Search

Time-dependent density functional theory (TDDFT) offers a tractable means to predict electronic excitation spectra of ices if sufficient care is taken in selecting the DFT functional, basis sets, and the number of excited states. In this work 48 functionals in conjunction with various correlation consistent basis sets were benchmarked for predicting electronic spectra. A training set of important astromolecules was chosen: carbon monoxide, water, hydrogen cyanide, ammonia, methanol, and the hydroxyl radical. Vertical excitation energies between the ground and first excited state and some higher excited states were calculated using multireference configuration interaction calculations to serve as benchmarks for gas phase TDDFT calculations. When used in conjunction with aug-cc-pVDZ quality correlation consistent basis sets, two functionals, MPW1K and ωB97, emerged as very good choices to model electronic excitations for most of the molecules in the training set. Cluster calculation predictions for the UV spectra of amorphous ices of water and ammonia were performed at the TDDFT-MPW1K/AVDZ and TDDFT-ωB97/AVDZ levels and then compared against experimental data. The calculations qualitatively reproduce the shapes of the spectra for the most part and quantitatively predict the position of the critical first absorption peak. [ABSTRACT FROM AUTHOR]

Structure determination of biological macromolecules using cryogenic electron microscopy is based on applying the phase object (PO) assumption and the weak phase object (WPO) approximation to reconstruct the 3D potential density of the molecule. To enhance the understanding of image formation of protein complexes embedded in glass-like ice in a transmission electron microscope, this study addresses multiple scattering in tobacco mosaic virus (TMV) specimens. This includes the propagation inside the molecule while also accounting for the effect of structural noise. The atoms in biological macromolecules are light but are distributed over several nanometres. Commonly, PO and WPO approximations are used in most simulations and reconstruction models. Therefore, dynamical multislice simulations of TMV specimens embedded in glass-like ice were performed based on fully atomistic molecular-dynamics simulations. In the first part, the impact of multiple scattering is studied using different numbers of slices. In the second part, different sample thicknesses of the ice-embedded TMV are considered in terms of additional ice layers. It is found that single-slice models yield full frequency transfer up to a resolution of 2.5 Å, followed by attenuation up to 1.4 Å. Three slices are sufficient to reach an information transfer up to 1.0 Å. In the third part, ptychographic reconstructions based on scanning transmission electron microscopy (STEM) and single-slice models are compared with conventional TEM simulations. The ptychographic reconstructions do not need the deliberate introduction of aberrations, are capable of post-acquisition aberration correction and promise benefits for information transfer, especially at resolutions beyond 1.8 Å.

Premelting of ice, a quasi-liquid layer (QLL) at the surface below the melting temperature, was first postulated by Michael Faraday 160 y ago. Since then, it has been extensively studied theoretically and experimentally through many techniques. Existing work has been performed predominantly on hexagonal ice, at conditions close to the triple point. Whether the same phenomenon can persist at much lower pressure and temperature, where stacking disordered ice sublimates directly into water vapor, remains unclear. Herein, we report direct observations of surface premelting on ice nanocrystals below the sublimation temperature using transmission electron microscopy (TEM). Similar to what has been reported on hexagonal ice, a QLL is found at the solid-vapor interface. It preferentially decorates certain facets, and its thickness increases as the phase transition temperature is approached. In situ TEM reveals strong diffusion of the QLL, while electron energy loss spectroscopy confirms its amorphous nature. More significantly, the premelting observed in this work is thought to be related to the metastable low-density ultraviscous water, instead of ambient liquid water as in the case of hexagonal ice. This opens a route to understand premelting and grassy liquid state, far away from the normal water triple point. [ABSTRACT FROM AUTHOR]

