start-ver=1.4
cd-journal=joma
no-vol=129
cd-vols=
no-issue=2
article-no=
start-page=726
end-page=735
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20241231
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Hydronium Ions Are Less Excluded from Hydrophobic Polymer?Water Interfaces than Hydroxide Ions
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The cloud point temperatures of aqueous poly(N-isopropylacrylamide) (PNIPAM) and poly(ethylene) oxide (PEO) solutions were measured from pH 1.0 to pH 13.0 at a constant ionic strength of 100 mM. This ionic strength was reached by mixing the appropriate concentration of NaCl with either HCl or NaOH. The phase transition temperature of both polymers was nearly constant between pH 2.0 and 12.0. However, the introduction of 100 mM HCl (pH 1.0) led to an increase in the cloud point temperature, although this value was still lower than the cloud point temperature in the absence of salt. By contrast, the introduction of 100 mM NaOH (pH 13.0) caused a decrease in the cloud point temperature, both relative to adding 100 mM NaCl and adding no salt. Nuclear magnetic resonance (NMR) studies of these systems were performed below the cloud point temperature, and the chemical shifts closely tracked the corresponding changes in the phase transition temperature. Specifically, the introduction of 100 mM HCl caused the 1H chemical shift to move downfield for the CH resonances from both PNIPAM and PEO, while 100 mM NaOH caused the same resonances to move upfield. Virtually no change in the chemical shift was seen between pH 2.0 and 12.0. These results are consistent with the idea that a sufficient concentration of H3O+ led to polymer swelling compared to Na+, while substituting Cl? with OH? reduced swelling. Finally, classical all-atom molecular dynamics (MD) simulations were performed with a monomer and 5-mer corresponding to PNIPAM. The results correlated closely with the thermodynamic and spectroscopic data. The simulation showed that H3O+ ions more readily accumulated around the amide oxygen moiety on PNIPAM compared with Na+. On the other hand, OH? was more excluded from the polymer surface than Cl?. Taken together, the thermodynamic, spectroscopic, and MD simulation data revealed that H3O+ was less depleted from hydrophobic polymer/water interfaces than any of the monovalent Hofmeister metal cations or even Ca2+ and Mg2+. As such, it should be placed on the far-right side of the cationic Hofmeister series. On the other hand, OH? was excluded from the interface and could be positioned in the anionic Hofmeister series between H2PO4? and SO42?.
en-copyright=
kn-copyright=
en-aut-name=MyersRyan L.
en-aut-sei=Myers
en-aut-mei=Ryan L.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=TairaAoi
en-aut-sei=Taira
en-aut-mei=Aoi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=YanChuanyu
en-aut-sei=Yan
en-aut-mei=Chuanyu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=LeeSeung-Yi
en-aut-sei=Lee
en-aut-mei=Seung-Yi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=WelshLauren K.
en-aut-sei=Welsh
en-aut-mei=Lauren K.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=IaniroPatrick R.
en-aut-sei=Ianiro
en-aut-mei=Patrick R.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=YangTinglu
en-aut-sei=Yang
en-aut-mei=Tinglu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=CremerPaul S.
en-aut-sei=Cremer
en-aut-mei=Paul S.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
affil-num=1
en-affil=Department of Chemistry, The Pennsylvania State University, University Park
kn-affil=
affil-num=2
en-affil=Department of Chemistry, Okayama University
kn-affil=
affil-num=3
en-affil=Department of Chemistry, The Pennsylvania State University, University Park
kn-affil=
affil-num=4
en-affil=Department of Chemistry, The Pennsylvania State University, University Park
kn-affil=
affil-num=5
en-affil=Department of Chemistry, The Pennsylvania State University, University Park
kn-affil=
affil-num=6
en-affil=Department of Chemistry, University of Pittsburgh at Bradford
kn-affil=
affil-num=7
en-affil=Department of Chemistry, The Pennsylvania State University, University Park
kn-affil=
affil-num=8
en-affil=Department of Chemistry, Okayama University
kn-affil=
affil-num=9
en-affil=Department of Chemistry, The Pennsylvania State University, University Park
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=161
cd-vols=
no-issue=21
article-no=
start-page=214501
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20241202
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=The nature of the hydrophobic interaction varies as the solute size increases from methanefs to C60fs
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The hydrophobic interaction, often combined with the hydrophilic or ionic interactions, makes the behavior of aqueous solutions very rich and plays an important role in biological systems. Theoretical and computer simulation studies have shown that the water-mediated force depends strongly on the size and other chemical properties of the solute, but how it changes with these factors remains unclear. We report here a computer simulation study that illustrates how the hydrophobic pair interaction and the entropic and enthalpic terms change with the solute size when the solute?solvent weak attractive interaction is unchanged with the solute size. The nature of the hydrophobic interaction changes qualitatively as the solute size increases from that of methane to that of fullerene. The potential of mean force between small solutes has several well-defined extrema, including the third minimum, whereas the potential of mean force between large solutes has the deep contact minimum and the large free-energy barrier between the contact and the water-bilayer separated configurations. The difference in the potential of mean force is related to the differences in the water density, energy, and hydrogen bond number distributions in the vicinity of the pairs of hydrophobic solutes.
