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We present a theory for the scanning tunneling microscope ͑STM͒ current based on a Keldysh Green function formalism. In our formalism, we solve self-consistently an ab initio linear combination of atomic orbitals Hamiltonian within a local density formalism. Total energy calculations for xenon deposited on metal surfaces are performed to obtain the equilibrium position, and the Green functions needed to compute the current are obtained at the same time. Structural and nonstructural effects that can influence the correct interpretation of experimental STM results are studied. We find good agreement between our calculations and experimental images taken under highly controlled conditions, and we conclude that STM images should be analyzed by comparing iteratively the theory and the experiment, much in the same way as it is usually done for other surface sensitive techniques like low-energy electron diffraction, photoelectron diffraction, surfaceextended x-ray-absorption fine structure spectroscopy, etc.

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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.

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