Global structure search for molecules on surfaces: Efficient sampling with curvilinear coordinates

Abstract

Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial moves. This approach has recently been shown to be efficient in structure determination of clusters [Nano Letters 15, 8044-8048 (2015)] and is here extended for its application to covalent, complex molecules and large adsorbates on surfaces. The employed automatically constructed delocalized internal coordinates are similar to molecular vibrations, which enhances the generation of chemically meaningful trial structures. By introducing flexible constraints and local translation and rotation of independent geometrical subunits we enable the use of this method for molecules adsorbed on surfaces and interfaces. For two test systems, trans-β-ionylideneacetic acid adsorbed on a Au(111) surface and methane adsorbed on a Ag(111) surface, we obtain superior performance of the method compared to standard optimization moves based on Cartesian coordinates.

First-principles calculations of hybrid inorganic–organic interfaces: from state-of-the-art to best practice

“…Moreover, the variation of adsorption geometries can introduce a notable (perceived) error bar on the calculations and significantly complicates the evaluation of the performance of the employed methodology compared to real-word experiments (see Chapter 4). Interestingly, recent advances in global structure optimization have finally put global structure search at hybrid interfaces including predictions of their atomistic structures [168][169][170] and even an assessment of different polymorphs, within reach. 165,[171][172][173] In passing, the authors note that their algorithm for global structure search at interfaces (SAMPLE) 165 is available as python package that can be downloaded from the author's homepage (www.if.tugraz.at/hofmann).…”

“…Thus, we recommend that the details of such a search are documented more often in the published literature). Even when systematic evaluations are done, they mostly rely on creating different starting points based on physical and chemical intuition followed by local geometry relaxations, rather than employing more unbiased and systematic approaches like Basin Hopping 168 or machine learning-based algorithms. 166 As a further complication, local relaxations have their own challenges, as will be shown in Section 5.…”

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

“…Hofmann and coworkers have used small‐scale versions of basin hopping and machine learning, to explore adsorption structures of tetracyanoethylene on Au(111), in a search space restricted strongly by several assumptions (almost rigid molecules, adsorption energy dominates over intermolecular interaction energy, predetermined small set of single‐molecule adsorption geometries). Krautgasser et al have also explored optimal poses of molecules on surfaces, with a basin‐hopping‐related strategy and targeted trial moves, but only for single molecules, not for assemblies of several molecules.…”

Reliable Computational Prediction of the Supramolecular Ordering of Complex Molecules under Electrochemical Conditions

“…To round up this section, it should be noted that a variety of techniques have been used in the literature for related optimization problems; among those are Monte Carlo or molecular dynamics-based techniques such as simulated annealing, 81 , 82 basin-hopping, 83 − 85 minima-hopping, 86 , 87 and eventually evolutionary approaches such as genetic algorithms. 61 − 67 , 79 , 80 , 88 − 91 The decision on the method of choice relies on the specific problem: for instance, as Hofmann et al.…”