Methane molecular dynamics simulation

The CH cation 1, protonated methane, is the parent of hypercoordinated carbocations containing a five coordinated carbon atom. It is elusive in solution and has not been observed by NMR spectroscopy but gas-phase infrared investigations have shown its fluxional structure which has been proven by ab initio molecular dynamic simulation.18... 

Methane Hydrate Formation via Molecular Dynamics Simulations. J Am. Chem. Soc., 127, 17852-17862. 

Figure 2.4 Simulated trajectories of helium, oxygen and methane molecules during a 200-ps time period in a poly(dimethylsiloxane) matrix [9]. Reprinted with permission from S.G. Charati and S.A. Stern, Diffusion of Gases in Silicone Polymers Molecular Dynamic Simulations, Macromolecules 31, 5529. Copyright 1998, American Chemical Society...

N.J. English et al., Molecular-dynamics simulations of methane hydrate dissociation. J. Chem. Phys. 123, 244503 (2005)... 

Molecular-dynamic simulations are characterized by a solution of Newton s laws of motion for the molecules travelling through the zeolite pore system under control of the force field given by the properties of the host lattice, by interactions between the host and the molecules, and by interactions between the molecules. To date this has been possible only for the diffusion of simple molecules (e.g. methane or benzene) inside a zeolite lattice of limited dimensions [29, 37, 54], To take into account the effects of a chemical reaction as well would require quantum-mechanical considerations however, such simulations are in their infancy. 

A. Alavi, Molecular Dynamics Simulation of Methane Adsorbed in MgO Evidence for a Kosterlitz-Thouless Transition, Mol. Phys. 71 (1990) 1173-1191 Evidence for a Kosterlitz-Thouless Transition in a Simulation of CD4 Adsorbed on MgO, Phys. Rev. Lett. 64 (1990), 2289-2292. A. Alavi and I. R. McDonald, Molecular Dynamics Simulation of Argon Physisorbed on Magnesium Oxide, Mol. Phys. 69 (1990) 703-713. 

Molecular dynamics simulations for the mixture water (1) + methane (2) + sodium chloride (3) revealed a similar local structure around an infinitely dilute gas molecule, namely the methane molecule is preferentially hydrated and sodium chloride is preferentially excluded from the vicinity of a methane molecule [72]. 

In the present paper, the method which the authors employed previously to derive an expression for the solubility of various proteins in aqueous solutions, has been extended to the solubility of gases in mixtures of water + strong electrolytes. One parameter equation for the solubility of gases has been derived, which was used to represent the solubilities of oxygen, carbon dioxide and methane in water -i- sodium chloride. In additions, the developed theory could be used to examine the local composition of the solvent around a gas molecule. The results revealed that the oxygen, carbon dioxide and methane molecules are preferentially hydrated in water-i-sodium chloride mixtures. A similar result was obtained for the water -i- methane -i- sodium chloride by molecular dynamics simulations [72]. 

Mitchell, M. C. Autry, J. D. Nenoflf, T. M. "Molecular Dynamics Simulations of Binary Mixtures of Methane and Hydrogen in Zeolite A and a Novel Zinc Phosphate". Mole. Physics, 2001, 99(22), 1831. 

Figure 15.4. Potential of mean force (PMF) between two methane molecules in water. This shows a first deeper minimum corresponding to the contact geometry of the two methane molecules. Another second (less deep) minimum is also observed in the PMF, corresponding to the solvent separated minimmn. Adapted from thesis entitled Molecular dynamics simulations of hydrophobic solutes in hquid water by Andy Hsu, Institute of Atomic and Molecular Sciences, Academia Sinica. (http //w3.iams.sinica.edu.tw/lab/jlli/thesis andy/%5d.)...

Lin, C. L. and R. H. Wood. 1996. Prediction of the free energy of dilute aqueous methane, ethane, and propane at temperatures from 600 to 1200 degrees C and densities from 0 to 1 g cm using molecular dynamics simulations. Journal of Physical Chemistry. 100, 16399. 

Early molecular dynamics simulations focused on spherically shaped particles in zeolites. These particles were either noble gases, such as argon, krypton, and xenon, or small molecules like methane. For these simulations, the sorbates were treated as soft spheres interacting with the zeolite lattice via a Lennard-Jones potential. Usually the aluminum and silicon atoms in the framework were considered to be shielded by the surrounding oxygen atoms, and no aluminum and silicon interactions with the sorbates were included. The majority of those studies have concentrated on commercially important zeolites such as zeolites A and Y and silicalite (all-silica ZSM-5), for which there is a wealth of experimental information for comparison with computed properties. 

Kinetic Separations. As discussed in Chapter 5, carbon molecular sieves have already been used for gas separation that is based on differences in diffusivities of different gas molecules. The same separations should also be possible with carbon nanotubes. To this end, a number of simulation studies have been carried out. Mao and Sinnott (2000 and 2001) have reported molecular dynamics simulation results for diffusion of methane, ethane, n-butane, and isobutene, as well as their binary mixtures, in SWNTs and their bundles. As expected, diffusion of smaller molecules is faster, for example a factor of 25 was obtained for melhane/isobutene in a (8,8) nanotube (Mao and Sinnott, 2001). 

Figure 2 Configurations of liquid water molecules near hydrophobic cavities in molecular dynamics simulations. The blue and white particles represent the oxygen (O) and hydrogen (H) atoms, respectively, of the water molecules. The dashed lines indicate hydrogen bonds. The space-filling size of the hydrophobic (red) particles in (a) is similar to the methane molecule. The hydrophobic cluster in (b) contains 135 methane-like particles that are hexagonally close-packed to form a roughly spherical unit of radius larger than 1 nm. (Reproduced from Ref. 8 American Chemical Society, 2005.)...

Morgan, W. L., Molecular dynamics simulation of geminate recombination by electrons in liquid methane, /. Chem. Phys., 84, 2298,1986. 

Such simple potential functions are widely used to study the properties of molecular clusters. For example, sulfur hexafluoride clusters [9], methane and ethane clusters [10], water droplets [11,12], methanol droplets [13], water/ethanol droplets [14], and acetonitrile clusters [15] have been investigated through molecular dynamics simulations using such potentials. Water clusters with ions have also been studied [16]. 

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