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Intracavity Conformational Changes in Clathrate Hydrates Yun-Ho Ahn, Hyung-Kyu Lim, Hyery Kang, Hyungjun Kim, Minjun Cha, Kyuchul Shin, and Huen Lee J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.6b04511 • Publication Date (Web): 25 Jul 2016 Downloaded from http://pubs.acs.org on August 2, 2016

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The Journal of Physical Chemistry

Intracavity Conformational Changes in Clathrate Hydrates Yun-Ho Ahn1, Hyung-Kyu Lim2, Hyery Kang1, Hyungjun Kim2, Minjun Cha3, Kyuchul Shin*4 and Huen Lee*1 1

Department of Chemical and Biomolecular Engineering (BK21+ program), Korea Advanced

Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea. 2

Graduate School of EEWS, Korea Advanced Institute of Science and Technology (KAIST),

291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea. 3

Department of Energy and Resources Engineering, Kangwon National University, 1

Kangwondaehak-gil, Chuncheon-si, Gangwon-do 200-701, Republic of Korea. 4

Major in Applied Chemistry, School of Applied Chemical Engineering, Kyungpook National

University, 80 Daehak-ro, Buk-gu, Daegu 702-701, Republic of Korea.

ACS Paragon Plus Environment

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ABSTRACT

Acyclic hydrocarbon molecules favor the gauche- or cis- conformation, more stable in terms of molecular geometry when they are enclathrated in clathrate hydrates. Once they are captured, they keep their conformation in the hydrate cavities. However, on the basis of Raman spectra and density functional theory (DFT) calculations, we observed the conformational changes of acyclic guest molecule (3-buten-2-one) occurring in the hydrate cavities induced by the intercavity electron transfer after γ-irradiation. This phenomenon is also accompanied by the enhanced thermodynamic stability of clathrate hydrate phases. These results contribute to understand the complex physicochemical properties of clathrate hydrates and to suggest practical application for hydrate-based gas storage and separation.


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INTRODUCTION Clathrate hydrates, which are composed of host water molecules and small gaseous or organic guest molecules,1 have been extensively investigated because of their potential for practical applications in energy and environmental engineering such as gas separation,2 methane production with carbon dioxide sequestration,3-6 and hydrogen storage.7-10 There are three widely known crystal structures of clathrate hydrates, structure-I (sI, cubic Pm-3n), structure-II (sII, cubic Fd-3m), and structure-H (sH, hexagonal P6/mmm), containing several types of large and small cavities.1 The sI clathrate hydrate is composed of six 51262 and two 512 cavities with 46 water molecules in a unit cell. On the other hand, the sII and sH clathrate hydrates are composed of eight 51264 and sixteen 512 cavities with 136 H2Os and one 51268, two 435663, and three 512 cavities with 34 H2Os, respectively.1 The hydrophobic guest-host interactions occurring in relatively larger cavities of sII (the 51264) and sH (the 51268) hydrates than sI (the 51262) hydrates often lead to higher thermodynamic stability of the clathrate structures.11-13 Many organic molecules having suitable molecular sizes to those cavities thus have been studied to form more stable clathrate hydrates with methane, carbon dioxide, or hydrogen gases for applications to gas storage and transportation.11-13 Several acyclic molecules having two or three rotational conformers are known to prefer the stable gauche conformation when those molecules are enclathrated in hydrate cavities. Isopentane, forming the sH hydrate with methane, was reported to show a gauche-gauche position in the 51268 cavity.14 Lee et al. also investigated several sH hydrate formers and their preferred conformer in the hydrate phases.15 One of other examples is n-butane, forming the sII hydrate with methane, hydrogen sulfide, or xenon.16-18 Although a trans conformer of n-butane is


