The middle atmosphere is an important area of the Earth's atmosphere, but our understanding of the dynamical and chemical processes in that region is still limited. Water vapour and methane both fulfil the requirements for tracers due to their long lifetimes and have frequently been used to study dynamical processes. However, the isotopic composition of water vapour and methane in the stratosphere is a relatively new area of interest that can give new insight to dynamical and microphysical processes in the stratosphere. The primary target would be the process of gas and particle exchange with the troposphere, but mixing within the stratosphere is also possible to study since the isotopic ratio can vary strongly between different atmospheric regions. Our current knowledge on the distribution of HDO and CH3D is rather poor but the few measurements that exist generally agree with the distribution expected from theory.

This thesis presents a first attempt to model the chemistry and dynamics of the less abundant isotopes of water vapour and methane in the stratosphere. A new oxidation scheme where CH3D is oxidised to form HDO has been implemented, and evaluated, in a one-dimensional model. The model is used to investigate how the D/H ratio of water vapour changes with altitude in the tropical stratosphere due to the influence of methane oxidation where the initial D/H ratio is higher. To reduce uncertainties in the model that are due to its one dimensionality, the study is extended such that the same chemical scheme is implemented in an existing two-dimensional model. A comparison in the tropical region shows good agreement between the two models. The differences that exist are related to the different transport descriptions in the two models. Compared to measurements the isotopic ratios in the two models are well represented in the tropical stratosphere up to ~45 km. At higher altitudes there are no measurements available and the very low amount of methane above 40-45 km makes the isotopic ratio very sensitive to errors, for example, in the reaction rates in the oxidation chain. Water vapour on the other hand is much less sensitive.

The simulations presented show that the isotopic ratio of water vapour and methane are good tracers of stratospheric transport and mixing between regions. The water vapour isotopic ratio can also be used to detect cloud formation in the stratosphere since the isotopic fractionation is very strong during phase changes in the cold lower stratosphere.