neb-ts

name	neb_ts
description	ORCA NEB-TS transition state search. Requires reactant and product structures. Handles NEB parameters, image count, and CI-NEB settings.

ORCA NEB-TS Transition State Skill

When to Use

Use this skill when the user wants to:

• Find a transition state between two structures
• Calculate a reaction barrier
• Map a minimum energy path (MEP) between reactant and product

Requirements: the user MUST provide both a reactant and a product structure. If only one structure is available, ask for the other before proceeding.

How NEB-TS Works

1. ORCA interpolates images between reactant and product geometries
2. NEB optimization finds the minimum energy path
3. Climbing-image NEB (CI-NEB) refines the highest-energy image
4. The TS is characterized by exactly one imaginary frequency

MCP Tool Examples

Step 1: Load reactant structure

catgo_fetch(action: "molecule", query: "reactant_name")

Or if the user provides a file:

catgo_structure(action: "load_file", file_content: "<xyz content>", file_format: "xyz")

Save the reactant -- get its structure from the viewer:

catgo_view(action: "get_state")

Step 2: Create NEB-TS workflow

catgo_workflow_engine(action: "create", params: {
  name: "SN2 reaction TS search"
})

Step 3: Add NEB-TS task

The orca_neb_ts node type requires both reactant and product structures provided as inputs. In the v2 engine, these come from upstream structure_input tasks:

catgo_workflow_engine(action: "add_task", params: {
  workflow_id: "<wf_id>",
  task_type: "orca_neb_ts",
  params: {
    software: "orca",
    orca_method: "B3LYP",
    orca_basis: "def2-SVP",
    charge: 0,
    multiplicity: 1,
    neb_images: 8,
    neb_convergence: "normal"
  }
})

Using the v1 workflow with explicit structures

In the graph-based workflow (v1), use the catgo_workflow tool:

catgo_workflow(action: "create", name: "NEB-TS Cl- + CH3Br")

catgo_workflow(action: "batch", workflow_id: "<wf_id>", operations: [
  {"op": "add_node", "node_type": "structure_input", "label": "reactant"},
  {"op": "add_node", "node_type": "structure_input", "label": "product"},
  {"op": "add_node", "node_type": "orca_neb_ts", "label": "neb",
   "params": {
     "orca_method": "B3LYP",
     "orca_basis": 
      
      
      
   
       
      
       
      
)

Step 4: Submit and monitor

catgo_workflow_engine(action: "submit", params: { workflow_id: "<wf_id>" })

catgo_workflow_engine(action: "status", params: { workflow_id: "<wf_id>" })

Step 5: Verify the TS

After NEB-TS completes, run a frequency calculation on the TS geometry to confirm exactly one imaginary frequency:

catgo_workflow_engine(action: "add_task", params: {
  workflow_id: "<wf_id>",
  task_type: "freq",
  depends_on: ["<neb_task_id>"],
  params: {
    software: "orca",
    orca_method: "B3LYP",
    orca_basis: "def2-SVP",
    charge: 0,
    multiplicity: 1
  }
})

A valid TS has exactly one imaginary frequency (negative value). If there are zero or more than one, the TS search failed.

NEB Parameters

Parameter	Default	Description
neb_images	8	Number of interpolated images
neb_convergence	"normal"	Convergence: "loose", "normal", "tight"
orca_extra_keywords	""	Additional keywords (e.g., "D3BJ")

Image count guidelines

System size	Recommended images
Small molecule (<15 atoms)	6-8
Medium molecule (15-50 atoms)	8-12
Large molecule (>50 atoms)	12-16

More images = smoother path but higher cost (each image is a full DFT calc).

Common Reaction Types

SN2 reaction

• Charge: -1 (incoming nucleophile)
• Check that leaving group bond elongates along path

Bond dissociation / formation

• Usually neutral, singlet
• Consider if radical pathway needs multiplicity: 3 (triplet)

Proton transfer

• Include dispersion: orca_extra_keywords: "D3BJ"
• Consider solvent: orca_extra_keywords: "D3BJ CPCM(Water)"

Troubleshooting

NEB does not converge

• Increase neb_images (more interpolation points)
• Use a better starting path (optimize reactant and product first)
• Try neb_convergence: "loose" for initial run, then tighten

Wrong TS found

• Check the imaginary frequency mode -- does it correspond to the expected bond breaking/forming?
• Try different initial interpolation (reorder atoms so they correspond)

Too expensive

• Screen with HF-3c or orca_method: "PBE", orca_basis: "def2-SVP" first
• Refine with better method only on the TS geometry (single-point)

Important Notes

• Reactant and product MUST have the same atoms in the same order
• Both structures should be pre-optimized at the same level of theory
• ORCA NEB-TS automatically switches to CI-NEB after initial convergence
• The barrier height is the energy difference between the TS and the reactant