{"action":"created","issue":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/514","labels_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/514/labels{/name}","comments_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/514/comments","events_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/514/events","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/514","id":125274921,"number":514,"title":"forbidden group N_birad_singlet_2singleBonds looks shady","user":{"login":"nickvandewiele","id":242147,"avatar_url":"https://avatars.githubusercontent.com/u/242147?v=3","gravatar_id":"","url":"https://api.github.com/users/nickvandewiele","html_url":"https://github.com/nickvandewiele","followers_url":"https://api.github.com/users/nickvandewiele/followers","following_url":"https://api.github.com/users/nickvandewiele/following{/other_user}","gists_url":"https://api.github.com/users/nickvandewiele/gists{/gist_id}","starred_url":"https://api.github.com/users/nickvandewiele/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nickvandewiele/subscriptions","organizations_url":"https://api.github.com/users/nickvandewiele/orgs","repos_url":"https://api.github.com/users/nickvandewiele/repos","events_url":"https://api.github.com/users/nickvandewiele/events{/privacy}","received_events_url":"https://api.github.com/users/nickvandewiele/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/labels/risk%20of%20error","name":"risk of error","color":"f57f31"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-01-06T22:11:20Z","updated_at":"2016-01-06T22:26:34Z","closed_at":null,"body":"e791c0a15ca49642cbf0f62577c88ef7461108ce shows a test in which the forbidden group (\r\nhttps://github.com/ReactionMechanismGenerator/RMG-database/blob/master/input/forbiddenStructures.py#L55)\r\n\r\n_N_birad_singlet_2singleBonds_\r\n\r\n```\r\n1 N u0 p1 {2,S} {3,S}\r\n2 R ux {1,S}\r\n3 R ux {1,S}\r\n```\r\nis successfully discovered in the \"normal\" looking molecule [CH2]-NH2\r\n\r\n```\r\nmultiplicity 2\r\n1 N u0 p1 c0 {2,S} {5,S} {6,S}\r\n2 C u1 p0 c0 {1,S} {3,S} {4,S}\r\n3 H u0 p0 c0 {2,S}\r\n4 H u0 p0 c0 {2,S}\r\n5 H u0 p0 c0 {1,S}\r\n6 H u0 p0 c0 {1,S}\r\n```\r\n\r\nAlthough the name of the group suggests the forbidden group should hit singlet biradical nitrogen, I am unsure whether this molecule qualifies as such. \r\n\r\nMy recommendation would be to remove that forbidden structure from the list, as it would prevent a lot of _normal_ nitrogen containing compounds from being formed.\r\n"},"comment":{"url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/comments/169482390","html_url":"https://github.com/ReactionMechanismGenerator/RMG-Py/issues/514#issuecomment-169482390","issue_url":"https://api.github.com/repos/ReactionMechanismGenerator/RMG-Py/issues/514","id":169482390,"user":{"login":"alongd","id":16158262,"avatar_url":"https://avatars.githubusercontent.com/u/16158262?v=3","gravatar_id":"","url":"https://api.github.com/users/alongd","html_url":"https://github.com/alongd","followers_url":"https://api.github.com/users/alongd/followers","following_url":"https://api.github.com/users/alongd/following{/other_user}","gists_url":"https://api.github.com/users/alongd/gists{/gist_id}","starred_url":"https://api.github.com/users/alongd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alongd/subscriptions","organizations_url":"https://api.github.com/users/alongd/orgs","repos_url":"https://api.github.com/users/alongd/repos","events_url":"https://api.github.com/users/alongd/events{/privacy}","received_events_url":"https://api.github.com/users/alongd/received_events","type":"User","site_admin":false},"created_at":"2016-01-06T22:26:34Z","updated_at":"2016-01-06T22:26:34Z","body":"I agree that *N_birad_singlet_2singleBonds* is problematic, I had to remove this structure (among others) from my *forbiddenStructures.py* file to be able to run N-chem in RMG.\r\n\r\nStill, shouldn't this forbidden structure restrict N p1 with 2 single bonds? The N atom in **[CH2]-NH2** has three."}}