Tip

All input files can be downloaded: Files.

opt

This keyword controls the search of geometry minimum, transistion state, and reaction path.

Options

type

Value	Min Search the geometry minimum.
	NEB Use the nudged elastic band (NEB) algorithm to search the reaction path and transition state.
	Dimer Use the dimer algorithm to search the transition state given the reactant and product geometry.
	QST2 Use the QST2 algorithm to search the transition state given the reactant and product geometry.
	TS Search the transition state from a single structure.
Default	Min

Determine what type of geometry optimization you want to do.

For Min and TS, the initial structure should be given in mol. The optimization process is output to x-opt-traj.xyz and the final minimum or transition state is output to x-opt.xyz.

For NEB, Dimer, and QST2, 2 structures have to be given in mol and mol2, which represent a reactant and product pose, respectively. Usually, one can first use NEB to rapidly find a reasonable path and transition state. If NEB is hard to converge, then use the structures from NEB result to do a Dimer or QST2 search. Dimer and QST2 require reactant and product structures of high quality.

For NEB, the reaction path is output to x-opt-traj.xyz and the final transition state is output to x-opt.xyz.

For Dimer and QST2, the transition state is output to x-opt.xyz. The x-opt-traj.xyz is NOT reaction path! It is just the optimization process as Min or TS.

max_step

Value	An integer
Default	1000

The maximum number of geometry optimization steps.

energy_cov

Value	A real number
Default	1.E-4

The energy convergence threshold. When the energy change is smaller than this value, this energy condition is satisfied.

grad_cov

Value	A real number
Default	1.E-3

The gradient convergence threshold. This actually determines 4 convergence thresholds:

Maximum gradient component	grad_cov
RMS gradient:	grad_cov * 2/3
Maximum atomic displacement	grad_cov * 4
RMS atomic displacement	grad_cov * 8/3

When all these 4 conditions are met, this gradient condition is satisfied.

max_dr

Value	A real number
Default	0.5

The maximum atomic displacement in an optimization step. If the molecule is highly flexible (Mathematically, the potential energy surface is very flat), or the structure (especially transition state) is very close to the stationary point but not converge, setting a smaller max_dr like 0.1 is very useful.

num_images

Value	An integer
Default	10

The number of images for NEB transition state search. This number canNOT be set too small, say, 5.

neb_k

Value	A real number
Default	0.01

The force constant for NEB transition state search. For a specific system, the optimal number of neb_k should be chose by trail-and-error.

fix_atoms

Value	Atom range
Default	None

Assign the atoms that are fixed during geometry optimization. For example:

opt
  fix_atom 2 5-9 23 26
end

The atoms 2,5,6,7,8,9,23,26 will be fixed during geometry optimization.

fix_bond

Value	2 integers
Default	None

Assign the bond that are fixed during geometry optimization. For example:

opt
  fix_bond 1 4
  fix_bond 2 6
end

The bonds (1,4) and (2,6) will be fixed during geometry optimization.

fix_angle

Value	3 integers
Default	None

Assign the angle that are fixed during geometry optimization. For example:

opt
  fix_angle 1 4 5
  fix_angle 2 6 7
end

The angles (1, 4, 5) and (2, 6, 7) will be fixed during geometry optimization.

fix_torsion

Value	4 integers
Default	None

Assign the torsion that are fixed during geometry optimization. For example:

opt
  fix_torsion 1 4 5 9
  fix_torsion 2 6 7 12
end

The torsions (1, 4, 5, 9) and (2, 6, 7, 12) will be fixed during geometry optimization.

Attention

Currently, the transition state search algorithm QST2 and TS do NOT support constraints. If you want to search a transition state with constraints, please use NEB or Dimer.

Theoretical Background

Minimum

The minimum is defined as a stable isomer on its potential energy surface (PES) of a molecule. The gradients on all atoms are zero. The optimization of minimum depends strongly on the initial structure. For different starters, one can get different isomers.

Transition State

Transition state is a short-lived configuration of atoms that in maximum on one direction but minimum on other directions. The gradients on all atoms are also zero. In Qbics, one can use NEB or dimer method to search the transition state. Only (unoptimized) reactant and product structures are needed. No exact Hessian needs to be computed.

A good strategy is:

• Use cheap method, like xTB, to find a reasonable path and transition state with NEB (type neb).

• Then, use standard DFT method to refine the transition state with dimer (type dimer) or QST2 (type QST2), even the previous NEB result is not converged.

This strategy is shown below:

Input Examples

Example: Minimum Structure of Aspirin

Search the minimum structure of aspirin at B3LYP/def2-SVP level of theory:

opt-1.inp

basis
    def2-svp
end

scf
    charge  0
    spin2p1 1
end

mol
    O    1.23330    0.55400    0.77920
    O    -0.69520    -2.71480    -0.75020
    O    0.79580    -2.18430    0.86850
    O    1.78130    0.81050    -1.48210
    C    -0.08570    0.60880    0.44030
    C    -0.79270    -0.55150    0.12440
    C    -0.72880    1.84640    0.41330
    C    -2.14260    -0.47410    -0.21840
    C    -2.07870    1.92380    0.07060
    C    -2.78550    0.76360    -0.24530
    C    -0.14090    -1.85360    0.14770
    C    2.10940    0.67150    -0.31130
    C    3.53050    0.59960    0.16350
    H    -0.18510    2.75450    0.65930
    H    -2.72470    -1.36050    -0.45640
    H    -2.57970    2.88720    0.05060
    H    -3.83740    0.82380    -0.50900
    H    3.72900    1.41840    0.85930
    H    4.20450    0.69690    -0.69240
    H    3.71050    -0.36590    0.64260
    H    -0.25550    -3.59160    -0.73370
end

task
    opt b3lyp
end

Example: Minimum Structure with Constraints

Search the minimum structure of a molecule “1UML” with a bond and a torsion fixed at xTB level of theory:

opt-2.inp1uml.xyz

opt-2.inp

opt
    fix_bond 7 51
    fix_torsion 2 9 12 13
end

mol
    1uml.xyz
end

task
    opt xtb
end

Check the constraints during optimization:

