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Okazawa A, Sanada N, Takahashi S, Sato H, Hiraoka S. Pathway selection in the self-assembly of Rh 4L 4 coordination squares under kinetic control. Commun Chem 2023; 6:248. [PMID: 37968322 PMCID: PMC10651846 DOI: 10.1038/s42004-023-01053-7] [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: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
Pathway selection principles in reversible reaction networks such as molecular self-assembly have not been established yet, because achieving kinetic control in reversible reaction networks is more complicated than in irreversible ones. In this study, we discovered that coordination squares consisting of cis-protected dinuclear rhodium(II) corner complexes and linear ditopic ligands are assembled under kinetic control, perfectly preventing the corresponding triangles, by modulating their energy landscapes with a weak monotopic carboxylate ligand (2,6-dichlorobenzoate: dcb-) as the leaving ligand. Experimental and numerical approaches revealed the self-assembly pathway where the cyclization step to form the triangular complex is blocked by dcb-. It was also found that one of the molecular squares assembled into a dimeric structure owing to the solvophobic effect, which was characterized by nuclear magnetic resonance spectroscopy and single-crystal X-ray analysis.
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Affiliation(s)
- Atsushi Okazawa
- Department of Electrical Engineering and Bioscience, Waseda University, Tokyo, 169-8555, Japan
| | - Naoki Sanada
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto, 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan.
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2
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Takahashi S, Iuchi S, Hiraoka S, Sato H. Theoretical and computational methodologies for understanding coordination self-assembly complexes. Phys Chem Chem Phys 2023; 25:14659-14671. [PMID: 37051715 DOI: 10.1039/d3cp00082f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
This perspective highlights three theoretical and computational methods to capture the coordination self-assembly processes at the molecular level: quantum chemical modeling, molecular dynamics, and reaction network analysis. These methods cover the different scales from the metal-ligand bond to a more global aspect, and approaches that are best suited to understand the coordination self-assembly from different perspectives are introduced. Theoretical and numerical researches based on these methods are not merely ways of interpreting the experimental studies but complementary to them.
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Affiliation(s)
- Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Satoru Iuchi
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8103, Japan
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3
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Piskorz TK, Martí-Centelles V, Young TA, Lusby PJ, Duarte F. Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and Opportunities. ACS Catal 2022; 12:5806-5826. [PMID: 35633896 PMCID: PMC9127791 DOI: 10.1021/acscatal.2c00837] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/09/2022] [Indexed: 01/18/2023]
Abstract
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Self-assembled
metallo-organic
cages have emerged as promising
biomimetic platforms that can encapsulate whole substrates akin to
an enzyme active site. Extensive experimental work has enabled access
to a variety of structures, with a few notable examples showing catalytic
behavior. However, computational investigations of metallo-organic
cages are scarce, not least due to the challenges associated with
their modeling and the lack of accurate and efficient protocols to
evaluate these systems. In this review, we discuss key molecular principles
governing the design of functional metallo-organic cages, from the
assembly of building blocks through binding and catalysis. For each
of these processes, computational protocols will be reviewed, considering
their inherent strengths and weaknesses. We will demonstrate that
while each approach may have its own specific pitfalls, they can be
a powerful tool for rationalizing experimental observables and to
guide synthetic efforts. To illustrate this point, we present several
examples where modeling has helped to elucidate fundamental principles
behind molecular recognition and reactivity. We highlight the importance
of combining computational and experimental efforts to speed up supramolecular
catalyst design while reducing time and resources.
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Affiliation(s)
- Tomasz K. Piskorz
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Vicente Martí-Centelles
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Valencia 46022, Spain
| | - Tom A. Young
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul J. Lusby
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, Scotland EH9 3FJ, United Kingdom
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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4
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Sun Y, Chen C, Liu J, Stang PJ. Recent developments in the construction and applications of platinum-based metallacycles and metallacages via coordination. Chem Soc Rev 2020; 49:3889-3919. [PMID: 32412574 PMCID: PMC7846457 DOI: 10.1039/d0cs00038h] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Coordination-driven suprastructures have attracted much interest due to their unique properties. Among these structures, platinum-based architectures have been broadly studied due to their facile preparation. The resultant two- or three-dimensional (2D or 3D) systems have many advantages over their precursors, such as improved emission tuning, sensitivity as sensors, and capture and release of guests, and they have been applied in biomedical diagnosis as well as in catalysis. Herein, we review the recent results related to platinum-based coordination-driven self-assembly (CDSA), and the text is organized to emphasizes both the synthesis of new metallacycles and metallacages and their various applications.
