Crystalline Ice Research Articles

Theoretical Determination of Binding Energies of Small Molecules on Interstellar Ice Surfaces

The adsorption of a series of atoms and small molecules and radicals (H, C, N, O, NH, OH, H2O, CH3, and NH3) on hexagonal crystalline and amorphous ice clusters were obtained via classical molecular dynamics and electronic structure methods. The geometry and binding energies were calculated using a QMHigh:QMLow hybrid method on model clusters. Several combination of basis sets, density functionals and semi-empirical methods were compared and tested against previous works. More accurate binding energies were also refined via single point Coupled Cluster calculations. Most species, except carbon atom, physisorb on the surface, leading to rather small binding energies. The carbon atom forms a COH2 molecule and in some cases leads to the formation of a COH-H3O+ complex. Amorphous ices are characterized by slightly stronger binding energies than the crystalline phase. A major result of this work is to also access the dispersion of the binding energies since a variety of adsorption sites is explored. The interaction energies thus obtained may serve to feed or refine astrochemical models. The present methodology could be easily extended to other types of surfaces and larger adsorbates.

Halophytes as a potential source of melanosis-inhibiting compounds. Mechanism of inhibition of a characterized polyphenol extract of purslane (Portulaca oleracea)

The market value of crustaceans depreciates during storage due to the appearance of melanosis caused by polyphenol oxidases. Sulfite derivatives are used as melanosis-inhibiting agents, but their unhealthy effects make it preferable to replace them with natural preservatives. In this work, a crude enzymatic extract from whiteleg shrimp (Penaeus vannamei) was characterized and used to test the diphenol oxidase-inhibiting activity of polyphenol extracts of five underutilized halophyte plants, namely crystalline ice plant, seaside arrowgrass, purslane, sea fennel, and seashore aster. The extracts inhibited diphenol oxidase activity more efficiently than sodium sulfite. The purslane extract was rich in isoorientins, isovitexin, and apigenin, and showed the highest inhibiting effect, being this classified as mixed or non-competitive. Hydroxyl groups in the phenyl B ring could be responsible for the inhibitory activity of the extract. The polyphenol extracts tested in this work could be promising melanosis-inhibiting agents of interest for seafood industries.

Adsorption of organic compounds at the surface of Enceladus’ ice grains. A grand canonical Monte Carlo simulation study

ABSTRACT In this paper, we characterise the adsorption of ethylene, propanol and hexanal molecules on crystalline ice by grand canonical Monte Carlo simulations performed at 236 K, a temperature which is typical of some Enceladus’ environments. We show that at low coverage of the ice surface, the adsorption of propanol and hexanal is driven by the interaction of these molecules with the ice phase and, as a consequence, the adsorbed molecules lie more or less parallel to the ice surface. On the other hand, upon saturation, the adsorbate–adsorbate interactions become more and more important and the molecules tend to become tilted with respect to the surface, the aliphatic chain pointing towards the gas phase, while the polar head of propanol and hexanal molecules always stays attached to the ice surface, irrespective of the coverage. By contrast, the ethylene molecules do not show any strong affinity for the ice surface because of the corresponding weak binding energy. These results are in good agreement with the major features provided by the available experiments on similar systems.

Brownian dynamics simulation of protofilament relaxation during rapid freezing.

Electron cryo-microscopy (Cryo-EM) is a powerful method for visualizing biological objects with up to near-angstrom resolution. Instead of chemical fixation, the method relies on very rapid freezing to immobilize the sample. Under these conditions, crystalline ice does not have time to form and distort structure. For many practical applications, the rate of cooling is fast enough to consider sample immobilization instantaneous, but in some cases, a more rigorous analysis of structure relaxation during freezing could be essential. This difficult yet important problem has been significantly under-reported in the literature, despite spectacular recent developments in Cryo-EM. Here we use Brownian dynamics modeling to examine theoretically the possible effects of cryo-immobilization on the apparent shapes of biological polymers. The main focus of our study is on tubulin protofilaments. These structures are integral parts of microtubules, which in turn are key elements of the cellular skeleton, essential for intracellular transport, maintenance of cell shape, cell division and migration. We theoretically examine the extent of protofilament relaxation within the freezing time as a function of the cooling rate, the filament's flexural rigidity, and the effect of cooling on water's viscosity. Our modeling suggests that practically achievable cooling rates are not rapid enough to capture tubulin protofilaments in conformations that are incompletely relaxed, suggesting that structures seen by cryo-EM are good approximations to physiological shapes. This prediction is confirmed by our analysis of curvatures of tubulin protofilaments, using samples, prepared and visualized with a variety of methods. We find, however, that cryofixation may capture incompletely relaxed shapes of more flexible polymers, and it may affect Cryo-EM-based measurements of their persistence lengths. This analysis will be valuable for understanding of structures of different types of biopolymers, observed with Cryo-EM.