en-copyright=
kn-copyright=
en-aut-name=NaitoHidefumi
en-aut-sei=Naito
en-aut-mei=Hidefumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=2
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=32
cd-vols=
no-issue=10
article-no=
start-page=e4763
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20230925
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2-trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent-dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2?M TFE and urea. As 2?M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse-micelle-like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.
en-copyright=
kn-copyright=
en-aut-name=NakataNoa
en-aut-sei=Nakata
en-aut-mei=Noa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=2
en-affil=Graduate School of Information Science, University of Hyogo
kn-affil=
affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=5
en-affil=Department of Chemistry, Graduate School of Science, Chiba University
kn-affil=
affil-num=6
en-affil=Department of Bio-Science, Nagahama Institute of Bio-Science and Technology
kn-affil=
en-keyword=2,2,2-trifluoroethanol
kn-keyword=2,2,2-trifluoroethanol
en-keyword=cosolvent effects
kn-keyword=cosolvent effects
en-keyword=preferential binding parameter
kn-keyword=preferential binding parameter
en-keyword=protein folding stability
kn-keyword=protein folding stability
en-keyword=urea
kn-keyword=urea
END
start-ver=1.4
cd-journal=joma
no-vol=249
cd-vols=
no-issue=
article-no=
start-page=440
end-page=452
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=2024
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=How do water-mediated interactions and osmotic second virial coefficients vary with particle size?
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=We examine quantitatively the solute-size dependences of the effective interactions between nonpolar solutes in water and in a simple liquid. The potential w(r) of mean force and the osmotic second virial coefficients B are calculated with high accuracy from molecular dynamics simulations. As the solute diameter increases from methane's to C60's with the solute?solute and solute?solvent attractive interaction parameters fixed to those for the methane?methane and methane?water interactions, the first minimum of w(r) lowers from ?1.1 to ?4.7 in units of the thermal energy kT. Correspondingly, the magnitude of B (<0) increases proportional to Ѓ with some power close to 6 or 7, which reinforces the solute-size dependence of B found earlier for a smaller range of [H. Naito, R. Okamoto, T. Sumi and K. Koga, J. Chem. Phys., 2022, 156, 221104]. We also demonstrate that the strength of the attractive interactions between solute and solvent molecules can qualitatively change the characteristics of the effective pair interaction between solute particles, both in water and in a simple liquid. If the solute?solvent attractive force is set to be weaker (stronger) than a threshold, the effective interaction becomes increasingly attractive (repulsive) with increasing solute size.
en-copyright=
kn-copyright=
en-aut-name=NaitoHidefumi
en-aut-sei=Naito
en-aut-mei=Hidefumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=2
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=18
cd-vols=
no-issue=1
article-no=
start-page=347
end-page=354
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20231218
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Close-Packed Ices in Nanopores
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Water molecules in any of the ice polymorphs organize themselves into a perfect four-coordinated hydrogen-bond network at the expense of dense packing. Even at high pressures, there seems to be no way to reconcile the ice rules with the close packing. Here, we report several close-packed ice phases in carbon nanotubes obtained from molecular dynamics simulations of two different water models. Typically they are in plastic states at high temperatures and are transformed into the hydrogen-ordered ice, keeping their close-packed structures at lower temperatures. The close-packed structures of water molecules in carbon nanotubes are identified with those of spheres in a cylinder. We present design principles of hydrogen-ordered, close-packed structures of ice in nanotubes, which suggest many possible dense ice forms with or without nonzero polarization. In fact, some of the simulated ices are found to exhibit ferroelectric ordering upon cooling.
