GenInfi

Generating infinitenes, kekulenes and clarenes

This is a handy program for generating structures of generalized infinitenes, generalized kekulenes, as well as clarenes. All constructed molecular structures are exported in Cartesian coordinates in *.xyz files.

Download link for the latest v1.0 version: https://github.com/yangwangmadrid/GenInfi/releases/download/v1.0/GenInfi_v1.0_release.zip

How to cite

If your research publications or presentations involve the use of GenInfi, it is obligatory to cite the following works:

1. Ke Du, Yang Wang. Infinitenes as the Most Stable Form of Cycloarenes: The Interplay Between π Delocalization, Strain, and π-π Stacking. J. Am. Chem. Soc. 2023, 145, 10763-10778. DOI:10.1021/jacs.3c01644

2. Yang Wang. The GenInfi program. 2023, https://github.com/yangwangmadrid/GenInfi.

Copyright and License

The Author of the Geninfi software is Yang Wang (yangwang@yzu.edu.cn; orcid.org/0000-0003-2540-2199). The Geninfi program is released under GNU General Public License v3 (GPLv3).

Disclaimer

The Geninfi software is provided as it is, with no warranties. The Author shall not be liable for any use derived from it. Feedbacks and bug reports are always welcome (yangwang@yzu.edu.cn). However, it is kindly reminded that the Author does not take on the responsibility of providing technical support.

How to Install

Requirements

• python >= 3.6
• numpy >= 1.18.0

Installation

This is a typical python program and requires no installation as long as Python 3 has been preinstalled in your computer. Upon downloading the Geninfi package, simply decompress it to any location as you like. Hereafter, we refer to the folder where the main program file, geninfi.py, is located as the source directory of Geninfi (denoted by SRC_GENINFI).

How to Use

It is very simple to use GenInfi to generate structures of infinitenes, kekulenes, and clarenes.

For a quick start, you can go to the examples/ folder and run the script*.sh files under each subfolder for tests.

You can also refer to the detailed instructions with examples in the next section.

I. General description of usage

1. Command line arguments

The program is executed at command line, as follows:

python SRC_GENINFI/geninfi.py <kinf|cinf|ccinf|kek|clr> <parameters>

where parameters can be either of the following options, depending on the types of constructions:

- Nring  (Number of rings for the molecules to enumerate)
- h1 h2 h3 h4 h5 h6  (Six side lengths for specifying a kekulene/clarene, or the clarene unit of CC-infinitenes)
- h1 h2 h3 h4 h5 h6 d  (Six side lengths and d-shift for specifying a CC-infinitene)
- h1 h2 h3 h4 h5 h6 k1 k2 k3 k4 k5 k6  (Twelve side lengths for enumeration of K- and C-infinitenes)
- h1 h2 h3 h4 h5 h6 k1 k2 k3 k4 k5 k6 d (Twelve side lengths and d-shift for specifying a K- or C-infinitene)

2. Types of structural constructions

(i) Direct generation of a specified structure

• By specifying 6 side lengths, h1 h2 h3 h4 h5 h6, one can construct the corresponding kekulene [h1,h2,h3,h4,h5,h6] or clarene <h1,h2,h3,h4,h5,h6>.

• For making a CC-infinitene <coronene|h1,h2,h3,h4,h5,h6>(d), one needs to provide an additional integer for the shift d.

• Likewise, given the 12 side lengths, h1 h2 h3 h4 h5 h6 k1 k2 k3 k4 k5 k6, and the shift d, the corresponding K-infinitene [h1,h2,h3,h4,h5,h6|k1,k2,k3,k4,k5,k6](d) or C-infinitene <h1,h2,h3,h4,h5,h6|k1,k2,k3,k4,k5,k6>(d) is obtained.

NOTE: All provided structural parameters must be valid for the desired molecule to construct. Otherwise, an error message will be prompted by GenInfi.

(ii) Enumeration of structures from specified kekulene/clarene units

One can enumerate all possible structures of K-infinitenes/C-infinitenes that are composed of two given kekulene/clarene units by specifying the side lengths for the corresponding kekulene/clarenes. Note that a given pair of kekulene (or clarene) units can have many different combinations to form K-infinitene (or C-infinitene) structures, depending on their contacting sides, relative shifts and relative orientation.

For CC-infinitenes, similar enumeration can be performed, but one only needs to provide the side lengths of the constituting clarene unit.

(iii) Enumeration of structures with a given number of rings

The simplest (but most exhaustive) way to generate these macrocyclic compounds is to tell GenInfi how many benzene rings you want the molecule to have. Given the number of rings, Nring, the program will conduct a full structural enumeration.

3. Outputs

• All generated structures are saved as Cartesian coordinates of atoms in *.xyz files, which can be visualized by many softwares such as JMol.
• Hydrogen atoms are automatically added to the carbon backbone in quite an intelligent way.
• For each structure, the simple Hückel π energy is computed and given in the title line of the *.xyz file.
• All detailed information is printed out to the screen during the execution of the program. This could be quite lengthy especially for a full enumeration of structures. It is thus recommended to redirect the screen output to a log file (using python SRC_GENINFI/geninfi.py ... > log_file).

