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Murata M, Koide T, Kobayashi O, Hiraoka S, Shimazaki T, Tachikawa M. Molecular Dynamics Study on the Structure-Property Relationship of Self-Assembled Gear-Shaped Amphiphile Molecules with/without Methyl Groups. J Phys Chem B 2023; 127:328-334. [PMID: 36542848 DOI: 10.1021/acs.jpcb.2c07444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gaining insight into the encapsulation mechanism is important for controlling the encapsulation rate toward the self-assembly of gear-shaped amphiphile molecules (GSAs). To this aim, we conducted molecular dynamics (MD) simulations for three different hexameric nanocubes (1612+, 2612+, and 3612+) of GSAs (12+, 22+, and 32+, respectively) to elucidate the quantitative structure-property relationship between the stability of the nanocubes and the rate of encapsulation of a guest molecule. The 12+, 22+, and 32+ monomers differ from each other in the number of methyl groups, having three, zero, and two methyl groups, respectively. The 3612+ hexamer has methyl groups only on the equatorial region. In the cases of the simulations of 1612+ and 3612+, the cubic structures are maintained due to a tight triple-π stacking around the equator region. Meanwhile, 2612+ deforms easily due to the occurrence of a large fluctuation. These results indicate that the methyl groups on the equator are crucial to stabilize the nanocubes. The encapsulation of an iodide ion as a guest molecule is revealed to occur through the pole region via a gap that is easily formed in the nanocubes without methyl groups on the poles. Our study clearly suggests that self-assembled nanocubes can be designed to attain a specific stability and encapsulation efficiency simultaneously.
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Affiliation(s)
- Moe Murata
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama236-0027, Kanagawa, Japan
| | - Takuya Koide
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama236-0027, Kanagawa, Japan
| | - Osamu Kobayashi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama236-0027, Kanagawa, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo153-8902Japan
| | - Tomomi Shimazaki
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama236-0027, Kanagawa, Japan
| | - Masanori Tachikawa
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama236-0027, Kanagawa, Japan
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2
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Sakowicz AM, Szumna A. Chiral Water-Soluble Molecular Capsules With Amphiphilic Interiors. Front Chem 2022; 10:883093. [PMID: 35494632 PMCID: PMC9047736 DOI: 10.3389/fchem.2022.883093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
We present the synthesis of new chiral water-soluble dimeric capsules by the multicomponent Mannich reaction between charged amino acids (glutamic acid or arginine), resorcinarene, and formaldehyde and by subsequent self-assembly. The zwitterionic character of the backbones enables electrostatic interactions between arms and induces self-assembly of dimeric capsules, namely, (L-ArgR)2 and (L-GluR)2, in water with a wide range of pH, as demonstrated by NMR, diffusion coefficient measurement, and circular dichroism. The assembly/disassembly processes are fast on the NMR timescale. This mode of dimerization leaves side chains available for additional interactions and creates chiral cavities of mixed hydrophobic/hydrophilic character. According to this characteristic, capsules do not bind fully nonpolar or fully polar guests but effectively encapsulate a variety of chiral molecules with mixed polar/apolar characters (aliphatic and aromatic aldehydes, epoxides, alcohols, carboxylic acids, amines, and amino acids) with moderate strength. We also demonstrate the formation of heterocapsules (GluR) (ArgR) (homo- and heterochiral) that utilize additional interactions between charged acidic and basic side chains and have better encapsulation properties than those of the homodimers.
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3
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Zhan YY, Hiraoka S. Molecular “Hozo”: Thermally Stable Yet Conformationally Flexible Self-Assemblies Driven by Tight Molecular Meshing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yi-Yang Zhan
- RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, 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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4
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Tsuchida Y, Aratsu K, Hiraoka S, Yoshizawa M. An Aromatic Oligomer Micelle: Large Enthalpic Stabilization and Selective Oligothiophene Uptake. Angew Chem Int Ed Engl 2021; 60:12754-12758. [PMID: 33773001 DOI: 10.1002/anie.202101453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/24/2021] [Indexed: 11/06/2022]
Abstract
An aromatic oligomer micelle, featuring both high stability and high uptake ability, was quantitatively formed in water from amphiphilic oligomers, composed of three bent polyaromatic amphiphiles connected alternately by two hydrophilic chains. The well-defined micelle, with a diameter of ca. 2 nm, remains intact even under highly diluted conditions (ca. 3 μM) and at elevated temperature (>130 °C), due to the polyaromatic chelate effect. The thermodynamic studies reveal that large enthalpic gain (ΔH=-110 kJ mol-1 ) is the key for the micelle formation. The oligomer micelle selectively encapsulates unsubstituted oligothiophenes (≥4-mer) to a high degree and the resultant, aqueous host-guest complexes display unusual emission derived from the multiply stacked oligomers. Furthermore, facile uptake and release of unsubstituted polythiophenes can be achieved using the oligomer micelle.
