Computational Characterization of the On-Surface Synthesis of Low-Dimensional Nanostructures
Authors: Gallardo Aurelio , Pérez Elvira Elena , Biswas Kalyan , Barragán Ana , Mendieta-Moreno Jesús , Björk Jonas , Jelínek Pavel , Urgel Jose , Ecija David 
Published: August 2024

On-surface chemistry represents a fast-growing field allowing to synthesize molecular structures not available by traditional wet chemistry. In this context, high-resolution scanning probe microscopy techniques are able to provide unprecedented spatial resolution, allowing to precisely identify individual products of the reactions. Nevertheless, a deep understanding of the reaction mechanism under the conditions imposed by the substrate remains unknown.
Nowadays, various computational strategies are employed to characterize the optimal reaction pathways of the chemical processes that take place on the surfaces of solids. For example, one of the most popular approaches is the nudged elastic band (NEB) as well as different transition state theory methods beyond it. These approaches had demonstrated their capability to characterize the potential energy landscape of the reaction pathways [1-2]. Another approach that had attracted the interest of the on-surface synthesis community is the application of molecular dynamics (MD) methods, within the canonical ensemble, and based on the QM/MM (quantum mechanics/molecular mechanics) of the interatomic forces [3-4]. This approach, which combines Density functional theory (DFT) and empirical force fields to describe the interaction forces, allows to simulate very large systems, at a very low computational cost while still accounting for the crucial quantum mechanics interactions. Also, such temperature-dependent simulations include the effect of entropy, vibrations modes, concerted motion, etc.
I will present the experimental and computational results of different projects in which we have made use of the aforementioned computational approaches to achieve a better understanding of the on-surface synthesis experiments performed by the group. For example, the rationalization of the selective cyclodehydrogenation of non-benzenoid nanographenes deposited on a Au(111) substrate by means of temperature-dependent MD calculations and the analysis of the obtained vibrational modes (See Figure 1a). The group had also studied the stepwise transformation of coronene-based organometallic networks into two-dimensional covalent patches through intermolecular homocoupling (See Figure 1b). We had as well investigated the transformation of indenyl precursors, through a triple C-H cleavage followed by a peripheral directed homocoupling, to form a polyacetylene backboned polymer that features a parity dependent and highly delocalized soliton in-gap state (See Figure 1c).
References:
1 - The Role of Metal Adatoms in a Surface-Assisted Cyclodehydrogenation Reaction on a Gold Surface. J. Björk, et al. Angew. Chem., 61, e2022123.1-7 (2022).
2 - Mechanisms of Halogen-Based Covalent Self-Assembly on Metal Surfaces. J. Björk, et al. J. Am. Chem. Soc. 135 (15) 5768–5775 (2013).
3 - fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems. J. I. Mendieta-Moreno, et al. J. Chem. Theory Comput., 10, 2185-2193 (2014).
4 - Strain‐induced isomerization in one‐dimensional metal–organic chains. M. Telychko Angewandte Chemie 131 (51), 18764-18770 (2019).