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Kuan KY, Hsu CP. Predicting Selectivity with a Bifurcating Surface: Inaccurate Model or Inaccurate Statistics of Dynamics? J Phys Chem A 2024; 128:6798-6805. [PMID: 39099446 DOI: 10.1021/acs.jpca.4c04039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Reactions on post-transition-state bifurcation (PTSB) energy surfaces are an important class of reaction in which classical rate theories, such as the transition state theory, fail to account for the selectivity. Quasiclassical trajectory molecular dynamic (QCT-MD) simulation is an important computational approach to understanding reactions mechanisms, especially for reactions that cannot be predicted from conventional rate theories. However, the applicability of direct dynamic simulations is hampered by huge computational costs for collecting a statistically meaningful set of trajectories, making it difficult to compare simulation results with theoretical or physical insights-based predictions (non-MD predictions). In this work, we examine the PTSB of Schmidt-Aubé reactions studied by Tantillo and co-workers. With machine-learning using kernel-ridge regression (KRR) to predict atomic forces, statistical reliability was enhanced by significantly increasing the number of trajectories. With KRR, the bottleneck of simulating dynamics (atomic forces in QCT-MD with density functional theory) was accelerated more than 100-fold. We found that this KRR-aided QCT-MD approach is successful in predicting branching ratios with a much larger number of trajectories. With our approach, statistical errors are greatly reduced, and hypothetical non-MD models for predicting selectivity are tested with much higher confidence. By comparison with non-MD models, dynamical properties that affect branching ratios become more clearly described.
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Affiliation(s)
- Kai-Yuan Kuan
- Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
- Physics Division, National Center for Theoretical Sciences, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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Lam CC, Goodman JM. Reaction dynamics as the missing puzzle piece: the origin of selectivity in oxazaborolidinium ion-catalysed reactions. Chem Sci 2023; 14:12355-12365. [PMID: 37969604 PMCID: PMC10631253 DOI: 10.1039/d3sc03009a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023] Open
Abstract
The selectivity in a group of oxazaborolidinium ion-catalysed reactions between aldehyde and diazo compounds cannot be explained using transition state theory. VRAI-selectivity, developed to predict the outcome of dynamically controlled reactions, can account for both the chemo- and the stereo-selectivity in these reactions, which are controlled by reaction dynamics. Subtle modifications to the substrate or catalyst substituents alter the potential energy surface, leading to changes in predominant reaction pathways and altering the barriers to the major product when reaction dynamics are considered. In addition, this study suggests an explanation for the mysterious inversion of enantioselectivity resulting from the inclusion of an orthoiPrO group in the catalyst.
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Affiliation(s)
- Ching Ching Lam
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jonathan M Goodman
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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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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Murakami T, Ibuki S, Hashimoto Y, Kikuma Y, Takayanagi T. Dynamics study of the post-transition-state-bifurcation process of the (HCOOH)H + → CO + H 3O +/HCO + + H 2O dissociation: application of machine-learning techniques. Phys Chem Chem Phys 2023; 25:14016-14027. [PMID: 37161528 DOI: 10.1039/d3cp00252g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The process of protonated formic acid dissociating from the transition state was studied using ring-polymer molecular dynamics (RPMD), classical MD, and quasi-classical trajectory (QCT) simulations. Temperature had a strong influence on the branching fractions for the HCO+ + H2O and CO + H3O+ dissociation channels. The RPMD and classical MD simulations showed similar behavior, but the QCT dynamics were significantly different owing to the excess energies in the quasi-classical trajectories. Machine-learning analysis identified several key features in the phase information of the vibrational motions at the transition state. We found that the initial configuration and momentum of a hydrogen atom connected to a carbon atom and the shrinking coordinate of the CO bond at the transition state play a role in the dynamics of HCO+ + H2O production.
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Affiliation(s)
- Tatsuhiro Murakami
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
- Department of Materials & Life Sciences, Faculty of Science & Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Shunichi Ibuki
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
| | - Yu Hashimoto
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
| | - Yuya Kikuma
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan.
