Topological Scission of the Chrysene Abiotic Loom: Dual Mastering, Structural Scaffolding, Sequential Catalytic Connectivity, and PCET-Enabled Prototype Enzyme Formation

Abstract

Papers 1 - 3 (Schaper, C. D. (2026). The Abiotic Loom: Discrete Morse Theory and the Geometric Resolution of Levinthal’s Paradox in the Chrysene Tensor Space. Annals of the Chrysene Formalism, 1(1), 273--282.  https://chrysene.com/index.php/acf/article/view/23, Schaper, C. D. (2026). Geometric Validation of the Abiotic Loom: Discrete Morse Predictions versus PDB Secondary-Structure Statistics and Ramachandran Densities. Annals of the Chrysene Formalism, 1(1), 283--291.  https://chrysene.com/index.php/acf/article/view/24, Schaper, C. D. (2026). Higher-Order Geometry of the Abiotic Loom: Axis Alignment, Pore Tethering, and Side-Chain Packing of Secondary-Structure Elements in the Chrysene Tensor Space. Annals of the Chrysene Formalism, 1(1), 292--304.  https://chrysene.com/index.php/acf/article/view/25) established that the Chrysene abiotic loom selects secondary-structure geometries, concentrates them in high-resolution public structures, and accommodates their three-dimensional shape, orientation and side-chain packing. The present paper extends the validated lattice into a multi-layer geometric and synthetic compiler. Controlled topological scission simultaneously generates residual voids and liberated fragments that function as dual catalytic masters, while the un-excised towers and rails remain as a rigid residual scaffold that holds every master in absolute spatial register. Successive masters may be placed so that the exit geometry of one coincides with the entrance geometry of the next, realizing metabolon-style sequential connectivity. The residual scaffold preserves the original proton-coupled electron transfer tethers; acting jointly with a scaffold-registered master, those tethers drive cooperative peptide-bond synthesis of a polypeptide conformal to the master. The assembled prototype enzyme is entropically stabilized relative to the disassembled state under aqueous conditions. The constructions are illustrated on segments of the glycolytic pathway (PFK-1 / isomerase) and the G6P-NADPH pathway. The prototype remains a geometric and covalent object only; its genetic tagging and replicative integration are deferred to a future paper. Continuous thermal fluctuations remain fully admissible inside the open cells of the residual lattice; the lattice walls and residual tethers supply absolute spatial and chemical bounds.