Exploring self‐organization of molecular tether molecules on a gold surface by global structure optimization

Abstract

We employ nondeterministic global cluster structure optimization, based on the evolutionary algorithms paradigm, to model the self-assembly of complex molecules on a surface. As a real-life application example directly related to many recent experiments, we use this approach for the assembly of triazatriangulene "platform" molecules on the Au(111) surface. Without additional restrictions like spatial discretizations, coarse-graining or precalculated adsorption poses, and despite the proof-of-principle character of this study, we achieve satisfactory qualitative agreement with several experimental observations and can provide answers to questions that experiments on these species had left open so far.

Particle formation and surface processes on atmospheric aerosols: A review of applied quantum chemical calculations

“…Configurational sampling has recently benefited from various applications of genetic algorithms (GA). [ 68–76 ] Temelso et al used the OGOLEM implementation of GA to characterize ternary prenucleation clusters [ 77 ] and glycine–water clusters. [ 78 ] The artificial bee colony (ABC) algorithm has recently been employed extensively to study atmospherically relevant clusters.…”

Disordered Two-Dimensional Self-Organization of Ethyl Pyruvate Molecules on the Pt(111) Surface

“…22,23 However, since a few decades, nondeterministic global optimization techniques 24−29 have been developed and applied to such vast search spaces, with considerable success. Tools like evolutionary algorithms (EA) are well established in chemistry, for example, for global cluster structure optimization in vacuo, 30 in solvents 31,32 and on surfaces, 33,34 and also for different aims like abstract point charges for catalysis by optimized external electric fields. 35,36 EAs have also been applied to simplified models of molecular interaction on surfaces, for example, to study complex, charged molecules under electrochemical conditions, by system-specific, simple force fields, 37 or to optimize graph representations for NO on Pt 2 Sn(111) and for propyne on a PdIn(021) step surface.…”

“…OGOLEM was originally designed for clusters in vacuo but was later extended to clusters in liquids 31 and recently to clusters on surfaces. 33,34 All EA techniques, including crossover and mutation operators, are the same as used in those previous on-surface applications. 33,34 The typical system behavior during global optimization is also very similar.…”

“…33,34 All EA techniques, including crossover and mutation operators, are the same as used in those previous on-surface applications. 33,34 The typical system behavior during global optimization is also very similar. The optimizations start from randomly generated, compact but noncolliding clusters of a prescribed number of EP molecules directly above the surface.…”

Computation of Atmospheric Concentrations of Molecular Clusters from <em>ab initio</em> Thermochemistry

“…Here, the shape of the PES and the evaluation of the energy at each point on the surface will be sensitive to the physical description of the system where a more accurate physical description results in a more computationally expensive energy calculation. We will specifically use the GA method implemented in the OGOLEM 25 program, which has been successfully applied to a variety of global optimization and configurational sampling problems 42,43,44,45 , to generate the initial set of sampling points. The PES will be described by the PM7 model 46 implemented in the MOPAC2016 program…”