openforcefield · jaclark5 · Aug 22, 2025 · Aug 22, 2025
@@ -263,6 +263,7 @@ These are currently used to compute properties of a minimum energy conformation
 | `OpenFF Optimization Hessians 2019-07 to 2025-03 v4.0` | [2025-04-14-OpenFF-Optimization-Hessians-2019-07-to-2025-03-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2025-04-14-OpenFF-Optimization-Hessians-2019-07-to-2025-03-v4.0) | Hessian single points for the final molecules in OpenFF optimization datasets from 2019-07 to 2025-03 |  S, H, O, Br, F, N, P, Cl, I, C ||
 | `OpenFF CX3-CX4 singlepoints v4.0"` | [2025-05-21-OpenFF-CX3-CX4-singlepoints-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2025-05-21-OpenFF-CX3-CX4-singlepoints-v4.0) | Single-points of molecules where Sage 2.2.1 torsions t17 and t18 have been driven |  Br, C, Cl, F, H, I, N, O, S ||
 |`MLPepper RECAP Optimized Fragments v1.1`| [2025-07-01-MLPepper-RECAP-Optimized-Fragments-v1.1](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2025-07-01-MLPepper-RECAP-Optimized-Fragments-v1.1) | Single point property calculations for charge models, expanded to include iodine | P ,B ,Cl ,Br ,C ,H ,I ,F ,O ,N ,Si ,S | |
+| `Curated tmQM-xtb Dataset: T=100K Dataset Restricted to Pd, Zn, Fe, Cu v0.0` | [2025-08-14-tmQM-xtb-Dataset-T=100K-Pd-Zn-Fe-Cu-low-mw-v0.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2025-08-14-tmQM-xtb-Dataset-T=100K-Pd-Zn-Fe-Cu-low-mw-v0.0) | BP86/def2-TZVP Conformers for single metal complexes with Pd, Fe, Zn, Cu, Mg, Li and change of {-1,0,+1}, MW <= 600 Da, generally high coordinate, and 30 geometry samples |  Br, C, Cl, Cu, F, Fe, H, N, O, P, Pd, S, Zn ||
 
 
 

@@ -0,0 +1,61 @@
+# tmQM xtb Dataset T=100K Pd Zn Fe Cu low mw v0.0
+
+### Description
+
+This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM). 
+This dataset contains 6,829 unique systems with 471,097 total configurations/spin states below 600 Da.  The molecules are 
+limited to containing transition metals d, Zn, Fe, or Cu, and also only contain elements C, H, P, S, O, N, F, Cl, 
+or Br with charges: {-1,0,+1}. The metal is restricted to greater than four coordination sites, except for Cu and Zn 
+must be greater than or equal to two. Each molecule was preprocessed using gfn2-xtb, and then a short MD simulation
+performed to provide ~30 additional configurations of per molecules at three different spin states, 1, 3, and 5. This
+singlepoint dataset was then run with the BP86/def2-TZVP for with those geometries from molecular dynamics using
+ gfn-xtb. Each configuration is reported with the following properties: 'energy', 'gradient', 'dipole', 'quadrupole',
+'wiberg_lowdin_indices', 'mayer_indices', 'lowdin_charges' 'dipole_polarizabilities', 'mulliken_charges'. SMILES
+strings where generated from tmos (https://github.com/openforcefield/tmos) when possible. These SMILES strings can be
+imported into RDKit for initial visualization, but will not reflect the coordinate geometries presented from tmQm.
+
+### General Information
+
+- Date: 2025-08-14
+- Purpose: BP86/def2-TZVP Conformers for single metal complexes with Pd, Fe, Zn, Cu, and change of {-1,0,+1}, MW <= 600 Da, generally high coordinate, and 30 geometry samples
+- Dataset Type: singlepoint
+- Name: tmQM xtb Dataset T=100K Pd Zn Fe Cu low mw v0.0
+- Number of unique molecules: 6,829
+- Number of filtered molecules: 0
+- Number of Conformers: 471,097
+- Number of conformers (min mean max): 30, 68, 88
+- Molecular Weight (min mean max): 95 455 600
+- Set of charges: -1.0, 0.0, 1.0
+- Dataset Submitter: Jennifer A. Clark
+- Dataset Curator: Christopher R. Iacovella
+
+### QCSubmit generation pipeline
+
+- `generate-dataset.ipynb`: A python notebook which shows how the dataset was prepared from the input files.