en-copyright=
kn-copyright=
en-aut-name=MochizukiKenji
en-aut-sei=Mochizuki
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=AdachiYuji
en-aut-sei=Adachi
en-aut-mei=Yuji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=Department of Chemistry, Zhejiang University
kn-affil=
affil-num=2
en-affil=Graduate School of Natural Sciences, Okayama University
kn-affil=
affil-num=3
en-affil=Department of Chemistry, Okayama University
kn-affil=
en-keyword=Close-packed ices
kn-keyword=Close-packed ices
en-keyword=Ice nanotubes
kn-keyword=Ice nanotubes
en-keyword=Carbon nanotubes
kn-keyword=Carbon nanotubes
en-keyword=Continuous freezing
kn-keyword=Continuous freezing
en-keyword=Ferroelectricices
kn-keyword=Ferroelectricices
END
start-ver=1.4
cd-journal=joma
no-vol=25
cd-vols=
no-issue=45
article-no=
start-page=31107
end-page=31117
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=2023
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Solvation free energies of alcohols in water: temperature and pressure dependences
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Solvation free energies * of amphiphilic species, methanol and 1,2-hexanediol, are obtained as a function of temperature or pressure based on molecular dynamics simulations combined with efficient free-energy calculation methods. In general, * of an amphiphile can be divided into Image ID:d3cp03799a-t1.gif and Image ID:d3cp03799a-t2.gif, the nonpolar and electrostatic contributions, and the former is further divided into Image ID:d3cp03799a-t3.gif and Image ID:d3cp03799a-t4.gif which are the work of cavity formation process and the free energy change due to weak, attractive interactions between the solute molecule and surrounding solvent molecules. We demonstrate that * of the two amphiphilic solutes can be obtained accurately using a perturbation combining method, which relies on the exact expressions for Image ID:d3cp03799a-t5.gif and Image ID:d3cp03799a-t6.gif and requires no simulations of intermediate systems between the solute with strong, repulsive interactions and the solute with the van der Waals and electrostatic interactions. The decomposition of * gives us several physical insights including that * is an increasing function of T due to Image ID:d3cp03799a-t7.gif, that the contributions of hydrophilic groups to the temperature dependence of * are additive, and that the contribution of the van der Waals attraction to the solvation volume is greater than that of the electrostatic interactions.
en-copyright=
kn-copyright=
en-aut-name=TairaAoi
en-aut-sei=Taira
en-aut-mei=Aoi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=2
en-affil=Graduate School of Information Science, University of Hyogo
kn-affil=
affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=156
cd-vols=
no-issue=22
article-no=
start-page=221104
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220614
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Osmotic second virial coefficients for hydrophobic interactions as a function of solute size
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=To gain quantitative insight into how the overall strength of the hydrophobic interaction varies with the molecular size, we calculate osmotic second virial coefficients B for hydrophobic spherical molecules of different diameters in water based on molecular simulation with corrections to the finite-size and finite-concentration effects. It is shown that B?(<0) changes by two orders of magnitude greater as increases twofold and its solute-size dependence is best fit by a power law B with the exponent ? 6, which contrasts with the cubic power law that the second virial coefficients of gases obey. It is also found that values of B for the solutes in a nonpolar solvent are positive but they obey the same power law as in water. A thermodynamic identity for B derived earlier [K. Koga, V. Holten, and B. Widom, J. Phys. Chem. B 119, 13391 (2015)] indicates that if B is asymptotically proportional to a power of , the exponent must be equal to or greater than 6.
en-copyright=
kn-copyright=
en-aut-name=NaitoHidefumi
en-aut-sei=Naito
en-aut-mei=Hidefumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=2
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=125
cd-vols=
no-issue=46
article-no=
start-page=12820
end-page=12831
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20211110
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Theory of Gas Solubility and Hydrophobic Interaction in Aqueous Electrolyte Solutions
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Ion-specific effects on the solubility of nonpolar solutes and on the solute?solute hydrophobic interaction in aqueous electrolyte solutions are studied on the basis of a continuum theory that incorporates the excluded volume of the molecules using the four-component (water, cations, anions, and solutes) Boubl??k?Mansoori?Carnahan?Starling?Leland model and ion hydration (electrostriction) using the Born model. We examine how the ordering of ions in the salt effect on the solubility as measured by the Sechenov coefficient KS changes with varying sizes of ions and solutes. Our calculation reproduces the general trend of experimentally measured KS and also provides insight into the irregular behavior of KS for lithium ion. The correlation between KS and the salt effect on the hydrophobic interaction that has been pointed out earlier is accounted for by an explicit connection between KS and the salt-enhanced-association coefficient CI in the expansion of the second osmotic virial coefficient B(ns) = B(0) ? CIns + ??? in powers of the salt density ns at fixed pressure and temperature. The quadratic relation is derived for ions and solutes that are not very large.
en-copyright=
kn-copyright=
en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=125
cd-vols=
no-issue=23
article-no=
start-page=6296
end-page=6305
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=202168
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=A general trend of the salting-out effect on hydrophobic solutes in aqueous solution is that the smaller the size of a dissolved ion, the larger the effect of reducing the solubility of a hydrophobe. An exception is that Li+, the smallest in alkali metal ions, has a notably weaker effect than Na+. To understand the reversed order in the cation series, we performed molecular dynamics simulations of aqueous solutions of salt ions and calculated the Setschenow coefficient of methane with the ionic radius of either a cation or an anion varied in a wide range. It is confirmed that the Setschenow coefficient is correlated with the packing fraction of salt solution, as observed in earlier studies, and also correlated with the partial molar volume of an ion. Analyses of correlation function integrals, packing fractions of solvation spheres, and orientations of water molecules surrounding an ion reveal the key differences in microscopic properties between the cation and anion series, which give rise to the reversed order in the cation series of the partial molar volumes of ions and ultimately that of the Setschenow coefficients.
