Mol Orb Reactivity Proposal Reaction Mixture Mol Orb Enumerator Molecular Orbital List Reduced Mol Orb List Stopping Criteria Analyzer Mol Orb Compatibility Scoring Revised Reaction Mixture Scored Orbital Compatibility List Reactor Iterator ReactionSimulator.runSimulation

Reaction Mixture 100 100 10 Reaction Conditions Solvent Properties Temperature ReactionSimulator.ReactionMixture

Orbital Enumerator Largely done for core atoms, but need extra logic to handle S,P atoms (d orbitals) Resonance structure enumerator Extended orbital chaining (e.g., E2, Sn2’) Orbital Reactivity Proposal Before full combinatorial reactivity compatibility check, pre-filter orbital list to exclude those are very unlikely to react OrbitalModel.orbitalIter OrbitalScore.OrbitalReactivityProbability

Molecular Orbital List Filled sp2 O p CO … Unfilled p* CO s* HC  p* CO Filled sp3 O s CO … Unfilled s* HO s* CO Filled sp3 O sp2 O … Unfilled p* SO s* HO  p* SO

Orbital Reactivity / Compatibility Core challenge (rest is mostly accounting) Thermodynamic Scoring Relative energy / stability of structures Reaction conditions may influence (particularly stabilization of ions by solvation) Components like bond energies, ring strain, entropy, aromaticity, conjugation and resonance, hyperconjugation, formal charges, octet rule ReactionScore.FreeEnergy

Orbital Reactivity / Compatibility Kinetics / Transition State Scoring Estimated barrier to structures to react based on proposed orbital interaction Thermodynamic basis + Klopman-Salem components like sterics, ionic character vs. orbital coefficients (HOMO-LUMO energies) Entropy considerations (number of molecules, rotatable bonds) OrbitalScore.TransitionStateEnergy

Scored Orbital Compatibility List sp2 O (reactant 1)  s* HO (reactant 3) ~ 2 kcal / mol sp3 O (reactant 2)  s* HO (reactant 3) ~ 3 kcal / mol …

Reactor Iterator Orbital Interaction Applicator Mostly done for core orbital interactions Generate / translate to curved arrows Need to implement stereospecificity logic Concentration / Prevalence model Use reactivity scores x concentrations to calculate probabilities on likely mechanistic steps (elementary reactions) Apply mechanistic steps to update reaction mix, but limit achievable transition states by reaction temperature ??? ReactionSimulator

Revised Reaction Mixture 97 94 1 3 6 9

GUI Input of reaction mixtures Output of resulting reaction mixtures Traceback of core mechanistic steps of major products Qualitative free energy diagrams from tracebacks Interactive exploration / explanation. Select mixtures or orbital combinations to see systems score report Systems bio style tracking of molecule concentrations over time (iterations) ??? Separate from reaction directory? Leave that for tutorial material?

Proposed Reaction Predictor Proposes complete arrow-pushing mechanisms, Including reaction intermediates and Electron flow schematics Qualitative reaction energy coordinate diagrams Benchmark: Solve problems that human experts can on paper Relative Energy DG‡ DG Reaction Coordinate +