We use low energy electron diffraction, scanning tunneling microscopy, first-principles densityfunctional theory, and molecular mechanics calculations to analyze the adsorption and growth of quinacridone derivatives (QA) with alkyl chains of 4 and 16 carbon atoms on a Ag(110) substrate. Surprisingly, we find that the alkyl chains determine the orientation of the molecular overlayers. While the interaction of QA and the Ag substrate is primarily due to chemical bonding of oxygen to the silver substrate, determining the molecular orientation and preferred adsorption site, the intermolecular arrangement can be adjusted via the length of alkyl chains. We are thus able to fabricate uniform QA films with very well controlled physical properties. DOI: 10.1103/PhysRevLett.96.226101 PACS numbers: 81.07.Nb, 68.43.ÿh, 81.16.Dn In recent years, the structure and growth of functional molecular thin films have been widely investigated due to their potential application for molecular devices [1][2][3][4]. However, understanding the interactions between organic molecules and noble metal substrates is not straightforward and has proven to be rather challenging [1][2][3][4][5]. In this respect, the ability to control the structure of molecular thin films provides a method of tuning the functional properties in a discrete manner. Previous work demonstrated that linear aromatic hydrocarbons attach to a silver substrate via interactions of the lowest unoccupied molecular orbital (LUMO) and silver 4d orbitals [6]. The match of the LUMO and the silver 4d orbitals also dominates the structural properties of the ensuing molecular film. Subsequent work concerned the lateral functional groups interacting with silver substrates, such as CN and CO groups in DMe-DCNQI and PTCDA [7]. The work suggested that the adsorbate-substrate geometry of large aromatic molecules on noble metal surfaces can be precisely controlled by functional groups of the molecule. However, the intermolecular geometry is less well researched due to lack of experimental data. Correspondingly, the understanding of intermolecular interaction is still somewhat shallow.For example, quinacridone and its derivatives (QA) are well-known chemically stable pigments. They display excellent photovoltaic and photoconductive properties [8][9][10]. The performance of organic light emitting devices based on QA have been widely investigated [11][12][13][14]. The QA molecular structure can be varied by the substitution of C atoms by N and O. QA can also be modified by attaching lateral alkyl chains to N heteroatoms and by the formation of QAnC, as shown in Fig. 1(a), where n denotes the number of carbon atoms in each alkyl chain. Accordingly, the photoelectric or electrical property can be adjusted by structural alterations of the molecule. It is quite possible that the lateral alkyl chains act as spacers and modulate the intermolecular distance. In this case the energy transfer between QAnC functional units is modified by noncovalent interactions between molecules, which are tuned ...