en-copyright=
kn-copyright=
en-aut-name=KatsutoHiroyuki
en-aut-sei=Katsuto
en-aut-mei=Hiroyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=153
cd-vols=
no-issue=11
article-no=
start-page=114501
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200916
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure and phase behavior of high-density ice from molecular-dynamics simulations with the ReaxFF potential
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=We report a molecular dynamics simulation study of dense ice modeled by the reactive force field (ReaxFF) potential, focusing on the possibility of phase changes between crystalline and plastic phases as observed in earlier simulation studies with rigid water models. It is demonstrated that the present model system exhibits phase transitions, or crossovers, among ice VII and two plastic ices with face-centered cubic (fcc) and body-centered cubic (bcc) lattice structures. The phase diagram derived from the ReaxFF potential is different from those of the rigid water models in that the bcc plastic phase lies on the high-pressure side of ice VII and does the fcc plastic phase on the low-pressure side of ice VII. The phase boundary between the fcc and bcc plastic phases on the pressure, temperature plane extends to the high-temperature region from the triple point of ice VII, fcc plastic, and bcc plastic phases. Proton hopping, i.e., delocalization of a proton, along between two neighboring oxygen atoms in dense ice is observed for the ReaxFF potential but only at pressures and temperatures both much higher than those at which ice VII?plastic ice transitions are observed.
en-copyright=
kn-copyright=
en-aut-name=AdachiYuji
en-aut-sei=Adachi
en-aut-mei=Yuji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=Graduate School of Natural Sciences, Okayama University
kn-affil=
affil-num=2
en-affil=2Department of Chemistry, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=9
cd-vols=
no-issue=
article-no=
start-page=5186
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=2019326
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Theoretical analysis on thermodynamic stability of chignolin
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann's hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small, designed protein, chignolin. The resulting free energy profile quantitatively agreed with the molecular dynamics simulations. Decomposition of the free energy profile indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with the site-directed mutagenesis and calorimetry experiments for globular proteins with hydrophobic interior cores.
en-copyright=
kn-copyright=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil= Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil= Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=150
cd-vols=
no-issue=16
article-no=
start-page=164701
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=20190424
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Three-phase equilibria in density-functional theory: Interfacial tensions
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= A mean-field density-functional model for three-phase equilibria in fluids (or other soft condensed matter) with two spatially varying densities is analyzed analytically and numerically. The interfacial tension between any two out of three thermodynamically coexisting phases is found to be captured by a surprisingly simple analytic expression that has a geometric interpretation in the space of the two densities. The analytic expression is based on arguments involving symmetries and invariances. It is supported by numerical computations of high precision, and it agrees with earlier conjectures obtained for special cases in the same model. An application is presented to three-phase equilibria in the vicinity of a tricritical point. Using the interfacial tension expression and employing the field variables compatible with tricritical point scaling, the expected mean-field critical exponent is derived for the vanishing of the critical interfacial tension as a function of the deviation of the noncritical interfacial tension from its limiting value, upon approach to a critical endpoint in the phase diagram. The analytic results are again confirmed by numerical computations of high precision.
en-copyright=
kn-copyright=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=IndekeuJoseph O.
en-aut-sei=Indekeu
en-aut-mei=Joseph O.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Institute for Theoretical Physics, KU Leuven
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=39
cd-vols=
no-issue=4
article-no=
start-page=202
end-page=217
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=20171108
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= Recently, we proposed a reference]modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard]sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard]sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water. We demonstrate that the RMDFT has high predictive ability for the temperature and pressure dependences of the SFE for small solute molecules in water when the optimal reference hard]sphere diameter determined for each thermodynamic condition is used. We also apply the RMDFT to investigate the temperature and pressure dependences of the thermodynamic stability of an artificial small protein, chignolin, and discuss the mechanism of high]temperature and high]pressure unfolding of the protein. ? 2017 Wiley Periodicals, Inc.