+
+### QCSubmit Manifest
+
+- `generate-dataset.ipynb`
+- `environment.yml`: Conda environment file to perform this workflow
+- `environment_full.yml`: All installed packages with versions for successful completion of this workflow
+- `scaffold.json.bz2`: A compressed json file of the target dataset
+
+### Metadata
+
+* Elements: {'Br', 'C', 'Cl', 'Cu', 'F', 'Fe', 'H', 'N', 'O', 'P', 'Pd', 'S', 'Zn'}
+* QC Specifications: BP86/def2-TZVP
+  * program: psi4
+  * method: BP86
+  * basis: def2-TZVP
+  * driver: gradient
+  * implicit_solvent: None
+  * keywords: {}
+  * maxiter: 500
+  * SCF Properties:
+    * dipole
+    * quadrupole
+    * wiberg_lowdin_indices
+    * mayer_indices
+    * lowdin_charges
+    * dipole_polarizabilities
+    * mulliken_charges
@@ -0,0 +1,22 @@
+name: qca-clean
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - numpy
+  - jupyter
+  - pandas
+  - h5py
+  - periodictable
+  - qcportal>=0.61
+  - qcfractal>=0.61
+  - qcfractalcompute>=0.59
+  - rdkit>=2025.3.3
+  - openbabel
+  - deepdiff
+  - py3Dmol
+  - scipy
+  - networkx
+  - pip:
+      - git+https://github.com/openforcefield/tmos.git
+      - git+https://github.com/MDAnalysis/mdanalysis.git@develop#subdirectory=package # delete after 2.10 is released
@@ -0,0 +1,242 @@
+name: qca-clean
+channels:
+  - conda-forge
+dependencies:
+  - anyio=4.10.0=pyhe01879c_0
+  - appnope=0.1.4=pyhd8ed1ab_1
+  - argon2-cffi=25.1.0=pyhd8ed1ab_0
+  - argon2-cffi-bindings=25.1.0=py311h3696347_0
+  - arrow=1.3.0=pyhd8ed1ab_1
+  - asttokens=3.0.0=pyhd8ed1ab_1
+  - async-lru=2.0.5=pyh29332c3_0
+  - attrs=25.3.0=pyh71513ae_0
+  - babel=2.17.0=pyhd8ed1ab_0
+  - beautifulsoup4=4.13.4=pyha770c72_0
+  - bleach=6.2.0=pyh29332c3_4
+  - bleach-with-css=6.2.0=h82add2a_4
+  - brotli=1.1.0=h5505292_3
+  - brotli-bin=1.1.0=h5505292_3
+  - brotli-python=1.1.0=py311h155a34a_3
+  - bzip2=1.0.8=h99b78c6_7
+  - c-ares=1.34.5=h5505292_0
+  - ca-certificates=2025.8.3=hbd8a1cb_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cairo=1.18.4=h6a3b0d2_0
+  - certifi=2025.8.3=pyhd8ed1ab_0
+  - cffi=1.17.1=py311h3a79f62_0
+  - chardet=5.2.0=pyhd8ed1ab_3
+  - charset-normalizer=3.4.3=pyhd8ed1ab_0
+  - comm=0.2.3=pyhe01879c_0
+  - contourpy=1.3.3=py311h57a9ea7_1
+  - cycler=0.12.1=pyhd8ed1ab_1
+  - cyrus-sasl=2.1.28=ha1cbb27_0
+  - debugpy=1.8.16=py311ha59bd64_0
+  - decorator=5.2.1=pyhd8ed1ab_0
