Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) hydrocarbon and torsional parameters and to the partial atomic charges and torsional parameters of the phosphate moiety. These changes were motivated by a combination of unexpected simulation results and recent high-level ab initio quantum mechanical calculations. The parameter optimization procedure is described, and the resulting energy function validated by an 11 ns molecular dynamics simulation of a hydrated phospholipid bilayer. Of note is the influence of the hydrocarbon LJ parameters on the conformational properties of the aliphatic tails, emphasizing the importance of obtaining the proper balance between the bonded and nonbonded portions of the force field. Compatibility with the CHARMM all-atom parameter sets for proteins and nucleic acids has been maintained such that high quality simulations of biologically interesting me...

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An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids

Gas clathrate hydrates were first identified in 1810 by Sir Humphrey Davy. However, it is believed that other scientists, including Priestley, may have observed their existence before this date. They are solid crystalline inclusion compounds consisting of polyhedral water cavities which enclathrate small gas molecules. Natural gas hydrates are important industrially because the occurrence of these solids in subsea gas pipelines presents high economic loss and ecological risks, as well as potential safety hazards to exploration and transmission personnel. On the other hand, they also have technological importance in separation processes, fuel transportation and storage. They are also a potential fuel resource because natural deposits of predominantly methane hydrate are found in permafrost and continental margins. To progress with understanding and tackling some of the technological challenges relating to natural gas hydrate formation, inhibition and decomposition one needs to
develop a fundamental understanding of the molecular mechanisms involved in these processes. This fundamental understanding is also important to the broader field of inclusion chemistry. The present article focuses on the application of a range of physico-chemical techniques and approaches for gaining a fundamental understanding of natural gas hydrate formation, decomposition and inhibition. This article is complementary to other reviews in this field, which have focused more on the applied, engineering and technological aspects of clathrate hydrates.

Towards a fundamental understanding of natural gas hydrates

Raman microspectrometry of fluid inclusions

The present study attempts to understand the use of the flexible porous chromium terephthalate Cr(OH)(O2C−C6H4−CO2) denoted MIL-53(Cr) (MIL = Material from Institut Lavoisier) for the separation of mixtures of CO2 and CH4 at ambient temperature. The coadsorption of CO2 and CH4 was studied by a variety of different techniques. In situ synchrotron X-ray Powder Diffraction allowed study of the breathing of the solid upon adsorption of the gas mixtures and simultaneously measured Raman spectra yielded an estimation of the adsorbed quantities of CO2 and CH4, as well as a quantification of the fraction of the narrow pore (NP) and the large pore (LP) form of MIL-53. Quantitative coadsorption data were then measured by gravimetry and by breakthrough curves. In addition, computer simulation was performed to calculate the composition of the adsorbed phase in comparison with experimental equilibrium isotherms and breakthrough results. The body of results shows that the coadsorption of CO2 and CH4 leads to a similar ...

Co-adsorption and separation of CO2-CH4 mixtures in the highly flexible MIL-53(Cr) MOF.

This review aims to introduce the chemistry of low dosage inhibitors of clathrate hydrate formation within the context of their role in the oil and gas industry. The review covers both kinetic hydrate inhibitors and anti-agglomerants from the point of view of structure–function relationships, focussing on recent refinements in mechanistic understanding and chemical design, and the consequently evolving and increasingly fine-tuned properties of these fascinating compounds.

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The chemistry of low dosage clathrate hydrate inhibitors

Raman spectra of clathrate hydrate guest molecules are presented for three known structures (I (sI), II (sII), and H (sH)) in the following systems:  CH4 (sI), CO2 (sI), C3H8 (sII), CH4 + CO2 (sI), CD4 + C3H8 (sII), CH4 + N2 (sI), CH4 + THF-d8 (sII), and CH4 + C7D14 (sH). Relative occupancy of CH4 in the large and small cavities of sI were determined by deconvoluting the ν1 symmetric bands, resulting in hydration numbers of 6.04 ± 0.03. The frequency of the ν1 bands for CH4 in structures I, II, and H differ statistically, so that Raman spectroscopy is a potential tool to identify hydrate crystal structure. Hydrate guest compositions were also measured for two vapor compositions of the CH4 + CO2 system, and they compared favorably with predictions. The large cavities were measured to be almost fully occupied by CH4 and CO2, whereas only a small fraction of the small cavities are occupied by CH4. No CO2 was found in the small cavities. Hydration numbers from 7.27 to 7.45 were calculated for the mixed hydrate.

and Robert C. Burruss

Papers

Measurement of Clathrate Hydrates via Raman Spectroscopy