The aim of a more precise knowledge about molecular structures and the nature of chemical bonds is the driving force behind the development of numerous experimental methods and theories. Recent soft X-ray based techniques provide novel opportunities for tackling the structure and the dynamics of chemical and biochemical systems in solution. In our research group we are developing experimental methods for mapping the electronic structure and dynamics of molecular systems in solution during bond-building and breaking using soft X-ray absorption and emission spectroscopy. The combination of such recent developments with conventional spectroscopy as well as theoretical modeling allows us to address open questions about hydrogen bonds, thermodynamics and active centers of biological systems. Based on the core-hole clock and pump–probe spectroscopy dynamics on the time scale from sub-femtoseconds up to picoseconds can be revealed.