Surface [4 + 2] Cycloaddition Reaction of Thymine on Si(111)7×7 Observed by Scanning Tunneling Microscopy

The early stage of thymine (Thy) adsorption on Si(111)7×7 surface is studied with scanning tunneling microscopy (STM) and density functional theory (DFT)-based computational method. Bright protrusions corresponding to the adsorbed thymine molecules are observed in both empty-state and filled-state STM images. These bright protrusions in the empty-state images exhibit three different degrees [lower (L), medium (M), and higher (H)] of intensities. The L and M protrusions are found on the adatom–restatom pairs in the 7 × 7 unit cell, indicating bidentate configurations for Thy adsorption. A free Thy molecule has been found to interact with the Si surface by a two-step process: Thy first undergoes keto–enol tautomerization to form the more stable dienol tautomer, which then binds to the Si adatom–restatom pair via the [4 + 2] cycloaddition reaction, leading to two different adproducts. Our DFT/B3LYP/6-31++G(d,p) calculations show three plausible cycloaddition products, with the 1,4-cyclohexadiene adproduct be...