Laboratory experiments have confirmed that the radiolytic decay rate of astrochemical ice analogues is dependent upon the solid phase of the target ice, with some crystalline molecular ices being more radio-resistant than their amorphous counterparts. The degree of radio-resistance exhibited by crystalline ice phases is dependent upon the nature, strength, and extent of the intermolecular interactions that characterise their solid structure. For example, it has been shown that crystalline CH3OH decays at a significantly slower rate when irradiated by 2 keV electrons at 20 K than does the amorphous phase due to the stabilising effect imparted by the presence of an extensive array of strong hydrogen bonds. These results have important consequences for the astrochemistry of interstellar ices and outer Solar System bodies, as they imply that the chemical products arising from the irradiation of amorphous ices (which may include prebiotic molecules relevant to biology) should be more abundant than those arising from similar irradiations of crystalline phases. In this present study, we have extended our work on this subject by performing comparative energetic electron irradiations of the amorphous and crystalline phases of the sulphur-bearing molecules H2S and SO2 at 20 K. We have found evidence for phase-dependent chemistry in both these species, with the radiation-induced exponential decay of amorphous H2S being more rapid than that of the crystalline phase, similar to the effect that has been previously observed for CH3OH. For SO2, two fluence regimes are apparent: a low-fluence regime in which the crystalline ice exhibits a rapid exponential decay while the amorphous ice possibly resists decay, and a high-fluence regime in which both phases undergo slow exponential-like decays. We have discussed our results in the contexts of interstellar and Solar System ice astrochemistry and the formation of sulphur allotropes and residues in these settings.

We investigate via numerical simulations of the TIP4P/Ice model the isothermal decompression of high density amorphous ice (HDA) mirroring the experimental protocol followed by recent experiments [H. K. Kim, et al., Science 370, 978, 2020]. Taking advantage of the recent determination of the TIP4P/Ice liquid-liquid critical point, we decompress our samples at temperatures both below and above the critical temperature. We follow the crossover between high and low density, complementing the time evolution of the structure factor with the time evolution of microscopic descriptors. Our results support the interpretation of the experimental pathway as a structural change from high to low density states through a first-order transition line. In the simulation study we do not observe nucleation events, but rather a spinodal-like non-equilibrium transformation, which offers an explanation on why the decompression process even at sub-critical temperatures may result in a continuous time evolution of the density and of the microscopic descriptors.

Because of the negative inclination of the solid–liquid phase separation line in water, ice Ih melts on compression. We carry out molecular dynamics simulations using TIP4P/Ice water model. We find that increase in pressure drives the liquid water into a high density metastable glassy state, at relatively high pressure (greater than ∼30 kbar). The crystal-to-glass transition is characterised by a rapid approach to a zero diffusion state and absence of crystalline order in the static structure factor. The vitrification is found to occur even at high temperatures (T > 250 K). We study this novel glass transition process at four temperatures (80, 250, 300 and 320 K). The transition pressure increases with an increase in temperature, as expected. Interestingly, we find that the total rate of change of entropy with pressure undergoes a change at/near the glass transition. We discover a pressure-induced realignment of water molecules resulting in two well-separated peaks in the O–O–O angle distribution among neighbouring molecules. The difference between the positions of these two peaks undergoes a sharp change at the vitrification pressure suggesting that it can serve as an appropriate order parameter to detect the glass transition point. [ABSTRACT FROM AUTHOR]

A recent experiment [K. H. Kim, et al., Science 370, 978 (2020)] showed that it may be possible to detect a liquid–liquid phase transition (LLPT) in supercooled water by subjecting high density amorphous ice (HDA) to ultrafast heating, after which the sample reportedly undergoes spontaneous decompression from a high density liquid (HDL) to a low density liquid (LDL) via a first-order phase transition. Here we conduct computer simulations of the ST2 water model, in which a LLPT is known to occur. We subject various HDA samples of this model to a heating and decompression protocol that follows a thermodynamic pathway similar to that of the recent experiments. Our results show that a signature of the underlying equilibrium LLPT can be observed in a strongly out-of-equilibrium process that follows this pathway despite the very high heating and decompression rates employed here. Our results are also consistent with the phase diagram of glassy ST2 water reported in previous studies.

