Hierarchical aggregation in a complex fluid; The Role of isomeric interconversion

Massey, D.*; Williams, C. D.*; Mu, J.*; Masters, A. J.*; Motokawa, Ryuhei; Aoyagi, Noboru; Ueda, Yuki; Antonio, M. R.*

Journal of Physical Chemistry B, 127(9), p.2052 - 2065, 2023/03

https://doi.org/10.1021/acs.jpcb.2c07527

Understanding competition of polyalcohol dehydration reactions in hot water

Chang, Y. L.*; Sasaki, Takehiko*; Ribas-Ario, J.*; Machida, Masahiko; Shiga, Motoyuki

Journal of Physical Chemistry B, 123(7), p.1662 - 1671, 2019/02

https://doi.org/10.1021/acs.jpcb.8b11615

Dehydration of biomass-derived polyalcohols has recently drawn attention in green chemistry as a prototype of selective reactions controllable in hot water or hot carbonated water, without any use of organic solvents or metal catalysts. Here, we report a free-energy analysis based on first-principles metadynamics and blue-moon ensemble simulations to understand the mechanism of competing intramolecular dehydration reactions of 1,2,5-pentanetriol in hot acidic water. The simulations consistently predict that the most dominant mechanism is the proton-assisted S2 process, where the protonation of the hydroxyl group by water and the C-O bond breaking and formation occur in a single step. The detailed mechanism found from the simulations shows how the reaction paths are selective in hot water and why the reaction rates are accelerated in acidic environments, thus giving a clear explanation of experimental findings for a broad class of competing dehydration processes of polyalcohols.

Nanoscopic structural investigation of physically cross-linked nanogels formed from self-associating polymers

Sekine, Yurina; Endo, Hitoshi*; Iwase, Hiroki*; Takeda, Shigeo*; Mukai, Sadaatsu*; Fukazawa, Hiroshi; Littrell, K. C.*; Sasaki, Yoshihiro*; Akiyoshi, Kazunari*

Journal of Physical Chemistry B, 120(46), p.11996 - 12002, 2016/11

https://doi.org/10.1021/acs.jpcb.6b06795

The detailed structure of a nanogel formed by self-association of cholesterol-bearing pullulans (CHP) was determined by contrast variation small-angle neutron scattering. The decomposition of scattering intensities into partial scattering functions of each CHP nanogel component, i.e., pullulan, cholesterol, and the cross-term between the pullulan and the cholesterol allows us to investigate the internal structure of the nanogel. The effective spherical radius of the skeleton formed by pullulan chains was found to be about 8.1 nm. In the CHP nanogel, there are about 19 cross-linking points where a cross-linking point is formed by aggregation of trimer cholesterol molecules with the spatially inhomogeneous distribution of the mass fractal dimension of 2.6. The average radius of the partial chains can also be determined to be 1.7 nm. As the result, the complex structure of the nanogels is coherently revealed at the nanoscopical level.

Comparative molecular dynamics study on tri--butyl phosphate in organic and aqueous environments and its relevance to nuclear extraction processes

Mu, J.*; Motokawa, Ryuhei; Williams, C. D.*; Akutsu, Kazuhiro*; Nishitsuji, Shotaro*; Masters, A. J.*

Journal of Physical Chemistry B, 120(23), p.5183 - 5193, 2016/06

https://doi.org/10.1021/acs.jpcb.6b00781

Dissociation free-energy profiles of specific and nonspecific DNA-protein complexes

Yonetani, Yoshiteru; Kono, Hidetoshi

Journal of Physical Chemistry B, 117(25), p.7535 - 7545, 2013/06

https://doi.org/10.1021/jp402664w

Self-assembly process of peptide amphiphile worm-like micelles

Shimada, Tomoko*; Sakamoto, Naoki*; Motokawa, Ryuhei; Koizumi, Satoshi*; Tirrell, M.*

Journal of Physical Chemistry B, 116(1), p.240 - 243, 2012/01

https://doi.org/10.1021/jp209105z

Determination of structural parameters of protein-containing reverse micellar solution by near-infrared absorption spectroscopy

Murakami, Hiroshi; Nishi, Takaki*; Toyota, Yuji*

Journal of Physical Chemistry B, 115(19), p.5877 - 5885, 2011/04

https://doi.org/10.1021/jp111852s

We present a method based on near-infrared absorption spectroscopy of the OH stretching vibration band of water around 3400 cm to examine if the aqueous cavity size of a protein-unfilled reverse micelle is affected by solubilization of protein, and it has been found for AOT (= bis (2-ethylhexyl) sulfosuccinate) reverse micellar solution with myoglobin that it does not change before and after solubilization of the protein in the water-to-surfactant molar ratio () from 2 to 18, that is, the values of the protein-filled and unfilled reverse micelles are the same as that of the reverse micellar solution regardless of size relation between the aqueous cavity of the unfilled reverse micelle and the protein. On the basis of this experimental fact, we propose a model to determine the structural parameters of protein-filled reverse micelles, such as the aqueous cavity radius and the aggregation number of surfactant molecules constituting the micelle, and the molar concentration of the unfilled reverse micelle that exists with the protein-filled reverse micelle in the reverse micellar solution, and derive their values for AOT reverse micellar solution with myoglobin in the range from 2 to 24. On the other hand, circular dichroism measurements and UV-visible absorption spectroscopy of myoglobin/AOT reverse micellar solution and myoglobin/AOT aqueous solution were carried out in order to examine the conformational state of myoglobin in the reverse micellar solution. These experimental results lead to the conclusion that myoglobin is located in the aqueous cavity of the reverse micelle, although the conformational state of the protein is to some extent distorted because of the interaction with AOT compared with that of native myoglobin. Finally, it is suggested that the proposed model is appropriate for reverse micellar solution with a hydrophilic protein molecule that is located in the aqueous cavity of the reverse micelle.

Anisotropic swelling behavior of the cornea

Matsuura, Toyoaki*; Ikeda, Hitoe*; Idota, Naokazu*; Motokawa, Ryuhei; Hara, Yoshiaki*; Annaka, Masahiko*

Journal of Physical Chemistry B, 113(51), p.16314 - 16322, 2009/12

https://doi.org/10.1021/jp907232h

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline Staphylococcal nuclease

Jochi, Yasumasa*; Nakagawa, Hiroshi; Kataoka, Mikio; Kitao, Akio*

Journal of Physical Chemistry B, 112(11), p.3522 - 3528, 2008/03

https://doi.org/10.1021/jp710039p

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K. In a full hydration state (hydration ratio in weight, h = 0.49), gaps are fully filled with water molecules, whereas only crystal waters are included in a minimal hydration state (h = 0.09). The inflection of the atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions, which are exposed to water, is much greater than in other regions in the full hydration state, but the mobility of the corresponding regions are relatively restricted in the minimal hydration state by inter-molecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is one order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water, and act as a lubricant for protein dynamics. In contrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein, restricting the fluctuation of these water molecules to the level of the protein. Thus, inter-molecular interaction and solvent mobility are important to understand the glass-like transition in proteins.

Reaction between diiodide anion radicals in ionic liquids

Takahashi, Kenji*; Sakai, Shingo*; Tezuka, Hiroaki*; Hiejima, Yusuke*; Katsumura, Yosuke; Watanabe, Masayoshi*

Journal of Physical Chemistry B, 111(18), p.4807 - 4811, 2007/05

https://doi.org/10.1021/jp0671087