Empty Clathrate Research Articles

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.

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.

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.

Structures, stabilities and phase diagram assessments of clathrate ices at negative pressures

Clathrate hydrates are ubiquitous in terrestrial oceans or asteroids in the solar system, attracting the attention of scientists and forming an unstoppable research wave. Here, we study 9 ice phases of the empty clathrate hydrates sII, sIII, sIV, sH, dtc, EMT, sL, ITT and ice XI at negative pressures based on the second-order Møller-Plesset perturbation (MP2) theory and the higher-level CCSD(T) theory. A renewed phase diagram at negative pressures is proposed, where the empty hydrates sII, dtc, and EMT are demonstrated to be thermodynamical stable from −0.26 to −0.80 GPa. The predicted lattice parameters and Raman spectra of empty clathrate ices are in excellent agreement with the observable results, which validates the accuracy of the proposed methods in predicting the structures and phase diagram. The proposed work is crucial to the exploration of ice polymorphs and the scientific understanding of the properties of molecular crystals at negative pressures.

Structure and thermodynamics of empty clathrate hydrates below the freezing point of water.

Recently prepared as a new H2O phase, ice XVI was obtained by degassing a Ne-sII clathrate hydrate under vacuum, however very little is known of that crystalline solid under temperatures (T ≤ 220 K) and pressures (p ≤ 5000 bar) relevant for the Earth's environment and geochemistry. In this work, atomically detailed calculations using long time-scale molecular simulations, seldom paralelled before, are employed to probe empty sII clathrate hydrates. It is found that the volumetric response to an applied pressure-temperature gradient is accurately described by the Parsafar and Mason equation of state with an accuracy of at least 99.7%. Structural deformation induced upon the crystals is interpreted by monitoring the unit cell length and isobaric thermal expansivity, whilst benchmarked against previous neutron diffraction measurements of ice XVI and hexagonal ice under room pressure conditions; a critical comparison is established with other sII guest occupied lattices (CH4, CO2 and CnH2n+2 with n = 2, 3, 4), often found in permafrost regions and in the margins of continental shelves. Such an analysis reveals that empty sII frameworks are slightly more stable to thermal deformation than their sI analogues and that hexagonal ice is the structurally most stable of the condensed H2O phases addressed here. Of paramount importance for the oil and natural gas industries, heat capacities obtained from enthalpy profiles are identical for the sI and sII empty clathrates up to 2000 bar and diverge by only ∼7.3% at 5000 bar. The canonical tetrahedral symmetry of water-bonded networks is analysed in terms of an angular and a distance order parameters, which are observed to decrease (increase) as pressure (temperature) increases (decreases). The results now being reported constitute a landmark for future studies dealing with high-pressure and very low-temperature conditions, characteristic of the Earth's permafrost environment and other planetary interiors, whilst contributing to expand our knowledge regarding the recently discovered ice XVI phase.

Reversible Li Insertion in Guest Free Type II Si Clathrates for Li-Ion Batteries

Stable intercalation anodes for Li-ion batteries are comprised of two groups: graphite and Ti/Nb oxides. Graphite electrodes are reversible but can’t be operated at high current rates because of particle fracture and dendrite formation as a result of volume expansion and a low reaction potential (0.1 V). Li4Ti5O12 is a popular insertion anode that demonstrates good stability (zero strain) and fast charging but its high reaction voltage (1.55 V) lowers the energy density of the full cell. A crystal framework that allows low strain Li-insertion at a lower potential (i.e. 0.2 -1.0 V) could allow for fast charging with less propensity for dendrite formation while also increasing the energy density of the cell. Intermetallic compounds have reaction voltages with Li between 0.2 V – 1.0 V, which makes them interesting candidates for insertion anodes. However, Li alloying accompanied by a large volume expansion is common in these materials (e.g. Si, Ge, Sn) so host frameworks that allow bulk Li insertion into the structure before a Li alloying reaction are needed. Intermetallic clathrates are crystal structures that are comprised of a group IV framework of cages which host alkali guest atoms in the center of the cages (e.g. Ba8Si46, K8Ge44). This structure type has led to many interesting materials properties such as thermoelectricity, superconductivity, hydrogen storage, and tunable optical properties. Recently, our group has been studying the electrochemical reactions of clathrates with Li to understand how the defects and characteristics of clathrates affect the electrochemical properties and if reversible Li insertion into the crystal structure is possible. Our previous work on Type I clathrates with filled cages indicate that guest atoms are frustrating Li mobility and that bulk Li diffusion between cages requires guest atom vacancies1,2. Type II Na-Si clathrates (NaxSi136 (0< x < 24)), composed of Si20 and Si28 cages (Figure 1a), are well known for having tunable guest atom occupancy based on the thermal treatment. Previous work has proven with nuclear magnetic resonance spectroscopy that Li can be inserted into the empty clathrate cages of Si136 when the guest atom occupancy is low (x = 0-1)3. This insertion process manifests as a potential plateau at 300 mV prior to the amorphization of the Si lattice. Lithiation of the clathrate cages has been demonstrated but delithiation and cycling of Si136 has not been investigated. In addition, the Li pathways and positions in the lithiated Si136 structure have not been concluded. In this work, the synthesis and electrochemical and structural characterization of guest free type II Si clathrate is reported. The type II Si clathrates (Si136) were synthesized via thermal decomposition of Na4Si4 under vacuum and then characterized with synchrotron powder XRD and transmission electron microscopy to confirm the low Na content. By applying a voltage cutoff (~260 mV) prior to the onset of the amorphization reaction, reversible Li insertion is demonstrated for the first time (Figure 1b). The delithiation shows uniquely asymmetric behavior indicating a different delithiation mechanism than from the lithiation. The Si136 structure can insert ~32 Li before beginning the Li alloying reaction which corresponds to a capacity of around 220 mAh/g (470 Ah/L). When cycled with a voltage cutoff prior to the Li alloying reaction, the electrode demonstrates a repeatable electrochemical profile demonstrating the reversible Li chemistry. In addition, we find that the capacity depends sensitively on the voltage cutoff used (Figure 1c). After 50 cycles, the electrode maintains the clathrate crystal structure, evidence of a reversible insertion reaction. Ex-situ XRD of the fully lithiated clathrate (Figure 1d), shows that the clathrate structure has a very low volume expansion of around 0.1%, indicating that the lithiation process could be considered zero-strain. Synchrotron powder XRD and X-ray pair distribution function analysis is used to confirm the positions of Li during insertion and elucidate the lithiation mechanism. Since the Li insertion voltage is 300 mV for Si136, the risk of dendrite formation at higher current rates could be reduced while maintaining higher energy density cell due to a low reaction voltage. These results are interesting for the future design of insertion anodes that maintain a higher full cell energy density similar to that of graphite while still providing rapid and reversible Li insertion. Zhao, R. et al. ACS Appl. Mater. Interfaces 9, 41246–41257 (2017).Dopilka, A. et al. ACS Appl. Mater. Interfaces acsami.8b11509 (2018). doi:10.1021/acsami.8b11509Langer, T. et al. J. Electrochem. Soc. 159159, 1318–1322 (2012). Figure 1

Computational analysis of vibrational spectrum and hydrogen bonds of ice XVII

Based on first-principles density functional theory, we investigated the relationship between the vibrational normal modes and the spectrum of the newest laboratory-prepared ice phase, an empty clathrate hydrate structure from gas hydrate named ice XVII. A 48-molecule supercell was designed to mimic the hydrogen-disordered structure. Despite its much lower density than ice Ih, its phonon density of states shows features very similar to those of that phase. In our previous studies of ice Ic and ice XIV, we found two basic hydrogen bond vibrational modes in these hydrogen-ordered ice phases, which contribute two sharp hydrogen bond peaks in the translation region. In this study, we found that this rule also holds in the hydrogen-disordered phase ice XVII. A water molecule vibrating along its angle bisector possesses strong energy, because this vibrational mode involves oscillation against four bonded neighbors. In contrast, a water molecule vibrating perpendicular to its angle bisector has low energy because this mode involves only two of the molecule’s hydrogen bonds. This is an evidence in hydrogen-disordered ice and strengthens our proposal that the existence of two basic hydrogen bond vibrational modes is a general rule among ice family.

A description of hydroquinone clathrates using molecular dynamics: Molecular model and crystalline structures for CH4 and CO2 guests.

