Recent experiments have shown that vacancy clusters are common defects in all types of monocrystalline brown diamond. This is believed to be due to an enhanced stability of the bounding (I 11) or (I 10) surfaces, arising from the formation of pi-bonded chains. These chains lead to broad bands of gap states with acceptor and donor levels around E-v + 2 eV. They also are likely to be responsible for the broad absorption continuum extending from the NIR through the visible and into the UV region which is characteristic of brown diamonds. High temperature treatment removes or transforms the clusters in CVD and type IIa diamonds leaving the diamond colourless. In type la brown diamonds, heat treatments up to 2500 degrees C lead to the breakup of the clusters and the formation of specific vacancy-nitrogen defects. We show that ab initio modelling of the interaction of nitrogen with the chains open a gap and leads to a threshold absorption energy in the 1-2 eV range. Finally, the calculations shed light on the identity of the vacancy-nitrogen defects observed.