Example: Transition State of S_N2 Reaction

Search the transion state of an S_N2 reaction with NEB algorithm at B3LYP/def2-SVP level of theory:

ts-1.inp

basis # Define basis set.
    def2-svp
end

opt
    type       NEB   # Type: Min, NEB, Dimer, QST2, TS
    num_images 10    # The number of images for NEB calculations.
    neb_k      0.01  # The force constant for NEB calculations.
end

scf
    charge     -1      # The net charge.
    spin2p1     1      # 2S+1
end

xtb
    chrg -1
end

mol
    C  -2.25147439    4.89406277   -1.00469981
    H  -1.89481996    3.88525277   -1.00469981
    H  -1.89480154    5.39846096   -0.13104831
    H  -3.32147439    4.89407596   -1.00469981
    Cl -1.66479756    5.72372709   -2.44173406
    Cl -2.67350651    4.09697871    0.73250622
end

mol2
    C  -2.36845504    4.69197207   -0.60149770
    H  -1.76657311    4.00286639   -1.15626927
    H  -1.80200132    5.57659799   -0.39786281
    H  -3.23625780    4.94775799   -1.17280492
    Cl -1.66479756    5.72372709   -2.44173406
    Cl -2.86278952    3.94963672    0.91579319
end

task
    opt b3lyp
    # opt xtb # You can also try this.
end

The reaction path is given in ts-1-opt-traj.xyz:

The energies can be found in the output file ts-1.out:

ts-1.out

NEB path updated in "ts-1-opt-traj.xyz":
----------------------------------------------------
   #          Energy      Dist     Gtang     Gperp
----------------------------------------------------
   0   -960.06873748   0.13968   0.00000   0.00000
   1   -960.06864683   0.11091   0.00029   0.00035
   2   -960.06738628   0.07888   0.00032   0.00028
   3   -960.06508634   0.07078   0.00008   0.00030
   4   -960.06240481   0.09854  -0.00028   0.00036
   5   -960.05912811   0.18516  -0.00087   0.00032
   6   -960.05781339   0.21042  -0.00025   0.00051
   7   -960.06424460   0.26756  -0.00057   0.00032
   8   -960.06880165   0.00000   0.00000   0.00000
   9   -960.05738746   0.06067   0.00014   0.00026
----------------------------------------------------

Geometry optimization step 34:
 Current energy:   -960.05738746
 Delta Energy:     8.34686E-08; Target: 1.00000E-04; Converged? Yes
 Max displacement: 2.30167E-04; Target: 4.00000E-03; Converged? Yes
 RMS displacement: 1.07545E-04; Target: 2.66667E-03; Converged? Yes
 Max gradient:     5.45965E-04; Target: 1.00000E-03; Converged? Yes
 RMS gradient:     2.56874E-04; Target: 6.66667E-04; Converged? Yes
Stationary point has reached.

In the table, structure 0 and 1 are the reactant and product, respectively, and structure 6 is the transition state, which is also given in ts-1-opt.xyz.

You can change b3lyp to xtb to perform the calculation in a much more rapid way.

You can also try type dimer, which is computationally cheaper than NEB but requires reactant and product structures must be of high quality.

Example: Transion State of Decarboxylation Reaction

Search the transion state of the following decarboxylation reaction with NEB algorithm at B3LYP/def2-SVP level of theory:

ts-2.inpa1.xyza2.xyz

ts-2.inp

mol
    a1.xyz
end

mol2
    a2.xyz
end

scf
    charge -1
    spin2p1 1
end

opt
    type neb  # You can also try "dimer".
    num_images 15
    neb_k 0.01
end

basis
    def2-svp
end

task
    opt b3lyp
end

Structures in a1.xyz and a2.xyz are shown below. They are put arbitrarily without optimization:

a1.xyza2.xyz

The optimized transtion state ts-2-opt.xyz and path ts-2-opt-traj.xyz are shown below:

ts-2-opt.xyzts-2-opt-traj.xyz

Example: Transion State of Pd(OAc)-Catalyzed Nucleopalladation

Search the transion state of the following Pd(OAc)-catalyzed nucleopalladation with DIMER algorithm at B3LYP/def2-SVP level of theory:

ts-3.inpa1.xyza2.xyz

ts-3.inp

mol
    a1.xyz
end

mol2
    a2.xyz
end

scf
    charge  0
    spin2p1 1
end

opt
    type dimer # You can also use qst2
end

basis
    def2-svp
end

pseudopotential
    def2-ecp # Since Pd is used, you need to use ECP.
end


task
    opt b3lyp
end

Structures in a1.xyz and a2.xyz are shown below. They are put arbitrarily without optimization:

a1.xyza2.xyz

The optimized transtion state is ts-3-opt.xyz, shown below: