Quick Reaction Coordinate (QRC) Jobs

The Quick Reaction Coordinate (QRC) method is a lightweight alternative to full Intrinsic Reaction Coordinate (IRC) calculations for linking a transition state (TS) to its adjacent minima.

Introduction

The QRC method was introduced by Jonathan M. Goodman and M. A. Silva in Tetrahedron Letters, 2003, 44, 8233.

The core idea:

  1. Start from a TS with a completed frequency calculation.

  2. Displace along the imaginary mode (negative eigenvalue direction) in both + and − directions by a small amplitude.

  3. Optimize each displaced geometry to find the adjacent minima.

  4. Plot energy vs. displacement for a quick reaction profile.

CHEMSMART automates this process, taking a TS frequency calculation output and directly submitting QRC jobs.

chemsmart sub [OPTIONS] gaussian [GAUSSIAN_OPTIONS] qrc [SUBCMD_OPTIONS]

QRC Options

Option

Type

Description

-j, --jobtype

string

Job type: opt, ts, modred, scan, sp, irc (default: opt)

-c, --coordinates

string

Coordinates to freeze/scan (1-indexed, for modred/scan)

-s, --step-size

float

Scan step size in Å or radians (for scan)

-n, --num-steps

int

Number of scan steps (for scan)

-m, --mode-idx

int

Vibrational mode index, 1-indexed (default: 1)

-a, --amp

float

Displacement amplitude in Å (default: 0.5)

-N, --nframes

int

Number of frames for vibrational movie

-p, --phase

float

Phase angle in radians (default: π/2)

--normalize/--no-normalize

flag

Normalize eigenvector to 1.0 Å max displacement

--return-xyz/--no-return-xyz

flag

Output multi-frame XYZ with --nframes

Workflow Overview

  1. Read TS geometry and modes

    Supply a Gaussian output (ts.log) or ORCA output (ts.out) containing an optimized TS and frequency calculation.

  2. Select eigenmode

    By default, mode 1 is used (the imaginary mode). Use -m to select a different mode.

  3. Generate displaced guesses

    Two geometries are created:

    \[R(\pm) = R_\mathrm{TS} \pm \mathrm{amp} \times v_\mathrm{mode}\]

    If --normalize is used, the eigenvector is rescaled so the largest single-atom displacement is 1.0 Å.

  4. Launch downstream jobs

    Each displaced structure is used for the specified job type:

    • opt: Optimize to find adjacent minima

    • ts: TS optimization (for removing extra imaginary frequencies)

    • modred/scan: Constrained optimizations or scans

    • sp: Single-point energy calculations

    • irc: Full IRC calculations

  5. (Optional) Generate movie

    With --nframes, sample multiple points along the vibrational mode. Use --return-xyz to output a multi-frame XYZ file.

Basic Usage

Standard QRC to find reactant and product minima:

chemsmart sub gaussian -p project -f ts.log qrc -j opt

Remove an extra imaginary frequency from a TS:

chemsmart sub gaussian -p project -f ts.log qrc -m 2 -a 1.2 -j ts

Generate a vibrational movie:

chemsmart sub gaussian -p project -f ts.log qrc -N 10 --return-xyz

Extended QRC Applications

Removing spurious imaginary frequencies from geometry optimizations:

If an optimization produces an unwanted imaginary frequency, use QRC to displace along that mode and re-optimize:

chemsmart sub gaussian -p project -f opt_with_imag.log qrc -m 1 -a 0.8 -j opt

Removing second imaginary frequency from TS:

If a TS has two imaginary frequencies, displace along the second mode:

chemsmart sub gaussian -p project -f ts.log qrc -m 2 -a 1.2 -j ts

Summary

CHEMSMART QRC automates the workflow of:

  • Extracting vibrational modes from TS calculations

  • Displacing the TS geometry by ± amplitude along a mode

  • Generating Gaussian inputs for downstream jobs

  • Submitting those jobs automatically

This provides:

  • Fast connectivity checks between TS and minima

  • Approximate reaction profiles without full IRC

  • Tools for removing spurious imaginary frequencies

  • Ready-to-visualize mode animations