The crystalline structure of hydroquinone clathrates has been studied using molecular dynamics. A flexible non-polarizable all-atom molecular model, based on the original Optimized Potentials for Liquid Simulations force field with recalculated point electric charges, has been used to describe the hydroquinone molecule, and the crystalline solid structure of the α native phase has been analyzed. Then, the β clathrates have been studied, considering CO2 and CH4 as guest molecules, and also the empty clathrate structure. In all cases, the lattice parameters obtained through molecular simulation show excellent agreement with reported experimental values, showing that the molecular model selected is able to reproduce both the native crystalline phase and also the clathrate structures. In addition, the process of clathrate guest molecule release upon heating has been characterized, and the simulations show a good correspondence with the very recent experimental trends observed for both guest molecules analyzed.

Unravelling the progressive role of rattlers in thermoelectric clathrate and strategies for performance improvement: Concurrently enhancing electronic transport and blocking phononic transport

Intermetallic clathrates, one class of guest-host systems with perfectly crystalline structures, hold great potential to be the “phonon glass – electron crystal” thermoelectric materials. Previous studies focus on revealing the atomistic origins of blocked phononic transport, yet little attention is drawn to the enhanced electronic transport. In this work, we investigate the binary type-I M8Si46 (M = Sr, Ba, Tl, and Pb) clathrates and unravel how rattlers concurrently block phononic transport and enhance electronic transport from first-principles. By comparing the empty and filled clathrates, the lattice thermal conductivity is greatly reduced by a factor of 21 due to the decrease in phonon relaxation time for propagative phonons over 0–6 THz by 1.5 orders of magnitude. On the other hand, rattlers bridge charge gaps among cages by donating electrons and thus drastically increase electrical conductivity. The concurrent realization of blocked phononic transport and enhanced electronic transport boosts the figure-of-merit (ZT) of empty clathrate by 4 orders of magnitude. Furthermore, by manipulating metallic rattlers and n-type doping, the power factor is markedly improved and ZT can reach 0.55 at 800 K. These results provide a quantitative description of the guest-host interaction and coupling dynamics from first-principles. The proposed strategy of manipulating ratting atoms and in-situ doping offers important guidance to engineer clathrates with high thermoelectric performance.

Equilibrium Born-Oppenheimer molecular-dynamics exploration of the lattice thermal conductivity of silicon clathrates

Thermal conductivity plays a critical rôle in determining the performance of a thermoelectric material. However, the computation of thermal conductivity from first principles is a challenging and laborious process, with pitfalls galore. Here, we present results on the calculation of the lattice thermal conductivities of silicon clathrates using a very efficient scheme based on the Einstein relationship for the energy moment, sampled from ab initio Born-Oppenheimer molecular dynamics employing linear-scaling Density Functional Theory. Both sI and sII silicon clathrates were studied using systems consisting of up to thousands of atoms. Instead of more glass-like behaviour reported for an empty sII clathrate, the present accurate first-principles calculations predict a thermal-conductivity temperature dependence more in keeping with that of a normal crystal for both clathrates polymorphs, essentially in agreement with a previous theoretical study on sI clathrate. Over the temperature range from 50 to 600K at ambient pressure, it is found that the sI-structure thermal conductivity is somewhat lower than sII, due probably to the greater proportion of larger tetrakaidecahedral 51262 cavities (vis-à-vis smaller dodecahedral 512 cages) therein leading to more substantial dissipation of heat-carrying acoustic phonons. However, the absolute conductivity of sII clathrate is itself limited due to the larger number of atoms per unit cell (136 versus 46 for sI) leading to significant zone-edge damping of acoustic phonons.