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Affiliation(s)
- Yan Sun
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, P. R. China.
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5
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Iioka T, Takahashi S, Yoshida Y, Matsumura Y, Hiraoka S, Sato H. A kinetics study of ligand substitution reaction on dinuclear platinum complexes: Stochastic versus deterministic approach. J Comput Chem 2019; 40:279-285. [PMID: 30299552 DOI: 10.1002/jcc.25588] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 02/03/2023]
Abstract
The kinetics on a basic ligand substitution reaction on dinuclear platinum complexes [Pt(PEt3 )2 PhPt(PEt3 )2 ]2+ and [Pt(PEt3 )2 PhCOPhPt(PEt3 )2 ]2+ , with the ligands pyridine and 3-chloropyridine, is studied. This is a fundamental step in a self-assembly, and the time evolution has been observed with a new experimental technique, QASAP (quantitative analysis of self-assembly process), which is recently developed by Hiraoka's group. As a result of numerical calculations based on master equation, we succeed in specifying the reaction rate constants with a simple reaction model. In addition, the time evolutions of all the intermediate components produced and consumed in chemical reaction are revealed, including those unobserved in the experiments. The convergence behavior of the existence ratios of specific chemical species calculated with the stochastic algorithm method is compared with those obtained from deterministic formalism based on rate equations, revealing a clear dependence on the number of constituent molecules. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Tatsuya Iioka
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yuichiro Yoshida
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yoshihiro Matsumura
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
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6
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Takahashi S, Sasaki Y, Hiraoka S, Sato H. A stochastic model study on the self-assembly process of a Pd2L4 cage consisting of rigid ditopic ligands. Phys Chem Chem Phys 2019; 21:6341-6347. [DOI: 10.1039/c8cp06102e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Numerical analysis considering explicit conformational difference revealed the self-assembly process of a Pd2L4 cage containing rigid ditopic ligands.
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Affiliation(s)
- Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Yuya Sasaki
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University
- Kyoto 615-8510
- Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University
- Kyoto 615-8510
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7
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Hiraoka S. Self‐Assembly Processes of Pd(II)‐ and Pt(II)‐Linked Discrete Self‐Assemblies Revealed by QASAP. Isr J Chem 2018. [DOI: 10.1002/ijch.201800073] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and SciencesThe University of Tokyo 3-8-1 Komaba, Meguro-ku Tokyo 153-8902 Japan
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8
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Hiraoka S. Unresolved Issues that Remain in Molecular Self-Assembly. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180008] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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9
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Chiral self-sorting process in the self-assembly of homochiral coordination cages from axially chiral ligands. Commun Chem 2018. [DOI: 10.1038/s42004-018-0020-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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10
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Kai S, Maddala SP, Kojima T, Akagi S, Harano K, Nakamura E, Hiraoka S. Flexibility of components alters the self-assembly pathway of Pd 2L 4 coordination cages. Dalton Trans 2018; 47:3258-3263. [PMID: 29442109 DOI: 10.1039/c8dt00112j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The self-assembly process of a Pd2L4 cage consisting of flexible ditopic ligands and Pd(ii) ions was revealed by QASAP (quantitative analysis of self-assembly process), which enables one to obtain information about the intermediates transiently produced during the self-assembly as the average composition of all the intermediates. It was found that the dominant pathway to the cage is the formation of a submicrometre-sized sheet structure, which was characterized by dynamic light scattering (DLS) and scanning transmission electron microscopy (STEM), followed by the addition of free ditopic ligands to the Pd(ii) centres of the sheet structure to trigger the cage formation. This assembly process is completely different from that of a Pd2L4 cage composed of rigid ditopic ligands, indicating that the flexibility of the components strongly affects the self-assembly process.
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Affiliation(s)
- Shumpei Kai
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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11
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Tateishi T, Kojima T, Hiraoka S. Multiple Pathways in the Self-Assembly Process of a Pd 4L 8 Coordination Tetrahedron. Inorg Chem 2018; 57:2686-2694. [PMID: 29469572 DOI: 10.1021/acs.inorgchem.7b03085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The self-assembly of a Pd418 coordination tetrahedron (Tet) from a ditopic ligand, 1, and palladium(II) ions, [PdPy*4]2+ (Py* = 3-chloropyridine), was investigated by a 1H NMR-based quantitative approach (quantitative analysis of self-assembly process, QASAP), which allows one to monitor the average composition of the intermediates not observed by NMR spectroscopy. The self-assembly of Tet takes place mainly through three pathways and about half of the Tet structures were produced through the reaction of a kinetically produced Pd3L6 double-walled triangle (DWT) and 200-nm-sized large intermediates (IntL). In two of the three pathways, the leaving ligand (Py*), which is not a component of Tet, catalytically assisted the self-assembly. Such a multiplicity of the self-assembly process of Tet suggests that molecular self-assembly takes place on an energy landscape like a protein-folding funnel.
