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

We have studied the applicability of the sigma enlarging bridge (SEB) correction method to the solvation of polyatomic solute molecules in a Lennard-Jones monatomic solvent using the three dimensional Ornstein–Zernike (3D-OZ) theory. It is found that the SEB correction improves the solvation free energy (SFE) significantly. It has been concluded from the analysis of the radial distribution function (RDF) that the parameter included in the SEB function can be transferred from the values of the monatomic solute to those of the polyatomic one for the 3D-OZ theory. The one dimensional reference interaction site model (1D-RISM) theory has also been examined. The SEB correction is found to be applicable to improve the SFE of the 1D-RISM theory. Except for buried or sterically hindered atoms of the solute, the transferability of the SEB parameter has been confirmed in terms of the RDF obtained by the 1D-RISM theory. This paper also examines the applicability of the hybrid closure between the molecular dynamics simulation and the one of the following closure equations—the hyper-netted chain, Kovalenko–Hirata, or Kobryn–Gusarov–Kovalenko equation—for preparing the solvent–solvent correlation function. Using the results of the hybrid closure in addition to the SEB-corrected closure, we discuss the effect of the quality of the correlation functions for the bulk solvent on the accuracy of the SFE.

DOI： 10.1063/5.0102003

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

We examined the accuracy of the reference interaction site model theory in terms of the thermodynamics of fluids consisting of single-component diatomic molecules, where we evaluated the internal energy, pressure, and isothermal compressibility. Two routes were tested for pressure. One is the differentiation of the Helmholtz free energy with respect to the density, and the other is the virial formula. We focused on hypernetted chain (HNC), Kovalenko–Hirata (KH), and Kobryn–Gusarov–Kovalenko (KGK) closure approximations. The most accurate closure relationship among the three is the KGK closure. The HNC and KH closures tend to overestimate the internal energy and pressure from the density derivative of the Helmholtz free energy. Moreover, it was found that the HNC closure significantly overestimated the isothermal compressibility, particularly at low density, or for molecular models with short bond lengths. The applicability of the sigma enlarging bridge (SEB) correction was also tested. After applying the SEB correction to the KH (SEB-KH) closure, a significant improvement was observed in the internal energy even for the model including the Coulomb potential.

DOI： 10.1063/5.0085014

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

DOI： 10.1063/5.0043388

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

DOI： 10.1246/cl.200521

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

DOI： 10.1016/j.cplett.2020.137777

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

© 2018 Elsevier B.V. We have examined a possibility of using canonical ensemble molecular dynamics (NVT-MD) simulation to prepare the solvent-solvent correlation function (VVCF), which is further utilized in the calculation of solute-solvent correlation function for the solvation free energy (SFE) of the Lennard-Jones (LJ) solution at the infinite dilution. We have employed a combined closure equation where the radial distribution function (RDF) of NVT-MD simulation is used for the short range and the hypernetted chain (HNC) closure for the long range. An appropriate separation for the boundary to switch the RDF of the MD simulation and the HNC closure is determined from the balance between the accuracy of the compressibility equation and the numerical stability. The appropriate separation is found to be from 2.0 to 3.0 in the unit of the LJ particle size. Furthermore, the isothermal compressibility evaluated from the combined NVT-MD closure agrees with those evaluated from the volume fluctuation in the isobaric isothermal ensemble MD simulation. The VVCF obtained from the combined NVT-MD closure is further used in the assessment of the sigma enlarging bridge (SEB) function that was proposed in our earlier works, e.g. [T. Miyata, Bull. Chem. Soc. Japan, 90 (2017) 1095], with which the first rising region of the RDF obtained from an approximate Ornstein-Zernike theory can be corrected by apparently adjusting (typically enlarging) the sigma parameters in the LJ potential. The following two points of view are considered in the assessment of the SEB function. One is the isothermal compressibility of the solvent, and the other is the SFE. It is found that the Kovalenko-Hirata closure with the SEB correction provides rather accurate VVCF, which leads to an accurate isothermal compressibility. The SFE is also improved when we apply the SEB correction to the solute-solvent calculation. While the SEB function includes one parameter, the numerical values of it are parameterized over a wide range of conditions in this study under the usage of the combined NVT-MD closure for the solvent-solvent calculation.

