From fed86de13240883442164d663839f63221f8b1bb Mon Sep 17 00:00:00 2001 From: Mark Payne Date: Wed, 29 Apr 2020 23:35:38 -0400 Subject: [PATCH] Fix species information for select reference species Likely due to an incorrect assignment of a smiles string that propagated to the other changes. It appears that the QM data is valid though, as the QM data has the correct number of atoms in each case --- input/reference_sets/main/Benzylide.yml | 39 +++++++++++---------- input/reference_sets/main/Ethynol anion.yml | 20 +++++------ input/reference_sets/main/Formyl anion.yml | 18 +++++----- input/reference_sets/main/Methanide.yml | 17 ++++----- input/reference_sets/main/Vinoxide.yml | 23 ++++++------ input/reference_sets/main/Vinyl anion.yml | 20 +++++------ 6 files changed, 70 insertions(+), 67 deletions(-) diff --git a/input/reference_sets/main/Benzylide.yml b/input/reference_sets/main/Benzylide.yml index c00458e1c1..205ad89f30 100644 --- a/input/reference_sets/main/Benzylide.yml +++ b/input/reference_sets/main/Benzylide.yml @@ -1,18 +1,19 @@ RMG_version: 3.0.0 adjacency_list: | - multiplicity 3 - 1 C u0 p0 c0 {2,D} {6,S} {7,S} - 2 C u0 p0 c0 {1,D} {3,S} {8,S} - 3 C u0 p0 c0 {2,S} {4,D} {9,S} - 4 C u0 p0 c0 {3,D} {5,S} {10,S} - 5 C u0 p0 c0 {4,S} {6,D} {11,S} - 6 C u0 p0 c0 {1,S} {5,D} {12,S} - 7 C u2 p1 c-1 {1,S} - 8 H u0 p0 c0 {2,S} - 9 H u0 p0 c0 {3,S} - 10 H u0 p0 c0 {4,S} - 11 H u0 p0 c0 {5,S} - 12 H u0 p0 c0 {6,S} + 1 C u0 p0 c0 {2,D} {6,S} {10,S} + 2 C u0 p0 c0 {1,D} {3,S} {11,S} + 3 C u0 p0 c0 {2,S} {4,D} {12,S} + 4 C u0 p0 c0 {3,D} {5,S} {7,S} + 5 C u0 p0 c0 {4,S} {6,D} {13,S} + 6 C u0 p0 c0 {1,S} {5,D} {14,S} + 7 C u0 p1 c-1 {4,S} {8,S} {9,S} + 8 H u0 p0 c0 {7,S} + 9 H u0 p0 c0 {7,S} + 10 H u0 p0 c0 {1,S} + 11 H u0 p0 c0 {2,S} + 12 H u0 p0 c0 {3,S} + 13 H u0 p0 c0 {5,S} + 14 H u0 p0 c0 {6,S} calculated_data: wb97m-v/def2-tzvpd: class: CalculatedDataEntry @@ -102,16 +103,16 @@ charge: -1 class: ReferenceSpecies datetime: 2020-02-24 11:05 default_xyz_chemistry: wb97m-v/def2-tzvpd -formula: C7H5 -inchi: InChI=1S/C7H5/c1-7-5-3-2-4-6-7/h2-6H/q-1 -inchi_key: WSUGBBJIWXKXIY-UHFFFAOYSA-N +formula: C7H7 +inchi: InChI=1S/C7H7/c1-7-5-3-2-4-6-7/h2-6H,1H2/q-1 +inchi_key: QJHNLKRMBCYQKX-UHFFFAOYSA-N index: 402 label: Benzylide molecular_weight: class: ScalarQuantity units: amu - value: 89.11460813569646 -multiplicity: 3 + value: 91.13048838065595 +multiplicity: 1 reference_data: ATcT: class: ReferenceDataEntry @@ -123,5 +124,5 @@ reference_data: units: kJ/mol value: 123.10000000000007 class: ThermoData -smiles: '[C-]C1=CC=CC=C1' +smiles: 'c1ccc(cc1)[CH2-]' symmetry_number: 2.0 diff --git a/input/reference_sets/main/Ethynol anion.yml b/input/reference_sets/main/Ethynol anion.yml index 7b42b19517..2ac2c1ddb8 100644 --- a/input/reference_sets/main/Ethynol anion.yml +++ b/input/reference_sets/main/Ethynol anion.yml @@ -1,9 +1,9 @@ RMG_version: 3.0.0 adjacency_list: | - multiplicity 2 - 1 O u0 p2 c0 {2,D} - 2 C u0 p0 c0 {1,D} {3,D} - 3 C u1 p1 c-1 {2,D} + 1 C u0 p1 c-1 {2,S} {3,D} + 2 H u0 p0 c0 {1,S} + 3 C u0 p0 c0 {1,D} {4,D} + 4 O u0 p2 c0 {3,D} calculated_data: wb97m-v/def2-tzvpd: class: CalculatedDataEntry @@ -43,16 +43,16 @@ charge: -1 class: ReferenceSpecies datetime: 2020-02-24 11:05 default_xyz_chemistry: wb97m-v/def2-tzvpd -formula: C2O -inchi: InChI=1S/C2O/c1-2-3/q-1 -inchi_key: BLDNDSGBHRVRNO-UHFFFAOYSA-N +formula: C2HO +inchi: InChI=1S/C2HO/c1-2-3/h1H/q-1 +inchi_key: BSJVBKBNZLEKLO-UHFFFAOYSA-N index: 119 label: Ethynol anion molecular_weight: class: ScalarQuantity units: amu - value: 40.02080261436369 -multiplicity: 2 + value: 41.028742736843434 +multiplicity: 1 reference_data: ATcT: class: ReferenceDataEntry @@ -64,5 +64,5 @@ reference_data: units: kJ/mol value: -47.26 class: ThermoData -smiles: '[C-]=C=O' +smiles: '[CH-]=C=O' symmetry_number: 1.0 diff --git a/input/reference_sets/main/Formyl anion.yml b/input/reference_sets/main/Formyl anion.yml index 2e70733d73..080279137c 100644 --- a/input/reference_sets/main/Formyl anion.yml +++ b/input/reference_sets/main/Formyl anion.yml @@ -1,8 +1,8 @@ RMG_version: 3.0.0 adjacency_list: | - multiplicity 2 - 1 O u0 p2 c0 {2,D} - 2 C u1 p1 c-1 {1,D} + 1 C u0 p1 c-1 {2,S} {3,D} + 2 H u0 p0 c0 {1,S} + 3 O u0 p2 c0 {1,D} calculated_data: wb97m-v/def2-tzvpd: class: CalculatedDataEntry @@ -37,16 +37,16 @@ charge: -1 class: ReferenceSpecies datetime: 2020-02-24 11:05 default_xyz_chemistry: wb97m-v/def2-tzvpd -formula: CO -inchi: InChI=1S/CO/c1-2/q-1 -inchi_key: DCMZLVSOPGZIFI-UHFFFAOYSA-N +formula: CHO +inchi: InChI=1S/CHO/c1-2/h1H/q-1 +inchi_key: CKJNUZNMWOVDFN-UHFFFAOYSA-N index: 44 label: Formyl anion molecular_weight: class: ScalarQuantity units: amu - value: 28.010101539606868 -multiplicity: 2 + value: 29.01804166208662 +multiplicity: 1 reference_data: ATcT: class: ReferenceDataEntry @@ -58,5 +58,5 @@ reference_data: units: kJ/mol value: 12.02 class: ThermoData -smiles: '[C-]=O' +smiles: '[CH-]=O' symmetry_number: 1.0 diff --git a/input/reference_sets/main/Methanide.yml b/input/reference_sets/main/Methanide.yml index 89e1d688a0..05c8f1dcb4 100644 --- a/input/reference_sets/main/Methanide.yml +++ b/input/reference_sets/main/Methanide.yml @@ -1,8 +1,9 @@ RMG_version: 3.0.0 adjacency_list: | - multiplicity 3 - 1 C u2 p1 c-1 {2,S} + 1 C u0 p1 c-1 {2,S} {3,S} {4,S} 2 H u0 p0 c0 {1,S} + 3 H u0 p0 c0 {1,S} + 4 H u0 p0 c0 {1,S} calculated_data: wb97m-v/def2-tzvpd: class: CalculatedDataEntry @@ -42,16 +43,16 @@ charge: -1 class: ReferenceSpecies datetime: 2020-02-24 11:05 default_xyz_chemistry: wb97m-v/def2-tzvpd -formula: CH -inchi: InChI=1S/CH/h1H/q-1 -inchi_key: VPIURJINGFGPNS-UHFFFAOYSA-N +formula: CH3 +inchi: InChI=1S/CH3/h1H3/q-1 +inchi_key: LGRLWUINFJPLSH-UHFFFAOYSA-N