Add hydrolysis TS adapter example input and documentation

docs/source/TS_search.rst

@@ -0,0 +1,57 @@
+.. _TS_search:
+
+Transition State Search
+=======================
+
+ARC can automatically search for and validate transition states (TSs) for selected reaction types.
+This section describes currently supported TS-search workflows and how to use them through ARC input files.
+
+Neutral hydrolysis TS search
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+ARC supports automated TS generation and validation for **neutral hydrolysis reactions**.
+This capability is designed to start from a high-level reaction definition (e.g., SMILES-defined reactants/products)
+and proceed through TS generation, optimization, and validation without requiring manual TS construction.
+
+Supported sub-families
+""""""""""""""""""""""
+The current implementation supports the following neutral hydrolysis sub-families:
+
+- Ester hydrolysis
+- Amide hydrolysis
+- Acyl halide hydrolysis
+- Ether hydrolysis
+- Nitrile hydrolysis
+
+How it is used
+""""""""""""""
+To run neutral hydrolysis TS search, define the reacting species and the overall reaction in the input file
+(see ARC's examples folder for an input file that executes a neutral hydrolysis TS search).
+At minimum, specify:
+
+- The participating species (e.g., SMILES, xyz, InChI, or adjacency list)
+- A reaction string connecting the species labels (e.g., ``A + H2O <=> products``)
+- The TS generation adapter(s) under ``ts_adapters`` (in this case, use: ``['heuristics']``)
+- The electronic structure levels used for optimization/validation (e.g., ``opt_level``, ``freq_level``, ``irc_level``)
+
+What ARC does
+""""""""""""""""""""""""""
+For neutral hydrolysis reactions, ARC performs the following general steps:
+
+1. Identify the relevant reactive atoms based on the reaction family definition.
+2. Generate one or more chemically reasonable TS guesses for the hydrolysis transformation.
+3. Optimize the TS candidates that passes internal filtration.
+4. Validate the TS using vibrational frequency and IRC calculations.
+
+Outputs and validation
+""""""""""""""""""""""
+Validated TS results are reported in the project output (log files and generated artifacts),
+together with the supporting calculations (optimization, frequency, and IRC).
+
+Reference
+"""""""""
+A detailed description of the methodology, design choices, and validation benchmarks is provided in:
+L. Fahoum, A. Grinberg Dana, *“Automated Reaction Transition State Search for Neutral Hydrolysis Reactions”*,
+Digital Discovery, 2026.
+
+.. include:: links.txt

docs/source/index.rst

@@ -38,6 +38,7 @@ Documentation Contents
    docker
    running
    examples
+   TS_search
    advanced
    output
    api/index

examples/Stationary/hydrolysis_TS/input.yml

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+# ------------------------------------------------------------
+# Example input file for automated transition-state search
+# of a neutral hydrolysis reaction.
+#
+# This example illustrates how to specify electronic structure
+# levels, molecular species, requested job types, and a reaction
+# definition for automated TS generation and validation.
+#
+# Species may be defined using SMILES, xyz coordinates, InChI
+# strings, or adjacency lists.
+# ------------------------------------------------------------
+
+project: hydrolysis_TS
+
+opt_level:
+  method: wb97xd
+  basis: jul-cc-pVTZ
+  solvation_method: smd
+  solvent: water
+
+freq_level:
+  method: wb97xd
+  basis: jul-cc-pVTZ
+  solvation_method: smd
+  solvent: water
+
+scan_level:
+  method: wb97xd
+  basis: jul-cc-pVTZ
+  solvation_method: smd
+  solvent: water
+
+irc_level:
+  method: wb97xd
+  basis: jul-cc-pVTZ
+  solvation_method: smd
+  solvent: water
+
+sp_level:
+  method: wb97xd
+  basis: jul-cc-pVTZ
+  solvation_method: smd
+  solvent: water
+
+ts_adapters: ['heuristics']
+freq_scale_factor: 1.0
+compute_thermo: false
+
+species:
+  - label: reactant
+    smiles: ClCC(=O)OC
+
+  - label: H2O
+    smiles: O
+
+  - label: ClCC(=O)O
+    smiles: ClCC(=O)O
+
+  - label: CO
+    smiles: CO
+
+job_types:
+  rotors: false
+  sp: true
+  opt: true
+  fine: true
+  freq: true
+  irc: true
+
+reactions:
+  - label: reactant + H2O <=> ClCC(=O)O + CO
+