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4.3 Following both IRC directions and validating endpoints

These are unexecuted teaching inputs and starting models. Original diagrams are schematics, not calculated results. Validate version-specific syntax, licensed or authorized data, numerical convergence and the scientific model before using this workflow.

4.3.1 Model, units and provenance

Geometry in Å; electronic energy in hartree; vibrational wavenumbers in cm⁻¹. Check each printed field and keep thermal and standard-state terms distinct.

Shared inputs, conventions and evidence

Original schematic: Following both IRC directions and validating endpoints. No numerical results are claimed.
Original schematic: Following both IRC directions and validating endpoints. No numerical results are claimed.

4.3.2 Unexecuted inputs and explicit deltas

Use the accompanying instructions to identify the parent calculation and placement of every delta; a snippet is not automatically a standalone input. Preserve all blank-line and file-provenance requirements.

4.3.2.1 Input block 1

%oldchk=case14_nh3_ts.chk
%chk=case15_nh3_irc_forward.chk
%mem=4GB
%nprocshared=2
#p B3LYP/6-31G(d) IRC=(RCFC,Forward,MaxPoints=50,StepSize=-5)
   Geom=AllCheck Guess=Read SCF=Tight Integral=UltraFine NoSymm

4.3.2.2 Input block 2

%oldchk=case14_nh3_ts.chk
%chk=case15_nh3_irc_reverse.chk
%mem=4GB
%nprocshared=2
#p B3LYP/6-31G(d) IRC=(RCFC,Reverse,MaxPoints=50,StepSize=-5)
   Geom=AllCheck Guess=Read SCF=Tight Integral=UltraFine NoSymm

4.3.2.3 Input block 3

%oldchk=case15_nh3_irc_forward.chk
%chk=case15_nh3_forward_min.chk
%mem=4GB
%nprocshared=2
#p B3LYP/6-31G(d) Opt=(Tight,CalcFC) Freq
   Geom=AllCheck Guess=Read SCF=Tight Integral=UltraFine NoSymm
   Temperature=298.15 Pressure=1.0

4.3.2.4 Input block 4

%oldchk=case15_nh3_irc_reverse.chk
%chk=case15_nh3_reverse_min.chk
%mem=4GB
%nprocshared=2
#p B3LYP/6-31G(d) Opt=(Tight,CalcFC) Freq
   Geom=AllCheck Guess=Read SCF=Tight Integral=UltraFine NoSymm
   Temperature=298.15 Pressure=1.0

4.3.3 Worked investigation

4.3.3.1 Question and intuition

A correct-looking transition-state vibration suggests a reaction direction, but where does the path actually go? The intrinsic reaction coordinate follows a steepest-descent path in mass-weighted coordinate space from a saddle. It is a geometrical path on the chosen potential-energy surface, not a time trajectory, solvent movie, or finite-temperature free-energy curve. For ammonia, the two branches should descend toward equivalent pyramidal configurations. This symmetry provides a useful built-in consistency test while still requiring both calculations.

Strict prerequisite: case14_nh3_ts.chk must be the untouched checkpoint from the completed and validated Case 14 TS frequency job, with the TS geometry and its calculated Cartesian force constants. A checkpoint left after another optimization, an IRC endpoint, or a single-point job may not contain the required compatible Hessian. RCFC reads Cartesian force constants from a preceding frequency calculation. It is the relevant IRC option; do not replace it with Freq=ReadFC or assume an optimization's approximate Hessian is sufficient.

4.3.3.2 Separate forward and reverse inputs

Both jobs copy the same preserved TS into separate new checkpoints. The source must not be the forward job when launching the reverse job. The explicit negative StepSize requests increments measured in hundredths of amu1/2 bohr; −5 denotes a nominal 0.05 amu1/2 bohr step. Numerical integration may involve additional internal steps, so the number of SCF evaluations is not the number of stored IRC points.

See input block 1 above.

See input block 2 above.

If compatible force constants are unavailable but the starting geometry is a verified TS, replace RCFC by CalcFC in each route to compute a new initial Hessian. This is a precise alternative, not an instruction to use both options or to skip the preceding TS validation. A new method, basis, solvent, or isotope convention requires revisiting compatibility and generally validating the saddle under that new model before following its path.

4.3.3.3 Workflow

  1. Read the Case 14 output and record the imaginary-mode identity, model chemistry, TS energy, and checkpoint provenance. Protect the TS source by always giving subsequent jobs new output checkpoint names.
  2. Run both branches. Inspect per-point progress, the reaction-path summary, and normal termination. MaxPoints=50 is a limit, not a guarantee that a minimum has been reached. If the path ends at the limit while still descending materially, extend it using the documented restart procedure or rerun from the original TS with a larger limit and a fresh output file.
  3. Plot relative electronic energy versus the signed IRC coordinate, stating its mass-weighted unit from the output. Set the TS to zero if using Gaussian's relative path table; do not subtract the TS again from a table already relative to it. Assign “forward” and “reverse” to physical endpoint structures only after inspecting them.
  4. Extract the final geometry from each branch and verify that it is displaced toward a pyramid, on opposite sides of the hydrogen plane in a consistent atom frame. A viewer may rotate the molecule, so compare a signed plane-distance definition rather than raw z coordinates.
  5. Reoptimize each endpoint without IRC constraints and run frequencies at the identical model. Verify six real internal modes at each endpoint, compare both with the independent Case 14 minimum, and retain all three stationary-point outputs for Case 16.

A reproducible signed coordinate is q = (rN − rH2) · n, where n is the normalized cross product (rH3 − rH2) × (rH4 − rH2); H2, H3, H4 refer to atoms 2, 3, 4 of the input, not hydrogen isotopes. With Cartesian coordinates in Å, q is in Å and differs from the mass-weighted IRC coordinate. This definition survives proper rigid rotations of the entire molecule, but swapping hydrogen labels or reflecting the coordinate frame can reverse its sign. Keep the mapping fixed and do not confuse these two horizontal-axis choices.

4.3.3.4 Endpoint reoptimization inputs

Use the following only after confirming that the named checkpoint holds the corresponding last IRC geometry. Check the molecule displayed when opening the checkpoint. If its stored geometry is ambiguous, export the final coordinates explicitly and use a fresh ordinary Opt Freq input with charge 0 and multiplicity 1 instead.

See input block 3 above.

See input block 4 above.

4.3.3.5 Interpretation pitfalls and exercise

Forward is defined by the phase of the transition vector, not by the chemist's preferred left-to-right equation. It is acceptable if your forward endpoint is the pyramid another run labels reverse. A terminal IRC point is not automatically an optimized minimum, and an IRC does not survey all possible reaction channels. For this isolated ammonia example, the endpoint energies and internal geometries should be equivalent within numerical accuracy; appreciable mismatch calls for checking completion, mode identity, atom mapping, and optimization tolerances.

EN exercise: Repeat the paths with a smaller mass-weighted step, then compare the final optimized minima and electronic barrier rather than only the number of path points. Explain why a denser path is not a faster or slower chemical reaction, and why a smooth IRC curve should not be labeled a Gibbs-energy profile.

4.3.5 Sources and further reading