Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules
In the current work, a comprehensive procedure for structural analysis of quasilinear organic molecules arranged in a polycrystalline sample generated by molecular dynamics is developed. A linear alkane, hexadecane, is used as a test case because of its interesting behavior upon cooling. Instead of...
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| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/28/5/2327 |
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| author | Stoyan Iliev Sonya Tsibranska Ilia Kichev Slavka Tcholakova Nikolai Denkov Anela Ivanova |
| author_facet | Stoyan Iliev Sonya Tsibranska Ilia Kichev Slavka Tcholakova Nikolai Denkov Anela Ivanova |
| author_sort | Stoyan Iliev |
| collection | DOAJ |
| description | In the current work, a comprehensive procedure for structural analysis of quasilinear organic molecules arranged in a polycrystalline sample generated by molecular dynamics is developed. A linear alkane, hexadecane, is used as a test case because of its interesting behavior upon cooling. Instead of a direct transition from isotropic liquid to the solid crystalline phase, this compound forms first a short-lived intermediate state known as a “rotator phase”. The rotator phase and the crystalline one are distinguished by a set of structural parameters. We propose a robust methodology to evaluate the type of ordered phase obtained after a liquid-to-solid phase transition in a polycrystalline assembly. The analysis starts with the identification and separation of the individual crystallites. Then, the eigenplane of each of them is fit and the tilt angle of the molecules relative to it is computed. The average area per molecule and the distance to the nearest neighbors are estimated by a 2D Voronoi tessellation. The orientation of the molecules with respect to each other is quantified by visualization of the second molecular principal axis. The suggested procedure may be applied to different quasilinear organic compounds in the solid state and to various data compiled in a trajectory. |
| first_indexed | 2024-03-11T07:16:15Z |
| format | Article |
| id | doaj.art-2408ebc627d64d9a99cb488d6b4bcf97 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-11T07:16:15Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-2408ebc627d64d9a99cb488d6b4bcf972023-11-17T08:15:06ZengMDPI AGMolecules1420-30492023-03-01285232710.3390/molecules28052327Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear MoleculesStoyan Iliev0Sonya Tsibranska1Ilia Kichev2Slavka Tcholakova3Nikolai Denkov4Anela Ivanova5Department of Physical Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, BulgariaDepartment of Chemical and Pharmaceutical Engineering, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, BulgariaDepartment of Physical Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, BulgariaDepartment of Chemical and Pharmaceutical Engineering, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, BulgariaDepartment of Chemical and Pharmaceutical Engineering, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, BulgariaDepartment of Physical Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, 1 James Bourchier Blvd., 1164 Sofia, BulgariaIn the current work, a comprehensive procedure for structural analysis of quasilinear organic molecules arranged in a polycrystalline sample generated by molecular dynamics is developed. A linear alkane, hexadecane, is used as a test case because of its interesting behavior upon cooling. Instead of a direct transition from isotropic liquid to the solid crystalline phase, this compound forms first a short-lived intermediate state known as a “rotator phase”. The rotator phase and the crystalline one are distinguished by a set of structural parameters. We propose a robust methodology to evaluate the type of ordered phase obtained after a liquid-to-solid phase transition in a polycrystalline assembly. The analysis starts with the identification and separation of the individual crystallites. Then, the eigenplane of each of them is fit and the tilt angle of the molecules relative to it is computed. The average area per molecule and the distance to the nearest neighbors are estimated by a 2D Voronoi tessellation. The orientation of the molecules with respect to each other is quantified by visualization of the second molecular principal axis. The suggested procedure may be applied to different quasilinear organic compounds in the solid state and to various data compiled in a trajectory.https://www.mdpi.com/1420-3049/28/5/2327structural analysisseparation of crystallitescrystallite eigenplanemolecular tilthexadecane-surfactant interfacemolecular dynamics |
| spellingShingle | Stoyan Iliev Sonya Tsibranska Ilia Kichev Slavka Tcholakova Nikolai Denkov Anela Ivanova Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules Molecules structural analysis separation of crystallites crystallite eigenplane molecular tilt hexadecane-surfactant interface molecular dynamics |
| title | Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules |
| title_full | Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules |
| title_fullStr | Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules |
| title_full_unstemmed | Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules |
| title_short | Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules |
| title_sort | computational procedure for analysis of crystallites in polycrystalline solids of quasilinear molecules |
| topic | structural analysis separation of crystallites crystallite eigenplane molecular tilt hexadecane-surfactant interface molecular dynamics |
| url | https://www.mdpi.com/1420-3049/28/5/2327 |
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