Faculty Profiles - Shinoda Wataru

Papers - Shinoda Wataru

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Li-Ion Transport and Solution Structure in Sulfolane-Based Localized High-Concentration Electrolytes Invited Reviewed

Taku Sudoh, Shuhei Ikeda, Keisuke Shigenobu, Seiji Tsuzuki, Kaoru Dokko, Masayoshi Watanabe, Wataru Shinoda, Kazuhide Ueno

JOURNAL OF PHYSICAL CHEMISTRY C 127 ( 25 ) 12295 - 12303 2023.6

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Localized high-concentration electrolytes (LHCEs), whichare mixturesof highly concentrated electrolytes (HCEs) and non-coordinating diluents,have attracted significant interest as promising liquid electrolytesfor next-generation Li secondary batteries, owing to their variousbeneficial properties both in the bulk and at the electrode/electrolyteinterface. We previously reported that the large Li+-iontransference number in sulfolane (SL)-based HCEs, attributed to theunique exchange/hopping-like Li+-ion conduction, decreasedupon dilution with the non-coordinating hydrofluoroether (HFE) despitethe retention of the local Li+-ion coordination structure.Therefore, in this study, we investigated the effects of HFE dilutionon the Li+ transference number and the solution structureof SL-based LHCEs via the analysis of dynamic ion correlations andmolecular dynamics simulations. The addition of HFE caused nano-segregationin the SL-based LHCEs to afford polar and nonpolar domains and fragmentationof the polar ion-conducting pathway into smaller clusters with increasingHFE content. Analysis of the dynamic ion correlations revealed thatthe anti-correlated Li+-Li+ motions weremore pronounced upon HFE addition, suggesting that the Li+ exchange/hopping conduction is obstructed by the non-ion-conductingHFE-rich domains. Thus, the HFE addition affects the entire solutionstructure and ion transport without significantly affecting the localLi(+)-ion coordination structure. Further studies on iontransport in LHCEs would help obtain a design principle for liquidelectrolytes with high ionic conductivity and large Li+-ion transference numbers.

DOI： 10.1021/acs.jpcc.3c02112

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Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy Reviewed

Hiromi Takahashi, Takao Yasui, Masaki Hirano, Keiko Shinjo, Yusuke Miyazaki, Wataru Shinoda, Takeshi Hasegawa, Atsushi Natsume, Yotaro Kitano, Mikiko Ida, Min Zhang, Taisuke Shimada, Piyawan Paisrisarn, Zetao Zhu, Fumiharu Ohka, Kosuke Aoki, Sakon Rahong, Kazuki Nagashima, Takeshi Yanagida, Yoshinobu Baba

Biosensors and Bioelectronics 234 115318 - 115318 2023.4

Fluorescence Turn‐on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, HeLa Cells, and E. coli Reviewed

Kosuke Masuda, Riku Omokawa, Riku Kawasaki, Yuta Mise, Yousuke Ooyama, Shogo Harada, Wataru Shinoda, Atsushi Ikeda

Chemistry – A European Journal 29 ( 10 ) e202203071 2023.2

Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes Reviewed

Dapeng Zhang, Qi Xiao, Mehrnoush Rahimzadeh, Matthew Liu, Cesar Rodriguez-Emmenegger, Yusuke Miyazaki, Wataru Shinoda, Virgil Percec

Journal of the American Chemical Society 145 ( 7 ) 4311 - 4323 2023.2

Liquid Structures and Ion Dynamics of Ionic Liquids viewed from Intermolecular Interactions Invited Reviewed

Seiji Tsuzuki, Wataru Shinoda

CHEMICAL RECORD 23 ( 8 ) e202200272 2023.2

Authorship：Last author Language：English Publishing type：Research paper (scientific journal) Publisher：WILEY-V C H VERLAG GMBH

The elucidation of the factors determining liquid structures and transport properties of ionic liquids is important for the design and development of ionic liquid electrolytes. This personal account introduces the importance of computational methods for studying ionic liquids. Molecular dynamics simulations provide detailed information on liquid structures of ionic liquid such as the structures of solvated cation complexes in equimolar mixtures of glymes and Li[TFSA] and the effects of the charges of electrode on liquid structure near the electrode. Ab initio calculations reveal that the magnitude of the attraction between ions and conformational flexibility ions play important roles in determining transport properties of ionic liquids. First principle molecular dynamics simulations elucidate why solvated cation complex is stable in the equimolar mixtures, although the Li+-[TFSA](-) interaction is greater than Li+-glyme interaction.

DOI： 10.1002/tcr.202200272

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Liquid Structures and Ion Dynamics of Ionic Liquids viewed from Intermolecular Interactions Invited Reviewed

Seiji Tsuzuki, Wataru Shinoda

THE CHEMICAL RECORD Chem.Rec.2023 e202200272 2023.1

Fluorescence Turn-on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, HeLa cells, and E. coli Reviewed

Kosuke Masuda, Riku Omokawa, Riku Kawasaki, Yuta Mise, Yousuke Ooyama, Shogo Harada, Wataru Shinoda, Atsushi Ikeda

Chemistry - A European Journal 2022.11

SPICA Force Field for Proteins and Peptides Reviewed International coauthorship

Shuhei Kawamoto, Huihui Liu, Yusuke Miyazaki, Sangjae Seo, Mayank Dixit, Russell DeVane, Christopher MacDermaid, Giacomo Fiorin, Michael L. Klein, Wataru Shinoda

Journal of Chemical Theory and Computation 18 ( 5 ) 3204 - 3217 2022.5

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulations with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. An elastic network model was adopted to maintain the secondary structure within a single chain. The side-chain analogues reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable association free energy (potential of mean force) in water compared to those from AA MD. A series of peptides/proteins adsorbed onto or penetrated into the membrane simulated by the CG MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins as comparable to those in the orientations of proteins in membranes (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated the good performance of the SPICA FF.

