Clathrate hydrates with hydrogen-bonding guests

Exploring vacancy defects in s-I clathrate hydrates

This study investigates the role of vacancy defects in s-I clathrate hydrate structures, particularly in the presence of ethylene oxide (EO) molecules, through first-principles calculations. The structural properties, formation energies, and guest-host interactions of these vacancy defects were examined in both periodic systems and finite-size clusters. Our findings demonstrate that EO molecules significantly stabilize vacancy defects via hydrogen bonding, especially when forming double hydrogen bonds with dangling hydrogens (d-Hs) arising from the molecular vacancy defect. The encapsulation of EO in defect-free cages and its interaction with dangling oxygens (d-Os) were also analyzed, highlighting the superior stabilizing effect of double hydrogen bonds. These results provide new insights into the behavior of vacancy defects in hydrate structures and the potential role of polar guest molecules in enhancing defect stability and facilitating hydrate formation processes.

Bjerrum defects in s-II gas hydrate

The energy and structure of Bjerrum defects in structure II gas hydrates were investigated by using first-principle calculations for finite-size clusters and periodic 3D lattice systems. The formation energies of these defects were calculated for the first time when the cages of the structure II structure were completely empty and the large cage was filled with a THF molecule. Analogous to findings in ice structures, one of the hydrogen atoms forming the D defect was noted to orient toward the cage. If the excess proton resides in the large cage, it acts as an attraction center for the polar guest molecule, i.e., THF. Therefore, the large cage guest THF molecule stabilizes the D/L defect pair and isolated D/L defect formation energies by forming hydrogen bonds with the D defect. In such cases, the defect structure representing a D/L defect pair containing a THF molecule interacting with one of the hydrogen atoms of the D defect mirrors the guest-induced ones. Notably, the classical Bjerrum defect and the guest-induced Bjerrum defect exhibit a similar phenomenon in defective structures. Contrary to existing literature, it is evident that guest-induced Bjerrum defects involve both the L and D components. The insights gained from this study could potentially offer an alternative perspective to understand various experimental observations, such as those related to dielectric and NMR properties.

Ion-specific ice provides a facile approach for reducing ice friction

HYPOTHESIS

Ice friction plays a crucial role in both basic study and practical use. Various strategies for controlling ice friction have been developed. However, one unsolved puzzle regarding ice friction is the effect of ion-ice interplay on its tribological properties.

EXPERIMENTS AND SIMULATIONS

Here, we conducted ice friction experiments and summarized the specific effects of hydrated ions on ice friction. By selecting cations and anions, the coefficient of ice friction can be reduced by more than 70 percent. Experimental spectra, low-field nuclear magnetic resonance (LF-NMR), density functional theory (DFT) calculations, and Molecular dynamics (MD) simulations demonstrated that the addition of ions could break the H-bonds in water.

FINDINGS

The link between the charge density of ions and the coefficients of ice friction was revealed. A part of the ice structure was changed from an ice-like to a liquid-like interfacial water structure with the addition of ions. Lower charge density ions led to weaker ionic forces with the water molecules in the immobilized water layer, resulting in free water molecules increasing in the lubricating layer. This study provides guidance for preparing ice-making solutions with low friction coefficients and a fuller understanding of the interfacial water structure at low temperatures.

The impact of alcohol and ammonium fluoride on pressure-induced amorphization of cubic structure I clathrate hydrates

We have investigated pressure-induced amorphization (PIA) of an alcohol clathrate hydrate (CH) of cubic structure type I (sI) in the presence of NH4F utilizing dilatometry and x-ray powder diffraction. PIA occurs at 0.98 GPa at 77 K, which is at a much lower pressure than for other CHs of the same structure type. The amorphized CH also shows remarkable resistance against crystallization upon decompression. While amorphized sI CHs could not be recovered previously at all, this is possible in the present case. By contrast to other CHs, the recovery of the amorphized CHs to ambient pressure does not even require a high-pressure annealing step, where recovery without any loss of amorphicity is possible at 120 K and below. Furthermore, PIA is accessible upon compression at unusually high temperatures of up to 140 K, where it reaches the highest degree of amorphicity. Molecular dynamics simulations confirm that polar alcoholic guests, as opposed to non-polar guests, induce cage deformation at lower pressure. The substitution of NH4F into the host-lattice stabilizes the collapsed state more than the crystalline state, thereby enhancing the collapse kinetics and lowering the pressure of collapse.

Formation and Transformation of Clathrate Hydrates under Interstellar Conditions

ConspectusContinuing efforts by many research groups have led to the discovery of ∼240 species in the interstellar medium (ISM). Observatory- and laboratory-based astrochemical experiments have led to the discovery of these species, including several complex organic molecules (COMs). Interstellar molecular clouds, consisting of water-rich icy grains, have been recognized as the primordial sources of COMs even at extremely low temperatures (∼10 K). Therefore, it is paramount to understand the chemical processes of this region, which may contribute to the chemical evolution and formation of new planetary systems and the origin of life.This Account discusses our effort to discover clathrate hydrates (CHs) of several molecules and their structural varieties, transformations, and kinetics in a simulated interstellar environment. CHs are nonstochiometric crystalline host-guest complexes in which water molecules form cages of different sizes to entrap guest molecules. CHs are abundant on earth and require moderate temperatures and high pressures for their formation. Our focus has been to form CHs at extremely low pressure and temperature as in the ISM, although their existence under such conditions has been a long-standing question since water and guest molecules (CH4, CO2, CO, etc.) exist in space. In multiple studies conducted at ∼10-10 mbar, we showed that CH4, CO2, and C2H6 hydrates could be formed at 30, 10, and 60 K, respectively. Well-defined IR spectroscopic features supported by quantum chemical simulations and temperature-programmed desorption mass spectrometric analyses confirmed the existence of the 512 (for CH4 and CO2) and 51262 (for C2H6) CH cages. Mild thermal activation for long periods under ultrahigh vacuum (UHV) allowed efficient molecular diffusion, which is crucial for forming CHs. We also explored the formation of THF hydrate (a promoter/stabilizer for binary CHs), and a spontaneous method was found for its formation under UHV. In a subsequent study, we observed a binary THF-CO2 hydrate and its thermal processing at 130 K leading to the transportation of CO2 from the hydrate cages to the matrix of amorphous water. The findings imply that such systems possess a dynamic setting that facilitates the movement of molecules, potentially accounting for the chemical changes observed in the ISM. Furthermore, an intriguing fundamental phenomenon is the consequences of these CHs and their dynamics. We showed that preformed acetone and formaldehyde hydrates dissociate to form cubic (Ic) and hexagonal (Ih) ices at 130-135 K, respectively. These unique processes could be the mechanistic routes for the formation of various ices in astrophysical environments.Other than adding a new entry, namely, CHs, to the list of species found in ISM, its existence opens new directions to astrochemistry, observational astronomy, and astrobiology. Our work provides a molecular-level understanding of the formation pathways of CHs and their transformation to crystalline ices, which sheds light on the chemical evolution of simple molecules to COMs in ISM. Furthermore, CHs can be potential candidates for studies involving radiation, ionization, and electron impact to initiate chemical transformations between the host and guest species and may be critical in understanding the origin of life.

Hydrogen bonding guest-water interactions in pinacolone, tert-butyl amine, and tert-butylmethyl ether: a theoretical study on energetics, structure, and topological +

CONTEXT

In guest-host interactions, guest molecules used for hydrogen bonding potential of clathrate hydrate cages are involved as "promoters" for hydrogen or methane storage. Among the promoter molecules, there are pinacolone and tert-butylmethyl ether containing oxygen atom, and tert-butyl amine among those containing nitrogen atom. The dimer and trimer interactions of these molecules with the water clusters were investigated. The cooperativity effect, which is a measure of the hydrogen bonding of these oxygen and nitrogen-containing complexes, was calculated and these complexes were analyzed. Moreover, molecular electrostatic potential (MEP) analysis was performed to determine intermolecular interactions. Clusters of several molecules may seem like a non-significant state of matter; however, in systematic studies with small clusters, important results can be obtained. Therefore, it is very useful to work with clusters to understand the properties of the dense phase, and this study aimed to examine the properties of structures, energies, infrared vibration frequencies, and topological parameters, which develop as a result of the interaction of structures in different clusters with water molecules.

METHODS

The MP2 level was performed using aug-cc-pVDZ basis set calculations for this study. Tight converting criteria were used in the optimization step. Harmonic vibrational modes were calculated at the MP2/aug-cc-pVDZ level. Each minima obtained from the MP2 level was subjected to single-point energy calculations using CCSD(T) levels with the aug-cc-pVDZ basis set by the Gaussian16 package program suite. The topological analyses were performed with non-covalent interaction (NCI). MEP surface of the complex was also composed by Gaussian program using the optimized geometry at a MP2/aug-cc-pvdz level.

Thermally Induced Phase Transition of Cubic Structure II Hydrate: Crystal Structures of Tetrahydropyran-CO2 Binary Hydrate

We report a thermally induced phase transition of cubic structure II hydrates of tetrahydropyran (THP) and CO₂ below about 140 K. The phase transition was characterized by powder X-ray diffraction measurements at variable temperatures. A dynamical ordering of the CO₂ guests in small pentagonal dodecahedral 5¹² host water cages, not previously observed in the simple CO₂ hydrate, occurs simultaneously with the symmetry lowering transition from a cubic structure II (space group Fd-3m with cell dimensions a = 17.3202(7) Å at 153 K) to a tetragonal (space group I4₁/amd with cell dimensions a = 17.484(4) Å and c = 12.145(1) Å at 138 K) unit cell. The effect of guest molecules on the phase transition at low temperatures is discussed, which demonstrates that the clathrate hydrate structures and thermodynamic properties can be modified by adjusting the size and chemical structure of larger and smaller guest molecules.

A temperature programmed desorption study of interactions between water and hydrophobes at cryogenic temperatures

It is considered that hydrophobic solutes dissolve in water via the formation of icelike cages in the first hydration shell. However, this conventional picture is currently under debate. We have investigated how hydrophobic species, such as D₂, Ne, Ar, Xe, CH₄, and C₃H₈, interact with water in composite films of amorphous solid water (ASW) based on temperature programmed desorption (TPD). The D₂ and Ne species tend to be incorporated in ASW without being caged, whereas two distinct peaks assignable to the caged species are identifiable for the other solutes examined here. The low-temperature peak is observed preferentially for Ar and CH₄ prior to crystallization. The hydrophobes are thought to be encapsulated in porous ASW films via reorganization of the hydrogen bond network up to 100 K; most of them are released in a liquidlike phase that occurs immediately before crystallization at ca. 160 K. The nature of hydrophobic hydration at cryogenic temperature appears to differ from that in normal water at room temperature because the former resembles crystalline ices in the local hydrogen-bond structure rather than the latter. No ordered structures assignable to clathrate hydrates were identified before and after crystallization.

Host-Guest Hydrogen Bonding in High-Pressure Acetone Clathrate Hydrates: In Situ Single-Crystal X-ray Diffraction Study

The phenomenon of host-guest hydrogen bonding in clathrate hydrate crystal structures and its effect on physical and chemical properties have become subjects of extensive research. Hydrogen bonding has been studied for cubic (sI and sII) and hexagonal (sH) binary clathrates, while it has not been addressed for clathrate structures that exist at elevated pressures. Here, four acetone hydrate clathrates have been grown at high-pressure and low-temperature conditions. In situ single-crystal X-ray diffraction revealed that the synthesized phases possess already known trigonal (sTr), orthorhombic (sO), and tetragonal (sT) crystal structures as well as a previously unknown orthorhombic structure, so-called sO-II. Only sO and sII have previously been reported for acetone clathrates. Structural analysis suggests that acetone oxygens are hydrogen-bonded to the closest water oxygens of the host frameworks. Our discoveries show that clathrate hydrates hosting polar molecules are not as exotic as previously thought and could be stabilized at high-pressure conditions through hydrogen bonding.

Comment on “Cage occupancy of methane clathrate hydrates in the ternary H2O–NH3–CH4 system” by C. Petuya, M. Choukroun, T. H. Vu, A. Desmedt, A. G. Davies, and C. Sotin, Chem. Commun., 2020, , 12391

Alternative interpretations of the experimental results given in the cited Communication are presented. There is evidence that under certain conditions, ammonia can be incorporated into clathrate hydrate cages.

To be or not to be? that is the entropic, enthalpic, and molecular interaction dilemma in the formation of (water)20 clusters and methane clathrate

A detailed analysis under a comprehensive set of theoretical and computational tools of the thermodynamical factors and of the intermolecular interactions behind the stabilization of a well known set of (water)20 cavities and of the methane clathrate is offered in this work. Beyond the available reports of experimental characterization at extreme conditions of most of the systems studied here, all clusters should be amenable to experimental detection at 1 atm and moderate temperatures since 280 K marks the boundary at which, ignoring reaction paths, formation of all clusters is no longer spontaneous from the 20H2O → (H2O)20 and CH4 + 20H2O → CH4@512 processes. As a function of temperature, a complex interplay leading to the free energy of formation occurs between the destabilizing entropic contributions, mostly due to cluster vibrations, and the stabilizing enthalpic contributions, due to intermolecular interactions and the PV term, is best illustrated by the highly symmetric 512 cage consistently showing signs of stronger intermolecular bonding despite having smaller binding energy than the other clusters. A fluxional wall of attractive non-covalent interactions, arising because of the cumulative effect of a large number of tiny individual charge transfers to the interstitial region, plays a pivotal role stabilizing the CH4@512 clathrate.

Local structure and distortions of mixed methane-carbon dioxide hydrates

A vast source of methane is found in gas hydrate deposits, which form naturally dispersed throughout ocean sediments and arctic permafrost. Methane may be obtained from hydrates by exchange with hydrocarbon byproduct carbon dioxide. It is imperative for the development of safe methane extraction and carbon dioxide sequestration to understand how methane and carbon dioxide co-occupy the same hydrate structure. Pair distribution functions (PDFs) provide atomic-scale structural insight into intermolecular interactions in methane and carbon dioxide hydrates. We present experimental neutron PDFs of methane, carbon dioxide and mixed methane-carbon dioxide hydrates at 10 K analyzed with complementing classical molecular dynamics simulations and Reverse Monte Carlo fitting. Mixed hydrate, which forms during the exchange process, is more locally disordered than methane or carbon dioxide hydrates. The behavior of mixed gas species cannot be interpolated from properties of pure compounds, and PDF measurements provide important understanding of how the guest composition impacts overall order in the hydrate structure.

Stability and NMR Chemical Shift of Amorphous Precursors of Methane Hydrate: Insights from Dispersion-Corrected Density Functional Theory Calculations Combined with Machine Learning

Clathrate hydrates of natural gases are important backup energy sources. It is thus of great significance to explore the nucleation process of hydrates. Hydrate clusters are building blocks of crystalline hydrates and represent the initial stage of hydrate nucleation. Using dispersion-corrected density functional theory (DFT-D) combined with machine learning, herein, we systematically investigate the evolution of stabilities and nuclear magnetic resonance (NMR) chemical shifts of amorphous precursors from monocage clusters CH₄(H₂O)_n (n = 16-24) to decacage clusters (CH₄)₁₀(H₂O)_n (n = 121-125). Compared with planelike configurations, the close-packed structures formed by the water-cage clusters are energetically favorable. The 5¹² cages are dominant, and the emerging amorphous precursors may be part of sII hydrates at the initial stage of nucleation. Based on our data set, the possible initial fusion pathways for water-cage clusters are proposed. In addition, the ¹³C NMR chemical shifts for encapsulated methane molecules also showed regular changes during the fusion of water-cage clusters. Machine learning can reproduce the DFT-D results well, providing a structure-energy-property landscape that could be used to predict the energy and NMR chemical shifts of such multicages with more water molecules. These theoretical results present vital insights into the hydrate nucleation from a unique perspective.

Formation of Cubic Ice via Clathrate Hydrate, Prepared in Ultrahigh Vacuum under Cryogenic Conditions

Cubic ice (ice I_c) is a crystalline phase of solid water, which exists in the earth's atmosphere and extraterrestrial environments. We provide experimental evidence that dissociation of acetone clathrate hydrate (CH) makes ice I_c in ultrahigh vacuum (UHV) at 130-135 K. In this process, we find that crystallization of ice I_c occurs below its normal crystallization temperature. Time-dependent reflection absorption infrared spectroscopy (RAIRS) and reflection high-energy electron diffraction (RHEED) were utilized to confirm the formation of ice I_c. Associated crystallization kinetics and activation energy (E_a) for the process were evaluated. We suggest that enhanced mobility or diffusion of water molecules during acetone hydrate dissociation enabled crystallization. Moreover, this finding implied that CHs might exist in extreme low-pressure environments present in comets. These hydrates, subjected to prolonged thermal annealing, transform into ice I_c. This unique process of crystallization hints at a possible mechanistic route for the formation of ice I_c in comets.

Energy and Environmental Analysis of Membrane-Based CH4-CO2 Replacement Processes in Natural Gas Hydrates

Natural gas hydrates are the largest reservoir of natural gas worldwide. This paper proposes and analyzes the CH4-CO2 replacement in the hydrate phase and pure methane collection through the use of membrane-based separation. The investigation uses a 1 L lab reactor, in which the CH4 hydrates are formed in a quartz sand matrix partially saturated with water. CH4 is subsequently dissociated with a CO2 stream supplied within the sediment inside the reactor. An energy and environmental analysis was carried out to prove the sustainability of the process. Results show that the process energy consumption constitutes 4.75% of the energy stored in the recovered methane. The carbon footprint of the CH4-CO2 exchange process is calculated as a balance of the CO2 produced in the process and the CO2 stored in system. Results provide an estimated negative value, equal to 0.004 moles sequestrated, thus proving the environmental benefit of the exchange process.

Clathrate hydrates in interstellar environment

Clathrate hydrates (CHs) are ubiquitous in earth under high-pressure conditions, but their existence in the interstellar medium (ISM) remains unknown. Here, we report experimental observations of the formation of methane and carbon dioxide hydrates in an environment analogous to ISM. Thermal treatment of solid methane and carbon dioxide-water mixture in ultrahigh vacuum of the order of 10^-10 mbar for extended periods led to the formation of CHs at 30 and 10 K, respectively. High molecular mobility and H bonding play important roles in the entrapment of gases in the in situ formed 5¹² CH cages. This finding implies that CHs can exist in extreme low-pressure environments present in the ISM. These hydrates in ISM, subjected to various chemical processes, may act as sources for relevant prebiotic molecules.

Macroscopic defects upon decomposition of CO2 clathrate hydrate crystals

Cracks and decomposition barriers observed in time-lapse micro-computed tomography measurements challenge existing models of gas hydrate decomposition.

NH3 as simple clathrate-hydrate catalyst: Experiment and theory

The catalytic action of NH₃ within the all-vapor approach for instant clathrate hydrate (CH) formation is studied using both FTIR spectroscopy and ab initio molecular dynamics simulations. A unique property of NH₃, namely, the rapid abundant penetration and occupation of the water network, creates defects, particularly Bjerrum D-defects, in the hydrate frame that are generally stabilized by guest NH₃ molecules in the cages. Furthermore, insertion of NH₃ seriously disturbs the hydrate network where the guest NH₃ molecules also make fluxional H-bonds with the host water molecules. These defects strongly facilitate a sub-second formation of the simple NH₃ s-II gas hydrate at 160 K. FTIR spectra of aerosols of the NH₃ s-II CH have been measured, and the displacement of both small and large cage NH₃ guests by CO₂ and tetrahydrofuran is examined.

Compatibility of Amino Acids in Ice Ih: Implications for the Origin of Life

Icy environments may have been common on early Earth due to the faint young sun. Previous studies have proposed that the formation of large icy bodies in the early ocean could concentrate the building blocks of life in eutectic fluids and, therefore, facilitate the polymerization of monomers. This hypothesis is based on the untested assumption that organic molecules are virtually incompatible in ice Ih (hexagonal ice). In this study, we conducted freezing experiments to explore the partitioning behavior of selected amino acids (AAs; glycine, l-alanine, l-proline, and l-phenylalanine) between ice Ih and aqueous solutions analogous to seawater. We allowed ice crystals to grow slowly from a few seeds in equilibrium with the solution and used Raman spectroscopy to analyze in situ the relative concentrations of AAs in the ice and aqueous solution. During freezing, there was no precipitation of AA crystals, indicating that the concentrations in solution never reached their solubility limit, even when the droplet was mostly frozen. Analyses of the Raman spectra of the ice and eutectic solution suggested that considerable amounts of AAs existed in the ice phase with partition coefficients varying between 0.2 and 0.5. These observations imply little incompatibility of AAs in ice Ih during the freezing of the solutions, rendering the concentration hypothesis in a eutectic system unwarranted. However, incorporation into ice Ih could protect AAs from decomposition or racemization and significantly improve the efficiency of extraterrestrial transport of small organics. Therefore, this study supports the hypothesis of extraterrestrial delivery of organic molecules in icy comets and asteroids to the primitive Earth as suggested by an increasing number of independent observations. Key Words: Ice Ih-Partition coefficient-Amino acids-Polymerization-Extraterrestrial transport of organics. Astrobiology 18, 381-392.

How Water's Properties Are Encoded in Its Molecular Structure and Energies

How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.

Kinetics of Trifluoromethane Clathrate Hydrate Formation from CHF3 Gas and Ice Particles

We report the formation kinetics of trifluoromethane clathrate hydrate (CH) from less than 75 μm diameter ice particles and CHF₃ gas. As previously observed for difluoromethane and propane hydrate formation, the initial stages of the reaction exhibit a strong negative correlation of the reaction rate with temperature, consistent with a negative activation energy of formation. The values obtained for trifluoromethane, ca. -6 kJ/mol (H₂O), are similar to those for difluoromethane, even though the two molecules have different intermolecular interactions and sizes. The activation energy is lesser per mole of H₂O, but greater per mole of guest molecule, than for propane hydrate, which has a different crystal structure. We propose a possible explanation for the negative activation barrier based on the stabilization of metastable structures at low temperature. A pronounced dependence of the formation kinetics on the gas flow rate into the cell is observed. At 253 K and a flow rate of 15 mmol/h, the stage II enclathration of trifluoromethane proceeds so quickly that the overpressure, the difference between the gas cell pressure and the hydrate vapor pressure, is only 0.06 MPa.

