Hi Marcella,
Thank you for your reply. Let me tell you a little bit about the system and why, although a negative HOMO-LUMO gap doesn't make sense, I'm no longer
worried about the situation.
The student is doing calculations on graphene quantum dots which (unlike graphene) are well-known to gave a gap. He is looking at the effect on the gap
of replacing hydrogens with either electron donating or electron withdrawing groups. He is also looking at the effect on the gap of replacing hydrogens with
bulkier groups at either armchair or zigzag positions since it has been suggested that a gap can form in graphene if it is strained and that the effect is different
for strain in the armchair versus zigzag directions.
The calculation for which he got the negative HOMO-LUMO gap, was one in which, due to too much strain or congestion, the "optimized" geometry was completely
nonphysical.
Best,
Ian