The input file for secondary carbocation looks very similar to input files of alkenes as this molecule is asymmetric and all the atoms are unique. However, the input for the tertiary carbocation will need futher editing because we now need to define only symmetry uniqe atoms. Your structure file is likely to be slightly asymmetric, and may look like this:
C 6 0.336947 1.268504 -0.402697 C 6 1.102716 0.000518 -0.102376 C 6 0.338491 -1.268755 -0.400995 C 6 -1.033078 -1.265344 0.289768 C 6 -1.827630 -0.001033 -0.048194 C 6 -1.034494 1.264623 0.288160 C 6 2.327449 0.001616 0.402001 H 1 3.198406 -0.008684 -0.231123 H 1 2.677601 0.801607 1.031974 H 1 0.187851 -1.341342 -1.478557 H 1 0.914726 -2.138007 -0.100974 H 1 -1.593370 -2.150090 -0.001667 H 1 -0.888418 -1.323860 1.367052 H 1 -2.071308 -0.001681 -1.110447 H 1 -2.773567 -0.001316 0.487422 H 1 -1.595730 2.148350 -0.004545 H 1 -0.890056 1.324689 1.365388 H 1 0.912323 2.138820 -0.104114 H 1 0.185922 1.339297 -1.480326 H 1 2.671717 -0.786671 1.049720
Notice that six atoms have nearly zero values for the Y-coordinate. These atoms -- the tertiary carbon, the methyl carbon, one of the methyl hydrogens, and the atoms of the central methylene unit -- lie on the symmetry plane. In totally symmetric structure these coordinate values should be all zeros. Second, notice how the remaining atoms form pairs: the first carbon and the third carbon have nearly identical X and Z coordinate values but opposite Y-coordinate values. Such atoms form a pair of symmetry-equivalent atoms because the position of the second atom can be generated from the position of the first atom after defining the molecular symmetry. To retain only symmetry-unique atoms, one of the atoms from each pair must be deleted. For example, all atoms that have a negative value for Y-coordinate could be deleted. Last, PC GAMESS expects that the symmetry axis is the Z-axis, and you should swap the values in the second and last columns. Remember to include a blank line after symmetry specification in case of this symmetric molecule. Thus, the input for the tertiary carbocation should look something like this:
$contrl scftyp=rhf runtyp=optimize coord=unique icharg=1 nprint=-5 $end $system mwords=64 timlim=600 $end $basis gbasis=N31 ngauss=6 ndfunc=1 npfunc=1 diffsp=1 $end $statpt nstep=50 hssend=.t. $end $data Tutorial: tertiary carbocation HF/6-31+G(d,p) geometry optimization Cs C 6 0.337000 -0.401000 1.266000 C 6 1.102716 -0.102376 0.000000 C 6 -1.827630 -0.048194 0.000000 C 6 -1.034000 0.289000 1.265000 C 6 2.327449 0.402001 0.000000 H 1 3.198406 -0.231123 0.000000 H 1 2.675000 1.040000 0.800000 H 1 -2.071308 -1.110447 0.000000 H 1 -2.773567 0.487422 0.000000 H 1 -1.594000 0.003000 2.150000 H 1 -0.890000 1.366000 1.324000 H 1 0.913000 -0.101000 2.138000 H 1 0.186000 -1.480000 1.340000 $end