Clathrate Cages Research Articles

Silicon Clathrate-Supported Catalysts with Low Work Functions for Ammonia Synthesis.

Diamond-type silicon has a work function of ≈4.8eV, and conventional n- or p-type doping modifies the value only between 4.6 and 5.05eV. Here, it is shown that the alkali clathrates AxSi46 have substantially lower work functions approaching 2.6eV, with clear trends between alkali electropositivity and clathrate cage size. The low work function enables alkali clathrates such as K8Si46 to be effective Haber-Bosch catalyst supports for NH3 synthesis. The catalytic properties of Si, Ge, and Sn-based clathrates are investigated while supporting Fe and Ru on the surface. The activity largely scales with the work function, and low activation energies below 60kJ mol-1 are observed due to strong electron donation effects from the support. Ru metal and Sn clathrates seem to be unsuitable for stability issues. Compared to other similar hydride/electride catalysts, the simple structure and composition combined with stability in air/water make a systematic study of these clathrates possible and open the door to other electron-rich Zintl phases and related intermetallics as low-work function materials suitable for catalysis. The observed low work function may also have implications for other existing electronic applications.

Mechanical properties and cage transformations in CO2-CH4 heterohydrates: a molecular dynamics and machine learning study

Abstract The substitution of natural gas hydrates with CO2 offers a compelling dual advantage by enabling the extracting of CH4 while simultaneously sequestering CO2. This process, however, is intricately tied to the mechanical stability of CO2-CH4 heterohydrates. In this study, we report the mechanical properties and cage transformations in CO2-CH4 heterohydrates subjected to uniaxial straining via molecular dynamics (MD) simulations and machine learning (ML). Results indicate that guest molecule occupancy, the ratio of CO2 to CH4 and their spatial arrangements within heterohydrate structure greatly dictate the mechanical properties of CO2–CH4 heterohydrates including Young’s modulus, tensile strength, and critical strain. Notable, the introduction of CO2 within clathrate cages, particularly within 512 small cages, weakens the stability of CO2–CH4 heterohydrates in terms of mechanical properties. Upon critical strains, unconventional clathrate cages form, contributing to loading stress oscillation before fracture of heterohydrates. Intriguingly, predominant cage transformations, such as 51262–4151063 or 425864 and 512–425861 cages, are identified, in which 4151062 appears as primary intermediate cage that is able to transform into 4151063, 425862, 425863, 512 and 51262 cages, unveiling the dynamic nature of heterohydrate structures under straining. Additionally, ML models developed using MD data well predict the mechanical properties of heterohydrates, and underscore the critical influence of the spatial arrangement of guest molecules on the mechanical properties. These newly-developed ML models serve as valuable tools for accurately predicting the mechanical properties of heterohydrates. This study provides fresh insights into the mechanical properties and cage transformations in heterohydrates in response to strain, holding significant implications for environmentally sustainable utilization of CO2–CH4 heterohydrates.

Predicted hot superconductivity in LaSc2H24 under pressure

The recent theory-driven discovery of a class of clathrate hydrides (e.g., CaH6, YH6, YH9, and LaH10) with superconducting critical temperatures (Tc) well above 200 K has opened the prospects for "hot" superconductivity above room temperature under pressure. Recent efforts focus on the search for superconductors among ternary hydrides that accommodate more diverse material types and configurations compared to binary hydrides. Through extensive computational searches, we report the prediction of a unique class of thermodynamically stable clathrate hydrides structures consisting of two previously unreported H24 and H30 hydrogen clathrate cages at megabar pressures. Among these phases, LaSc2H24 shows potential hot superconductivity at the thermodynamically stable pressure range of 167 to 300 GPa, with calculated Tcs up to 331 K at 250 GPa and 316 K at 167 GPa when the important effects of anharmonicity are included. The very high critical temperatures are attributed to an unusually large hydrogen-derived density of states at the Fermi level arising from the newly reported peculiar H30 as well as H24 cages in the structure. Our predicted introduction of Sc in the La-H system is expected to facilitate future design and realization of hot superconductors in ternary clathrate superhydrides.

