Two-dimensional structures of pyrimido[5,4-d]pyrimidine derivatives (PD) were studied by scanning tunneling microscopy (STM) at solid/liquid interface. In order to tune the intervals of functional unit (hydrogen bonding site) in the molecule, the PD with different numbers and length of alkyl chain were designed and synthesized. STM observation at highly oriented pyrolytic graphite (HOPG)/1-phenyloctane interface revealed that the PD with four alkyl chains formed a columnar structure, and the alkyl chains were not interdigitated. By contrast, the PD with two alkyl chains formed similar columnar structure, whereas the alkyl chains were interdigitated. These structural features of the PD indicates that the intervals of the functional unit, i.e., hydrogen bonding sites in the PD can be controlled by changing not only the length but also the number of alkyl chains. (c) 2008 Elsevier B.V. All rights reserved.