Details of a Researcher

Optimization of zwitterionic polymers for cell cryopreservation Reviewed International journal

Yui Kato, Takuya Uto, Takeru Ishizaki, Daisuke Tanaka, Kojiro Ishibashi, Yuya Matsuda, Issei Onoda, Akiko Kobayashi, Masaharu Hazawa, Richard W. Wong, Kenji Takahashi, Eishu Hirata, Kosuke Kuroda

Macromolecular Bioscience 24 ( 7 ) Article number: e2300499 2024.7

Language：English Publishing type：Research paper (scientific journal)

DOI： 10.1002/mabi.202300499

Extended ensemble simulation study of structural polysaccharide crystal structures Invited

Toshifumi Yui, Takuya Uto

Cellulose Communications 31 18 - 21 2024.3

Authorship：Last author Language：Japanese Publishing type：Research paper (scientific journal)

Physicochemical properties of pyrrolidinium-based room temperature ionic liquids with propoxyethyl, ethoxypropyl, or (methoxymethoxy)ethyl group Reviewed International journal

Kazuki Yoshii, Takuya Uto

Electrochemistry 92 ( 4 ) Article number: 043007 2024.2

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：The Electrochemical Society of Japan

Room temperature ionic liquids (RTILs) with ether oxygen atoms in the side chain have been investigated for electrochemical applications because they show favorable transport properties compared with alkyl analogs. However, the influence of the position and number of ether oxygen atoms on physical properties has not yet been fully clarified. In the present study, the physicochemical properties of RTILs consisting of bis(trifluoromethanesulfonyl)amide (TFSA−) with 1-methy-1-propoxyethylpyrrolidinium (Pyr1,2O3+), 1-methyl-1-ethoxypropylpyrrolidinium (Pyr1,3O2+), and 1-methyl-1-(methoxymethoxy)ethylpyrrolidinium (Pyr1,2O1O1+) was investigated using experimental and computational approach. Pyr1,2O3TFSA exhibited the lowest viscosity and highest ionic conductivity. Pyr1,2O1O1TFSA with two oxygen atoms in the side chain showed relatively high viscosity, indicating the physicochemical properties were affected sensitively by the position and number of ether oxygen atoms. Furthermore, by comparing with the structural isomers reported so far, we were able to systematically discuss the introduction effect of ether oxygen on the physicochemical properties of RTILs.

DOI： 10.5796/electrochemistry.23-69154

Protein cryoprotectant ability of the aqueous zwitterionic solution Reviewed International journal

Takahiro Takekiyo, Shuto Yamada, Takuya Uto, Masaharu Nakayama, Tetsuya Hirata, Takeru Ishizaki, Kosuke Kuroda, Yukihiro Yoshimura

Journal of Physical Chemistry B 128 ( 2 ) 526 - 535 2024.1

Language：English Publishing type：Research paper (scientific journal)

DOI： 10.1021/acs.jpcb.3c05614

Cell-compatible isotonic freezing media enabled by thermo-responsive osmolyte-adsorption/exclusion polymer matrices Reviewed International journal

Yui Kato, Yuya Matsuda, Takuya Uto, Daisuke Tanaka, Kojiro Ishibashi, Takeru Ishizaki, Akio Ohta, Akiko Kobayashi, Masaharu Hazawa, Richard W. Wong, Kazuaki Ninomiya, Kenji Takahashi, Eishu Hirata, Kosuke Kuroda

Communications Chemistry 6 ( 1 ) Article number: 260 2023.12

Language：English Publishing type：Research paper (scientific journal)

DOI： 10.1038/s42004-023-01061-7

Control of thermal diffusivity of nanocellulose papers by introduction of metal ions Invited

Kojiro Uetani, Takuya Uto

Journal of the Japan Society of Colour Material 96 ( 7 ) 228 - 232 2023.7

Authorship：Last author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japan Society of Colour Material

Crystalline cellulose nanofibers (nanocelluloses) are produced through chemical purification and nanofibrillation of biomass such as ascidian mantles and wood flour. Nanocellulose with carboxy groups introduced on the surface is dried to make a freestanding paper, and when immersed in an aqueous solution of metal chloride, metal ions can be introduced into the nanocellulose paper. The thermal diffusivity of these metal ion-introduced papers was measured in a low-humidity environment and found to vary depending on the ionic radius and electronegativity. This review outlines the recently revealed thermal conductive properties of nanocellulose papers and the control of thermal diffusivity by ion introduction.

DOI： 10.4011/shikizai.96.228

Extended ensemble molecular dynamics study of ammonia-cellulose I complex crystal models: Free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase Reviewed International journal

Toshifumi Yui, Takuya Uto, Kotaro Noda

Journal of Chemical Information and Modeling 63 ( 13 ) 4088 - 4099 2023.7

Language：English Publishing type：Research paper (scientific journal)

DOI： 10.1021/acs.jcim.3c00106

Strong attractive interaction between finite element models of twisted cellulose nanofibers by intermeshing of twists Reviewed International journal

Kojiro Uetani, Takuya Uto

RSC Advances 13 ( 24 ) 16387 - 16395 2023.5

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

DOI： 10.1039/d3ra01784b

Molecular dynamics simulation study of chitosan−zinc chloride complex model Reviewed

Kotaro Noda, Takuya Uto, Toshifumi Yui

Journal of Fiber Science and Technology 79 ( 2 ) 24 - 31 2023.3

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Society of Fiber Science and Technology, Japan

