Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages.     

Stability and reactivity of methane clathrate hydrates: insights from density functional theory

The sI methane clathrate hydrate consists of methane gas molecules encapsulated as dodecahedron (5(12)CH(4)) and tetrakaidecahedron (5(12)6(2)CH(4)) water cages. The characterization of the stability of these cages is crucial to an understanding of the mechanism of their formation. In the present work, we perform calculations using density functional theory to calculate interaction energies, free energies, and reactivity indices of these cages. The contributions from polarization functions to interaction energies is more than diffuse functions from Pople basis sets, though both functions from the correlation-consistent basis sets contribute significantly to interaction energies. The interaction energies and free energies show that the formation of the 5(12)CH(4) cage (from the 5(12) cage) is more favored compared to the 5(12)6(2)CH(4) cage (from the 5(12)6(2) cage). The pressure-dependent study shows a spontaneous formation of the 5(12)CH(4) cage at 273 K (P ≥ 77 bar) and the 5(12)6(2)CH(4) cage (P = 100 bar). The reactivity of the 5(12)CH(4) cage is similar to that of the 5(12) cage, but the 5(12)6(2)CH(4) cage is more reactive than the 5(12)6(2) cage.     

Vibrational spectra of methane clathrate hydrates from molecular dynamics simulation

Molecular dynamics simulations were performed on methane clathrate hydrates at ambient conditions. Thermal expansion results over the temperature range 60-300 K show that the unit cell volume increases with temperature in agreement with experiment. Power spectra were obtained at 273 K from velocity autocorrelation functions for selected atoms, and normal modes were assigned. The spectra were further classified according to individual atom types, allowing the assignment of contributions from methane molecules located in small and large cages within the structure I unit cell. The symmetric C-H stretch of methane in the small cages occurs at a higher frequency than for methane located in the large cages, with a peak separation of 14 cm(-1). Additionally, we determined that the symmetric C-H stretch in methane gas occurs at the same frequency as methane in the large cages. Results of molecular dynamics simulations indicate the use of power spectra obtained from the velocity autocorrelation function is a reliable method to investigate the vibrational behavior of guest molecules in clathrate hydrates.     

Heterogeneous crystal growth of methane hydrate on its sII [001] crystallographic face

This paper presents a systematic molecular simulation study of the heterogeneous crystal growth of methane hydrate sII from supersaturated aqueous methane solutions. The growth of sII hydrate on the [001] crystallographic face is achieved through utilization of a recently proposed methodology, and rates of crystal growth of 1 A/ns were sustained for the molecular models and specific conditions employed in this work. Characteristics of the crystals grown as well as properties and structure of the interface are examined. Water cages with a 5(12)6(3) arrangement, which are improper to both sI and sII structures, are identified during the heterogeneous growth of sII methane hydrate. We show that the growth of a [001] face of sII hydrate can produce an sI crystalline structure, confirming that cross-nucleation of methane hydrate structures is possible. Defects consisting of two methane molecules trapped in large 5(12)6(4) cages and water molecules trapped in small and large cages are observed, where in one instance we have found a large 5(12)6(4) cage containing three water molecules.     

IR and FTMW-IR spectroscopy and vibrational relaxation pathways in the CH stretch region of CH3OH and CH3OD

Infrared spectra of jet-cooled CH(3)OD and CH(3)OH in the CH stretch region are observed by coherence-converted population transfer Fourier transform microwave-infrared (CCPT-FTMW-IR) spectroscopy (E torsional species only) and by slit-jet single resonance spectroscopy (both A and E torsional species, CH(3)OH only). Twagirayezu et al. reported the analysis of ν(3) symmetric CH stretch region (2750-2900 cm(-1); Twagirayezu et al. J. Phys. Chem. A 2010, 114, 6818), and the present work addresses the more complicated higher frequency region (2900-3020 cm(-1)) containing the two asymmetric CH stretches (ν(2) and ν(9)). The additional complications include a higher density of coupled states, more extensive mixing, and evidence for Coriolis as well as anharmonic coupling. The overall observed spectra contain 17 interacting vibrational bands for CH(3)OD and 28 for CH(3)OH. The sign and magnitude of the torsional tunneling splittings are deduced for three CH stretch fundamentals (ν(3), ν(2), ν(9)) of both molecules and are compared to a model calculation and to ab initio theory. The number and distribution of observed vibrational bands indicate that the CH stretch bright states couple first to doorway states that are binary combinations of bending modes. In the parts of the spectrum where doorway states are present, the observed density of coupled states is comparable to the total density of vibrational states in the molecule, but where there are no doorway states, only the CH stretch fundamentals are observed. Above 2900 cm(-1), the available doorway states are CH bending states, but below, the doorway states also involve OH bending. A time-dependent interpretation of the present FTMW-IR spectra indicates a fast (～200 fs) initial decay of the bright state followed by a second, slower redistribution (about 1-3 ps). The qualitative agreement of the present data with the time-dependent experiments of Iwaki and Dlott provides further support for the similarity of the fastest vibrational relaxation processes in the liquid and gas phases.     

