diff --git a/docs/source/TS_search.rst b/docs/source/TS_search.rst new file mode 100644 index 0000000000..73513c9afb --- /dev/null +++ b/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 diff --git a/docs/source/index.rst b/docs/source/index.rst index e3d6a5518c..3672c4ce40 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -38,6 +38,7 @@ Documentation Contents docker running examples + TS_search advanced output api/index diff --git a/examples/Stationary/TS/input.yml b/examples/Stationary/TS_with_xyz/input.yml similarity index 100% rename from examples/Stationary/TS/input.yml rename to examples/Stationary/TS_with_xyz/input.yml diff --git a/examples/Stationary/hydrolysis_TS/input.yml b/examples/Stationary/hydrolysis_TS/input.yml new file mode 100644 index 0000000000..056d84ce75 --- /dev/null +++ b/examples/Stationary/hydrolysis_TS/input.yml @@ -0,0 +1,72 @@ +# ------------------------------------------------------------ +# 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 +