We report molecular dynamics simulation study of chitosan－zinc chloride complex crystal model to predict a hydrated structure and to evaluate the potential of mean force (PMF), namely, the free energy difference, in migration of a guest zinc chloride molecule in the crystal model. The accelerated molecular dynamics method was adopted to predict the hydrate structure of the crystal model, which proposed the crystal model interior involving four to five water molecules per a unit cell. The water molecules were mostly located in the crystal void surrounded by the functional groups of D-glucosamine and zinc chloride molecules, where the water molecules were mostly coordinated to zinc atoms. The PMF profile, obtained by using adaptive steered molecular dynamics method, exhibited continuously increase in the base line accompanied with appreciable minima, each of which corresponded to formations of interactions between the zinc chloride molecule and the polar functional groups, suggesting that the zinc chloride molecule on migration was handed over the C6 hydroxyl and C2 amino groups, while C3 hydroxyl groups were irrelevant to such an interaction. It was suggested that a zinc chloride molecule was more readily accommodated in the void through coordination with a C6 hydroxyl group which was more spatially mobile through C5-C6 bond rotation.

DOI： 10.2115/fiberst.2023-0004

Tunability of the thermal diffusivity of cellulose nanofibril films by addition of multivalent metal ions Reviewed International journal

Kojiro Uetani, Keitaro Kasuya, Soh Yoshikawa, Takuya Uto

Carbohydrate Polymers 297 Article number: 120010 2022.12

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

DOI： 10.1016/j.carbpol.2022.120010

Theoretical study on dissolution mechanism of chitin crystal in ionic liquids Reviewed

Takuya Uto

Chitin and Chitosan Research 28 16 - 21 2022.4

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

Off-axis photoelasticity by anisotropic molecular deformation of uniaxially aligned cellulose nanofiber films Invited Reviewed International journal

Kojiro Uetani, Takuya Uto

Carbohydrate Polymer Technologies and Applications 2 ( 25 ) Article number: 100166 2021.12

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

We report the angle dependence of the photoelasticity for unidirectionally aligned films of bacterial cellulose nanofibers (CNFs) by applying the off-axis stress at 0°–90° with respect to the CNF orientation. The photoelastic coefficient was positive when the stress direction was close to the CNF axial direction, and it was negative when the stress was applied close to the lateral direction. The positive to negative photoelasticity was also observed in the off-axis photoelasticity of the cellophane film and in the density functional theory (DFT) calculations for the stretching between two atoms in the cellobiose model. On the other hand, unlike the cellophane film, the CNF film showed a positively and negatively asymmetric photoelasticity of 5 to −10 TPa−1, reflecting the anisotropy of the crystal modulus tensor. We found that the presence or absence of cellulose crystals controls the anisotropy of photoelasticity by constraining the molecular deformation.

DOI： 10.1016/j.carpta.2021.100166

Synthetic zwitterions as efficient non-permeable cryoprotectants Reviewed International journal

Yui Kato, Takuya Uto, Daisuke Tanaka, Kojiro Ishibashi, Akiko Kobayashi, Masaharu Hazawa, Richard W. Wong, Kazuaki Ninomiya, Kenji Takahashi, Eishu Hirata, Kosuke Kuroda

Communications Chemistry 4 Article number: 151 2021.10

Language：English Publishing type：Research paper (scientific journal) Publisher：Nature Research

Cryopreservation of cells is necessary for long periods of storage. However, some cell lines cannot be efficiently cryopreserved, even when optimized commercial cryoprotectants are employed. Previously, we found that a low-toxic synthetic zwitterion aqueous solution enabled good cryopreservation. However, this zwitterion solution could not cryopreserve some cells, such as human kidney BOSC cells, with good efficiency. Therefore, details of the cryoprotective effect of the zwitterions and optimization based on its mechanisms are required. Herein, we synthesized 18 zwitterion species and assessed the effects of the physical properties of water/zwitterion mixtures. Non-cell-permeable zwitterions can inhibit ice crystal formation extracellularly via direct interaction with water and intracellularly via dehydration of cells. However, cells that could not be cryopreserved by zwitterions were insufficiently dehydrated in the zwitterion solution. Dimethyl sulfoxide (DMSO) was combined as a cell-permeable cryoprotectant to compensate for the shortcomings of non-cell-permeable zwitterions. The water/zwitterion/DMSO (90/10/15, v/w/w) could cryopreserve different cells, for example freezing-vulnerable K562 and OVMANA cells; yielding ~1.8-fold cell viability compared to the case using a commercial cryoprotectant. Furthermore, molecular dynamics simulation indicated that the zwitterions protected the cell membrane from the collapse induced by DMSO.

DOI： 10.1038/s42004-021-00588-x

Extended ensemble molecular dynamics study of cellulose I–ethylenediamine complex crystal models: Atomistic picture of desorption behaviors of ethylenediamine Invited Reviewed International journal

Toshifumi Yui, Takuya Uto

Cellulose 29 2855 - 2867 2021.8

Authorship：Last author Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Nature

Cellulose I crystals swell on exposure to ethylenediamine (EDA) molecules to form a cellulose I–EDA complex, and successive extraction of EDA molecules converts the complex crystalline phase to either original cellulose I or cellulose IIII, depending on the treatment procedure. The present study reports the extended ensemble molecular dynamics (MD) simulation of the cellulose I–EDA complex models. An accelerated MD simulation allows most of the EDA molecules to desorb from the crystal model through a hydrophilic channel between the piles of cellulose chains, one at a time. Migration of a single EDA molecule along the channel is simulated by the adopted steered MD method combined with the umbrella sampling method to evaluate the potential of mean force (PMF) or free energy change on its movement. The PMF continues to increase during the migration of an EDA molecule to give a final PMF value of more than 30 kcal/mol. The PMF profiles are largely lowered by the removal of EDA molecules in the neighboring channels and by the widening of the channel. The former suggests that the EDA desorption cooperates with that in the neighboring channels, and, in the latter case, an EDA migration is efficiently promoted by solvation with water molecules in the expanded channel. We conclude that the atomistic picture of the EDA desorption behaviors observed in the crystal models is applicable to the real crystalline phase.