Experimental Simulation of Titan's Stratospheric Photochemistry: Benzene (C6H6) Ices

AbstractWe performed laboratory experiments to study the photochemical evolution induced by long‐UV irradiation of benzene ices in Titan's atmosphere. The aim of this study was to investigate whether photo‐processed benzene ices could lead to the formation of aerosols analogs to those observed in Titan's stratosphere. Prior to that, spectroscopic properties of amorphous and crystalline benzene ices were studied as a function of temperature, using infrared spectroscopy. UV photolysis experiments (λ > 230 nm) of benzene ices led to the formation of volatile photo‐products, among which fulvene is identified, and of a residue dominated by νCH IR features, demonstrating that pure aromatic‐based polymeric structures are not sufficient to explain the composition of Titan's stratospheric haze layer. However, we provide a characterization of long‐UV‐induced benzene‐containing aerosol analogs, which will contribute to Titan's surface organics layer. These data are of prime interest in the context of the future Dragonfly space mission.

Infalling thermally destroyed bodies as a possible explanation for the KIC 8462852 phenomenon

ABSTRACT Using the analytical solution of the heat diffusion equation, we calculate the components of the thermal stress tensor and analyse the process of thermal destruction of bodies consisting of crystalline ice with radii ranging from 10 m to 10 km around KIC 8462852. As a body approaches the star in a high-eccentricity orbit, compressive stresses increase on its surface, making tensile stresses increase in its interior and causing catastrophic body destruction. The processes of destruction near the surface of bodies that occur as a result of compressive stress and contribute to the appearance of coma are most severe in large bodies (10 km or more). We show that, for bodies with radii from 20 m to 10 km, internal tensile strengths exceed the limit of material strength at different distances from the star. Bodies with a size of r ≈ 1.8–2.1 km are among the first to experience catastrophic destruction, being at a distance of 80–100 au from the star. Subsequent cascading destruction of fragments can lead to the formation of dust. Closest to the star, being at a distance of 7.44 au, both the biggest and smallest bodies with a radius of more than 10 km and less than 20 m, respectively, begin to break apart. The infalling thermally destroyed body (ITDB) mechanism is capable of explaining the main details of both the short-term and long-term photometric behaviour of KIC 8462852.

Infrared spectra of amorphous and crystalline urea ices.

Urea is a molecule of great interest in chemistry and biology. In particular, it is considered a key building block in prebiotic chemistry on Earth. The hypothesis of its possible exogenous origin has been reinforced after the recent detection of this molecule in the interstellar medium, where it is believed to form in the ice mantles of dust grains. In this work the infrared spectra of urea ices and urea:H2O ice mixtures have been studied both experimentally and theoretically. Urea ices were generated by vapour deposition at temperatures between 10 K and 270 K. It was found that an amorphous phase is formed at temperatures below 200 K. A theoretical modelling of crystalline urea and of a tentative amorphous urea solid phase, as well as of amorphous urea:H2O ice mixtures, has been performed. The corresponding infrared spectra were simulated with density functional theory. The main spectral features observed in the various solid samples are interpreted with the help of the theoretical results. Infrared band strengths are also provided for amorphous and crystalline urea. The infrared spectroscopic information given in this work is expected to be useful for the detection and quantification of urea in astrophysical ices.

The freezing behavior of aqueous n-alcohol nanodroplets.

