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The kinetic Monte Carlo method as a way to solve the master equation for interstellar grain chemistry.

Cuppen HM, Karssemeijer LJ, Lamberts T - Chem. Rev. (2013)

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Affiliation: Theoretical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen , 6525 AJ Nijmegen, The Netherlands.

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Some of the icespecies accrete from the gas phase, but as mentioned before, manyof the simple important molecules such as H2 and H2O and also several complex organic molecules are not formedin the gas phase, but rather on the grain surfaces themselves... These include sticking fractions, diffusionbarriers, binding energies, and activation energies for reaction.The sticking fraction is the fraction of impingements that leads toadsorption... Fractions lower than 1 effectively decrease the flux ofincoming particles... A diffusive model was appliedto fit the results of Pirronello et al., which couldonly give a lower limit for the desorption energy of H atoms... Highervalues for this energy were found to give degenerate results... Simulating bulk diffusion using lattice-gasKMC simulations is however hard, since the exact mechanism is unclear.The discrepancy between simulations and experiments in the cases ofboth CO and O2 hydrogenation is probably mainly due to a missingbulk diffusion mechanism... Here diffusion rates for H2O on hexagonalice were determined using NEB and subsequently included in a lattice-gasKMC model to determine the diffusion constant which is in agreementwith the experimental diffusivity at the same temperature... Therefore, thesix possible directions of diffusion on the honeycomb structure wereassigned different weights, with the highest probability for the atomto continue in its original direction... This directional bias was foundto have very little effect on the final results... Good agreement was obtained between KMC simulations and experimentsfor low surface temperatures where only the top few monolayers ofthe deposited CO ice were chemically altered as can be seen in thetop left panel of Figure 15... At higher temperatures,the hydrogen atoms were found to be able to penetrate the CO ice deeper,but this penetration effect was not fully reproduced by the KMC simulations,which resulted in a lower final yield in the simulations... The latter model included preferred sticking atpara sites as discussed in section 5.1, althougha square lattice was used instead of an hexagonal grid... Rate equationresults were compared with microscopic KMC results... Return to thegas phase occurs through photodesorption and chemical desorption.To model these energetic processes, molecular dynamics would probablybe better suited, although the required time scales cannot be reached.At a low dust temperature of T = 10 K, hydrogenationreactions leading to species such as H2 and H2O are found to dominate; for higher temperatures (T = 30 K) oxygenation starts to take over, leading to the formationof O2 and O3... With this method, it is possible to run off-latticekinetic Monte Carlo simulations without having to define the eventtable beforehand.

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Schematic representation of the honeycomb lattice of a graphenelayer with a hydrogen atom attached (gray circle). Stable dimer configurationscan be formed by attachment of a second hydrogen atom at the o(rtho)or p(ara) position.
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fig13: Schematic representation of the honeycomb lattice of a graphenelayer with a hydrogen atom attached (gray circle). Stable dimer configurationscan be formed by attachment of a second hydrogen atom at the o(rtho)or p(ara) position.

Mentions: The formation of themost abundant molecule in the universe, H2, occurs mainlythrough surface reactions, and as such it has received considerableattention. These reactions have been the topic of several astrochemicalmodeling studies as mentioned in previous sections, but also of experimentsand quantum chemical calculations. A model system for H2 formation on carbonaceous grains is the deposition of H atoms ona graphite surface or a graphene layer. Figure 13 shows a schematic representation of the honeycomb lattice of a graphenelayer. Hydrogen atoms can be chemically attached to the carbon atomsin this hexagonal lattice. The gray circle represents such an atom.Molecular hydrogen can be formed by a process called “abstraction”,where the atom chemisorbed to the surface reacts with another H atomto form H2. Hydrogen abstraction from graphite has beenstudied extensively both experimentally103,104 and by density functional theory (DFT) and quantum wave packet calculations.105−110


The kinetic Monte Carlo method as a way to solve the master equation for interstellar grain chemistry.

