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  • 1.
    Camisasca, Gaia
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum. Università Roma Tre, Italy.
    Iorio, Antonio
    De Marzio, Margherita
    Gallo, Paola
    Structure and slow dynamics of protein hydration water2018Ingår i: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 268, s. 903-910Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report results on the structure, local order and dynamics of water surrounding a lysozyme protein. The local order of water molecules is as much tetrahedral as in bulk water already at close vicinity of the protein but the number of hydrogen bonds depends more on the distance from the protein and gradually recovers bulk value upon moving outer. The dynamics of water seems in general to be more affected than its structure by the presence of the protein. An extremely long-relaxation detected in hydration water appears in the first monolayer around the protein, and the slow down is enhanced at low temperature. The dynamics of water within a layer of thickness 6 A is sub-diffusive up to about similar to 1 ns, above 1 ns we observe a crossover toward a hopping regime over a length-scale larger than that of nearest neighbors molecules. This hopping seems connected to transient trapping of water molecules on some specific protein domains.

  • 2. Iorio, Antonio
    et al.
    Camisasca, Gaia
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Gallo, Paola
    Slow dynamics of hydration water and the trehalose dynamical transition2019Ingår i: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 282, s. 617-625Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present results from molecular dynamics simulations of a solution of water and trehalose, a cryoprotecting disaccharide, upon cooling. We focus our attention on both the dynamics of hydration water and of the trehalose. Hydration water presents two slow relaxations. One is the a relaxation typical of glass formers and the second one is a long relaxation that was also found in proteins hydration water and appears coupled to the movement of the surface of trehaloses. Below 280 K trehalose aggregates and upon further cooling we find a dynamical transition for the trehalose aggregate at around 250 K similar to the well known Protein Dynamical Transition. When this transition happens the long relaxation time has a dynamical crossover. We hypothesize that this dynamical transition is a general feature that can be found not only in proteins but also in aggregates that interact with water and that have a flexible structure. In fact this feature has already been found not only in proteins hydration water but also in a colloidal microgel. In the known cases, including the one that we present here, water enhances movements of the surface of these aggregates above a certain temperature. The temperature of this dynamical transition ranges between 260 K and 220 K in all known cases.

  • 3.
    Nilsson, Anders
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Huang, Congcong
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Fluctuations in ambient water2012Ingår i: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 176, nr SI, s. 2-16Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We emphasize the importance in simulations of water of reproducing the isothermal compressibility, dependent on density fluctuations in the liquid, for a correct description of structural fluctuations in simulated water. From x-ray spectroscopy a strict bimodality in terms of fluctuations between high- (HDL) and low-density (LDL) forms of the liquid has been reported. The inherent structure in simulations, i.e. the structure quenched to 0 K, is found to be bimodal in terms of HDL and LDL in close correspondence to x-ray spectroscopy. This is, however, smeared out in the real structure where temperature is included. We suggest that the local minima for the HDL and LDL local structures in the simulation need to be deeper and propose that many-body electronic structure effects and non-local van der Waals interactions will be important in this respect. Much larger simulations than hitherto considered are likely necessary to catch the effects of both thermal and structural fluctuations in the simulated liquid. Since structural fluctuations can be expected to significantly affect the dynamics in the liquid it is important that these are taken properly into account when discussing hydrogen-bond breaking and reformation. Here it is essential that the model used correctly reproduces the temperature and pressure dependence in thermodynamic response functions.

  • 4. Pogorelov, V.
    et al.
    Doroshenko, I.
    Pitsevich, G.
    Balevicius, V.
    Sablinskas, V.
    Krivenko, B.
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    From clusters to condensed phase - FT IR studies of water2017Ingår i: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 235, s. 7-10Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Intermolecular hydrogen bonding, which is formed between water molecules in the condensed state, causes a variety of unique properties of liquid water. In this paper the results of experimental FT IR studies of water trapped in an Ar matrix as well as condensed water at temperatures from 133 to 293 K are presented. It is shown that the temperature evolution of the FTIR-spectra of water trapped in low-temperature matrices can be considered as an experimental model of the structure transformation of water during the phase transition from gas phase to condensed confined water. The comparison of the vibrational spectra of water in matrix isolation with the corresponding spectra of condensed water gives information about the peculiarities of H-bonded structures of water.

  • 5. Pogorelov, Valeriy
    et al.
    Chernolevska, Yelyzaveta
    Vaskivskyi, Yevhenii
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Doroshenko, Iryna
    Sablinskas, Valdas
    Balevicius, Vytautas
    Ceponkus, Justinas
    Kovaleva, Kristina
    Malevich, Alex
    Pitsevich, George
    Structural transformations in bulk and matrix-isolated methanol from measured and computed infrared spectroscopy2016Ingår i: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 216, s. 53-58Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    FTIR spectra of methanol trapped in an Ar matrix were registered during gradual heating of the sample. The spectral changes observed in these experiments indicate a transformation from isolated methanol monomers to small hydrogen-bonded clusters, allowing us to consider such experiments as an experimental model of the gas-liquid phase transition. The liquid-solid phase transition for methanol was investigated by analysing the temperature dependence of the registered FTIR spectra of methanol during cooling from 70 degrees C to 115 degrees C. Comparing the experimental spectra in the C-O stretching region with results of quantum-chemical calculations using the method of principal component analysis we draw conclusions about the size and structure of the methanol clusters formed in the sample at different temperatures.

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