Investigation of Mesoscopic Clathrate Hydrate Structures within Graphene Liquid Cells Using Transmission Electron Microscopy

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Dissolution of gases in liquid water is a general and fundamental phenomenon across living and nonliving things. Conventionally it has been assumed that dissolved gas molecules are well dispersed as monomers. The concentration of gas molecules at a given time and position, C(r,t), has been used to describe the gas condition in aqueous solutions, even when the dissolved gas concentration is near or above the saturation level. Despite numerous studies over the last century, there remain many mysteries about gas dissolved in water, such as the nucleation mechanism of gas bubbles in water, whether nanobubbles exist in bulk water, the abnormal thermodynamic properties of gas-saturated water, and more. Recent experiments suggest that gas concentration alone is not sufficient to describe gas dissolved in water, thus we sought to examine whether dissolved gas forms any microstructure in water. Transmission electron microscopy (TEM) of graphene liquid cells (GLCs) can reveal structures in liquid with sub-nanometer or atomic resolution [1]. We thus encapsulated water between two laminated graphene layers spanning the holes in TEM grids; we investigated degassed water, deionized water, and water supersaturated with pure gas (N2, O2, Ar, Xe, CO2, and SF6) at room temperature (RT). While neither degassed water nor deionized water yielded specific features, two major microscopic structures were evident in gas-supersaturated water: (1) individual polycrystalline nanoparticles (typically several nanometers in diameter) in liquid water, and (2) mesoscopic clathrate structures (often ∼100 nm or larger in lateral size). The latter was seen much more frequently than the former [2]. The observations indicate that gas molecules may not be homogeneously dispersed as monomers in liquid water. Fig. 1 shows bright-field and dark-field TEM of a mesoscopic clathrate structure for N2-supersaturated water encapsulated in a GLC. This state features a high density of tiny cells: these cells appear as white spots at underfocus (Fig. 1a) and as dark spots at overfocus (Fig. 1b) [2]. Similar structures were visualized in GLCs containing water supersaturated with other gases. Interestingly, selected area electron diffraction (SAED) patterns acquired on the clathrate structures contained additional diffraction spots other than those associated with graphene (Fig. 1c). These diffraction spots were consistently observed in all water pockets containing this intriguing state. Diffraction spots with interplanar spacing (d-spacing) of 2.6–2.8, 3.4–3.6, 3.7––3.9, or 4.5-4.8 Å are commonly detected with different gases in this state [2], suggesting that water molecules form the crystalline structures that produce diffraction spots. Dark-field TEM imaging revealed regions of honeycomb-like structures with water molecules forming a solid matrix hosting the tiny gas-containing cells (Fig. 1d). It also indicates that water molecules form crystalline structures surrounding or between gas-containing cavities. This novel clathrate state differs from typical states of gas clathrates in several aspects: (1) it exists at RT, (2) the cages are larger (typically 2–4 nm), (3) the honeycomb-like cell morphology has neither long-ranged translational nor orientational order, and (4) the state has a lateral size smaller than 1 μm. Observation of the mesoscopic clathrate structures may resolve many long-standing puzzles about the dissolution of gases in water, such as abnormal thermodynamic properties, the iceberg model, bulk nanobubbles. The mesoscopic clathrate structures were observed in GLCs, but they may also be present in bulk water. We did observe the coexistence of liquid water with the clathrate structures inside the same water pocket [2]. A study of liquid water in equilibration with high-pressure gas using infrared spectroscopy indicated the existence of structures with water hydrogen bonds strengthened to levels observed in ice and clathrates [3], consistent with our observation of clathrate hydrate structures. Almost identical clathrate structures were observed when ethanol-water (EW) mixtures at ∼10% volume fraction ethanol, which is also gas supersaturated, were sandwiched between two laminated graphene layers [4]. Vibrational spectroscopies based on Raman scattering and infrared absorption techniques have also demonstrated a sharp increase in strength of hydrogen bonds with increasing ethanol concentration in EW mixtures [5]. The presence of mesoscopic clathrate structures explains many long-standing puzzles related to EW mixtures [4]. The crystalline water structure in this novel clathrate state has a d-spacing of 4.5–4.8 Å [2,4], which has not been reported for any other water ice or clathrate hydrate structure. Determining this new crystalline water structure is thus of considerable scientific interest. Because of the small size and low concentration of the mesoscopic clathrate hydrate structures, techniques such as X-ray diffraction and neutron diffraction, which are predominantly used to determine crystalline water structures, are not applicable. We derived the crystalline water structure in the mesoscopic clathrate structures by recording and analyzing in-zone electron diffraction patterns (IZEDPs) and by performing first-principles calculations [6]. The IZEDP evidence confirmed that the clathrate structures that formed in gas-supersaturated water and in EW mixtures have the same crystalline water structure [6]. Many of the mesoscopic clathrate structures exhibited a single crystal grain. We tilted the samples to acquire IZEDPs for each clathrate structure; more than one IZEDPs could often be acquired in the range of our TEM goniometer (x, y ± 30°). Figure 2 a–d presents a set of IZEDPs acquired for a clathrate structure in 10% EW mixture. We derived the lattice parameters of the structure and indexed the IZEDPs by using the CONOGRAPH software; a hexagonal lattice with a = b = 5.40 Å and c = 7.12 Å was determined. First-principles calculations were performed to locate the equilibrium positions of atoms. Six water molecules were placed inside the unit cell because the mass density (0.99 g/cm3) is close to that of liquid water. Fig. 3a shows the structure derived from the first-principles calculation, referred to as CW-RT, representing crystalline water structure at RT [6]. In the CW-RT structure, all water molecules are hydrogen-bonded to four others, and some distortions from the perfect tetrahedral structure are evident. The structure comprises only five-membered (pentagonal) rings of hydrogen-bonded water molecules, in contrast to the six-membered rings in hexagonal ice. The space group of the structure is P21. The structure viewed along the a- or b-axis is presented in Fig. 3b. The spiraling channels formed by water molecules can be identified along the c-axis (Fig. 3c). Fig. 2e–h shows the simulated IZEDPs; the related angles and d-spacings of the simulated patterns agree well with those of the experimental IZEDPs. This study suggests that water may form a matrix that actively interacts with gas molecules in complex and subtle ways. Because the samples were prepared under ambient conditions, the results offer insights into the local structures of ambient liquid water. The present findings may resolve many mysteries regarding ambient water as well as gas in water [7]. Bright-field TEM images were acquired at (a) underfocus and (b) overfocus. Insets: enlarged views of the regions outlined in yellow. (c) SAED pattern of the region shown in (a) and (b). The dashed circle indicates the first-order diffraction spots of the multi-layer graphene. Inset: enlarged view of the diffraction beam indicated with d-spacing of 3.4 Å. (d) Dark-field TEM image acquired from the diffracted beam indicated with d-spacing of 3.4 Å in (c) [2]. Four types of IZEDP acquired for a clathrate structure and the corresponding simulated diffraction patterns. (a–d) Experimental IZEDPS categorized as Types α–δ, respec

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