DOI： 10.1007/s10570-021-04136-7

Essential requirements of biocompatible cellulose solvents Reviewed International coauthorship International journal

Tetsuo Komori, Heri Satria, Kyohei Miyamura, Ai Ito, Magoto Kamiya, Ayumi Sumino, Takakazu Onishi, Kazuaki Ninomiya, Kenji Takahashi, Jared L. Anderson, Takuya Uto, Kosuke Kuroda

ACS Sustainable Chemistry & Engineering 9 ( 35 ) 11825 - 11836 2021.8

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

Energy-efficient bioethanol production from plant biomass is in high demand, and one of the most promising procedures reported to date is one-pot ethanol production, that is, the production of ethanol from biomass in the same reaction pot, such as industrial first-generation bioethanol. This process requires cellulose solvents whose toxicity toward fermentative microorganisms is extremely low. Herein, we have developed a low-toxic zwitterionic cellulose solvent known as 4-(1-(2-(2-methoxyethoxy)ethyl)imidazol-3-io)butyrate (OE2imC3C). OE2imC3C is the only reported solvent that satisfies the following properties: being liquid at mild temperature and having good cellulose dissolution ability and low toxicity, even when including other types of solvents. We here investigated the relationship between the chemical structures and properties by synthesizing 22 zwitterions. Long alkyl- or oligoether chains attached to the cation (cation tails) were necessary to be a liquid. The zwitterions, except for that with an octyl tail, exhibited biocompatibility. Interestingly, the spacers of the zwitterions, alkyl chains between the cations and anions, were expected to be inert, but affected the toxicity. The molecular mechanisms were investigated using molecular dynamics simulations. The zwitterions exhibiting low toxicity scarcely inserted their cation tails into cell membrane and thus did not rupture the cell membrane. Ionic liquids, which have free cations and anions, induced molecular-level disruption of the cell membrane, suggesting that the zwitterion structure is a critical factor for low toxicity. The spacers, which were expected to be inert, shifted the solvent cluster structures in the bulk phase and induced molecular-level disruption of the cell membrane. The requirements for low-toxic cellulose solvents are zwitterionic structures, carboxylate anions, long polar cation tails, and in some cases, short spacers.

DOI： 10.1021/acssuschemeng.1c03438

Ether‐functionalized pyrrolidinium‐based room temperature ionic liquids: Physicochemical properties, molecular dynamics, and the lithium ion coordination environment Reviewed International journal

Kazuki Yoshii, Takuya Uto, Takakazu Onishi, Daichi Kosuga, Naoki Tachikawa, Yasushi Katayama

ChemPhysChem 22 ( 15 ) 1584 - 1594 2021.7

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：John Wiley & Sons, Inc.

The physicochemical properties of room temperature ionic liquids (RTILs) consisting of bis(trifluoromethanesulfonyl)amide (TFSA−) combined with 1-hexyl-1-methylpyrrolidinium (Pyr1,6+), 1-(butoxymethyl)-1-methylpyrrolidinium (Pyr1,1O4+), 1-(4-methoxybutyl)-1-methyl pyrrolidinium (Pyr1,4O1+), and 1-((2-methoxyethoxy)methyl)-1-methylpyrrolidinium (Pyr1,1O2O1+) were investigated using both experimental and computational approaches. Pyr1,1O2O1TFSA, which contains two ether oxygen atoms, showed the lowest viscosity, and the relationship between its physicochemical properties and the position and number of the ether oxygen atoms was discussed by a careful comparison with Pyr1,1O4TFSA and Pyr1,4O1TFSA. Ab initio calculations revealed the conformational flexibility of the side chain containing the ether oxygen atoms. In addition, molecular dynamics (MD) calculations suggested that the ion distributions have a significant impact on the transport properties. Furthermore, the coordination environments of the Li ions in the RTILs were evaluated using Raman spectroscopy, which was supported by MD calculations using 1000 ion pairs. The presented results will be valuable for the design of functionalized RTILs for various applications.

DOI： 10.1002/cphc.202100380

Molecular and crystal structure of a chitosan−zinc chloride complex Reviewed International journal

Toshifumi Yui, Takuya Uto, Kozo Ogawa

Nanomaterials 11 ( 6 ) Article number: 1407 2021.5

Language：English Publishing type：Research paper (scientific journal) Publisher：MDPI

We determined the molecular and packing structure of a chitosan–ZnCl2 complex by X-ray diffraction and linked-atom least-squares. Eight D-glucosamine residues—composed of four chitosan chains with two-fold helical symmetry, and four ZnCl2 molecules—were packed in a rectangular unit cell with dimensions a = 1.1677 nm, b = 1.7991 nm, and c = 1.0307 nm (where c is the fiber axis). We performed exhaustive structure searches by examining all of the possible chain packing modes. We also comprehensively searched the positions and spatial orientations of the ZnCl2 molecules. Chitosan chains of antiparallel polarity formed zigzag-shaped chain sheets, where N2···O6, N2···N2, and O6···O6 intermolecular hydrogen bonds connected the neighboring chains. We further refined the packing positions of the ZnCl2 molecules by theoretical calculations of the crystal models, which suggested a possible coordination scheme of Zn(II) with an O6 atom.