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Murakami T, Matsumoto N, Takayanagi T, Fujihara T. The importance of nuclear dynamics in reaction mechanisms of acetylene cyclotrimerization catalyzed by Fe+-compounds. J Organomet Chem 2023. [DOI: 10.1016/j.jorganchem.2023.122643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Abstract
Differences in entropies of competing transition states can direct kinetic selectivity. Understanding and modeling such entropy differences at the molecular level is complicated by the fact that entropy is statistical in nature; i.e., it depends on multiple vibrational states of transition structures, the existence of multiple dynamically accessible pathways past these transition structures, and contributions from multiple transition structures differing in conformation/configuration. The difficulties associated with modeling each of these contributors are discussed here, along with possible solutions, all with an eye toward the development of portable qualitative models of use to experimentalists aiming to design reactions that make use of entropy to control kinetic selectivity.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Ave, Davis, California 95616, United States
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Park KHK, Frank N, Duarte F, Anderson EA. Collective Synthesis of Illudalane Sesquiterpenes via Cascade Inverse Electron Demand (4 + 2) Cycloadditions of Thiophene S, S-Dioxides. J Am Chem Soc 2022; 144:10017-10024. [PMID: 35609003 PMCID: PMC9185749 DOI: 10.1021/jacs.2c03304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiophene S,S-dioxides are underutilized tools for the de novo construction of benzene rings in organic synthesis. We report a collective synthesis of nine illudalane sesquiterpenes using bicyclic thiophene S,S-dioxides as generalized precursors to the indane core of the natural products. Exploiting furans as unusual dienophiles in this inverse electron demand Diels-Alder cascade, this concise and convergent approach enables the synthesis of these targets in as little as five steps. Theoretical studies rationalize the reactivity of thiophene S,S-dioxides with both electron-poor and electron-rich dienophiles and reveal reaction pathways involving either nonpolar pericyclic or bifurcating ambimodal cycloadditions. Overall, this work demonstrates the wider potential of thiophene S,S-dioxides as convenient and flexible precursors to polysubstituted arenes.
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Affiliation(s)
- Kun Ho Kenny Park
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Nils Frank
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Fernanda Duarte
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Edward A Anderson
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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Bharadwaz P, Maldonado-Domínguez M, Srnec M. Bifurcating reactions: distribution of products from energy distribution in a shared reactive mode. Chem Sci 2021; 12:12682-12694. [PMID: 34703554 PMCID: PMC8494029 DOI: 10.1039/d1sc02826j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/21/2021] [Indexed: 11/21/2022] Open
Abstract
Bifurcating reactions yield two different products emerging from one single transition state and are therefore archetypal examples of reactions that cannot be described within the framework of the traditional Eyring's transition state theory (TST). With the growing number and importance of these reactions in organic and biosynthetic chemistry, there is also an increasing demand for a theoretical tool that would allow for the accurate quantification of reaction outcome at low cost. Here, we introduce such an approach that fulfils these criteria, by evaluating bifurcation selectivity through the energy distribution within the reactive mode of the key transition state. The presented method yields an excellent agreement with experimentally reported product ratios and predicts the correct selectivity for 89% of nearly 50 various cases, covering pericyclic reactions, rearrangements, fragmentations and metal-catalyzed processes as well as a series of trifurcating reactions. With 71% of product ratios determined within the error of less than 20%, we also found that the methodology outperforms three other tested protocols introduced recently in the literature. Given its predictive power, the procedure makes reaction design feasible even in the presence of complex non-TST chemical steps. Reactive Mode Composition Factor (RMCF) analysis is a powerful tool to forecast the product distribution of bifurcating reactions through analysis of the kinetic energy distribution within the first transition state traversed by the reacting system.![]()
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Affiliation(s)
- Priyam Bharadwaz
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences Dolejškova 3 Prague 8 18223 Czech Republic
| | - Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences Dolejškova 3 Prague 8 18223 Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences Dolejškova 3 Prague 8 18223 Czech Republic
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Tantillo DJ, Laconsay CJ. Melding of Experiment and Theory Illuminates Mechanisms of Metal-Catalyzed Rearrangements: Computational Approaches and Caveats. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/s-0040-1720451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThis review summarizes approaches and caveats in computational modeling of transition-metal-catalyzed sigmatropic rearrangements involving carbene transfer. We highlight contemporary examples of combined synthetic and theoretical investigations that showcase the synergy achievable by integrating experiment and theory.1 Introduction2 Mechanistic Models3 Theoretical Approaches and Caveats3.1 Recommended Computational Tools3.2 Choice of Functional and Basis Set3.3 Conformations and Ligand-Binding Modes3.4 Solvation4 Synergy of Experiment and Theory – Case Studies4.1 Metal-Bound or Free Ylides?4.2 Conformations and Ligand-Binding Modes of Paddlewheel Complexes4.3 No Metal, Just Light4.4 How To ‘Cope’ with Nonstatistical Dynamic Effects5 Outlook
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