DOI： 10.1021/acs.jctc.1c01207

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Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study. Reviewed International journal

Yusuke Miyazaki, Wataru Shinoda

Biochimica et biophysica acta. Biomembranes 1864 ( 9 ) 183955 - 183955 2022.5

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.

DOI： 10.1016/j.bbamem.2022.183955

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Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study Reviewed

Hari O. S. Yadav, An-Tsung Kuo, Shingo Urata, Kosuke Funahashi, Yutaka Imamura, Wataru Shinoda

Physical Chemistry Chemical Physics 24 14805 - 14815 2022.5

Effects of Li ion-solvent interaction on ionic transport and electrochemical properties in highly concentrated cyclic carbonate electrolytes Reviewed

Keisuke Shigenobu, Taku Sudoh, Mayu Tabuchi, Seiji Tsuzuki, Wataru Shinoda, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno

Journal of Non-Crystalline Solids: X 11-12 100071 2021.11

Domain Formation in Charged Polymer Vesicles Reviewed International coauthorship

Kaushik Chakraborty, Prabir Khatua, Wataru Shinoda, Sharon M. Loverde

Macromolecules 54 ( 20 ) 9258 - 9267 2021.10

Hemimicelle formation of semi-fluorocarbon chains at air–water interface: coarse-grained molecular dynamics study with an extension of the SPICA force field Reviewed

Hari O. S. Yadav, Shogo Harada, An-Tsung Kuo, Shingo Urata, Wataru Shinoda

Molecular Physics 119 ( 19-20 ) e1910355 2021.10

All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution Reviewed

Kazushi Fujimoto, Youhei Yamaguchi, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki

The Journal of Chemical Physics 155 ( 14 ) 145101 2021.10

Analyzing the Role of Surfactants in the Colloidal Stability of Nanoparticles in Oil through Coarse-Grained Molecular Dynamics Simulations Reviewed

Mark Z. Griffiths, Wataru Shinoda

The Journal of Physical Chemistry B 125 ( 23 ) 6315 - 6321 2021.6

Chain-End Modification: A Starting Point for Controlling Polymer Crystal Nucleation Reviewed

Kyle Wm. Hall, Simona Percec, Wataru Shinoda, Michael L. Klein

Macromolecules 54 ( 4 ) 1599 - 1610 2021.2

Thermodynamic aspect of sulfur, polysulfide anion and lithium polysulfide: plausible reaction path during discharge of lithium–sulfur battery Reviewed

Seiji Tsuzuki, Tomoaki Kaneko, Keitaro Sodeyama, Yasuhiro Umebayashi, Wataru Shinoda, Shiro Seki, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe

Physical Chemistry Chemical Physics 23 ( 11 ) 6832 - 6840 2021

GLASS MICROFLUIDIC PLATFORM FOR NANOWIRE-ASSISTED URINARY CELL-FREE DNA ISOLATION

Hiromi Takahashi, Takao Yasui, Keiko Shinjo, Yusuke Miyazaki, Wataru Shinoda, Takeshi Hasegawa, Yotaro Kitano, Yoshinobu Baba

MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences 1401 - 1402 2021

Publishing type：Research paper (international conference proceedings)

Driven by the importance of urinary cell-free DNA (cfDNA) as cancer biomarkers, the effectiveness of cfDNA isolation from body fluids can impact clinical usability, especially for molecular diagnostic. However, cfDNA isolations are currently hampered by the dilution of small fragmented cfDNA in body fluids. In this work, we report the unique properties of nanowires assisting the isolation of urinary cfDNA based on specific chemical interactions, maximizing the effectiveness of the platform that could never be achieved with the conventional methods.

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Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement Reviewed

Tetsuro Nagai, Shuhei Tsurumaki, Ryo Urano, Kazushi Fujimoto, Wataru Shinoda, Susumu Okazaki

Journal of Chemical Theory and Computation 16 ( 12 ) 7239 - 7254 2020.12

Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})

The authors propose a novel method to evaluate the position-dependent diffusion constant by analyzing unperturbed segments of a trajectory determined by the additional flat-bottom potential. The accuracy of this novel method is first established by studying homogeneous systems, where the reference value can be obtained by the Einstein relation. The applicability of this new method to heterogeneous systems is then demonstrated by studying a hydrophobic solute near a hydrophobic wall. The proposed method is also comprehensively compared with popular conventional methods, whereby the significance of the present method is illustrated. The novel method is powerful and useful for studying kinetics in heterogeneous systems based on molecular dynamics calculations.

DOI： 10.1021/acs.jctc.0c00448

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Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure Reviewed

Valeria Zoni, Wataru Shinoda, Stefano Vanni

Proceedings of the National Academy of Sciences 118 ( 10 ) e2017205118 2020.10

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Papers - Shinoda Wataru