DOI： 10.3390/nano11061407

Molecular dynamics simulation of cellulose synthase subunit D octamer with cellulose chains from acetic acid bacteria: Insight into dynamic behaviors and thermodynamics on substrate recognition Reviewed International journal

Takuya Uto, Yuki Ikeda, Naoki Sunagawa, Kenji Tajima, Min Yao, Toshifumi Yui

Journal of Chemical Theory and Computation 17 ( 1 ) 488 - 496 2021.1

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)

The present study reports the building of a computerized model and molecular dynamics (MD) simulation of cellulose synthase subunit D octamer (CesD) from Komagataeibacter hansenii. CesD was complexed with four cellulose chains having DP = 12 (G12) by model building, which revealed unexpected S-shaped pathways with bending regions. Combined conventional and accelerated MD simulations of CesD complex models were carried out, while the pyranose ring conformations of the glucose residues were restrained to avoid undesirable deviations of the ring conformation from the 4C1 form. The N-terminal regions and parts of the secondary structures of CesD established appreciable contacts with the G12 chains. Hybrid quantum mechanical (QM) and molecular mechanical (MM) simulations of the CesD complex model were performed. Glucose residues located at the pathway bends exhibited reversible changes to the ring conformation into either skewed or boat forms, which might be related to the function of CesD in regulating microfibril production.

DOI： 10.1021/acs.jctc.0c01027

Irregular and suppressed elastic deformation by a structural twist in cellulose nanofibre models Reviewed International journal

Kojiro Uetani, Takuya Uto, Nozomu Suzuki

Scientific Reports 11 Article number: 790 2021.1

Language：English Publishing type：Research paper (scientific journal) Publisher：Nature research

The elastic responsiveness of single cellulose nanofibres is important for advanced analysis of biological tissues and their use in sophisticated functional materials. However, the mechanical responsiveness derived from the twisted structure of cellulose nanofibres (CNFs) has remained unexplored. In this study, finite element simulations were applied to characterize the deformation response derived from the torsional structure by performing tensile and bending tests of an unconventionally very long and twisted rod model, having the known dimensional parameters and properties of CNFs. The antagonistic action of two types of structural elements (a contour twist and a curvilinear coordinate) was found to result in an irregular deformation response but with only small fluctuations. The contour twist generated rotational displacements under tensile load, but the curvilinear coordinate suppressed rotational displacement. Under bending stress, the contour twist minimized irregular bending deformation because of the orthotropic properties and made the bending stress transferability a highly linear response.

DOI： 10.1038/s41598-020-80890-1

Non-aqueous, zwitterionic solvent as an alternative for dimethyl sulfoxide in the life sciences Reviewed International journal

Kosuke Kuroda, Tetsuo Komori, Kojiro Ishibashi, Takuya Uto, Isao Kobayashi, Riki Kadokawa, Yui Kato, Kazuaki Ninomiya, Kenji Takahashi, Eishu Hirata

Communications Chemistry 3 Article number: 163 2020.11

Language：English Publishing type：Research paper (scientific journal) Publisher：Nature Research

Dimethyl sulfoxide (DMSO) is widely used as a solvent in the life sciences, however, it is somewhat toxic and affects cell behaviours in a range of ways. Here, we propose a zwitterionic liquid (ZIL), a zwitterion-type ionic liquid containing histidine-like module, as a new alternative to DMSO. ZIL is not cell permeable, less toxic to cells and tissues, and has great potential as a vehicle for various hydrophobic drugs. Notably, ZIL can serve as a solvent for stock solutions of platinating agents, whose anticancer effects are completely abolished by dissolution in DMSO. Furthermore, ZIL possesses suitable affinity to the plasma membrane and acts as a cryoprotectant. Our results suggest that ZIL is a potent, multifunctional and biocompatible solvent that compensates for many shortcomings of DMSO.

DOI： 10.1038/s42004-020-00409-7

Nanocellulose enriches enantiomers in asymmetric aldol reactions Reviewed International journal

Naliharifetra Jessica Ranaivoarimanana, Xin Habaki, Takuya Uto, Kyohei Kanomata, Toshifumi Yui, Takuya Kitaoka

RSC Advances 10 ( 61 ) 37064 - 37071 2020.10

Language：English Publishing type：Research paper (scientific journal) Publisher：Royal Society of Chemistry (RSC)

Cellulose nanofibers obtained from wood pulp by TEMPO-mediated oxidation acted as a chiral enhancer in direct aldol reactions of 4-nitrobenzaldehyde and cyclopentanone with (S)-proline as an organocatalyst. Surprisingly, catalytically inactive TEMPO-oxidized cellulose nanofibers enriched the (R,R)-enantiomer in this reaction, affording 89% ee in the syn form with a very high yield (99%). Conversely, nanocellulose-free (S)-proline catalysis resulted in poor selectivity (64% ee, syn form) with a low yield (18%). Green organocatalysis occurring on nanocellulose solid surfaces bearing regularly aligned chiral carbons on hydrophobic crystalline facets will provide new insight into asymmetric synthesis strategies for interfacial catalysis.

