CoNTub v2.0 - Algorithms for Constructing C3-Symmetric Models of Three-Nanotube Junctions

CONAN─Novel Tool to Create and Analyze Liquids in Confined Space

Modeling of complex liquids at solid surfaces and in confinement is gaining attention due to an increase in computer power and advancement of simulation techniques. Therefore, tools to set up structures and for analysis are needed. In this paper, we present CONAN─a Python code designed to facilitate the study of liquids interacting with solid structures, such as walls or pores. Among other things, the program provides the option to generate a variety of different structures, including carbon walls and nanotubes and their boron nitride analogs, as well as the ability to analyze various structural properties of confined and interfacial liquids. In the case of the ionic liquid 1-butyl-3-methylimidazolium acetate in carbon nanotubes of different sizes, we demonstrate the abilities of our tool. The average density within the confinement highly depends on the carbon nanotube size, and it is generally lower than the density of the bulk liquid. The arrangement of the individual species within the tube also depends on size, with radial layers forming within the tubular confinement. The density is largely increased in the respective layers, while it is drastically reduced between the layers.

Junction-Producing Algorithm Connecting Carbon Nanotube to Carbon Nanocone to Obtain Funnel-Like Nanostructure: Nanochimney Generator

This study aims to provide a computational algorithm which contributes to the understanding and implementation of carbon nanochimneys. The structure resembles a tube ending with an inverted funnel, with a connection region that uses non-hexagonal rings as defects in order to match the boundaries of the two linked nanostructures. They are important for applications such as thermal transport, gas storage, or separation. The algorithm is written in Python 3.7 and provides a .pdb file with the coordinates of all the atoms included in the system. The parameters that can be specified are the carbon nanotube dimensions, for either armchair or zigzag conformations, five levels of disclination for the carbon nanocone along with the base diameter of the latter.

Developing nanotube junctions with arbitrary specifications

Experimentally synthesized carbon nanotube (CNTs) junctions (either single or with 2D/3D CNT network topology) are expected to have random orientation of defect sites (non-hexagonal rings) around the junction. This random and irregular nature of the junction topology and defect characteristics is expected to affect their strength and durability as well as impact the associated mesoscopic and macroscopic properties. On the contrary, theoretical and computational studies often investigate structure-property relationships of pristine and regular junctions of carbon nanostructures. In this study, we developed a computational framework to model a variety of junction structures between CNTs with arbitrary spatial (orientation and degree of overlap) and intrinsic (chirality) specifications. The developed computational model also has the ability to tune the degree of topological defects around the junction via a variety of defect annihilation approaches. Our method makes use of the primal/dual meshing concept, where the development and manipulation of the junction nodes occur using triangular meshes (primal mesh), which is eventually converted to its dual mesh (honeycomb mesh) to render a fully covalently bonded CNT junction. Here each carbon atom has 3 bonded neighbors (mimicking sp² hybridization). Under a given set of CNT orientation, overlap and chirality specifications, the approach creates a number of CNT junction configurations with varying degrees of energetic stability, offering an opportunity to investigate the effect of topological arrangement of defects around the junction on mechanical, electrical and thermal properties. In addition, it is shown via few examples that the discussed methodology can easily be extended to create multi-junction nanotube clusters, multi-wall nanotube junctions, as well as true 3D random network structures.

Unique ring families: a chemically meaningful description of molecular ring topologies

The perception of a set of rings forms the basis for a number of chemoinformatics applications, e.g. the systematic naming of compounds, the calculation of molecular descriptors, the matching of SMARTS expressions, and the generation of atomic coordinates. We introduce the concept of unique ring families (URFs) as an extension of the concept of relevant cycles (RCs). URFs are consistent for different atom orders and represent an intuitive description of the rings of a molecular graph. Furthermore, in contrast to RCs, URFs are polynomial in number. We provide an algorithm to efficiently calculate URFs in polynomial time and demonstrate their suitability for real-time applications by providing computing time benchmarks for the PubChem Database. URFs combine three important properties of chemical ring descriptions, for the first time, namely being unique, chemically meaningful, and efficient to compute. Therefore, URFs are a valuable alternative to the commonly used concept of the smallest set of smallest rings (SSSR) and would be suited to become the standard measure for ring topologies of small molecules.