diff --git a/.github/workflows/base-ci.yaml b/.github/workflows/base-ci.yaml
new file mode 100644
index 00000000..f6fcac98
--- /dev/null
+++ b/.github/workflows/base-ci.yaml
@@ -0,0 +1,77 @@
+name: Base tests
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    # weekly tests, Sundays at midnight
+    - cron: "0 0 * * 0"
+
+concurrency:
+  # Specific group naming so CI is only cancelled
+  # within same PR or on merge to main
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+env:
+  OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+
+jobs:
+  main_tests:
+    name: CI (${{ matrix.os }}, py-${{ matrix.python-version }}, openeye=${{ matrix.include-openeye }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+          os: [macOS-13, macOS-latest, ubuntu-latest]
+          python-version: ["3.10", "3.11", "3.12"]
+          include-openeye: [false, true]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build information
+      run: |
+        uname -a
+        df -h
+        ulimit -a
+
+    - name: Install environment
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: devtools/conda-envs/base.yaml
+        create-args: >-
+          python=${{ matrix.python-version }}
+
+    - name: Install package
+      run: |
+        python -m pip install . --no-deps
+
+    - uses: ./.github/actions/include-openeye
+      if: matrix.include-openeye == true
+      with:
+        openeye-license-text: ${{ secrets.OE_LICENSE }}
+        openeye-license-file: ${{ env.OE_LICENSE }}
+
+      
+    - name: Uninstall OpenEye
+      if: matrix.include-openeye == false
+      run: conda remove --force openeye-toolkits --yes || echo "openeye not installed"
+
+    - name: Check toolkit installations
+      shell: bash -l -c "python -u {0}"
+      run: |
+        from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
+        assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}'
+        assert str(RDKIT_AVAILABLE).lower() == 'true'
+
+    - name: Run tests
+      run: |
+        python -m pytest -n 4 -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/
diff --git a/.github/workflows/dev-ci.yaml b/.github/workflows/dev-ci.yaml
index dfa6c369..6b4e4407 100644
--- a/.github/workflows/dev-ci.yaml
+++ b/.github/workflows/dev-ci.yaml
@@ -14,6 +14,10 @@ concurrency:
 defaults:
   run:
     shell: bash -l {0}
+  
+env:
+  OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+  DGL_HOME: ${{ github.workspace }}/dgl
 
 jobs:
   nightly_check:
@@ -22,8 +26,8 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          os: [macOS-12, ubuntu-latest]
-          python-version: ["3.10", "3.11", "3.12"]
+          os: [macOS-13, macOS-latest, ubuntu-latest]
+          python-version: ["3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -42,25 +46,63 @@ jobs:
           python=${{ matrix.python-version }}
           pydantic=2
     
-    - name: Install nightly pytorch-lightning and DGL
+    - name: Install nightly pytorch
       run: |
-        python -m pip install --pre dgl -f https://data.dgl.ai/wheels-test/repo.html
-        python -m pip install --pre dglgo -f https://data.dgl.ai/wheels-test/repo.html
-        python -m pip install https://github.com/Lightning-AI/lightning/archive/refs/heads/master.zip -U  
+        python -m pip install https://github.com/Lightning-AI/lightning/archive/refs/heads/master.zip -U 
 
-    - name: Install package
+    - name: Download DGL source
       run: |
-        python -m pip install . --no-deps
+        git clone --recurse-submodules https://github.com/dmlc/dgl.git
+      
+    - name: Set up DGL
+      if: matrix.os != 'ubuntu-latest'
+      run: |
+        # from https://docs.dgl.ai/en/latest/install/index.html#macos
+        cd dgl/
+        mkdir build && cd build
+        cmake -DUSE_OPENMP=off -DUSE_LIBXSMM=OFF ..
+        make -j4
+        cd ../..
+    
+    - name: Set up DGL (Ubuntu)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        cd dgl/
+        mkdir build && cd build
+        cmake -DBUILD_TYPE=dev -DUSE_CUDA=OFF -DUSE_LIBXSMM=OFF ..
+        make
+        cd ../..
+    
+    - name: Install DGL Python bindings
+      run: |
+        cd dgl/python
+        python setup.py install
+        python setup.py build_ext --inplace
+        cd ../..
 