We generate water-rich aerosols containing 1-propanol and 1-pentanol in a supersonic nozzle to study the effects of these solutes on the freezing behavior of water. Condensation and freezing are characterized by two complementary techniques, pressure trace measurements and Fourier Transform Infrared spectroscopy. When 1-pentanol and 1-propanol are present, condensation occurs at higher temperatures because particle formation from the vapor phase is enhanced by the decrease in interfacial free energy of mixed aqueous-alcohol critical clusters relative to those of pure water. FTIR results suggest that when ∼6 nm radius droplets freeze, the tetrahedral structure of the ice is well preserved up to an overall alcohol mole fraction of 0.031 for 1-propanol and 0.043 for 1-pentanol. In this concentration range, the ice nucleation temperature decreases continuously with increasing 1-propanol concentration, whereas the onset of freezing is not significantly perturbed by 1-pentanol up to a mole fraction of 0.03. Furthermore, once freezing starts the ice nucleation rates in the aqueous-alcohol droplets are very close to those for pure water. In contrast, at the highest mole fractions of either alcohol it is not clear whether droplets freeze to form crystalline ice since the final state of the particles cannot be adequately characterized with the available experimental techniques.

ALMA chemical survey of disk-outflow sources in Taurus (ALMA-DOT)

Context. Planet formation starts around Sun-like protostars with ages ≤1 Myr, but the chemical compositions of the surrounding discs remains unknown. Aims. We aim to trace the radial and vertical spatial distribution of a key species of S-bearing chemistry, namely H2CS, in protoplanetary discs. We also aim to analyse the observed distributions in light of the H2CS binding energy in order to discuss the role of thermal desorption in enriching the gas disc component. Methods. In the context of the ALMA chemical survey of disk-outflow sources in the Taurus star forming region (ALMA-DOT), we observed five Class I or early Class II sources with the o-H2CS(71,6−61,5) line. ALMA-Band 6 was used, reaching spatial resolutions ≃40 au, that is, Solar System spatial scales. We also estimated the binding energy of H2CS using quantum mechanical calculations, for the first time, for an extended, periodic, crystalline ice. Results. We imaged H2CS emission in two rotating molecular rings in the HL Tau and IRAS 04302+2247 discs, the outer radii of which are ~140 au (HL Tau) and 115 au (IRAS 04302+2247). The edge-on geometry of IRAS 04302+2247 allows us to reveal that H2CS emission peaks at radii of 60–115 au, at z = ±50 au from the equatorial plane. Assuming LTE conditions, the column densities are ~1014 cm−2. We estimate upper limits of a few 1013 cm−2 for the H2CS column densities in DG Tau, DG Tau B, and Haro 6–13 discs. For HL Tau, we derive, for the first time, the [H2CS]/[H] abundance in a protoplanetary disc (≃10−14). The binding energy of H2CS computed for extended crystalline ice and amorphous ices is 4258 and 3000–4600 K, respectively, implying thermal evaporation where dust temperatures are ≥50–80 K. Conclusions. H2CS traces the so-called warm molecular layer, a region previously sampled using CS and H2CO. Thioformaldehyde peaks closer to the protostar than H2CO and CS, plausibly because of the relatively high excitation level of the observed 71,6−61,5 line (60 K). The H2CS binding energy implies that thermal desorption dominates in thin, au-sized, inner and/or upper disc layers, indicating that the observed H2CS emitting up to radii larger than 100 au is likely injected in the gas phase due to non-thermal processes.

Influence of ice structure on the soft UV photochemistry of PAHs embedded in solid water

Context. The UV photoreactivity of polycyclic aromatic hydrocarbons (PAHs) in porous amorphous solid water has long been known to form both oxygenated photoproducts and photofragments. Aims. The aim of this study is to examine the influence of ice structure on reactivity under soft UV irradiation conditions. Methods. Mixtures of PAHs with amorphous solid water (porous and compact) and crystalline (cubic and hexagonal) ices were prepared in a high vacuum chamber and irradiated using a mercury lamp for up to 2.5 h. Results. The results show that the production of oxygenated PAHs is efficient only in amorphous water ice, while fragmentation can occur in both amorphous and crystalline ices. We conclude that the reactivity is driven by PAH–water interactions in favourable geometries, notably where dangling bonds are available at the surface of pores. Conclusions. These results suggest that the formation of oxygenated PAH molecules is most likely to occur in interstellar environments with porous (or compact) amorphous solid water and that this reactivity could considerably influence the inventory of aromatics in meteorites.