Water ice clouds form in the mesospheres of terrestrial planets in the solar system (and most likely elsewhere) by vapor deposition at low pressures and temperatures. Under these conditions a range of crystalline and amorphous phases of ice might form. The phase is important because it influences nucleation kinetics, density, vapor pressure over the solid, growth rates and particle shape. In the past, the temperature range over which these different phases exist has been defined on the basis of depositing ice at low temperature and warming it while observing phase changes. However, the direct deposition of ice at a range of temperatures relevant for the terrestrial planets has not been systematically investigated. Here we present X‐ray Diffraction (XRD) measurements of water ice deposited at temperature intervals between 88 and 145 K in a vacuum chamber. XRD patterns showed that low density amorphous ice was formed at ≤120 K, stacking disordered ice I formed from 121 to 135 K and hexagonal ice I formed at 140 and 145 K. Direct deposition results in the stable hexagonal phase at much lower temperatures than when warming stacking disordered ice. All three phases of water ice observed here are possible in clouds in the mesospheres of Earth and Mars, while on Venus only amorphous ice is likely to form. Plain Language Summary: Ice clouds made up of water ice crystals can form in the thin upper atmospheres (mesospheres) of terrestrial planets where it can be extremely cold. Under these conditions a range of crystalline (hexagonal, cubic, or stacking disordered) and amorphous (lacking long range order) phases of ice might form. The phase is important because it influences a range of cloud properties. Experimentally, rather than warming ice formed at low temperature (as has been done in the past) we deposit the ice directly. We did this because an understanding of how the structure of ice evolves on warming as well as what structure forms when ice is deposited at specific temperatures is necessary to understand the properties of these clouds. Measurements showed that the amorphous, stacking disordered and hexagonal phases of water ice (ice I) can form depending on the specific temperature. Direct deposition yields the hexagonal phase at much lower temperatures than when warming ice deposited at lower temperatures. All three phases of water ice observed here are possible in clouds in the mesospheres of Earth and Mars. In contrast, on Venus clouds form at lower temperatures and so only amorphous ice is likely to form. Key Points: Low density amorphous ice was formed at 88–120 K, stacking disordered ice I formed from 121 to 135 K and hexagonal ice I formed at 140–145 KDirect deposition results in the stable hexagonal phase at much lower temperatures than when warming stacking disordered iceAll three phases of ice are possible in clouds in the mesospheres of Earth and Mars, while on Venus only amorphous ice is likely to form [ABSTRACT FROM AUTHOR]

• Molecular dynamics simulations including the largest model of a protein in ice. • A gaussian random field approach to modelling the amorphous ice potential. • The gaussian random field and molecular dynamics models results in identical images. • Simulations with the gaussian random field model are two orders of magnitude faster. Simulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datasets to support the development of instrumentation, methods, and software, as well as to assess data acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice model produced using molecular dynamics simulations. Although practical for small sample volumes; for simulation of cryo-EM data from large sample volumes, this can be too computationally expensive. We have evaluated a Gaussian Random Field (GRF) ice model which is shown to be more computationally efficient for large sample volumes. The simulated EM images are compared with the gold standard atom-based ice model approach and shown to be directly comparable. Comparison with experimentally acquired data shows the Gaussian random field ice model produces realistic simulations. The software required has been implemented in the Parakeet software package and the underlying atomic models are available online for use by the wider community. [ABSTRACT FROM AUTHOR]

We here report isotope substitution neutron diffraction experiments on two variants of high-density amorphous ice (HDA): its unannealed form prepared via pressure-induced amorphization of hexagonal ice at 77 K, and its expanded form prepared via decompression of very-high density amorphous ice at 140 K. The latter is about 17 K more stable thermally, so that it can be heated beyond its glass-to-liquid transition to the ultraviscous liquid form at ambient pressure. The structural origin for this large thermal difference and the possibility to reach the deeply supercooled liquid state has not yet been understood. Here we reveal that the origin for this difference is found in the intermediate range structure, beyond about 3.6 Å. The hydration shell markedly differs at about 6 Å. The local order, by contrast, including the first as well as the interstitial space between first and second shell is very similar for both. 'eHDA' that is decompressed to 0.20 GPa instead of 0.07 GPa is here revealed to be rather far away from well-relaxed eHDA. Instead it turns out to be roughly halfway between VHDA and eHDA – stressing the importance for decompressing VHDA to at least 0.10 GPa to make an eHDA sample of good quality. [ABSTRACT FROM AUTHOR]