-    - name: Python information
+    - uses: ./.github/actions/include-openeye
+      with:
+        openeye-license-text: ${{ secrets.OE_LICENSE }}
+        openeye-license-file: ${{ env.OE_LICENSE }}
+
+    - name: Check toolkit installations
+      shell: bash -l -c "python -u {0}"
       run: |
-        which python
-        conda info
-        conda list
+        from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
+        assert str(OPENEYE_AVAILABLE).lower() == 'true'
+        assert str(RDKIT_AVAILABLE).lower() == 'true'
 
+    - name: Check Python environment
+      run: |
+        pip list
+    
     - name: Import DGL
       run: |
-        python -c "import dgl"
+        python -c "import dgl; import dgl.nn"
+
+    - name: Install package
+      run: |
+        python -m pip install . --no-deps
 
     - name: Run tests
       run: |
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
index 296cc6d4..fe3ae8e4 100644
--- a/.github/workflows/gh-ci.yaml
+++ b/.github/workflows/gh-ci.yaml
@@ -30,7 +30,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          os: [macOS-12, ubuntu-latest]
+          os: [macOS-13, macOS-latest, ubuntu-latest]
           python-version: ["3.10", "3.11", "3.12"]
           pydantic-version: ["1", "2"]
           include-rdkit: [false, true]
@@ -39,12 +39,6 @@ jobs:
           exclude:
             - include-rdkit: false
               include-openeye: false
-            # no openeye for 3.12 yet
-            - include-openeye: true
-              python-version: "3.12"
-            # no builds?
-            - include-dgl: true
-              python-version: "3.12"
 
 
     steps:
@@ -57,7 +51,7 @@ jobs:
         ulimit -a
 
     - name: Install environment
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: devtools/conda-envs/test_env_dgl_${{ matrix.include-dgl }}.yaml
         create-args: >-
@@ -77,11 +71,11 @@ jobs:
       
     - name: Uninstall OpenEye
       if: matrix.include-openeye == false
-      run: conda remove --force openeye-toolkits --yes || echo "openeye not installed"
+      run: micromamba remove --force openeye-toolkits --yes || echo "openeye not installed"
 
     - name: Uninstall RDKit
       if: matrix.include-rdkit == false
-      run: conda remove --force rdkit --yes || echo "rdkit not installed"
+      run: micromamba remove --force rdkit --yes || echo "rdkit not installed"
 
     # See https://github.com/openforcefield/openff-nagl/issues/103
     - name: Rewrite DGL config
@@ -90,12 +84,6 @@ jobs:
         mkdir -p ~/.dgl
         echo '{"backend": "pytorch"}' > ~/.dgl/config.json
 
-    - name: Python information
-      run: |
-        which python
-        conda info
-        conda list
-
     - name: Check toolkit installations
       shell: bash -l -c "python -u {0}"
       run: |
@@ -103,9 +91,14 @@ jobs:
         assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}'
         assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}'
 
+    - name: Check DGL installation
+      if: matrix.include-dgl == true
+      run: |
+        python -c "import dgl"
+
     - name: Run tests
       run: |
-        python -m pytest -n 4 -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/
+        python -m pytest -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/
 
     - name: codecov
       uses: codecov/codecov-action@v4
@@ -177,29 +170,19 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Install conda
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
-        python-version: ${{ matrix.python-version }}
-        add-pip-as-python-dependency: true
-        architecture: x64
-        miniforge-variant: Mambaforge
-        use-mamba: true
-        auto-update-conda: true
-        show-channel-urls: true
-        channels: conda-forge, defaults
+        environment-name: openff-nagl
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Build from source
       run: |
-        conda create --name openff-nagl
-        conda activate openff-nagl
-        conda list
-    
-        mamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml
+        micromamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml
         python --version
         python -m pip install . --no-deps
-        conda list
+        micromamba list
 