Bayesian analysis of Juno/JIRAM's NIR observations of Europa

Decades of observations of Europa's surface in the near-infrared (NIR), spanning spacecrafts like Galileo, Cassini and New Horizons, along with ground based observations, have revealed a rich mixture of species on Europa's surface. Adding to the NIR data of Europa, Juno spacecraft's spectrometer JIRAM has observed it in the 2–5 μm wavelength region. Here we present analysis of select spectra from this dataset, focusing on the two forms of water-ice - amorphous and crystalline. We were limited in our ability to include other dominant Europan species, like acid hydrate, due to unavailability of their optical constants over the entire JIRAM wavelength range. We also take this as an opportunity to present a novel Bayesian spectral inversion framework. Traditional spectral fitting methods, for example a grid-based search of parameter space, lack a systematic way to quantify detection significances of the species included in the model, statistically constrain surface properties and explore degenerecies of solution. Our Bayesian inference framework overcomes these shortcomings by confidently detecting amorphous and crystalline ice in the JIRAM data and permits probabilistic constraints on their compositions and average grain sizes to be obtained. We first validate our analysis framework using simulated spectra of amorphous and crystalline ice mixtures and a laboratory spectrum of crystalline ice. We next analyze the JIRAM data and, through Bayesian model comparisons, find that a two-component, intimately mixed model of amorphous and crystalline ice, henceforth referred to as TC-IM, is strongly preferred (at 26σ confidence) over a two-component model of the same materials but where their spectra are areally/linearly mixed. We also find that the TC-IM model is strongly preferred (at > 30σ confidence) over single-component models with only amorphous or crystalline ice, indicating the presence of both these phases of water ice in the data. Given the high SNR of the JIRAM data, abundances and grain sizes of amorphous and crystalline ice are very tightly constrained for the analysis with the TC-IM model. The solution corresponds to a mixture with a very large number density fraction (99.952−0.001+0.001 %) of small (23.12−1.01+1.01 microns) amorphous ice grains, and a very small fraction (0.048−0.001+0.001 %) of large (565.34−1.01+1.01 microns) crystalline ice grains. The overabundance of small amorphous ice grains we find is consistent with previous studies. The maximum-likelihood spectrum of the TC-IM model, however, is in tension with the data in the regions around 2.5 and 3.6 μm, and indicates the presence of non-ice components not currently included in our model. Our new technique therefore holds the promise of being able to identify these minor species hiding in Europan reflectance data in future work and constrain their abundances and physical properties.

Electron-stimulated desorption from molecular ices in the 0.15–2 keV regime

Electron-stimulated desorption (ESD) of cryosorbed molecules on surfaces is a process of relevance to fields as varied as vacuum dynamics in accelerators and astrochemistry. While desorption from such molecular systems induced by keV electrons and fast ions has been extensively studied, the sub-keV electron regime is comparatively little known. We measured and quantified electron-stimulated desorption from molecular ice systems (layers of N2, CO, CO2, Ar, and H2O/D2O condensed at cryogenic temperatures) in the 150–2000 eV electron energy range. In this regime, stopping power is no longer sufficient to explain the electron energy dependence of ESD yields. We introduce the notion of desorption-relevant depth, which characterizes the transition between two energy deposition regimes near the surface. We then apply this notion to the different systems, showing how ESD in the sub-keV regime can, for example, reveal the differences in species diffusion in crystalline and porous amorphous CO2 ices.

Predicting the refractive index of amorphous materials using the Bruggeman effective medium approximation.

Previous studies have shown that the Lorentz-Lorenz relationship, or molar refractivity/specific refractivity effective medium approximation, enables a reasonable prediction of the refractive index of amorphous water ice, given the refractive index of crystalline water ice. In the current study, we show that the Bruggeman effective medium approximation provides an even closer match to measurements of the refractive index of several amorphous materials, given the refractive index of their crystalline phase. We show that the Bruggeman effective medium approximation provides a good match to measurements of the refractive index of amorphous ice as well. Thus, assuming that the volume fraction of the scattering centers is a constant for a given amorphous material (with respect to a given range of wavelengths) seems to be a more robust assumption than assuming that the molar mass and molar refractivity or specific refractivity are preserved in going from the crystalline state to the amorphous state of the same material. Our results have implications for astrophysics applications, as well as for the optics of non-crystalline materials in general.