DOI： 10.1016/j.molliq.2019.111167

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

© 2019 Author(s). We study the applicability of sigma enlarging bridge (SEB) function to a homonuclear Lennard-Jones (LJ) diatomic solute molecule solvated in an LJ monatomic solvent, where the SEB was originally proposed for a monatomic solute molecule to improve the accuracy of the solvation free energy (SFE) [T. Miyata, Bull. Chem. Soc. Jpn. 90, 1095 (2017)]. Our interest is focused on the transferability of the SEB parameter, which is a parameter included in the SEB function. We employ the two-dimensional Ornstein-Zernike (OZ) theory. Hypernetted chain (HNC), Kovalenko-Hirata (KH) and Percus-Yevick (PY) closures are considered. The HNC closure with the SEB correction (SEB-HNC) and the counterpart for the KH closure (SEB-KH) are also examined in terms of the SFE. It is found that by comparing with the molecular dynamics simulation, the SFE is overestimated under both HNC and KH closures, whereas it tends to be underestimated under PY closures. These results are similar to those obtained for systems of LJ monatomic solute molecules. Both the SEB-HNC and the SEB-KH closures provide quite an accurate SFE, when the SEB parameter values that were originally evaluated for a monatomic solute molecule are applied to the homonuclear LJ diatomic solute. This indicates that the SEB parameter is transferable. The transferability of the SEB parameter is also confirmed in terms of the angular-dependent one-dimensional distribution function, which is obtained from the two-dimensional distribution function. The validity of the partial molar volume correction is also discussed by examining the dependence of the SFE errors on the solute volume.

DOI： 10.1063/1.5087935

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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

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier B.V.  

The performance of Kobryn-Gusarov-Kovalenko (KGK) closure was examined in terms of the thermodynamics for one-component Lennard-Jones fluids. The result was compared to molecular dynamics simulation as well as to hypernetted chain, Kovalenko-Hirata (KH), Percus-Yevick and Verlet-modified closures. As the density increases, the error of KGK closure shows a turnover, regarding the excess internal energy, pressure and isothermal compressibility. On the other hand, it was numerically confirmed that the energy and the virial equations are consistent under both KH and KGK closures. The accuracies of density-derivative and temperature-derivative of the radial distribution function are also discussed.

DOI： 10.1016/j.cplett.2018.04.013

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

We have studied the accuracy of Ornstein-Zemike (OZ) integral equation theory in terms of the solvation free energy (SFE) for a two-component Lennard-Jones system at the infinite dilution limit. We have employed the hypernetted chain (HNC), Kovalenko-Hirata (KH), Kobryn-Gusarov-Kovalenko (KGK), and Percus-Yevick (PY) closure equations. Further, we have extended the Verlet-modified (VM) closure to the two-component system to examine the accuracy of this method in terms of the SFE. Molecular dynamics simulations were employed to compare the results with the above mentioned OZ theories. The HNC and KH approximations significantly overestimate the SFE, whereas the PY approximation tends to underestimate it. The overestimation of the SFE by the KGK approximation becomes significant when the solvent density is relatively high. In contrast, the VM approximation is found to be rather accurate at all studied conditions. An analysis of the integrand for the SFE reveals that, to improve the SFE, the first rising (FR) region in the radial distribution function (RDF) must be corrected. We have also tested the sigma-enlarging-bridge (SEB) function that we proposed previously [T.Miyata and Y.Ebato, J.Mol.Liq.217 (2016) 75] for the correction of the FR region of the RDF. In this study, we applied the SEE function to both HNC-type and KH-type closures and found that these combinations (SEB-HNC and SEB-KH) improve the SFE significantly. (C) 2017 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.molliq.2017.05.134

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

We report the parameter values included in the sigma enlarging bridge (SEB) function for two-component Lennard-Jones fluids within the Ornstein-Zernike (OZ) integral equation framework, which was first proposed in our previous study [T. Miyata, Y. Ebato, J. Molec. Liquids, 217 (2016) 75] to improve the accuracy of the solvation free energy (SFE). In this article, we consider a wide range of thermodynamic states, with varying the solute size and the solute-solvent interaction strength. The SEB parameter was evaluated via the least square fitting of the first rising region of the radial distribution function obtained from OZ theory to that from molecular dynamics simulation. The SEB function was applied to both the hypernetted chain (HNC) and Kovalenko-Hirata (KH) closures. It is found that the SEB parameter increases monotonically with the solute size, whereas it hardly depends on the solute-solvent interaction strength. Also, the performance of bare HNC, bare KH, Percus-Yevick, and Verlet-modified closures are also examined, to report the relationship between the solute volume and the error of the SFE obtained from OZ theory. We found that the SFE errors under both HNC and KH closures are not necessarily proportional to the solute volume.

