chemistry-tools

# Chemistry Tools Computational chemistry and cheminformatics. Venv: `source /Users/zhangmingda/clawd/.venv/bin/activate` ## Molecular Properties ```python # Using RDKit if available, otherwise manual calculations from sympy import symbols, Eq, solve # Molecular weight calculation (manual) ATOMIC_WEIGHTS = { 'H': 1.008, 'He': 4.003, 'Li': 6.941, 'Be': 9.012, 'B': 10.81, 'C': 12.011, 'N': 14.007, 'O': 15.999, 'F': 18.998, 'Ne': 20.180, 'Na': 22.990, 'Mg': 24.305, 'Al': 26.982, 'Si': 28.086, 'P': 30.974, 'S': 32.065, 'Cl': 35.453, 'Ar': 39.948, 'K': 39.098, 'Ca': 40.078, 'Fe': 55.845, 'Cu': 63.546, 'Zn': 65.38, 'Br': 79.904, 'Ag': 107.868, 'I': 126.904, 'Au': 196.967, } import re def molecular_weight(formula): """Calculate MW from chemical formula like 'C6H12O6'""" elements = re.findall(r'([A-Z][a-z]?)(\d*)', formula) mw = sum(ATOMIC_WEIGHTS.get(el, 0) * (int(n) if n else 1) for el, n in elements) return mw # Example print(f"Glucose (C6H12O6): {molecular_weight('C6H12O6'):.3f} g/mol") ``` ## Chemical Equation Balancing ```python from sympy import Matrix, lcm def balance_equation(reactants_elements, products_elements): """ Balance using linear algebra (null space method). Each compound is a dict of {element: count}. """ all_elements = set() for compound in reactants_elements + products_elements: all_elements.update(compound.keys()) all_elements = sorted(all_elements) n_compounds = len(reactants_elements) + len(products_elements) matrix = [] for el in all_elements: row = [] for comp in reactants_elements: row.append(comp.get(el, 0)) for comp in products_elements: row.append(-comp.get(el, 0)) matrix.append(row) M = Matrix(matrix) null = M.nullspace() if null: coeffs = null[0] # Make integer coefficients denom = lcm(*[c.q for c in coeffs if hasattr(c, 'q')] or [1]) coeffs = [int(c * denom) for c in coeffs] return coeffs return None ``` ## Thermodynamics ```python import numpy as np # Ideal gas law: PV = nRT R = 8.314 # J/(mol·K) def ideal_gas(P=None, V=None, n=None, T=None): """Solve for the missing variable. Units: Pa, m³, mol, K""" if P is None: return n * R * T / V if V is None: return n * R * T / P if n is None: return P * V / (R * T) if T is None: return P * V / (n * R) # Gibbs free energy def gibbs(dH, T, dS): """ΔG = ΔH - TΔS (kJ/mol, K, kJ/(mol·K))""" return dH - T * dS # Nernst equation def nernst(E0, n_electrons, Q, T=298.15): """E = E° - (RT/nF)ln(Q)""" F = 96485 # C/mol return E0 - (R * T / (n_electrons * F)) * np.log(Q) # Arrhenius equation def arrhenius(A, Ea, T): """k = A * exp(-Ea/RT), Ea in J/mol""" return A * np.exp(-Ea / (R * T)) ``` ## Chemical Databases ### PubChem ```bash # Search by name curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/JSON" | python3 -m json.tool # Search by SMILES curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/CC(=O)OC1=CC=CC=C1C(=O)O/JSON" # Get properties curl -s "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/caffeine/property/MolecularFormula,MolecularWeight,IUPACName/JSON" ``` ### ChEBI (Chemical Entities of Biological Interest) ```bash curl -s "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377" # water ``` ## Spectroscopy Reference | Technique | What it measures | Key info | |-----------|-----------------|----------| | IR | Bond vibrations | Functional groups (cm⁻¹) | | NMR (¹H) | H environments | Chemical shift (δ ppm), splitting | | NMR (¹³C) | C environments | Chemical shift (δ ppm) | | UV-Vis | Electronic transitions | λmax, absorbance | | Mass Spec | m/z ratio | Molecular weight, fragmentation | ### Common IR Absorptions - O-H stretch: 3200-3600 cm⁻¹ (broad) - N-H stretch: 3300-3500 cm⁻¹ - C-H stretch: 2850-3000 cm⁻¹ - C=O stretch: 1650-1750 cm⁻¹ - C=C stretch: 1600-1680 cm⁻¹ - C-O stretch: 1000-1300 cm⁻¹ ## Tips - Always check units (SI vs CGS vs practical) - Use IUPAC nomenclature - For complex reactions, break into elementary steps - Verify thermodynamic data against NIST WebBook - For computational chemistry (DFT, MD), recommend specialized software (Gaussian, ORCA, GROMACS)