Much of the dense gas in molecular clouds has a filamentary structure but the detailed structure and evolution of this gas is poorly known. We have observed 54 cores in infrared dark clouds (IRDCs) using N2H+ (1-0) and (3-2) to determine the kinematics of the densest material, where stars will form. We also observed N2D+ (3-2) towards 29 of the brightest peaks to analyse the level of deuteration which is an excellent probe of the quiescent of the early stages of star formation. There were 13 detections of N2D+ (3-2). This is one of the largest samples of IRDCs yet observed in these species. The deuteration ratio in these sources ranges between 0.003 and 0.14. For most of the sources the material traced by N2D+ and N2H+ (3-2) still has significant turbulent motions, however three objects show subthermal N2D+ velocity dispersion. Surprisingly the presence or absence of an embedded 70 mu m source shows no correlation with the detection of N2D+ (3-2), nor does it correlate with any change in velocity dispersion or excitation temperature. Comparison with recent models of deuteration suggest evolutionary time-scales of these regions of several free-fall times or less.