Determination of the hydrogen species in hydrogen in vein quartz using infrared spectroscopy shows that samples containing a significant fluid inclusion population also yield a 'normal' hydrogen isotope signature (-39‰). Samples generating an anomalous 8D signature (-103%o) contain a significant quantity of structurally incorporated defect hydrogen species. Additional experiments different hydrogen reservoirs are liberated from quartz at temperatures that correlate with those described previously as generating anomalous hydrogen isotope signatures during stepped heating isotopic experiments. The findings suggest that hydrogen isotope signatures decoupled from that suggested by accompanying oxygen isotopes may be attributable to a significant defect hydrogen reservoir in the sample. Using mid-infrared spectroscopy, the frequencies of the fundamental molecular vibrations obtained using standard and field-based sample preparation techniques are the same. Bands generated using infrared absorbance and reflectance spectroscopic techniques are also in good agreement. Micro-infrared spectroscopy was used to characterise the products of hydrothermally altered plagioclase phenocrysts from the Chelopech Au deposit, Bulgaria. Samples from inside and outside the main silicified zone are dominated by kaolinite and beidellite respectively. Mineral characterisation was confirmed using XRD analysis. Cathodoluminescence images of quartz phenocrysts from a porphyry copper related intrusion elucidate numerous growth zones. Dendritic morphologies, indicative of periods of rapid growth, are found in the inner regions of individual zones. These regions also display a bright luminescence response. Outer regions of an individual zone may display morphologies indicative of euhedral growth and are of lower luminescence response. The observed growth patterns record numerous periods of cyclic growth, which are interpreted to be associated with periodic phases of magmatic volatile exsolution. Concentrations of H-OH groups, measured using micro-infrared spectroscopy during a traverse of a magmatic quartz crystal, show significant spatial variability. This is attributed to irregular incorporation of these species during crystal growth. Regions recording high H-OH contents also correlate with those displaying bright luminescence response and quartz habits indicative of rapid growth. The results of this study suggest that SEM-CL images may provide a rapid technique for interpreting the relative rates of quartz growth in a crystal. Apatite and biotite crystals are found as inclusions in quartz phenocrysts. Calculations using the elemental composition of these phases enables log fugacity ratios log(fH2o)/(fHCI), log(fH2o)/(fHF), and log(fHF)/fHci) to be calculated for the precipitating medium. A comparison between log fugacity ratios of the studied intrusion, with those from other porphyry copper settings, shows halogen bearing minerals in many porphyry systems have crystallised under a similar fugacity regime.