Adsorption structures of the 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecule on the clean Si(001) - 2 × 1 surface were investigated using scanning tunneling microscopy (STM) experiments in conjunction with first principles theoretical calculations. Four dominant adsorption structures were observed in the STM experiments and their atomic coordinates on the Si(001) surface were determined by comparison between the experimental STM images and the theoretical simulations. Maximizing the number of the Si-O bonds is more crucial than that of the Si-C bonds in the PTCDA adsorption.
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