nx_chem_isotope_pattern.nx

nx_chem_isotope_pattern.nx -- C2.8b milestone: isotopologue M+1/M+2 peak intensity prediction. MS adulterant identification relies on more than exact mass: the natural-abundance isotopologue pattern (M, M+1, M+2 peaks) is a fingerprint of elemental composition. Famous halogen signatures: * Cl in molecule -> M:M+2 ratio approximately 3:1 (75.78% : 24.22%) * Br in molecule -> M:M+2 ratio approximately 1:1 (50.69% : 49.31%) * No Cl/Br -> M+2 small (sub-1% per atom) Sulfur has notable M+2 contribution (~4.5% per S; from 34-S). Carbon has notable M+1 contribution (~1.08% per C; from 13-C). Approach: first-order linear approximation -- each atom contributes its single-substitution probability to M+1 / M+2. Accurate for 0-1 of each halogen + low atom counts; overestimates for multiple halogens (binomial expansion needed; deferred to C2.8b.1). Returns Q4 fraction of M-peak intensity (10000 = 100% of M, so e.g., ethanol M+1 = 232 means M+1 is 2.32% the height of M). Constants pinned (IUPAC 2021 isotopic compositions): ¹H 99.985%, ²H 0.015% ¹²C 98.93%, ¹³C 1.07% ¹⁴N 99.636%, ¹⁵N 0.364% ¹⁶O 99.757%, ¹⁷O 0.038%, ¹⁸O 0.205% ³²S 94.99%, ³³S 0.75%, ³⁴S 4.25% ³⁵Cl 75.78%, ³⁷Cl 24.22% ⁷⁹Br 50.69%, ⁸¹Br 49.31% (¹⁹F, ³¹P, ¹²⁷I monoisotopic -- contribute 0 to M+1/M+2) Honest gaps (deferred): - Multi-halogen binomial expansion: a molecule with 4 Cl atoms gives M+2 = 4 * (37Cl/35Cl) * (35Cl/35Cl)^3 = 4 * 0.3196 = 128% by first-order, but binomial says 4 * 0.3196 * (1 - 0.2422)^3 = ~32% normalized. C2.8b.1 will ship binomial. - M+3, M+4 peaks: relevant for Cl2, Br2, mixed halogen species. C2.8b.2.