A General Method for Determining Molecular Interfaces and Layers.

0480914 - ÚCHP 2018 RIV US eng J - Článek v odborném periodiku
Škvor, J. - Škvára, J. - Jirsák, Jan - Nezbeda, Ivo
A General Method for Determining Molecular Interfaces and Layers.
Journal of Molecular Graphics & Modelling. Roč. 76, SEP 2017 (2017), s. 17-35. ISSN 1093-3263. E-ISSN 1873-4243
Grant CEP: GA ČR GA15-19542S
Institucionální podpora: RVO:67985858
Klíčová slova: interface * molecular layers * percolating cluster
Obor OECD: Physical chemistry
Impakt faktor: 1.885, rok: 2017

A general and direct computational scheme to locate the surface separating arbitrarily shaped domains made up of molecules (or any other particles) has been developed and is described and illustrated for several, both artificial and physical examples. The proposed scheme consists of two modules: (i) triangulation and (ii) assignment of simplices to domains. Three different triangulation methods are employed, viz., the Delaunay triangulation, regular triangulation, and quasi-triangulation. In the triangulated system, the assignment step is carried out in two different ways, one based on the characteristic metric of a particular triangulation procedure and the other on the concept of a touching sphere. Some of the combinations of the triangulation and assignment steps lead to methods already used by others to find interfacial or surface molecules, namely the alpha-shape-based method of Usabiaga nad Duque. The resulting surface is defined not only as a discrete set of particles, but it is build up of facets of the triangulation forming a broken line in two dimensions or a polyhedral surface in three dimensions. Individual molecular layers are identified in a very straightforward manner, starting with the interfacial layer itself and proceeding into the interior of the phase. The proposed scheme is illustrated first by identifying border molecules of pre-sampled domains of several shapes in a plane and then applied to five physically meaningful examples: thin films, near critical water, liquid water slab in an electric field, liquid water at a solid wall, and water at condition of electric-field-induced jetting. Performance of the considered methods is critically assessed. Treatment of domains forming percolating clusters through periodic boundary conditions is also described along with the determination of their periodicity and dimensionality.
Trvalý link: http://hdl.handle.net/11104/0276573