diff --git a/input/reference_sets/main/Bromofluoromethane.yml b/input/reference_sets/main/Bromofluoromethane.yml
deleted file mode 100644
index 38aabfc84d..0000000000
--- a/input/reference_sets/main/Bromofluoromethane.yml
+++ /dev/null
@@ -1,74 +0,0 @@
-RMG_version: 3.0.0
-adjacency_list: |
-  1 Br u0 p3 c0 {3,S}
-  2 F  u0 p3 c0 {3,S}
-  3 C  u0 p0 c0 {1,S} {2,S} {4,S} {5,S}
-  4 H  u0 p0 c0 {3,S}
-  5 H  u0 p0 c0 {3,S}
-calculated_data:
-  wb97m-v/def2-tzvpd:
-    class: CalculatedDataEntry
-    thermo_data:
-      H298:
-        class: ScalarQuantity
-        units: kcal/mol
-        value: -50.95823941818229
-      class: ThermoData
-    xyz_dict:
-      coords:
-        class: np_array
-        object:
-        - - 1.9378368722
-          - -0.4571093956
-          - 0.0
-        - - 1.0682068489
-          - 0.5914838627
-          - 0.0
-        - - -0.7504198703999999
-          - -0.0510603655
-          - 0.0
-        - - 1.2074623692
-          - 1.1760980128999998
-          - 0.903877525
-        - - 1.2074623692
-          - 1.1760980128999998
-          - -0.903877525
-      isotopes:
-      - 19
-      - 12
-      - 79
-      - 1
-      - 1
-      symbols:
-      - F
-      - C
-      - Br
-      - H
-      - H
-charge: 0
-class: ReferenceSpecies
-datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
-formula: CH2BrF
-inchi: InChI=1S/CH2BrF/c2-1-3/h1H2
-inchi_key: LHMHCLYDBQOYTO-UHFFFAOYSA-N
-index: 148
-label: Bromofluoromethane
-molecular_weight:
-  class: ScalarQuantity
-  units: amu
-  value: 112.9289901816446
-multiplicity: 1
-reference_data:
-  CCCBDB:
-    class: ReferenceDataEntry
-    thermo_data:
-      H298:
-        class: ScalarQuantity
-        uncertainty: 0.12
-        uncertainty_type: +|-
-        units: kJ/mol
-        value: 11.63
-      class: ThermoData
-smiles: FCBr
-symmetry_number: 1.0
diff --git a/input/reference_sets/main/Dinitrogen dioxide.yml b/input/reference_sets/main/Dinitrogen dioxide.yml
index 6dc8454c94..af1502f001 100644
--- a/input/reference_sets/main/Dinitrogen dioxide.yml	
+++ b/input/reference_sets/main/Dinitrogen dioxide.yml	
@@ -11,24 +11,24 @@ calculated_data:
       H298:
         class: ScalarQuantity
         units: kcal/mol
-        value: 61.9022178309892
+        value: 42.1384750201032
       class: ThermoData
     xyz_dict:
       coords:
         class: np_array
         object:
-        - - 1.7562573254
-          - -0.11125283589999997
-          - 0.10237003999999997
-        - - 0.5430836993
-          - -0.0399046657
-          - 0.1275879637
-        - - -0.543083709
-          - 0.0399047752
-          - -0.1275880057
-        - - -1.7562573157
-          - 0.1112527262
-          - -0.1023699979
+        - - 1.6662469432
+          - -0.1024431763
+          - 0.0337055878
+        - - 0.5312424355
+          - -0.024632855299999996
+          - -0.11480881989999998
+        - - 0.3380517243
+          - 0.0907318637
+          - -1.9470706107
+        - - 1.4162228077
+          - 0.0495853245
+          - -2.3368879394
       isotopes:
       - 16
       - 14
diff --git a/input/reference_sets/main/Mercaptomethyl.yml b/input/reference_sets/main/Mercaptomethyl.yml
deleted file mode 100644
index b1d89a93e5..0000000000
--- a/input/reference_sets/main/Mercaptomethyl.yml
+++ /dev/null
@@ -1,75 +0,0 @@
-RMG_version: 3.0.0
-adjacency_list: |
-  multiplicity 2
-  1 S u0 p2 c0 {2,S} {5,S}
-  2 C u1 p0 c0 {1,S} {3,S} {4,S}
-  3 H u0 p0 c0 {2,S}
-  4 H u0 p0 c0 {2,S}
-  5 H u0 p0 c0 {1,S}
-calculated_data:
-  wb97m-v/def2-tzvpd:
-    class: CalculatedDataEntry
-    thermo_data:
-      H298:
-        class: ScalarQuantity
-        units: kcal/mol
-        value: 35.502902632106284
-      class: ThermoData
-    xyz_dict:
-      coords:
-        class: np_array
-        object:
-        - - 1.1285584801
-          - -0.0217105324
-          - -0.0001341992
-        - - -0.5774037449
-          - 0.0887582516
-          - 8.52863e-05
-        - - 1.6352127212
-          - -0.9708630549
-          - 0.0010073963
-        - - 1.6799504805
-          - 0.9034922582
-          - -0.0005060904
-        - - -0.8480541632999999
-          - -1.2224980339
-          - -0.0010606917
-      isotopes:
-      - 12
-      - 32
-      - 1
-      - 1
-      - 1
-      symbols:
-      - C
-      - S
-      - H
-      - H
-      - H
-charge: 0
-class: ReferenceSpecies
-datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
-formula: CH3S
-inchi: InChI=1S/CH3S/c1-2/h2H,1H2
-inchi_key: YYOGAOHWUDJBLM-UHFFFAOYSA-N
-index: 79
-label: Mercaptomethyl
-molecular_weight:
-  class: ScalarQuantity
-  units: amu
-  value: 47.09952451133177
-multiplicity: 2
-reference_data:
-  Cioslowski:
-    class: ReferenceDataEntry
-    thermo_data:
-      H298:
-        class: ScalarQuantity
-        uncertainty: 1.7
-        uncertainty_type: +|-
-        units: kJ/mol
-        value: 124.7
-      class: ThermoData
-smiles: '[CH2]S'
-symmetry_number: 2.0