DFT Calculations with Avogadro and ORCA

Generating ORCA Input Files:
- Use Avogadro to create input files.
- Access ORCA input generation via Extensions > ORCA > Generate ORCA Input.
- Always select "Advanced" options.
Charge and Multiplicity:
- Charge: Net charge of the molecule (e.g., -1 for a carboxyl group).
- Multiplicity: Defined as $2S+1$ , where $S$ is the total spin angular momentum; corresponds to singlet, doublet, and triplet states (1, 2, 3).
- Alternatively, use the number of unpaired electrons + 1.
- Learn how to determine both charge and multiplicity in your theory class.
Basis Set:
- Using a basis set introduces a basis set error in quantum chemical calculations.
- DEF2-SVP is generally suitable for most elements.
- ECP (Effective Core Potential) is only needed for heavy metals.
- Calculations on heavy elements can be performed using ECPs.
Functional:
- A functional is a function of another function.
- B3LYP is a popular functional.
Selecting Methods (HF vs. DFT vs. MP2):
- DFT: Uses a variational approach.
- MP2: Uses perturbation theory.
- DFT: Bypasses the many-electron wave function in favor of electron density.
- Hartree-Fock (HF): Does not fully incorporate electronic correlation; resulting energies tend to be too high.
CPCM Solvation:
- Conductor-like Polarizable Continuum Model (CPCM) accounts for solvent effects.
- Treats the solvent as an implicit solvent.
- No need to treat the solvent as discrete molecules unless higher levels of analysis are required.

Types of Calculations:
- Geometry Optimization (Opt).
- Single Point Energy.
- Frequency.
Workflow:
- Always optimize the structure first.
- Then perform single point energy calculations.
- Single point energy is the potential energy of a molecule for a given arrangement of the atoms—useless unless optimized first.
- Harmonic vibrational frequencies can be calculated using the Frequency option.

SCF Iterations:
- An iterative procedure refines an initial guess to reach a self-consistent field (SCF) solution.
- Higher iterations increase accuracy.
- Add custom commands directly to the input file as needed.

Running ORCA from Terminal:
- Submit ORCA calculations through the terminal/command line (no UI).
- Perform both Geometry Optimization and Single Point Energy calculations.
Viewing the Output File:
- Open the output file in Avogadro.
Viewing Final Energies:
- Find final energies in the output file.

Generating ORCA Input Files:
- Use Avogadro to create input files.
- Access ORCA input generation via Extensions > ORCA > Generate ORCA Input.
- Always select "Advanced" options.
Charge and Multiplicity:
- Charge: Net charge of the molecule (e.g., -1 for a carboxyl group).
- Multiplicity: Defined as $2S+1$ , where $S$ is the total spin angular momentum; corresponds to singlet, doublet, and triplet states (1, 2, 3).
  - Alternatively, use the number of unpaired electrons + 1.
- Learn how to determine both charge and multiplicity in your theory class.
Basis Set:
- Using a basis set introduces a basis set error in quantum chemical calculations.
  - DEF2-SVP is generally suitable for most elements.
  - ECP (Effective Core Potential) is only needed for heavy metals.
    - Calculations on heavy elements can be performed using ECPs.
Functional:
- A functional is a function of another function.
  - B3LYP is a popular functional.
Selecting Methods (HF vs. DFT vs. MP2):
- DFT: Uses a variational approach.
- MP2: Uses perturbation theory.
- DFT: Bypasses the many-electron wave function in favor of electron density.
- Hartree-Fock (HF): Does not fully incorporate electronic correlation; resulting energies tend to be too high.
CPCM Solvation:
- Conductor-like Polarizable Continuum Model (CPCM) accounts for solvent effects.
  - Treats the solvent as an implicit solvent.
  - No need to treat the solvent as discrete molecules unless higher levels of analysis are required.

Types of Calculations:
- Geometry Optimization (Opt).
- Single Point Energy.
- Frequency.
Workflow:
- Always optimize the structure first.
- Then perform single point energy calculations.
  - Single point energy is the potential energy of a molecule for a given arrangement of the atoms—useless unless optimized first.
- Harmonic vibrational frequencies can be calculated using the Frequency option.

SCF Iterations:
- An iterative procedure refines an initial guess to reach a self-consistent field (SCF) solution.
  - Higher iterations increase accuracy.
- Add custom commands directly to the input file as needed.

Running ORCA from Terminal:
- Submit ORCA calculations through the terminal/command line (no UI).
  - Perform both Geometry Optimization and Single Point Energy calculations.
Viewing the Output File:
- Open the output file in Avogadro.
Viewing Final Energies:
- Find final energies in the output file.