Here we report about the structural evolution during the conversion from high-density amorphous ices at ambient pressure to the low-density state. Using high-energy X-ray diffraction, we have monitored the transformation by following in reciprocal space the structure factor SOO(Q) and derived in real space the pair distribution function gOO(r). Heating equilibrated high-density amorphous ice (eHDA) at a fast rate (4 K min–1), the transition to the low-density form occurs very rapidly, while domains of both high- and low-density coexist. On the other hand, the transition in the case of unannealed HDA (uHDA) and very-high-density amorphous ice is more complex and of continuous nature. The direct comparison of eHDA and uHDA indicates that the molecular structure of uHDA contains a larger amount of tetrahedral motives. The different crystallization behaviour of the derived low-density amorphous states is interpreted as emanating from increased tetrahedral coordination present in uHDA. This article is part of the theme issue 'The physics and chemistry of ice: scaffolding across scales, from the viability of life to the formation of planets'. [ABSTRACT FROM AUTHOR]

• Molecular dynamics calculations of amorphous ice were performed. • The surface diffusion of protons on amorphous ice was analyzed. • The mechanisms of surface diffusion of protons were determined. To investigate the surface diffusion of protons on amorphous ice, we performed molecular dynamics calculations. The diffusion mechanisms were analyzed by observing the trajectories of protons on the surface. The results show that the protons diffuse on the surface of amorphous ice via repeated formation and dissociation of H 3 O+. From the frequencies of the formation and dissociation of H 3 O+, the diffusion coefficients and activation energy were estimated in the temperature range of 40–130 K. The surface diffusion is an important factor for chemical reactions that occur on ice dust in interstellar molecular clouds. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The infrared spectra of vapor-deposited H 2 O CO 2 amorphous ice were measured. • The formation mechanisms of CO 2 clathrate hydrate from amorphous ice were analyzed. • The phase diagram of the H 2 O CO 2 system including vacuum conditions was predicted. Abstract To investigate the formation mechanisms of CO 2 clathrate hydrate under vacuum conditions, infrared spectra of vapor-deposited H 2 O CO 2 amorphous ice were measured. From analyses of variations in the spectral features with warming, remarkable changes were found at ∼100 K. The results indicate that the deposited amorphous ice is transformed into CO 2 clathrate hydrate at around ∼100 K. From the results, a phase diagram of CO 2 clathrate hydrate from vapor deposited amorphous ice was predicted. The results suggest the existence of pure CO 2 clathrate hydrates in space. [ABSTRACT FROM AUTHOR]

Premelting of ice, a quasi-liquid layer (QLL) at the surface below the melting temperature, was first postulated by Michael Faraday 160 y ago. Since then, it has been extensively studied theoretically and experimentally through many techniques. Existing work has been performed predominantly on hexagonal ice, at conditions close to the triple point. Whether the same phenomenon can persist at much lower pressure and temperature, where stacking disordered ice sublimates directly into water vapor, remains unclear. Herein, we report direct observations of surface premelting on ice nanocrystals below the sublimation temperature using transmission electron microscopy (TEM). Similar to what has been reported on hexagonal ice, a QLL is found at the solid-vapor interface. It preferentially decorates certain facets, and its thickness increases as the phase transition temperature is approached. In situ TEM reveals strong diffusion of the QLL, while electron energy loss spectroscopy confirms its amorphous nature. More significantly, the premelting observed in this work is thought to be related to the metastable low-density ultraviscous water, instead of ambient liquid water as in the case of hexagonal ice. This opens a route to understand premelting and grassy liquid state, far away from the normal water triple point.

We review the recent research on supercooled and glassy water, focusing on the possible origins of its complex behavior. We stress the central role played by the strong directionality of the water-water interaction and by the competition between local energy, local entropy and local density. In this context we discuss the phenomenon of polyamorphism (i.e., the existence of more than one disordered solid state), emphasizing both the role of the preparation protocols and the transformation between the different disordered ices. Finally, we present the ongoing debate on the possibility of linking polyamorphism with a liquid-liquid transition that could take place in the no-man's land, the temperature-pressure window in which homogeneous nucleation prevents the investigation of water in its metastable liquid form. [ABSTRACT FROM AUTHOR]

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 nano-meter 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. [ABSTRACT FROM AUTHOR]

To investigate the surface structure, we performed molecular dynamics calculations of amorphous ice. The result shows that a low density layer, which forms a few hydrogen bonds with weaker strength, exists in the surface. Furthermore, the sintering processes were simulated to investigate the structure of grain boundary formed from the adsorption of two surfaces. The result indicates that a low density region exists in a boundary between amorphous ice grains. The structures of surface and interface of amorphous ice have important implications for adsorption, diffusion, and chemical reaction in ice grains of interstellar molecular clouds. [ABSTRACT FROM AUTHOR]