     - name: Check success
       run: |
-        conda activate openff-nagl
         python -c "import openff.nagl ; print(openff.nagl.__version__)"
diff --git a/devtools/conda-envs/base.yaml b/devtools/conda-envs/base.yaml
new file mode 100644
index 00000000..a26378f8
--- /dev/null
+++ b/devtools/conda-envs/base.yaml
@@ -0,0 +1,35 @@
+name: openff-nagl-test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+    # Base depends
+  - python
+  - pip
+  - importlib_resources
+
+  # UI
+  - click
+  - click-option-group
+  - rich
+  - tqdm
+
+  # chemistry
+  - openff-toolkit-base >=0.11.1
+  - openff-units
+  - pydantic <3
+  - rdkit
+  - scipy
+
+  # files
+  - pyyaml
+
+  # gcn
+  - pytorch >=2.0
+  - pytorch-lightning
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  - codecov
diff --git a/devtools/conda-envs/nightly.yaml b/devtools/conda-envs/nightly.yaml
index 0cdad8f2..61e71e85 100644
--- a/devtools/conda-envs/nightly.yaml
+++ b/devtools/conda-envs/nightly.yaml
@@ -1,8 +1,8 @@
 name: openff-nagl-test
 channels:
   - openeye
-  - pytorch-nightly
   - conda-forge
+  - pytorch-nightly
   - defaults
 dependencies:
     # Base depends
@@ -18,13 +18,16 @@ dependencies:
   - pydantic <3
   - rdkit
   - scipy
+  - openeye-toolkits
+
+  # gnn
+  - pytorch
+  - torchvision
+  - torchaudio
 
   # database
   - pyarrow
 
-  # gcn
-  - pytorch
-
   # parallelism
   - dask-jobqueue
 
@@ -49,6 +52,11 @@ dependencies:
   - sqlite
   - xmltodict
 
+  # building
+  - make
+  - cmake
+  - cython
+
   # Pip-only installs
   - pip:
     - git+https://github.com/openforcefield/openff-utilities.git@main
diff --git a/devtools/conda-envs/test_env_dgl_false.yaml b/devtools/conda-envs/test_env_dgl_false.yaml
index 4ee79048..ebee3a64 100644
--- a/devtools/conda-envs/test_env_dgl_false.yaml
+++ b/devtools/conda-envs/test_env_dgl_false.yaml
@@ -2,7 +2,6 @@ name: openff-nagl-test
 channels:
   - openeye
   - conda-forge
-  - defaults
 dependencies:
     # Base depends
   - python
diff --git a/devtools/conda-envs/test_env_dgl_true.yaml b/devtools/conda-envs/test_env_dgl_true.yaml
index 4536289d..9376d111 100644
--- a/devtools/conda-envs/test_env_dgl_true.yaml
+++ b/devtools/conda-envs/test_env_dgl_true.yaml
@@ -1,9 +1,7 @@
 name: openff-nagl-test
 channels:
   - openeye
-  - dglteam
   - conda-forge
-  - defaults
 dependencies:
     # Base depends
   - python
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index ec5acf35..4c921d87 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -27,6 +27,7 @@ The rules for this file:
 - Removed unused, undocumented code paths, and updated docs (PR #132)
 
 ### Fixed
+- Fixed molecule normalization issues (Issue #119, PR #149)
 - Check lookup tables for allowed molecules before ChemicalDomain for forbidden ones (PR #145, Issue #144)
 - Add support for single atoms (PR #146, Issue #138)
 
diff --git a/openff/nagl/nn/_dataset.py b/openff/nagl/nn/_dataset.py
index 8551cdbd..2fe03d3e 100644
--- a/openff/nagl/nn/_dataset.py
+++ b/openff/nagl/nn/_dataset.py
@@ -268,9 +268,15 @@ class _LazyDGLMoleculeDataset(Dataset):
 
     @property
     def schema(self):
+        self.get_schema()
+    
+    @classmethod
+    def get_schema(cls):
         import pyarrow as pa
 
         return pa.schema([pa.field("pickled", pa.binary())])
+    
+
 
     def __len__(self):
         return self.n_entries
@@ -370,7 +376,7 @@ def from_arrow_dataset(
         input_dataset = ds.dataset(path, format=format)
 
         with pa.OSFile(str(output_path), "wb") as sink:
-            with pa.ipc.new_file(sink, cls.schema) as writer:
+            with pa.ipc.new_file(sink, cls.get_schema()) as writer:
                 input_batches = input_dataset.to_batches(columns=columns)
                 for input_batch in input_batches:
                     with get_mapper_to_processes(n_processes=n_processes) as mapper:
@@ -378,7 +384,7 @@ def from_arrow_dataset(
 
                     output_batch = pa.RecordBatch.from_arrays(
                         [pa.array(pickled)],
-                        schema=cls.schema
+                        schema=cls.get_schema()
                     )
                     writer.write_batch(output_batch)
                     
