QM Agent

Expert agent for quantum chemistry calculations using ORCA, including DFT, geometry optimization, and property calculations.

Table of Contents

• Overview
• Capabilities
• Available Tools
• Workflow
• Example Prompts
• Configuration
• See Also

Overview

The QM Agent specializes in running quantum chemistry calculations using ORCA. It handles structure preparation, DFT calculations, geometry optimization, frequency calculations, and various property predictions relevant to HEM design.

Expertise Areas

• DFT calculations (B3LYP, PBE0, M06-2X)
• Geometry optimization
• Frequency calculations and thermochemistry
• Electronic structure calculations
• Proton affinity and pKa estimation
• Binding energy calculations
• NMR chemical shift prediction

MCP Server

The QM Agent connects to the OHMind-ORCA MCP server for tool access.

Important Note

The QM Agent runs calculations. For analysis of results (HOMO/LUMO energies, orbital properties), the Multiwfn Agent should be used after calculations complete.

Capabilities

Capability	Description	Expensive
SMILES to XYZ	Convert molecular structures	No
Single Point Energy	Calculate energy at fixed geometry	No
Geometry Optimization	Find minimum energy structure	⚠️ Yes
Frequency Calculation	Vibrational analysis, thermochemistry	⚠️ Yes
Charge Analysis	Mulliken, Löwdin, Hirshfeld charges	No
Proton Affinity	pKa estimation	No
Binding Energy	Ion-functional group interactions	No
NMR Shifts	Chemical shift prediction	⚠️ Yes
Transition State	TS search and verification	⚠️ Yes

Available Tools

Core Tools

smiles_to_xyz

Convert SMILES to 3D XYZ coordinates using RDKit.

Parameters:

• smiles (str): Input SMILES string

Returns: XYZ coordinate string

Note: Always use this tool first before running calculations.

calculate_single_point_energy

Single-point energy calculation at fixed geometry.

Parameters:

• xyz_string (str): XYZ coordinates
• method (str): DFT functional (default: B3LYP)
• basis (str): Basis set (default: def2-SVP)
• dispersion (str): Dispersion correction (default: D3BJ)

Returns: Energy in Hartree, output file paths

optimize_geometry

⚠️ EXPENSIVE OPERATION - Requires user approval

Optimize molecular geometry to find minimum energy structure.

Parameters:

• xyz_string (str): Initial XYZ coordinates
• method (str): DFT functional
• basis (str): Basis set
• dispersion (str): Dispersion correction

Returns: Optimized coordinates, final energy, results directory

Estimated Time: 5-30 minutes

calculate_frequencies

⚠️ EXPENSIVE OPERATION - Requires user approval

Vibrational frequency calculation for thermochemistry.

Parameters:

• xyz_string (str): XYZ coordinates (should be optimized)
• method (str): DFT functional
• basis (str): Basis set
• temperature (float): Temperature in K (default: 298.15)

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

Estimated Time: 5-30 minutes

IEM-Focused Tools

calculate_proton_affinity

Proton affinity and approximate pKa for acidic groups.

Parameters:

• xyz_string (str): XYZ coordinates
• acidic_site (int): Atom index of acidic proton
• solvent (str, optional): Solvent for implicit solvation

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

calculate_binding_energy

Ion-functional group binding energies.

Parameters:

• complex_xyz (str): Ion-molecule complex coordinates
• ion_xyz (str): Isolated ion coordinates
• molecule_xyz (str): Isolated molecule coordinates
• bsse_correction (bool): Apply BSSE correction
• solvent (str, optional): Implicit solvation

Returns: Binding energy with/without corrections

calculate_ionic_solvation_energy

Solvation/hydration energies for ions.

Parameters:

• xyz_string (str): Ion or ion-water cluster coordinates
• charge (int): Total charge
• solvent (str): Solvent model

Returns: Solvation energy and free energy

analyze_atomic_charges

Calculate atomic charges using various methods.

Parameters:

• xyz_string (str): XYZ coordinates
• methods (list): Charge methods (mulliken, loewdin, hirshfeld)

Returns: Charges per atom, dipole/quadrupole moments

search_transition_state

⚠️ EXPENSIVE OPERATION - Requires user approval

Transition state search with optional frequency verification.

Parameters:

• xyz_string (str): Initial TS guess coordinates
• method (str): DFT functional
• verify_frequencies (bool): Run frequency calculation to verify

Returns: TS geometry, activation energy, imaginary frequency

predict_nmr_chemical_shifts

⚠️ EXPENSIVE OPERATION - Requires user approval

NMR shielding and chemical shifts.

Parameters:

• xyz_string (str): XYZ coordinates
• nuclei (list): Nuclei to calculate (1H, 13C, 19F, 31P)
• reference (str): Reference compound

Returns: Chemical shifts for selected nuclei

calculate_polymer_reactivity

HOMO/LUMO energies and conceptual DFT descriptors.

Parameters:

• xyz_string (str): Monomer XYZ coordinates

Returns: HOMO/LUMO energies, gap, chemical potential, hardness

Workflow

Standard QM Calculation Workflow

graph TD
    A[SMILES Input] --> B[smiles_to_xyz]
    B --> C[XYZ Coordinates]
    C --> D{Calculation Type}
    D --> |Single Point| E[calculate_single_point_energy]
    D --> |Optimization| F[Request Approval]
    F --> G[optimize_geometry]
    G --> H[Optimized Structure]
    H --> I{Need Frequencies?}
    I --> |Yes| J[calculate_frequencies]
    I --> |No| K[Results]
    J --> K
    K --> L[Multiwfn Analysis]

Validation Flow

Expensive operations require user approval:

# Validation message format
"⚠️ **Quantum Chemistry Calculation requires approval**

**Requested operations:**
- optimize_geometry: {'method': 'B3LYP', 'basis': 'def2-SVP'}

**Results will be saved to:** `/OHMind_workspace/ORCA`

This calculation is computationally expensive and may take 5-30 minutes.

Please approve to continue."

Multi-Turn Tool Calling

The QM Agent supports iterative tool calling (up to 5 iterations) to handle complex workflows that require multiple sequential calculations.

Example Prompts

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.

Configuration

Environment Variables

Variable	Purpose	Default
OHMind_ORCA	Path to ORCA binary	Required
OHMind_MPI	Path to MPI binaries	Required for parallel
QM_WORK_DIR	Working directory	$OHMind_workspace/ORCA

Results Storage

QM results are saved to:

$QM_WORK_DIR/
├── temp_*/           # Per-job temporary directories
│   ├── input.inp     # ORCA input file
│   ├── input.out     # ORCA output file
│   ├── input.gbw     # Wavefunction file
│   └── input.xyz     # Final geometry
└── results/          # Preserved results

Expensive Operations

The following tools require validation before execution:

• optimize_geometry
• calculate_frequencies
• predict_nmr_chemical_shifts
• search_transition_state

See Also

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

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