II. Detailed instructions with examples

The following examples can be found in the examples/ folder. The execution command in each case is given in the script*.sh file. The generated the *.xyz output files are in the same folder.

1. Kekulenes

• Generate kekulene [1,3,2,3,1,4]:

python ../../geninfi.py kek 1 3 2 3 1 4

NOTE: All side lengths of a kekulene must form a valid equiangular hexagon.

The output file kek_R14-1_3_2_3_1_4.xyz will be generated.

• Enumerate all possible [15]kekulene structures:

python ../../geninfi.py kek 15

As we will see, four structures are generated: kek_R15-1_2_4_2_1_5.xyz, kek_R15-1_3_3_2_2_4.xyz, kek_R15-1_4_1_4_1_4.xyz, and kek_R15-2_3_2_3_2_3.xyz.

2. Clarenes

• Generate clarene <2,4,4,4,2,6>:

python ../../geninfi.py clr 2 4 4 4 2 6

NOTE: All side lengths of a clarene must be even numbers and form a valid equiangular hexagon.

The output file clr_R22-2_4_4_4_2_6.xyz will be generated.

• Enumerate all possible [26]clarene structures:

python ../../geninfi.py clr 26

Two possible isomers, clr_R26-2_4_6_4_2_8.xyz and clr_R26-2_6_4_4_4_6.xyz will be created. The structure of the first one is shown in the figure below.

3. K-infinitenes

• Generate K-infinitene [2,4,3,4,2,5|3,3,4,5,1,6](1):

python ../../geninfi.py kinf 2 4 3 4 2 5 3 3 4 5 1 6 1

The constructed molecule contains 42 rings, as written in kinf_R42-2_4_3_4_2_5-3_3_4_5_1_6_d1.xyz and depicted as the following picture.

• Enumerate all possible K-infinitenes composed of kekulenes [1,1,2,1,1,2] and [1,2,3,1,2,3]:

python ../../geninfi.py kinf 1 1 2 1 1 2 1 2 3 1 2 3

As GenInfi outputs, there are as many as 30 enumerated structures: kinf_R20-1_1_2_1_1_2-1_2_3_1_2_3_d-1.xyz, ..., kinf_R20-1_2_1_1_2_1-3_2_1_3_2_1_d0.xyz.

• Enumerate all possible K-infinitenes containing 14 rings:

python ../../geninfi.py kinf 14

Four possible isomers will be found: kinf_R14-1_1_1_1_1_1-1_1_2_1_1_2_d-1.xyz, kinf_R14-1_1_1_1_1_1-1_1_2_1_1_2_d0.xyz, kinf_R14-1_1_1_1_1_1-1_1_2_1_1_2_d1.xyz, and kinf_R14-1_1_1_1_1_1-2_1_1_2_1_1_d-1.xyz.

4. C-infinitenes

• Generate C-infinitene <2,4,2,4,2,4|6,4,2,6,4,2>(-2):

python ../../geninfi.py cinf 2 4 2 4 2 4 6 4 2 6 4 2 -2

The obtained 42-ring infinitene, cinf_R42-2_4_2_4_2_4-6_4_2_6_4_2_d-2.xyz, shows a structure as follows.

• Enumerate all possible C-infinitenes composed of clarenes <2,4,2,4,2,4> and <6,4,2,6,4,2>:

python ../../geninfi.py cinf 2 4 2 4 2 4 6 4 2 6 4 2

GenInfi will produce 36 different possible structures: cinf_R42-2_4_2_4_2_4-2_4_6_2_4_6_d-2.xyz, ..., cinf_R42-4_2_4_2_4_2-6_4_2_6_4_2_d0.xyz.

• Enumerate all possible C-infinitenes with 32 rings:

python ../../geninfi.py cinf 32

We will obtain 27 isomers of [32]C-infinitenes with different combinations of clarene units: cinf_R32-2_2_2_2_2_2-2_2_6_2_2_6_d-2.xyz, ..., cinf_R32-4_2_2_4_2_2-4_2_2_4_2_2_d0.xyz.

5. CC-infinitenes

• Generate CC-infinitene <coronene|6,2,4,4,4,2>(-6):

python ../../geninfi.py ccinf 6 2 4 4 4 2 -6

The generated [28]CC-infinitene will be stored in ccinf_R28-1_1_1_1_1_1-6_2_4_4_4_2_d-6.xyz, as shown in the figure below.

• Enumerate all CC-infinitenes composed of coronene and clarene <4,2,2,4,2,2>:

python ../../geninfi.py ccinf 4 2 2 4 2 2

We will get four possible structures: ccinf_R22-1_1_1_1_1_1-2_2_4_2_2_4_d-2.xyz, ccinf_R22-1_1_1_1_1_1-2_2_4_2_2_4_d0.xyz, ccinf_R22-1_1_1_1_1_1-4_2_2_4_2_2_d-2.xyz, and ccinf_R22-1_1_1_1_1_1-4_2_2_4_2_2_d-4.xyz.

• Enumerate all possible [26]CC-infinitenes:

python ../../geninfi.py ccinf 26

Eventually, eight structures will be created: ccinf_R26-1_1_1_1_1_1-2_2_6_2_2_6_d-2.xyz, ..., ccinf_R26-1_1_1_1_1_1-6_2_2_6_2_2_d-6.xyz.