Phase equilibrium measurements and crystallographic analyses on structure-H type gas hydrate formed from the CH4-CO2-neohexane-water system

Phase equilibrium conditions and the crystallographic properties of structure-H type gas hydrates containing various amounts of methane (CH4), carbon dioxide (CO2), neohexane (2,2-dimethylbutane; NH), and liquid water were investigated. When the CH4 concentration was as high as approximately 70%, the phase equilibrium pressure of the structure-H hydrate, which included NH, was about 1 MPa lower at a given temperature than that of the structure-I hydrate with the same composition (except for a lack of NH). However, as the CO2 concentration increased, the pressure difference between the structures became smaller and, at CO2 concentrations below 50%, the phase equilibrium line for the structure-H hydrate crossed that for the structure I. This cross point occurred at a lower temperature at higher CO2 concentration. Extrapolating this relation between the cross point and the CO2 concentration to 100% CO2 suggests that the cross-point temperature would be far below 273.2 K. It is then difficult to form structure-H hydrates in the CO2-NH-liquid water system. To examine the structure, guest composition, and formation process of structure-H hydrates at various CH4-CO2 compositions, we used the methods of Raman spectroscopy, X-ray diffraction, and gas chromatography. Raman spectroscopic analyses indicated that the CH4 molecules were found to occupy both 5(12) and 4(3)5(6)6(3) cages, but they preferably occupied only the 5(12) cages. On the other hand, the CO2 molecules appeared to be trapped only in the 4(3)5(6)6(3) cages. Thus, the CO2 molecules aided the formation of structure-H hydrates even though they reduced the stability of that structure. This encaged condition of guest molecules was also compared with the theoretical calculations. In the batch-type reactor, this process may cause the fractionation of the remaining vapor composition in the opposite sense as that for CH4-CO2 hydrate (structure-I), and thus may result in an alternating formation of structure-H hydrates and structure-I in the same batch-type reactor.     

The structure of methane hydrate under geological conditions a combined Rietveld and maximum entropy analysis

We present a study of the structure of a fully deuterated methane hydrate under the geological conditions found in the world's oceans. In situ high-resolution neutron diffraction experiments have been performed at temperatures of 220, 275, and 280 K and a pressure of 100 bar, corresponding to the conditions at 1000 m water depth. The data were analyzed with a combination of Rietveld refinement and maximum entropy methods. From the Rietveld refinement, precise atomic parameters of the host lattice could be determined, indicating increasing distortions of the structure of the cages at elevated temperatures and pressures. Debye-Waller factors of the encaged CD(4) molecules have been found to exceed the values of the Debye-Waller factors of the D(2)O molecules considerably. In the large cage of structure type I the thermal center-of-mass displacements of the guests are 5-10 times larger than those of the water molecules. From the maximum entropy analysis maps of the scattering length density have been obtained, showing details of the vibrational amplitudes of the atoms in methane hydrate. The Debye-Waller factors of all molecules have been found to deviate considerably from a simple spherical geometry.     

Crystal lattice size and stability of type H clathrate hydrates with various large-molecule guest substances

To gain a better understanding of the effects of guest molecules on the lattice and stability of type H hydrates, we performed powder X-ray diffraction (PXRD) measurements and semiempirical molecular orbital calculations. The unit cell parameters and cohesive energies of various type H hydrates that contain methane (CH4) were analyzed. PXRD measurements indicated that an increase in the large-molecule guest volume caused the unit cell volume to increase. It was also indicated that a large-molecule guest substance caused the a-axis-direction of the unit cell to increase with little decrease in the c-axis direction. Calculations of cohesive energy by means of a semiempirical molecular orbital method indicated that the functional group and configuration of large-molecule guest substances affects the stability of type H hydrates. It was concluded that the icosahedron (5(12)6(8)) cages do not easily increase in length along the c-axis direction when larger guest molecules are used to form the hydrate, but the 5(12)6(8) cage and the layer of dodecahedron (5(12)) cages can easily increase in length along the a-axis direction due to interactions of the guest-host molecule.     