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thermodynamically preferred in the gas phase, only the gauche form is observed in its clathrate hydrate.19-22 At this stage, a question arises: Is it possible that a guest molecule changes its conformation in a hydrate cavity? Isopentane and n-butane are converted to suitable conformations for hydrate cavities when they are enclathrated.14, 16-18 After enclathration, guest molecules keep the conformations and no cases of intracavity changes of guest conformation in clathrate hydrates have been reported to date. Recently, Ohgaki et al. reported that the interconversions between npropyl and i-propyl radicals or between i-butyl and tert-butyl radicals induced by hydrogen transfer to an adjacent cavity were observed in the annealing process of γ-irradiated propane and isobutane hydrates,23-24 but there is no conformational change of the propane and isobutane molecules. In this study, we report for the first time intracavity conformational changes of guest molecules in clathrate hydrates. For the study, 3-buten-2-one (also called methyl vinyl ketone), having a suitable molecular size to fit into the 51264 cavity, was chosen. 3-buten-2-one is a α,β-unsaturated carbonyl compound containing both a carbon-carbon double bond and a carbonyl group. The two conjugated double bonds can rotate 180° on the axis of a carbon-carbon single bond resulting in two conformers, s-cis and s-trans, in nature (Figure S1).25-26 It was reported that the existence ratio of s-cis and s-trans conformers is temperature dependent and that s-trans is the favored conformer at a low temperature condition on the basis of IR and Raman spectroscopic studies.2527

In this study, we attempted to form the clathrate hydrate of 3-buten-2-one with methane as a

help guest and investigate the conformational changes of 3-buten-2-one in the hydrate cavity by Raman spectroscopy.


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EXPERIMENTAL SECTION Synthesis of binary (3-buten-2-one + CH4) hydrate samples Deionized water of ultrahigh purity was supplied from Merck (Germany) and 3-buten-2-one was supplied by Sigma-Aldrich Inc. CH4 gas was purchased from Special Gas (Korea) with stated minimum purities of 99.99 mol %. An amount of 10 g of 3-buten-2-one solution having 5 mol % of concentration was initially loaded into the stirring cell. The stirring cell has a vertical magnetic drive agitator so that continuous stirring is possible when making binary hydrates. A four-wire type Pt-100Ω probe was used for the temperature sensing, and a pressure transducer (Druck, PMP5073) was also used for the pressure sensing inside the cell. After loading the solution, air existed inside the cell was flushed out by continuous injecting of CH4. After few seconds, CH4 was pressurized up to around 120 bar by using microflow syringe pump (Teledyne, ISCO 260D). Then, temperature of stirring cell was lowered with a circulating bath (Jeio Tech., RW-2025G) until binary hydrates were formed. After binary hydrate formation detected with increased temperature and decreased pressure, the cell was kept in a 263 K bath for sufficient time (3 days) to produce binary hydrate without any icy impurities. To recover the binary hydrate sample, the stirring cell was quenched in liquid nitrogen and after a few seconds, the pressure was released to atmospheric pressure. The binary hydrate particles were ground (~200 µm) in a mortar and pestle in liquid nitrogen. These binary hydrate samples were used for HRPD and Raman analysis without γ-ray irradiation. A part of sample was irradiated at 90 kGy dose (15 kGy per 1 h) by a 60Co γ-ray source at KAERI in Jeongeup, Korea. The sample was being immersed in liquid nitrogen during the irradiation. These γ-ray irradiated binary hydrate samples were used for Raman and ESR analysis.


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Structure Analysis Using Synchrotron High Resolution Powder Diffraction (HRPD) The HRPD patterns were measured using the High-Resolution Powder Diffraction beamline (9B) at Pohang Accelerator Laboratory (PAL) in Korea. During the measurements, the θ/2θ scan mode with a fixed time of 2 s, and a step size of 0.005° for 2θ = 0-120° and the beamline with a wavelength of 1.5472 Å were used for each samples. The binary hydrate powder stored in liquid nitrogen was quickly transferred to the sample stage cooled down to 80 K in air, and experiment was carried out at around 77 K to minimize the possible sample damage. Conformational Characterization Using Raman Spectroscopy Raman spectra were measured using the Horiba Jobin Yvon LabRAM HR UV/Vis/NIR high resolution dispersive Raman microscope equipped with CCD detector and cooled by liquid nitrogen. The resolution of recorded spectra was 0.75 cm-1 at 1800 grating mode. The excitation source was an Ar-ion laser emitting a 514.53 nm line. The intensity of laser was typically 30 mW. For variable temperature experiment, LINKAM unit was used to control the sample temperature. At each temperature, sufficient time was provided to reach the equilibrium state. Radical Characterization Using Electron Spin Resonance (ESR) The electron spin resonance (ESR) spectrum were measured using the JEOL PX2300 equipment. The samples were kept under liquid nitrogen to maintain the radical species during the experiment. Multi-component fitting and simulation of the ESR spectrum were performed using the Garlic function with the Gaussian line broadening factor, implemented in EasySpin 5.0.19 software.28


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Calculation Methods Density Functional Theory (DFT) calculations for assigning Raman peaks have been carried out by using Jaguar 8.4.29 We used the Becke three-parameter functional (B3) combined with the correlation functional of Lee, Yang, and Parr (LYP) 30, and the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional 31 along with 6-31+G** basis sets. After fully optimizing the molecular structures of 3-buten-2-one in gas-phase state, we calculated the Hessians for vibrational frequencies by evaluating analytic gradients. From these gas-phase vibrational frequency data, we derived the scaling factors for each C=C and C=O peaks to match with the experimental gas-phase Raman peaks (Table S1). In order to estimate the peak shifts of vibrational modes when the guest molecules are in aqueous and enclathrated phase, we employed Poisson-Boltzmann (PB) implicit solvation method for aqueous phase and explicit 51264 water cage which is sampled from sII clathrate structure with experimentally refined lattice parameter in this work. Before inserting guest molecules into the 51264 cage, the positions of hydrogen atoms in cage were fully optimized while the oxygen atoms were fixed. We note that the frequency calculations of enclathrated guest molecule, we diagonalized the partial Hessian matrix of guest molecule with fixing the position of host cage structure. For direct and quantitative comparison with inducing an appropriate error cancellation, we scaled the calculated Raman frequencies a priori. The scaling factors were slightly differently chosen depending on peaks to align gas-phase experimental frequencies and DFT calculated frequencies, ranging from 0.96 to 1.01 as listed in Table S1. The final scaled and unscaled DFT calculated Raman frequencies are listed in Table S2.


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RESULTS AND DISCUSSION From a synchrotron high resolution powder diffraction (HRPD) analysis, the binary 3-buten-2one + CH4 clathrate hydrate sample was proven to be sII clathrate hydrate of a cubic Fd-3m space group with a small amount of ice impurity (Figure 1). The lattice parameter obtained from pattern refinement by the Le Bail fitting method32 was 17.1959(3) Å at 80 K. Because we used a 5 mol % 3-buten-2-one solution, which is slightly less concentrated than the stoichiometric 5.6 mol % concentration for the complete occupation of 51264 cavities in the sII hydrate phase, so as to minimize unreacted 3-buten-2-one, methane molecules might occupy a fraction of the 51264 cavity. Although the molecular size of 3-buten-2-one is slightly larger than the mean-free diameter of 51264 cavities, it possibly occupies large cages of sII hydrates as other large molecules do due to the flexibility of water frameworks.33-34 As the next step, we checked the conformations of 3-buten-2-one in the aqueous solution and in the clathrate hydrate by Raman spectroscopy. The Raman spectra of the binary 3-buten-2-one + CH4 clathrate hydrate were measured with various initial temperatures from 93 to 213 K shown in Figure 2. The C‒H stretching modes of methane occupying the 512 and 51264 cavities of sII hydrate were observed at 2914 cm-1 and 2904 cm-1, respectively, and the sII 3-buten-2-one + CH4 hydrate kept the clathrate structure stable until 133 K. However, as the temperature increased, the hydrate started to dissociate and a large amount of methane already disappeared at 153 K. By the way, considering both the C=C band (1623 cm-1, s-trans; 1627 cm-1, s-cis) and the C=O band (1705 cm-1, s-trans; 1715 cm-1, s-cis) of neat 3-buten-2-one,26, 35 two bands of the binary 3-buten-2-one + CH4 clathrate hydrate observed at 1626 cm-1 and 1692 cm-1 imply that they are from the C=C bond and C=O bond of one 3-buten-2-one conformer, which is dominantly favored in the cavity (shown in the spectra recorded at 93 K, 113 K, and 133 K of


