Faculty Profiles - Shinoda Wataru

PubMed

A coarse-grain model for entangled polyethylene melts and polyethylene crystallization Reviewed

Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup Reviewed

Shinya Hanashima, Kazuhiro Murakami, Michihiro Yura, Yo Yano, Yuichi Umegawa, Hiroshi Tsuchikawa, Nobuaki Matsumori, Sangjae Seo, Wataru Shinoda, Michio Murata

Biophysical Journal 117 ( 2 ) 307 - 318 2019.7

Kyle Wm. Hall, Timothy W. Sirk, Michael L. Klein, Wataru Shinoda

The Journal of Chemical Physics 150 ( 24 ) 244901 - 244901 2019.6

Molecular mechanism of material deformation and failure in butadiene rubber: Insight from all-atom molecular dynamics simulation using a bond breaking potential model Reviewed

Rajdeep Singh Payal, Kazushi Fujimoto, Changwoon Jang, Wataru Shinoda, Yuki Takei, Hiroshi Shima, Katsuhiko Tsunoda, Susumu Okazaki

Polymer 170 113 - 119 2019.4

SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol Reviewed

Sangjae Seo, Wataru Shinoda

Journal of Chemical Theory and Computation 151 ( 10 ) 762 - 774 2019.1

Direct Evidence for Li Ion Hopping Conduction in Highly Concentrated Sulfolane-Based Liquid Electrolytes Reviewed

Kaoru Dokko, Daiki Watanabe, Yosuke Ugata, Morgan L. Thomas, Seiji Tsuzuki, Wataru Shinoda, Kei Hashimoto, Kazuhide Ueno, Yasuhiro Umebayashi, Masayoshi Watanabe

The Journal of Physical Chemistry B 122 ( 47 ) 10736 - 10745 2018.11

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids Reviewed

Wataru Shinoda, Yuta Hatanaka, Masashi Hirakawa, Susumu Okazaki, Seiji Tsuzuki, Kazuhide Ueno, Masayoshi Watanabe

The Journal of Chemical Physics 148 ( 19 ) 193809 - 193809 2018.5

Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals Reviewed

Soumya Lipsa Rath, Huihui Liu, Susumu Okazaki, Wataru Shinoda

Journal of Chemical Information and Modeling 58 ( 2 ) 328 - 337 2018.2

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

Around 270 million individuals currently live with hepatitis B virus (HBV) infection. Heteroaryldihydropyrimidines (HAPs) are a family of antivirals that target the HBV capsid protein and induce aberrant self-assembly. The capsids formed resemble the native capsid structure but are unable to propagate the virus progeny because of a lack of RNA/DNA. Under normal conditions, self-assembly is initiated by the viral genome. The mode of action of HAPs, however, remains largely unknown. In this work, using molecular dynamics simulations, we attempted to understand the action of HAP by comparing the dynamics of capsid proteins with and without HAPs. We found that the inhibitor is more stable in higher oligomers. It retains its stability in the hexamer throughout 1 μs of simulation. Our results also show that the inhibitor might help in stabilizing the C-terminus, the HBc 149-183 arginine-rich domain of the capsid protein. The C-termini of dimers interact with each other, assisted by the HAP inhibitor. During capsid assembly, the termini are supposed to directly interact with the viral genome, thereby suggesting that the viral genome might work in a similar way to stabilize the capsid protein. Our results may help in understanding the underlying molecular mechanism of HBV capsid self-assembly, which should be crucial for exploring new drug targets and structure-based drug design.

DOI： 10.1021/acs.jcim.7b00471

Polymer Electrolytes Containing Solvate Ionic Liquids: A New Approach to Achieve High Ionic Conductivity, Thermal Stability, and a Wide Potential Window Reviewed

Yuzo Kitazawa, Kaori Iwata, Ryosuke Kido, Satoru Imaizumi, Seiji Tsuzuki, Wataru Shinoda, Kazuhide Ueno, Toshihiko Mandai, Hisashi Kokubo, Kaoru Dokko, Masayoshi Watanabe

