmospheric particulate matter and has even been detected as a new disinfection byproduct in wastewaters. NNN generally requires metabolic activation by cytochrome P450 enzymes to exert its genotoxicity, but the respective biotransformation pathways have not been described in detail. In this work, we performed density functional theory (DFT) calculations to unravel possible NNN activation pathways including α-hydroxylation, β-hydroxylation, pyridine N-oxidation, and norcotinine formation. The results reveal an initial rate-determining Hα-atom abstraction step for α-hydroxylation, followed by an unexpected kinetic competition between denitrosation and OH rebound, leading to ( iso-)myosmine as a detoxified product and α-hydroxyNNNs as the precursor of carcinogenic diazohydroxides, respectively. Further detoxification routes are given by β-hydroxylation with relative high reaction barrier and N-oxidation with comparable barrier to the toxifying α-hydroxylation. Moreover, we show for the first time how norcotinine can be generated as a minor NNN metabolite that is formed from iso-myosmine through a unique porphyrin-assisted H atom 1,2-transfer mechanism. These results demonstrate that the carcinogenic potential of NNN is subject to a kinetic competition between activating and deactivating metabolic routes, and identify respective biomarkers to inform about the individual risk associated with NNN exposure.
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Affiliation(s)
- Guangcai Ma
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Haiying Yu
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Ting Xu
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Xiaoxuan Wei
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Jianrong Chen
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Hongjun Lin
- College of Geography and Environmental Sciences , Zhejiang Normal University , Yingbin Avenue 688 , 321004 , Jinhua , China
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry , Helmholtz Centre for Environmental Research , Permoserstrasse 15 , 04318 , Leipzig , Germany
- Institute of Organic Chemistry , Technical University Bergakademie Freiberg , Leipzig Strasse 29 , 09596 Freiberg , Germany
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35
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Heshmat M. Unraveling the Origin of Solvent Induced Enantioselectivity in the Henry Reaction with Cinchona Thiourea as Catalyst. J Phys Chem A 2018; 122:7974-7982. [PMID: 30230831 DOI: 10.1021/acs.jpca.8b04589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we report an energy decomposition and electronic structure analysis using DFT calculations for the C-C coupling step in the Henry reaction with cinchona thiourea as catalyst and DMF solvent to unravel the origin of enantioselectivity. We found that the conformation of flexible thiourea moiety is affected by the solvent, and in the preferred conformation of thiourea in strong Lewis basic DMF solvent, the N-H sites are in the opposite direction, i.e., in trans conformation. Hence, the thiourea moiety acts via single hydrogen bonding with substrates. The conformation of the substrates with respect to the forming C-C bond plays critical role to increase orbital interaction between two substrates and enhances hydrogen bond strength between substrates and catalyst, which in turn stabilizes the positive charge developing on the catalyst at the transition state for one of the enantiomers ( S). Thus, the enantioselectivity has electronic structure origin. The stronger H-bond formation in the S enantiomer has been confirmed by the calculated IR spectra and is in agreement with thus far experimental and computational results.
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Affiliation(s)
- Mojgan Heshmat
- Department of Organic Chemistry , Stockholm University , Stockholm , 10691 , Sweden.,Theoretical Chemistry , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
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36
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Comparing quantitative prediction methods for the discovery of small-molecule chiral catalysts. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0040-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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37
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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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38
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Zhang M, Hu L, Lang Y, Cao Y, Huang G. Mechanism and Origins of Regio- and Enantioselectivities of Iridium-Catalyzed Hydroarylation of Alkenyl Ethers. J Org Chem 2018; 83:2937-2947. [DOI: 10.1021/acs.joc.8b00377] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mei Zhang
- Department
of Chemistry, School of Science and Tianjin Key Laboratory of Molecular
Optoelectronic Sciences, Tianjin University, Tianjin 300072, P. R. China
| | - Lingfei Hu
- Department
of Chemistry, School of Science and Tianjin Key Laboratory of Molecular
Optoelectronic Sciences, Tianjin University, Tianjin 300072, P. R. China
| | - Yanmin Lang
- Department
of Chemistry, School of Science and Tianjin Key Laboratory of Molecular
Optoelectronic Sciences, Tianjin University, Tianjin 300072, P. R. China
| | - Yang Cao
- Institute of New Energy, Shenzhen, Guangdong 518031, P.R. China
| | - Genping Huang
- Department
of Chemistry, School of Science and Tianjin Key Laboratory of Molecular
Optoelectronic Sciences, Tianjin University, Tianjin 300072, P. R. China
- National
Demonstration Center for Experimental Chemistry and Chemical Engineering
Education, National Virtual Simulation Experimental Teaching Center
for Chemistry and Chemical Engineering Education, Tianjin University, Tianjin 300072, P. R. China
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39
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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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40
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Li X, Wu H, Lang Y, Huang G. Mechanism, selectivity, and reactivity of iridium- and rhodium-catalyzed intermolecular ketone α-alkylation with unactivated olefinsviaan enamide directing strategy. Catal Sci Technol 2018. [DOI: 10.1039/c8cy00290h] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DFT calculations were performed to investigate the title reaction, focusing on detailed reaction mechanism and origins of selectivity and reactivity.
