ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

ARC didn't find a correct conformer for a singlet carbene species

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#700 0 comments 0 reactions 0 assignees View on GitHub

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Type: Bug
Dominant language
Python
Stars
51
Forks
25
Avg merge
4d 5h
Merged PRs (30d)
15

Description

The species is:

Smiles: CCCC=CC[C]C=O
adjlist:

    1  O u0 p2 c0 {8,D}
    2  C u0 p0 c0 {3,S} {5,S} {10,S} {11,S}
    3  C u0 p0 c0 {2,S} {6,S} {12,S} {13,S}
    4  C u0 p0 c0 {7,S} {9,S} {14,S} {15,S}
    5  C u0 p0 c0 {2,S} {16,S} {17,S} {18,S}
    6  C u0 p0 c0 {3,S} {7,D} {19,S}
    7  C u0 p0 c0 {4,S} {6,D} {20,S}
    8  C u0 p0 c0 {1,D} {9,S} {21,S}
    9  C u0 p1 c0 {4,S} {8,S}
    10 H u0 p0 c0 {2,S}
    11 H u0 p0 c0 {2,S}
    12 H u0 p0 c0 {3,S}
    13 H u0 p0 c0 {3,S}
    14 H u0 p0 c0 {4,S}
    15 H u0 p0 c0 {4,S}
    16 H u0 p0 c0 {5,S}
    17 H u0 p0 c0 {5,S}
    18 H u0 p0 c0 {5,S}
    19 H u0 p0 c0 {6,S}
    20 H u0 p0 c0 {7,S}
    21 H u0 p0 c0 {8,S}

We expected to get a linear geometry:
1%20%20O%20u0%20p2%20c0%20%7B8%2CD%7D%0A2%20%20C%20u0%20p0%20c0%20%7B3%2CS%7D%20%7B5%2CS%7D%20%7B10%2CS%7D%20%7B11%2CS%7D%0A3%20%20C%20u0%20p0%20c0%20%7B2%2CS%7D%20%7B6%2CS%7D%20%7B12%2CS%7D%20%7B13%2CS%7D%0A4%20%

But got:

O       1.35356100   -2.04187600   -0.27751400
C      -1.66813300   -0.61628700    0.36007000
C      -0.88428900    0.26015900   -0.62633800
C       2.50264900    1.51850400    0.21895400
C      -2.89996100   -1.26465400   -0.27629700
C       0.29557000    0.96714800    0.01116200
C       1.45071300    1.42849700   -0.82461700
C       2.07072500   -1.07058000   -0.16582800
C       1.63488300    0.28123000    0.16956100
H      -1.97601000   -0.00811600    1.21948400
H      -0.99715000   -1.39131700    0.73916300
H      -0.53981600   -0.35715300   -1.46151200
H      -1.55178600    1.02271800   -1.04707500
H       2.35964100    2.19995200    1.05689000
H       3.53495600    1.41092800   -0.10274500
H      -3.43976800   -1.88219100    0.44642200
H      -2.61580000   -1.90890700   -1.11384300
H      -3.59778100   -0.51151900   -0.65688400
H       0.02304000    1.62941700    0.83723200
H       1.57229400    1.34849200   -1.89467900
H       3.17073700   -1.15771700   -0.31276600

which looks like this:

image

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing issue #700 with the supplied SMILES and adjacency list, then compare the generated coordinates with the expected linear geometry. Trace the conformer-generation path used for this singlet carbene species. Done means ARC finds and returns a correct conformer with the expected geometry.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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