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Figure 2). The two tiny shoulders appearing at 1618 and 1672 cm-1 are considered to be from the unreacted 3-buten-2-one molecules that exist outside the hydrate media, or possibly from another geometrically less favored conformer in the cavity. As the hydrate started to dissociate from 153 K, two tiny peaks at 1618 cm-1 (C=C stretching mode) and 1672 cm-1 (C=O stretching mode) rapidly grew, implying that they are from the 3-buten-2-one released from the clathrate cavity. In Figure S2, the Raman spectra of the frozen 5 mol % 3-buten-2-one solution in the region from 1600 to 1725 cm-1 show two same peaks, at 1618 cm-1 for C=C and at 1672 cm-1 for C=O stretching modes, indicating that only one conformer exists from 93 K to 253 K. At this stage, we checked the conformation of 3-buten-2-one in the aqueous solution and in the clathrate hydrate by assigning the Raman band with the help of density functional theory (DFT) calculation. We adopted two different B3LYP and PBE exchange-correlation functionals for cross-checking the results, and the detailed calculation methods and assigned Raman frequencies are in the calculation methods of experimental section and the supporting information, respectively. First, both the B3LYP and PBE methods predicted that the Raman peaks will show a slight blue-shift (2~10 cm-1) from the aqueous solution to the clathrate phase for both s-cis and s-trans forms. However, both the C=C and C=O stretching modes of the Raman spectra (Figure 2) show larger peak shifts than the predicted shifts for the enclathration while retaining conformations of guests (8 cm-1 (1618→1626 cm-1) and 20 cm-1 (1672→1692 cm-1), respectively). The calculation results for the peak shifts from the aqueous s-trans form to the enclathrated s-cis form predicted a similar degree of peak shifts to the experimental observations. Therefore, it is reasonable that assigning s-cis form to observed peaks in clathrate phase. Considering the calculated Raman peaks in aqueous phase, it is also confirmed that solvated 3buten-2-one by water molecules prefers the s-trans form and the band observed in the aqueous


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solution showed redshift due to the solvation effect compared to the bands of gas-phase 3-buten2-one.26, 35 Therefore, from the Raman spectra and DFT calculation results shown in Figure 2, the conformation change of 3-buten-2-one from the s-cis to s-trans is due to the hydrate dissociation and there is no intracavity conformational transformation. By the way, recent studies reported hydrogen atom transfer (referred to as the ‘hydrogenpicking’ phenomenon) through a hexagonal face of a 51264 cavity between hydrocarbon guests of γ-irradiated hydrates.23-24 In order to provide driving force for conformational transformation in a hydrate cavity, the 3-buten-2-one + CH4 clathrate hydrate was γ-irradiated to 90 kGy at 77 K and analysed again by Raman spectroscopy. At 93 K, the obtained Raman spectrum of the γ-irradiated sample is similar to that of the nonirradiated sample (Figure 3). As the temperature increases, however, two peaks at 1620 cm-1 and at 1674 cm-1 newly appear and increase until 133 K even though the hydrate phase does not start to dissociate. As shown in Figure 3, most of the methane stays in the 512 and the 51264 cavities of sII hydrate until the temperature increases to 173 K. Thus, newly appearing two peaks at 1620 cm-1 and at 1674 cm-1 strongly imply the existence of the s-trans form of 3-buten-2-one in the 51264 cavity of sII hydrate, corresponding to the slight calculated peak shifts of s-trans form from aqueous to hydrate phase. Meanwhile, calculation results predict that enclathrated s-cis and strans forms are slightly distorted around 10 and 5 degree, respectively in order to have geometrically optimized configuration in the cavity (Figure 4). However, this slight distortion does not induce high energy increment comparable with the third conformer of 3-buten-2-one, having a nonplanar or gauche structure.26


