7.2. Example: C6H12

Tip

The sample input and output files can be found in testfiles/geom/9-c6h12-xTB.

Cyclohexane \(\left(\mathrm{C}\right)_{6}\left(\mathrm{H}\right)_{12}\) is a classical example in organic chemistry. In this section, we try to find its many isomers. Its structure is

c6h12.xyz

18
C6H12
C                 -1.18651427   -0.82443489   -0.22810126
C                  0.12072442   -1.43976894    0.22810126
C                  1.30723869   -0.61533405   -0.22810126
C                  1.18651427    0.82443489    0.22810126
C                 -0.12072442    1.43976894   -0.22810126
C                 -1.30723869    0.61533405    0.22810126
H                  2.25289806   -1.06033269    0.17609354
H                  0.12760438   -1.51078637    1.34823193
H                  0.20817399   -2.48123329   -0.17609354
H                 -1.24457718   -0.86590182   -1.34823193
H                 -2.04472407   -1.42090061    0.17609354
H                  1.24457718    0.86590182    1.34823193
H                  2.04472407    1.42090061   -0.17609354
H                 -0.20817399    2.48123329    0.17609354
H                 -0.12760438    1.51078637   -1.34823193
H                 -1.37218156    0.64488455    1.34823193
H                 -2.25289806    1.06033269   -0.17609354
H                  1.37218156   -0.64488455   -1.34823193

1 2 1.0 6 1.0 11 1.0 10 1.0
2 3 1.0 8 1.0 9 1.0
3 4 1.0 7 1.0 18 1.0
4 5 1.0 12 1.0 13 1.0
5 6 1.0 14 1.0 15 1.0
6 17 1.0 16 1.0
7
8
9
10
11
12
13
14
15
16
17
18

Note that we have already use topgen to add bonding information. Since we want to find its isomers, we will explicitly let its cycle deform during conformation search.

c6h12.inp

lm_dir          c6h12    # Save the local minima to this folder.
num_calcs       100      # Total number of calculations.
do_coarse_opt   yes      # no: Do NOT the coarse optimization.
min_energy_gap  5.E-4    # When two energies differ smaller than
                         # this value, they are treated as identical.
                         # A negative number means do not remove
                         # energetically degenerated ones.
max_geom_iters  3000     # The maximum number of iterations for local optimization.
                         # If it is less or equal than zero, then the number is unlimited.

components
  c6h12.xyz 1
  fix 0 0 0 0 0 0
  1 2 3 4 5 6
  ****
end

xtb
  0 0 2
end

commands
  $xtb$
end

We fix the molecule in space, and assign a deformable ring 1 2 3 4 5 6. We use xTB to do local optimization. Now run the conformation search:

$ geom c6h12.inp > c6h12.out

After the optimization, the end of c6h12.out is

c6h12.out

 -- Result Report --
Results are energy-increasingly reordered.
Structures of energies within 1.000E-04 are treated as degenerate.
All minima are saved to "c6h12".
-------------------------------------------------------------------
     #  index               Energy            NaiveRMSD
-------------------------------------------------------------------
     0     50         -18.98671582           0.00000000
     1     65         -18.97813291           1.53121941

Note that there are only two isomers. They are the chair and boat isomer, respectively. See below.