HTR+: a novel algorithm for identifying type and polycrystal of gas hydrates

In this work, the hierarchical topology ring (HTR+) algorithm, an extension of the HTR algorithm, was developed for identifying gas hydrate types, cage structures, and grain boundaries (GBs) within polycrystalline structures. Utilizing molecular dynamics trajectories of polycrystalline hydrates, the accuracy of the HTR+ algorithm is validated in identifying sI, sII and sH hydrate types, hydrate grains, and GBs in multi-hydrate polycrystals, as well as clathrate cages at GBs. Additionally, during the hydrate nucleation and growth processes, clathrate cages, hydrate type, hydrate grains and ice structures are accurately recognized. Significantly, this algorithm demonstrates high efficiency, particularly for large hydrate systems. HTR+ algorithm emerges a powerful tool for identifying micro/mesoscopic structures of gas hydrates, enabling an in-depth understanding of the formation mechanisms and properties of gas hydrates.

Interplay between the Formation of Colloidal Clathrate and Cubic Diamond Crystals.

Controlling the valency of directional interactions of patchy particles is insufficient for the selective formation of target crystalline structures due to the competition between phases of similar free energy. Examples of such are stacking hybrids of interwoven hexagonal and cubic diamonds with (i) its liquid phase, (ii) arrested glasses, or (iii) clathrates, all depending on the relative patch size, despite being within the one-bond-per-patch regime. Herein, using molecular dynamics simulations, we demonstrate that although tetrahedral patchy particles with narrow patches can assemble into clathrates or stacking hybrids in the bulk, this behavior can be suppressed by the application of external surface potential. Depending on its strength, the selective growth of either cubic diamond crystals or empty sII clathrate cages can be achieved. The formation of a given ordered network depends on the structure of the first adlayer, which is commensurate with the emerging network.

Superconducting ternary hydrides in Ca-U-H under high pressure

The research on hydrogen-rich ternary compounds attract tremendous attention for it paves new route to room-temperature superconductivity at lower pressures. Here, we study the crystal structures, electronic structures, and superconducting properties of the ternary Ca-U-H system, combining crystal structure predictions with ab-initio calculations under high pressure. We found four dynamically stable structures with hydrogen clathrate cages: CaUH12-Cmmm, CaUH12-Fd-3m, Ca2UH18-P-3m1, and CaU3H32-Pm-3m. Among them, the Ca2UH18-P-3m1 and CaU3H32-Pm-3m are likely to be synthesized below 1 megabar. The f electrons in U atoms make dominant contribution to the electronic density of states around the Fermi energy. The electron-phonon interaction calculations reveal that phonon softening in the mid-frequency region can enhance the electron–phonon coupling significantly. The T c value of Ca2UH18-P-3m1 is estimated to be 57.5–65.8 K at 100 GPa. Our studies demonstrate that introducing actinides into alkaline-earth metal hydrides provides possibility in designing novel superconducting ternary hydrides.

Two-photon chemistry of tetrahydrofuran in clathrate hydrates.

High-lying electronic states hold the potential for new and unusual photochemical reactions. However, for conventional single-photon excitation in the condensed phase, reaching these states is often not possible because the vacuum-ultraviolet (VUV) light required is competitively absorbed by the surrounding matrix rather than the molecule of interest. Here, this hurdle is overcome by leveraging nonresonant two-photon absorption (2PA) at 265 nm to achieve preferential photolysis of tetrahydrofuran (THF) trapped within a clathrate hydrate network at 77 K. Electron spin resonance (ESR) spectroscopy enables direct observation and identification of otherwise short-lived organic radicals stabilized by the clathrate cages, providing clues into the rapid dynamics that immediately follow photoexcitation. 2PA induces extensive fragmentation of enclathrated THF yielding 1-alkyl, acyl, allyl and methyl radicals-a stark departure from the reactive motifs commonly reported in γ-irradiated hydrates. We speculate on the undetected transient dynamics and explore the potential role of trapped electrons generated from water and THF. This demonstration of nonresonant two-photon chemistry presents an alternative approach to targeted condensed phase photochemistry in the VUV energy range.

