ORCA pKa Calculations

This page covers ORCA pKa job submission. The command structure mirrors Gaussian pKa for a consistent experience.

Note

Output-file analysis is backend-independent. After calculations finish, use chemsmart run pka analyze or chemsmart run pka batch-analyze. See pKa Calculations for the full analysis workflow, table formats, and thermochemistry options.

Quick Start 

Proton exchange (default)

Unless -s direct is given, CHEMSMART uses the proton exchange scheme and expects a reference acid.

chemsmart run orca -p my_project -f acid.xyz -c 0 -m 1 pka \
    -pi 10 \
    -r ref_acid.xyz \
    -rpi 21 \
    -rc 1 \
    -rm 1

Where:

-p my_project: ORCA project settings
-f acid.xyz: Input geometry
-c 0 -m 1: Charge and multiplicity of HA
-pi 10: 1-based proton index
-r / -rpi / -rc / -rm: Reference acid HRef

This runs gas-phase opt+freq and CPCM/water solvent single-points for HA, A⁻, HRef, and Ref⁻.

Direct cycle

chemsmart run orca -p my_project -f acid.xyz -c 0 -m 1 pka \
    -pi 10 \
    -s direct

ChemDraw CDXML / CDX input

ChemDraw .cdxml and .cdx files are supported. Colour the acidic proton in ChemDraw; CHEMSMART reads the drawing and detects it automatically, so -pi can be omitted for single-fragment inputs.

chemsmart run orca -p my_project -f phenol.cdxml -c 0 -m 1 pka \
    -r ref_acid.xyz -rpi 21 -rc 1 -rm 1

chemsmart run orca -p my_project -f phenol.cdxml -c 0 -m 1 pka \
    -r ref_acid.cdxml -rc 1 -rm 1

See pKa Calculations for multi-molecule CDXML workflows and colour-code options.

Job Output File Naming 

ORCA batch submission appends _pka to the input stem when forming the job label. For input acid1.xyz the label is acid1_pka and typical outputs are:

acid1_pka_HA_opt.out
acid1_pka_A_opt.out
acid1_pka_HA_sp.out
acid1_pka_A_sp.out
acid1_pka_HRef_opt.out    # proton exchange
acid1_pka_Ref_opt.out
acid1_pka_HRef_sp.out
acid1_pka_Ref_sp.out

These names align with the batch-analyze autodiscovery convention <basename>_pka_* when basename is acid1.

Batch Processing with Input Tables 

Proton exchange (default — reference acid required):

chemsmart run orca -p my_project -f pka_input_table.csv pka \
    -r ref_acid.xyz -rpi 5 -rc 0 -rm 1 batch

Direct cycle:

chemsmart run orca -p my_project -f pka_input_table.csv pka -s direct batch

Note

When -f is a submission table, the parent orca command does not require -c / -m.

Note

For proton exchange with multiple batch rows, only the first row uses the reference acid; subsequent rows switch to the direct cycle (same behaviour as Gaussian batch).

On HPC clusters, chemsmart sub ... pka batch writes one scheduler script per row or CDXML fragment with reconstructed pka submit arguments. See HPC Cluster Submission (chemsmart sub).

Table Format 

Required columns: filepath, proton_index, charge, multiplicity. See Gaussian pKa Calculations for CSV examples. For single-molecule .cdxml / .cdx rows, proton_index may be left blank for coloured-proton auto-detection.

ChemDraw CDXML / CDX batch input 

Pass a multi-molecule CDXML file directly as -f with pka batch. Each ChemDraw fragment becomes one pKa job with per-fragment coloured-proton detection. Labels are <basename>_frag<N>_pka (outputs such as acids_frag1_pka_HA_opt.out).

chemsmart run orca -p my_project -f acids.cdxml -c 0 -m 1 pka \
    -r ref_acid.xyz -rpi 21 -rc 1 -rm 1 batch

chemsmart run orca -p my_project -f acids.cdxml -c 0 -m 1 pka -s direct batch

For cluster submission of multi-fragment CDXML, see HPC Cluster Submission (chemsmart sub).

Computing pKa from Existing Output Files 

chemsmart run pka analyze \
    -ha acid1_pka_HA_opt.out \
    -hr ref_acid_pka_HRef_opt.out \
    -rp 6.75 \
    -T 298.15

ORCA .out and Gaussian .log files can be combined in batch-analyze. See pKa Calculations.

Parameters 

ORCA pKa options mirror Gaussian submission options. The main default difference is the solvent model (CPCM instead of SMD).

Short	Long	Description
`-pi`	`--proton-index`	Required in single-molecule mode (unless CDXML auto-detection applies).
`-cc`	`--color-code`	CDXML colour-table index for the target proton.
`-s`	`--scheme`	`direct` or `proton exchange` (default).
	`--conjugate-base-charge`	Charge of A⁻. Defaults to `charge - 1`.
	`--conjugate-base-multiplicity`	Multiplicity of A⁻.
`-sm`	`--solvent-model`	Solvation model for solvent SP. Default: `CPCM`.
`-si`	`--solvent-id`	Solvent identifier. Default: `water`.
`-r`	`--reference`	Reference acid geometry (proton exchange).
`-rpi`	`--reference-proton-index`	Proton index on HRef.
`-rcc`	`--reference-color-code`	CDXML colour index for the reference proton.
`-rc` / `-rm`	`--reference-charge` / `--reference-multiplicity`	Required with `-r` for proton exchange batch/submit.
	`--reference-conjugate-base-charge`	Charge of Ref⁻.
	`--reference-conjugate-base-multiplicity`	Multiplicity of Ref⁻.
`-rp`	`--reference-pka`	Experimental pKa of HRef (required for `chemsmart run pka analyze` only).
`-T`	`--temperature`	Default: `298.15` K.
`-c`	`--concentration`	Default: `1.0` mol/L.
`-P`	`--pressure`	Default: `1.0` atm.
`-csg` / `-cst` / `-ch`	`--cutoff-entropy-grimme`, etc.	Entropy and enthalpy cutoffs (cm⁻¹). See pKa Calculations.
`-dG`	`--delta-g-proton`	Default `-265.9` kcal/mol for submission; explicit for direct-cycle analysis.

Examples 

Example 1: Direct Cycle Submission 

chemsmart run orca -p orca_m062x -f phenol.xyz -c 0 -m 1 pka \
    -pi 13 \
    -s direct \
    -T 298.15

Example 2: Proton Exchange Submission 

chemsmart run orca -p orca_m062x -f benzoic_acid.xyz -c 0 -m 1 pka \
    -pi 15 \
    -r acetic_acid.xyz \
    -rpi 10 \
    -rc 0 \
    -rm 1 \
    -T 310.15 \
    -sm CPCM \
    -si water

Example 3: Batch Submission from CSV 

chemsmart run orca -p orca_m062x -f pka_scale.csv pka \
    -r ref_acid.xyz \
    -rpi 21 \
    -rc 1 \
    -rm 1 \
    batch

Example 4: Analyze Completed ORCA Outputs 

chemsmart run pka analyze \
    -ha phenol_pka_HA_opt.out \
    -hr ref_acid_pka_HRef_opt.out \
    -rp 6.75 \
    -T 298.15 -c 1.0 -csg 100 -ch 100

Example 5: Mixed Gaussian/ORCA Batch Analysis 

chemsmart run pka batch-analyze -o pka_output.csv

With -p auto (default), ORCA target .out files and Gaussian reference .log files in the same table are supported. See pKa Calculations.