The description of various amorphous phases of ices has been performed on a molecular level in order to study the nature of amorphous polymorphism in a water system. The models of very high-, high- and low-density amorphous (VHDA, HDA and LDA, respectively) ices have been constructed. The molecules are located in their equilibrium states and the structure of the networks is characterized by the absence of long-range atomic order, but short-range order is still present. The thermodynamic properties of VHDA, HDA and LDA ices have been determined using the molecular dynamics and lattice dynamics methods. It has been found that at low temperatures the transformation LDA → HDA is a real phase transition in the classical sense. In the case of HDA → VHDA, the same transition has been found only in negative pressure regions. At positive pressure the transformation from the metastable phase HDA to the thermodynamically stable phase VHDA can be classified as a continuous one. [ABSTRACT FROM AUTHOR]

This work is a study of CO and H 2 O molecules as adsorbates that interact on the surface of olivine dust grains. Olivine (forsterite) is present on the Earth, planetary dust, in the interstellar medium (ISM) and in particular in comets. The composition of amorphous ice is very important for the interpretation of processes that occur in the solar system and the ISM. Dust particles in ISM are composed of a heterogeneous mixture of amorphous or crystalline silicates ( e.g. olivine) organic material, carbon, and other minor constituents. These dust grains are embedded in a matrix of ices, such as H 2 O, CO, CO 2 , NH 3 , and CH 4 . We consider that any amorphous ice will interact and grow faster on dust grain surfaces. In this work we explore the adsorption of CO-H 2 O amorphous ice onto several (100) forsterite surfaces (dipolar and non-dipolar), by using first principle calculations based on density functional theory (DFT). These models are applied to two possible situations: i ) adsorption of CO molecules mixed into an amorphous ice matrix (gas mixture) and adsorbed directly onto the forsterite surface. This interaction has lower adsorption energy than polar molecules (H 2 O and NH 3 ) adsorbed on this surface; ii ) adsorption of CO when the surface has previously been covered by amorphous water ice (onion model). In this case the calculations show that adsorption energy is low, indicating that this interaction is weak and therefore the CO can be desorbed with a small increase of temperature. Vibration spectroscopy for the most stable complex was also studied and the frequencies were in good agreement with experimental frequency values. [ABSTRACT FROM AUTHOR]

Structure determination of biological macromolecules using cryogenic electron microscopy is based on applying the phase object (PO) assumption and the weak phase object (WPO) approximation to reconstruct the 3D potential density of the molecule. To enhance the understanding of image formation of protein complexes embedded in glass-like ice in a transmission electron microscope, this study addresses multiple scattering in tobacco mosaic virus (TMV) specimens. This includes the propagation inside the molecule while also accounting for the effect of structural noise. The atoms in biological macromolecules are light but are distributed over several nanometres. Commonly, PO and WPO approximations are used in most simulations and reconstruction models. Therefore, dynamical multislice simulations of TMV specimens embedded in glass-like ice were performed based on fully atomistic molecular-dynamics simulations. In the first part, the impact of multiple scattering is studied using different numbers of slices. In the second part, different sample thicknesses of the ice-embedded TMV are considered in terms of additional ice layers. It is found that single-slice models yield full frequency transfer up to a resolution of 2.5 Å, followed by attenuation up to 1.4 Å. Three slices are sufficient to reach an information transfer up to 1.0 Å. In the third part, ptychographic reconstructions based on scanning transmission electron microscopy (STEM) and single-slice models are compared with conventional TEM simulations. The ptychographic reconstructions do not need the deliberate introduction of aberrations, are capable of post-acquisition aberration correction and promise benefits for information transfer, especially at resolutions beyond 1.8 Å., (open access.)

The coexistence of the amorphous structure and crystalline hexagonal structure of ice near its melting point at normal pressure is confirmed by comparing the diffraction patterns of diffuse X-ray scattering for different amorphous structures. The diffuse X-ray scattering at an ice sample maintained at a temperature of-10°C is continuously recorded for a long time. Continual variations in the nature of diffuse scattering until its complete disappearance are revealed. The disappearance of diffuse scattering indicates the metastability of amorphous ice near its melting point with a lifetime of about 15 days. [ABSTRACT FROM AUTHOR]