Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water

Maddalena Bin; Rafat Yousif; Sharon Berkowicz; Sudipta Das; Daniel Schlesinger; Fivos Perakis
2021 | Phys Chem Chem Phys

Understanding the mechanism responsible for the protein low-temperature crossover observed at T ≈ 220 K can help us improve current cryopreservation technologies. This crossover is associated with changes in the dynamics of the system, such as in the mean-squared displacement, whereas experimental evidence of structural changes is sparse. Here we investigate hydrated lysozyme proteins by using a combination of wide-angle X-ray scattering and molecular dynamics (MD) simulations. Experimentally we suppress crystallization by accurate control of the protein hydration level, which allows access to temperatures down to T = 175 K. The experimental data indicate that the scattering intensity peak at Q = 1.54 Å−1, attributed to interatomic distances, exhibits temperature-dependent changes upon cooling. In the MD simulations it is possible to decompose the water and protein contributions and we observe that, while the protein component is nearly temperature independent, the hydration water peak shifts in a fashion similar to that of bulk water. The observed trends are analysed by using the water–water and water-protein radial distribution functions, which indicate changes in the local probability density of hydration water.

Molecular Perspective on Water Vapor Accommodation into Ice and Its Dependence on Temperature

Daniel Schlesinger; Samuel J. Lowe; Tinja Olenius; Xiangrui Kong; Jan B. C. Pettersson; Ilona Riipinen
2020 | JOURNAL OF PHYSICAL CHEMISTRY A | 124 (51) (10879-10889)

Anisotropic X-Ray Scattering of Transiently Oriented Water

Kim, K. H.; Späh, A.; Pathak, H.; Yang, C.; Bonetti, S.; Amann-Winkel, K.; Mariedahl, D.; Schlesinger, D.; Sellberg, J. A.; Mendez, D.; van der Schot, G.; Hwang, H. Y.; Clark, J.; Shigeki, O.; Tadashi, T.; Harada, Y.; Ogasawara, H.; Katayama, T.; Nilsson, A.; Perakis, F.
2020 | Phys. Rev. Lett. | 125, 076002

We study the structural dynamics of liquid water by time-resolved anisotropic x-ray scattering under the optical Kerr effect condition. In this way, we can separate the anisotropic scattering decay of 160 fs from the delayed temperature increase of ∼0.1  K occurring at 1 ps and quantify transient changes in the O-O pair distribution function. Polarizable molecular dynamics simulations reproduce well the experiment, indicating transient alignment of molecules along the electric field, which shortens the nearest-neighbor distances. In addition, analysis of the simulated water local structure provides evidence that two hypothesized fluctuating water configurations exhibit different polarizability.

Brine rejection and hydrate formation upon freezing of NaCl aqueous solutions

Ifigeneia Tsironi; Daniel Schlesinger; Alexander Späh; Lars Eriksson; Mo Segad; Fivos Perakis
2020 | Phys Chem Chem Phys | 22 ( 7625-7632)

Studying the freezing of saltwater on a molecular level is of fundamental importance for improving freeze desalination techniques. In this study, we investigate the freezing process of NaCl solutions using a combination of X-ray diffraction and molecular dynamics simulations (MD) for different salt-water concentrations, ranging from seawater conditions to saturation. A linear superposition model reproduces well the brine rejection due to hexagonal ice Ih formation and allows us to quantify the fraction of ice and brine. Furthermore, upon cooling at T = 233 K, we observe the formation of NaCl·2H2O hydrates (hydrohalites), which coexist with ice Ih. MD simulations are utilized to model the formation of NaCl crystal hydrates. From the simulations, we estimate that the salinity of the newly produced ice is 0.5% mass percent (m/m) due to ion inclusions, which is within the salinity limits of fresh water. In addition, we show the effect of ions on the local ice structure using the tetrahedrality parameter and follow the crystallite formation using the ion coordination parameter and cluster analysis.

