{"action":"created","issue":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/issues/257","repository_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database","labels_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/issues/257/labels{/name}","comments_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/issues/257/comments","events_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/issues/257/events","html_url":"https://github.com/ReactionMechanismGenerator/RMG-database/pull/257","id":304581855,"number":257,"title":"Added Kinetics Data for Hydrogen Abstraction by Chlorine Atom","user":{"login":"zjburas","id":12465817,"avatar_url":"https://avatars0.githubusercontent.com/u/12465817?v=4","gravatar_id":"","url":"https://api.github.com/users/zjburas","html_url":"https://github.com/zjburas","followers_url":"https://api.github.com/users/zjburas/followers","following_url":"https://api.github.com/users/zjburas/following{/other_user}","gists_url":"https://api.github.com/users/zjburas/gists{/gist_id}","starred_url":"https://api.github.com/users/zjburas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zjburas/subscriptions","organizations_url":"https://api.github.com/users/zjburas/orgs","repos_url":"https://api.github.com/users/zjburas/repos","events_url":"https://api.github.com/users/zjburas/events{/privacy}","received_events_url":"https://api.github.com/users/zjburas/received_events","type":"User","site_admin":false},"labels":[{"id":698086978,"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/labels/Twin%20RMG-Py%20PR","name":"Twin RMG-Py PR","color":"b60205","default":false},{"id":860469152,"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/labels/chlorine","name":"chlorine","color":"d130d1","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":16,"created_at":"2018-03-12T23:56:41Z","updated_at":"2018-03-18T03:00:18Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/pulls/257","html_url":"https://github.com/ReactionMechanismGenerator/RMG-database/pull/257","diff_url":"https://github.com/ReactionMechanismGenerator/RMG-database/pull/257.diff","patch_url":"https://github.com/ReactionMechanismGenerator/RMG-database/pull/257.patch"},"body":"Companion to [RMG-Py PR #1310](https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1310).\r\n\r\nConsists of 3 chlorine-related additions to the database:\r\n\r\n1. 41 training reactions for hydrogen abstraction reactions by chlorine (Cl+RH=HCl+R), all taken from either NIST Kinetics or [IUPAC](http://iupac.pole-ether.fr/htdocs/show_datasheets.php?category=Gas-phase+organics%3A+X+%2B+VOC). Most of the kinetics are based on temperature-dependent experimental measurements, although for a few of the slow reactions without any reported measurements (e.g., Cl+CH3OH=HCl+CH3O) theoretical predictions from literature were used. These types of reactions should not be pressure-dependent.\r\n\r\n2. 11 Benson GAV's for carbon bonded to at least one chlorine atom. These all come from Benson's 1976 book \"Thermochemical Kinetics\", which were fit to experimental measurements. For many of the groups, Cp was not determined up to 1500 K, so as an approximation I padded the missing data points with the Cp value measured at the highest T. \r\n\r\n3. Thermo library containing experimental measurements for 17 chloroalkanes. These were the species used by Benson to fit the original GAV's, and could perhaps be used in a unit test.\r\n\r\nCurrently, the purpose of this branch is to estimate initial radical pools in chlorine-initiated oxidation experiments. In these experiments the Cl is first generated by photolysis of a chemical precursor (e.g. Cl2=2Cl at 351 nm) and then abstracts hydrogens from different sites on the fuel molecule (e.g., heptane) to initiate the chemistry. I have tested this branch for Cl+n-heptane, i-octane and 1-butanol and have obtained reasonable product branching in each case. For example, in the butanol case very little H-abstraction from the O-H site is predicted relative to the C-H sites. \r\n\r\nTechnically the additions to the thermochemical database are unnecessary, because the only chlorine-containing species involved in H-abstraction are Cl and HCl, both of which cannot be estimated by GAV and appear in the primary thermo library instead. However, I decided to include Benson's Cl-containing GAV's in this PR to facilitate future additions to chlorine chemistry. For example, R-recombination (R+Cl=RCl), \"Cl-abstraction\" (RCl+X=R+XCl) and SN2 reactions (RCl+X=RX+Cl) involving chlorine (and other halogens) could all be added in the future. \r\n\r\nI have not forbid Cl from reacting in any families, but maybe I should until we actually have kinetics data for Cl reacting in those families. \r\n\r\nI suppose some unit tests are in order next. @alongd , can you give me some guidance?"},"comment":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/issues/comments/373969193","html_url":"https://github.com/ReactionMechanismGenerator/RMG-database/pull/257#issuecomment-373969193","issue_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-database/issues/257","id":373969193,"user":{"login":"zjburas","id":12465817,"avatar_url":"https://avatars0.githubusercontent.com/u/12465817?v=4","gravatar_id":"","url":"https://api.github.com/users/zjburas","html_url":"https://github.com/zjburas","followers_url":"https://api.github.com/users/zjburas/followers","following_url":"https://api.github.com/users/zjburas/following{/other_user}","gists_url":"https://api.github.com/users/zjburas/gists{/gist_id}","starred_url":"https://api.github.com/users/zjburas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zjburas/subscriptions","organizations_url":"https://api.github.com/users/zjburas/orgs","repos_url":"https://api.github.com/users/zjburas/repos","events_url":"https://api.github.com/users/zjburas/events{/privacy}","received_events_url":"https://api.github.com/users/zjburas/received_events","type":"User","site_admin":false},"created_at":"2018-03-18T03:00:17Z","updated_at":"2018-03-18T03:00:17Z","author_association":"CONTRIBUTOR","body":"After reviewing the sources of @faribas H-abstraction rate rules ([Goldfinger](http://pubs.rsc.org/en/content/articlelanding/TF/1967/tf9676301631#!divAbstract) and [Senkan](https://pubs.acs.org/doi/abs/10.1021/j100205a044)) I do think they could be converted to training reactions. However, the new training reactions that I would add are all for Cl + some chlorinated hydrocarbon (e.g., hexachloroethane). The Cl + hydrocarbon rates in the above references are already included in the current PR (e.g., Cl + ethane). Adding training reactions for the Cl + chlorinated hydrocarbon reactions would require the addition of new groups in the H-abstraction family, and because these reactions are not of immediate interest to my current project I would like to leave this to @skrsna and @rwest for a later PR.\r\n\r\nIf that's ok, then I'm done with the data entry portion of this PR, and you can run the test again @alongd . Also I will think about what unit tests to add. \r\n\r\n@KEHANG , didn't you have a test to check whether changes to the thermo database made estimations for some benchmark species better or worse? If so, I have a library of ~50 experimentally measured chlorinated species that could be added to this benchmark."}}
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