Nonstandard cages in the formation process of methane clathrate: stability, structure, and spectroscopic implications from first-principles

Endohedral CH(4)@(H(2)O)(n) (n = 16, 18, 20, 22, 24) clusters with standard and nonstandard cage configurations containing four-, five-, six-, seven-membered rings were generated by spiral algorithm and were systematically explored using DFT-D methods. The geometries of all isomers were optimized in vacuum and aqueous solution. In vacuum, encapsulation of methane molecules can stabilize the hollow (H(2)O)(n) cage by 2.31~5.44 kcal/mol; but the endohedral CH(4)@(H(2)O)(n) cages are still less stable than the pure (H(2)O)(n) clusters. Aqueous environment could promote the stabilities of the hollow (H(2)O)(n) cages as well as the CH(4)@(H(2)O)(n) clusters, and the CH(4)@(H(2)O)(n) clusters possess larger stabilization energies with regard to the pure (H(2)O)(n) clusters except for n = 24. The lowest energy structures of the CH(4)@(H(2)O)(20) and CH(4)@(H(2)O)(24) cages are identical to the building units in the crystalline sI clathrate hydrate. All of the low-energy cages (including both regular and irregular ones) have large structural similarity and can be connected by "dimer-insertion" operation and Stone-Wales transformation. Our calculation also showed that in the range of cluster size n = 16-24, the relative energies of cage isomers tend to decrease with increasing number of the adjacent pentagons in the oxygen skeleton structures. In addition to the regular endohedral CH(4)@(H(2)O)(20) and CH(4)@(H(2)O)(24) cage structures, some nonstandard CH(4)@(H(2)O)(n) (n = 18, 20, 22, 24) cages have lower energies and might appear during nucleation process of methane hydrate. For the methane molecules in these low-energy cage isomers, we found that the C-H symmetric stretching frequencies show a red-shift trend and the (13)C NMR chemical shifts generally move toward negative values as the cavity size increases. These theoretical results are comparable to the available experimental data and might help experimental identification of the endohedral water cages during nucleation.     

First-principles calculations of the structural and dynamic properties, and the equation of state of crystalline iodine oxides I2O4, I2O5, and I2O6

The structural and dynamical correlations, and the equation of state of crystalline I(2)O(4), I(2)O(5), and I(2)O(6) are investigated by first-principles calculations based on the density functional theory (DFT). The lattice dynamics results reveal distinctive features in the phonon density of states among the three crystals. The frequencies of the stretch modes in I(2)O(4) and I(2)O(5) are clearly separated from those of the other (e.g., bending) modes by a gap, with all stretch modes above the gap. In contrast, the gap in I(2)O(6) separates the highest-frequency stretch modes with other stretch modes, and there is no gap between the stretch and the other modes in I(2)O(6). The motion of iodine atoms is involved in all vibrational modes in I(2)O(5), but only in low-frequency lattice modes in I(2)O(6). In I(2)O(4), iodine atoms are involved in modes with frequency below 700 cm(-1). Van der Waals correction within our DFT calculations is found to reduce the overestimation of the equilibrium volume, with its effect on structure similar to the pressure effect. Namely, both effects significantly decrease the inter-molecular distances, while slightly increasing the bond lengths within the molecules. This causes the frequencies of some vibrational modes to decrease with pressure, resulting in negative "modes Gru?neisen parameters" for those modes. Thermodynamic properties, derived from the equation of state, of crystalline I(2)O(4), I(2)O(5), and I(2)O(6) are discussed within the quasi-harmonic approximation.     