en-copyright=
kn-copyright=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=Mochizuki Kenji
en-aut-sei=Mochizuki
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
affil-num=1
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=2
en-affil=Co-Design Team, FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science
kn-affil=
affil-num=3
en-affil= Department of Physics, Keio University
kn-affil=
affil-num=4
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=5
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
en-keyword=3D-RISM theory
kn-keyword=3D-RISM theory
en-keyword=chignolin
kn-keyword=chignolin
en-keyword=classical density functional theory
kn-keyword=classical density functional theory
en-keyword=high-pressure unfolding
kn-keyword=high-pressure unfolding
en-keyword=hydrophobic solute
kn-keyword=hydrophobic solute
en-keyword=protein
kn-keyword=protein
en-keyword=temperature and pressure dependences of solvation free energy
kn-keyword=temperature and pressure dependences of solvation free energy
en-keyword=thermal denaturation
kn-keyword=thermal denaturation
END
start-ver=1.4
cd-journal=joma
no-vol=144
cd-vols=
no-issue=22
article-no=
start-page=224104
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2016
dt-pub=20160610
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.
en-copyright=
kn-copyright=
en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
affil-num=2
en-affil=Co-Design Team, Exascale Computing Project, RIKEN Advanced Institute for Computational Science
kn-affil=
affil-num=3
en-affil=Co-Design Team, Exascale Computing Project, RIKEN Advanced Institute for Computational Science
kn-affil=
affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=112
cd-vols=
no-issue=27
article-no=
start-page=8221
end-page=8226
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150707
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Solid-liquid critical behavior of water in nanopores
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Nanoconfined liquid water can transform into low-dimensional ices whose crystalline structures are dissimilar to any bulk ices and whose melting point may significantly rise with reducing the pore size, as revealed by computer simulation and confirmed by experiment. One of the intriguing, and as yet unresolved, questions concerns the observation that the liquid water may transform into a low-dimensional ice either via a first-order phase change or without any discontinuity in thermodynamic and dynamic properties, which suggests the existence of solid?liquid critical points in this class of
nanoconfined systems. Here we explore the phase behavior of a model of water in carbon nanotubes in the temperature?pressure?diameter space by molecular dynamics simulation and provide unambiguous evidence to support solid?liquid critical phenomena of nanoconfined water. Solid?liquid first-order phase boundaries are
determined by tracing spontaneous phase separation at various temperatures. All of the boundaries eventually cease to exist at the critical points and there appear loci of response function maxima, or the Widom lines, extending to the supercritical region. The finite-size scaling analysis of the density distribution supports the
presence of both first-order and continuous phase changes between solid and liquid. At around the Widom line, there are microscopic domains of two phases, and continuous solid?liquid phase changes
occur in such a way that the domains of one phase grow and those of the other evanesce as the thermodynamic state departs from the Widom line.
en-copyright=
kn-copyright=
en-aut-name=MochizukiKenji
en-aut-sei=Mochizuki
en-aut-mei=Kenji
kn-aut-name=]
kn-aut-sei=]
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=bꌤY
kn-aut-sei=b
kn-aut-mei=Y
aut-affil-num=2
ORCID=
affil-num=1
en-affil=
kn-affil=Rww@RȊw
affil-num=2
en-affil=
kn-affil=Rww@RȊw
en-keyword=water
kn-keyword=water
en-keyword=solid?liquid critical point
kn-keyword=solid?liquid critical point
en-keyword=carbon nanotube
kn-keyword=carbon nanotube
en-keyword=ice
kn-keyword=ice
en-keyword=Widom line
kn-keyword=Widom line
END
start-ver=1.4
cd-journal=joma
no-vol=104
cd-vols=
no-issue=22-24
article-no=
start-page=3469
end-page=3477
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2006
dt-pub=20061001
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Line adsorption in a mean-field density functional model
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Recent ideas about the analog for a three-phase contact line of the Gibbs adsorption equation for interfaces are illustrated in a mean-field density-functional model. With $d?tau$ the infinitesimal change in the line tension $?tau$ that accompanies the infinitesimal changes $d?mu_i$ in the thermodynamic field variables $?mu_i$ and with $?Lambda_i$ the line adsorptions, the sum $d?tau + ?Sigma ?Lambda_i d?mu_i$, unlike its surface analog, is not 0. An equivalent of this sum in the model system is evaluated numerically and analytically. A general line adsorption equation, which the model results illustrate, is derived.
en-copyright=
kn-copyright=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=WidomBenjamin
en-aut-sei=Widom
en-aut-mei=Benjamin
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=
kn-affil=Okayama University
affil-num=2
en-affil=
kn-affil=Cornell University
en-keyword=line tension
kn-keyword=line tension
en-keyword=line adsorption
kn-keyword=line adsorption
en-keyword=adsorption equation
kn-keyword=adsorption equation
en-keyword=three-phase equilibria
kn-keyword=three-phase equilibria
en-keyword=partial wetting
kn-keyword=partial wetting
END
start-ver=1.4
cd-journal=joma
no-vol=123
cd-vols=
no-issue=9
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2005
dt-pub=20050901
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Formation of ice nanotube with hydrophobic guests inside carbon nanotube
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=A composite ice nanotube inside a carbon nanotube has been explored by molecular dynamics and grandcanonical Monte Carlo simulations. It is made from an octagonal ice nanotube whose
hollow space contains hydrophobic guest molecules such as neon, argon, and methane. It is shown that the attractive interaction of the guest molecules stabilizes the ice nanotube. The guest occupancy of the hollow space is calculated by the same method as applied to clathrate hydrates.