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Affiliation(s)
- Xiaojie Li
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
| | - Hongli Wu
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
| | - Yanmin Lang
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
| | - Genping Huang
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
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41
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Wu H, Li X, Tang X, Huang G. Mechanism and origins of chemo- and regioselectivities of (NHC)NiH-catalyzed cross-hydroalkenylation of vinyl ethers with α-olefins: a computational study. Org Chem Front 2018. [DOI: 10.1039/c8qo01020j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theory calculations were performed to investigate the (NHC)NiH-catalyzed cross-hydroalkenylation of vinyl ethers with α-olefins.
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Affiliation(s)
- Hongli Wu
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
| | - Xiaojie Li
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
| | - Xiangyang Tang
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
| | - Genping Huang
- Department of Chemistry
- School of Science and Tianjin Key Laboratory of Molecular Optoelectronic Sciences
- Tianjin University
- Tianjin 300072
- P. R. China
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42
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Heshmat M, Privalov T. Theory-Based Extension of the Catalyst Scope in the Base-Catalyzed Hydrogenation of Ketones: RCOOH-Catalyzed Hydrogenation of Carbonyl Compounds with H 2 Involving a Proton Shuttle. Chemistry 2017; 23:18193-18202. [PMID: 28981175 DOI: 10.1002/chem.201702149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Indexed: 11/09/2022]
Abstract
As an extension of the reaction mechanism describing the base-catalyzed hydrogenation of ketones according to Berkessel et al., we use a standard methodology for transition-state (TS) calculations in order to check the possibility of heterolytic cleavage of H2 at the ketone's carbonyl carbon atom, yielding one-step hydrogenation path with involvement of carboxylic acid as a catalyst. As an extension of the catalyst scope in the base-catalyzed hydrogenation of ketones, our mechanism involves a molecule with a labile proton and a Lewis basic oxygen atom as a catalyst-for example, R-C(=O)OH carboxylic acids-so that the heterolytic cleavage of H2 could take place between the Lewis basic oxygen atom of a carboxylic acid and the electrophilic (Lewis acidic) carbonyl carbon of a ketone/aldehyde. According to our TS calculations, protonation of a ketone/aldehyde by a proton shuttle (hydrogen bond) facilitates the hydride-type attack on the ketone's carbonyl carbon atom in the process of the heterolytic cleavage of H2 . Ketones with electron-rich and electron-withdrawing substituents in combination with a few carboxylic and amino acids-in total, 41 substrate-catalyst couples-have been computationally evaluated in this article and the calculated reaction barriers are encouragingly moderate for many of the considered substrate-catalyst couples.