+  - deepdiff=8.6.0=pyhe01879c_0
+  - defusedxml=0.7.1=pyhd8ed1ab_0
+  - exceptiongroup=1.3.0=pyhd8ed1ab_0
+  - executing=2.2.0=pyhd8ed1ab_0
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=h77eed37_3
+  - fontconfig=2.15.0=h1383a14_1
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.59.1=py311h2fe624c_0
+  - fqdn=1.5.1=pyhd8ed1ab_1
+  - freetype=2.13.3=hce30654_1
+  - freetype-py=2.3.0=pyhd8ed1ab_0
+  - greenlet=3.2.4=py311hf719da1_0
+  - h11=0.16.0=pyhd8ed1ab_0
+  - h2=4.2.0=pyhd8ed1ab_0
+  - h5py=3.14.0=nompi_py311h8470beb_100
+  - hdf5=1.14.6=nompi_he65715a_103
+  - hpack=4.1.0=pyhd8ed1ab_0
+  - httpcore=1.0.9=pyh29332c3_0
+  - httpx=0.28.1=pyhd8ed1ab_0
+  - hyperframe=6.1.0=pyhd8ed1ab_0
+  - icu=75.1=hfee45f7_0
+  - idna=3.10=pyhd8ed1ab_1
+  - importlib-metadata=8.7.0=pyhe01879c_1
+  - ipykernel=6.30.1=pyh92f572d_0
+  - ipython=9.4.0=pyhfa0c392_0
+  - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
+  - ipywidgets=8.1.7=pyhd8ed1ab_0
+  - isoduration=20.11.0=pyhd8ed1ab_1
+  - jedi=0.19.2=pyhd8ed1ab_1
+  - jinja2=3.1.6=pyhd8ed1ab_0
+  - json5=0.12.1=pyhd8ed1ab_0
+  - jsonpointer=3.0.0=py311h267d04e_1
+  - jsonschema=4.25.0=pyhe01879c_0
+  - jsonschema-specifications=2025.4.1=pyh29332c3_0
+  - jsonschema-with-format-nongpl=4.25.0=he01879c_0
+  - jupyter=1.1.1=pyhd8ed1ab_1
+  - jupyter-lsp=2.2.6=pyhe01879c_0
+  - jupyter_client=8.6.3=pyhd8ed1ab_1
+  - jupyter_console=6.6.3=pyhd8ed1ab_1
+  - jupyter_core=5.8.1=pyh31011fe_0
+  - jupyter_events=0.12.0=pyh29332c3_0
+  - jupyter_server=2.16.0=pyhe01879c_0
+  - jupyter_server_terminals=0.5.3=pyhd8ed1ab_1
+  - jupyterlab=4.4.6=pyhd8ed1ab_0
+  - jupyterlab_pygments=0.3.0=pyhd8ed1ab_2
+  - jupyterlab_server=2.27.3=pyhd8ed1ab_1
+  - jupyterlab_widgets=3.0.15=pyhd8ed1ab_0
+  - kiwisolver=1.4.9=py311h63e5c0c_0
+  - krb5=1.21.3=h237132a_0
+  - lark=1.2.2=pyhd8ed1ab_1
+  - lcms2=2.17=h7eeda09_0
+  - lerc=4.0.0=hd64df32_1
+  - libaec=1.1.4=h51d1e36_0
+  - libblas=3.9.0=34_h10e41b3_openblas
+  - libboost=1.86.0=hc9fb7c5_3
+  - libboost-python=1.86.0=py311h8fc16d6_3
+  - libbrotlicommon=1.1.0=h5505292_3
+  - libbrotlidec=1.1.0=h5505292_3
+  - libbrotlienc=1.1.0=h5505292_3
+  - libcblas=3.9.0=34_hb3479ef_openblas
+  - libcurl=8.14.1=h73640d1_0
+  - libcxx=20.1.8=hf598326_1
+  - libdeflate=1.24=h5773f1b_0
+  - libedit=3.1.20250104=pl5321hafb1f1b_0
+  - libev=4.33=h93a5062_2
+  - libexpat=2.7.1=hec049ff_0
+  - libffi=3.4.6=h1da3d7d_1
