Gas-Phase Reaction Mechanisms

Thanks to Rohit Mathur of MCNC-North Carolina Supercomputing Center for the use of his writings on gas-phase reaction mechanism which form the basis of these readings.

Background

Gas-phase reaction mechanisms are a set of reactions that represent all of the most significant chemical reactions occuring in the troposphere. Significant increases in the understanding of these mechanisms occurred with the understanding of the role of the hydroxyl radical (OH) in the lower atmosphere, especially in its role in the reaction pathways of reactive hydrocarbons and oxides of nitrogen.

Mechanisms consist of two parts:

Inorganic chemistry
Organic chemistry

The inorganic chemistry of the atmosphere is fairly well understood; the complexity lies in the representation of the organic part of the mechanism. Thousands of chemical reactions, reactants, and products are found in the lower atmosphere. Mechanisms which attempt to treat all chemical species and reactions individually are known as explicit mechanisms. The difficulties with explicit mechanisms is twofold:

difficulties in identifying the reactants, intermediates, products, and rate constants for the reactions
the computational complexity of integrating the large number of equations each reaction requires

As a method to remove some of the complexities of explicit mechanisms, most photochemical models use a lumped chemical mechanism. In these mechanisms, a surrogate species is created to represent a group of individual species. These condensed mechanisms have as their goal the representation of all of the reactive organic chemistry in a form that is both quantifiable and computable. Obviously, loss of accuracy is a product of this simplification!

A number of modeling principles are used in the derivation of these condensed mechanisms:

Generalization: different real-world species are treated as if they were identical or at least similar: Example: urban alkanes, alkenes, and aromatic species (about 120 routinely observed species) are represented by 10-15 model species
Distortion: some real-world operation is represented in the model in an inexact manner: Example: a two-step reaction may be represented through a single reaction (e.g., formation of RO₂radicals)
Deletion: some real-world chemical processes are totally absent from the modeled mechanism: Example: when simulating urban and regional domains it is common to omit the chemistry of many slowly reacting organic species, but when simulating global domains over extended periods, the chemistry of fast-reacting species may be omitted.

The two processes of distortion and deletion may be intentional or unintentional, for several reasons:

due to limited laboratory studies, the mechanisms may contain what the authors believe is an accurate representation of the process
due to limited knowledge and/or lack of evidence, certain chemicals and chemical pathways may be totally absent
though there is general consensus on the reaction rates of most reactions, there remain reactions for which rate coefficients are either unknown or over which there is considerable disagreement (e.g., aromatics)

There are several methods for creating a generalized condensed or lumped mechanism:

Lumped structure: based on structural components of molecules (e.g., single bonds, double bonds, etc.)
Lumped molecule: based on representative molecules of each classification
Surrogate species: single specie hydrocarbon used to represent a larger reactivity group
Reactivity-based lumping: extension of the lumped molecule approach, in which all hydrocarbons are represented by a small subset of hydrocarbons which react according to their known rate constants.

Current Mechanisms:

There are a variety of mechanisms currently being used in photochemical models:

Carbon Bond IV (CB4 or CB-IV)
Regional Acid Deposition Model (RADM)
SAPRC90

The mechanisms available for this scenario include a slightly older versions of the CB4 and RADM mechanisms. The CB4 mechanism is used in the EKMA/OZIP model, the Urban Airshed Model, and the Regional Oxidant Model. The RADM mechanism is used in the Regional Acid Deposition Model, and is an option in this version of OZIP. The SAPRC90 mechanism is used in a model known as SARMAP, not discussed in this scenario.

Some similarities and differences in these mechanisms are as follows:

each mechanism represents the inorganic chemistry with approximately the same set of reactions, based on photochemical and chemical kinetics data developed by NASA in 1988 and 1990.
each method uses a different method for generalizing the organic chemistry.
approximately the same set of kinetic and smog chamber databases were available to each author, but these were utilized differently by each.
regardeless of the generalization (lumping) techniques used, implicit to each condensed mechanism are assumptions of some expected hydrocarbon mix in the atmosphere and their subsequent degradation through chemical transformations.

The Carbon Bond 4 Mechanism

In this mechanism, the reactants are lumped depending on their bonding structure. Fundamentally, there are approximately 15 classes of reactive organic species, each with its own designation. Several of the common classes are shown below:

PAR: single bond carbon atoms, such as alkanes
OLE: fast doubly bonded atoms, such as olefins (with the exception of ethylene)
ARO: slow doubly bonded atoms, such as aromatics and ethylene
CAR: carbonyl carbon atoms, such as aldehydes and ketones
XO₂: NO to NO₂ operation

In this mechanism, there are approximately 89 reactions among 33 modeled species. Lumping is based on reactions of similar carbon bonds.

The RADM Mechanism

The RADM mechanism provides 158 reactions among 58 species, with 15 classes of reactive mechanisms. The lumping is based on a lumped molecule approach, in which molecules with similar reactivities are represented by a lumped surrogate. The reactivity weighting scheme used is based on the assumption that the effect of volatile organic compound (VOC) emissions on the model simulation results is approximately proportional to the amount of the compound that reacts on a daily basis. Some examples of the surrogates used are as follows:

HC3: alkanes with an OH-reactivity rate constant between 2.7 x 10^-13 and 3.4 x 10^-12
HC5: alkanes with an OH-reactivity rate constant between 3.4 x 10^-12 and 6.8 x 10^-12
HC8: alkanes with an OH-reactivity rate constant greater than 6.8 x 10^-12

Note! If you use the RADM files (mechanism, zenith set, reactivities), you should ONLY use VOCs, NO_x, and CO in your emissions inventories.

Back to Command Options

Developed by