The Real Time Flipping Dynamics Studies of Dipolar Diflourophenylene Rotator (Compass Needle) of Crystalline Siloxaalkane Molecular Compass

Anant Babu Marahatta


One of the most indispensable strategies of nanotechnology is to integrate the networks of molecular arrays and their explicit functionalizable physicochemical properties of those type crystalline materials that exhibit unique amphidynamic behavior at wide range temperature regimes, and respond genuinely to the external stimuli owing to the inventions of smart, and intelligent nanomachines. The recently synthesized macroscopic compass like macrocyclic crystalline compound with a completely closed structural topology possessing a Si-C spin axis, and a dipolar diflourophenylene (rotator) ring encapsulated into the peripheral -(Si-O)x- & -Si-O-Si- made siloxaalkane spokes (stator) is one of such type materials whose central rotator is experimentally observed as 1p-flipped in two degenerate positions (b and b') at T = 273 K. Herein, all the associated rotary dynamical assets of this gyrotop molecular arrays are probed under crystalline conditions by employing the NCC-DFTB/MD simulation scheme. The general results achieved in this study are found to justify the X-ray/1H-NMR predicted flipping motions and temporal behavior of the central dipolar rotator in real-time scales. When the average kinetic temperatures T of the molecular ensemble are set to 1200 K & 600 K, the rotator is found to consume @8 ps & @45 ps with the flipping rates of  = 0.022 ps-1 &  = 0.125 ps-1 respectively for the specific b®b' 1p-flipping, but when T is reduced to 273 K, this flipping motion is completely forbidden within the present simulation timeframe of £ 200 ps. The flipping barrier value Ea = 4.3 kcal/mol obtained from the Arrhenius equation is also found to lie in well agreeable range to that determined through the Gaussian-external PES techniques (Ea = 4.9 kcal/mol). The results presented here are quite essential to understand the compass/gyroscope like functions of the siloxaalkane molecular analogues which in turn speculate their functionalizing masterplans comprehensively.

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. 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:

. 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; 14(1):1231.

. Available:

. Balzani V, Venturi M, Credi A. Molecular Devices and machines: A Journey into the Nano World; Wiley-VCH: Weinheim, Germany, 2003.

. Kelley TR. Molecular Machines. Topics in Current Chemistry, Springer, Berlin, Heidelberg, New York, 2005.

. Dominguez Z, Dang H, Strouse MJ, Garcia-Garibay MA. Molecular "compasses" and "gyroscopes." III. Dynamics of a phenylene rotor and clathrated benzene in a slipping-gear crystal lattice. Journal of American Chemical Society. 2002; 124(26):77197727.

. Available:

. Horansky RD, Clarke LI, Price JC, Karlen SD, Jarowski PD, Santillan R, Garcia-Garibay MA. Dipolar rotor-rotor interactions in a difluorobenzene molecular rotor crystal. Physical Review B. 2006; 74:054306(112).

. Available:

. O’Brien ZJ, Natarajan A, Khan S, Garcia-Garibay MA. Synthesis and Solid-State Rotational Dynamics of Molecular Gyroscopes with a Robust and Low Density Structure Built with a Phenylene Rotator and a Tri(meta-terphenyl)methyl Stator. Crystal Growth & Design. 2011; 11(6): 26542659.

. Available:

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

. Available: From=fulltext

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

. Available:

. Setaka W, Yamaguchi K. Thermal modulation of birefringence observed in a crystalline molecular gyrotop. The Proceedings of the National Academy of Sciences. 2012; 109(24), 92719275.

. Available:

. Akimov AV, Kolomeisky A. Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes. Journal of Physical Chemistry C. 2011; 115(1), 125131.

. Available:

. Marahatta AB, Kanno M, Hoki K, Setaka W, Irle S. Theoretical Investigation of the Structures and Dynamics of Crystalline Molecular Gyroscopes. Journal of physical chemistry C. 2012; 116, 4845−24854.

. Available:

. 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:

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

. Available:chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/ ad/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:

. Marahatta AB. DFTB1 and DFTB2 Based RealTime Flipping Motion Studies of Central Phenylene Rotator of Crystalline Siloxaalkane Molecular Gyroscope. International Journal of Progressive Sciences and Technologies. 2024; 42(2):1939.

. Available:

. Elstner M, Hobza P, Frauenheim T, Suhai S, Kaxiras E. Hydrogen bonding and stacking interactions of nucleic acid base pairs: a density-functional-theory based treatment. Journal of Chemical Physics. 2001; 114:51495155.

. Available: ng-and-stacking-interactions-of?redirectedFrom=fulltext

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

. Available:

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

. Available:

. DFTB+ Version 1.3 User Manual.

. Available:



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