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Organic and biological macromolecules have attracted great interest within nanotechnology research due to properties that can be useful in future devices. Interesting functionalities such as optical activity, host-guest binding and molecular recognition are based on effects at the single molecular level. To study the properties and functions of molecules at submolecular scale, an atomically defined environment with low contamination is of great advantage. This can for instance be provided on a clean surface in ultrahigh vacuum (UHV), where surface sensitive analytical techniques and advanced nanostructure fabrication can be applied. Atoms and small organic molecules are easily transferred to a surface in vacuum by thermal sublimation. Many large, functional molecules, however, are nonvolatile and disintegrate at an elevated temperature, which hinders their application and investigation within the UHV environment. To explore the properties of nonvolatile molecules adsorbed at surface as well as the nanostructure fabricated from such molecules, electrospray ion beam deposition (ES-IBD), a technique capable of transferring nonvolatile molecules intact to surfaces in UHV, and in situ scanning tunneling microscopy (STM) are combined. A home-built ES-IBD setup allows molecular beam deposition with an unprecedented level of control: the ion beam composition is monitored by time-of-flight mass spectrometry (TOF-MS) prior to the deposition, molecular flux and coverage controlled via the ion beam current and the beam energy can be measured and adjusted. The modified surfaces are characterized in situ by STM, which reveals structural and electronic properties with submolecular resolution. Moreover, ex situ analysis by atomic force microscopy (AFM) allows to access meso-scale structural formation. In addition, Laser Desorption Ionization (LDI), Matrix-Assisted Laser Desorption Ionization (MALDI) and Secondary Ion Mass Spectrometry (SIMS) are performed to check the chemical composition and purity of the adsorbed materials. This work first introduces the principles of our experiments and reviews of the literature on molecular ion beam deposition. In the following, the experimental method is characterized in detail using Rhodamine 6G, an organic dye, as a model system. It is shown that homogeneous layers of adsorbed, intact molecules are formed on the surface and single molecule adsorbates are observed by STM. An investigation by SIMS and LDI reveals that the kinetic energy of the molecular ions upon collision with the surface determines whether intact or fragment ions are deposited. Molecular layer growth was studied using cluster ion beams of the nonvolatile surfactant SDS, resulting in an arrangement of the molecules typical for surfactants in a head-to-head and tail-to-tail manner based on the structural motive. Crystalline structures are observed by AFM resembling inverted bilayer-membranes formed on graphite and SiOx surfaces. A similar structural feature revealed by STM is a flat-laying double row of the molecules on Cu(100) surface showing the robustness of the structural motive. The properties of single molecular functional systems are studied on two types of large functional molecules: macrocycle complexes and proteins. Macrocyclic host-guest complexes of the three cations: Na+, Cs+ and H+ trapped in the cavity of dibenzo-24-crown-8 (DB24C8) are formed in the electrospray solutions and transferred intact to the surface. Characterization by STM and density functional theory calculations shows the structure of the complexes with the alkali ion present in the cavity. The shape of the complex at the surface is also determined. Cytochrome c, an electron transfer protein is deposited on surfaces in UHV as an ion beam of high or low charge-state. STM reveals unfolded strands with distinguishable submolecular structural features after the deposition of high charge states. When low charge states are deposited, two significantly different structures are observed. Folded proteins appear as globular features of 2-3 nm diameter, while unfolded proteins are imaged as at strands. On Au(111) the unfolded strands fold into compact two-dimensional patches. Additionally, the variation in kinetic energy upon deposition and elevated surface temperature are also studied regarding the change in conformation of the adsorbed proteins. The results of this thesis open up new opportunities for the creation of functional nanostructures on surfaces. Both the preparation of layers and thin films as well as the controlled immobilization of single functional molecules were demonstrated with ES-IBD and characterized at submolecular resolution in situ by STM. A great variety of nonvolatile substances from small to large functional molecules with different binding motives like covalent, complex coordination or hydrogen bonds, is compatible with ESI and thus can be used as building blocks to construct new materials in a well-controlled manner.