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Affiliation(s)
- Yamato Tsuchida
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, 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
| | - 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
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
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5
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Tsuchida Y, Aratsu K, Hiraoka S, Yoshizawa M. An Aromatic Oligomer Micelle: Large Enthalpic Stabilization and Selective Oligothiophene Uptake. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yamato Tsuchida
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 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
| | - 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
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life Science Institute of Innovative Research Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
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Takase Y, Yamazaki Y, Hayashi Y, Toma-Fukai S, Kamikubo H. Structure elements can be predicted using the contact volume among protein residues. Biophys Physicobiol 2021; 18:50-59. [PMID: 33954082 PMCID: PMC8049775 DOI: 10.2142/biophysico.bppb-v18.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 12/01/2022] Open
Abstract
Previously, the structure elements of dihydrofolate reductase (DHFR) were determined using comprehensive Ala-insertion mutation analysis, which is assumed to be a kind of protein “building blocks.” It is hypothesized that our comprehension of the structure elements could lead to understanding how an amino acid sequence dictates its tertiary structure. However, the comprehensive Ala-insertion mutation analysis is a time- and cost-consuming process and only a set of the DHFR structure elements have been reported so far. Therefore, developing a computational method to predict structure elements is an urgent necessity. We focused on intramolecular residue–residue contacts to predict the structure elements. We introduced a simple and effective parameter: the overlapped contact volume (CV) among the residues and calculated the CV along the DHFR sequence using the crystal structure. Our results indicate that the CV profile can recapitulate its precipitate ratio profile, which was used to define the structure elements in the Ala-insertion mutation analysis. The CV profile allowed us to predict structure elements like the experimentally determined structure elements. The strong correlation between the CV and precipitate ratio profiles indicates the importance of the intramolecular residue–residue contact in maintaining the tertiary structure. Additionally, the CVs between the structure elements are considerably more than those between a structure element and a linker or two linkers, indicating that the structure elements play a fundamental role in increasing the intramolecular adhesion. Thus, we propose that the structure elements can be considered a type of “building blocks” that maintain and dictate the tertiary structures of proteins.
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Affiliation(s)
- Yasumichi Takase
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoichi Yamazaki
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yugo Hayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Sachiko Toma-Fukai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
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7
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Hanayama H, Yamada J, Tomotsuka I, Harano K, Nakamura E. Rim Binding of Cyclodextrins in Size-Sensitive Guest Recognition. J Am Chem Soc 2021; 143:5786-5792. [PMID: 33826331 DOI: 10.1021/jacs.1c00651] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyclodextrins (CDs) are doughnut-shaped cyclic oligosaccharides having a cavity and two rims. Inclusion binding in the cavity has long served as a classic model of molecular recognition, and rim binding has been neglected. We found that CDs recognize guests by size-sensitive binding using the two rims in addition to the cavity, using single-molecule electron microscopy and a library of graphitic cones as a solid-state substrate for complexation. For example, with its cavity and rim binding ability combined, γ-CD can recognize a guest of radius between 4 and 9 Å with a size-recognition precision of better than 1 Å, as shown by structural analysis of thousands of individual specimens and statistical analysis of the data thereof. A 2.5 ms resolution electron microscopic video provided direct evidence of the process of size recognition. The data suggest the occurrence of the rim binding mode for guests larger than the size of the CD cavity and illustrate a unique application of dynamic molecular electron microscopy for deciphering the spatiotemporal details of supramolecular events.
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Affiliation(s)
- Hiroki Hanayama
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Junya Yamada
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Issei Tomotsuka
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koji Harano
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Eiichi Nakamura
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Zhan YY, Jiang QC, Ishii K, Koide T, Kobayashi O, Kojima T, Takahashi S, Tachikawa M, Uchiyama S, Hiraoka S. Polarizability and isotope effects on dispersion interactions in water. Commun Chem 2019. [DOI: 10.1038/s42004-019-0242-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractTrue understanding of dispersion interaction in solution remains elusive because of difficulty in the precise evaluation of its interaction energy. Here, the effect of substituents with different polarizability on dispersion interactions in water is discussed based on the thermodynamic parameters determined by isothermal titration calorimetry for the formation of discrete aggregates from gear-shaped amphiphiles (GSAs). The substituents with higher polarizability enthalpically more stabilize the nanocube, which is due to stronger dispersion interactions and to the hydrophobic effect. The differences in the thermodynamic parameters for the nanocubes from the GSAs with CH3 and CD3 groups are also discussed to lead to the conclusion that the H/D isotope effect on dispersion interactions is negligibly small, which is due to almost perfect entropy-enthalpy compensation between the two isotopomers.
