Folding, isomerization, and dissociation of molecules, i. e., bond breaking and bond formation, is happening on ultrafast timescales. Femtoseconds (1 fs = 10^(−15) s) are the timescale on which atoms move. Hence, the observation of a chemical process on that timescale allows not only to measure the reactants and products of a chemical reaction, but also to observe the systems far from equilibrium. Within this dissertation several complementary measurements are presented, which are designed to measure chemical reactions of controlled gas-phase molecules at synchrotrons, high-harmonic generation based radiation sources, and the 4th generation x-ray light sources, x-ray free-electron lasers. Gas-phase molecular ensembles are cooled in molecular beams and purified by either spatial separation of different rotational isomers, or size-selection of molecular clusters to provide a clean sample for the experiments. Furthermore, control is gained by the alignment of the initially isotropically distributed molecular sample to the laboratory frame. The controlled molecular samples, or their fragments, are imaged by several techniques, ranging from one-dimensional ion time-of-flight measurements, over two-dimensional velocity-map imaging of electrons and ions, to the measurement of scattered x-ray photons by an x-ray camera. At first it is demonstrated that the cis- and trans-conformer of 3-fluorophenol can be purified in the interaction region to more than 90 % via spatial separation, and thus providing an ideal sample to study isomerization dynamics (chapter 3). The sample was chosen such that it is possible measure the ultrafast isomerization dynamics via photoelectron diffraction by using a free-electron laser. In addition to the spatial control of the molecular beam, the alignment of the gas-phase molecular sample is demonstrated at the full repetition rate of a free-electron laser by the use of an in-house Ti:Sapphire laser system (chapter 4). Since most facilities have synchronized Ti:Sapphire laser systems at their corresponding end stations, this approach is demonstrating an alignment technique which can be easily implemented in most experiments. The controlled gas-phase molecules were probed by hard x-ray photons to determine their structure via diffractive imaging (chapter 5). Diffractive imaging of gas-phase molecules at free-electron lasers is a highly promising approach to image ultrafast molecular dynamics of gas-phase molecules. The alignment of the molecular sample does have the advantage that, providing the molecules are perfectly aligned (or more general perfectly oriented), its diffraction pattern is equal to the diffraction pattern of a single molecule, which allows for the reconstruction of bond distances and bond angles of the molecule. Furthermore, the x-ray photophysics of indole and indole-water clusters measured at a synchrotron are presented in chapter 6 and chapter 7. Indole and microsolvated indole-water clusters were spatially separated and both locally ionized by soft x-ray radiation. The ionic fragments as well as emitted electrons were recorded in coincidence. The fragmentation patterns of both species are compared to learn about the influence of the hydrogen-bonded water on the fragmentation of indole. This experiment was aiming at the difference between isolated molecules and molecules in solvation, and also to study hydrogen bonds which are of universal importance in chemistry and biochemistry. The potential use of a high-harmonic generation based radiation as a further source—next to the established accelerator-based facilities—for extreme ultraviolet photons is demonstrated in section 8.1 to study ultrafast dynamics of gas-phase molecules. Moreover, the sample preparation of the amino acid glycine is shown in section 8.2 for future studies of ultrafast charge migration in conformer-selected molecular samples by the use of attosecond pulses generated by higher harmonics.