Self-assembly of organic molecules is a mechanism crucial for design of molecular nanodevices. We demonstrate unprecedented control over the self-assembly, which could allow switching and patterning at scales accessible by lithography techniques. We use the scanning tunneling microscope (STM) to induce a reversible 2D-gas-solid phase transition of copper phthalocyanine molecules on technologically important silicon surface functionalized by a metal monolayer. By means of ab-initio calculations we show that the charge transfer in the system results in a dipole moment carried by the molecules. The dipole moment interacts with a non-uniform electric field of the STM tip and the interaction changes the local density of molecules. To model the transition, we perform kinetic Monte Carlo simulations which reveal that the ordered molecular structures can form even without any attractive intermolecular interaction.

The state of matter in fluid phases, determined by the interactions between particles, can be characterized by a pair correlation function (PCF). At the nanoscale, the PCF has been so far obtained experimentally only by means of reciprocal-space techniques. We use scanning tunneling microscopy (STM) at room temperature in combination with lattice-gas kinetic Monte Carlo (KMC) simulations to study a two-dimensional gas of highly mobile molecules of fluorinated copper phthalocyanine on a Si(111)/Tl-(1×1) surface. A relatively slow mechanism of STM image acquisition results in time-averaging of molecular occurrence under the STM tip. We prove by the KMC simulations that in the proximity of fixed molecules STM images represent the PCF. We demonstrate that STM is capable of visualizing directly the pair correlation function in real space.

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