Chemistry of Materials 30 ( 1 ) 252 - 261 2018.1

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

We describe here the electrochemical properties and battery performance of polymer electrolytes composed of ABA-triblock copolymers and Li-glyme solvate ionic liquids (SILs), which consist of the [Li(glyme)]+ complex cation and bis(trifluoromethanesulfoly)amide ([TFSA]-) anion, to simultaneously achieve high ionic conductivity, thermal stability, and a wide potential window. Three different block copolymers, consisting of a SIL-incompatible A segment (polystyrene, PSt) and SIL-compatible B segments (poly(methyl methacrylate) (PMMA), poly(ethylene oxide) (PEO), and poly(butyl acrylate) (PBA)) were synthesized. The SILs were solidified with the copolymers through physical cross-linking by the self-assembly of the PSt segment. The thermal and electrochemical properties of the polymer electrolytes were significantly affected by the stability of the [Li(glyme)]+ complex in the block copolymer B segments, and the preservation of the SILs contributed to their thermal stabilities and oxidation stabilities greater than 4 V vs Li/Li+. Pulsed-field gradient spin-echo nuclear magnetic resonance measurements of the polymer electrolytes and molecular dynamics simulation indicate that the [Li(glyme)]+ complex cation is unstable in the PEO matrix because of the competitive coordination of the PEO chain and glyme with Li+. On the other hand, the complex structure of [Li(glyme)]+ is stable in the PMMA- and PBA-based polymer electrolytes because of the weak interaction between Li+ and the polymer chains. By use of the PMMA- and PBA-based polymer electrolytes, 4-V class Li batteries with a LiCoO2 cathode and a Li metal anode could be operated stably at 60 °C
in contrast, this was not possible using the PEO-based electrolyte.

DOI： 10.1021/acs.chemmater.7b04274

Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction Reviewed

Morishita, T., Nakamura, T., Shinoda, W., Ito, A.M.

Chemical Physics Letters 706 633 - 640 2018

Exploring the effect of pendent side chain length on the structural and mechanical properties of hydrated perfluorosulfonic acid polymer membranes by molecular dynamics simulation Reviewed

Kuo, A.-T., Takeuchi, K., Tanaka, A., Urata, S., Okazaki, S., Shinoda, W.

Polymer 146 53 - 62 2018

Molecular Dynamics Study on the Mechanical Deformation of Hydrated Perfluorosulfonic Acid Polymer Membranes Reviewed

An-Tsung Kuo, Atsushi Tanaka, Jun Irisawa, Wataru Shinoda, Susumu Okazaki

JOURNAL OF PHYSICAL CHEMISTRY C 121 ( 39 ) 21374 - 21382 2017.10

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

Mechanical deformation has been proposed to influence the proton conduction of perfluorosulfonic acid (PFSA) polymer membranes. We conducted a series of all-atom molecular dynamics simulations to understand how stretching affects the structural and dynamic properties of hydrated membranes composed of different equivalent weights (EWs) of PFSA at different water contents. The simulations reveal that the Young's modulus and yield stress of the membrane decreases with increasing water content, which is qualitatively in good agreement with experimental observations. When the PFSA membrane was stretched along a particular axis, the ionomer backbone chains became extended along the stretching direction and were aligned parallel to each other. The elongation of the ionomer backbone enhances hydronium ion diffusivity in the stretching direction at low water content. However, at high water content, the side chains orient themselves perpendicularly to the stretching direction in order to associate with free hydronium ions; this results in lower hydronium ion mobility. Furthermore, the higher EW PFSA is better aligned along the direction of stretching than the lower EW PFSA. The effect of stretching on proton transport is more pronounced in the higher EW PFSA membrane.

DOI： 10.1021/acs.jpcc.7b05719

Transferable coarse-grained model for perfluorosulfonic acid polymer membranes Reviewed

An-Tsung Kuo, Susumu Okazaki, Wataru Shinoda

JOURNAL OF CHEMICAL PHYSICS 147 ( 9 ) 2017.9

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

Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes. (C) 2017 Author(s).

DOI： 10.1063/1.4986287

Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission Reviewed

Qi Xiao, Samuel E. Sherman, Samantha E. Wilner, Xuhao Zhou, Cody Dazen, Tobias Baumgart, Ellen H. Reed, Daniel A. Hammer, Wataru Shinoda, Michael L. Klein, Virgil Percec

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 ( 34 ) E7045 - E7053 2017.8

Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES

A three-component system of Janus dendrimers (JDs) including hydrogenated, fluorinated, and hybrid hydrogenated-fluorinated JDs are reported to coassemble by film hydration at specific ratios into an unprecedented class of supramolecular Janus particles (JPs) denoted Janus dendrimersomes (JDSs). They consist of a dumbbell-shaped structure composed of an onion-like hydrogenated vesicle and an onion-like fluorinated vesicle tethered together. The synthesis of dye-tagged analogs of each JD component enabled characterization of JDS architectures with confocal fluorescence microscopy. Additionally, a simple injection method was used to prepare sub-micron JDSs, which were imaged with cryogenic transmission electron microscopy (cryo-TEM). As reported previously, different ratios of the same three-component system yielded a variety of structures including homogenous onion-like vesicles, core-shell structures, and completely self-sorted hydrogenated and fluorinated vesicles. Taken together with the JDSs reported herein, a self-sorting pathway is revealed as a function of the relative concentration of the hybrid JD, which may serve to stabilize the interface between hydrogenated and fluorinated bilayers. The fission-like pathway suggests the possibility of fusion and fission processes in biological systems that do not require the assistance of proteins but instead may result from alterations in the ratios of membrane composition.