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9
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Zhan YY, Liao J, Kajita M, Kojima T, Takahashi S, Takaya T, Iwata K, Hiraoka S. Supramolecular fluorescence sensor for liquefied petroleum gas. Commun Chem 2019. [DOI: 10.1038/s42004-019-0212-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Sensing systems of nonpolar gas molecules without functional groups such as natural gas and liquefied petroleum gas (LPG) remain difficult to develop because of lacking selective detection of such molecules over other gas molecules. Here we report a supramolecular fluorescence sensor for LPG using a 2-nm-sized cube-shaped molecular container i.e. a nanocube self-assembled from six molecules of gear-shaped amphiphiles (GSA) in water. The nanocube selectively encapsulates LPG, while it does not bind other gas molecules. Upon encapsulation of LPG in the nanocube, the fluorescence from the nanocube is enhanced by 3.9 times, which is caused by the restricted motion of the aromatic rings of GSA in the nanocube based on aggregation-induced emission. Besides the high selectivity, high sensitivity, quick response, high stability of the nanocube for LPG, and easy preparation of GSA satisfy the requirement for its practical use for an LPG sensor.
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10
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Nishioka T, Kuroda K, Akita M, Yoshizawa M. A Polyaromatic Gemini Amphiphile That Assembles into a Well‐Defined Aromatic Micelle with Higher Stability and Host Functions. Angew Chem Int Ed Engl 2019; 58:6579-6583. [DOI: 10.1002/anie.201814624] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/28/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Tomoya Nishioka
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Kiyonori Kuroda
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Munetaka Akita
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
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11
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Nishioka T, Kuroda K, Akita M, Yoshizawa M. A Polyaromatic Gemini Amphiphile That Assembles into a Well‐Defined Aromatic Micelle with Higher Stability and Host Functions. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Tomoya Nishioka
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Kiyonori Kuroda
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Munetaka Akita
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life ScienceInstitute of Innovative ResearchTokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
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12
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Zhan YY, Kojima T, Ishii K, Takahashi S, Haketa Y, Maeda H, Uchiyama S, Hiraoka S. Temperature-controlled repeatable scrambling and induced-sorting of building blocks between cubic assemblies. Nat Commun 2019; 10:1440. [PMID: 30926927 PMCID: PMC6441092 DOI: 10.1038/s41467-019-09495-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/12/2019] [Indexed: 12/28/2022] Open
Abstract
Separation of a homogeneous mixture of different components to reach an ordered out-of-equilibrium state in solution has attracted continuous attention. While this can be achieved using external chemical fuels or photo energy, an alternative energy source is heat. Here we realize a temperature-controlled cycle of transitions between ordered and disordered states based on a mixture of two kinds of building blocks that self-assemble into cubic structures (nanocubes). An almost statistical mixture of nanocubes (disordered state) is thermodynamically most stable at lower temperature (25 °C), while homoleptic assemblies composed of single components are preferentially produced at higher temperature (100 °C) followed by rapid cooling. The scrambling of the building blocks between the nanocubes takes place through the exchange of free building blocks dissociated from the nanocubes. Based on this mechanism, it is possible to accelerate, retard, and perfectly block the scrambling by the guest molecules encapsulated in the nanocubes. In this paper, the authors study the temperature-controlled dynamic behavior of a system of nanocubes self-assembled from two different building blocks. Non-intuitively, the disordered, equilibrium state (a mixture of heteroleptic cubes) and the ordered, out-of-equilibrium state (a mixture of homoleptic cubes) are cycled by heating and subsequent rapid cooling.
