Transition State Search (Gaussian)

This page covers transition state optimization, IRC calculations, and potential energy surface scanning using Gaussian.

Transition State Optimization

Run transition state optimization to find saddle points on the potential energy surface:

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

TS Options

Option	Type	Description
`-f, --freeze-atoms`	string	Atom indices to freeze (1-based indexing)

Basic Usage

Standard TS optimization:

chemsmart sub gaussian -p project -f ts_guess.xyz -c 0 -m 1 ts

TS optimization with frozen atoms:

chemsmart sub gaussian -p project -f ts_guess.xyz ts -f 2,5,8

Using semiempirical method for pre-screening:

chemsmart sub gaussian -p project -f ts_guess.gjf -c 0 -m 2 -s PM6 ts

Modified Redundant Coordinate (Modred) Jobs

Run constrained geometry optimization using modified redundant coordinates:

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

Modred Options

Option	Type	Description
`-c, --coordinates`	string	Coordinate indices to constrain (1-based indexing)

Basic Usage

Constrain a bond between atoms 4 and 17:

chemsmart sub gaussian -p project -f input.com modred -c [[4,17]]

Constrain multiple bonds:

chemsmart sub gaussian -p project -f input.gjf -c 0 -m 2 modred -c [[85,100],[100,101],[101,89]]

Intrinsic Reaction Coordinate (IRC) Calculations

Run IRC calculations to follow the reaction path from a transition state:

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

IRC Options

Option	Type	Description
`-fl, --flat-irc/--no-flat-irc`	bool	Run flat IRC (default: disabled)
`-pt, --predictor`	string	Predictor type: LQA, HPC, EulerPC, DVV, Euler
`-rc, --recorrect`	string	Recorrection step: Never, Always, Test
`-rs, --recalc-step`	int	Hessian recalculation frequency (default: 6)
`-mp, --maxpoints`	int	Points along reaction path (default: 512)
`-mc, --maxcycles`	int	Maximum IRC steps (default: 128)
`-ss, --stepsize`	int	Step size in 0.01 Bohr units (default: 20)
`-d, --direction`	string	Direction: forward, reverse, or both (default: both)

Basic Usage

Standard IRC calculation:

chemsmart sub gaussian -p project -f ts.xyz irc

Potential Energy Surface Scanning

Run coordinate scanning to explore potential energy surfaces:

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

Note

Scanning coordinates, step size, and number of steps are all required.

Scan Options

Option	Type	Description
`-c, --coordinates`	string	Coordinates to scan (1-based indexing)
`-s, --step-size`	float	Step size for scanning
`-n, --num-steps`	int	Number of scan steps
`-cc, --constrained-coordinates`	string	Coordinates to keep fixed (1-based indexing)

Basic Usage

Scan a bond distance:

chemsmart sub gaussian -p project -f molecule.xyz scan -c [[2,3]] -s 0.1 -n 10

This scans the bond between atoms 2 and 3 for 10 steps of 0.1 Å each.

Multi-coordinate scan:

chemsmart sub gaussian -p project -f molecule.xyz scan -c [[2,3],[5,6]] -s [0.1,0.15] -n [10,12]

Scan with constraints:

# Keep bond 5-8 fixed while scanning bond 2-3
chemsmart sub gaussian -p project -f molecule.xyz scan -c [[2,3]] -s 0.1 -n 10 -cc [[5,8]]

# Multiple constraints
chemsmart sub gaussian -p project -f molecule.xyz scan -c [[2,3]] -s 0.1 -n 10 -cc [[5,8],[1,4,6]]