en-copyright=
kn-copyright=
en-aut-name=TanakaHideki
en-aut-sei=Tanaka
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
en-keyword=ice nanotubes
kn-keyword=ice nanotubes
en-keyword=carbon nanotubes
kn-keyword=carbon nanotubes
END
start-ver=1.4
cd-journal=joma
no-vol=127
cd-vols=
no-issue=6
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2007
dt-pub=20070814
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Line and boundary tensions on approach to the wetting transition
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=A mean-field density-functional model often used in the past in the study of line and boundary tensions at wetting and prewetting transitions is reanalyzed by extensive numerical calculations, approaching the wetting transition much more closely than had previously been possible. The results are what are now believed to be definitive for the model. They include strong numerical evidence for the presence of the logarithmic factors predicted by theory both in the mode of approach of the prewetting line to the triple-point line at the point of the first-order wetting transition and in the line tension itself on approach to that point. It is also demonstrated with convincing numerical precision that the boundary tension on the prewetting line and the line tension on the triple-point line have a common limiting value at the wetting transition, again as predicted by theory. As a by product of the calculations, in the model's symmetric three-phase state, far from wetting, it is found that certain properties of the model's line tension and densities are almost surely given by simple numbers arising from the symmetries, but proving that these are exact for the model remains a challenge to analytical theory.
en-copyright=
kn-copyright=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=WidomB.
en-aut-sei=Widom
en-aut-mei=B.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Baker Laboratory, Cornell University
en-keyword=SURFACE PHASES
kn-keyword=SURFACE PHASES
en-keyword=FLUID PHASES
kn-keyword=FLUID PHASES
en-keyword=SUBSTRATE
kn-keyword=SUBSTRATE
en-keyword=ADSORPTION
kn-keyword=ADSORPTION
en-keyword=INTERFACE
kn-keyword=INTERFACE
en-keyword=CONTACT
kn-keyword=CONTACT
en-keyword=MODEL
kn-keyword=MODEL
en-keyword=ICE
kn-keyword=ICE
END
start-ver=1.4
cd-journal=joma
no-vol=124
cd-vols=
no-issue=13
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2006
dt-pub=20060407
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Close-packed structures and phase diagram of soft spheres in cylindrical pores
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=It is shown for a model system consisting of spherical particles confined in cylindrical pores that the first ten close-packed phases are in one-to-one correspondence with the first ten ways of folding a triangular lattice, each being characterized by a roll-up vector like the single-walled carbon nanotube. Phase diagrams in pressure-diameter and temperature-diameter planes are obtained by inherent-structure calculation and molecular dynamics simulation. The phase boundaries dividing two adjacent phases are infinitely sharp in the low-temperature limit but are blurred as temperature is increased. Existence of such phase boundaries explains rich, diameter-sensitive phase behavior unique for cylindrically confined systems.
en-copyright=
kn-copyright=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=TanakaHideki
en-aut-sei=Tanaka
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
en-keyword=WALLED CARBON NANOTUBES
kn-keyword=WALLED CARBON NANOTUBES
en-keyword=NANOCAPILLARITY
kn-keyword=NANOCAPILLARITY
en-keyword=MICROTUBULES
kn-keyword=MICROTUBULES
en-keyword=CAPILLARITY
kn-keyword=CAPILLARITY
en-keyword=CRYSTALS
kn-keyword=CRYSTALS
END
start-ver=1.4
cd-journal=joma
no-vol=122
cd-vols=
no-issue=10
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2005
dt-pub=20050308
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Phase diagram of water between hydrophobic surfaces
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Molecular dynamics simulations demonstrate that there are at least two classes of quasi-two-dimensional solid water into which liquid water confined between hydrophobic surfaces freezes spontaneously and whose hydrogen-bond networks are as fully connected as those of bulk ice. One of them is the monolayer ice and the other is the bilayer solid which takes either a crystalline or an amorphous form. Here we present the phase transformations among liquid, bilayer amorphous (or crystalline) ice, and monolayer ice phases at various thermodynamic conditions, then determine curves of melting, freezing, and solid-solid structural change on the isostress planes where temperature and intersurface distance are variable, and finally we propose a phase diagram of the confined water in the temperature-pressure-distance space.