DOI： 10.1246/bcsj.20170203

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

The accuracy of the temperature derivative of radial distribution function obtained under hypernetted chain (HNC), Kovalenko-Hirata (KH), Percus-Yevick (PY) and Verlet-modified (VM) closure approximations is examined for one-component Lennard-Jones fluid. As relevant thermodynamic quantities, constant-volume heat capacity and thermal pressure coefficient are investigated in terms of their accuracy under the above four approximations. It is found that HNC and KH closures overestimate these quantities, whereas PY closure tends to underestimate them. VM closure predicts rather accurately the quantities. A significant cancellation is observed along the integration for the above quantities under HNC and KH closures, especially at high density state. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2016.06.049

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

We have calculated the excess internal energy, U-ex, pressure through the virial route, Pv, and excess chemical potential, mu(ex), for one-component Lennard-Jones (LJ) fluids by using hypernetted chain (HNC), Kovalenko-Hirata (KH), Percus-Yevick (PY) and Verlet modified (VM) approximations in an Ornstein-Zernike (OZ) integral equation theory. The results have been compared with molecular dynamics simulation to examine the accuracy of each approximation at relatively high density region. HNC and KH approximations significantly overestimate the above three thermodynamic quantities, whereas PY and VM approximations give relatively accurate results. The analysis upon the integrand to evaluate U-ex,Pv and mu(ex) has revealed that the precise location of the first rising (FR) region in radial distribution function is the most important for the accurate evaluation of these quantities. We have applied an approximate bridge function pretending to adjust a parameter in the LJ potential both to HNC and KH approximations, to obtain satisfactorily corrected results regarding U-ex, Pv, and mu(ex). Thus, we propose one of the necessary conditions for accurately evaluating thermodynamic quantities by using some approximated OZ theories: it is the proper location of the FR region in radial distribution functions. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.molliq.2015.11.054

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

Ornstein-Zernike (OZ) integral equation theory is known to overestimate the excess internal energy, U-ex, pressure through the virial route, P-v, and excess chemical potential, mu(ex), for one-component Lennard-Jones (LJ) fluids under hypernetted chain (HNC) and Kovalenko-Hirata (KH) approximatons. As one of the bridge correction methods to improve the precision of these thermodynamic quantities, it was shown in our previous paper that the method to apparently adjust sigma parameter in the LJ potential is effective [T. Miyata and Y. Ebato, J. Molec. Liquids. 217, 75 (2016)]. In our previous paper, we evaluated the actual variation in the sigma parameter by using a fitting procedure to molecular dynamics (MD) results. In this article, we propose an alternative method to determine the actual variation in the sigma parameter. The proposed method utilizes a condition that the virial and compressibility pressures coincide with each other. This method can correct OZ theory without a fitting procedure to MD results, and possesses characteristics of keeping a form of HNC and/or KH closure. We calculate the radial distribution function, pressure, excess internal energy, and excess chemical potential for one-component LJ fluids to check the performance of our proposed bridge function. We discuss the precision of these thermodynamic quantities by comparing with MD results. In addition, we also calculate a corrected gas-liquid coexistence curve based on a corrected KH-type closure and compare it with MD results. (C) 2016 Author(s).

