Clathrate Hydrate Structure Research Articles

Generating proton-disordered ice configurations using orientational simulated annealing.

We examine an algorithm for the creation of proton-disordered ice cells based on a simulated-annealing (SA) scheme for molecular orientations. Application to defect-free ice Ih, a clathrate-hydrate structure, and a random polycrystalline ice Ih sample demonstrates the SA technique to be effective, attaining maximum HB connectivity using relatively short cooling simulations, thus serving as an alternative method for those cases in which the application of topology-based methods is inhibited.

Harnessing Nuclear Magnetic Resonance Spectroscopy to Decipher Structure and Dynamics of Clathrate Hydrates in Confinement: A Perspective.

This perspective outlines recent developments in the field of NMR spectroscopy, enabling new opportunities for in situ studies on bulk and confined clathrate hydrates. These hydrates are crystalline ice-like materials, built up from hydrogen-bonded water molecules, forming cages occluding non-polar gaseous guest molecules, including CH4, CO2 and even H2 and He gas. In nature, they are found in low-temperature and high-pressure conditions. Synthetic confined versions hold immense potential for energy storage and transportation, as well as for carbon capture and storage. Using previous studies, this report highlights static and magic angle spinning NMR hardware and strategies enabling the study of clathrate hydrate formation in situ, in bulk and in nano-confinement. The information obtained from such studies includes phase identification, dynamics, gas exchange processes, mechanistic studies and the molecular-level elucidation of the interactions between water, guest molecules and confining interfaces.

Phase equilibria and crystallographic structure of clathrate hydrate formed with carbon dioxide and cyclohexanone

This paper reports the phase equilibrium and crystallographic data of the hydrate formed in the CO2 + cyclohexanone + water system. We measured the phase equilibrium condition and conducted the powder X-ray diffraction measurements. The formation of the structure II hydrate in the system of CO2 + cyclohexanone + water was observed at the temperature from 270.0 K to 275.6 K, under the pressure from 0.62 MPa to 1.70 MPa.At 270.0 K – 275.6 K and 0.62 MPa – 1.70 MPa, the structure II hydrate formed, and the phase equilibrium condition alleviated in the system of CO2 + cyclohexanone + water, while the hydrate formed at 276.5 K - 280.7 K and 2.02 MPa – 3.33 MPa, displayed structure I and cyclohexanone acted as an inhibitor. Equilibrium conditions were measured using the isochoric method, revealing different p-T slopes at high and low temperatures. The high-temperature slope closely resembled that of structure I CO2 hydrate reported previously. We continuously monitored temperature and pressure during the structural phase transition, resulting in a slope change. To directly determine the hydrate structure, PXRD measurements were conducted on two samples: one from the high-temperature side and the other from the low-temperature side. The sample from the high-temperature side exhibited structure I with a lattice constant of 11.8749 (9) Å at 153 K, while the low-temperature sample displayed structure II with a lattice constant of 17.443(1) Å at 153 K.

Large-cage occupation and quantum dynamics of hydrogen molecules in sII clathrate hydrates.

Hydrogen clathrate hydrates are ice-like crystalline substances in which hydrogen molecules are trapped inside polyhedral cages formed by the water molecules. Small cages can host only a single H2 molecule, while each large cage can be occupied by up to four H2 molecules. Here, we present a neutron scattering study on the structure of the sII hydrogen clathrate hydrate and on the low-temperature dynamics of the hydrogen molecules trapped in its large cages, as a function of the gas content in the samples. We observe spectral features at low energy transfer (between 1 and 3meV), and we show that they can be successfully assigned to the rattling motion of a single hydrogen molecule occupying a large water cage. These inelastic bands remarkably lose their intensity with increasing the hydrogen filling, consistently with the fact that the probability of single occupation (as opposed to multiple occupation) increases as the hydrogen content in the sample gets lower. The spectral intensity of the H2 rattling bands is studied as a function of the momentum transfer for partially emptied samples and compared with three distinct quantum models for a single H2 molecule in a large cage: (i) the exact solution of the Schrödinger equation for a well-assessed semiempirical force field, (ii) a particle trapped in a rigid sphere, and (iii) an isotropic three-dimensional harmonic oscillator. The first model provides good agreement between calculations and experimental data, while the last two only reproduce their qualitative trend. Finally, the radial wavefunctions of the three aforementioned models, as well as their potential surfaces, are presented and discussed.

