1
|
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.
Collapse
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
| |
Collapse
|
2
|
Srivastava A, Naik RM, Rai J, Kumar I, Yaseen B, Gangwar C. Kinetic study of Hg(
II
)‐promoted substitution of cyanide from hexacyanoferrate(
II
) in an anionic surfactant medium by 2,2′‐bipyridine. J SURFACTANTS DETERG 2022. [DOI: 10.1002/jsde.12622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Radhey Mohan Naik
- Department of Chemistry Lucknow University Lucknow Uttar Pradesh India
| | - Jyoti Rai
- Department of Chemistry Lucknow University Lucknow Uttar Pradesh India
| | - Indresh Kumar
- Department of Chemistry Lucknow University Lucknow Uttar Pradesh India
| | - Bushra Yaseen
- Department of Chemistry Lucknow University Lucknow Uttar Pradesh India
| | - Chinky Gangwar
- Department of Chemistry Lucknow University Lucknow Uttar Pradesh India
| |
Collapse
|
3
|
Zhang X, Takahashi S, Aratsu K, Kikuchi I, Sato H, Hiraoka S. Cyclization or bridging: which occurs faster is the key to the self-assembly mechanism of Pd 6L 3 coordination prisms. Phys Chem Chem Phys 2022; 24:2997-3006. [PMID: 35037923 DOI: 10.1039/d1cp04448f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-assembly processes of Pd6L3 coordination prisms consisting of cis-protected Pd(II) complexes and porphyrin-based tetratopic ligands with four 3-pyridyl or 4-pyridyl groups (L) were investigated by experimental and numerical methods, QASAP (quantitative analysis of self-assembly process) and NASAP (numerical analysis of self-assembly process), respectively. It was found that contrary to common intuition macrocyclization takes place faster than the bridging reaction in the prism assembly and that the bridging reaction occurring before the macrocyclization tends to produce kinetically trapped species. A numerical simulation demonstrates that the relative magnitude of the rate constants between the macrocyclization and the bridging reaction is the key factor that determines whether the self-assembly leads to the thermodynamically most stable prism or to kinetically trapped species. Finding the key elementary reactions that largely affect the selection of the major assembly pathway is helpful to rationally control the products under kinetic control via modulation of the energy landscape.
Collapse
Affiliation(s)
- Xinman Zhang
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, 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.
| | - Keisuke Aratsu
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Isamu Kikuchi
- 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.,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, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| |
Collapse
|
4
|
Srivastava A, Naik RM, Rai J, Asthana A. Ag(I)-Promoted Substitution of Cyanide from Hexacyanoferrate(II) with Pyrazine: A Kinetic and Mechanistic Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2021. [DOI: 10.1134/s0036024421130227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Tateishi T, Takahashi S, Kikuchi I, Aratsu K, Sato H, Hiraoka S. Unexpected Self-Assembly Pathway to a Pd(II) Coordination Square-Based Pyramid and Its Preferential Formation beyond the Boltzmann Distribution. Inorg Chem 2021; 60:16678-16685. [PMID: 34652136 DOI: 10.1021/acs.inorgchem.1c02570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Experimental and theoretical investigations of the self-assembly process of a Pd(II) coordination M6L4 square-based pyramid (SP) were conducted. It was found that the probable self-assembly pathway, in which the dimerization of M2L2 with two M leads to SP, expected from the connectivity of the building blocks is not a major self-assembly pathway to the M6L4 SP. Whether the M6L4 SP is assembled or M2L2 is trapped is determined by an inter- or intramolecular reaction in a chain-like M2L2X, where X is a leaving ligand. The kinetically trapped state where the M6L4 SP is produced from M2L2 beyond the Boltzmann distribution was realized by a concentration-induced process and was kept for at least 2 months at 298 K.
Collapse
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
| | - 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
| | - Isamu Kikuchi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Keisuke Aratsu
- 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.,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, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| |
Collapse
|
6
|
Ulitin N, Kharlampidi K, Tereshchenko К, Novikov N, Shiyan D, Nurmurodov T, Nurullina N, Ziyatdinov N, Miroshkin N. The cumene oxidation and cumene hydroperoxide decomposition in the presence of Zn, Cd or Hg 2-ethylhexanoate: Kinetic model and analysis of its sensitivity. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
7
|
Takahashi S, Tateishi T, Sasaki Y, Sato H, Hiraoka S. Towards kinetic control of coordination self-assembly: a case study of a Pd 3L 6 double-walled triangle to predict the outcomes by a reaction network model. Phys Chem Chem Phys 2020; 22:26614-26626. [PMID: 33201952 DOI: 10.1039/d0cp04623j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Numerical analysis of self-assembly process (NASAP) was performed for a [Pd3L6]6+ double-walled triangle (DWT) complex. With a chemical reaction network and a parameter set of the reaction rate constants obtained from a numerical search in an eighteen-dimensional parameter space to obtain a good fit to the data from the experimental counterpart (quantitative analysis of self-assembly process, QASAP), a refined calculation resulted in a detailed time evolution of each molecular species. Analysis based on those clues revealed dominant self-assembly pathways and a balance between inter- and intramolecular reactions, and enabled prediction of the reaction outcomes depending on the initial stoichiometric ratio under kinetic control.
Collapse
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.
| | | | | | | | | |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|