OHMind-ORCA MCP Server

Quantum chemistry tools for DFT calculations, geometry optimization, and property predictions using ORCA.

Overview
Server Configuration
Tools Reference
Usage Examples
Results Format
Troubleshooting
See Also

Overview

The OHMind-ORCA MCP server provides 10 tools for quantum chemistry calculations using ORCA. It handles structure preparation, DFT calculations, geometry optimization, and various property predictions relevant to HEM design.

Server Details

Property	Value
Server Name	`OHMind-ORCA`
Entry Point	`python -m OHMind_agent.MCP.ORCA.server`
Tool Count	10
Dependencies	ORCA, RDKit, cclib

Capabilities

SMILES to 3D coordinate conversion
Single point energy calculations
Geometry optimization
Frequency calculations and thermochemistry
Proton affinity and pKa estimation
Binding energy calculations
Charge analysis (Mulliken, Löwdin, Hirshfeld)
NMR chemical shift prediction
Transition state search

Server Configuration

Starting the Server

# stdio transport (default)
python -m OHMind_agent.MCP.ORCA.server --transport stdio

# HTTP transport
python -m OHMind_agent.MCP.ORCA.server --transport streamable-http --port 8103

Environment Variables

Variable	Purpose	Required
`PYTHONPATH`	Path to OHMind project	Yes
`OHMind_ORCA`	Path to ORCA binary	Yes
`OHMind_MPI`	Path to MPI binaries	For parallel
`QM_WORK_DIR`	Working directory	Yes

mcp.json Configuration

{
  "OHMind-ORCA": {
    "command": "python",
    "args": ["-m", "OHMind_agent.MCP.ORCA.server", "--transport", "stdio"],
    "env": {
      "PYTHONPATH": "/path/to/OHMind",
      "OHMind_ORCA": "/path/to/orca",
      "OHMind_MPI": "/usr/local/bin",
      "QM_WORK_DIR": "/OHMind_workspace/ORCA"
    }
  }
}

Tools Reference

Structure Preparation

`SmilesToXYZ`

Convert SMILES to 3D XYZ coordinates using RDKit.

Parameters:

Name	Type	Required	Description
`smiles`	string	Yes	Input SMILES string

Returns: XYZ coordinate string

Note: Always use this tool first before running calculations.

Example:

{
  "smiles": "C[N+]1(C)CCCCC1"
}

Core Calculation Tools

`SinglePointEnergy`

Single-point energy calculation at fixed geometry.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	XYZ coordinates
`method`	string	No	DFT functional (default: `B3LYP`)
`basis`	string	No	Basis set (default: `def2-SVP`)
`dispersion`	string	No	Dispersion correction (default: `D3BJ`)

Returns: Energy in Hartree, output file paths

Available Methods:

B3LYP - Hybrid functional (default)
PBE0 - Hybrid functional
M06-2X - Minnesota functional
wB97X-D3 - Range-separated with dispersion

Available Basis Sets:

def2-SVP - Double-zeta (default, fast)
def2-TZVP - Triple-zeta (accurate)
def2-QZVP - Quadruple-zeta (very accurate)

`GeometryOptimization`

⚠️ EXPENSIVE OPERATION - Requires user approval

Optimize molecular geometry to find minimum energy structure.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	Initial XYZ coordinates
`method`	string	No	DFT functional
`basis`	string	No	Basis set
`dispersion`	string	No	Dispersion correction

Returns: Optimized coordinates, final energy, results directory

Estimated Time: 5-30 minutes

`FrequencyCalculation`

⚠️ EXPENSIVE OPERATION - Requires user approval

Vibrational frequency calculation for thermochemistry.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	XYZ coordinates (should be optimized)
`method`	string	No	DFT functional
`basis`	string	No	Basis set
`temperature`	float	No	Temperature in K (default: 298.15)

Returns: Frequencies, IR spectrum, thermochemistry, Gibbs free energy

Estimated Time: 5-30 minutes

IEM-Focused Tools

`ProtonAffinityCalculation`

Proton affinity and approximate pKa for acidic groups.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	XYZ coordinates
`acidic_site`	integer	Yes	Atom index of acidic proton
`solvent`	string	No	Solvent for implicit solvation

Returns: Gas-phase and solution-phase proton affinity, estimated pKa

`BindingEnergyCalculation`

Ion-functional group binding energies.

Parameters:

Name	Type	Required	Description
`complex_xyz`	string	Yes	Ion-molecule complex coordinates
`ion_xyz`	string	Yes	Isolated ion coordinates
`molecule_xyz`	string	Yes	Isolated molecule coordinates
`bsse_correction`	boolean	No	Apply BSSE correction
`solvent`	string	No	Implicit solvation

Returns: Binding energy with/without corrections

`IonicSolvationEnergy`

Solvation/hydration energies for ions.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	Ion or ion-water cluster coordinates
`charge`	integer	Yes	Total charge
`solvent`	string	Yes	Solvent model

Returns: Solvation energy and free energy

`ChargeAnalysis`

Calculate atomic charges using various methods.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	XYZ coordinates
`methods`	array	No	Charge methods (default: all)

Available Methods:

mulliken - Mulliken population analysis
loewdin - Löwdin population analysis
hirshfeld - Hirshfeld charges

Returns: Charges per atom, dipole/quadrupole moments

`TransitionStateSearch`

⚠️ EXPENSIVE OPERATION - Requires user approval

Transition state search with optional frequency verification.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	Initial TS guess coordinates
`method`	string	No	DFT functional
`verify_frequencies`	boolean	No	Run frequency calculation to verify

Returns: TS geometry, activation energy, imaginary frequency

`NMRChemicalShift`

⚠️ EXPENSIVE OPERATION - Requires user approval

NMR shielding and chemical shifts.