DOI： 10.1063/1.4950703

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

The accuracy of both hypernetted chain (HNC) and Kovalenko-Hirata (KH) approximations assumed in an Ornstein-Zernike integral equation theory has been studied in terms of the solvation free energy (SFE) by comparing with molecular dynamics simulation for Lennard-Jones liquid. The Lennard-Jones parameters for the solute, epsilon(u) and sigma(u), were systematically varied. epsilon(u)-dependence of the relative SFE is found to be hardly dependent on the approximations. However, sigma(u)-dependences of the SFE obtained both from HNC and KH approximations considerably differ from those by molecular dynamics simulation. The source of the error in the SFE from both approximations is also discussed. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2014.05.002

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

We report the generation of a nano-scale tubular structure of cellulose molecules (CelNT), through density functional theory (DFT) calculations. When a cellulose IIII (1 0 0) 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

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

We propose the thermodynamic integration along a spatial reaction coordinate using the molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. This method provides a free energy calculation in solution along the reaction coordinate defined by the Cartesian coordinates of the solute atoms. The proposed method is based on the blue moon algorithm which can, in principle, handle any reaction coordinate as far as it is defined by the solute atom positions. In this article, we apply the present method to the complex formation process of the crown ether 18-Crown-6 (18C6) with the potassium ion in an aqueous solution. The separation between the geometric centers of these two molecules is taken to be the reaction coordinate for this system. The potential of mean force (PMF) becomes the maximum at the separation between the molecular centers being similar to 4 angstrom, which can be identified as the free energy barrier in the process of the molecular recognition. In a separation further than the free energy barrier, the PMF is slightly reduced to exhibit a plateau. In the region closer than the free energy barrier, approach of the potassium ion to the center of 18C6 also decreases the PMF. When the potassium ion is accommodated at the center of 18C6, the free energy is lower by -5.7 +/- 0.7 kcal/mol than that at the above mentioned plateau or converged state. By comparing the results with those from the free energy calculation along the coupling parameters obtained in our previous paper [T. Miyata, Y. Ikuta, and F. Hirata, J. Chem. Phys. 133, 044114 (2010)], it is found that the effective interaction in water between 18C6 and the potassium ion vanishes beyond the molecular-center-separation of 10 angstrom. Furthermore, the conformation of 18C6 is found to be significantly changed depending upon the 18C6-K(+) distance. A proper conformational sampling and an accurate solvent treatment are crucial for realizing the accurate PMF, and we believe that the proposed method is useful to evaluate the PMF in a solution. A discussion upon the PMF in terms of the three-dimensional distribution function for the solvent is also presented. (C) 2011 American Institute of Physics. [doi:10.1063/1.3532078]

DOI： 10.1063/1.3532078

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

Although it has been suggested that the tacticity affects the hydrophilicity of poly(N-isopropylacrylamide) (PNiPA), little is known about the physical background of this phenomenon. In this study, we investigated the solubility of the dimer model compounds (DNiPA). The partition coefficient of DNiPA in the two phases of a water/chloroform mixture has indicated that DNiPA with the racemo configuration (r-DNiPA) is more soluble in water than DNiPA with the meso configuration (m-DNiPA). The difference of the hydration free energy between m- and r-DNiPA is estimated to be 1.2 kJ mol(-1). The molecular mechanics (MM) calculations with the GB/SA model have revealed that r-DNiPA in water is more stable by ca. 1 kJ mol(-1) than m-DNiPA, which is in excellent agreement with the experimental result. The MM calculations have also indicated that the intramolecular interaction of m-DNiPA is stronger than that of r-DNiPA, while r-DNiPA is advantageous in terms of the hydration free energy and conformational entropy.

DOI： 10.1021/jp107442h

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

This article proposes a free energy calculation method based on the molecular dynamics simulation combined with the three dimensional reference interaction site model theory. This study employs the free energy perturbation (FEP) and the thermodynamic integration (TDI) along the coupling parameters to control the interaction potential. To illustrate the method, we applied it to a complex formation process in aqueous solutions between a crown ether molecule 18-Crown-6 (18C6) and a potassium ion as one of the simplest model systems. Two coupling parameters were introduced to switch the Lennard-Jones potential and the Coulomb potential separately. We tested two coupling procedures: one is a "sequential-coupling" to couple the Lennard-Jones interaction followed by the Coulomb coupling, and the other is a "mixed-coupling" to couple both the Lennard-Jones and the Coulomb interactions together as much as possible. The sequential-coupling both for FEP and TDI turned out to be accurate and easily handled since it was numerically well-behaved. Furthermore, it was found that the sequential-coupling had relatively small statistical errors. TDI along the mixed-coupling integral path was to be carried out carefully, paying attention to a numerical behavior of the integrand. The present model system exhibited a nonmonotonic behavior in the integrands for TDI along the mixed-coupling integral path and also showed a relatively large statistical error. A coincidence within a statistical error was obtained among the results of the free energy differences evaluated by FEP, TDI with the sequential-coupling, and TDI with the mixed-coupling. The last one is most attractive in terms of the computer power and is accurate enough if one uses a proper set of windows, taking the numerical behavior of the integrands into account. TDI along the sequential-coupling integral path would be the most convenient among the methods we tested, since it seemed to be well-balanced between the computational load and the accuracy. The numerical results reported in this article qualitatively agree with the experimental data for the potassium ion recognition by the 18C6 in aqueous solution. (C) 2010 American Institute of Physics.[doi:10.1063/1.3462276]

