CoNTub

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CoNTub
Contub logo.gif

Contub v1.0 01.png

Screenshot of the main view in CoNTub 1.0.
Developer(s) Grupo de Modelización y Diseño Molecular [1] [2]
Initial release April 2004;14 years ago (2004-04)
Stable release
2.0 / September 2011;6 years ago (2011-09)
Operating system Cross-platform.
Type Cheminformatics / Molecular modelling
License freeware
Website www.ugr.es/local/gmdm/contub.htm

CoNTub is a software project written in Java which runs on Windows, Mac OS X, Linux and Unix Operating systems through any Java-enabled web browser. It is the first implementation of an algorithm for generating 3D structures of arbitrary carbon nanotube connections by means of the placement of non-hexagonal (pentagonal or heptagonal) rings, also referred as defects or disclinations.

Java (programming language) Object-oriented programming language

Java is a general-purpose computer-programming language that is concurrent, class-based, object-oriented, and specifically designed to have as few implementation dependencies as possible. It is intended to let application developers "write once, run anywhere" (WORA), meaning that compiled Java code can run on all platforms that support Java without the need for recompilation. Java applications are typically compiled to "bytecode" that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The language derives much of its original features from SmallTalk, with a syntax similar to C and C++, but it has fewer low-level facilities than either of them. As of 2016, Java was one of the most popular programming languages in use, particularly for client-server web applications, with a reported 9 million developers.

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Linux Family of free and open-source software operating systems based on the Linux kernel

Linux is a family of free and open-source software operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution.

Contents

The software is a set of tools dedicated to the construction of complex carbon nanotube structures for use in computational chemistry. CoNTub 1.0[1] was the first implementation for building these complex structures and included nanotube heterojunctions, while CoNTub 2.0[2] is mainly devoted to three-nanotube junctions. Its aim is to help in the design and research about new nanotube-based devices. CoNTub is based on the strip algebra, and is able to find the unique structure for connecting two specific and arbitrary carbon nanotubes and many of the possible three-tube junctions.

Carbon nanotube allotropes of carbon with a cylindrical nanostructure

Carbon nanotubes (CNTs) are allotropes of carbon with a cylindrical nanostructure. These cylindrical carbon molecules have unusual properties, which are valuable for nanotechnology, electronics, optics, and other fields of materials science and technology. Owing to the material's exceptional strength and stiffness, nanotubes have been constructed with a length-to-diameter ratio of up to 132,000,000:1, significantly larger than that for any other material.

Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids. It is necessary because, apart from relatively recent results concerning the hydrogen molecular ion, the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials.

Strip Algebra is a set of elements and operators for the description of carbon nanotube structures, considered as a subgroup of polyhedra, and more precisely, of polyhedra with vertices formed by three edges. This restriction is imposed on the polyhedra because carbon nanotubes are formed of sp2 carbon atoms. Strip Algebra was developed initially for the determination of the structure connecting two arbitrary nanotubes, but has also been extended to the connection of three identical nanotubes

CoNTub generates the geometry of various types of nanotube junctions, i.e., nanotube heterojunctions and three-nanotube junctions, including also single-walled nanotubes (SWNTs) and multi-walled nanotubes (MWNTs).

Geometry branch of mathematics that measures the shape, size and position of objects

Geometry is a branch of mathematics concerned with questions of shape, size, relative position of figures, and the properties of space. A mathematician who works in the field of geometry is called a geometer.

Although the current version of CoNTub is v2.0, this version does not supersedes v1.0, as v2.0 is dedicated currently to only three-nanotube junctions, although the incorporation of v1.0 functionality into v.2.0 is planned. Nanotube heterojunctions can be generated only with v1.0.

CoNTub v1.0 is organized in five Tabbed panels CoNTub[1], the first three being dedicated to structure generation, the fourth to the output in PDB format, and the fifth contains a short help section.

The Protein Data Bank (pdb) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed sidechain rotamers, secondary structure assignments, as well as atomic connectivity. Structures are often deposited with other molecules such as water, ions, nucleic acids, ligands and so on, which can be described in the pdb format as well. The Protein Data Bank also keeps data on biological macromolecules in the newer mmCIF file format.

CoNTub v2.0 has experimented a major redesign, and the panes have been removed, instead, a conventional menubar has been added where the type of structure to be generated can be chosen. Although the menu item for heterojunction generation appears in the menu, the button is disabled, so NTHJ's can be only generated with v1.0

Features

In solid-state physics, the electronic band structure of a solid describes the range of energies that an electron within the solid may have and ranges of energy that it may not have.

