Voronoi Tessellation Analysis of Clathrate Hydrates

Chakraborty, Somendra Nath; Grzelak, Eric M.; Barnes, Brian C.; Wu, David T.; Sum, Amadeu K.

doi:10.1021/jp304612f

Cited by 21 publications

(18 citation statements)

References 39 publications

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“…59,60 Nucleation and growth of hydrates are usually characterized by order parameters that distinguish the phase of water molecules, structure of cages, and coordinates of guest molecules. [27][28][29][30][31]61 However, it is difficult to identify clusters that have formed initially using these order parameters due to the complex molecular geometries. Most recently, Barnes et al developed an order parameter, called the Mutually Coordinated Guest (MCG) order parameter, that identies guest molecules separated by water clusters consisting of ve or six-member rings.…”

Section: Analysis Of Nucleationmentioning

confidence: 99%

“…The nucleation rate calculated by Walsh et al is from the maximum likelihood estimate. 31 They performed the six replications at T ¼ 250 K, P ¼ 50 MPa and the induction times were veried by analyzing the evolution of the global F 4 61 order parameter as well as the appearance of cages larger than seven through the MD trajectories. The nucleation rate from Walsh et al is around J sim ¼ 5.00 Â 10 24 cm À3 s À1 .…”

Section: Survival Probabilitymentioning

confidence: 99%

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Nucleation rate analysis of methane hydrate from molecular dynamics simulations

et al. 2015

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Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Various analysis methods for nucleation have been developed through MD to analyze nucleation. In particular, the mean first-passage time (MFPT) and survival probability (SP) methods have proven to be effective in procuring the nucleation rate and critical nucleus size for monatomic systems. This study assesses the MFPT and SP methods, previously used for monatomic systems, when applied to analyzing clathrate hydrate nucleation. Because clathrate hydrate nucleation is relatively difficult to observe in MD simulations (due to its high free energy barrier), these methods have yet to be applied to clathrate hydrate systems. In this study, we have analyzed the nucleation rate and critical nucleus size of methane hydrate using MFPT and SP methods from data generated by MD simulations at 255 K and 50 MPa. MFPT was modified for clathrate hydrate from the original version by adding the maximum likelihood estimate and growth effect term. The nucleation rates calculated by MFPT and SP methods are within 5%, and the critical nucleus size estimated by the MFPT method was 50% higher, than values obtained through other more rigorous but computationally expensive estimates. These methods can also be extended to the analysis of other clathrate hydrates.

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Section: Analysis Of Nucleationmentioning

confidence: 99%

Section: Survival Probabilitymentioning

confidence: 99%

Nucleation rate analysis of methane hydrate from molecular dynamics simulations

et al. 2015

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“…Many hydrate order parameters have relied solely on water molecule coordinates, whether locally (a clustering metric) or globally (a system structure metric), 14,21,22 or solely on guest molecule coordinates. 23 None have been demonstrated to be a reaction coordinate (RC) in the sense of accurately quantifying progress along the nucleation pathway. Recently, we introduced the Mutually Coordinated Guest (MCG) order parameter, that quantifies the evolution of hydrate incipient formation and growth while considering the local structure of both water and methane molecules.…”

Section: ■ Introductionmentioning

confidence: 99%

Reaction Coordinate of Incipient Methane Clathrate Hydrate Nucleation

et al. 2014

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Nucleation from solution is a ubiquitous phenomenon with relevance to myriad scientific disciplines, including pharmaceuticals, biomineralization, and disease. One prominent example is the nucleation of clathrate hydrates, multicomponent crystalline inclusion compounds relevant to the energy industry where they block pipelines and also constitute a potential vast energy resource. Despite their importance, the molecular mechanism of incipient hydrate formation remains unknown. Herein, we employ advanced molecular simulation tools (pB histogram, equilibrium path sampling) to provide a statistical-mechanical basis for extracting physical insight into the molecular steps by which clathrates form. Through testing the Mutually Coordinated Guest (MCG) order parameter, we demonstrate that both guest (methane) and host (water) structuring are crucial to accurately describe the nucleation of hydrates and determine a critical nucleus size of MCG-1 = 16 at 255 K and 500 bar. Equipped with a validated (and novel) reaction coordinate, subsequent equilibrium path sampling simulations yield the free energy barrier and nucleation rate. The resulting quantitative nucleation process is described by the MCG clustering mechanism. This constitutes a significant advance in the field of hydrates research, as the fitness of a molecular descriptor has never been statistically verified. More broadly, this work has significance to a wide range of multicomponent nucleation contexts wherein the formation mechanism depends on contributions from both solute and solvent.

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“…32 Chakraborty et al defined Voronoi tessellation of the space centred around guest molecules. 33 In hydrates crystals, the water molecules are at the vertexes of Voronoi tessellation. Thus, in simulations, water molecules are considered hydrates-like if they are within a prescribed distance from the Voronoi vertexes.…”

Section: Introductionmentioning

confidence: 99%

Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation

Lauricella

Meloni

Liang

et al. 2015

The Journal of Chemical Physics

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For clathrate-hydrate polymorphic structure-type (sI versus sII), geometric recognition criteria have been developed and validated. These are applied to the study of the rich interplay and development of both sI and sII motifs in a variety of hydrate-nucleation events for methane and H2S hydrate studied by direct and enhanced-sampling molecular dynamics (MD) simulations. In the case of nucleation of methane hydrate from enhanced-sampling simulation, we notice that already at the transition state, ∼80% of the enclathrated CH4 molecules are contained in a well-structured (sII) clathrate-like crystallite. For direct MD simulation of nucleation of H2S hydrate, some sI/sII polymorphic diversity was encountered, and it was found that a realistic dissipation of the nucleation energy (in view of non-equilibrium relaxation to either microcanonical (NVE) or isothermal-isobaric (NPT) distributions) is important to determine the relative propensity to form sI versus sII motifs.

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Voronoi Tessellation Analysis of Clathrate Hydrates

Cited by 21 publications

References 39 publications

Nucleation rate analysis of methane hydrate from molecular dynamics simulations

Nucleation rate analysis of methane hydrate from molecular dynamics simulations

Reaction Coordinate of Incipient Methane Clathrate Hydrate Nucleation

Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation

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