DOI： 10.1039/D0RA07412H

The effects of the position of the ether oxygen atom in pyrrolidinium-based room temperature ionic liquids on their physicochemical properties Reviewed International journal

Kazuki Yoshii, Takuya Uto, Naoki Tachikawa, Yasushi Katayama

Physical Chemistry Chemical Physics 22 ( 35 ) 19480 - 19491 2020.9

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Royal Society of Chemistry (RSC)

Room temperature ionic liquids (RTILs) containing ether oxygen atoms have been investigated for a gamut of science and technology applications owing to their superior physicochemical properties. However, the effect of the position of the ether oxygen atom in the side chain on their physicochemical properties is not clearly understood. This study investigates, using both experimental and computational approaches, the effect of ether oxygen atoms on the physicochemical properties of RTILs consisting of bis(trifluoromethylsulfonyl)amide (TFSA−) with 1-methyl-1-propylpyrrolidinium (MPP+), 1-butyl-1-methylpyrrolidinium (BMP+), 1-methoxymethyl-1-methylpyrrolidinium (MOMMP+), 1-ethoxymethyl-1-methylpyrrolidinium (EOMMP+), and 1-methoxyethyl-1-methylpyrrolidinium (MOEMP+). The viscosity of the RTILs containing the ether oxygen atom was lower than that of the alkyl analogues. Moreover, the viscosity of EOMMPTFSA was lower than that of MOEMPTFSA, albeit EOMMPTFSA and MOEMPTFSA have the same molecular weight with ether oxygen atoms at different positions. Ab initio calculations reveal that the number of methylene groups between nitrogen and oxygen atoms in the cation structure profoundly impacts the local stable structure of the cation. Furthermore, we discussed the relationship between the transport properties and the spatial distribution of ions obtained by MD simulations. This result will be valuable in the design of functionalized RTILs, via the judicious tuning of the conformational flexibility of ether oxygen atoms in related ionic liquids.

DOI： 10.1039/d0cp02662j

Docking and molecular dynamics study of the carbohydrate binding module from Trichoderma reesei Cel7A on the surfaces of the cellulose III_I crystal Invited Reviewed International journal

Toshifumi Yui, Takuya Uto

Journal of Renewable Materials 8 ( 8 ) 863 - 878 2020.7

Authorship：Last author Language：English Publishing type：Research paper (scientific journal) Publisher：Tech Science Press (TSP)

We report the systematic survey of the binding free energies at the interface between a carbohydrate binding module (CBM) of Cel7A and the cellulose III_I crystal model using grid docking searches and molecular dynamics simulations. The two hydrophobic crystal surfaces were involved in the distinct energy minima of the binding free energy. The complex models, each with the CBM at the minimum energy position, stably formed in the solution state. The binding free energies of the cellulose III_I complex models, based on both static and dynamics states, were comparable to those of the native cellulose complex models. However, the cellulose III_I crystal had a larger binding surface, which is compatible with the observed high enzymatic activity of Cel7A for the cellulose III_I substrate.

DOI： 10.32604/jrm.2020.010830

Evaluation of artificial crystalline structure from amylose analog polysaccharide without hydroxy groups at C-2 position Reviewed International journal

Takuya Uto, Shota Nakamura, Kazuya Yamamoto, Jun-ichi Kadokawa

Carbohydrate Polymers 240 ( 15 ) Article number: 116347 2020.7

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier Ltd.

In this study, we found that a new artificial crystalline structure was fabricated from an amylose analog polysaccharide without hydroxy groups at the C-2 position, i.e., 2-deoxyamylose. The polysaccharide with a well-defined structure was synthesized by facile thermostable α-glucan phosphorylase-catalyzed enzymatic polymerization. Powder X-ray diffraction (XRD) analysis of the product indicated the formation of a specific crystalline structure that was completely different from the well-known double helix of the natural polysaccharide, amylose. Molecular dynamics simulations showed that the isolated chains of 2-deoxyamylose spontaneously assembled to a novel double helix based on building blocks with controlled hydrophobicity arising from pyranose ring stacking. The simulation results corresponded with the XRD patterns.

DOI： 10.1016/j.carbpol.2020.116347

Development of supplemental force field parameters for molecular mechanics calculations Invited

Takuya Uto, Toshifumi Yui

Cellulose Communications 27 ( 1 ) 28 - 33 2020.3

Authorship：Lead author,　Corresponding author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Cellulose Society of Japan

現在,セルロース材料の分子動力学研究で広く利用されるAMBER,CHARMMおよびGROMACSに装備された分子力場パラメータは,計算化学を専門とする研究グループによって開発され,長期間にわたって改良が重ねられてきた.本稿はトピックスを限定し,既存パラメータセットの利用を前提として,それに装備されていないパラメータを補完する方法について解説する.筆者らがAMBER力場の糖質分子パラメータGLYCAMを用いたセルロース材料計算で実施した,セルロース複合体ゲスト分子であるエチレンジアミン(EDA)およびセルロース誘導体のパラメータ作成事例を報告する.

