Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations

被引:1
|
作者
Higuchi, Yuji [1 ]
Abu Saleh, Md. [2 ]
Anada, Takahisa [2 ,3 ]
Tanaka, Masaru [2 ,3 ]
Hishida, Mafumi [4 ]
机构
[1] Kyushu Univ, Res Inst Informat Technol, Fukuoka 8190395, Japan
[2] Kyushu Univ, Grad Sch Engn, Dept Appl Chem, Fukuoka 8190395, Japan
[3] Kyushu Univ, Inst Mat Chem & Engn, Fukuoka 8190395, Japan
[4] Tokyo Univ Sci, Fac Sci, Dept Chem, Tokyo 1628601, Japan
基金
日本学术振兴会;
关键词
HYDROGEN-BONDS; LIQUID WATER; PROTEIN; HYDRATION; MECHANISM; DFTB3; SHELL;
D O I
10.1021/acs.jpcb.3c08470
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.
引用
收藏
页码:5008 / 5017
页数:10
相关论文
共 50 条
  • [21] Molecular Dynamics Simulations of Water Sorption in a Perfluorosulfonic Acid Membrane
    Daly, Kevin B.
    Benziger, Jay B.
    Debenedetti, Pablo G.
    Panagiotopoulos, Athanassios Z.
    JOURNAL OF PHYSICAL CHEMISTRY B, 2013, 117 (41) : 12649 - 12660
  • [22] Molecular Dynamics Simulations of Water Structure and Diffusion in Silica Nanopores
    Bourg, Ian C.
    Steefel, Carl I.
    JOURNAL OF PHYSICAL CHEMISTRY C, 2012, 116 (21) : 11556 - 11564
  • [23] Structure of Hexafluoroisopropanol-Water Mixtures by Molecular Dynamics Simulations
    Yamaguchi, Toshio
    Imura, Shinya
    Kai, Tadashi
    Yoshida, Koji
    ZEITSCHRIFT FUR NATURFORSCHUNG SECTION A-A JOURNAL OF PHYSICAL SCIENCES, 2013, 68 (1-2): : 145 - 151
  • [24] Anisotropic structure and dynamics of the solvation shell of a benzene solute in liquid water from ab initio molecular dynamics simulations
    Choudhary, Ashu
    Chandra, Amalendu
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2016, 18 (08) : 6132 - 6145
  • [25] Polarizable Molecular Dynamics Simulations of Aqueous Dipeptides
    Kucukkal, Tugba G.
    Stuart, Steven J.
    JOURNAL OF PHYSICAL CHEMISTRY B, 2012, 116 (30) : 8733 - 8740
  • [26] Ultrafast Vibrational Dynamics of Water Disentangled by Reverse Nonequilibrium Ab Initio Molecular Dynamics Simulations
    Nagata, Yuki
    Yoshimune, Seiji
    Hsieh, Cho-Shuen
    Hunger, Johannes
    Bonn, Mischa
    PHYSICAL REVIEW X, 2015, 5 (02):
  • [27] Structure and Dynamics of Collagen Hydration Water from Molecular Dynamics Simulations: Implications of Temperature and Pressure
    Madhavi, W. A. Monika
    Weerasinghe, Samantha
    Fullerton, Gary D.
    Momot, Konstantin, I
    JOURNAL OF PHYSICAL CHEMISTRY B, 2019, 123 (23) : 4901 - 4914
  • [28] Dynamics of water confined in lyotropic liquid crystals: Molecular dynamics simulations of the dynamic structure factor
    Mantha, Sriteja
    Yethiraj, Arun
    JOURNAL OF CHEMICAL PHYSICS, 2016, 144 (08)
  • [29] Dynamics of water and solute transport in polymeric reverse osmosis membranes via molecular dynamics simulations
    Shen, Meng
    Keten, Sinan
    Lueptow, Richard M.
    JOURNAL OF MEMBRANE SCIENCE, 2016, 506 : 95 - 108
  • [30] Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study
    Jahan, Ishrat
    Nayeem, Shahid M.
    RSC ADVANCES, 2020, 10 (46) : 27598 - 27614