Effect of nucleation on icy pebble growth in protoplanetary discs

Katrin Ros; Anders Johansen; Ilona Riipinen; Daniel Schlesinger
2019 | Astron Astrophys | 629 (A65)

Solid particles in protoplanetary discs can grow by direct vapour deposition outside of ice lines. The presence of microscopic silicate particles may nevertheless hinder growth into large pebbles, since the available vapour is deposited predominantly on the small grains that dominate the total surface area. Experiments on heterogeneous ice nucleation, performed to understand ice clouds in the Martian atmosphere, show that the formation of a new ice layer on a silicate surface requires a substantially higher water vapour pressure than the deposition of water vapour on an existing ice surface. In this paper, we investigate how the difference in partial vapour pressure needed for deposition of vapour on water ice versus heterogeneous ice nucleation on silicate grains influences particle growth close to the water ice line. We developed and tested a dynamical 1D deposition and sublimation model, where we include radial drift, sedimentation, and diffusion in a turbulent protoplanetary disc. We find that vapour is deposited predominantly on already ice-covered particles, since the vapour pressure exterior of the ice line is too low for heterogeneous nucleation on bare silicate grains. Icy particles can thus grow to centimetre-sized pebbles in a narrow region around the ice line, whereas silicate particles stay dust-sized and diffuse out over the disc. The inhibition of heterogeneous ice nucleation results in a preferential region for growth into planetesimals close to the ice line where we find large icy pebbles. The suppression of heterogeneous ice nucleation on silicate grains may also be the mechanism behind some of the observed dark rings around ice lines in protoplanetary discs, as the presence of large ice pebbles outside ice lines leads to a decrease in the opacity there.

A proposal for the structure of high- and low-density fluctuations in liquid water

Camisasca, G; Schlesinger, D; Zhovtobriukh, I; Pitsevich, G; Pettersson, LGM
2019 | J. Chem. Phys. | 151 (3)
1st-order transition , absorption-spectroscopy , basis-sets , hydrogen-bond network , rearrangements , scattering , spectra , supercooled water , temperature-dependence , x-ray-emission
Based on recent experimental data that can be interpreted as indicating the presence of specific structures in liquid water, we build and optimize two structural models which we compare with the available experimental data. To represent the proposed high-density liquid structures, we use a model consisting of chains of water molecules, and for low-density liquid, we investigate fused dodecahedra as templates for tetrahedral fluctuations. The computed infrared spectra of the models are in very good agreement with the extracted experimental spectra for the two components, while the extracted structures from molecular dynamics (MD) simulations give spectra that are intermediate between the experimentally derived spectra. Computed x-ray absorption and emission spectra as well as the O-O radial distribution functions of the proposed structures are not contradicted by experiment. The stability of the proposed dodecahedral template structures is investigated in MD simulations by seeding the starting structure, and remnants found to persist on an similar to 30 ps time scale. We discuss the possible significance of such seeds in simulations and whether they can be viable candidates as templates for structural fluctuations below the compressibility minimum of liquid water.

Cloud droplet activation of black carbon particles with organic compounds of varying solubility

Dalirian, M.; Ylisirnio, A.; Buchholz, A.; Schlesinger, D.; Strom, J.; Virtanen, A.; Riipinen, I.
2018 | Atmos. Chem. Phys. | 18 (12477-12489)

X-ray Scattering and O-O Pair-Distribution Functions of Amorphous Ices

Mariedahl, D; Perakis, F; Spah, A; Pathak, H; Kim, KH; Camisasca, G; Schlesinger, D; Benmore, C; Pettersson, LGM; Nilsson, A; Amann-Winkel, K
2018 | J. Phys. Chem. B | 122 (30) (7616-7624)
1st-order transition , diffraction , dynamics , high-density , hyperquenched glassy water , liquid water , neutron-scattering , phases , pressure-induced amorphization , xii