en-copyright=
kn-copyright=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=TanakaHideki
en-aut-sei=Tanaka
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Okayama University
en-keyword=MOLECULAR-DYNAMICS SIMULATION
kn-keyword=MOLECULAR-DYNAMICS SIMULATION
en-keyword=CONFINED WATER
kn-keyword=CONFINED WATER
en-keyword=LIQUID WATER
kn-keyword=LIQUID WATER
en-keyword=SOLVATION FORCES; CARBON NANOTUBES
kn-keyword=SOLVATION FORCES; CARBON NANOTUBES
en-keyword=BILAYER ICE
kn-keyword=BILAYER ICE
en-keyword=EQUILIBRIA
kn-keyword=EQUILIBRIA
en-keyword=TRANSITION
kn-keyword=TRANSITION
en-keyword=WALLS
kn-keyword=WALLS
en-keyword=INTERFACE
kn-keyword=INTERFACE
END
start-ver=1.4
cd-journal=joma
no-vol=127
cd-vols=
no-issue=8
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2007
dt-pub=20070828
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Phase equilibria and interfacial tension of fluids confined in narrow pores
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Correlation between phase behaviors of a Lennard-Jones fluid in and outside a pore is examined over wide thermodynamic conditions by grand canonical Monte Carlo simulations. A pressure tensor component of the confined fluid, a variable controllable in simulation but usually uncontrollable in experiment, is related with the pressure of a bulk homogeneous system in equilibrium with the confined system. Effects of the pore dimensionality, size, and attractive potential on the correlations between thermodynamic properties of the confined and bulk systems are clarified. A fluid-wall interfacial tension defined as an excess grand potential is evaluated as a function of the pore size. It is found that the tension decreases linearly with the inverse of the pore diameter or width.
en-copyright=
kn-copyright=
en-aut-name=HamadaYoshinobu
en-aut-sei=Hamada
en-aut-mei=Yoshinobu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=TanakaHideki
en-aut-sei=Tanaka
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=3
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
en-keyword=MONTE-CARLO-SIMULATION
kn-keyword=MONTE-CARLO-SIMULATION
en-keyword=CARBON NANOTUBES
kn-keyword=CARBON NANOTUBES
en-keyword=WATER
kn-keyword=WATER
en-keyword=TRANSITION
kn-keyword=TRANSITION
en-keyword=NANOSPACES
kn-keyword=NANOSPACES
en-keyword=ADSORPTION
kn-keyword=ADSORPTION
en-keyword=NANOPORES
kn-keyword=NANOPORES
en-keyword=SURFACE
kn-keyword=SURFACE
en-keyword=LIQUID
kn-keyword=LIQUID
en-keyword=WALLS
kn-keyword=WALLS
END
start-ver=1.4
cd-journal=joma
no-vol=121
cd-vols=
no-issue=15
article-no=
start-page=7304
end-page=7312
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2004
dt-pub=20041015
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Hydrophobic effect in the pressure-temperature plane
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The free energy of the hydrophobic hydration and the strength of the solvent-mediated attraction between hydrophobic solute molecules are calculated in the pressure-temperature plane. This is done in the framework of an exactly soluble model that is an extension of the lattice model proposed by Kolomeisky and Widom [A. B. Kolomeisky and B. Widom, Faraday Discuss. 112, 81 (1999)]. The model takes into account both the mechanism of the hydrophobic effect dominant at low temperatures and the opposite mechanism of solvation appearing at high temperatures and has the pressure as a second thermodynamic variable. With this model, two boundaries are identified in the pressure-temperature plane: the first one within which the solubility, or the Ostwald absorption coefficient, decreases with increasing temperature at fixed pressure and the second one within which the strength of solvent-mediated attraction increases with increasing temperature. The two are nearly linear and parallel to each other, and the second boundary lies in the low-temperature and low-pressure side of the first boundary. It is found that a single, near-linear relation between the hydration free energy and the strength of the hydrophobic attraction holds over the entire area within the second boundary in the pressure-temperature plane. (C) 2004 American Institute of Physics.
en-copyright=
kn-copyright=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
en-keyword=FREE-ENERGY
kn-keyword=FREE-ENERGY
en-keyword=AQUEOUS ARGON
kn-keyword=AQUEOUS ARGON
en-keyword=DEPENDENCE
kn-keyword=DEPENDENCE
en-keyword=WATER
kn-keyword=WATER
en-keyword=HYDRATION
kn-keyword=HYDRATION
en-keyword=ENTROPY
kn-keyword=ENTROPY
en-keyword=MODEL
kn-keyword=MODEL
en-keyword=DENATURATION
kn-keyword=DENATURATION
en-keyword=SIMULATIONS
kn-keyword=SIMULATIONS
en-keyword=ATTRACTION
kn-keyword=ATTRACTION
END
start-ver=1.4
cd-journal=joma
no-vol=127
cd-vols=
no-issue=4
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2007
dt-pub=20070728
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=On the thermodynamic stability of hydrogen clathrate hydrates
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The cage occupancy of hydrogen clathrate hydrate has been examined by grand canonical Monte Carlo (GCMC) simulations for wide ranges of temperature and pressure. The simulations are carried out with a fixed number of water molecules and a fixed chemical potential of the guest species so that hydrogen molecules can be created or annihilated in the clathrate. Two types of the GCMC simulations are performed; in one the volume of the clathrate is fixed and in the other it is allowed to adjust itself under a preset pressure so as to take account of compression by a hydrostatic pressure and expansion due to multiple cage occupancy. It is found that the smaller cage in structure II is practically incapable of accommodating more than a single guest molecule even at pressures as high as 500 MPa, which agrees with the recent experimental investigations. The larger cage is found to encapsulate at most 4 hydrogen molecules, but its occupancy is dependent significantly on the pressure of hydrogen.
