Gaussian pKa Calculations

This page covers Gaussian pKa job submission — generating input files and running the dual-level HA / A⁻ / (optional) HRef / Ref⁻ workflow.

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.

Theory 

For thermodynamic cycles, the dual-level approach, and analysis methodology, see pKa Calculations.

Quick Start 

Proton exchange (default)

Unless -s direct is given, CHEMSMART uses the proton exchange scheme and expects a reference acid. Provide -r, -rpi, -rc, and -rm (or a coloured-proton CDXML reference with auto-detected -rpi).

chemsmart run gaussian -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: Project settings (functional, basis set, etc.)
-f acid.xyz: Input geometry (XYZ, LOG, COM, CDXML, …)
-c 0 -m 1: Charge and multiplicity of the protonated acid (HA)
-pi 10: 1-based index of the proton to remove
-r / -rpi / -rc / -rm: Reference acid HRef and its deprotonation settings

This runs gas-phase opt+freq and solvent single-points for HA, A⁻, HRef, and Ref⁻ (default solvent: SMD/water from project or CLI).

Direct cycle

Use -s direct when you do not want a reference acid. Only HA and A⁻ calculations are submitted.

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

ChemDraw CDXML / CDX input

Structures drawn in ChemDraw can be submitted directly. Mark the acidic proton with a distinct atom colour; CHEMSMART reads the drawing and auto-detects it, so -pi is optional for single-fragment files.

# Single fragment — proton index auto-detected from colour
chemsmart run gaussian -p my_project -f phenol.cdxml -c 0 -m 1 pka \
    -r ref_acid.xyz -rpi 21 -rc 1 -rm 1

# Reference acid can also be CDXML (omit -rpi when uniquely coloured)
chemsmart run gaussian -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 batch submission and the -cc / -rcc colour options.

Job Output File Naming 

Sub-job labels determine output filenames. For a job with label acid1 (the default when submitting acid1.xyz):

acid1_HA_opt.log      # HA gas-phase opt+freq
acid1_A_opt.log       # A- gas-phase opt+freq
acid1_HA_sp.log       # HA solvent single-point
acid1_A_sp.log        # A- solvent single-point
acid1_HRef_opt.log    # HRef gas-phase (proton exchange)
acid1_Ref_opt.log     # Ref- gas-phase (proton exchange)
acid1_HRef_sp.log     # HRef solvent SP (proton exchange)
acid1_Ref_sp.log      # Ref- solvent SP (proton exchange)

When building a batch-analyze output table, either list these paths explicitly or use a basename and suffix convention documented in pKa Calculations (the _pka_* autodiscovery pattern matches ORCA-labelled outputs; Gaussian-labelled outputs are typically given as explicit paths).

Batch Processing with Input Tables 

Pass a .csv or whitespace-delimited .txt file via -f and invoke pka batch (or omit the subcommand — batch is selected automatically when -f points to a submission table).

Proton exchange (default — reference acid required on the pka group):

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

Direct cycle (-s direct must be set explicitly):

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

Note

When -f is a submission table, the parent gaussian command does not require -c / -m; charge and multiplicity are read from each table row.

Note

In batch mode, each table row becomes an independent pKa job.

On HPC clusters, use chemsmart sub instead of chemsmart run; each row receives its own scheduler script with a reconstructed single-row pka submit command. See HPC Cluster Submission (chemsmart sub).

Table Format 

Required columns (comma or whitespace delimited):

filepath: Path to the input geometry for HA
proton_index: 1-based index of the proton to remove
charge: Charge of HA
multiplicity: Multiplicity of HA

Example pka_input_table.csv:

filepath,proton_index,charge,multiplicity
/path/to/acid1.xyz,12,0,1
/path/to/acid2.xyz,8,-1,2
/path/to/acid3.cdxml,,0,1

Note

For single-molecule .cdxml / .cdx table rows, leave proton_index blank to auto-detect the coloured proton. Multi-fragment CDXML expansion applies only when the CDXML file is passed directly as -f (see ChemDraw CDXML / CDX batch input below).

Note

For proton exchange with batch input (the default scheme), -r, -rpi, -rc, and -rm are required on the pka group. When the table has multiple rows, only the first row uses the reference acid; later rows switch to the direct cycle automatically.

ChemDraw CDXML / CDX batch input 

When -f is a .cdxml or .cdx file (not a CSV table), pka batch reads every ChemDraw fragment in the file, auto-detects the coloured proton in each fragment independently, and submits one pKa job per molecule. Labels follow <basename>_frag<N>_pka (e.g. acids_frag1_pka_HA_opt.log).

