mims-harvard/tooluniverse-inorganic-physical-chemistry
plugin/skills/tooluniverse-inorganic-physical-chemistry/SKILL.md
Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, lattice parameters, thermodynamic properties, electronic structure. Use for unit cell volume calculations, coordination geometry, materials property estimation, and inorganic-mechanism reasoning. Complementary to tooluniverse-organic-chemistry.
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SKILL.md
- name:
- tooluniverse-inorganic-physical-chemistry
- description:
- Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, lattice parameters, thermodynamic properties, electronic structure. Use for unit cell volume calculations, coordination geometry, materials property estimation, and inorganic-mechanism reasoning. Complementary to tooluniverse-organic-chemistry.
- disable-model-invocation:
- true
Inorganic & Physical Chemistry
Reasoning Strategy
1. Crystal Structure Questions
When given crystal structure data, always COMPUTE don't guess:
-
Calculate unit cell volume for the crystal system:
- Cubic: V = a^3
- Tetragonal: V = a^2 * c
- Orthorhombic: V = a * b * c
- Monoclinic: V = a * b * c * sin(beta)
- Triclinic: V = abc * sqrt(1 - cos^2(alpha) - cos^2(beta) - cos^2(gamma) + 2*cos(alpha)*cos(beta)*cos(gamma))
- Hexagonal: V = a^2 * c * sqrt(3)/2
-
Verify density: d = (Z * M) / (V * Na * 1e-24) where V in ų, M in g/mol, Na = 6.022e23
-
Preferred: Use
CrystalStructure_validatetool (via MCP/SDK). Fallback:python3 skills/tooluniverse-organic-chemistry/scripts/crystal_validator.py --a X --b Y --c Z --alpha A --beta B --gamma G --Z N --MW M --density D -
For batch comparison (find the wrong dataset): Save datasets as JSON array and use
--datasets path/to/datasets.json
2. Bonding & Covalency Questions
Key reasoning patterns:
- Covalency = orbital mixing between metal and ligand. Greater overlap = more covalent.
- Lanthanide/actinide: 4f orbitals of Ce(IV) typically show ENHANCED covalent mixing vs Ce(III) — more contracted 4f in higher oxidation states increases overlap with ligand orbitals
- But: Enhanced covalency does NOT always mean stronger bonds — it depends on the specific orbital interactions
- d-block vs f-block: d-orbitals have more radial extension → stronger covalent bonds than f-orbitals
- Nephelauxetic effect: Reduced electron-electron repulsion in complexes → indicates covalency. Larger effect = more covalent.
3. Noble Gas Chemistry
- Xe compounds: XeF2 (linear), XeF4 (square planar), XeF6 (distorted octahedral)
- XeF4 synthesis: Requires Xe + F2 at elevated temperature (400°C) and pressure. Can also form at lower temperatures with specific methods (UV photolysis, electric discharge)
- Key: Temperature thresholds matter for synthesis efficiency. LOOK UP DON'T GUESS — search literature for specific synthesis conditions.
4. Symmetry & Point Groups
- Identify the molecular shape
- Find symmetry elements: C_n axes, mirror planes (σ_h, σ_v, σ_d), inversion center (i), improper rotation (S_n)
- Use
python3 skills/tooluniverse-organic-chemistry/scripts/chemistry_facts.py point_groupsfor point group lookup - Optical activity: Requires absence of improper rotation axes (S_n, including σ = S_1 and i = S_2). Chiral point groups: C_1, C_n, D_n, T, O, I
- Crystal classes with optical activity: Piezoelectric non-centrosymmetric classes that lack mirror planes and inversion
5. Thermodynamics & Kinetics
COMPUTE DON'T ESTIMATE — write Python code for:
- Gibbs free energy: ΔG = ΔH - TΔS
- Equilibrium constant: K = exp(-ΔG/RT)
- Arrhenius equation: k = A * exp(-Ea/RT)
- Nernst equation: E = E° - (RT/nF) * ln(Q)
- Clausius-Clapeyron: ln(P2/P1) = -ΔH_vap/R * (1/T2 - 1/T1)
6. Solubility & Equilibrium Calculations
Preferred: Use EquilibriumSolver_calculate tool (via MCP/SDK) with type, ksp, stoich, and other parameters. Fallback: run equilibrium_solver.py directly.
# Simple Ksp: MaXb(s) <-> aM + bX
python3 skills/tooluniverse-inorganic-physical-chemistry/scripts/equilibrium_solver.py \
--type ksp_simple --ksp 5.3e-27 --stoich 1:3
# Ksp + complex formation (e.g., Al(OH)3 in water with Al(OH)4- complex)
python3 skills/tooluniverse-inorganic-physical-chemistry/scripts/equilibrium_solver.py \
--type ksp_kf --ksp 5.3e-27 --kf 1.1e33 --stoich 1:3
# Common ion effect (e.g., AgCl in 0.1M NaCl)
python3 skills/tooluniverse-inorganic-physical-chemistry/scripts/equilibrium_solver.py \
--type common_ion --ksp 1.77e-10 --stoich 1:1 --common-ion 0.1
Key points:
ksp_kfmode solves the full charge-balance system numerically (Newton's method) — accounts for free cation, complex anion, and OH-/H+ simultaneously- For
MX_b + X- <-> MX_(b+1)-, K_overall = Ksp * Kf common_ionmode uses bisection to solve the exact Ksp expression with extra ion concentration- Always specify
--stoich a:bmatching the salt formula (e.g., 1:3 for Al(OH)3, 1:2 for CaF2, 1:1 for AgCl)
7. Spectroscopy Interpretation
- UV-Vis: d-d transitions (weak, Laporte forbidden), LMCT/MLCT (strong), π→π* (organic)
- IR: Functional group region (4000-1500 cm⁻¹), fingerprint (1500-400 cm⁻¹)
- NMR: Chemical shift indicates electronic environment. For counting peaks, identify symmetry-equivalent protons.
- For peak counting: Draw the structure, identify all symmetry operations, group equivalent H atoms. Use
python3 skills/tooluniverse-organic-chemistry/scripts/chemistry_facts.pyfor reference data.
Available Tools
| Tool | Use For |
|------|---------|
| PubChem_get_CID_by_compound_name | Get compound CID from name |
| PubChem_get_compound_properties_by_CID | Detailed compound data by CID |
| ChEMBL_search_molecules | Bioactive compounds |
| PubMed_search_articles | Literature on synthesis conditions, properties |
| CrystalStructure_validate tool (or crystal_validator.py fallback) | Verify crystal structure data consistency |
| EquilibriumSolver_calculate tool (or equilibrium_solver.py fallback) | Ksp, complex formation, common-ion solubility |
LOOK UP DON'T GUESS
- Noble gas compound synthesis conditions vary by method — search literature before answering
- Crystal structure parameters must be computed, not estimated
- Bonding descriptions (covalent vs ionic) require specific orbital considerations — don't generalize from one system to another
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