Influence of temperature on methane hydrate formation

During gas hydrate formation process, a phase transition of liquid water exists naturally, implying that temperature has an important influence on hydrate formation. In this study, methane hydrate was formed within the same media. The experimental system was kept at 1.45, 6.49, and 12.91 °C respectively, and then different pressurization modes were applied in steps. We proposed a new indicator, namely the slope of the gas flow rates against time (dν g /dt), to represent the intrinsic driving force for hydrate formation. The driving force was calculated as a fixed value at the different stages of formation, including initial nucleation/growth, secondary nucleation/growth, and decay. The amounts of gas consumed at each stage were also calculated. The results show that the driving force during each stage follows an inverse relation with temperature, whereas the amount of consumed gas is proportional to temperature. This opposite trend indicates that the influences of temperature on the specific formation processes and final amounts of gas contained in hydrate should be considered separately. Our results also suggest that the specific ambient temperature under which hydrate is formed should be taken into consideration, when explaining the formation of different configurations and saturations of gas hydrates in natural reservoirs.

NH3 as unique non-classical content-former within clathrate hydrates

High quality FTIR spectra of aerosols of NH₃-THF and NH₃-TMO binary clathrate hydrates (CHs) have been measured. Our recently developed all-vapor sub-second approach to clathrate-hydrate formation combined with computational studies has been used to identify vibrational spectroscopic signatures of NH₃ within the gas hydrates. The present study shows that there are three distinct NH₃ types, namely, classical small-cage NH₃, nonclassical small-cage NH₃, and NH₃ within the hydrate network. The network ammonia does not directly trigger the non-classical CH structure. Rather, the ammonia within the network structure perturbs the water bonding, introducing orientational defects that are stabilized by small and/or large cage guest molecules through H-bonding. This unusual behavior of NH₃ within CHs opens a possibility for catalytic action of NH₃ during CH-formation. Furthermore, impacts over time of the small-cage NH₃-replacement molecules CO₂ and CH₄ on the structure and composition of the ternary CHs have been noted.

Ion-specific ice recrystallization provides a facile approach for the fabrication of porous materials

Ice recrystallization is of great importance to both fundamental research and practical applications, however understanding and controlling ice recrystallization processes remains challenging. Here, we report the discovery of an ion-specific effect on ice recrystallization. By simply changing the initial type and concentration of ions in an aqueous solution, the size of ice grains after recrystallization can be tuned from 27.4±4.1 to 277.5±30.9 μm. Molecular dynamics simulations show that the ability of the ion to be incorporated into the ice phase plays a key role in the ultimate size of the ice grains after recrystallization. Moreover, by using recrystallized ice crystals as templates, 2D and 3D porous networks with tuneable pore sizes could be prepared from various materials, for example, NaBr, collagen, quantum dots, silver and polystyrene colloids. These porous materials are suitable for a wide range of applications, for example, in organic electronics, catalysis and bioengineering.

Thermodynamic Stability of Structure II Methyl Vinyl Ketone Binary Clathrate Hydrates and Effects of Secondary Guest Molecules on Large Guest Conformation

Clathrate hydrates have received massive attention because of their potential application as energy storage materials. Host water frameworks of clathrate hydrates provide empty cavities that can capture not only small molecular guests but also radical species induced by γ-irradiation. In this work, we investigated structure II methyl vinyl ketone (MVK) binary clathrate hydrates with CH₄, O₂, and N₂ and the effects of secondary guest species on MVK conformation in the cavity of hydrate and on the thermodynamic stability of unirradiated and γ-irradiated hydrate phases. The present findings provide meaningful information to understand the nature of guest-host interactions in γ-irradiated clathrate hydrates and to open up practical applications for hydrate-based nanoreactors.

Dense Semi-Clathrates at High Pressure: A Study of the Water-tert-Butylamine System

In situ high-pressure crystallization and diffraction techniques have been applied to obtain two very structurally distinct semi-clathrates of the tert-butylamine-water system with hydration numbers 5.65 and 5.8, respectively, thereby considerably reducing a notable hydration gap between the monohydrate and the 71/4 -hydrate that results when crystallization space is explored by temperature alone. Both structures can be considered as an intriguing solid-state example of hydrophobic hydration, in which the water network creates wide tert-butylamine-filled channels stabilized by cross-linking hydrogen bonds. The existence of interconnected channels might also add low hydration structures to a list of potential targets for hydrogen storage. A detailed analysis of the topology of host water and host-guest interactions is reported and extended to those of other hydrates of the compound. This analysis offers new insight into properties of the tert-butylamine-water system and provides some clues as to the occurrence of the sizable number of hydrates of this compound.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates

Clathrate hydrate phases of Cl₂ and Br₂ guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen–halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen–halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme–substrate compounds. The nature of the halogen–water interactions for the Cl₂ and Br₂ molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl₂ and Br₂ guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

Fast crystalline ice formation at extremely low temperature through water/neon matrix sublimation

Crystalline ice formation requires water molecules to be sufficiently mobile to find and settle on the thermodynamically most stable site.

