The adsorption of molecular and atomic hydrogen as well as other molecules in the atmosphere on vacancies in the (0001) graphite surface are investigated using density functional theory. Atomic hydrogen adsorbs with energies ranging from 4.7 to 2.3 eV. The validity of the model is confirmed by the good agreement between calculated vibrational spectra and those of high-resolution electron energy loss spectroscopy. It is shown that molecular hydrogen dissociates with a barrier of 1.1 eV on this model system. Water and oxygen also dissociate with respective barriers of 1.6 and 0.2 eV. Carbon dioxide and nitrogen have no interaction with the defect whereas carbon monoxide is incorporated into the vacancy with an activation energy of 1.5 eV. A comparison is made with the reactivity of graphene edges, both zigzag and armchair. (c) 2006 Elsevier Ltd. All rights reserved.