DOI： 10.1063/1.3462276

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

A computer docking study has been carried out on the crystal surfaces of cellulose I alpha crystal models for the carbohydrate binding module (CBM) protein of the cellobiohydrolase Cel7A produced by Trichoderma reesei. Binding Free energy maps between the CBM and the crystal Surface were obtained by calculating the noncovalent interactions and the solvation free energy at grid points covering the area of the unit cell dimensions at the crystal surface. The potential maps obtained from grid searches of the hydrophobic (110) crystal surface exhibited two distinct potential wells. These reflected the 2-fold helical symmetry of the cellulose chain and had lower binding energies at the minimum positions than those for the hydrophilic (100) and (010) crystal surfaces. The CBM-cellulose crystal complex models derived from the minimum positions were then subjected to molecular dynamics (MD) simulation Under an explicit solvent system. The (110) complex models exhibited larger affinities at the interface than the (100) and (010) ones. The CBM was more stably bound to the (110) surface when it was placed in all antiparallel orientation with respect to the cellulose fiber axis. In the solvated dynamics state, the Curved (110) Surface resulting from the fiber twist somewhat assisted a complementary fit with the CBM at the interface. In addition to the conventional Generalized Born (GB) method, the three-dimensional reference interaction site model (3D-RISM) theory was adopted to assess a solvent effect for the solvated MD trajectories. Large exothermic values for the noncovalent interactions appeared correlated to and were mostly Compensated by endothermic values for the solvation free energy. These gave total binding free energies of -13 to -28 kcal/mol. Results also suggested that the hydrogen bonding scheme was not essential for Substrate specificity.

DOI： 10.1021/jp908249r

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We have developed an algorithm for sampling the conformational space of large flexible molecules in solution, which combines the molecular dynamics (MD) method and the three-dimensional reference interaction site model (3D-RISM) theory. The solvent-induced force acting on solute atoms was evaluated as the gradient of the solvation free energy with respect to the solute-atom coordinates. To enhance the computation speed, we have applied a multiple timestep algorithm based on the RESPA (Reversible System Propagator Algorithm) to the combined MD/ 3D-RISM method. By virtue of the algorithm, one can choose a longer timestep for renewing the solvent-induced force compared with that of the conformational update. To illustrate the present MD/3D-RISM simulation, we applied the method to a model of acetylacetone in aqueous solution. The multiple timestep algorithm succeeded in enhancing the computation speed by 3.4 times for this model case. Acetylacetone possesses an intramolecular hydrogen-bonding capability between the hydroxyl group and the carbonyl oxygen atom, and the molecule is significantly stabilized due to this hydrogen bond, especially in gas phase. The intramolecular hydrogen bond was kept intact during almost entire course of the MD simulation in gas phase, while in the aqueous solutions the bond is disrupted in a significant number of conformations. This result qualitatively agrees with the behavior on a free energy barrier lying upon the process for rotating a torsional degree of freedom of the hydroxyl group, where it is significantly reduced in aqueous solution by a cancellation between the electrostatic interaction and the solvation free energy. © 2007 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.20844

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：INST CONDENSED MATTER PHYSICS NATL ACAD SCIENCES UKRAINE  

The anomeric equilibrium of D-glucose in aqueous solution was studied by the extended reference interaction site model (XRISM) theory. In this study, all of the rotational degrees of freedom were considered upon the exocyclic hydroxyl and hydroxymethyl groups, namely 729 stereoisomers for each anomer. The free energy differences between the alpha and beta anomers were calculated from partition functions. The XRISM theory predicts that beta-D-glucose is more stable in aqueous solution than alpha-D-glucose, which agrees with an experimental result qualitatively It is found that the solvation free energy stabilizes the beta anomer more preferably than alpha, and that the intramolecular electrostatic energy of the beta anomer in solution is remarkably higher than that of alpha. The beta anomer in aqueous solution would favor an interaction with water molecules through hydrogen bonds, compared to the a anomer.