Novel approach for designing order parameters of clathrate hydrate structures by graph neural network.

Clathrate hydrates continue to be the focus of active research efforts due to their use in energy resources, transportation, and storage-related applications. Therefore, it is crucial to define their essential characteristics from a molecular standpoint. Understanding molecular structure in particular is crucial because it aids in understanding the mechanisms that lead to the formation or dissociation of clathrate hydrates. In the past, a wide variety of order parameters have been employed to classify and evaluate hydrate structures. An alternative approach to inventing bespoke order parameters is to apply machine learning techniques to automatically generate effective order parameters. In earlier work, we suggested a method for automatically designing novel parameters for ice and liquid water structures with Graph Neural Networks (GNNs). In this work, we use a GNN to implement our method, which can independently produce feature representations of the molecular structures. By using the TeaNet-type model in our method, it is possible to directly learn the molecular geometry and topology. This enables us to build novel parameters without prior knowledge of suitable order parameters for the structure type, discover structural differences, and classify molecular structures with high accuracy. We use this approach to classify the structures of clathrate hydrate structures: sI, sII, and sH. This innovative approach provides an appealing and highly accurate replacement for the traditional order parameters. Furthermore, our method makes clear the process of automatically designing a universal parameter for liquid water, ice, and clathrate hydrate to analyze their structures and phases.

Geometric and Hydrophilic Effects of Oxirane Compounds with a Four-Carbon Backbone on Clathrate Hydrate Formation.

The physicochemical properties of clathrate hydrates are influenced by the chemical nature and three-dimensional (3D) geometry of the added molecules. This study investigates the effects of five oxirane compounds: cis-2,3-epoxybutane (c23EB), trans-2,3-epoxybutane (t23EB), 1,2-epoxybutane (12EB), 1,2,3,4-diepoxybutane (DEB), and 3,3-dimethylepoxybutane (33DMEB) on CH4 hydrate formation. Despite having a four-carbon backbone, these compounds differ in their 3D geometries. The structures and stabilities of CH4 hydrates containing each compound were analyzed using high-resolution powder diffraction, solid-state 13C NMR, and phase equilibrium measurements. The experimental results revealed that c23EB, 12EB, and 33DMEB act as sII/sH hydrate formers and thermodynamic promoters, whereas t23EB and DEB have opposite roles. These results were analyzed in relation to the 3D geometries and relative stabilities of various rotational isomers using DFT calculations. Hydrate structure was influenced by both the length and thickness of the added compounds. Moreover, an appropriate level of (not excessive) hydrophilicity induced by an oxirane group appeared to enhance the thermodynamic stability of the hydrates. This study provides insights into how the chemical nature of additives influences the structure and stability of clathrate hydrates.

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.

Topological dual and extended relations between networks of clathrate hydrates and Frank-Kasper phases

Clathrate hydrates are a class of ordered structures that are stabilized via the delicate balance of hydrophobic interactions between water and guest molecules, of which the space-filling network of hydrogen-bonded (H-bonded) water molecules are closely related to tetrahedrally close-packed structures, known as Frank-Kasper (FK) phases. Here we report an alternative way to understand the intricate structures of clathrate hydrates, which unveils the diverse crystalline H-bonded networks that can be generated via assembly of one common building block. In addition to the intrinsic relations and pathways linking these crystals, we further illustrate the rich structural possibilities of clathrate hydrates. Given that the topological dual relations between networks of clathrate hydrates and tetrahedral close-packed structures, the descriptors presented for clathrate hydrates can be directly extended to other ordered materials for a more thorough understanding of their nucleation, phases transition, and co-existence mechanisms.

Neutron scattering study of polyamorphic THF·17(H2O) - toward a generalized picture of amorphous states and structures derived from clathrate hydrates.