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Affiliation(s)
- Tomoki Tateishi
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba, Meguro-ku , Tokyo 153-8902 , Japan
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba, Meguro-ku , Tokyo 153-8902 , Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba, Meguro-ku , Tokyo 153-8902 , Japan
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12
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Kai S, Nakagawa M, Kojima T, Li X, Yamashina M, Yoshizawa M, Hiraoka S. Self-Assembly Process of a Pd2
L4
Capsule: Steric Interactions between Neighboring Components Favor the Formation of Large Intermediates. Chemistry 2018; 24:3965-3969. [DOI: 10.1002/chem.201705253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Shumpei Kai
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
| | - Masanori Nakagawa
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
| | - Tatsuo Kojima
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
| | - Xin Li
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
| | - Masahiro Yamashina
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259 Nagatsuta Midori-ku Yokohama 226-8503 Japan
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life Science; Institute of Innovative Research; Tokyo Institute of Technology; 4259 Nagatsuta Midori-ku Yokohama 226-8503 Japan
| | - Shuichi Hiraoka
- Department of Basic Science; Graduate School of Arts and Sciences; The University of Tokyo; 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan
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13
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Matsumura Y, Iuchi S, Hiraoka S, Sato H. Chiral effects on the final step of an octahedron-shaped coordination capsule self-assembly. Phys Chem Chem Phys 2018; 20:7383-7386. [DOI: 10.1039/c7cp08237a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The final step of the self-assembly of an octahedron-shaped coordination capsule was investigated by a novel theoretical method.
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Affiliation(s)
- Y. Matsumura
- Department of Molecular Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - S. Iuchi
- Graduate School of Informatics
- Nagoya University
- Nagoya 464-8601
- Japan
| | - S. Hiraoka
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo
- Japan
| | - H. Sato
- Department of Molecular Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
- Elements Strategy Initiative for Catalysts and Batteries
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14
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Kai S, Martí-Centelles V, Sakuma Y, Mashiko T, Kojima T, Nagashima U, Tachikawa M, Lusby PJ, Hiraoka S. Quantitative Analysis of Self-Assembly Process of a Pd 2 L 4 Cage Consisting of Rigid Ditopic Ligands. Chemistry 2017; 24:663-671. [PMID: 29044811 DOI: 10.1002/chem.201704285] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Indexed: 12/20/2022]
Abstract
The self-assembly process of a Pd2 L4 cage complex consisting of rigid ditopic ligands, in which two 3-pyridyl groups are connected to a benzene ring through acetylene bonds and PdII ions was revealed by a recently developed quantitative analysis of self-assembly process (QASAP), with which the self-assembly process of coordination assemblies can be investigated by monitoring the evolution with time of the average composition of all the intermediates. QASAP revealed that the rate-determining steps of the cage formation are the intramolecular ligand exchanges in the final stage of the self-assembly: [Pd2 L4 Py*2 ]4+ →[Pd2 L4 Py*1 ]4+ +Py* and [Pd2 L4 Py*1 ]4+ →[Pd2 L4 ]4+ +Py* (Py*: 3-chloropyridine, which was used as a leaving ligand on the metal source). The energy barriers for the two reactions were determined to be 22.3 and 21.9 kcal mol-1 , respectively. DFT calculations of the transition-state (TS) structures for the two steps indicated that the distortion of the trigonal-bipyramidal PdII center at the TS geometries increases the activation free energy of the two steps.
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Affiliation(s)
- Shumpei Kai
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Vicente Martí-Centelles
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, Scotland, EH9 3FJ, UK
| | - Yui Sakuma
- Quantum Chemistry Division, Graduate School of Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama-city, Kanagawa, 236-0027, Japan
| | - Takako Mashiko
- Quantum Chemistry Division, Graduate School of Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama-city, Kanagawa, 236-0027, Japan
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Umpei Nagashima
- Foundation for Computational Science (FOCUS), 7-1-28, Minatojimaminatomachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division, Graduate School of Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama-city, Kanagawa, 236-0027, Japan
| | - Paul J Lusby
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, Scotland, EH9 3FJ, UK
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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