index: 16 label: Methanide molecular_weight: class: ScalarQuantity units: amu - value: 13.018641197236564 -multiplicity: 3 + value: 15.034521442196064 +multiplicity: 1 reference_data: ATcT: class: ReferenceDataEntry @@ -63,5 +64,5 @@ reference_data: units: kJ/mol value: 137.63 class: ThermoData -smiles: '[CH]' +smiles: '[CH3-]' symmetry_number: 3.0 diff --git a/input/reference_sets/main/Vinoxide.yml b/input/reference_sets/main/Vinoxide.yml index 0f746e915c..4e4953aaf3 100644 --- a/input/reference_sets/main/Vinoxide.yml +++ b/input/reference_sets/main/Vinoxide.yml @@ -1,10 +1,11 @@ RMG_version: 3.0.0 adjacency_list: | - multiplicity 3 - 1 O u0 p2 c0 {2,D} - 2 C u0 p0 c0 {1,D} {3,S} {4,S} - 3 C u2 p1 c-1 {2,S} - 4 H u0 p0 c0 {2,S} + 1 C u0 p1 c-1 {2,S} {3,S} {4,S} + 2 H u0 p0 c0 {1,S} + 3 H u0 p0 c0 {1,S} + 4 C u0 p0 c0 {1,S} {5,D} {6,S} + 5 O u0 p2 c0 {4,D} + 6 H u0 p0 c0 {4,S} calculated_data: wb97m-v/def2-tzvpd: class: CalculatedDataEntry @@ -54,16 +55,16 @@ charge: -1 class: ReferenceSpecies datetime: 2020-02-24 11:05 default_xyz_chemistry: wb97m-v/def2-tzvpd -formula: C2HO -inchi: InChI=1S/C2HO/c1-2-3/h2H/q-1 -inchi_key: FKOCRZRGMPDZME-UHFFFAOYSA-N +formula: C2H3O +inchi: InChI=1S/C2H3O/c1-2-3/h2H,1H2/q-1 +inchi_key: MGKBHFTXPZTTHS-UHFFFAOYSA-N index: 157 label: Vinoxide molecular_weight: class: ScalarQuantity units: amu - value: 41.028742736843434 -multiplicity: 3 + value: 43.04462298180294 +multiplicity: 1 reference_data: ATcT: class: ReferenceDataEntry @@ -75,5 +76,5 @@ reference_data: units: kJ/mol value: -160.63 class: ThermoData -smiles: '[C-]C=O' +smiles: '[CH2-]C=O' symmetry_number: 1.0 diff --git a/input/reference_sets/main/Vinyl anion.yml b/input/reference_sets/main/Vinyl anion.yml index 7b96e06065..628ddb7974 100644 --- a/input/reference_sets/main/Vinyl anion.yml +++ b/input/reference_sets/main/Vinyl anion.yml @@ -1,10 +1,10 @@ RMG_version: 3.0.0 adjacency_list: | - multiplicity 2 - 1 C u0 p0 c0 {2,D} {3,S} {4,S} - 2 C u1 p1 c-1 {1,D} - 3 H u0 p0 c0 {1,S} + 1 C u0 p0 c0 {2,D} {4,S} {5,S} + 2 C u0 p1 c-1 {1,D} {3,S} + 3 H u0 p0 c0 {2,S} 4 H u0 p0 c0 {1,S} + 5 H u0 p0 c0 {1,S} calculated_data: wb97m-v/def2-tzvpd: class: CalculatedDataEntry @@ -49,16 +49,16 @@ charge: -1 class: ReferenceSpecies datetime: 2020-02-24 11:05 default_xyz_chemistry: wb97m-v/def2-tzvpd -formula: C2H2 -inchi: InChI=1S/C2H2/c1-2/h1H2/q-1 -inchi_key: VSVANFQZMKLBSU-UHFFFAOYSA-N +formula: C2H3 +inchi: InChI=1S/C2H3/c1-2/h1H,2H2/q-1 +inchi_key: IEARPTNIYZTWOZ-UHFFFAOYSA-N index: 70 label: Vinyl anion molecular_weight: class: ScalarQuantity units: amu - value: 26.037282394473127 -multiplicity: 2 + value: 27.04522251695288 +multiplicity: 1 reference_data: ATcT: class: ReferenceDataEntry @@ -70,5 +70,5 @@ reference_data: units: kJ/mol value: 232.59 class: ThermoData -smiles: '[C-]=C' +smiles: 'C=[CH-]' symmetry_number: 2.0