UV-ray irradiation never causes amorphization of crystalline CO2: A transmission electron microscopy study

The Crystallinity of ices, amorphous and crystalline, can be altered not only by heat but also by irradiation of UV-rays or charged particles. In this work, the effect of UV-irradiation on the crystallinity of CO2 ice was investigated by using a transmission electron microscope. A crystalline CO2 ice was produced by annealing amorphous CO2 ice. We found that UV-ray irradiation of CO2 crystals at approximately 10 K does not cause amorphization in contrast to the reported amorphization of crystalline water ice below 70 K. We discuss the difference based on the expected UV photochemistry of CO2 ice.

Chemical Desorption versus Energy Dissipation: Insights from Ab Initio Molecular Dynamics of HCO· Formation

Abstract Molecular clouds are the cold regions of the Milky Way where stars form. They are enriched by rather complex molecules. Many of these molecules are believed to be synthesized on the icy surfaces of the interstellar submicron-sized dust grains that permeate the Galaxy. At 10 K thermal desorption is inefficient and, therefore, why these molecules are found in the cold gas has tantalized astronomers for years. The assumption of the current models, called chemical desorption, is that the molecule formation energy released by the chemical reactions at the grain surface is partially absorbed by the grain and the remaining energy causes the ejection of the newly formed molecules into the gas. Here we report accurate ab initio molecular dynamics simulations aimed at studying the fate of the energy released by the first reaction of the H· addition chain to CO, H· + CO HCO·, occurring on a crystalline ice surface model. We show that about 90% of the HCO· formation energy is injected toward the ice in the first picosecond, leaving HCO· with an energy content (10–15 kJ mol−1) of less than half its binding energy (30 kJ mol−1). As a result, in agreement with laboratory experiments, we conclude that chemical desorption is inefficient for this specific system, namely H· + CO on crystalline ice. We suspect this behavior to be quite general when dealing with hydrogen bonds, which are responsible for both the cohesive energy of the ice mantle and the interaction with adsorbates, as HCO·, even though ad hoc simulations are needed to draw specific conclusions on other systems.

Transmission and Trapping of Low-Energy (1–10 eV) Electrons in Crystalline Ice Films

We studied the interactions between low-energy (1–10 eV) electrons and a crystalline ice film in a low fluence condition, where incident electrons interacted mostly with the pristine ice lattice. The electron beams were irradiated onto an ice film sample of large thickness (>100 monolayers) at 95 K. The kinetic energy and flux of incident electrons were maintained constant by applying an offset bias potential to the sample to compensate the charging voltage of an ice film developed by electron trapping. A Kelvin work-function probe was used to measure the charging voltage and estimate the electron trapping efficiency. The measurements for ice films with different thicknesses showed that low energy electrons transmitted through the ice films very efficiently. When electrons were trapped in the ice films, the trapping occurred preferentially at the surface of ice films. The electron trapping cross-section for the ice surface was estimated to be ≤(2.6 ± 0.3) × 10–23 m2 at the incident electron energy of 1–10 eV. The electron trapping cross-section for the ice interior was below ∼10–25 m2. In comparison, adsorbed SO2 and CFCl3 molecules on the ice surface were able to trap incident electrons much more efficiently than the surface water molecules, with corresponding cross sections of (1.1 ± 0.4) × 10–21 m2 and (2.8 ± 0.3) × 10–21 m2, respectively.

Amorphous and crystalline thioacetamide ice: Infrared spectra as a probe for temperature and structure

In this work we report the effect of intermolecular interactions on the structure of thioacetamide (CH3CSNH2) as a function of temperature, monitored by IR spectroscopy. Thin films of amorphous thioacetamide ice were deposited at 10 K and gradually warmed up to 260 K. Irreversible spectral changes between 180 and 200 K provide evidence for crystallization of the ice. Quantum chemical computations on a dodecamer of thioacetamide aided the assignment of the IR spectrum of the amorphous ice for the first time and allowed reassessing some of the earlier vibrational assignments of the crystalline form. This provides fundamental knowledge regarding the structure determination of thioacetamide (amorphous or crystalline). Upon repeated cooling and annealing of the crystalline sample, reversible spectral changes could also be detected, indicating that at temperatures below 150 K the methyl group undergoes a hindered torsional motion, while at higher temperatures the vibrationally excited methyl group exhibits virtually barrierless torsion. This interpretation was supported by computations, which have also provided estimates for the mean H-bond energies in the crystal. Investigation of low-temperature thioacetamide ice might be of interest from the astrophysical point of view. Moreover, the reversible temperature dependence of the vibrational spectra for the compounds with internal methyl rotor, such as thioacetamide, could serve as a molecular thermometer for cryogenic crystals.