diff --git a/openff/nagl/tests/nn/__init__.py b/openff/nagl/tests/nn/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/openff/nagl/tests/utils/test_openff.py b/openff/nagl/tests/utils/test_openff.py
index 831260f1..a988e548 100644
--- a/openff/nagl/tests/utils/test_openff.py
+++ b/openff/nagl/tests/utils/test_openff.py
@@ -7,7 +7,7 @@
 from openff.nagl.toolkits import NAGLRDKitToolkitWrapper
 from openff.toolkit import RDKitToolkitWrapper
 from openff.toolkit.utils.toolkit_registry import toolkit_registry_manager, ToolkitRegistry
-from openff.toolkit.utils.toolkits import RDKIT_AVAILABLE, OPENEYE_AVAILABLE, AMBERTOOLS_AVAILABLE
+from openff.toolkit.utils.toolkits import RDKIT_AVAILABLE, OPENEYE_AVAILABLE
 from openff.units import unit
 
 from openff.nagl.toolkits.openff import (
@@ -26,6 +26,36 @@
 )
 from openff.nagl.utils._utils import transform_coordinates
 
+def _load_rdkit_molecule_exactly(mapped_smiles: str):
+    """
+    Load a molecule from a mapped SMILES string using RDKit, without any normalization.
+    """
+    from rdkit import Chem
+
+    # load into RDKit
+    params = Chem.SmilesParserParams()
+    params.removeHs = False
+    params.sanitize = False
+    rdmol = Chem.MolFromSmiles(mapped_smiles, params)
+    Chem.MolToSmiles(rdmol)
+
+    atom_indices = [atom.GetAtomMapNum() - 1 for atom in rdmol.GetAtoms()]
+    ordering = [atom_indices.index(i) for i in range(rdmol.GetNumAtoms())]
+    rdmol = Chem.RenumberAtoms(rdmol, ordering)
+    Chem.SanitizeMol(rdmol, Chem.SANITIZE_SYMMRINGS)
+    Chem.Kekulize(rdmol)
+
+    molecule = Molecule.from_rdkit(rdmol, allow_undefined_stereo=True)
+
+    # copy over formal charges and bonds again; from_rdkit sanitizes the rdmol
+    for atom, rdatom in zip(molecule.atoms, rdmol.GetAtoms()):
+        atom.formal_charge = rdatom.GetFormalCharge() * unit.elementary_charge
+    for rdbond in rdmol.GetBonds():
+        i, j = rdbond.GetBeginAtomIdx(), rdbond.GetEndAtomIdx()
+        bond = molecule.get_bond_between(i, j)
+        bond._bond_order = int(rdbond.GetBondTypeAsDouble())
+
+    return molecule
 
 def test_get_openff_molecule_bond_indices(openff_methane_charged):
     bond_indices = get_openff_molecule_bond_indices(openff_methane_charged)
@@ -46,21 +76,86 @@ def test_smiles_to_inchi_key(smiles, expected):
     assert smiles_to_inchi_key(smiles) == expected
 