Insights into the mechanical stability of tetrahydrofuran hydrates from experimental, machine learning, and molecular dynamics perspectives.

Natural gas hydrates (NGHs) hold immense potential as a future energy resource and for sustainable applications such as gas capture and storage. Due to the challenging formation conditions, however, their mechanical properties remain poorly understood. Herein, the mechanical characteristics of tetrahydrofuran (THF) hydrates, a proxy for methane hydrates, were investigated at different ice contents, strain rates, and temperatures using uniaxial compressive experiments. The results unveil a distinct behavior in the peak strength of THF hydrates with a varying ice content, strain rate and temperature, exhibiting an increase as the strain rate and temperature decrease, in contrast to the peak strength-strain rate relationship observed in polycrystalline ice. Based on the experimental data, four machine learning (ML) models including extreme gradient boosting (XGboost), multilayer perceptron (MLP), gradient boosting decision tree (GBDT) and decision tree (DT) were developed to predict the peak strength. The XGboost model demonstrates superior predictive performance, emphasizing the significant influence of ice content and temperature on the peak strength of hydrates. Furthermore, molecular dynamics (MD) simulations were employed to gain insights into the dissociation and formation processes of clathrate cages, as well as phase transitions and amorphization occurring at grain boundaries (GBs) involving diverse unconventional clathrate cages, including 51265, 4151062, 4151064, 425861 and 425862, with 425861 and 425862 cages being predominant. This study enhances our understanding of the mechanical properties and deformation mechanisms of hydrates and provides a ML-based predictive framework for estimating the compressive strength of hydrates under diverse coupling conditions. The findings have significant implications for stability assessments of NGHs and the exploitation of NGH resources.

Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein.

Methane clathrates on continental margins contain the largest stores of hydrocarbons on Earth, yet the role of biomolecules in clathrate formation and stability remains almost completely unknown. Here, we report new methane clathrate-binding proteins (CbpAs) of bacterial origin discovered in metagenomes from gas clathrate-bearing ocean sediments. CbpAs show similar suppression of methane clathrate growth as the commercial gas clathrate inhibitor polyvinylpyrrolidone and inhibit clathrate growth at lower concentrations than antifreeze proteins (AFPs) previously tested. Unlike AFPs, CbpAs are selective for clathrate over ice. CbpA3 adopts a nonglobular, extended structure with an exposed hydrophobic surface, and, unexpectedly, its TxxxAxxxAxx motif common to AFPs is buried and not involved in clathrate binding. Instead, simulations and mutagenesis suggest a bipartite interaction of CbpAs with methane clathrate, with the pyrrolidine ring of a highly conserved proline residue mediating binding by filling empty clathrate cages. The discovery that CbpAs exert such potent control on methane clathrate properties implies that biomolecules from native sediment bacteria may be important for clathrate stability and habitability.

Unconventional growth of methane hydrates: A molecular dynamics and machine learning study

Natural gas hydrate reservoirs in natural settings subjected to external driving forces are deformed and locally dissociated, while they reform due to endothermic dissociation reaction. Here we report a molecular dynamics (MD) and machine learning (ML) study of unconventional growth characteristics of methane hydrates (MH). MD results show that depending on the strain of MH substrate, methane clathrate hydrates grow via four distinct growth modes, in which diverse unconventional cages are critically involved. Interestingly, a novel new MH structure named as MH-VII composed of 51263, 51472 and 425861 polyhedral cages is discovered. Moreover, a long short-term memory (LSTM) neural network-based ML model using short-time MD information is developed to effectively predict the complex dynamic growth of MH in terms of clathrate cages and F4 order parameter. This work provides new insights and perspectives into the growth of clathrate hydrates, and as-developed LSTM-based ML model opens a critical pathway for exploring time-dependent behaviors of clathrate hydrates under complex conditions.