Methane clathrate: CH(4) quantum rotor state dependent rattling potential

In methane hydrate the dominant peak in the density of states above 3 meV represents a rattling mode of the guest molecule CH(4) in the large ice cages. This mode shifts from 6.7 meV at T=4.5 K to T=30 K to 7.14 meV with conversion of CH(4) guest molecules into the tunneling ground state. The less symmetric angular density distribution PsiPsi(*) in the excited rotational state compared to the ground state allows the methane to fit better in the orientation dependent cage potential surface. This leads to a larger average distance to the cage-forming molecules with a weaker potential and a reduced rattling energy. A two state single particle model with characteristic rattling energies of 5.20 meV for pure T-methane and 7.3 meV for pure A-methane weighted by the population factors can fit the data.     

水合物CH4-CO2置换的双重机理:空位辅助与竞争

过去的CO2置换甲烷水合物的微观机理研究,主要集中在客体分子(CH4、CO2)之间的交换、占据状态,孤立地研究分解过程或生成过程,忽视主体-客体之间的作用、主体分子(H2O)的空位辅助和客体分子的多重竞争通道。本文基于水合物分解的过冷水及其水空位辅助,以及水合物生成的串滴链及其客体分子竞争的研究,进一步评论水合物CH4-CO2置换的双重机理。然后,对微观机理的动态性和未来研究的相关问题进行讨论。通过综述和评论,文章得出以下初步结果:过冷水通过水空位推动客体分子的跳跃、扩散,实现置换过程的自组装;CO2分子在分解前沿形成一个有序结构的CO2串滴链,其动态性伴随水的组织到获取包合物笼的结构,以及非晶形包合物转变成晶形包合物的生长过程;CO2和CH4在中晶穴中必然产生竞争,并且存在多种竞争类型;成核过程中,不稳定簇导致竞争结构,且有多重竞争通道。最后,结果表明水合物的CH4-CO2置换机理具有双重性,即主体分子的空位辅助和客体分子的竞争,是分解过程和生成过程的自然统一。     

The cages, dynamics, and structuring of incipient methane clathrate hydrates

Interest in describing clathrate hydrate formation mechanisms spans multiple fields of science and technical applications. Here, we report findings from multiple molecular dynamics simulations of spontaneous methane clathrate hydrate nucleation and growth from fully demixed and disordered two-phase fluid systems of methane and water. Across a range of thermodynamic conditions and simulation geometries and sizes, a set of seven cage types comprises approximately 95% of all cages formed in the nucleated solids. This set includes the ubiquitous 5(12) cage, the 5(12)6(n) subset (where n ranges from 2-4), and the 4(1)5(10)6(n) subset (where n also ranges from 2-4). Transformations among these cages occur via water pair insertions/removals and rotations, and may elucidate the mechanisms of solid-solid structural rearrangements observed experimentally. Some consistency is observed in the relative abundance of cages among all nucleation trajectories. 5(12) cages are always among the two most abundant cage types in the nucleated solids and are usually the most abundant cage type. In all simulations, the 5(12)6(n) cages outnumber their 4(1)5(10)6(n) counterparts with the same number of water molecules. Within these consistent features, some stochasticity is observed in certain cage ratios and in the long-range ordering of the nucleated solids. Even when comparing simulations performed at the same conditions, some trajectories yield swaths of multiple adjacent sI unit cells and long-range order over 5 nm, while others yield only isolated sI unit cells and little long-range order. The nucleated solids containing long-range order have higher 5(12)6(2)/5(12) and 5(12)6(3)/4(1)5(10)6(2) cage ratios when compared to systems that nucleate with little long-range order. The formation of multiple adjacent unit cells of sI hydrate at high driving forces suggests an alternative or addition to the prevailing hydrate nucleation hypotheses which involve formation through amorphous intermediates.     

Spectroscopic signatures of halogens in clathrate hydrate cages. 1. Bromine

We report the first UV-vis spectroscopic study of bromine molecules confined in clathrate hydrate cages. Bromine in its natural hydrate occupies 51262 and 51263 lattice cavities. Bromine also can be encapsulated into the larger 51264 cages of a type II hydrate formed mainly from tetrahydrofuran or dichloromethane and water. The visible spectra of the enclathrated halogen molecule retain the spectral envelope of the gas-phase spectra while shifting to the blue. In contrast, spectra of bromine in liquid water or amorphous ice are broadened and significantly more blue-shifted. The absorption bands shift by about 360 cm-1 for bromine in large 51264 cages of type II clathrate, by about 900 cm-1 for bromine in a combination of 51262 and 51263 cages of pure bromine hydrate, and by more than 1700 cm-1 for bromine in liquid water or amorphous ice. The dramatic shift and broadening in water and ice is due to the strong interaction of the water lone-pair orbitals with the halogen sigma* orbital. In the clathrate hydrates, the oxygen lone-pair orbitals are all involved in the hydrogen-bonded water lattice and are thus unavailable to interact with the halogen guest molecule. The blue shifts observed in the clathrate hydrate cages are related to the spatial constraints on the halogen excited states by the cage walls.     

