DFTB1 and DFTB2 Based Real-Time Flipping Motion Studies of Central Phenylene Rotator of Crystalline Siloxaalkane Molecular Gyroscope

Anant Babu Marahatta


Despite adopting ab initio functionalities comprising mathematical formulations and many unique complex computational features, the density-functional based tight-binding (DFTB) scheme presents itself as the standalone, versatile, and efficient quantum mechanical application. The recognizably low-cost, & extremely faster MD simulation parser codes of it run under the DFTB+ atomic simulation environment interface plus the noticeably methodical long ranged molecular interactions addressing 'non-self-consistent-charge' (DFTB1) & 'self-consistent-charge' (DFTB2) formulations adds a substantial value to its rational applications. Herewith, both the DFTB2/ & DFTB1/ MD simulation schemes are employed separately to simulate the siloxaalkane molecular gyroscope under crystalline condition with and without 'dispersion energy corrections' features at wide temperature regimes & the experimentally observed facile flipping motions of its central phenylene rotator are confirmed theoretically in real-time scales. The concerned rotary trajectories depict that: (a) at 800 K ³ T £ 1200 K, the rotator exhibits 1p inversions & frequent flipping motions easily with sub-picoseconds to picoseconds lifetimes; (b) at T = 600 K, the rotator flips between its stable positions at the intervals of several tens of picoseconds; but (c) at T = 300 K, the rotator flips more demonstratively with longer lifespans only after addressing the dispersion energies in DFTB2 scheme. Additionally, the flipping rates of the rotator;  = 0.018 ps-1 & = 0.021 ps-1 predicted at T = 800 K & 1200 K respectively are retarded to 0.009 ps-1 & 0.013 ps-1, and the flipping barrier estimated by using  & as Ea1 = 0.66 kcal/mol is increased to Ea2 = 1.84 kcal/mol after treating dispersion energies; the quite consistent values to those retrieved from the respectively derived potential energy surface (Ea1 =0.70 kcal/mol & Ea2 =1.2 kcal/mol). These quantitative results illuminate that the DFTB2/MD simulation scheme is more demandable than the DFTB1/MD especially for simulating crystalline molecular assembly.

Full Text:



Seifert G. Tight-Binding Density Functional Theory: An Approximate Kohn−Sham DFT Scheme. Journal of Physical Chemistry A. 2007; 111:5609−5613.

Available:https://pubs.acs.org/doi/10.1021/jp069056r#:~:text=The%20DFTB%20method% 20is%20an,and%20to%20the%20Harris%20functional.

Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Physical Review B. 1998; 58:7260−7268.

Available: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.58.7260

Aradi B, Hourahine B, Frauenheim T. DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method. Journal of Physical Chemistry A. 2007; 111:5678−5684.


Elstner M, Frauenheim T, Kaxiras E, Seifert G, Suhai S. A Self‐Consistent Charge Density‐Functional Based Tight‐Binding Scheme for Large Biomolecules. Physica Status Solidi B. 2000; 217:357−376.

Available: https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1521-3951(200001)217: 1% 3C41::AID-PSSB41%3E3.0.CO;2-V

Frauenheim T, Seifert G, Elstner M, Niehaus T, Kohler C, Amkreutz M, Sternberg M, Hajnal Z, Di Carlo A, Suhai S. Atomistic simulations of complex materials: groundstate and excited-state properties. Journal of Physics Condensed Matter. 2002; 14(11):3015–3047.

Available: https://iopscience.iop.org/article/10.1088/0953-8984/14/11/313/meta

Marahatta AB. Performance Evaluation of DFTB1 and DFTB2 Methods in reference to the Crystal Structures and Molecular Energetics of Siloxaalkane Molecular Compass. International Journal of Progressive Sciences and Technologies. 2023; 41(1):1231.

Marahatta AB, Kono H. Performance of NCC- And SCC- DFTB Methods for Geometries and Energies of Crystalline Molecular Gyroscope. International Journal of Innovative Research and Advanced Studies. 2019; 6(5):180185.

Available: http://www.ijiras.com/2019/Vol_6-Issue_5/paper_28.pdf

Zheng G, Irle S, Morokuma K. Performance of the DFTB method in comparison to DFT and semiempirical methods for geometries and energies of C20–C86 fullerene isomers. Chemical Physics Letter. 2005; 412: 210−216.

Available: https://www.sciencedirect.com/science/article/abs/pii/S0009261405009334

Ohta Y, Okamoto Y, Irle S, Morokuma K. Single-walled carbon nanotube growth from a cap fragment on an iron nanoparticle: Density-functional tight-binding molecular dynamics simulations. Physical Review B. 2009; 79:195415 (17).