 
+NORMALIZATION_MOLECULE_TESTS = [
+    (
+        r"[H:6][C:1]([H:7])([H:8])[S+2:2]([C:5]([H:9])([H:10])[H:11])([O-:3])[O-:4]",
+        r"[H:6][C:1]([H:7])([H:8])[S:2](=[O:3])(=[O:4])[C:5]([H:9])([H:10])[H:11]",
+
+    ),
+    (
+        r"[H:22][c:7]1[c:6]([c:12]([n:10](=[O:11])[c:9]([n:8]1)[H:23])[C:13]([H:24])([H:25])[N:14](=[O:15])=[O:16])[C:5]([H:20])([H:21])[S+2:2]([C:1]([H:17])([H:18])[H:19])([O-:3])[O-:4]",
+        r"[H:22][c:7]1[c:6]([c:12]([n+:10]([c:9]([n:8]1)[H:23])[O-:11])[C:13]([H:24])([H:25])[N+:14](=[O:16])[O-:15])[C:5]([H:20])([H:21])[S:2](=[O:3])(=[O:4])[C:1]([H:17])([H:18])[H:19]"
+    ),
+    # Issue 119
+    (
+        r"[H:1][C:2]([H:3])([H:4])[c:5]1[c:6]2=[N:7][O:8][N+:9](=[c:10]2[c:11]([n+:12]([n+:13]1[O-:14])[O-:15])[C:16]([H:17])([H:18])[H:19])[O-:20]",
+        r"[H:1][C:2]([H:3])([H:4])[c:5]1[c:6]2=[N:7][O:8][N+:9](=[c:10]2[c:11]([n:12](=[O:15])[n:13]1=[O:14])[C:16]([H:17])([H:18])[H:19])[O-:20]",
+    ),
+    (
+        r"[H:1][c:2]1[c:3]([c:4]([c:5]2[c:6]([c:7]1[H:8])/[C:9](=[N:10]/[C:11](=[O:12])[c:13]3[c:14]([c:15]([c:16]([c:17]([c:18]3[N+:19](=[O:20])[O-:21])[H:22])[N+:23](=[O:24])[O-:25])[H:26])[H:27])/[N-:28][c:29]4[c:30]([c:31]([c:32]([c:33]([n+:34]4[C:35]2([H:36])[H:37])[H:38])[Br:39])[H:40])[H:41])[H:42])[H:43]",
+        r"[H:1][c:2]1[c:3]([c:4]([c:5]2[c:6]([c:7]1[H:8])/[C:9](=[N:10]/[C:11](=[O:12])[c:13]3[c:14]([c:15]([c:16]([c:17]([c:18]3[N+:19](=[O:20])[O-:21])[H:22])[N+:23](=[O:24])[O-:25])[H:26])[H:27])/[N:28]=[C:29]4[C:30](=[C:31]([C:32](=[C:33]([N:34]4[C:35]2([H:36])[H:37])[H:38])[Br:39])[H:40])[H:41])[H:42])[H:43]"
+    ),
+    (
+        r"[H:21][c:1]1[c:2]([c:3]([c:4]([c:5]([c:6]1[C:7]2=[N:8][N+:9]3=[C:15]([S:16]2)[N:14]([C:12](=[O:13])[C:11](=[C:10]3[O-:17])[H:25])[H:26])[H:24])[H:23])[N:18](=[O:19])=[O:20])[H:22]",
+        r"[H:21][c:1]1[c:2]([c:3]([c:4]([c:5]([c:6]1[C:7]2=[N:8][N:9]3[C:10](=[C:11]([C:12](=[O:13])[N+:14](=[C:15]3[S:16]2)[H:26])[H:25])[O-:17])[H:24])[H:23])[N+:18](=[O:20])[O-:19])[H:22]"
+    )
+
+]
+
+@pytest.mark.skipif(not OPENEYE_AVAILABLE, reason="requires openeye")
 @pytest.mark.parametrize(
-    "expected_smiles, given_smiles",
-    [
-        ("CS(=O)(=O)C", "C[S+2]([O-])([O-])C"),
-    ],
+    "given_smiles, expected_smiles",
+    NORMALIZATION_MOLECULE_TESTS
 )
-def test_normalize_molecule(expected_smiles, given_smiles):
+def test_normalize_molecule_openeye(given_smiles, expected_smiles):
     from openff.toolkit.topology.molecule import Molecule
-    expected_molecule = Molecule.from_smiles(expected_smiles)
+    expected_molecule = Molecule.from_mapped_smiles(expected_smiles)
 
-    molecule = Molecule.from_smiles(given_smiles)
+    molecule = Molecule.from_mapped_smiles(given_smiles)
     assert not Molecule.are_isomorphic(molecule, expected_molecule)[0]
 