Exploring Host-Guest Interactions: a Single Crystal High-Pressure study

Single crystal X-ray diffraction data from several Hydroquinone clathrate systems, with various small guest molecules (e.g. HCOOH, MeOH), have been obtained up to a pressure of 10 GPa, using a diamond anvil cell (DAC). Hydroquinone clathrates are key examples of supramolecular aggregates, having a diverse structural chemistry controlled, to a large extent, by the detailed intermolecular interactions between the host and the guest molecules. Although supramolecular chemistry is the foundation for the design and development of advanced materials (e.g. for catalysis, targeted drug delivery, chemical separation and nonlinear optics) the basic understanding leading to such complex systems are often lacking. High pressure (HP) crystallography is an excellent method of systematically increasing host-guest interactions by forcing the molecules closer together, often leading to interesting and unexpected results. At ambient pressure smaller guest molecules are often disordered inside the clathrate cavities. As the external pressure increases the cavities shrink, and it seems likely that guest molecules will order inside the cavity breaking the host symmetry. Guest ordering transitions are also found upon cooling. In this work, results from HP studies of the hydroquinone – formic acid system reveal that the structure is stable up to 10 GPa, at which pressure the guest cavity volume is reduced by more than 50 % without ordering of the guest atoms. Earlier studies have shown that the empty Hydroquinone clathrate undergoes a phase transition into a nonporous structure already at 0.4 GPa. [1] This indicates that formic acid stabilizes the host framework through strong intermolecular host-guest interactions, but without lowering the host symmetry.

Stability and Metastability of Bromine Clathrate Polymorphs

Clathrate hydrates are crystals in which water forms a network of fully hydrogen-bonded polyhedral cages that contain small guests. Clathrate hydrates occur mostly in two cubic crystal polymorphs, sI and sII. Bromine is one of two guests that yield a hydrate with the tetragonal structure (TS), the topological dual of the Frank-Kasper σ phase. There has been a long-standing disagreement on whether bromine hydrate also forms metastable sI and sII crystals. To date there are no data on the thermodynamic range of stability (e.g., the melting temperatures) of the metastable polymorphs. Here we use molecular dynamics simulations with the coarse-grained model of water mW to (i) investigate the thermodynamic stability of the empty and guest-filled the sI, sII, TS, and HS-I hydrate polymorphs, (ii) develop a coarse-grained model of bromine compatible with mW water, and (iii) evaluate the stability of the bromine hydrate polymorphs. The mW model predicts the same relative energy of the empty clathrate polymorphs and the same phase diagram as a function of water-guest interaction than the fully atomistic TIP4P water model. There is a narrow region in water-guest parameter space for which TS is marginally more stable than sI or sII. We parametrize a coarse-grained model of bromine compatible with mW water and use it to determine the order of stability of the bromine hydrate polymorphs. The melting temperatures of the bromine hydrate polymorphs predicted by the coarse-grained model are 281 ± 1 K for TS, 279 ± 1 K for sII, and 276 ± 1 K for sI. The closeness of the melting temperatures supports the plausibility of formation of metastable sII and sI bromine hydrates.

A Simple Method for Calculation of the Composition of Type I Clathrate Hydrates

AbstractA simple and generalized method for calculating the composition of the Type I clathrate gas hydrates is discussed. It is suggested that the use of additive terms in the known temperature dependent molar volume values of hexagonal ice is useful in calculating the molar volume of the empty clathrate cage. Since the molecular weight of the gas hydrate is dependent on the occupation, the degree of occupation can be expressed by using the experimental density values of each hydrate. The results so obtained are in fair agreement with the results calculated from experimental density and X‐ray lattice constants, and with the values of the experimentally measured compositions.

The Minimal Occupancy Level of the Clathrate Hydrate Host Lattice and the Intercalation Heat of the Guest Molecules in the Chlorine Hydrates

AbstractThe minimal occupancy level (θmin) of the clathrate lattice of gas molecules is defined as the number of guest molecules in the host clathrate lattice, which can stabilize the thermodynamically unstable empty cage by covering the energy demand of the transformation of hexagonal ice into empty clathrate lattice (ΔHtrans). The θmin values for chlorine hydrate were determined from the n = f(p)T=const. relationship and the average molar intercalation heat of chlorine in the type I clathrate lattice was also calculated for both type of cavities.

On the Thermodynamic Stability of Clathrate Hydrates V: Phase Behaviors Accommodating Large Guest Molecules with New Reference States

We present a method that brings prediction of phase behaviors of various clathrate hydrates with firm statistical mechanical ground adopting a different reference state from the usual one. Accommodation of a large guest molecule makes the frequencies of the lattice vibrational motions higher, which is one of the breakdowns of the assumptions in the original van der Waals and Platteeuw theory. The frequency modulations are incorporated in the free energy of cage occupation in the present method. Moreover, the reference state, which is originally the corresponding empty clathrate structure, is alternated to a state where cages of at least one sort are fully occupied. This meets the stability condition of clathrate hydrates that most of the cages should be accommodated. Owing to this new reference state, the thermodynamic stability is evaluated with reasonable accuracy from the free energy of cage occupation especially by a large guest molecule without considering its dependence on the cage occupancy. This conversion is also beneficial to establish a relation between the chemical potential of water and the cage occupancy from grandcanonical Monte Carlo simulation. We show a new method indeed works well in predicting the dissociation pressures of clathrate hydrates containing isobutane, propane, ethane, Xe, and CF(4).