CH stretch vibrations of adsorbed molecules studied by infrared spectroscopy; CH3O on Cu(100)

The first high-resolution CH stretch vibrations in submonolayers of molecules adsorbed on a single-crystalline surface have been obtained by infrared spectroscopy. Investigation of symmetric and asymmetric vibrational modes of CH₃O adsorbed on Cu(l00) shows that the molecules are tilted on the surface, that nearest-neighbour interactions are important and that the intrinsic peak widths are large.     

聚乙烯唑啉作用下甲烷水合物分解的分子动力学模拟

利用分子动力学模拟系统研究了不同质量浓度下(1.25%、2.50%、6.06%)聚乙烯唑啉(PEtO)对甲烷水合物的分解作用. 模拟体系为甲烷水合物2′2′2的超胞和聚合物对接体系. 模拟发现水分子间氢键构架的水合物笼型结构在PEtO的作用下出现扭曲, 最终导致水合物笼型结构完全坍塌. 通过氧原子径向分布函数、均方位移以及扩散系数比较不同浓度PEtO的作用, 证实在一定浓度范围内, PEtO的浓度越高, 其水合物分解作用越强. 此外, PEtO 具有一定的可生物降解性. PEtO 对水合物的作用为: PEtO 吸附在水合物表面, 其中的酰胺基(N―C＝O)与成笼的水分子形成氢键, 破坏邻近的笼形结构, 令水合物分解; PEtO不断分解表面的水合物, 直到水合物笼完全分解.     

Molecular dynamics simulations for the growth of CH_4-CO_2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xCO2= 75%, xCO2= 50%, and xCO2= 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.     

Molecular dynamics simulations for the growth of CH4-CO2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.     

Reaction dynamics and vibrational spectroscopy of CH3D molecules with both C-H and C-D stretches excited

State-resolved reactions of CH3D molecules containing both C-H and C-D stretching excitation with Cl atoms provide new vibrational spectroscopy and probe the consumption and disposal of vibrational energy in the reactions. The vibrational action spectra have three different components, the combination of the C-H symmetric stretch and the C-D stretch (nu1 + nu2), the combination of the C-D stretch and the C-H antisymmetric stretch (nu2 + nu4), and the combination of the C-D stretch and the first overtone of the CH3 bend (nu2 + 2nu5). The simulation for the previously unanalyzed (nu2 + nu4) state yields a band center of nu0 = 5215.3 cm(-1), rotational constants of A = 5.223 cm(-1) and B = 3.803 cm(-1), and a Coriolis coupling constant of zeta = 0.084. The reaction dynamics largely follow a spectator picture in which the surviving bond retains its initial vibrational excitation. In at least 80% of the reactive encounters of vibrationally excited CH3D with Cl, cleavage of the C-H bond produces CH2D radicals with an excited C-D stretch, and cleavage of the C-D bond produces CH3 radicals with an excited C-H stretch. Deviations from the spectator picture seem to reflect mixing in the initially prepared eigenstates and, possibly, collisional coupling during the reaction.     

Crown ethers at the aqueous solution-air interface: 1. Assignments and surface spectroscopy

The surface of aqueous solutions of 4-Nitro Benzo-15-Crown-5 (NB15C5) and Benzo-15-Crown-5 (B15C5) has been studied using the surface sensitive technique vibrational sum frequency spectroscopy (VSFS). The NO, CN, COC and CH vibrational modes of these compounds at the air-water interface as well as OH vibrational modes of the surface water hydrating this compound have been targeted in order to obtain molecular information about arrangement and conformation of the adsorbed crown ether molecules at the air-water interface. The CH(2) vibrational modes of crown ethers have been identified and found to be split due to interaction with ether oxygen. The spectra provide evidence for the existence of a protonated crown complex moiety at the surface leading to the appearance of strongly ordered water species. The interfacial water species are influenced by the resulting charged interface and by the strong Zundel polarizability due to tunneling of the proton species between equivalent sites within the crown ring.