# Multi-molecule CDXML — proton exchange (default)
chemsmart run gaussian -p my_project -f acids.cdxml -c 0 -m 1 pka \
    -r ref_acid.xyz -rpi 21 -rc 1 -rm 1 batch

# Multi-molecule CDXML — direct cycle
chemsmart run gaussian -p my_project -f acids.cdxml -c 0 -m 1 pka -s direct batch

# Optional: pin the colour table index when auto-detection is ambiguous
chemsmart run gaussian -p my_project -f acids.cdxml -c 0 -m 1 pka -cc 4 -s direct batch

A CSV table may list single-molecule .cdxml paths per row (see Table Format above); blank proton_index triggers coloured-proton auto-detection for that row. charge and multiplicity still come from the table columns for CSV rows; for multi-fragment CDXML passed directly as -f, see pKa Calculations (Charge and multiplicity).

On clusters, chemsmart sub ... pka batch with a CDXML file creates one submission per fragment; each run script targets a single fragment via --index. See HPC Cluster Submission (chemsmart sub).

Computing pKa from Existing Output Files 

Use the backend-independent analysis command (not gaussian pka):

chemsmart run pka analyze \
    -ha acid1_HA_opt.log \
    -hr ref_acid_HRef_opt.log \
    -rp 6.75 \
    -T 298.15 -c 1.0 -csg 100 -ch 100

See pKa Calculations for auto-discovery rules, direct-cycle syntax, and batch-analyze.

Parameters 

Core Options 

Short	Long	Description
`-pi`	`--proton-index`	Required in single-molecule mode (unless CDXML auto-detection applies). 1-based proton index.
`-cc`	`--color-code`	CDXML colour-table index for the proton to remove. Auto-detected when uniquely coloured.
`-s`	`--scheme`	`direct` or `proton exchange` (default).
	`--conjugate-base-charge`	Charge of A⁻. Defaults to `charge - 1`.
	`--conjugate-base-multiplicity`	Multiplicity of A⁻. Defaults to HA multiplicity.

Reference Acid Options (Proton Exchange)

Short	Long	Description
`-r`	`--reference`	Geometry file for HRef.
`-rpi`	`--reference-proton-index`	1-based proton index on HRef. Required with `-r` (unless CDXML auto-detection applies).
`-rcc`	`--reference-color-code`	CDXML colour index for the reference proton.
`-rc`	`--reference-charge`	Charge of HRef. Required with `-r`.
`-rm`	`--reference-multiplicity`	Multiplicity of HRef. Required with `-r`.
	`--reference-conjugate-base-charge`	Charge of Ref⁻. Defaults to `reference_charge - 1`.
	`--reference-conjugate-base-multiplicity`	Multiplicity of Ref⁻. Defaults to reference multiplicity.
`-rp`	`--reference-pka`	Experimental pKa of HRef. Required for `chemsmart run pka analyze` (not for job submission).

Solvent Options 

Short	Long	Description
`-sm`	`--solvent-model`	Solvation model for solvent SP. Default: `SMD` (or project setting).
`-si`	`--solvent-id`	Solvent identifier. Default: `water`.

Thermochemistry Options 

Short	Long	Description
`-T`	`--temperature`	Temperature in Kelvin. Default: `298.15` K.
`-c`	`--concentration`	Concentration in mol/L. Default: `1.0` mol/L.
`-P`	`--pressure`	Pressure in atm. Default: `1.0` atm.
`-csg`	`--cutoff-entropy-grimme`	Grimme quasi-RRHO entropy cutoff (cm⁻¹). Default: `100.0`.
`-cst`	`--cutoff-entropy-truhlar`	Truhlar quasi-RRHO entropy cutoff (cm⁻¹). Mutually exclusive with `-csg`.
`-ch`	`--cutoff-enthalpy`	Head-Gordon enthalpy cutoff (cm⁻¹). Default: `100.0`.
`-dG`	`--delta-g-proton`	\(\Delta G^{\circ}(\text{H}^{+})_{\text{aq}}\) in kcal/mol for direct-cycle submission. Default: `-265.9`. For output analysis, pass explicitly with `-s direct` (see pKa Calculations).

Examples 

Example 1: Direct Cycle Submission 

chemsmart run gaussian -p b3lyp_project -f phenol.xyz -c 0 -m 1 pka \
    -pi 13 \
    -s direct \
    -T 298.15

Example 2: Proton Exchange with Custom Temperature 

chemsmart run gaussian -p m062x_project -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 SMD \
    -si water

Example 3: Batch Submission from CSV 

chemsmart run gaussian -p m062x_project -f pka_scale.csv pka \
    -r ref_acid.xyz \
    -rpi 21 \
    -rc 1 \
    -rm 1 \
    batch

Example 4: Analyze Completed Gaussian Outputs 

chemsmart run pka analyze \
    -ha phenol_HA_opt.log \
    -hr ref_acid_HRef_opt.log \
    -rp 6.75 \
    -T 298.15 -c 1.0 -csg 100 -ch 100

Example 5: Direct-Cycle Analysis 

chemsmart run pka -s direct -dG -265.9 analyze \
    -ha phenol_HA_opt.log \
    -T 298.15 -csg 100 -ch 100