[en] The Division of Theoretical Chemistry at the University of Innsbruck is focused on the study of chemical compounds in aqueous solution, in terms of mainly hybrid quantum mechanical / molecular mechanical molecular dynamics simulations (QM/MM MD). Besides the standard means of data analysis employed for such simulations, this study presents several advanced and capable algorithms for the description of structural and dynamic properties of the simulated species and its hydration. The first part of this thesis further presents selected exemplary simulations, in particular a comparative study of Formamide and N-methylformamide, Guanidinium, and Urea. An included review article further summarizes the major advances of these studies. The computer programs developed in the course of this thesis are by now well established in the research field. The second part of this study presents the theory and a development guide for a quantum chemical program, QuMuLuS, that is by now used as a QM program for recent QM/MM simulations at the division. In its course, this part presents newly developed algorithms for electron integral evaluation and point charge embedding. This program is validated in terms of benchmark computations. The associated theory is presented on a detailed level, to serve as a source for contemporary and future studies in the division. In the third and final part, further investigations of related topics are addressed. This covers additional schemes of molecular simulation analysis, new software, as well as a mathematical investigation of a non-standard two-electron integral. (author)