Parameter-free coordination numbers for solutions and interfaces

Abstract

Coordination numbers are among the central quantities to describe the local environment of atoms and are thus used in various applications such as structure analysis, fingerprints and parameters. Yet, there is no consensus regarding a practical algorithm, and many proposed methods are designed for specific systems. In this work, we propose a scale-free and parameter-free algorithm for nearest neighbor identification. This algorithm extends the powerful Solid-Angle based Nearest-Neighbor (SANN) framework to explicitly include local anisotropy. As such, our Anisotropically corrected Solid-Angle based Nearest-Neighbor (ASANN) algorithm provides with a fast, robust and adaptive method for computing coordination numbers. The ASANN algorithm is applied to flat and corrugated metallic surfaces to demonstrate that the expected coordination numbers are retrieved without the need for any system-specific adjustments. The same applies to the description of the coordination numbers of metal atoms in AuCu nano-particles and we show that ASANN based coordination numbers are well adapted for automatically counting neighbors and the establishment of cluster expansions. Analysis of classical molecular dynamics simulations of an electrified graphite electrode reveals a strong link between the coordination number of Cs + ions and their position within the double layer, a relation that is absent for Na + , which keeps its first solvation shell even close to the electrode.

Water adlayers on noble metal surfaces: Insights from energy decomposition analysis

“…Having established the "universal" character of the nonadditivity interaction, we now focus on the case of Pt(111) to obtain a geometric understanding of its origin. Since the structures are essentially two-dimensional, we do not simply determine the coordination number, 55 but perform a directional analysis: in each structure, the H-bond (H• • • O distance below 2.5 Å) acceptors are identified. Then, they are classified according to the Pt-O distance (<3.0 Å for chemisorbed water molecules, > 3.0 Å for physisorbed molecules).…”

Atomistic modeling of electrocatalysis: Are we there yet?

“…Furthermore, we have shown that the solvation shell of cations indeed fluctuate significantly, and cation specifically, at the electrified interface. 183 For electrocatalytic reactions, where both the electrolyte and the adsorbate have to rearrange, the situation is less clear: During the reaction, the adsorbate undergoes a bond-breaking/formation process (horizontal axis of Figure 5) and the electrolyte (vertical axis) has to adapt to the new arrangement. If the solvent rearrangement is fast (flat solvation free energy surface in y-direction) compared to the nuclear reorganization, then the adiabatic approximation applied to the stationary states can also be applied to the transition state (TS) and no special treatment is necessary.…”

DockOnSurf: A Python Code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces

“…Hence, we enable the use of DockOnSurf for adsorption sites that differ in orientation. For every adsorption site, a normal vector to the surface is either provided by the user, or, more conveniently, automatically determined using the Anisotropically corrected Solid-Angle based Nearest-Neighbors (ASANN) 63 algorithm.…”

“…The generalized coordination numbers of their surface atoms ranged from 1.6-5, making it an ideal test-case, as already observed in our previous study on coordination numbers. 63 For the identification of adsorption modes on corrugated surfaces, we chose a 3×3 supercell of the (0001) facet of hematite in its Fe-O 3 -Fe-termination when hydrated by one dissociated water molecule per unit cell. 68 Its lowest four atomic layers were kept frozen in its bulk arrangement.…”

“…DockOnSurf can automatically guess the local surface normal using the ASANN algorithm. 63 To illustrate this capability, we have defined all surface atoms of a low-energy non-crystaline Au 38 nanoparticle as adsorption sites to be screened. The CO molecule was chosen as a typical and simple adsorbate.…”