From crystalline tetrahydrofuran clathrate hydrate, THF-CH (THF·17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF-CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77-140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, VHDA, upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third form, recovered amorphous (RA). Results from neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF-CH and liquid THF·17H2O solution (∼2.5 M). Although fully amorphous, HDA is heterogeneous with two length scales for water-water correlations (less dense local water structure) and guest-water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest-host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ∼23H2O. The local water structure in HDA is reminiscent of pure HDA-ice featuring 5-coordinated H2O. In VHDA, the hydration structure of HDA is maintained but the local water structure is densified and resembles pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ∼18 H2O molecules and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous.

A Clathrate Hydrate Structure Hidden in Plain Sight.

Clathrate hydrates have diverse crystal structures, and among them, the three (sI, sII, and sH) most prevalent ones cover nearly all known structures, while the norm is to consider other structures only when specific guest molecules are present. Here we report the observation of a hidden clathrate structure: the tetragonal structure (TS-I) in commonly formed gas hydrates, as evidenced from molecular dynamics simulations. We show that when two (or more) sI crystal grains with different growth directions come into contact or when the growth of a sI crystal encounters geometrical frustration, the TS-I results as a cocrystal. We give evidence that TS-I may also play an important role in the combination and/or transition between sI and sII. These results imply that this previously neglected structure may be commonly present whenever sI or sII is formed. This hidden structure must be identified, experimentally and in simulations; confining the possible structures may hinder an in-depth understanding of clathrate hydrates.

Experimental Study on Hydrate Structure Transition Using an In Situ High-Pressure Powder X-ray Diffractometer: Application in CO2 Capture

Clathrate (gas) hydrates as materials have received great interest due to their high-density gas storage potential and separation applications for their ability to preferentially separate a targeted component such as CO2 from waste streams. Among the three clathrate hydrate structures, only sH (structure H) hydrates require a large molecule such as neohexane (NH) or tert-butyl methyl ether (TBME) as well as a “help-gas” molecule such as methane (CH4) to form a stable structure. However, attempts to use CO2 as a help-gas came up with mixed results where it appeared that the sH hydrate formed was stable only at temperatures below the ice point, whereas the compound formed with CH4 was considerably more stable. sH hydrates have considerable potential for gas separation, for instance, of CH4–CO2 mixtures. Thus, in this work, several compositions were tested for their hydrate forming ability. The large cage guests tested were NH and TBME, the help-gas mixtures were a CO2-rich mixture (76% CO2 and 24% CH4), and a CO2 lean mixture (24% CO2 and 76% CH4). The phase behavior of hydrates formed from the various combinations was tested by measuring the endo- and exotherms associated with hydrate formation and decomposition in a high-pressure differential calorimeter. The different phases indicated from the DSC results were identified by employing an in situ high-pressure cell on a powder X-ray diffractometer. Powder patterns were recorded to identify the crystal phase arising from nucleation and possible re-crystallization events after annealing. It was confirmed that the CO2 lean mixture (24% CO2 and 76% CH4) forms structure H (sH) hydrate, while the CO2-rich mixture (76% CO2 and 24% CH4) forms structure I (sI) hydrate presenting a structure transition pattern across the gas mixtures investigated. Further, it was observed that the CO2 lean mixture, which forms sH hydrate, also starts as sI hydrate and gradually converts to the thermodynamically stable sH hydrate. This study, in essence, helps to understand the preference of CH4 and CO2 for three different types of cages in sH hydrates and presents a design framework for a suitable gas separation mechanism for this gas mixture of interest.

Structural changes due to the ordered guest molecules in deuterated ethane hydrate

Ethane hydrate, a natural gas hydrate, has been considered to only have a cubic symmetry known as structure I. Neutron diffraction measurement of deuterated ethane hydrate was performed from 10 K to 150 K. The diffraction patterns of deuterated ethane hydrate drastically changed below 30 K. A new hexagonal crystal structure with ordered ethane molecules was found as a clathrate hydrate structure. This phase transition was concerned with the thermal motion of the ethane molecules.