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One interesting aspect in Figure 3 is that the Raman signals of the s-trans form disappear at 153 K and reappear as the temperature rises to 173 K. Here, we note that the spectroscopic results shown in Figure 3 were reproducible for the other samples obtained from two additionally repeated experiments (Figure S3). Reappearing s-trans signals over 173 K are due to 3-buten-2one molecules released from the hydrate cavities because the intensities of C‒H stretching modes at 2904 and 2914 cm-1, originating from enclathrated methane molecules, start to decrease from 173 K. Therefore, we can conclude that there would be a defined temperature window (~ 133 K) where the s-trans conformer could exist stably in the hydrate phase, and the intracavity conformational transformation of 3-buten-2-one occurs in this defined temperature window. In order to identify the mechanism underlying this phenomenon, we obtained the electron spin resonance (ESR) spectrum of γ-irradiated 3-buten-2-one + CH4 hydrate at 77 K (Figure 5). The spectrum shows strong 1:3:3:1 hyperfine signals, indicating methyl radicals generated from the dissociation of CH4 molecules (coupling constant: 2.35 mT).36 The presence of small peaks merged in the signal of the methyl radical in the spectrum imply that there exist at least two different radicals in the irradiated sample, but the relatively low intensities of these peaks make identification of them difficult. One possible radical for the irradiated (3-buten-2-one + CH4) hydrate system is a ketyl radical anion (Figure 5), which is generated when the 3-buten-2one molecule captures a solvated electron in liquid ammonia.37 In order to check whether this ketyl radical was formed by the γ-irradiation, we simulated the ESR spectrum containing both a methyl radical and a ketyl radical anion. The EasySpin program was used for this simulation with the coupling constants of radicals obtained from the literature (2.3 mT for methyl radical36 and 0.92 mT for ‒CH3, 1.17 mT for =CH2, and 0.05 mT for =CH‒ groups of ketyl radical37) for the initial input. As shown in Figure 5, the simulated spectrum is well-matched with the


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experimental spectrum and the refined values of the coupling constants after the simulation (2.35 mT for methyl radical and 1.11 mT / 1.42 mT / 0.07 mT for ‒CH3 / =CH2 / =CH‒ groups of ketyl radical) were in good agreement with the values in the literature, although there are small uncertain shoulders. Slight differences in the coupling constants between the literature and the simulation are ascribed to the enclathration effect of the ketyl radical. Therefore, we conclude that γ-irradiation generated methyl radicals from CH4 and ketyl radical anions from 3-buten-2one guest molecules, respectively. From the ESR spectroscopic results, a possible mechanism for the conformational change is as follows (Scheme 1): (1) A few 3-buten-2-one molecules are changed to ketyl radicals by γirradiation. (2) The carbon atom of the carbonyl group has a pyramidal geometry rather than triangular and freely rotates. (3) The electron of the ketyl radical transfers to neighboring 3buten-2-one as the temperature increases and forms a new ketyl radical. (4) After the electron transfer, the old ketyl radical is returned to 3-buten-2-one with either the s-cis or s-trans form. Because the mechanism proposed above is a kind of chain reaction, a few ketyl radical anions only can initiate a considerable number of conformational changes as observed in the Raman spectroscopy (Figure 3). Another remarkable feature of this phenomenon is that the dissociation temperature of 3-buten2-one + CH4 hydrate increases by over 20 degrees after γ-irradiation. As shown in Figure 2, most methane molecules of 3-buten-2-one + CH4 hydrate were already released at 153 K. On the other hand, after γ-irradiation, a large amount of methane was still inside the cages even at 173 K (Figure 3). Although the exact mechanism has not been revealed yet, this enhanced thermodynamic stability of the 3-buten-2-one hydrate by γ-irradiation can provide an important contribution to the modification of clathrate materials.