Parameters:

Name	Type	Required	Description
`xyz_string`	string	Yes	XYZ coordinates
`nuclei`	array	No	Nuclei to calculate
`reference`	string	No	Reference compound

Available Nuclei:

1H - Proton
13C - Carbon-13
19F - Fluorine-19
31P - Phosphorus-31

Returns: Chemical shifts for selected nuclei

Usage Examples

End-to-End QM Descriptor Pipeline

Using your OHMind-ORCA QM tools, start from the SMILES `C[N+]1(C)CCCCC1` and:

1) Convert to a reasonable 3D geometry.
2) Optimize the structure at B3LYP/def2-SVP with D3BJ.
3) Compute frequencies to confirm there are no imaginary modes.
4) Report LUMO energy and any descriptors relevant to alkaline stability, 
   and interpret them qualitatively.

Proton Affinity and pKa Estimation

For a sulfonic-acid-containing fragment, use your proton affinity tool to 
estimate gas-phase and solution-phase proton affinity and the corresponding pKa.

Explain what these values imply for acid strength and membrane behavior.

Binding and Solvation Comparison

Compare the binding energy and hydration energy of OH⁻ vs Cl⁻ to a model 
quaternary ammonium site using your ORCA binding and solvation tools.

Summarize which ion binds more strongly and how solvation competes with binding.

Simple Single Point Calculation

Calculate the single point energy for this cation: C[N+]1(C)CCCCC1
Use B3LYP/def2-SVP with D3BJ dispersion correction.

Results Format

Output Directory Structure

QM results are saved to $QM_WORK_DIR/:

$QM_WORK_DIR/
├── temp_<timestamp>/     # Per-job temporary directories
│   ├── input.inp         # ORCA input file
│   ├── input.out         # ORCA output file
│   ├── input.gbw         # Wavefunction file
│   ├── input.xyz         # Final geometry
│   └── input.hess        # Hessian (for frequencies)
└── results/              # Preserved results

Output File Contents

File	Contents
`input.inp`	ORCA input with method, basis, coordinates
`input.out`	Full ORCA output with energies, properties
`input.gbw`	Binary wavefunction for Multiwfn analysis
`input.xyz`	Optimized geometry (if optimization)

Energy Units

Property	Unit
Total energy	Hartree
Binding energy	kcal/mol
Proton affinity	kcal/mol
Frequencies	cm⁻¹
Gibbs free energy	Hartree

Troubleshooting

Common Issues

ORCA Not Found

Error: ORCA executable not found

Solution: Set the ORCA path:

export OHMind_ORCA=/path/to/orca

MPI Not Available

Warning: MPI not found, running in serial mode

Solution: Set MPI path for parallel calculations:

export OHMind_MPI=/usr/local/bin

Calculation Failed

Error: ORCA calculation failed

Solutions:

Check input.out for error messages
Verify input geometry is reasonable
Try a smaller basis set
Check disk space in QM_WORK_DIR

Memory Error

Error: Not enough memory

Solution: Reduce basis set size or molecule size. ORCA memory is controlled in the input file.

Expensive Operations

The following tools require validation before execution:

Tool	Estimated Time
`GeometryOptimization`	5-30 minutes
`FrequencyCalculation`	5-30 minutes
`NMRChemicalShift`	10-60 minutes
`TransitionStateSearch`	15-60 minutes

Debug Mode

Run the server with verbose logging:

PYTHONPATH=/path/to/OHMind \
  OHMind_ORCA=/path/to/orca \
  QM_WORK_DIR=/OHMind_workspace/ORCA \
  python -m OHMind_agent.MCP.ORCA.server --transport stdio 2>&1 | tee orca_debug.log

OHMind-ORCA MCP Server

Table of Contents

Overview

Server Details

Capabilities

Server Configuration

Starting the Server

Environment Variables

mcp.json Configuration

Tools Reference

Structure Preparation

SmilesToXYZ

Core Calculation Tools

SinglePointEnergy

GeometryOptimization

FrequencyCalculation

IEM-Focused Tools

ProtonAffinityCalculation

BindingEnergyCalculation

IonicSolvationEnergy

ChargeAnalysis

TransitionStateSearch

NMRChemicalShift

Usage Examples

End-to-End QM Descriptor Pipeline

Proton Affinity and pKa Estimation

Binding and Solvation Comparison

Simple Single Point Calculation

Results Format

Output Directory Structure

Output File Contents

Energy Units

Troubleshooting

Common Issues

ORCA Not Found

MPI Not Available

Calculation Failed

Memory Error

Expensive Operations

Debug Mode

See Also

`SmilesToXYZ`

`SinglePointEnergy`

`GeometryOptimization`

`FrequencyCalculation`

`ProtonAffinityCalculation`

`BindingEnergyCalculation`

`IonicSolvationEnergy`

`ChargeAnalysis`

`TransitionStateSearch`

`NMRChemicalShift`