+  - libfreetype=2.13.3=hce30654_1
+  - libfreetype6=2.13.3=h1d14073_1
+  - libgfortran=15.1.0=hfdf1602_0
+  - libgfortran5=15.1.0=hb74de2c_0
+  - libglib=2.84.3=h587fa63_0
+  - libiconv=1.18=h23cfdf5_2
+  - libintl=0.25.1=h493aca8_0
+  - libjpeg-turbo=3.1.0=h5505292_0
+  - liblapack=3.9.0=34_hc9a63f6_openblas
+  - liblzma=5.8.1=h39f12f2_2
+  - libnghttp2=1.64.0=h6d7220d_0
+  - libntlm=1.8=h5505292_0
+  - libopenblas=0.3.30=openmp_h60d53f8_1
+  - libpng=1.6.50=h280e0eb_1
+  - libpq=17.6=h6846fd6_0
+  - librdkit=2025.03.5=hafd8b29_0
+  - libsodium=1.0.20=h99b78c6_0
+  - libsqlite=3.50.3=hf8de324_1
+  - libssh2=1.11.1=h1590b86_0
+  - libtiff=4.7.0=h025e3ab_6
+  - libwebp-base=1.6.0=h07db88b_0
+  - libxcb=1.17.0=hdb1d25a_0
+  - libxml2=2.13.8=h4a9ca0c_1
+  - libzlib=1.3.1=h8359307_2
+  - llvm-openmp=20.1.8=hbb9b287_1
+  - markupsafe=3.0.2=py311h4921393_1
+  - matplotlib-base=3.10.5=py311h66dac5a_0
+  - matplotlib-inline=0.1.7=pyhd8ed1ab_1
+  - mistune=3.1.3=pyh29332c3_0
+  - munkres=1.1.4=pyhd8ed1ab_1
+  - nbclient=0.10.2=pyhd8ed1ab_0
+  - nbconvert-core=7.16.6=pyh29332c3_0
+  - nbformat=5.10.4=pyhd8ed1ab_1
+  - ncurses=6.5=h5e97a16_3
+  - nest-asyncio=1.6.0=pyhd8ed1ab_1
+  - networkx=3.5=pyhe01879c_0
+  - notebook=7.4.5=pyhd8ed1ab_0
+  - notebook-shim=0.2.4=pyhd8ed1ab_1
+  - numpy=2.3.2=py311h0856f98_0
+  - openbabel=3.1.1=py311h292ccdb_9
+  - openjpeg=2.5.3=h889cd5d_1
+  - openldap=2.6.10=hbe55e7a_0
+  - openssl=3.5.2=he92f556_0
+  - orderly-set=5.5.0=pyhe01879c_0
+  - overrides=7.7.0=pyhd8ed1ab_1
+  - packaging=25.0=pyh29332c3_1
+  - pandas=2.3.1=py311hff7e5bb_0
+  - pandocfilters=1.5.0=pyhd8ed1ab_0
+  - parso=0.8.4=pyhd8ed1ab_1
+  - pcre2=10.45=ha881caa_0
+  - periodictable=1.7.1=pyhd8ed1ab_0
+  - pexpect=4.9.0=pyhd8ed1ab_1
+  - pickleshare=0.7.5=pyhd8ed1ab_1004
+  - pillow=11.3.0=py311hb9ba9e9_0
+  - pip=25.2=pyh8b19718_0
+  - pixman=0.46.4=h81086ad_1
+  - platformdirs=4.3.8=pyhe01879c_0
+  - prometheus_client=0.22.1=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.51=pyha770c72_0
+  - prompt_toolkit=3.0.51=hd8ed1ab_0
+  - psutil=7.0.0=py311h917b07b_0
+  - pthread-stubs=0.4=hd74edd7_1002
+  - ptyprocess=0.7.0=pyhd8ed1ab_1
+  - pure_eval=0.2.3=pyhd8ed1ab_1
+  - py3dmol=2.5.2=pyhd8ed1ab_0
+  - pycairo=1.28.0=py311h8a0deb1_0
+  - pycparser=2.22=pyh29332c3_1
+  - pygments=2.19.2=pyhd8ed1ab_0
+  - pyobjc-core=11.1=py311hf0763de_0