Molecular dynamics simulation of cellulose I-ethylenediamine complex crystal models Reviewed International journal

Takuya Uto, Meguru Minamizaki, Toshifumi Yui

Journal of Physical Chemistry B 124 ( 1 ) 134 - 143 2019.12

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)

Cellulose I fibrils swell on exposure to ethylenediamine (EDA), which forms the cellulose I-EDA complex. These are regarded as host materials with guest intercalation. The present study reports molecular dynamics (MD) simulations of cellulose I-EDA crystal models with finite fiber to reproduce desorption of EDA molecules. The force field parameters for EDA were improved. Part of the EDA molecules was desorbed only from the surfaces of the crystal models, not from their interiors. The EDA molecules diffused through a hydrophilic channel composed of the hydrophilic edges of the cellulose chains, and their conformations and orientations changed. With the configuration of the cellulose chains being held, the vacant hydrophilic channel was immediately filled with water molecules. The innermost part of the crystal models, defined as a core unit, was partly deformed from the initial crystal structure, including the changes in the exocyclic group conformations of the cellulose chains and the orientations of the EDA molecules, coupled with partial reconfiguration of the intermolecular hydrogen bonding scheme. A possible crystalline conversion scheme after complete desorption of EDA has been discussed based on the present findings.

DOI： 10.1021/acs.jpcb.9b08153

Theoretical study on crystal structure of structural polysaccharides and their dissolution mechanisms Invited

Takuya Uto

Journal of The Society of Fiber Science and Technology 75 ( 9 ) 497 - 500 2019.9

Authorship：Lead author,　Last author,　Corresponding author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Society of Fiber Science and Technology, Japan

セルロースの結晶構造を3次元分解した分子鎖シートモデルに対して,密度汎関数理論計算を適用した.その結果,天然セルロース繊維について,長年議論されてきた変形特性の要因が,Iα型(110)/Iβ型(100)面の平面状分子鎖シートに由来することを明らかにした.さらに,III_I型(100)面シートモデルが自発的にチューブ形態へと変化する現象を観察した.このチューブ状分子(セルロースナノチューブ)は,分子鎖シート両端が水素結合によって閉じた新たなセルロース高次構造となる可能性を見出し,非極性溶媒中で安定に存在し得ることを提案した. 最近,構造多糖を溶解するイオン液体に注目がされている.異なるイオン液体のセルロースやキチンに対する溶解性を関連づけるために,イオン液体中におけるセルロース・キチン溶解の分子動力学計算を実施した.その結果,イオン液体のカチオンとアニオンが協同的にセルロース・キチンの分子間水素結合を切断する溶解過程を観察した.特に,界面に存在する臭化物イオンがキチン溶解に寄与することが計算によって示唆されたため,微量の臭化物イオン存在下でもキチン溶解性が向上することを実験によって検証した.また,水素結合切断量と実際のセルロース・キチン溶解度が強く相関し,文献情報の無いイオン液体の溶解度を予測した.

DOI： 10.2115/fiber.75.p-497

Higher ordered structure of cellulose predicted by computational chemistry: Cellulose nanotube in cyclohexane and ethyl acetate Reviewed

Takuya Uto, Toshifumi Yui

Journal of Fiber Science and Technology 74 ( 8 ) 171 - 176 2018.8

Authorship：Lead author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Society of Fiber Science and Technology, Japan

Nanotubes are remarkable nanoscale architectures for a wide range of potential applications. Recently, we have predicted a nanoscale, tubular structure of cellulose molecules (CelNT), through density functional theory (DFT) calculation. In the present paper, we report a molecular dynamics (MD) study of the theoretical CelNT models to evaluate their dynamic behavior in solution (cyclohexane or ethyl acetate). Based on the one-quarter chain staggering relationship predicted by DFT calculations, we constructed six CelNT models by combining the two chain polarities (parallel (P) and antiparallel (AP)) and three symmetry operations (helical right (HR), helical left (HL), and rotation (R)) to generate a circular arrangement of molecular chains. The tubular structure of the CelNT models quickly collapsed in ethyl acetate with cleavages of intermolecular hydrogen bonds, indicating that ethyl acetate was not appropriate for the solvent of CelNTs. The four models (P-HR, P-HL, P-R, and AP-R) retained the tubular form in cyclohexane and the P-R and AP-R models exhibited relatively continuous tubular forms with the largest binding energies. The structural features of the CelNT models in cyclohexane were characterized in terms of intermolecular hydrogen bond and the hydroxymethyl group conformation. Solvent structuring clearly occurred, suggesting that the CelNT models may stably disperse in cyclohexane.

DOI： 10.2115/fiberst.2018-0024

Understanding dissolution process of chitin crystal in ionic liquids: Theoretical study Reviewed International journal

Takuya Uto, Satoshi Idenoue, Kazuya Yamamoto, Jun-ichi Kadokawa

Physical Chemistry Chemical Physics 20 ( 31 ) 20669 - 20677 2018.8

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Royal Society of Chemistry (RSC)

Chitin is a promising biomass resource and has high potential for industrial applications owing to its huge annual production in nature. However, it exhibits poor processability and solubility due to its very stable and crystalline character. Recently, ionic liquids (ILs) have attracted attention as solvents for structural polysaccharides - for example, 1-allyl-3-methylimidazolium bromide (AMIMBr) has been found to dissolve chitin. As few ILs are known to dissolve chitin, little research has been conducted on the dissolution mechanism involved. In this study, we have adopted a molecular dynamics (MD) approach to study the dissolution of chitin crystals in imidazolium-based ILs. The MD simulation in AMIMBr has demonstrated that the dissolution process involved peeling of chitin chains from the crystal surface, with Br- cleaving the chitin hydrogen bonds, and AMIM+ preventing a return to the crystalline phase after the peeling. By contrast, in imidazolium acetates, which has also been reported to dissolve chitin, although the molecular chains are peeled off, the peeled chains occasionally return to the crystalline phase. Furthermore, the MD trajectory analysis has revealed that the solubility of chitin is well correlated with the number of intermolecular hydrogen bonds by acetamido groups in the chitin crystal. It has been experimentally proven that mixing a small amount of 2-bromoethyl acetate, as a bromide generator, with 1-allyl-3-methylimidazolium chloride can enhance chitin solubility, which supports the dissolution mechanism indicated by the above theoretical results.

DOI： 10.1039/c8cp02749h

Molecular dynamics simulations of theoretical cellulose nanotube models Reviewed International journal

Takuya Uto, Yuta Kodama, Tatsuhiko Miyata, Toshifumi Yui

Carbohydrate Polymers 190 ( 15 ) 331 - 338 2018.7

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier Ltd.

Nanotubes are remarkable nanoscale architectures for a wide range of potential applications. In the present paper, we report a molecular dynamics (MD) study of the theoretical cellulose nanotube (CelNT) models to evaluate their dynamic behavior in solution (either chloroform or benzene). Based on the one-quarter chain staggering relationship, we constructed six CelNT models by combining the two chain polarities (parallel (P) and antiparallel (AP)) and three symmetry operations (helical right (HR), helical left (HL), and rotation (R)) to generate a circular arrangement of molecular chains. Among the four models that retained the tubular form (P-HR, P-HL, P-R, and AP-R), the P-R and AP-R models have the lowest steric energies in benzene and chloroform, respectively. The structural features of the CelNT models were characterized in terms of the hydroxymethyl group conformation and intermolecular hydrogen bonds. Solvent structuring more clearly occurred with benzene than chloroform, suggesting that the CelNT models may disperse in benzene.

DOI： 10.1016/j.carbpol.2018.03.004

Double helix formation from non-natural amylose analog polysaccharides Reviewed International journal

Toshifumi Yui, Takuya Uto, Takuya Nakauchida, Kazuya Yamamoto, Jun-ichi Kadokawa

Carbohydrate Polymers 189 ( 1 ) 184 - 189 2018.7

Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier Ltd.

Double helix formation from the non-natural anionic and cationic amylose analog polysaccharides (amylouronic acid and amylosamine, respectively) was achieved through electrostatic interactions. A water-insoluble complex was obtained by simply mixing the two polysaccharides in water. The 1H NMR analysis indicated that the formation of the complexes with an approximately equimolar unit ratio from the two polysaccharides was resulted regardless of feed ratios for mixing. The powder X-ray diffraction (XRD) measurement suggested that the helix had larger sizes both in diameter and pitch compared with well-known amylose double helix. The formation of the double helical structure was also examined by theoretical calculations. The double helix models, differing in a chain polarity and a charge state of the residues, were constructed based on the 6-fold left-handed amylose chain of the A-amylose crystal structure. Molecular dynamics calculations indicated that those with an antiparallel chain polarity retained an intertwined form. The antiparallel double helical model with the free form residues was suggested to be the most likely structure for the non-natural polysaccharides.

DOI： 10.1016/j.carbpol.2018.02.026

DFT optimization of isolated molecular chain sheet models constituting native cellulose crystal structures Reviewed International journal

Takuya Uto, Toshifumi Yui

ACS Omega 3 ( 7 ) 8050 - 8058 2018.7

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)

Because of high crystallinity and natural abundance, the crystal structures of the native cellulose allomorphs have been theoretically investigated to elucidate the cellulose chain packing schemes. Here, we report systematic structure optimization of cellulose chain sheet models isolated from the cellulose Iα and Iβ crystals by density functional theory (DFT). For each allomorph, the three-dimensional chain packing structure was partitioned along each of the three main crystal planes to construct either a flat chain sheet model or two stacked chain sheet models, each consisting of four cello-octamers. Various combinations of the basis set and DFT functional were investigated. The flat chain sheet models constituting the cellulose Iα (110) and Iβ (100) planes, where the cellulose chains are mainly linked by intermolecular hydrogen bonds, exhibit a right-handed twist. More uniform and symmetrical sheet twists are observed when the flat chain sheet models are optimized using a basis set with diffuse functions (6-31+G(d,p)). The intermolecular interactions are more stable when the chain sheet models are optimized with the two hybrid functionals CAM-B3LYP and M06-2X. Optimization of the two stacked chain sheet models, where van der Waals interactions predominated between adjacent chains, gave differing results; those retaining the initial structures and those losing the sheet appearance, corresponding to the cellulose Iα/Iβ (010)/(1-10) and (100)/(110) chain sheet models, respectively. The cellulose Iβ (1-10) chain sheet model is more stable using the M06-2X functional than using the CAM-B3LYP functional.

DOI： 10.1021/acsomega.8b00834

Structural stability of the molecular chain sheets composing the crystal structures of cellulose allomorphs: A theoretical study Invited

Takuya Uto, Tsutomu Yonekura, Toshifumi Yui

Cellulose Communications 25 ( 1 ) 20 - 23 2018.3

Authorship：Lead author,　Corresponding author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Cellulose Society of Japan

The structural stabilities of the molecular chain sheet models isolated from the crystal structures of the four cellulose allomorphs, Iα, Iβ, II, and III_I, were studied by density functional theory (DFT) optimization. Intermolecular hydrogen bonds connect molecular chains to form a molecular chain sheet. The DFT-optimized (110) and (100) chain sheet models of the cellulose Iα and Iβ allomorphs, respectively, developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models oppositely twisted with right- and left-handed chirality, respectively. The cellulose III_I (1−10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models reflected those of the parent crystal models observed in solvated molecular dynamics (MD) simulations.

Cellulose crystal dissolution in imidazolium-based ionic liquids: A theoretical study Reviewed International journal

Takuya Uto, Kazuya Yamamoto, Jun-ichi Kadokawa

The Journal of Physical Chemistry B 122 ( 1 ) 258 - 266 2018.1

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)

The highly crystalline nature of cellulose results in poor processability and solubility, necessitating the search for solvents that can efficiently dissolve this material. Thus, ionic liquids (ILs) have recently been shown to be well suited for this purpose, although the corresponding dissolution mechanism has not been studied in detail. Herein, we adopt a molecular dynamics (MD) approach to study the dissolution of model cellulose crystal structures in imidazolium-based ILs and gain deep mechanistic insights, demonstrating that dissolution involves IL penetration-induced cleavage of hydrogen bonds between cellulose molecular chains. Moreover, we reveal that in ILs with high cellulose dissolving power (powerful solvents, such as 1-allyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium chloride), the above molecular chains are peeled from the crystal phase and subsequently dispersed in the solvent, whereas no significant structural changes are observed in poor-dissolving-power solvents. Finally, we utilize MD trajectory analysis to show that the solubility of microcrystalline cellulose is well correlated with the number of intermolecular hydrogen bonds in cellulose crystals. The obtained results allow us to conclude that both anions and cations of high-dissolving-power ILs contribute to the stepwise breakage of hydrogen bonds between cellulose chains, whereas this breakage does not occur to a sufficient extent in poorly solubilizing ILs.

DOI： 10.1021/acs.jpcb.7b09525

Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs Reviewed International journal

Takuya Uto, Sho Mawatari, Toshifumi Yui

The Journal of Physical Chemistry B 118 ( 31 ) 9313 - 9321 2014.7

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)

The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iβ, II, and III_I were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively. The cellulose III_I (1-10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models were reflected in the structures of the parent crystal models observed in solvated molecular dynamics (MD) simulations. The minor conformations of the hydroxymethyl groups proposed in the real crystal structures were detected in the MD crystal models and the DFT-optimized (010) model of cellulose II. The crystal chain packing and crystal conversions are interpreted in terms of principal chain sheet stacking.

DOI： 10.1021/jp503535d

Prediction of cellulose nanotube models through density functional theory calculations Reviewed International journal

Takuya Uto, Tatsuhiko Miyata, Toshifumi Yui

Cellulose 21 ( 1 ) 87 - 95 2014.2

Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Nature

We report the generation of a nano-scale tubular structure of cellulose molecules (CelNT), through density functional theory (DFT) calculations. When a cellulose III_I (100) chain sheet model is optimized by DFT calculations, the sheet models spontaneously roll into tubes. The oligomers arrange in a right-handed, four-fold helix with one-quarter chain staggering, oriented with parallel polarity similar to the original crystal structure. Based on a one-quarter chain staggering relationship, six large CelNT models, consisting of 16 cellulose chains with DP = 80, are constructed by combinations of two types of chain polarities and three types of symmetry operations to generate a circular arrangement of molecular chains. All six CelNT models are examined by molecular dynamics (MD) calculations in chloroform. While four CelNT models retain a tubular form throughout MD calculations, the remaining two deform. 3D-RISM theory model is used to estimate the solvation free energies of the four CelNT models. The results suggest that the CelNT model with a chain arrangement of parallel polarity and right-handed helical symmetry forms the most stable tube structure.

DOI： 10.1007/s10570-013-0125-y

Enhancement of ethanol production from Napiergrass (Pennisetum purpureum Schumach) by a low-moisture anhydrous ammonia pretreatment Reviewed International journal

Masahide Yasuda, Keisuke Takeo, Hayato Nagai, Takuya Uto, Toshifumi Yui, Tomoko Matsumoto, Yasuyuki Ishii, Kazuyoshi Ohta

Journal of Sustainable Bioenergy Systems 3 ( 3 ) 179 - 185 2013.9

Language：English Publishing type：Research paper (scientific journal) Publisher：Scientific Research Publishing

Napiegrass (Pennisetum purpureum Schumach) was treated with a low-moisture anhydrous ammonia (LMAA) pretreatment by adding an equal weight of water and keeping it under atmospheric ammonia gas at room temperature for four weeks. After the removal of ammonia and washing with water, a simultaneous saccharification and fermentation (SSF) was conducted for the LMAA-pretreated napiergrass (1.33 g) in a buffer solution (8 mL) using a mixture of a cellulase (80 mg) and a xylanase (53 mg) as well as the cell suspension (0.16 mL) of Saccharomyces cerevisiae. Ethanol and xylose resulted in 91.2% and 62.9% yields, respectively. The SSF process was scaled up using LMAA-pretreated napiergrass (100.0 g) to give ethanol (77.2%) and xylose (52.8%). After the removal of ethanol, the pentose fermentation of the SSF solution (40 mL), which contained 1.00 g of xylose, using cell suspension of Escherichia coli KO11 (70 mL) gave 86.3% yield of ethanol. Total ethanol yield reached 68.9% based on xylan (21.4 wt%) and glucan (39.7 wt%) of the LMAA-pretreated napiergrass.

DOI： 10.4236/jsbs.2013.33025