majiayu000 name: molecular-qchem description: Molecular Quantum Chemistry (1 sub-skills: gaussian-qchem-workflow)
Molecular Quantum Chemistry
Quantum chemistry calculations for molecules and molecular clusters (non-periodic systems). This skill group covers geometry optimization, vibrational analysis, thermochemistry, solvation, excited states, and reaction energetics using open-source quantum chemistry engines (PySCF, Psi4) that can be installed via pip/conda. Inspired by the atomate2 Q-Chem module but adapted for the open-source tools available in MatClaw's container environment.
Unlike the periodic electronic-structure skills (which target crystals with Quantum ESPRESSO), this group targets isolated molecules, molecular complexes, and cluster models where Gaussian-type orbital (GTO) basis sets are natural and efficient.
Sub-Skills
| Sub-Skill | Directory | Description |
|---|---|---|
| Molecular QChem Workflows | gaussian-qchem-workflow/ |
Complete workflows for geometry optimization + frequency, solvation energy, reaction profiles, and excited-state (TD-DFT) calculations using PySCF |
Method Decision Guide
What kind of system are you studying?
Periodic crystal or slab?
--> Use electronic-structure/ skills (Quantum ESPRESSO / MACE)
Isolated molecule, molecular cluster, or reaction?
--> This skill group (molecular-qchem/)
What property do you need?
Optimized geometry + thermochemistry (ZPE, H, G)?
--> gaussian-qchem-workflow/ : Workflow 1
Solvation free energy (gas vs solution)?
--> gaussian-qchem-workflow/ : Workflow 2
Reaction energy or barrier (A + B -> C)?
--> gaussian-qchem-workflow/ : Workflow 3
UV-Vis absorption spectrum / excited states?
--> gaussian-qchem-workflow/ : Workflow 4
What level of theory?
Quick screening or large molecule (> 50 atoms)?
--> DFT: B3LYP/def2-SVP or PBE0/def2-SVP
Accurate thermochemistry (small molecule, < 20 atoms)?
--> MP2/cc-pVTZ or CCSD(T)/cc-pVTZ (single-point on DFT geometry)
Organic reaction energetics?
--> B3LYP-D3/def2-TZVP (DFT with dispersion)
Transition metal complex?
--> PBE0/def2-SVP or B3LYP/def2-SVP with ECPs (automatic in def2 basis)
Common Prerequisites
- PySCF:
pip install pyscf-- the primary quantum chemistry engine used in all workflows. - geomeTRIC:
pip install geometric-- geometry optimizer that interfaces with PySCF. - RDKit (optional):
pip install rdkit-- for building molecules from SMILES strings. - ASE (optional): pre-installed in container -- for reading/writing molecular structures in various formats.
- NumPy / SciPy / matplotlib: pre-installed -- for post-processing and plotting.