Molecular Dynamic Simulations of Clathrate Hydrate Structures I: Lattice Constant and Thermal Expansion

Molecular Dynamic Simulations of Clathrate Hydrate Structures I: Lattice Constant and Thermal Expansion

Structural and mechanical stability of clathrate hydrates encapsulating monoatomic guest species

Clathrate hydrate (CH) structures find diversely promising applications such as gas and energy storage and transport, carbon capture and storage, gas separation, water desalination, and food and pharmaceutical engineering. However, the influence of guest molecules on their properties remains largely uncharacterized. Here, the critical roles of monoatomic guest size and interaction strength with water molecule in the structural and mechanical stability of clathrate hydrates are explicitly examined by classical molecular dynamics simulations. With increasing guest size or its interaction strength, the lattice constant and mechanical properties such as Young’s modulus, tensile strength, Poisson’s ratio of CHs vary nonlinearly. Based on the characteristics of the contour map of lattice constant, four regions of lattice constant of CHs can be divided. Interestingly, there are crossovers in the iso-lattice constant lines and tensile strength. Upon uniaxial tension, CH destabilizes via brittle or ductile failure, relying on the size and interaction strength of monoatomic guest. The guest size and interaction strength dependent properties can be critically understood by radial distribution function, cage volume and distribution of guest@cages.

Pyrazine Analogues on Clathrate Hydrates in Methane–Water Systems

This paper reports the change in equilibrium pressure–temperature (pT) boundaries in a methane (CH4)–water system by adding three pyrazine analogues: 2-methylpyrazine, 2,3-dimethylpyrazine, and 2,3,5-trimethylpyrazine. The 2-methylpyrazine, 2,3-dimethylpyrazine, and 2,3,5-trimethylpyrazine showed no effect on the clathrate hydrate structure that formed in the CH4–water system upon analysis via Raman spectroscopy. Raman spectra revealed that clathrate crystals that formed in the CH4–pyrazine analogue–water system were of a structure-I CH4 hydrate. Phase equilibrium pT boundaries in the three CH4–pyrazine analogue–water systems shifted to a higher p and lower T condition than that for the CH4–water system with no additive. The higher p/lower T shift confirmed that 2-methylpyrazine, 2,3-dimethylpyrazine, and 2,3,5-trimethylpyrazine act as thermodynamic inhibitors for hydrate formation. The order of ΔT, a lower T shift from the CH4–water system, was as follows: 2-methylpyrazine–water > 2,3-dimethylpyrazine > 2,3,5-trimethylpyrazine. This order is in agreement with the number of −CH3 groups in the molecules.

Molecular dynamics simulations on dissociation of CO2 hydrate in the presence of inhibitor

The dissociation kinetics of CO2 hydrate are investigated by molecular dynamics (MD) simulation in the presence of thermodynamic inhibitor glycine (5 wt%, 10 wt%, 15 wt%, 20 wt%) and kinetic inhibitor glucose (1.2 wt%, 2.0 wt%, 3.8 wt%). The molecular dynamics simulations are performed at 273.15 K and 3 MPa under the isothermal-isobaric (NPT) ensemble. The configuration, radial distribution functions, mean square displacement, and density are analyzed respectively. It is found that the dissociation rate of CO2 hydrate is increased in the presence of two inhibitors. The optimal concentration of glycine is 10 wt% and that is 1.2 wt% for glucose. The results indicate different mechanisms for two inhibitors. Glycine accumulates on the solid–liquid surface of the initial structure, and the clathrate hydrate structure is destroyed due to the aggregation of hydroxyl (OH) and amidogen (NH2) with water hydrogen bond in the hydrate structure. While glucose accelerates the dissociation of hydrates because of the synergistic effect of steric hindrance, owing to its ring-shaped structure and the disruption of functional groups.

Propane and Water: The Cooperativity of Unlikely Molecules to Form Clathrate Structures.

Many unanswered questions still exist at the molecular level to understand the nucleation process and mechanism of clathrate hydrates, especially for larger guest molecules that would result in the structure II crystal. Here, we report on molecular dynamics simulations for propane and water to describe the molecular mechanism leading to a structure II system. Through a large number (30) of long (5 μs) and coupled annealing (20 μs) simulations, we detail the prenucleation, nucleation, growth, and annealing of propane clathrate hydrate structures at 250 K and 1800 bar. The results demonstrate the equal importance of the empty and occupied cages in the nucleation of propane hydrates. The critical nucleus size is identified to be eight cages. While separate distinct clusters may exist during the prenucleation period, only one survives to grow beyond the critical nucleus size, with the others remaining subcritical. From the annealing simulations, it is clear that solid rearrangement is a very slow process, and 20 μs is still not long enough to capture long-range ordering resembling the structure II crystal. These results, along with the developed analysis method, have a significant impact in advancing our understanding of the nucleation process for unlike molecules.