Competitive and synergistic mechanisms of adsorption-hydration during methane storage in the wet ZIF-8 fixed bed

The natural gas storage technology based on wet ZIF-8 fixed bed has been proved to have excellent methane storage performance. To reveal the internal competition and synergism mechanism of adsorption-hydration, molecular dynamics technique was employed to simulate the microscopic dynamics process of methane hydrate formation in the ZIF-8 fixed bed with saturated water. Our results indicated that when the diameter of ZIF-8 particles were small, the low water content of the bed would induce the strong adsorption-hydration competition, and apparently inhibit the formation of methane hydrates. When the water content was sufficient, the gas adsorption performance of ZIF-8 solid particles could significantly accelerate the hydrate nucleation, exhibiting the adsorption - hydration synergy. In this case, the hydrate nucleus always took shape outside the region affected by ZIF-8 (within the range of about 10 Å from the surface of ZIF-8) and continuously grew away from the solid surface. Moreover, the simulation results also showed that the particle sizes of ZIF-8 played a vital role on hydrate nucleation/growth velocities and the types of clathrate cages formed, but had little impact on the conversion ratio of water and methane to hydrates.

Confining CO2 inside sI clathrate‐hydrates: The impact of the CO2–water interaction on quantized dynamics

We report new results on the translational-rotational (T-R) states of the CO2 molecule inside the sI clathrate-hydrate cages. We adopted the multiconfiguration time-dependent Hartree methodology to solve the nuclear molecular Hamiltonian, and to address issues on the T-R couplings. Motivated by experimental X-ray observations on the CO2 orientation in the D and T sI cages, we aim to evaluate the effect of the CO2 -water interaction on quantum dynamics. Thus, we first compared semiempirical and ab initio-based pair interaction model potentials against first-principles DFT-D calculations for ascertaining the importance of nonadditive many-body effects on such guest-host interactions. Our results reveal that the rotational and translational excited states quantum dynamics is remarkably different, with the pattern and density of states clearly affected by the underlying potential model. By analyzing the corresponding the probability density distributions of the calculated T-R eigenstates on both semiempirical and ab initio pair CO2 -water nanocage potentials, we have extracted information on the altered CO2 guest local structure, and we discussed it in connection with experimental data on the orientation of the CO2 molecule in the D and T sI clathrate cages available from neutron diffraction and solid-state NMR studies, as well as in comparison with previous molecular dynamics simulations. Our calculations provide a very sensitive test of the potential quality by predicting the low-lying T-R states and corresponding transitions for the encapsulated CO2 molecule. As such spectroscopic observables have not been measured so far, our results could trigger further detailed experimental and theoretical investigations leading to a quantitative description of the present guest-host interactions.

Formation of Type II Silicon Clathrate with Lithium Guests through Thermal Diffusion.

At low guest atom concentrations, Si clathrates can be viewed as semiconductors, with the guest atoms acting as dopants, potentially creating alternatives to diamond Si with exciting optoelectronic and spin properties. Studying Si clathrates with different guest atoms would not only provide insights into the electronic structure of the Si clathrates but also give insights into the unique properties that each guest can bring to the Si clathrate structure. However, the synthesis of Si clathrates with guests other than Na is challenging. In this study, we have developed an alternative approach, using thermal diffusion into type II Si clathrate with an extremely low Na concentration, to create Si clathrate with Li guests. Using time-of-flight secondary-ion mass spectroscopy, X-ray diffraction, and Raman scattering, thermal diffusion of Li into the nearly empty Si clathrate framework is detected and characterized as a function of the diffusion temperature and time. Interestingly, the Si clathrate exhibits reduced structural stability in the presence of Li, converting to polycrystalline or disordered phases for anneals at temperatures where the starting Na guest Si clathrate is quite stable. The Li atoms inserted into the Si clathrate lattice contribute free carriers, which can be detected in Raman scattering through their effect on the strength of Si-Si bonds in the framework. These carriers can also be observed in electron paramagnetic resonance (EPR). EPR shows, however, that Li guests are not simple analogues of Na guests. In particular, our results suggest that Li atoms, with their smaller size, tend to doubly occupy cages, forming "molecular-like" pairs with other Li or Na atoms. Results of this work provide a deeper insight into Li guest atoms in Si clathrate. These findings are also relevant to understanding how Li moves through and interacts with Si clathrate anodes in Li-ion batteries. Additionally, techniques presented in this work demonstrate a new method for filling the Si clathrate cages, enabling studies of a broad range of other guests in Si clathrates.