Cuppen HM, Karssemeijer LJ, Lamberts T - Chem. Rev. (2013)

Schematic representation of the honeycomb lattice of a graphenelayer with a hydrogen atom attached (gray circle). Stable dimer configurationscan be formed by attachment of a second hydrogen atom at the o(rtho)or p(ara) position.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC3934372&req=5

fig13: Schematic representation of the honeycomb lattice of a graphenelayer with a hydrogen atom attached (gray circle). Stable dimer configurationscan be formed by attachment of a second hydrogen atom at the o(rtho)or p(ara) position.
Mentions: The formation of themost abundant molecule in the universe, H2, occurs mainlythrough surface reactions, and as such it has received considerableattention. These reactions have been the topic of several astrochemicalmodeling studies as mentioned in previous sections, but also of experimentsand quantum chemical calculations. A model system for H2 formation on carbonaceous grains is the deposition of H atoms ona graphite surface or a graphene layer. Figure 13 shows a schematic representation of the honeycomb lattice of a graphenelayer. Hydrogen atoms can be chemically attached to the carbon atomsin this hexagonal lattice. The gray circle represents such an atom.Molecular hydrogen can be formed by a process called “abstraction”,where the atom chemisorbed to the surface reacts with another H atomto form H2. Hydrogen abstraction from graphite has beenstudied extensively both experimentally103,104 and by density functional theory (DFT) and quantum wave packet calculations.105−110

View Article: PubMed Central - PubMed

Affiliation: Theoretical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen , 6525 AJ Nijmegen, The Netherlands.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Some of the icespecies accrete from the gas phase, but as mentioned before, manyof the simple important molecules such as H2 and H2O and also several complex organic molecules are not formedin the gas phase, but rather on the grain surfaces themselves... These include sticking fractions, diffusionbarriers, binding energies, and activation energies for reaction.The sticking fraction is the fraction of impingements that leads toadsorption... Fractions lower than 1 effectively decrease the flux ofincoming particles... A diffusive model was appliedto fit the results of Pirronello et al., which couldonly give a lower limit for the desorption energy of H atoms... Highervalues for this energy were found to give degenerate results... Simulating bulk diffusion using lattice-gasKMC simulations is however hard, since the exact mechanism is unclear.The discrepancy between simulations and experiments in the cases ofboth CO and O2 hydrogenation is probably mainly due to a missingbulk diffusion mechanism... Here diffusion rates for H2O on hexagonalice were determined using NEB and subsequently included in a lattice-gasKMC model to determine the diffusion constant which is in agreementwith the experimental diffusivity at the same temperature... Therefore, thesix possible directions of diffusion on the honeycomb structure wereassigned different weights, with the highest probability for the atomto continue in its original direction... This directional bias was foundto have very little effect on the final results... Good agreement was obtained between KMC simulations and experimentsfor low surface temperatures where only the top few monolayers ofthe deposited CO ice were chemically altered as can be seen in thetop left panel of Figure 15... At higher temperatures,the hydrogen atoms were found to be able to penetrate the CO ice deeper,but this penetration effect was not fully reproduced by the KMC simulations,which resulted in a lower final yield in the simulations... The latter model included preferred sticking atpara sites as discussed in section 5.1, althougha square lattice was used instead of an hexagonal grid... Rate equationresults were compared with microscopic KMC results... Return to thegas phase occurs through photodesorption and chemical desorption.To model these energetic processes, molecular dynamics would probablybe better suited, although the required time scales cannot be reached.At a low dust temperature of T = 10 K, hydrogenationreactions leading to species such as H2 and H2O are found to dominate; for higher temperatures (T = 30 K) oxygenation starts to take over, leading to the formationof O2 and O3... With this method, it is possible to run off-latticekinetic Monte Carlo simulations without having to define the eventtable beforehand.

No MeSH data available.