Available: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.79.195415

Lee KH, Schnupf U, Sumpter BG, and Irle S. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution. American Chemical Society Omega. 2018; 3(12):16899–16915.


Pekka Koskinen, Ville Mäkinen. Density-functional tight-binding for beginners. Computational Materials Science. 2009; 47:237–253.

Available: https://www.sciencedirect.com/science/article/abs/pii/S0927025609003036

D. Frenkel, B. Smit. Understanding molecular simulation, From Algorithms to

Applications, Academic Press, 2002.

Available: https://www.sciencedirect.com/book/9780122673511/understanding-molecular-


Setaka W, Ohmizu S, Kabuto C, Kira, MA. Molecular Gyroscope Having Phenylene Rotator Encased in Three-spoke Silicon-based Stator. Chemistry Letters. 2007; 36(8):1076 1077.

Available: https://www.journal.csj.jp/doi/epdf/10.1246/cl.2007.1076

Setaka W, Ohmizu S, Kabuto C, Kira M. Molecular Gyroscope Having a Halogen-substituted p-Phenylene Rotator and Silaalkane Chain Stators. Chemistry Letter. 2010; 39(5):468469.

Available: https://www.journal.csj.jp/doi/pdf/10.1246/cl.2010.468

Setaka W, Yamaguchi K. Thermal modulation of birefringence observed in a crystalline molecular gyrotop. Proceedings of the National Academy of Sciences of the USA. 2012; 109:9271–9275.

Available: https://www.pnas.org/doi/10.1073/pnas.1114733109

Michl J, Charles E, Sykes H. Molecular Rotors and Motors: Recent Advances and Future Challenges. American Chemical Society Nano. 2009; 3(5):1042–1048

Available: https://pubs.acs.org/doi/10.1021/nn900411n

Marahatta AB, Kanno M, Hoki K, Setaka W, Irle S, Kono H. Theoretical Investigation of the Structures and Dynamics of Crystalline Molecular Gyroscopes. Journal of Physical Chemistry C. 2012; 116:24845–24854.

Available: https://pubs.acs.org/doi/10.1021/jp308974j

Marahatta AB. GaussianExternal Methodology Predicted Crystal Structures, Molecular Energetics, and Potential Energy Surface of the Crystalline Molecular Compass. Asian Journal of Applied Chemistry Research. 2023; 14(1):825.

Available: https://journalajacr.com/index.php/AJACR/article/view/255

Marahatta AB, Kono H. SCCDFTB Study for the Structural Analysis of Crystalline Molecular Compasses. Chemistry Research Journal. 2022; 7(4):7794.

Available: https://chemrj.org/download/vol-7-iss-4-2022/chemrj-2022-07-04-77-94.pdf

Marahatta AB, Kono H. Structural Characterization of Isolated Siloxaalkane Molecular Gyroscopes via DFTB-based Quantum Mechanical Model. International Journal of Progressive Sciences and Technologies. 2021; 26(1):526541.

Available: https://ijpsat.org/index.php/ijpsat/article/view/2950/0

Marahatta AB, Kono H. Comparative Theoretical Study on the Electronic Structures of the Isolated Molecular Gyroscopes with Polar and Nonpolar Phenylene Rotator. International Journal of Progressive Sciences and Technologies. 2020; 20(1):109122.

Available: https://ijpsat.org/index.php/ijpsat/article/view/1716

Macrae CF, Edgington PR, McCabe P, Pidcock E, Shields GP, Taylor R, Towler M, van de Streek J. Mercury: visualization and analysis of crystal structures. Journal of Applied Crystallography. 2006; 39:453–457.

Available: https://onlinelibrary.wiley.com/doi/abs/10.1107/S002188980600731X

(a) Verlet L. Computer “Experiments” on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Physical Review. 1967; 159:98-103.

Available: https://journals.aps.org/pr/pdf/10.1103/PhysRev.159.98

(b) Verlet L. Computer “Experiments” on Classical Fluids. II. Equilibrium Correlation Functions. Physical Review. 1968; 165:201:214

Available: https://journals.aps.org/pr/abstract/10.1103/PhysRev.165.201

DFTB+ Version 1.3 User Manual.

Available: https://dftbplus.org/fileadmin/DFTB-Plus/public/dftb/current/manual.pdf

DOI: http://dx.doi.org/10.52155/ijpsat.v42.2.5732


  • There are currently no refbacks.

Copyright (c) 2024 Anant Babu Marahatta

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.