Interaction energy of Cl2 and Br2 with H2 O: Exchange, dispersion and density the crucial ingredients.

Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X2 -H2 O with X=Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl2 and Br2 inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl2 @512 , -5.3 ± 0.3kcal/mol; Cl2 @512 62 , -5.5 ± 0.1kcal/mol; Br2 @512 62 , -7.6 ± 1.0kcal/mol; Br2 @512 63 , -10.6 ± 1.0kcal/mol; Br2 @512 64 , -10.9 ± 0.8kcal/mol.

Interfacial mechanical properties of tetrahydrofuran hydrate-solid surfaces: Implications for hydrate management

Understanding the interfacial mechanical properties between hydrate and solids is vital to designing and fabricating surfaces for hydrate management. Herein, the role of the surface wettability, the type of solid substrate and temperature on the interfacial adhesion properties of tetrahydrofuran (THF) hydrate and ice were examined by force analysis based shearing measurements and molecular dynamics (MD) simulations. The results showed that the adhesion strength of THF hydrate and ice on silica varies with the compositions of coating, and the adhesion strength of ice is larger than that of THF hydrate for all investigated solid substrates. Particularly, in contrast to a linear relationship between 1 + cosθr and hydrate adhesion on organic silanes/thiols/polymer surfaces, the hydrate adhesion on the coated inorganic glass surfaces is enhanced as a function of 1 + cosθr, in which θr is the receding contact angle. MD simulations uncovered that the adhesion strength of ice on solid substrates is dominated by the quasi-liquid water layer, however, that of hydrate is governed not only by the quasi-liquid layer but also newly formed unconventional clathrate cages. This study provides new insights and perspectives into the hydrate adhesion on solid surfaces, which is of help to develop hydrate-phobic coatings for advanced hydrate management.

Mechanical stability of fluorinated-methane clathrate hydrates

• Lattice constant of clathrate hydrates formed by encapsulating fluorinated methane derivatives is greatly dictated by the number of fluorine atoms. • Polar fluorinated methane derivatives@cage show distinct rotational dynamics that vary with global strain. • Mechanical properties of clathrate hydrates are greatly influenced by the size and dipole moment of guests. • Unconventional water cages form as clathrate hydrates are mechanically failed via fractures of water cages. Clathrate hydrates recently find important practical applications in the capture and recovery of greenhouse gases, cold storage and refrigeration systems. Nevertheless, their properties at microscopic scale remains largely insufficient yet. Herein, the structure and stability of clathrate hydrates encapsulating fluorinated methane derivatives under mechanical load are investigated by molecular dynamics simulations. All investigated clathrate hydrates are structurally stable host-guest molecular crystals yet show distinct structural and mechanical behaviors. Lattice constant of those clathrate hydrates is dictated by the size and dipole moment of fluorinated methane, for example, it is initially enlarged with increasing fluorine atom in the methane guest molecule but followed by reduction as the guest molecule becomes tetrafluoromethane. However, clathrate hydrates encapsulating non-polar fluorinated methane show superior mechanical properties over those encapsulating polar ones. Polar fluorinated methane derivatives@clathrate cages exhibit distinct rotational dynamics that are influenced by strain. Moreover, all studied clathrate hydrates are mechanically failed by fractures of water cage accompanied by formation of unconventional clathrate cages. Those findings give insights into understanding the structural, thermodynamic stability and mechanical properties of clathrate hydrates encapsulating fluorinated guests.

Temperature-dependent crystal structure investigation of 4f hybridized thermoelectric clathrate Ba8-xCexAuySi46-y.