Terahertz and mid-infrared spectroscopy of matrix-isolated clusters and matrix-sublimation ice of D2O.

We have established an apparatus for terahertz and mid-infrared spectroscopy in an ultrahigh vacuum and have measured absorption spectra of D2O clusters trapped in solid Ar. To assign terahertz absorption peaks due to the D2O dimer, trimer, and tetramer, the dependence of the spectrum on the annealing temperature and D2O dilution was analyzed. The assignment was also examined by ab initio calculations with the use of the "our own N-layered integrated molecular orbital and molecular mechanics" method, where the flexibility of surrounding Ar atoms was systematically incorporated. We identified all the intermolecular fundamentals of the dimer and those with significant intensities of the trimer and tetramer, whose structural symmetries were revealed to be broken down. After isolating the D2O clusters in solid Ar, we sublimated only Ar atoms to leave behind matrix-sublimation ice, which was found to be amorphous- or crystal-like depending on the formation conditions: the dilution and sublimation temperature. The crystallinity of matrix-sublimation ice was determined by decomposing its terahertz spectrum into the spectra of amorphous and crystalline ices. Since the crystallinity got higher by raising the dilution and sublimation temperature, the diffusion of the D2O monomer on the surface of sublimating solid Ar was found to be crucial to the crystallization of the sublimation ice.

Electronic, dielectric, and optical properties of two-dimensional and bulk ice: A multiscale simulation study

The intercalated water into nanopores exhibits anomalous properties such as ultralow dielectric constant.~Multi-scale modeling and simulations are used to investigate the dielectric properties of various crystalline two-dimensional ices and bulk ices. Although, the structural properties of two-dimensional (2D-) ices have been extensively studied, much less is known about their electronic and optical properties. First, by using density functional theory (DFT) and density functional perturbation theory (DFPT), we calculate the key electronic, optical and dielectric properties of 2D-ices. Performing DFPT calculations, both the ionic and electronic contributions of the dielectric constant are computed. The in-plane electronic dielectric constant is found to be larger than the out-of-plane dielectric constant for all the studied 2D-ices. The in-plane dielectric constant of the electronic response is found to be isotropic for all the studied ices. Secondly, we determined the dipolar dielectric constant of 2D-ices using molecular dynamics simulations (MDS) at finite temperature. The total out-of-plane dielectric constant is found to be larger than 2 for all the studied 2D-ices. Within the framework of the random-phase approximation (RPA), the absorption energy ranges for 2D-ices are found to be in the ultraviolet spectra. For the comparison purposes, we also elucidate the electronic, dielectric and optical properties of four crystalline ices (ice VIII, ice XI, ice Ic and ice Ih) and bulk water.

Thermal Formation of Ammonium Carbamate on the Surface of Laboratory Analogs of Carbonaceous Grains in Protostellar Envelopes and Planet-forming Disks

Abstract The catalytic role of dust grain surfaces in the thermal reaction CO2 + 2NH3 → NH4 +NH2COO− was recently demonstrated by our group. The rate coefficients for the reaction at 80 K on the surface of nanometer-sized carbon and silicate grains were measured to be up to three times higher compared to the reaction rate coefficients measured on KBr. In this study, the reaction was performed on carbon grains and on KBr in the extended temperature range of 50–80 K and with the addition of water ice. The reaction activation energy was found to be about three times lower on grains compared to the corresponding ice layer on KBr. Thus, the catalytic role of the dust grain surface in the studied reaction can be related to a reduction of the reaction barrier. Addition of water to NH3:CO2 ice on grains slowed the reaction down. At the H2O:CO2 ratio of 5:1, the reaction was not detected on the experimental timescale. This result calls into question the thermal formation of ammonium carbamate in dense molecular clouds and outer regions of protostellar and protoplanetary environments with dominating water ice mantle chemistry. However, it can still happen in inner regions of protostellar and protoplanetary environments in crystalline ices.