Chemistry Layer Reference
Molecules and Bond Diagrams
Bond Legend
Bond notation is structural, not decorative. The legend below is shared across the molecule browser so covalent, ionic, double-bond, protocol, absence, and feedback semantics stay consistent.
Covalent
Solid line · Load-bearing; removing it collapses molecule function.
Double Bond
Parallel solid lines · Primary structural constraint that defines molecule identity.
Ionic
Dashed line · Optional extension; the molecule remains valid with reduced capability.
Protocol Bond
Short dashed connector · Boson-mediated exchange surface for tool, delegation, or human closure.
Absent by Design
Ghosted dashed link · Intentional structural absence that acts as a guarantee, not a missing feature.
Feedback Loop
Curved return path · Adaptive cycle where prior outcomes condition future routing or behavior.
Confirmed Molecules
The stable set currently includes the minimum viable agent, planning agents, memory-augmented retrieval, restartable persistence, and orchestrated delegation.
ReAct Agent
Lm - Wm - Es - (Rt · Wt) [Mc]
Minimum viable agent with a fully load-bearing chain and no optional elements.
Defining Constraint
Every bond is covalent; no optional elements or absent-by-design constraints are present.
Observed Property
Smallest stable agent configuration and the most brittle: every element is a single point of failure.
Implementation Examples
None yet documented.
Working Memory is scoped to active execution only. Each invocation begins with a clean state with no accumulated knowledge from prior tasks.
Plan-and-Execute Agent
Lm - Pm - Lt - Ws= - Ds [Mc]
Separates planning from execution through an identity-defining workflow-state bond.
Defining Constraint
Ws= is the double bond. Removing Workflow State transforms the molecule into a reactive loop rather than degrading the same agent.
Observed Property
Supports step separation, plan tracking, and conditional routing through the Lm=Ws coupling.
Implementation Examples
None yet documented.
Every property that makes this a planning agent lives in the Workflow State coupling, not in the presence of additional tools alone.
Memory-Augmented Agent (RAG)
Lm - Ec - Sm - Wm - (Rt · Em·) - Is [Mc]
Semantic retrieval agent whose memory layer depends on an explicit encoder.
Defining Constraint
Ec is load-bearing. Semantic Memory without an Encoder is storage, not semantic retrieval.
Observed Property
Supports retrieval-grounded reasoning, with Episodic Memory adding optional adaptive behavior through an ionic bond.
Implementation Examples
None yet documented.
Ec was the critical missing element before v0.3. The stress-test showed that embedding cannot be treated as an implementation detail of Semantic Memory.
Persistent Agent
Lm - Ws= - Cp - (Rt · Wt) - Es [Mc]
Long-running execution molecule built to survive process boundaries.
Defining Constraint
Workflow State and Checkpoint State form the defining structural pair; neither is sufficient on its own.
Observed Property
Supports restartable execution with retained position and state continuity after interruption.
Implementation Examples
None yet documented.
Checkpoint State without Workflow State can restart but not resume position. Workflow State without Checkpoint State tracks position but loses it on restart.
Orchestrator
Lm - Ws= - Ds - (Ag1 · Ag2 · Agn·) [Mc][A2][A3]
First multicellular composition with governed delegation and configurable sub-agent sets.
Defining Constraint
A2 is structurally required. Using Mc instead strips sub-agents of intent chain and governance surface.
Observed Property
Supports delegating across a configurable population of sub-agents while preserving authority and human-closure channels.
Implementation Examples
None yet documented.
The distinction between Mc and A2 is structural, not stylistic: tools are invoked, delegates inherit task, authority, and traceable intent.
Predicted Molecules
These entries preserve the predicted frontier from the engineering brief. Where a canonical diagram has not yet been authored, the card remains text-complete and explicitly marked as pending.
Reflexive Agent
Lm - Em - Ds - [Em⟲Ds]
Predicted learning-oriented configuration with a feedback loop between episodic record and decision routing.
Defining Constraint
The Em⟲Ds feedback loop is identity-defining; adaptation emerges from the quality of that loop.
Predicted Property
Each execution adds to Episodic Memory, and each addition shifts future routing behavior through Decision Skill.
Implementation Examples
None yet documented.
The loop also introduces a new failure mode: biased episodic records can recursively bias routing decisions and amplify their own errors.
Stateless Catalyst
Lm - Pm - Lt ∅state
Lowest-mass agent configuration for deterministic transformation with explicit state absence.
Defining Constraint
State elements are absent by design; that absence is the specification, not a temporary omission.
Predicted Property
Produces identical behavior on every invocation with no cross-run dependencies or accumulated side effects.
Implementation Examples
None yet documented.
This pattern fits high-frequency transformation tasks where statelessness is a correctness guarantee rather than a convenience.
Sensory Agent
Lm - Rt - Ss - Is ∅Wt, ∅A2
Purely observational molecule that reads, classifies, and records without mutation or delegation.
Defining Constraint
Write Tool and A2 are absent by design, making non-mutating observation an architectural guarantee.
Predicted Property
Supports monitoring and classification workflows whose non-delegating, non-mutating behavior must be structurally enforced.
Implementation Examples
None yet documented.
Configured restrictions can be removed at runtime. Architectural absence cannot; that distinction is the entire point of the molecule.
Evaluator Agent
Formal notation pending
Predicted evaluation-centric molecule that supplies corrective signal quality for adaptive and reflexive systems.
Predicted Molecule
Diagram in preparation
The Evaluator Agent remains part of the Phase 1 molecule set, but its canonical structural diagram is not yet published. This placeholder preserves the catalogue without presenting a guessed geometry as final.
Defining Constraint
Final structural notation and bond geometry are still being authored; the role is known, the canonical diagram is not yet published.
Predicted Property
Expected to generate the corrective signal that keeps episodic feedback loops aligned rather than self-reinforcing error.
Implementation Examples
None yet documented.
Diagram in preparation. This entry remains in Phase 1 so the predicted set matches the engineering brief without presenting a guessed structure as final.
Chemistry References
Reference samples stay separate from the agent catalogue so the molecule browser can show both stable molecules and structural proofs without conflating them.
Tool Molecule Completeness Sample
Rt+Ex · Wt+Db · Lt+Ce · Ct+Cp+Ex+Rt
Reference sample showing that tools reduce to action archetypes bonded with infrastructure substrates.
The four action archetypes (Rt, Wt, Lt, Ct) over the four infrastructure substrates (Ce, Fs, Db, Ex) form a closed space. No tool requires an element outside the table.