Thermoelectric materials allow for conversion of waste heat into electrical energy, and they represent a green solution for improving our energy efficiency. Inclusion of 4f electrons near the Fermi level may boost the Seebeck coefficient, which is essential for high thermoelectric performance. In this study, Ce was successfully substituted for Ba on the guest atom sites in the type-I clathrate Ba8-xCexAuySi46-y and the material was characterized using high-resolution synchrotron powder X-ray diffraction data measured from 100 K to 1000 K to investigate potential structural implications of the inclusion of a 4f element. The thermal expansion and bonding of the host structure are not affected by the presence of Ce, as seen from the linear coefficient of unit-cell thermal expansion of 7.30 (8) × 10-6 K-1 and the average host Debye temperature of 404 (7) K determined from the multi-temperature atomic displacement parameters, both of which are similar to values obtained for pure Ba8AuySi46-y. The anisotropic atomic displacement parameters on the guest atom site in the large clathrate cage populated by Ba surprisingly reveals isotropic behavior, which is different from all other clathrates reported in literature, and thus represents a unique host-guest bonding situation.

HTR: An ultra-high speed algorithm for cage recognition of clathrate hydrates

Abstract Clathrate hydrates find diverse significant applications including but not limited to future energy resources, gas storage and transport, gas separation, water desalination, and refrigeration. Studies on the nucleation, growth, dissociation, and micro/nanoscale properties of clathrate hydrates that are of utmost importance for those applications are challenging by experiments but can be accessible by molecular simulations. By this method, however, identification of cage structures to extract useful insights is highly required. Herein, we introduce a hierarchical topology ring (HTR) algorithm to recognize cage structures with high efficiency and high accuracy. The HTR algorithm can identify all types of complete cages and is particularly optimized for hydrate identification in large-scale systems composed of millions of water molecules. Moreover, topological isomers of cages and n × guest@cage can be uniquely identified. Besides, we validate the use of HTR for the identification of cages of clathrate hydrates upon mechanical loads to failure.

From Three-Dimensional Clathrates to Two-Dimensional Zintl Phases AMSb2 (A = Rb, Cs; M = Ga, In) Composed of Pentagonal M-Sb Rings.

Three new antimonide Zintl phases, RbGaSb2, CsGaSb2, and CsInSb2, were discovered during exploration of corresponding A-M-Sb (A = Rb, Cs; M = Ga, In) ternary systems while searching for new clathrates. The AGaSb2 phases crystallize in the tetragonal space group P42/nmc (No. 137) in the LiBS2 structure type, while CsInSb2 crystallizes in lower symmetry in the orthorhombic space group Cmce (No. 64) in the KGaSb2 structure type with additional disorder of one of the Cs sites. The crystal structures of all three reported AMSb2 compounds are composed of two-dimensional [MSb2]- tetrahedral layers separated by Rb+ or Cs+ cations. [MSb2]- layers are built from fused M-Sb pentagons and hexagons, which are also the main structural units for A8M27Sb19 clathrate cages. The semiconductor nature of AMSb2 was suggested by band structure calculations and confirmed by transport property characterization. CsGaSb2 is a rare example of an n-type pnictide Zintl phase. All reported compounds exhibit low thermal conductivity typical for complex antimonides of heavy elements.

An experimental FTIR-ATR and computational study of H-bonding in ethanol/water mixtures

• FTIR-ATR spectra show that certain peaks shift as a function of concentration of ethanol in water. • A cyclic H-bonded network can explain the strong IR shift of the peaks corresponding to the H 2 O bending. • Molecular mechanics calculations support the formation of a cyclic cage-like H-bonded network. Ethanol/water mixtures have served as a model to study the hydrophobic effect and the formation of clathrate and other cage like water formations around the hydrophobic end of ethanol. We have studied the evolution of FTIR-ATR spectra of ethanol/water mixtures as a function of the content of water in the mixture. The experimental spectra show redshift of primarily the H-O-H bending vibration, which is 18.9 cm −1 in total width. It also shows a blueshift of 9.0 cm −1 of the asymmetric stretching vibration of C-H groups of β-CH 3 . These infrared spectral shifts are consistent with the formation of a cyclic H-bonded network between ethanol and H-bonded water molecules. This hypothesis has been supported by full optimizations of high-level B3LYP/aug-cc-pVQZ calculations in implicit and explicit water and ethanol solvents as well as MMFF94s simulations of ethanol in explicit water clusters with up to 30 water molecules.