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Affiliation(s)
- Mojgan Heshmat
- Department of Organic Chemistry, Stockholm University, Stockholm, 10691, Sweden
| | - Timofei Privalov
- Department of Organic Chemistry, Stockholm University, Stockholm, 10691, Sweden
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43
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Bhaskararao B, Jindal G, Sunoj RB. Exploring the Mechanism and Stereoselectivity in Chiral Cinchona-Catalyzed Heterodimerization of Ketenes. J Org Chem 2017; 82:13449-13458. [DOI: 10.1021/acs.joc.7b02517] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Bangaru Bhaskararao
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai,
Mumbai 400076, India
| | - Garima Jindal
- Department
of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, United States
| | - Raghavan B. Sunoj
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai,
Mumbai 400076, India
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44
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Jover J. Quantitative DFT modeling of product concentration in organometallic reactions: Cu-mediated pentafluoroethylation of benzoic acid chlorides as a case study. Phys Chem Chem Phys 2017; 19:29344-29353. [PMID: 29075697 DOI: 10.1039/c7cp05709a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DFT calculations are widely used for computing properties, reaction mechanisms and energy profiles in organometallic reactions. A qualitative agreement between the experimental and the calculated results seems to usually be enough to validate a computational methodology but recent advances in computation indicate that a nearly quantitative agreement should be possible if an appropriate DFT study is carried out. Final percent product concentrations, often reported as yields, are by far the most commonly reported properties in experimental metal-mediated synthesis studies but reported DFT studies have not focused on predicting absolute product amounts. The recently reported stoichiometric pentafluoroethylation of benzoic acid chlorides (R-C6H4COCl) with [(phen)Cu(PPh3)C2F5] (phen = 1,10-phenanthroline, PPh3 = triphenylphosphine) has been used as a case study to check whether the experimental product concentrations can be reproduced by any of the most popular DFT approaches with high enough accuracy. To this end, the Gibbs energy profile for the pentafluoroethylation of benzoic acid chloride has been computed using 14 different DFT methods. These computed Gibbs energy profiles have been employed to build kinetic models predicting the final product concentration in solution. The best results are obtained with the D3-dispersion corrected B3LYP functional, which has been successfully used afterwards to model the reaction outcomes of other simple (R = o-Me, p-Me, p-Cl, p-F, etc.) benzoic acid chlorides. The product concentrations of more complex reaction networks in which more than one position of the substrate may be activated by the copper catalyst (R = o-Br and p-I) are also predicted appropriately.
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Affiliation(s)
- Jesús Jover
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain and Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
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45
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Li M, Xue XS, Cheng JP. Mechanism and Origins of Stereoinduction in Natural Cinchona Alkaloid Catalyzed Asymmetric Electrophilic Trifluoromethylthiolation of β-Keto Esters with N-Trifluoromethylthiophthalimide as Electrophilic SCF3 Source. ACS Catal 2017. [DOI: 10.1021/acscatal.7b03007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Man Li
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry,
Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, People’s Republic of China
| | - Xiao-Song Xue
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry,
Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, People’s Republic of China
| | - Jin-Pei Cheng
- State
Key Laboratory of Elemento-Organic Chemistry, College of Chemistry,
Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, People’s Republic of China
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
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46
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Aoto YA, de Lima Batista AP, Köhn A, de Oliveira-Filho AGS. How To Arrive at Accurate Benchmark Values for Transition Metal Compounds: Computation or Experiment? J Chem Theory Comput 2017; 13:5291-5316. [DOI: 10.1021/acs.jctc.7b00688] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yuri A. Aoto
- Institut
für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring
55, D-70569 Stuttgart, Germany
| | - Ana Paula de Lima Batista
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, SP, Brazil
| | - Andreas Köhn
- Institut
für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring
55, D-70569 Stuttgart, Germany
| | - Antonio G. S. de Oliveira-Filho
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
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47
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Bhaskararao B, Sunoj RB. Asymmetric Dual Chiral Catalysis using Iridium Phosphoramidites and Diarylprolinol Silyl Ethers: Insights into Stereodivergence. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02776] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Bangaru Bhaskararao
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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48
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Zou H, Wang ZL, Huang G. Mechanism and Origins of the Chemo- and Regioselectivities in Nickel-Catalyzed Intermolecular Cycloadditions of Benzocyclobutenones with 1,3-Dienes. Chemistry 2017; 23:12593-12603. [DOI: 10.1002/chem.201702316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Hongyan Zou
- Tianjin Key Laboratory of Water Resources and Environment; Tianjin Normal University; Tianjin 300387 P.R. China
| | - Zhong-Liang Wang
- Tianjin Key Laboratory of Water Resources and Environment; Tianjin Normal University; Tianjin 300387 P.R. China
| | - Genping Huang
- Department of Chemistry; School of Science; National Demonstration Center for Experimental Chemistry & Chemical engineering Education; National Virtual Simulation Experimental Teaching Center for Chemistry & Chemical engineering Education; Tianjin Key Laboratory of Molecular Optoelectronic Sciences; Tianjin University, Tianjin; 300072 P.R. China
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49
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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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50
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Ji L, Wang C, Ji S, Kepp KP, Paneth P. Mechanism of Cobalamin-Mediated Reductive Dehalogenation of Chloroethylenes. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00540] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Ji
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Chenchen Wang
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Shujing Ji
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Kasper P. Kepp
- DTU
Chemistry, Technical University of Denmark, Building 206, Kgs. Lyngby DK-2800, Denmark
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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