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Affiliation(s)
- Yi-Yang Zhan
- 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
| | - Kentaro Ishii
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, 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
| | - Yohei Haketa
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hiromitsu Maeda
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Susumu Uchiyama
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, 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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Adamantane template effect on the self-assembly of a molecular tetrahedron: A theoretical analysis. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.10.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Zhan YY, Kojima T, Nakamura T, Takahashi T, Takahashi S, Haketa Y, Shoji Y, Maeda H, Fukushima T, Hiraoka S. Induced-fit expansion and contraction of a self-assembled nanocube finely responding to neutral and anionic guests. Nat Commun 2018; 9:4530. [PMID: 30382098 PMCID: PMC6208372 DOI: 10.1038/s41467-018-06874-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/27/2018] [Indexed: 01/03/2023] Open
Abstract
Induced-fit or conformational selection is of profound significance in biological regulation. Biological receptors alter their conformation to respond to the shape and electrostatic surfaces of guest molecules. Here we report a water-soluble artificial molecular host that can sensitively respond to the size, shape, and charged state of guest molecules. The molecular host, i.e. nanocube, is an assembled structure consisting of six gear-shaped amphiphiles (GSAs). This nanocube can expand or contract its size upon the encapsulation of neutral and anionic guest molecules with a volume ranging from 74 to 535 Å3 by induced-fit. The responding property of this nanocube, reminiscent of a feature of biological molecules, arises from the fact that the GSAs in the nanocubes are connected to each other only through the hydrophobic effect and very weak intermolecular interactions such as van der Waals and cation-π interactions.
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Affiliation(s)
- Yi-Yang Zhan
- 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
| | - Takashi Nakamura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
- Division of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Toshihiro 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
| | - 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
| | - Yohei Haketa
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yoshiaki Shoji
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiromitsu Maeda
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takanori Fukushima
- 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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15
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Yamamoto T, Arefi H, Shanker S, Sato H, Hiraoka S. Self-Assembly of Nanocubic Molecular Capsules via Solvent-Guided Formation of Rectangular Blocks. J Phys Chem Lett 2018; 9:6082-6088. [PMID: 30274518 DOI: 10.1021/acs.jpclett.8b02624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We investigate the mechanism underlying the self-assembly of gear-shaped amphiphilic molecules into a highly ordered nanocubic capsule ("nanocube") in aqueous methanol. Simulation results show that the solvent molecules play a significant role in the assembly process by directing the primitive intermediates to orthogonal/rectangular shapes, thus creating appropriate building blocks for cubic assembly while avoiding off-pathway stacked aggregates. Free-energy analyses reveal that the interplay of the direct intermonomer interaction and the solvent-mediated repulsion between large aromatic cores (via preferential solvation of methanol on hydrophobic surfaces) leads to the strong trend for perpendicular binding of monomers and hence the solvent-guided formation of rectangular blocks. Furthermore, we report the self-assembly simulation of the nanocube using replica exchange with solute tempering and demonstrate that the simulation can predict a highly ordered nanocapsule structure, assembly intermediates, and encapsulated molecules, which helps promote computer-aided design of functional molecular self-assemblies in explicit solvent.
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Affiliation(s)
- Takeshi Yamamoto
- Department of Chemistry , Graduate School of Science, Kyoto University , Kyoto 606-8502 , Japan
| | - Hadi Arefi
- Department of Chemistry , Graduate School of Science, Kyoto University , Kyoto 606-8502 , Japan
| | - Sudhanshu Shanker
- Department of Chemistry , Graduate School of Science, Kyoto University , Kyoto 606-8502 , Japan
| | - Hirofumi Sato
- Department of Molecular Engineering , Graduate School of Engineering, Kyoto University , Kyoto 615-8510 , Japan
| | - Shuichi Hiraoka
- Department of Basic Science , Graduate School of Arts and Science, The University of Tokyo , Tokyo 153-8902 , Japan
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16
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Liao J, Kojima T, Takahashi S, Hiraoka S. Gram-Scale Synthesis of a C
2v
-Symmetric Hexaphenylbenzene with Three Different Types of Substituents. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201800448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jingyuan Liao
- 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
| | - 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
| | - 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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17
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Kosaka T, Iwai S, Inoue Y, Moriuchi T, Mori T. Solvent and Temperature Effects on Dynamics and Chiroptical Properties of Propeller Chirality and Toroidal Interaction of Hexaarylbenzenes. J Phys Chem A 2018; 122:7455-7463. [PMID: 30102034 DOI: 10.1021/acs.jpca.8b06535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Because of the unique interaction of radial aromatic blades, propeller-shaped hexaarylbenzenes (HABs) attract much research interest and find various practical applications. By introducing a small point-chiral group at the tip of aromatic blade(s), HAB becomes propeller-chiral to exhibit strong Cotton effects. Because of the dynamic nature of propeller chirality, the chiroptical properties of HAB critically responded to minute changes in the environment. Using a series of chiral HABs with one to six ( R)-1-methylpropyloxy substituent(s) introduced at the blade tip, we elucidated how the smallest chiral auxiliary at the HAB periphery progressively and cooperatively boosts the overall chiroptical properties and also how subtle changes in temperature and solvent structure affect the propeller dynamics and thus the chiroptical responses. The unique features of propeller-chiral HABs further enabled us to switch on/off their circularly polarized luminescence.