DOI： 10.1073/pnas.1708380114

Effect of the cation on the stability of cation-glyme complexes and their interactions with the [TFSA](-) anion Reviewed

Seiji Tsuzuki, Toshihiko Mandai, Soma Suzuki, Wataru Shinoda, Takenobu Nakamura, Tetsuya Morishita, Kazuhide Ueno, Shiro Seki, Yasuhiro Umebayashi, Kaoru Dokko, Masayoshi Watanabe

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19 ( 28 ) 18262 - 18272 2017.7

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

The interactions of glymes with alkali or alkaline earth metal cations depend strongly on the metal cations. For example, the stabilization energies (E-form) calculated for the formation of cation-triglyme (G3) complexes with Li+, Na+, K+, Mg2+, and Ca2+ at the MP2/6-311G** level were -95.6, -66.4, -52.5, -255.0, and -185.0 kcal mol(-1), respectively, and those for the cation-tetraglyme (G4) complexes were -107.7, -76.3, -60.9, -288.3 and -215.0 kcal mol(-1), respectively. The electrostatic and induction interactions are the major source of the attraction in the complexes; the contribution of the induction interactions to the attraction is especially significant in the divalent cationglyme complexes. The binding energies of the cation-G3 complexes with Li+, Na+, K+, Mg2+, and Ca2+ and the bis(trifluoromethylsulfonyl)amide anion ([TFSA](-)) were -83.9, -86.6, -80.0, -196.1, and -189.5 kcal mol(-1), respectively, and they are larger than the binding energies of the corresponding cation-G4 complexes (-73.6, -75.0, -77.4, -172.1, and -177.2 kcal mol(-1), respectively). The binding energies and conformational flexibility of the cation-glyme complexes also affect the melting points of equimolar mixtures of glyme and TFSA salts. Furthermore, the interactions of the metal cations with the oxygen atoms of glymes significantly decrease the HOMO energy levels of glymes. The HOMO energy levels of glymes in the cation-glyme-TFSA complexes are lower than those of isolated glymes, although they are higher than those of the cation-glyme complexes.

DOI： 10.1039/c7cp02779f

Molecular Dynamics Study of the Morphology of Hydrated Perfluorosulfonic Acid Polymer Membranes Reviewed

An-Tsung Kuo, Wataru Shinoda, Susumu Okazaki

JOURNAL OF PHYSICAL CHEMISTRY C 120 ( 45 ) 25832 - 25842 2016.11

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

Many morphological models have been proposed to describe the water swelling behavior and proton transport mechanism of perfluorosulfonic acid (PFSA) polymer membranes through experimental and modeling studies. However, the ongoing structural debate has not been completely resolved yet. We here conducted a series of all-atom molecular dynamics simulations of hydrated PFSA membranes to evaluate changes in the membrane morphology at different water contents. We found a similar dependence of the morphology on the water content between PFSA membranes with equivalent weight (EW) of 844 and 1144 g/equiv. That is, the morphology of the aqueous domain changes with increasing water content from a channel-network structure to a tortuous layered structure, and once attaining the tortuous layered structure, the water layer just thickened gradually by further increasing water content. Furthermore, we found more heterogeneous water domains in the higher-EW PFSA membrane, demonstrating the stronger aggregation behavior of the aqueous domains in the high-EW membranes. The variation of the PFSA membrane morphology observed here is useful to understand the proton transport mechanism and design new materials suitable for polymer electrolyte fuel cells in the near future.

DOI： 10.1021/acs.jpcc.6b08015

Permeability across lipid membranes Invited Reviewed

Wataru Shinoda

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 1858 ( 10 ) 2254 - 2265 2016.10

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Rog. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbamem.2016.03.032

Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism Reviewed

Shuhei Kawamoto, Michael L. Klein, Wataru Shinoda

JOURNAL OF CHEMICAL PHYSICS 143 ( 24 ) 2015.12

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

The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion. (C) 2015 AIP Publishing LLC.

DOI： 10.1063/1.4933087