Structural Correlation between Crystal Lattice and Lamellar Morphology in the Phase Transitions of Uniaxially Oriented Syndiotactic Polystyrene (δ and δe Forms) As Revealed by Simultaneous Measurements of Wide-Angle and Small-Angle X-ray Scatterings

The simultaneous measurement of wide-angle (WAXS) and small-angle X-ray scattering (SAXS) patterns has been made successfully for the first time for the uniaxially oriented δ (filled clathrate) and δe (emptied clathrate) forms during the heating process. The basic idea behind these measurements is to clarify the correlation between the crystal structure change and the morphological change of the stacked lamella. At room temperature the δ and δe forms showed a two-point scattering pattern, indicating the stacked lamellar structure. However, in the δe form the two-point scattering pattern was completely masked by strong diffused scattering because of the empty cavities in the crystal lattice due to the removal of solvent molecules. WAXS and SAXS results revealed that the δ to γ phase transition occurs smoothly without disturbing the stacked lamellar structure very much. On the other hand, a major reorganization in the stacked lamellar structure was observed in the case of δe to γ transition through a disord...

Structural Study of Methane Hydrate

The authors present a structural study of methane hydrate by using MP2 calculations and the QTAIM method. Two different structures are analyzed for the empty clathrate molecule. Both structures exhibit 30 hydrogen bonds and they differ in the position of the 10 O–H bonds that are not involved in hydrogen bonds. As the available space in the middle of the structure, where the guest could be located, is the same in both cases, most stable molecule is considered to be filled with methane. We also try to establish similarities and differences between methane occupied and empty units by analyzing geometrical and density charge properties, particularly what is related to the hydrogen bonds among water molecules in the clathrate. Our results allow us to conclude that the introduction of methane does not vary the main structural properties of this molecule.

Account of three-body interactions in the lattice dynamics method

The lattice dynamics method is extended with the account of three-body interaction potential in the harmonic approximation. Analytic expressions for the force constants and dynamical matrix elements are presented. Dynamical matrix element responsible for indirect interaction of atoms is single out. Modeling calculations of phonon spectra at the center of Brillouin zone for empty silicon clathrate structures Si 34 and Si 46 have been performed.

Structure and properties of the mesophase of syndiotactic polystyrene. II. Effect of stepwise extraction on the preparation of the mesophase

AbstractIn this study, a novel stepwise extraction method has been examined. The guest molecules housed between the helices of the clathrate δ form of syndiotactic polystyrene can be removed completely with this method. A systematic study of the preparation of a solvent‐free mesophase (emptied clathrate) membrane, its helical and residual solvent contents, and its structural transformations has been performed. In this first attempt, an enhancement in the TTGG helical content has been observed in the extracted membrane, and a conceptual mechanism is proposed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 269–273, 2003

Crystalline Transitions of the Clathrate (δ) Form of Syndiotactic Polystyrene during Heating: Studies Using High-Temperature X-ray Diffraction

The structural changes occurring during heating in a syndiotactic polystyrene (sPS)−solvent complex were monitored in situ by X-ray diffraction. The room temperature δ form transformed into the γ form on heating above the glass transition temperature of the sPS. The transition temperature showed a linear dependency on the amount of solvent absorbed; the higher the solvent molecules absorbed, the higher the transition temperature. However, the transition temperature does not depend on the nature of the solvent. The emptied clathrate form transformed into the γ form at the glass transition temperature. The γ form transformed into the α‘ ‘ form at ∼200 °C on heating and is independent of the δ to γ form transition. Calorimetric studies showed an endotherm followed by an exotherm during these transitions and indicated that the transitions are first order in nature.The studies provided information on the stability of various crystalline forms of sPS.