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Affiliation(s)
- Tomoyo Kosaka
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , 2-1 Yamada-oka , Suita 565-0871 , Japan
| | - Satono Iwai
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , 2-1 Yamada-oka , Suita 565-0871 , Japan
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , 2-1 Yamada-oka , Suita 565-0871 , Japan
| | - Toshiyuki Moriuchi
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , 2-1 Yamada-oka , Suita 565-0871 , Japan
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , 2-1 Yamada-oka , Suita 565-0871 , Japan
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18
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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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19
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Zhan YY, Kojima T, Koide T, Tachikawa M, Hiraoka S. A Balance between van der Waals and Cation-π Interactions Stabilizes Hydrophobic Assemblies. Chemistry 2018; 24:9130-9135. [DOI: 10.1002/chem.201801376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Yi-Yang Zhan
- 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
| | - Takuya Koide
- Quantum Chemistry Division; Graduate School of Science; Yokohama City University; 22-2 Seto Kanazawa-ku Yokohama Kanagawa 236-0027 Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division; Graduate School of Science; Yokohama City University; 22-2 Seto Kanazawa-ku Yokohama Kanagawa 236-0027 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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20
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Zhan YY, Tanaka N, Ozawa Y, Kojima T, Mashiko T, Nagashima U, Tachikawa M, Hiraoka S. Importance of Molecular Meshing for the Stabilization of Solvophobic Assemblies. J Org Chem 2018; 83:5132-5137. [PMID: 29644858 DOI: 10.1021/acs.joc.8b00495] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of the methyl groups in neutral gear-shaped amphiphiles (GSAs) on the stability of nanocubes was investigated using a novel C2 v-symmetric GSA, which was synthesized using selective alternate trilithiation of a pentabrominated hexaphenylbenzene derivative. The lack of only one methyl group in the GSA decreased the association constant for the assembly of the nanocube by 3 orders of magnitude. A surface analysis recently developed by the authors (SAVPR: surface analysis with varying probe radii) was carried out for characteristic isomers of the nanocube consisting of C2 v-symmetric GSAs. It was found that the methyl groups near the equator of the nanocube play a significant role in the stabilization of the nanocubes.
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Affiliation(s)
- Yi-Yang Zhan
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro-ku , Tokyo 153-8902 , Japan
| | - Naru Tanaka
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba , Meguro-ku , Tokyo 153-8902 , Japan
| | - Yuka Ozawa
- 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
| | - Takako Mashiko
- Quantum Chemistry Division, Graduate School of Science , Yokohama City University , 22-2 Seto , Kanazawa-ku, Yokohama-city , Kanagawa 236-0027 , Japan
| | - Umpei Nagashima
- Foundation for Computational Science (FOCUS) , 7-1-28, Minatojimaminamimachi , 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
| | - 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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21
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Tanaka N, Zhan YY, Ozawa Y, Kojima T, Koide T, Mashiko T, Nagashima U, Tachikawa M, Hiraoka S. Semi-quantitative evaluation of molecular meshing via surface analysis with varying probe radii. Chem Commun (Camb) 2018; 54:3335-3338. [DOI: 10.1039/c8cc00695d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular meshing in molecular recognition and assembly can be assessed by plotting the distribution of contact surfaces against the contact distance.
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Affiliation(s)
- Naru Tanaka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Yi-Yang Zhan
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Yuka Ozawa
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Takuya Koide
- Quantum Chemistry Division, Graduate School of Science, Yokohama City University
- Yokohama
- Japan
| | - Takako Mashiko
- Quantum Chemistry Division, Graduate School of Science, Yokohama City University
- Yokohama
- Japan
| | | | - Masanori Tachikawa
- Quantum Chemistry Division, Graduate School of Science, Yokohama City University
- Yokohama
- 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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22
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Harada R, Mashiko T, Tachikawa M, Hiraoka S, Shigeta Y. Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study. Phys Chem Chem Phys 2018; 20:9115-9122. [DOI: 10.1039/c8cp00284c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-organization processes of a gear-shaped amphiphile molecule (1) to form a hexameric structure (nanocube,16) were inferred from sequential dissociation processes by using molecular dynamics (MD) simulations.
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Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences
- University of Tsukuba
- Ibaraki 305-8577
- Japan
| | - Takako Mashiko
- Quantum Chemistry Division
- Graduate School of NanobioScience
- Yokohama City University
- Yokoyama City
- Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division
- Graduate School of NanobioScience
- Yokohama City University
- Yokoyama City
- Japan
| | - Shuichi Hiraoka
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences
- University of Tsukuba
- Ibaraki 305-8577
- Japan
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