Unraveling Mixed Hydrate Formation: Microscopic Insights into Early Stage Behavior

The molecular-level details of mixed hydrate nucleation remain unclear despite the broad implications of this process for a variety of scientific domains. Through analysis of mixed hydrate nucleation in a prototypical CH₄/H₂S/H₂O system, we demonstrate that high-level kinetic similarities between mixed hydrate systems and corresponding pure hydrate systems are not a reliable basis for estimating the composition of early stage mixed hydrate nuclei. Moreover, we show that solution compositions prior to and during nucleation are not necessarily effective proxies for the composition of early stage mixed hydrate nuclei. Rather, microscopic details, (e.g., guest-host interactions and previously neglected cage types) apparently play key roles in determining early stage behavior of mixed hydrates. This work thus provides key foundational concepts and insights for understanding mixed hydrate nucleation.

Characterization of Free Radicals in Clathrate Hydrates of Furan, 2,3-Dihydrofuran, and 2,5-Dihydrofuran by Muon Spin Spectroscopy

In addition to their importance as abundant hydrocarbon deposits in nature, clathrate hydrates are being studied as potential media for hydrogen and carbon dioxide storage and as "nano-reactors" for small molecules. However, little is known about the behavior of reactive species in such materials. We have employed muon spin spectroscopy to characterize various organic free radicals that reside as isolated guests in structure II clathrates. The radicals are formed by reaction of atomic muonium (Mu) with the guest molecules furan and two isomeric dihydrofurans. Muonium is essentially a light isotope of hydrogen and adds to unsaturated molecules in the same manner as H. We have determined muon and proton hyperfine coupling constants for the muoniated radicals formed in the clathrates and also in neat liquids at the same temperature. DFT calculations were used to guide the spectral assignments and distinguish between competing radical products for Mu addition to furan and 2,3-dihydrofuran. Relative signal amplitudes provide yields and thus the relative reactivities of the C4 and C5 addition sites in these molecules. Spectral features, hyperfine constants, and reactivities all indicate that the radicals do not tumble freely in the clathrate cages in the same way that they do in liquids.

Evidence from mixed hydrate nucleation for a funnel model of crystallization

The molecular-level details of crystallization remain unclear for many systems. Previous work has speculated on the phenomenological similarities between molecular crystallization and protein folding. Here we demonstrate that molecular crystallization can involve funnel-shaped potential energy landscapes through a detailed analysis of mixed gas hydrate nucleation, a prototypical multicomponent crystallization process. Through this, we contribute both: (i) a powerful conceptual framework for exploring and rationalizing molecular crystallization, and (ii) an explanation of phenomenological similarities between protein folding and crystallization. Such funnel-shaped potential energy landscapes may be typical of broad classes of molecular ordering processes, and can provide a new perspective for both studying and understanding these processes.

Micro-Tomographic Investigation of Ice and Clathrate Formation and Decomposition under Thermodynamic Monitoring

Clathrate hydrates are inclusion compounds in which guest molecules are trapped in a host lattice formed by water molecules. They are considered an interesting option for future energy supply and storage technologies. In the current paper, time lapse 3D micro computed tomographic (µCT) imaging with ice and tetrahydrofuran (THF) clathrate hydrate particles is carried out in conjunction with an accurate temperature control and pressure monitoring. µCT imaging reveals similar behavior of the ice and the THF clathrate hydrate at low temperatures while at higher temperatures (3 K below the melting point), significant differences can be observed. Strong indications for micropores are found in the ice as well as the THF clathrate hydrate. They are stable in the ice while unstable in the clathrate hydrate at temperatures slightly below the melting point. Significant transformations in surface and bulk structure can be observed within the full temperature range investigated in both the ice and the THF clathrate hydrate. Additionally, our results point towards an uptake of molecular nitrogen in the THF clathrate hydrate at ambient pressures and temperatures from 230 K to 271 K.

Propane Clathrate Hydrate Formation Accelerated by Methanol

The role of methanol as both an inhibitor and a catalyst for the formation of clathrate hydrates (CHs) has been a topic of intense study. We report a new quantitative study of the kinetics of propane CH formation at 253 K from the reaction of propane gas with <75 μm ice particles that have been doped with varying amounts of methanol. We find that methanol significantly accelerates the formation reaction with quite small doping quantities. Even for only 1 methanol molecule per 10 000 water molecules, the maximum uptake rate of propane into CHs is enhanced and the initiation pressure is reduced. These results enable more efficient production of CHs for gas storage. This remarkable acceleration of the CH formation reaction by small quantities of methanol may place constraints on the mechanism of the inhibition effect observed under other conditions, usually employing much larger quantities of methanol.