Density of states a system describes the number of states per interval of energy at each energy level available to be occupied

In solid state physics and condensed matter physics, the density of states (DOS) of a system describes the number of states per an interval of energy at each energy level available to be occupied. It is mathematically represented by a density distribution and it is generally an average over the space and time domains of the various states occupied by the system. A high 'DOS' at a specific energy level means that there are many states available for occupation. A DOS of zero means that no states can be occupied at that energy level. The DOS is usually represented by one of the symbols g, ρ, D, n, or N.

Cartesian coordinate system coordinate system

A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a set of numerical coordinates, which are the signed distances to the point from two fixed perpendicular oriented lines, measured in the same unit of length. Each reference line is called a coordinate axis or just axis of the system, and the point where they meet is its origin, at ordered pair (0, 0). The coordinates can also be defined as the positions of the perpendicular projections of the point onto the two axes, expressed as signed distances from the origin.

Nanotube generation

To generate a SWNT, it is only necessary to introduce the indices of the tube, its desired length (Angstrom), and the type of atom for termination of dangling bonds. ConTub displays the resulting nanotube, as well as its electronic band structure and density of states (DOS), following a tight binding model. [3]

MWNT - multiple tubes with the same axis and length - are created by providing the indices of the most inner tube (i,j), the desired length (l), the number of shells (N), and the approximate distance between shells or spacing (S) in Angstrom. The default value for spacing corresponds to the standard distance between layers in crystalline graphite (3.4 Å). ConTub automatically selects the indices of the remaining tubes, trying to adjust the interlayer spacing, and tries to use tubes with the same chirality as that of the inner nanotube.

Heterojunction generation

This is the core of the CoNTub[1] program. Strip algebra was implemented, [4] which allows two perfect carbon nanotubes to be joined, independently of their geometry, radius or chirality, with the simplest geometry possible, i.e. with the lowest number of non-hexagonal rings (a pentagon and a heptagon), also called defects or disclinations. There is always a possible connection between two tubes and strip algebra ensues that the solution is unique and depending only of the indices (i,j) of both tubes.

C3 Symmetric Three-Nanotube Junction generation

A further implementation of the Strip Algebra has been released in the second version of CoNTub, in order to elucidate the precise location of atoms and rings that lead to a junction of three nanotubes.

Connection between three nanotubes requires, at least, the presence of six heptagons, instead of the single pentagon and heptagon required for an heterojunction. In this case, the set of equations that rule the geometry has more variables to solve than restrictions, so the possible geometries constitute an infinite set. The detailed procedure for the nanotube construction has been also published,

Imposing additional restrictions to the geometry can ease the finding of viable geometries, and this is what is applied in the current version of CoNTub: Forcing the tubes connected to be of the same kind, and forcing an additional C3 symmetry, an automated way to construct the geometry can be found. However, even with these restrictions, the possibilities are still infinite. Therefore, a way to estimate the viability of the junction, even before constructing it, had to be developed. Given that non-hexagonal rings

See also

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Vertically aligned carbon nanotube arrays (VANTAs) are a unique microstructure consisting of carbon nanotubes oriented along their longitudinal axis normal to a substrate surface. These VANTAs effectively preserve and often accentuate the unique anisotropic properties of individual carbon nanotubes and possess a morphology that may be precisely controlled. VANTAs are consequently widely useful in a range of current and potential device applications.


AA'-graphite is an allotrope of carbon similar to graphite, but where the layers are positioned differently to each other as compared to the order in graphite.

References

  1. ↑ Melchor, S.; Dobado, J.A. (2004). "CoNTub: An Algorithm for Connecting Two Arbitrary Carbon Nanotubes". J. Chem. Inf. Comput. Sci. 44 (5): 1639–1646. doi:10.1021/ci049857w. PMID   15446821.
  2. ↑ Melchor, S.; Martin-Martinez, F.J.; Dobado, J.A. (2011). "CoNTub v2.0 - Algorithms for Constructing C3-Symmetric Models of Three-Nanotube Junctions". J. Chem. Inf. Model. 51: 1492–1505. doi:10.1021/ci200056p.
  3. ↑ Savinskii, S.S.; Khokhriakov, N.V. Characteristic Features of the Pi-Electron States of Carbon Nanotubes. J. Exp. Theor. Phys. 1997, 84, 1131-1137.
  4. ↑ Melchor, S.; Khokhriakov, N.V.; Savinskii, S.S. (1999). "Geometry of Multi-Tube Carbon Clusters and Electronic Transmission in Nanotube Contacts". Molecular Engineering. 8 (4): 315–344. doi:10.1023/A:1008342925348.
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