en-copyright=
kn-copyright=
en-aut-name=KatsumasaKeisuke
en-aut-sei=Katsumasa
en-aut-mei=Keisuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=TanakaHideki
en-aut-sei=Tanaka
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=3
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
en-keyword=OCCUPANCY
kn-keyword=OCCUPANCY
en-keyword=CLUSTERS
kn-keyword=CLUSTERS
en-keyword=STORAGE
kn-keyword=STORAGE
en-keyword=CAGES
kn-keyword=CAGES
en-keyword=WATER
kn-keyword=WATER
END
start-ver=1.4
cd-journal=joma
no-vol=122
cd-vols=
no-issue=7
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2005
dt-pub=20050215
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=On the thermodynamic stability and structural transition of clathrate hydrates
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Gas mixtures of methane and ethane form structure II clathrate hydrates despite the fact that each of pure methane and pure ethane gases forms the structure I hydrate. Optimization of the interaction potential parameters for methane and ethane is attempted so as to reproduce the dissociation pressures of each simple hydrate containing either methane or ethane alone. An account for the structural transitions between type I and type II hydrates upon changing the mole fraction of the gas mixture is given on the basis of the van der Waals and Platteeuw theory with these optimized potentials. Cage occupancies of the two kinds of hydrates are also calculated as functions of the mole fraction at the dissociation pressure and at a fixed pressure well above the dissociation pressure.
en-copyright=
kn-copyright=
en-aut-name=KoyamaYuji
en-aut-sei=Koyama
en-aut-mei=Yuji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=TanakaHideki
en-aut-sei=Tanaka
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=3
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
en-keyword=STRUCTURE-II
kn-keyword=STRUCTURE-II
en-keyword=POTENTIAL FUNCTIONS
kn-keyword=POTENTIAL FUNCTIONS
en-keyword=ETHANE
kn-keyword=ETHANE
en-keyword=METHANE
kn-keyword=METHANE
en-keyword=GAS
kn-keyword=GAS
en-keyword=MOLECULES
kn-keyword=MOLECULES
en-keyword=MIXTURES
kn-keyword=MIXTURES
en-keyword=PROPANE
kn-keyword=PROPANE
en-keyword=WATER
kn-keyword=WATER
END
start-ver=1.4
cd-journal=joma
no-vol=121
cd-vols=
no-issue=11
article-no=
start-page=5488
end-page=5493
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2004
dt-pub=20040915
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=On the thermodynamic stability of clathrate hydrates IV: Double occupancy of cages
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=We have extended the van der Waals and Platteeuw theory to treat multiple occupancy of a single cage of clathrate hydrates, which has not been taken into account in the original theory but has been experimentally confirmed as a real entity. We propose a simple way to calculate the free energy of multiple cage occupancy and apply it to argon clathrate structure II in which a larger cage can be occupied by two argon atoms. The chemical potential of argon is calculated treating it as an imperfect gas, which is crucial to predict accurate pressure dependence of double occupancy expected at high pressure. It is found that double occupancy dominates over single occupancy when the guest pressure in equilibrium with the clathrate hydrate exceeds 270 MPa. (C) 2004 American Institute of Physics.
en-copyright=
kn-copyright=
en-aut-name=TanakaHideki
en-aut-sei=Tanaka
en-aut-mei=Hideki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=NakatsukaTakeharu
en-aut-sei=Nakatsuka
en-aut-mei=Takeharu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
affil-num=1
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=2
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
affil-num=3
en-affil=
kn-affil=Department of Chemistry, Faculty of Science, Okayama University
en-keyword=RAMAN-SCATTERING
kn-keyword=RAMAN-SCATTERING
en-keyword=HIGH-PRESSURES
kn-keyword=HIGH-PRESSURES
en-keyword=LIQUID WATER
kn-keyword=LIQUID WATER
en-keyword=AR HYDRATE
kn-keyword=AR HYDRATE
en-keyword=MOLECULES
kn-keyword=MOLECULES
END