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CONCLUSION The guest conformation in the hydrate cavity often provides abundant information for the guesthost interactions. This work demonstrates the first example of the intracavity conformational change of an acyclic guest molecule enclathrated in a hydrate cage. The 3-buten-2-one molecule favors enclathration in the s-cis form in the 51264 cavity, similarly to the gauche form of n-butane in the sII hydrate,22 while the neat or solvated 3-buten-2-one prefers the s-trans over the s-cis conformation. The γ-irradiation can induce the intracavity conformational change of 3-buten-2one, i.e., from the s-cis to the s-trans form in the hydrate cavity. The γ-irradiation causes a few 3buten-2-one molecules to form ketyl radicals and the s-trans conformation appears when the ketyl radical returns to the 3-buten-2-one by electron transfer to the neighboring 3-buten-2-one guest in the 51264 cavity. This work also shows the possibility that the conformational transformation enhances the thermodynamic stability of clathrate hydrate phases. The present findings provide an important key to understand the radiolysis chemistry occurring in the clathrate phase and to modify the clathrate hydrate materials.


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Figure 1. Synchrotron HRPD patterns of the 3-buten-2-one + CH4 hydrate recorded at 80 K. (Red circles, observed HRPD pattern; Black solid line, calculated HRPD pattern; tick marks, cubic Fd-3m (top) and hexagonal P63/mmc phases (bottom)).


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Figure 2. Raman spectra of 3-buten-2-one + CH4 hydrate measured at various temperatures. Enclathrated s-cis 3-buten-2-one (1626, 1692 cm-1) and CH4 molecule (2904, 2914 cm-1) were observed from 93 K to 153 K. Green and blue tick marks indicate the calculated Raman shifts for s-trans and s-cis conformers in the aqueous solution (top) and in the clathrate hydrate (bottom), respectively.


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Figure 3. Raman spectra of the γ-irradiated 3-buten-2-one + CH4 hydrate measured at various temperatures. Enclathrated s-trans 3-buten-2-one was detected (1620, 1674 cm-1) from 93 K to 133 K. Green and blue tick marks indicate the calculated Raman shifts for s-trans and s-cis conformer in the aqueous solution (top) and in the clathrate hydrate (bottom), respectively.


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Figure 4. Geometrically optimized configurations of s-cis and s-trans forms in the clathrate hydrate cavities. (distortion angles: 9.5º and 5.1 º for s-cis and s-trans, respectively, using PBE; 10.6 º and 5.4 º for s-cis and s-trans, respectively, using B3LYP)


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Figure 5. Experimental and simulated ESR spectra of the γ-irradiated 3-buten-2-one + CH4 hydrate measured at 77 K. The inset figure shows simulated ESR patterns from each guest molecule in the hydrate system.


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Scheme 1. A schematic illustration of the conformational change mechanism in large cavities of sII hydrates.


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ASSOCIATED CONTENT Supporting Information. Structures of 3-buten-2-one conformers and their size, Raman spectra of 3-buten-2-one solution, Scaling factors used in DFT calculation, and Detailed results of Raman shifts from both experiment and calculations. This material is available free of charge via the Internet at http://pubs.acs.org.

AUTHOR INFORMATION Corresponding Author * (H.L.) E-mail: [email protected], Phone: +82-42-350-3917 * (K.S.) E-mail: [email protected], Phone: +82-53-950-5587 Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. Notes Any additional relevant notes should be placed here.

ACKNOWLEDGMENT This research was funded by the the Nuclear Energy Research Infrastructure Program (NRF2015M2B2A4031401) through a National Research Foundation Korea (NRF) grant funded by


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the Ministry of Science, ICT and Future Planning (MSIP). HRPD experiments at PLS (Beamline 9B) were supported by POSTECH.

ABBREVIATIONS sI, Structure-I; sII, Structure-II; sH, Structure-H; HRPD, High Resolution Powder Diffraction; ESR, Electron Spin Resonance; DFT, Density Functional Theory; B3LYP, Becke 3-Parameter (Exchange), Lee, Yang and Parr; PBE, Perdew-Burke-Ernzerhof.


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Intracavity Conformational Changes in Clathrate Hydrates - The

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