+  - pyobjc-framework-cocoa=11.1=py311hab620ed_0
+  - pyparsing=3.2.3=pyhe01879c_2
+  - pysocks=1.7.1=pyha55dd90_7
+  - python=3.11.13=hc22306f_0_cpython
+  - python-dateutil=2.9.0.post0=pyhe01879c_2
+  - python-fastjsonschema=2.21.1=pyhd8ed1ab_0
+  - python-json-logger=2.0.7=pyhd8ed1ab_0
+  - python-tzdata=2025.2=pyhd8ed1ab_0
+  - python_abi=3.11=8_cp311
+  - pytz=2025.2=pyhd8ed1ab_0
+  - pyyaml=6.0.2=py311h4921393_2
+  - pyzmq=27.0.1=py311h2637eca_0
+  - qhull=2020.2=h420ef59_5
+  - rdkit=2025.03.5=py311h1da7121_0
+  - readline=8.2=h1d1bf99_2
+  - referencing=0.36.2=pyh29332c3_0
+  - reportlab=4.4.1=py311h917b07b_0
+  - requests=2.32.4=pyhd8ed1ab_0
+  - rfc3339-validator=0.1.4=pyhd8ed1ab_1
+  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
+  - rfc3987-syntax=1.1.0=pyhe01879c_1
+  - rlpycairo=0.2.0=pyhd8ed1ab_0
+  - rpds-py=0.27.0=py311h1c3fc1a_0
+  - scipy=1.16.1=py311hffedffa_0
+  - send2trash=1.8.3=pyh31c8845_1
+  - setuptools=80.9.0=pyhff2d567_0
+  - six=1.17.0=pyhe01879c_1
+  - sniffio=1.3.1=pyhd8ed1ab_1
+  - soupsieve=2.7=pyhd8ed1ab_0
+  - sqlalchemy=2.0.43=py311h3696347_0
+  - stack_data=0.6.3=pyhd8ed1ab_1
+  - terminado=0.18.1=pyh31c8845_0
+  - tinycss2=1.4.0=pyhd8ed1ab_0
+  - tk=8.6.13=h892fb3f_2
+  - tomli=2.2.1=pyhe01879c_2
+  - tornado=6.5.2=py311h3696347_0
+  - traitlets=5.14.3=pyhd8ed1ab_1
+  - types-python-dateutil=2.9.0.20250809=pyhd8ed1ab_0
+  - typing-extensions=4.14.1=h4440ef1_0
+  - typing_extensions=4.14.1=pyhe01879c_0
+  - typing_utils=0.1.0=pyhd8ed1ab_1
+  - tzdata=2025b=h78e105d_0
+  - unicodedata2=16.0.0=py311h917b07b_0
+  - uri-template=1.3.0=pyhd8ed1ab_1
+  - urllib3=2.5.0=pyhd8ed1ab_0
+  - wcwidth=0.2.13=pyhd8ed1ab_1
+  - webcolors=24.11.1=pyhd8ed1ab_0
+  - webencodings=0.5.1=pyhd8ed1ab_3
+  - websocket-client=1.8.0=pyhd8ed1ab_1
+  - wheel=0.45.1=pyhd8ed1ab_1
+  - widgetsnbextension=4.0.14=pyhd8ed1ab_0
+  - xorg-libxau=1.0.12=h5505292_0
+  - xorg-libxdmcp=1.1.5=hd74edd7_0
+  - yaml=0.2.5=h925e9cb_3
+  - zeromq=4.3.5=hc1bb282_7
+  - zipp=3.23.0=pyhd8ed1ab_0
+  - zstandard=0.23.0=py311h917b07b_2
+  - zstd=1.5.7=h6491c7d_2
+  - pip:
+    - MDAnalysis==2.10.0.dev0
+    - qcarchivetesting==0.62.post11+g5735f6503
+    - qcfractal==0.62.post11+g5735f6503
+    - qcfractalcompute==0.62.post11+g5735f6503
+    - qcportal==0.62.post11+g5735f6503
+    - tmos==1.0.0+33.g2b4f7f8
+
+prefix: "/Users/jenniferclark/mamba/envs/qca-clean"