The structure factor and oxygen-oxygen pair distribution functions of amorphous ices at liquid nitrogen temperature (T = 77 K) have been derived from wide-angle X-ray scattering (WAXS) up to interatomic distances of r = 23 angstrom, where local structure differences between the amorphous ices can be seen for the entire range. The distances to the first coordination shell for low-, high-, and very-high-density amorphous ice (LDA, HDA, VHDA) were determined to be 2.75, 2.78, and 2.80 angstrom, respectively, with high accuracy due to measurements up to a large momentum transfer of 23 angstrom(-1). Similarities in pair-distribution functions between LDA and supercooled water at 254.1 K, HDA and liquid water at 365.9 K, and VHDA and high-pressure liquid water were found up to around 8 angstrom, but beyond that at longer distances, the similarities were lost. In addition, the structure of the high-density amorphous ices was compared to high-pressure crystalline ices IV, IX, and XII, and conclusions were drawn about the local ordering.

Cloud droplet activation of black carbon particles coated with organic compounds of varying solubility

Dalirian, M; Ylisirnio, A; Buchholz, A; Schlesinger, D; Strom, J; Virtanen, A; Riipinen, I
2018 | Atmos. Chem. Phys. | 18 (16) (12477-12489)
Atmospheric black carbon (BC) particles are a concern due to their impact on air quality and climate. Their net climate effect is, however, still uncertain. This uncertainty is partly related to the contribution of coated BC particles to the global cloud condensation nuclei (CCN) budgets. In this study, laboratory measurements were performed to investigate CCN activity of BC (REGAL 400R pigment black) particles, in pure state or coated through evaporating and subsequent condensation of glutaric acid, levoglucosan (both water-soluble organics) or oleic acid (an organic compound with low solubility). A combination of soot particle aerosol mass spectrometer (SP-AMS) measurements and size distribution measurements with a scanning mobility particle sizer (SMPS) showed that the studied BC particles were nearly spherical agglomerates with a fractal dimension of 2.79 and that they were coated evenly by the organic species. The CCN activity of BC particles increased after coating with all the studied compounds and was governed by the fraction of organic material. The CCN activation of the BC particles coated by glutaric acid and levoglucosan were in good agreement with the theoretical calculations using the shell-and-core model, which is based on a combination of the CCN activities of the pure compounds. The oleic acid coating enhanced the CCN activity of the BC particles, even though the pure oleic acid particles were CCN inactive. The surprising effect of oleic acid might be related to the arrangement of the oleic acid molecules on the surface of the BC cores or other surface phenomena facilitating water condensation onto the coated particles. Our results show that present theories have potential for accurately predicting the CCN activity of atmospheric BC coated with organic species, given that the identities and amounts of the coating species are known. Furthermore, our results suggest that even relatively thin soluble coatings (around 2 nm for the compounds studied here) are enough to make the insoluble BC particles CCN active at typical atmospheric supersaturations and thus be efficiently taken up by cloud droplets. This highlights the need for an accurate description of the composition of atmospheric particles containing BC to unravel their net impact on climate.

Diffusive dynamics during the high-to-low density transition in amorphous ice

Perakis, F; Amann-Winkel, K; Lehmkuhler, F; Sprung, M; Mariedahl, D; Sellberg, JA; Pathak, H; Spaeh, A; Cavalca, F; Schlesinger, D; Ricci, A; Jain, A; Massani, B; Aubree, F; Benmore, CJ; Loerting, T; Grubel, G; Pettersson, LGM; Nilsson, A
2017 | Proc. Natl. Acad. Sci. U.S.A. | 114 (31) (8193-8198)
1st-order transition , amorphous ice , behavior , glass transition , glass-liquid transition , liquid-liquid transition , phases , photon-correlation spectroscopy , pressure , reorientation , speckle , supercooled water , water , x-ray photon-correlation spectroscopy
Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high(HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distribution function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. The diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid-liquid transition in the ultraviscous regime.

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