jing.rxn.RateConstantNotFoundException

[mrharper]

Yushi Suzuki was running a RMG job and received the titled exception, followed by RMG terminating the simulation. He and Greg Magoon determined the exception was thrown when RMG attempted to react the following species with the core:

1 C 0 {2,D} 2 C 0 {1,D} {3,S} {7,S} 3 C 0 {2,S} {4,D} 4 C 0 {3,D} {5,S} 5 C 0 {4,S} {6,S} {8,D} 6 C 1 {5,S} {7,S} {8,S} 7 C 0 {6,S} {2,S} {9,D} 8 C 0 {5,D} {6,S} 9 O 0 {7,D}

Here's the InChI: InChI=1/C8H5O/c1-5-2-3-6-4-7(6)8(5)9/h2-4H,1H2

In particular, the exception was thrown when trying to react this species with the core, against the Diels_alder_addition reaction family. For Yushi's case, the reaction that caused the problem was the above radical + isobutylene --> following radical

1 C 0 {2,S} {20,S} {5,S} {6,S} 2 C 0 {1,S} {16,S} {3,S} {4,S} 3 C 0 {2,S} {7,S} {8,S} {9,S} 4 C 0 {2,S} {10,S} {11,S} {12,S} 5 H 0 {1,S} 6 H 0 {1,S} 7 H 0 {3,S} 8 H 0 {3,S} 9 H 0 {3,S} 10 H 0 {4,S} 11 H 0 {4,S} 12 H 0 {4,S} 13 C 1 {14,S} {22,S} {23,S} 14 C 0 {15,D} {19,S} {13,S} 15 C 0 {14,D} {16,S} {24,S} 16 C 0 {15,S} {17,S} {2,S} {25,S} 17 C 0 {16,S} {18,D} {20,S} 18 C 0 {17,D} {19,S} {20,S} 19 C 0 {21,D} {18,S} {14,S} 20 C 0 {17,S} {18,S} {1,S} {26,S} 21 O 0 {19,D} 22 H 0 {13,S} 23 H 0 {13,S} 24 H 0 {15,S} 25 H 0 {16,S} 26 H 0 {20,S}

Here's the InChI: InChI=1/C12H13O/c1-6-4-8-9-7(5-12(8,2)3)10(9)11(6)13/h4,7-8H,1,5H2,2-3H3

Greg and Mike determined that the exception was being thrown because RMG could not match the input radical against the "diene_out" node in the tree.

The general "diene_out" is a union of groups, one of which is:

diene_unsub_unsub_out 1 *3 Cd 0 {2,D}, {5,S}, {6,S} 2 *4 Cd 0 {1,D}, {3,S} 3 *5 Cd 0 {2,S}, {4,D} 4 *6 Cd 0 {3,D}, {7,S}, {8,S} 5 H 0 {1,S} 6 H 0 {1,S} 7 H 0 {4,S} 8 H 0 {4,S}

The problem arises in that the definition assumes *3 atom is bound to two atoms (not including *4, *5, or *6) and likewise, *6 atom is bound to two atoms (not including *3, *4, or *5). However, in this specific case, our *4 is bound to *6.

Temporary solution: Coming soon

[mrharper]

The following commit resolves the specific exception being thrown in Yushi's RMG run:

http://github.com/GreenGroup/RMG-Java/commit/d492cb6dd10e81f50b679a4bdf50b1254c0cce80

I am choosing not to close the issue, so that we can attempt to address the bigger issue at hand (namely, what should we do when RMG cannot find a rate constant ... other than terminate the program).

[gmagoon]

Just wanted to point out that another issue we identified that we haven't been able to explain yet is why RMG identifies the reaction in the first place, given that there is a radical on the "outskirts" of the diene_out group such that it doesn't look like any of the diene_out groups should match. One possibility that I just thought of while writing this: Maybe it is identifying the reaction of a resonance form where the radical is not part of the diene_out group?