Thin film growth of molecules on substrates are governed by the convolution of inter-molecular forces and template-adsorbate interactions. Often the initial dimer formation plays a crucial role in the outcome of the molecular structure on the surface. Here, the behavior of naphtho-merocyanine on an Au(111) substrate was investigated using computational chemistry methods and Scanning Tunneling Microscopy. The experiments show a strong preference of dimer formation of the merocyanine molecules. Topographical measurements are used to identify two distinguished configurations, an elongated/oval dimer and a compact/rectangular dimer. With the addition of computational chemistry calculations including Density Functional Theory (DFT) and Molecular Mechanics calculations using the AMBER 3 force field, these two configurations of two specific merocyanine conformers, namely CTC and CTT, could be identified. Intermolecular binding energy calculations could be performed. This is a first step in understanding the possible island/thin film growth of naphtho-merocyanine and subsequently possible pathways toward the switching behavior of merocyanine and spiropyran on this substrate.

分子在基板上的薄膜生长受分子间力和模板-吸附物相互作用的卷积支配。通常，最初的二聚体形成在表面分子结构的结果中起着至关重要的作用。在这里，使用计算化学方法和扫描隧道显微镜研究了萘甲基花青在Au（111）衬底上的行为。实验表明，花青素分子的二聚体形成具有强烈的偏爱性。形貌测量用于识别两个不同的配置，一个细长的/卵形的二聚体和一个紧凑的/矩形的二聚体。在添加化学计算计算（包括密度泛函理论（DFT））和使用AMBER 3力场的分子力学计算之后，可以确定两个特定的花菁构象体的这两种构型，即CTC和CTT。可以进行分子间结合能的计算。这是了解萘-花青素可能的岛/薄膜生长以及随后在该底物上向花青素和螺吡喃转换行为的可能途径的第一步。