Disorder of Hydrofluorocarbon Molecules Entrapped in the Water Cages of Structure I Clathrate Hydrate

Water versus fluorine: Clathrate hydrates encaging hydrofluorocarbons as guests show both isotropic and anisotropic distributions within host water cages, depending on the number of fluorine atoms in the guest molecule; this is caused by changes in intermolecular interactions to host water molecules in the hydrates.

Molecular Modes and Dynamics of HCl and DCl Guests of Gas Clathrate Hydrates

Recent years have yielded advances in the placement of unusual molecules as guests within clathrate hydrates (CHs) without severe distortion of the classic lattice structures. Reports describing systems for which observable but limited distortion does occur are available for methanol, ammonia, acetone, and small ether molecules. In these particular examples, the large-cage molecules often participate as non-classical guests H-bonded to the cage walls. Here, we expand the list of such components to include HCl/DCl and HBr as small-cage guests. Based on FTIR spectra of nanocrystalline CHs from two distinct preparative methods combined with critical insights derived from on-the-fly molecular dynamics and ab initio computational data, a coherent argument emerges that these strong acids serve as a source of molecular small-cage guests, ions, and orientational defects. Depending on the HCl/DCl content the ions, defects and molecular guests determine the CH structures, some of which form in sub-seconds via an all-vapor preparative method.

Towards Clathrates: Frozen States of Hydration of tert-Butylamine

The dilution of tert-butylamine (tBA) with water and subsequent cooling leads to a large series of different crystalline hydrates by an in situ IR laser melting-zone procedure. The crystal structures were determined for tBA⋅n H2 O, with n=0, 1/4, 1, 7 1/4, 7 3/4, 9 3/4, 11, and 17. For the two lower hydrates (n= 1/4, 1), one- and two-dimensional hydrogen-bonded networks are formed, respectively. The higher hydrates (n>1) exhibit a clathrate-like three-dimensional water framework with the tBA molecules as part of, or sitting inside, the cages. In all cases, tBA is hydrogen-bonded to the H2 O framework. In the intermediate range (1<n<7 1/4), crystallization is hindered, and no crystalline phases could be observed. The crystal structures that are achieved from the dilution of tBA with water are considered to be frozen stages of hydration, describing the genesis of such clathrate-like structures, finally ending at ice as an example of an infinitely diluted hydrate.

The nucleation of gas hydrates near silica surfaces

Understanding the nucleation and crystal growth of gas hydrates near mineral surfaces and in confinement are critical to the methane recovery from gas hydrate reservoirs. In this work, through molecular dynamics simulation studies, we present an exploration of the nucleation behavior of methane hydrates near model hydroxylated silica surfaces. Our simulation results indicate that the nucleation of methane hydrates can initiate from the silica surfaces despite of the structural mismatch of the two solid phases. A layer of intermediate half-cage structures was observed between the gas hydrate and silica surfaces, apparently helping to minimize the free energy penalty. These results have important implications to our understanding of the effects of solid surfaces on hydrate nucleation processes.

A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates

Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

Catalytic activity of methanol in all-vapor subsecond clathrate-hydrate formation

Methanol's property as a catalyst in the formation of gas clathrate hydrates has been recognized for several years and was recently employed in a broad ranging study [K. Shin, K. A. Udachin, I. L. Moudrakovski, D. M. Leek, S. Alavi, C. I. Ratcliffe, and J. A. Ripmeester, Proc. Natl. Acad. Sci. U.S.A. 110, 8437 (2013)]. A new measure of that activity is offered here from comparative rates of formation of methanol (MeOH) clathrate hydrates within our all-vapor aerosol methodology for which tetrahydrofuran (THF) and other small ethers have set a standard for catalytic action. We have previously described numerous examples of the complete conversion of warm all-vapor mixtures to aerosols of gas clathrate hydrates on a sub-second time scale, generally with the catalyst confined primarily to the large cage of either structure-I (s-I) or structure-II (s-II) hydrates. THF has proven to be the most versatile catalyst for the complete subsecond conversion of water to s-II hydrate nanocrystals that follows pulsing of appropriate warm vapor mixtures into a cold chamber held in the 140-220 K range. Here, the comparative ability of MeOH to catalyze the formation of s-I hydrates in the presence of a small-cage help-gas, CO2 or acetylene, is examined. The surprising result is that, in the presence of either help gas, CH-formation rates appear largely unchanged by a complete replacement of THF by MeOH in the vapor mixtures for a chamber temperature of 170 K. However, as that temperature is increased, the dependence of effective catalysis by MeOH on the partial pressure of help gases also increases. Nevertheless, added MeOH is shown to markedly accelerate the s-II THF-CO2 CH formation rate at 220 K.