How Does the Guest—Host Hydrogen Bonding Affect the Thermal Properties of Clathrate Hydrates?

Herein, molecular dynamics simulations are performed to study the effect of the guest-host hydrogen bonding on the thermal properties, such as isothermal compressibility, isobaric thermal expansivity, and heat capacity, in the sI clathrate hydrate phases of trimethylene oxide (TMO), ethylene oxide (EO), and formaldehyde (FA) as polar guests. The results of these simulations are compared with those of nonpolar guests with analogous structures, cyclobutane (CB), cyclopropane (CP), and ethane (Et). Binary hydrates are constructed with the above guests in large 14-sided cages and methane placed in small 12-sided cages of the structure of sI clathrate hydrates. We present the temperature dependence of the lattice parameter and also the pressure dependence of the unit cell volume for variety guests with different sizes, polarity, and guest-host hydrogen bonding capability. The lattice parameters for some of the guest species obtained in this work are in good agreement with experimental values. The oxygen atom of the formaldehyde carbonyl group and the ether oxygen atoms of TMO and EO molecules can form hydrogen bonds with sI large cage water hydrogen atoms while CB, CP and Et molecules do not. The consequences of the guest-host hydrogen bonding on the isothermal compressibility, thermal expansivity, and heat capacity of the clathrate are discussed.

The water molecule arrangement over the side chain of some aliphatic amino acids: A quantum chemical and bottom‐up investigation

AbstractThe geometry of surrounding water molecules on the side chain of glycine, alanine, α‐aminoisobutyric acid, α‐aminobutyric acid, valine, and related hydrocarbons has been analyzed combining bottom‐up and quantum chemical methodologies. To minimize the cavity size and to prevent water‐water hydrogen bonding loss, the water molecules adopt a shape, resembling the one found in crystal structure of gas clathrate hydrates, with water molecules tangentially oriented to the surface of hydrophobic side chain. The cage is directly hydrogen bonded to the backbone's polar groups, thus hydration shells around hydrophobic and hydrophilic groups are folded together in amphiphilic molecules. The hydrophobe enclathration implies a substantial freedom degree reduction which makes it entropically disfavored. This disadvantageous entropic contribution is partially compensated by the favorable van der Waals interactions with guest in stabilizing clathrate hydrate formation. The water shell around the side chain relates intimately with the side‐chain rotational isomerism. Present data are correlated with the experimental determined populations of the three rotamers, yielding promising results for both α‐aminobutyric acid and valine.

How does the guest—host hydrogen bonding affect the thermal properties of clathrate hydrates?

Herein, molecular dynamics simulations are performed to study the effect of the guest—host hydrogen bonding on the thermal properties, such as isothermal compressibility, isobaric thermal expansivity, and heat capacity, in the sI clathrate hydrate phases of trimethylene oxide (TMO), ethylene oxide (EO), and formaldehyde (FA) as polar guests. The results of these simulations are compared with those of nonpolar guests with analogous structures, cyclobutane (CB), cyclopropane (CP), and ethane (Et). Binary hydrates are constructed with the above guests in large 14-sided cages and methane placed in small 12-sided cages of the structure of sI clathrate hydrates. We present the temperature dependence of the lattice parameter and also the pressure dependence of the unit cell volume for variety guests with different sizes, polarity, and guest—host hydrogen bonding capability. The lattice parameters for some of the guest species obtained in this work are in good agreement with experimental values. The oxygen atom of the formaldehyde carbonyl group and the ether oxygen atoms of TMO and EO molecules can form hydrogen bonds with sI large cage water hydrogen atoms while CB, CP and Et molecules do not. The consequences of the guest—host hydrogen bonding on the isothermal compressibility, thermal expansivity, and heat capacity of the clathrate are discussed.