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

The fabrication of metal-oxide-pillared clay by a simple, environmentally friendly method is reported. The interlayer space within the clay (vermiculite, VMT) is first modified, followed by the intercalation of metal alkoxides dissolved in supercritical CO2 (see Figure), which are then hydrolyzed. Large electrostatic charges on VMT help resist delamination during intercalation and maintain ordered structures after calcination. Basal spacing and porosity are controllable by the intercalation time.

DOI： 10.1002/adma.200400469

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

The energetic heterogeneity effect of a solid surface on the phase behavior of a confined fluid within a narrow cylindrical pore was studied by means of Gibbs Ensemble Monte Carlo (GEMC) and canonical ensemble Monte Carlo (MC) simulations. The energetic heterogeneity was modeled as a local adsorbing site, and all the interactions considered were described by Lennard-Jones (LJ) potentials, i.e. 12-6 and 9-3 type. From the changes in the apparent shapes of isotherms, energetic heterogeneity on the solid surface was found to smear the phase transition region. The energetic heterogeneity of the solid internal surface causes an additive effect to pull the fluid particles toward the solid surface in the entire relative pressure region, leading to higher packing of the fluid particle layered in the vicinity of the pore wall compared with the homogeneous surface case at the same mean fluid density within the pore.

DOI： 10.1080/08927020310001645246

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：KLUWER ACADEMIC PUBL  

DOI： 10.1023/B:JMSC.0000012958.40071.50

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

A new method for the synthesis of pillared clays using supercritical carbon dioxide (scCO(2)) has been developed. This scheme consists of two steps: ( 1) the hydrophobitization of the clay interlayer space, using an organic ion exchange method with interlayer cations in aqueous solution, and ( 2) the intercalation of a metal alkoxide dissolved in scCO(2) followed by hydrolysis with adsorbed water present in the interlayer space. This method is expected to be advantageous in the structural and chemical design of pillared clays by allowing specific tailoring of the organic ions and metal alkoxides used during preparation. In this work, the synthesis of titania-pillared clay using montmorillonite (MNT) and titanium isopropoxide was investigated. Alkyltrimethylammonium cations were used to study the effect of organic ions on the clay structure. Titania pillared MNT were successfully prepared with the presence of hydrophobic interlayer ions, whereas intercalation was not successful on MNT without hydrophobitization of the interlayer space. Nano-sized anatase was observed on the calcined samples and the titania content was related to the hydrophobic nature of the organic ion used. The intercalated samples have both meso- and microporous structures and the microporosity was considered to be a factor related to the variety of organic ion used. An optimised pillared clay sample showed potential as a catalytic adsorbent for toxic volatile organic compounds in air.

DOI： 10.1039/b404584j

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE  

This paper discusses an accurate method of pore size distribution evaluation in boundary regions of micropores and mesopores using the gas adsorption process on the basis of the capillary condensation theory, which is liable to be underestimated with the existing BJH and DH methods. A typical nitrogen adsorption isotherm for highly ordered mesoporous silica, which has cylindrical pores with diameter smaller than 4 nm, is considered to be type IV and it is well known for the steep increase of the amount adsorbed through capillary condensation in the region of the relative pressure P/P-0 smaller than 0.4. In calculating the distribution of the pore size from the change of the amount adsorbed due to capillary condensation, it is important to accurately predict both the multilayer thickness I of the adsorbed nitrogen molecules and the critical radius r(c) where capillary condensation occurs. It is necessary to consider the curvature of the adsorption layer-gas phase interface when predicting the multilayer thickness t of nitrogen adsorbed within the pore of highly ordered mesoporous silica. Revision of the Kelvin equation is also required when rc is to be predicted. While the predicted value of t based on the Broekhoff and de Boer theory is matched well with the value of t which is actually measured using highly ordered mesoporous silica, and the predicted value of rc based on the GTKB-Kelvin-cylindrical equation that has been revised considering the effect of the interfacial curvature on the interfacial tension of the adsorption layer-gas phase interface is matched with the value of rc which is actually measured using highly ordered mesoporous silica. A combination method of the Broekhoff and de Boer equation and the GTKB-Kelvin-cylindrical equation is proposed as a means of accurately evaluating, from the nitrogen adsorption isotherm, the pore size distribution in the highly ordered mesoporous silica in boundary region of micropore and mesopore. The proposed new method of pore size evaluation features high accuracy and offers the convenience of obtaining the pore size distribution without repeated calculations by employing the same algorithm as DH method. The pore size predicted by the Halsey equation and the Kelvin equation of the conventional DH method is about 20% smaller than the pore size predicted by the newly proposed evaluation method. (C) 2003 Elsevier Science (USA). All rights reserved.

