OHMind-ORCA MCP Server

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

Table of Contents

• 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:

1. Check input.out for error messages
2. Verify input geometry is reasonable
3. Try a smaller basis set
4. 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

See Also

• MCP Server Reference - Overview of all servers
• QM Agent - Agent documentation
• Multiwfn Server - For result analysis
• QM Calculations Tutorial - Step-by-step guide
• OHQM Module - QM utilities

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Last updated: 2025-12-22 | OHMind v1.0.0