     output_molecule = normalize_molecule(molecule)
-    assert Molecule.are_isomorphic(output_molecule, expected_molecule)[0]
+    output_smiles = output_molecule.to_smiles(mapped=True)
+    # reload molecule to avoid spurious failures from different kekulization
+    output_molecule = Molecule.from_mapped_smiles(output_smiles)
+    is_isomorphic = Molecule.are_isomorphic(
+        output_molecule, expected_molecule,
+    )[0]
+    assert is_isomorphic, output_molecule.to_smiles(mapped=True)
+
+
+@pytest.mark.skipif(not RDKIT_AVAILABLE, reason="requires rdkit")
+@pytest.mark.parametrize(
+    "given_smiles, expected_smiles",
+    NORMALIZATION_MOLECULE_TESTS
+)
+def test_normalize_molecule_bypasses_rdkit_normalization(
+    given_smiles,
+    expected_smiles,
+):
+    from openff.toolkit.topology.molecule import Molecule
+
+    expected_molecule = _load_rdkit_molecule_exactly(expected_smiles)
+    molecule = _load_rdkit_molecule_exactly(given_smiles)
+    
+    assert not Molecule.are_isomorphic(molecule, expected_molecule)[0]
+    output_molecule = normalize_molecule(molecule)
+    is_isomorphic = Molecule.are_isomorphic(output_molecule, expected_molecule)[0]
+
+    # this may fail spuriously due to kekulization error, in which case
+    # we reload the molecule and try again
+    if not is_isomorphic:
+        output_smiles = output_molecule.to_smiles(mapped=True)
+        # reload molecule to avoid spurious failures from different kekulization
+        output_molecule = _load_rdkit_molecule_exactly(output_smiles)
+        is_isomorphic = Molecule.are_isomorphic(
+            output_molecule, expected_molecule,
+        )[0]
+
+    assert is_isomorphic, output_molecule.to_smiles(mapped=True)
+
+
+        
 
 
 @pytest.mark.parametrize(
diff --git a/openff/nagl/toolkits/openeye.py b/openff/nagl/toolkits/openeye.py
index 4e081f43..89e642ed 100644
--- a/openff/nagl/toolkits/openeye.py
+++ b/openff/nagl/toolkits/openeye.py
@@ -47,6 +47,7 @@ def _run_normalization_reactions(
 
         for reaction_smarts in normalization_reactions:
             reaction = oechem.OEUniMolecularRxn(reaction_smarts)
+            reaction.SetValidateKekule(False)
             reaction(oemol)
 
         molecule = self.from_openeye(
diff --git a/openff/nagl/toolkits/rdkit.py b/openff/nagl/toolkits/rdkit.py
index 874962ef..85d1285d 100644
--- a/openff/nagl/toolkits/rdkit.py
+++ b/openff/nagl/toolkits/rdkit.py
@@ -76,7 +76,16 @@ def _run_normalization_reactions(
                     )
 
                 for atom in rdmol.GetAtoms():
-                    atom.SetAtomMapNum(atom.GetIntProp("react_atom_idx") + 1)
+                    # reorder the rdkit mol following mapping
+                    original_atom_indices = [
+                        atom.GetIntProp("react_atom_idx")
+                        for atom in rdmol.GetAtoms()
+                    ]
+                new_order = [original_atom_indices.index(i) for i in range(rdmol.GetNumAtoms())]
+                rdmol = Chem.RenumberAtoms(rdmol, new_order)
+                # RDKit can assign stereochemistry differently
+                # and toolkit doesn't allow STEREOCIS and STEREOTRANS bonds
+                Chem.AssignStereochemistry(rdmol, cleanIt=True)
 
                 new_smiles = Chem.MolToSmiles(Chem.AddHs(rdmol))
                 # stop changing when smiles converges to same product
@@ -87,12 +96,28 @@ def _run_normalization_reactions(
                     f"Reaction {reaction_smarts} did not converge after "
                     f"{max_iter} iterations for molecule {original_smiles}"
                 )
+            
+        for i, atom in enumerate(rdmol.GetAtoms(), 1):
+            atom.SetAtomMapNum(i)
 
+        # required to calculate explicit atom valence
+        # for kekulize call
+        Chem.SanitizeMol(rdmol, Chem.SANITIZE_SYMMRINGS)
+        Chem.Kekulize(rdmol)
+        Chem.AssignStereochemistry(rdmol)
+            
         new_mol = self.from_rdkit(
             rdmol,
             allow_undefined_stereo=True,
-            _cls=molecule.__class__,
         )
+        # copy over formal charges and bonds again; from_rdkit sanitizes the rdmol
+        for atom, rdatom in zip(new_mol.atoms, rdmol.GetAtoms()):
+            atom.formal_charge = rdatom.GetFormalCharge() * unit.elementary_charge
+        for rdbond in rdmol.GetBonds():
+            i, j = rdbond.GetBeginAtomIdx(), rdbond.GetEndAtomIdx()
+            bond = new_mol.get_bond_between(i, j)
+            bond._bond_order = int(rdbond.GetBondTypeAsDouble())
+
         mapping = new_mol.properties.pop("atom_map")
         adjusted_mapping = dict((current, new - 1) for current, new in mapping.items())