DOI： 10.1016/S0021-9797(02)00254-0

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PubMed

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：SOC CHEMICAL ENG JAPAN  

The tracer diffusion of a charged particle in an oppositely charged cubic lattice as a simplest model of charged hydrogel was studied by a Brownian dynamics simulation. The effect of the electrostatic attractive interaction between the tracer particle and the cubic lattice on the self-diffusion coefficient was mainly discussed, when the mesh size of the cubic lattice was sufficiently larger than the diameter of the particle. The charge density of the cubic lattice structure and the electrolyte concentration in the solvent were varied. The electrostatic force acting on the tracer particle was calculated using the potential screened by an electric double layer. The self-diffusion coefficient of the tracer particle significantly decreases as the charge density of the cubic lattice increases, while the increase in the electrolyte concentration in the solvent induces the disappearance of the effect of electrostatic attractive interaction on the self-diffusion coefficient, resulting into the asymptotical behavior to those observed in the non-charged cubic lattice. 2-Order reduction in the self-diffusion coefficient was obtained in this simulation and this shows the applicability of the control of diffusivity of ionic solutes in the swollen hydrogel by means of introducing ionic species covalently into the hydrogels. In the spatial distribution of the probability density of the charged tracer particle, the stochastic path along which the tracer particle tends to move was observed in the charged cubic lattice, which is caused by electrostatic potentials. The reduction of the self-diffusion coefficient in the charged cubic lattice is due to the transient entrapment at the point of local minimum of potential energy inside the stochastic paths.

DOI： 10.1252/jcej.35.640

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

The successful preparation of TiO2-montmorillonite mesoporous composites using intercalation of titanium isopropoxide dissolved in supercritical carbon dioxide involved ion exchange of interlayer cations by hydrophobic cations.

DOI： 10.1039/b202589b

Web of Science

PubMed

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Authorship：Lead author,　Corresponding author  

DOI： 10.1252/kakoronbunshu.27.42

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Language：Japanese   Publisher：The Society of Chemical Engineers, Japan  

The diffusion of polystyrene latex microparticles dispersed in gels formed from worm-like molecular assemblies of surfactant cetyltrimethylammonium-bromide (CTAB) was studied using dynamic light scattering (DLS). The initial relaxation mode of the field correlation function obtained by DLS corresponds to the localized translational displacement of the microparticle entrapped by the gel structure. The frictional coefficient for this localized movement is dominated by the viscosity of the solvent (water), irrespective of CTAB concentration determining the density of cross-links. On the other hand, the final relaxation mode was attributed to the net translational displacement of the microparticle in the gel. The diffusion coefficient for this net displacement differs much from the value evaluated from shear viscosity of the gel. The net displacement was visually illustrated as a step-wise displacement whose rate is dominated by an activation energy determining the average time interval of the step-wise motion. The interval is estimated as 0.2-0.3s assuming that the step-length corresponds to the gel mesh size obtained as the correlation length of the CTAB gel free from the microparticles.

DOI： 10.1252/kakoronbunshu.26.347

CiNii Books

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Other Link： https://jlc.jst.go.jp/DN/JALC/00066768401?from=CiNii

Event date： 2021.12

Language：English   Presentation type：Oral presentation (general)  

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Event date： 2019.10 - 2019.11

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Language：English   Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (invited, special)  

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Language：English   Presentation type：Oral presentation (invited, special)  

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Presentation type：Oral presentation (invited, special)  

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Language：English   Presentation type：Poster presentation  

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