Getting started with web access - SAPRC/MechGen GitHub Wiki

MechGen is a computer program that can be used to generate gas-phase reactions of volatile organic compounds and the products they form at temperatures at or near 298 K and pressures at or near 1 atmosphere. The reactions can be generated in either in "single step" mode to see the predictions and documentation for a single reaction, or in "react completely" mode to also react the intermediates formed to obtain a complete mechanism leading to stable products. The stable products can then be reacted as separate operations. Results are displayed to the user or can be downloaded for further analysis.

MechGen can be accessed using the web interface that is currently available at: http://mechgen.cert.ucr.edu. This quick guide will walk through the basic operations for web users. If you are unable to access this website, please contact the author, William P. L. Carter: [email protected]. Documents giving more information on MechGen and how it derives chemical mechanisms are available through the MechGen web site.

When first accessing the MechGen website, the user is presented with a login page shown on Figure 1. It includes a form to give a username and a password for new users to create a user-specific “reactor” system, or for returning users to access that reactor. Once created, the username and password are necessary to login back to your own reactor system in the future.

Main Menu

When first logged into the system, the user is presented with a web page with a reactor with the default settings when a new user reactor is created. In Figure 2, one reactant has been created and fully reacted for illustration. These sections of the web page in Figure 2 are as follows:

Header

Identifies the user and reactor and gives links to reload, log out, or restore reactor defaults. Also indicates the current lumping method that controls how mechanisms are generated and processed.

Create VOC or radical reactant

This section has a form to create a reactant. You can input SMILES directly, or use MechGen structure notation (similar to SMILES but displays all atoms). Click the links on the website for detailed explanations of "structure" and "assigned name".

Get information on reactants in contents

This lists reactants that were previously created by the user. It has links to go to the “Reactant Information” page for the reactant (discussed later). If a reactant has been fully reacted, there are links to access the reaction results. Note that radical reactants are not displayed in this list unless they have been completely reacted.

Reactor options

This contains links to change options that control mechanism generation and lumping options. Restoring reactor defaults sets all these options to those for a new user.

Other information

This section includes links to obtain general information about MechGen and SAPRC.

Advanced options

Users can employ "user assignments" to add to or override the default mechanism assignments. This might be useful for advanced users for the purpose of developing new mechanisms consistent with new data or theories, or modeling experimental data that appear to be inconsistent with default MechGen predictions. This section is not covered in this quick startup guide; please read the complete user manual on MechGen website for further details.

User Account Section

This section has links to log out, change user password, enable telnet logins, or completely delete this web and (if applicable) telnet account, or provide optional user information.

Reactant Information Pages

Reactant information pages are shown when new reactants are created, or existing reactions are selected from the main menu. The content of these pages varies depending on whether the reactant is a stable compound or an intermediate, and whether the reactant has undergone a "react completely" operation. Figure 3 and Figure 4 illustrate examples of a stable reactant methyl ethyl ketone and of one of the radicals formed after it reacts. The contents of these pages are as follows:

Header

The top section gives basic information about the reactant, including its structure in both MechGen and SMILES format, and lumping information if applicable.

Generate Reactions

In the case of stable compounds, this section gives links to generate single step reactions or complete reactions of the various type that this reactant can undergo, which is reaction with OH, NO3, and photolysis in the case of MEK, but can also include unimolecular reactions or reactions with O3, O3P, depending on the compound. If reactions of this compound have previously been used in deriving a SAPRC mechanism, the page also includes a "Get Reaction Assignments" link to obtain information about the assignments that were used in previous complete mechanism generations for this compound.

In the case of reactant pages for intermediates, this section gives the results of a single step reaction of this radical, and a link to react this radical completely.

Groups

This section lists MechGen groups in the molecule and how they were used to estimate the heat of formation.

Estimated vapor pressure (stable reactants only)

Information about how the vapor pressure is estimated.

Generating Single Step Reactions

Generating single step reactions is the best means to obtain information about reactions of individual compounds or radicals, and obtaining documentation information about how the results are derived or assigned. Once a single step reaction is generated, an associated single step reaction results page will be displayed.

These consist of lists of reactions and estimation methods, or mechanism assignments used. Example of single step reaction output for a stable reactant is shown in Figure 5.

Full Mechanism Generation

The full mechanism generation process involves reacting all radicals formed in the initial reactions, then reacting the intermediates formed that need to be reacted, until only stable or species or basic species that do not need to be reacted remain. This can take a significant amount of time for larger molecules.

Once the full reaction generation is complete a page showing the generated reaction is displayed with links for downloading the reaction or product lists. An example of the portions of such a page is shown as Figure 6.

The top part of the page has links for downloading the list of products and reactants in the explicit, minimally processed, and (if applicable) lumped mechanisms in various formats. The download options include the following:

Full Mechanism Generation

If the compound has more than 9 groups, the "Generate Reaction" section will not contain any active links to generate full reactions -- only single step reactions can be generated using the web system for such compounds. Telnet logins are required to generate mechanisms for login compounds. The main menu (Figure 1) has links to create a telnet login.

Once the full reaction generation is completed, a page showing the generated reaction is displayed with links for downloading the reaction or product lists. An example of the portions of such a page is shown as Figure 6.

In Figure 6, the top part of the page has links for downloading the list of products and reactants in the explicit, minimally processed, and (if applicable) lumped mechanisms in various formats. The download options include the following:

Full mechanism (reactions)

Reactions, rate constant parameters, and branching ratios in tab-separated format. Columns in this spreadsheet include reaction number, A, Ea, and B parameters for calculating temperature dependences where k(T)=Aexp(-Ea/T)(T/300)B, the weighting factor used during mechanism generation, the rate constant at the default temperature, and the reaction itself. For photolysis reactions, the name of the SAPRC-22 photolysis file is given in the column used for Ea and the overall quantum yield is in the column used for B, and the rate constant is shown for overhead sunlight for standard reaction conditions.

Full mechanism (Products)

List of products and their estimated yields for the standard environmental conditions.

Processed mechanism (reactions & tab-separated format)

List of products and intermediates (steady state species) in the minimally reduced processed mechanism. The product and intermediate listings include columns with the product or intermediate number, the name used for the product or intermediate in the reaction listings (either a standard SAPRC name or system generated), and the structure. The reaction section includes columns with the reaction number, A, Ea, and B parameters and rate constant at the default temperature (or photolysis file names and quantum yields and photolysis rates for overhead sunlight for photolysis reactions), and the reactions.

Processed mechanism in (SAPRC .RXN format)

This gives the processed mechanism in the format that can be used with SAPRC base mechanism and the SAPRC box modeling software. Links to obtain the SAPRC mechanism files and software are available at: https://intra.engr.ucr.edu/~carter/SAPRC/SAPRCfiles.htm

Modifying Mechanism Generation Options

The options that affect mechanism generation and results processing in the reactor that the user can modify are listed and summarized in Table 1, which also gives the defaults for these options. These can be modified using links or input boxes in the "Reactor options" or "Advanced Options" sections of the main menu. Note that changing the lumping method or creating or deleting user mechanisms will delete any previous full reaction results that may have been generated.